From 25f0640f6ae77f393990488c99335cff55c22270 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Wed, 22 Jan 2014 11:13:13 -0500 Subject: [PATCH 0001/1033] Fix for installing migrated tools with dependencies. --- lib/tool_shed/galaxy_install/migrate/common.py | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/lib/tool_shed/galaxy_install/migrate/common.py b/lib/tool_shed/galaxy_install/migrate/common.py index c20580090aa..948a4003ef1 100644 --- a/lib/tool_shed/galaxy_install/migrate/common.py +++ b/lib/tool_shed/galaxy_install/migrate/common.py @@ -2,7 +2,7 @@ import ConfigParser import os import sys import galaxy.config -from tool_shed.galaxy_install import install_manager +from tool_shed.galaxy_install import install_manager, installed_repository_manager class MigrateToolsApplication( object, galaxy.config.ConfiguresGalaxyMixin ): @@ -41,6 +41,8 @@ class MigrateToolsApplication( object, galaxy.config.ConfiguresGalaxyMixin ): self._configure_toolbox() self._configure_tool_shed_registry() + + self.installed_repository_manager = installed_repository_manager.InstalledRepositoryManager( self ) # Get the latest tool migration script number to send to the Install manager. latest_migration_script_number = int( tools_migration_config.split( '_' )[ 0 ] ) From 7f58614225d9a29d3770f0700dde55757bc9bdb7 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Wed, 22 Jan 2014 11:28:49 -0500 Subject: [PATCH 0002/1033] Point rsync at a cname rather than scofield. --- lib/galaxy/config.py | 2 +- universe_wsgi.ini.sample | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index 3ce11476fc9..f023b64823d 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -58,7 +58,7 @@ class Configuration( object ): self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) self.genome_data_path = kwargs.get( "genome_data_path", "tool-data/genome" ) - self.rsync_url = kwargs.get( "rsync_url", "rsync://scofield.bx.psu.edu/indexes" ) + self.rsync_url = kwargs.get( "rsync_url", "rsync://datacache.galaxyproject.org/indexes" ) # Galaxy OpenID settings self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) self.openid_config = kwargs.get( 'openid_config_file', 'openid_conf.xml' ) diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample index 961098bd3a6..50062e575b6 100644 --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -124,7 +124,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory #genome_data_path = tool-data/genome # URL for rsync server to download pre-built indexes. -#rsync_url = rsync://scofield.bx.psu.edu/indexes +#rsync_url = rsync://datacache.galaxyproject.org/indexes # Dataset files are stored in this directory. #file_path = database/files From 96b74f7e1f5e8d051f8ee8348ee681cf77f6e13f Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Wed, 22 Jan 2014 11:30:32 -0500 Subject: [PATCH 0003/1033] Tool Shed install and test framework fixes. --- .../base/util.py | 51 ++++++++++++------- 1 file changed, 34 insertions(+), 17 deletions(-) diff --git a/test/install_and_test_tool_shed_repositories/base/util.py b/test/install_and_test_tool_shed_repositories/base/util.py index acb27939c92..dd7347dc5b2 100644 --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -753,7 +753,9 @@ def populate_dependency_install_containers( app, repository, repository_identifi owner = str( missing_repository_dependency.owner ) changeset_revision = str( missing_repository_dependency.changeset_revision ) error_message = unicodify( missing_repository_dependency.error_message ) - print 'Revision %s of repository %s owned by %s:\n%s' % ( changeset_revision, name, owner, error_message ) + print 'Revision %s of repository %s owned by %s has the following installation error:' % ( changeset_revision, name, owner ) + # Use log.debug here instead of print because print will throw UnicodeEncodeError exceptions. + log.debug( '%s' % error_message ) missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, name=name, owner=owner, @@ -774,7 +776,9 @@ def populate_dependency_install_containers( app, repository, repository_identifi type = str( missing_tool_dependency.type ) version = str( missing_tool_dependency.version ) error_message = unicodify( missing_tool_dependency.error_message ) - print 'Version %s of tool dependency %s %s:\n%s' % ( version, type, name, error_message ) + print 'Version %s of tool dependency %s %s has the following installation error:' % ( version, type, name ) + # Use log.debug here instead of print because print will throw UnicodeEncodeError exceptions. + log.debug( '%s' % error_message ) missing_tool_dependency_info_dict = dict( type=type, name=name, version=version, @@ -870,25 +874,38 @@ def populate_install_containers_for_repository_dependencies( app, repository, re ( changeset_revision, name, owner ) print 'due to the following error getting tool_test_results:\n%s' % str( error_message ) else: - # Check the required repository's time_last_tested value to see if its tool_test_results column - # has been updated within the past 12 hours. The RepositoryMetadata class's to_dict() method - # returns the value of time_last_tested in datetime.isoformat(). - twenty_hours_ago = ( datetime.utcnow() - timedelta( hours=20 ) ).isoformat() + # The assumption is that the Tool SHed's install and test framework is executed no more than once per 24 hour + # period, so check the required repository's time_last_tested value to see if its tool_test_results column + # has been updated within the past 24 hours. The RepositoryMetadata class's to_dict() method returns the value + # of time_last_tested in datetime.isoformat(). time_last_tested, error_message = get_time_last_tested( galaxy_tool_shed_url, required_repository_metadata_id ) - if time_last_tested is not None and time_last_tested < twenty_hours_ago: - print 'The install containers for version %s of repository dependency %s owned by %s have been ' % \ - ( changeset_revision, name, owner ) - print 'populated within the past 20 hours (likely in this test run), so skipping this check.' - continue - elif time_last_tested is None: + print 'Value of time_last_tested: %s' % str( time_last_tested ) + if time_last_tested is None: print 'The time_last_tested column value is None for version %s of repository dependency %s owned by %s.' % \ ( changeset_revision, name, owner ) - elif time_last_tested < twenty_hours_ago: - print 'Version %s of repository dependency %s owned by %s was last tested less than 20 hours ago.' % \ - ( changeset_revision, name, owner ) else: - print 'Version %s of repository dependency %s owned by %s was last tested more than 20 hours ago.' % \ - ( changeset_revision, name, owner ) + twenty_four_hours_ago = ( datetime.utcnow() - timedelta( hours=24 ) ).isoformat() + print 'Value of twenty_four_hours_ago: %s' % str( twenty_four_hours_ago ) + # This is counter intuitive because the following check is on strings like this: '2014-01-21T19:46:06.953741', + # so if "time_last_tested > twenty_four_hours_ago" is True, then it implies that the time_last_tested column + # was actually updated less than 24 hours ago, and should not be updated again because we're likely processing + # another dependent repository, many of which can have the same repository dependency. + try: + # Be very conservative here. Our default behavior will be to assume containers have not been populated + # during the current test run. + already_populated = time_last_tested > twenty_four_hours_ago + except Exception, e: + log.exception( 'Error attempting to set already_populated: %s' % str( e ) ) + already_populated = False + print 'Value of already_populated: %s' % str( already_populated ) + if already_populated: + print 'The install containers for version %s of repository dependency %s owned by %s have been ' % \ + ( changeset_revision, name, owner ) + print 'populated within the past 24 hours (likely in this test run), so skipping this check.' + continue + else: + print 'Version %s of repository dependency %s owned by %s was last tested more than 24 hours ago.' % \ + ( changeset_revision, name, owner ) # Inspect the tool_test_results_dict for the last test run to see if it has not yet been populated. if len( tool_test_results_dicts ) == 0: tool_test_results_dict = {} From 427ad65d9aff6c6fc5a885889ee065e4ae7856b3 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 22 Jan 2014 10:35:31 -0600 Subject: [PATCH 0004/1033] Adjust logic related to_posix_lines to make optionally specified. Fixes library uploads and restores backward-compatiblity to create_paramfile interface to rest of Galaxy. This is an alternative to pull request #305. --- lib/galaxy/tools/actions/upload_common.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py index e134e63fe22..98d267ef4ae 100644 --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -332,7 +332,7 @@ def create_paramfile( trans, uploaded_datasets ): is_binary=is_binary, link_data_only=link_data_only, uuid=uuid_str, - to_posix_lines=uploaded_dataset.to_posix_lines, + to_posix_lines=getattr(uploaded_dataset, "to_posix_lines", True), space_to_tab=uploaded_dataset.space_to_tab, in_place=trans.app.config.external_chown_script is None, path=uploaded_dataset.path ) From 2fbb93ba34b6580a32b421ea86b6d4fa21cd2344 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Wed, 22 Jan 2014 11:48:12 -0500 Subject: [PATCH 0005/1033] Fix tool shed functional test broken when the pull request resulting in changeset 329f9ac was accepted. --- test/tool_shed/functional/test_1140_tool_help_images.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/test/tool_shed/functional/test_1140_tool_help_images.py b/test/tool_shed/functional/test_1140_tool_help_images.py index fcc9f1413d1..86315e32257 100644 --- a/test/tool_shed/functional/test_1140_tool_help_images.py +++ b/test/tool_shed/functional/test_1140_tool_help_images.py @@ -109,10 +109,10 @@ class TestToolHelpImages( ShedTwillTestCase ): In the center tool panel, look for the image string similar to the following string where the encoded_repository_id is previously determined as the installed ToolShedRepository id: - src="/admin_toolshed/static/images//count_modes.png" + src="admin_toolshed/static/images//count_modes.png" ''' repository = self.test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) - image_path = 'src="/admin_toolshed/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) + image_path = 'src="admin_toolshed/static/images/%s/count_modes.png"' % self.security.encode_id( repository.id ) # The repository uploaded in this test should only define one tool, which should be the tool that contains a link to an image. repository_metadata = repository.metadata tool_id = repository_metadata[ 'tools' ][ 0 ][ 'guid' ] From 89e959bb1a160da522f94abfc25a8d9728624680 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 22 Jan 2014 11:06:26 -0600 Subject: [PATCH 0006/1033] Allow adjusting the reset password length in unvierse_wsgi.ini. Purposely not annotated in universe_wsgi.ini.sample - though could be persuaded to add it. --- lib/galaxy/config.py | 1 + lib/galaxy/webapps/galaxy/controllers/user.py | 3 ++- 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index f023b64823d..2164bf8d0f9 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -151,6 +151,7 @@ class Configuration( object ): h, m, s = [ int( v ) for v in self.job_walltime.split( ':' ) ] self.job_walltime_delta = timedelta( 0, s, 0, 0, m, h ) self.admin_users = kwargs.get( "admin_users", "" ) + self.reset_password_length = int( kwargs.get('reset_password_length', '15') ) self.mailing_join_addr = kwargs.get('mailing_join_addr',"galaxy-announce-join@bx.psu.edu") self.error_email_to = kwargs.get( 'error_email_to', None ) self.activation_email = kwargs.get( 'activation_email', None ) diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py index 09b72f0d5cd..5fba76e25c8 100644 --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -1083,7 +1083,8 @@ class User( BaseUIController, UsesFormDefinitionsMixin, CreatesUsersMixin, Creat else: chars = string.letters + string.digits new_pass = "" - for i in range(15): + reset_password_length = getattr( trans.app.config, "reset_password_length", 15 ) + for i in range(reset_password_length): new_pass = new_pass + random.choice(chars) host = trans.request.host.split(':')[0] if host == 'localhost': From 78661d6561f7735eeedc0950d7cdcf98adf33b97 Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Wed, 22 Jan 2014 12:06:59 -0500 Subject: [PATCH 0007/1033] Circster: (a) add style sheet and (b) update styles to use smaller labels. --- static/scripts/viz/circster.js | 23 +++++++++++++++++------ static/style/Gruntfile.js | 8 ++++---- static/style/blue/circster.css | 2 ++ static/style/src/less/circster.less | 7 +++++++ 4 files changed, 30 insertions(+), 10 deletions(-) create mode 100644 static/style/blue/circster.css create mode 100644 static/style/src/less/circster.less diff --git a/static/scripts/viz/circster.js b/static/scripts/viz/circster.js index 3d5222b1887..6a1d10ea668 100644 --- a/static/scripts/viz/circster.js +++ b/static/scripts/viz/circster.js @@ -1,4 +1,7 @@ -define(["libs/underscore", "libs/d3", "viz/visualization"], function(_, d3, visualization) { +define(["utils/utils", "libs/underscore", "libs/d3", "viz/visualization"], function(utils, _, d3, visualization) { + +// Load needed CSS. +utils.cssLoadFile("static/style/circster.css"); /** * Utility class for working with SVG. @@ -652,7 +655,7 @@ var CircsterChromLabelTrackView = CircsterTrackView.extend({ this.bg_fill = 'fff'; // Minimum arc distance for labels to be applied. - this.min_arc_len = 0.08; + this.min_arc_len = 0.05; }, /** @@ -673,9 +676,9 @@ var CircsterChromLabelTrackView = CircsterTrackView.extend({ }) .attr('text-anchor', 'middle') .append("svg:textPath") + .attr("class", "chrom-label") .attr("xlink:href", function(d) { return "#label-" + d.data.chrom; }) .attr('startOffset', '25%') - .attr('font-weight', 'bold') .text(function(d) { return d.data.chrom; }); @@ -791,11 +794,16 @@ var CircsterQuantitativeTrackView = CircsterTrackView.extend({ return "rotate(90)"; }; + // Draw min, max on first chrom only. + this.drawTicks(this.parent_elt, [ this.chroms_layout[0] ], this._data_bounds_ticks_fn(), textTransform, true); + + /* // Filter for visible chroms, then for every third chrom so that labels attached to only every // third chrom. var visibleChroms = _.filter(this.chroms_layout, function(c) { return c.endAngle - c.startAngle > 0.08; }), labeledChroms = _.filter(visibleChroms, function(c, i) { return i % 3 === 0; }); this.drawTicks(this.parent_elt, labeledChroms, this._data_bounds_ticks_fn(), textTransform, true); + */ }, /** @@ -868,7 +876,8 @@ var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({ if (d) { // Each data point has the form [position, value], so return all values. return _.map(d.data, function(p) { - return p[1]; + // Null is used for a lack of data; resolve null to 0 for comparison. + return parseInt(p[1], 10) || 0; }); } else { @@ -876,7 +885,9 @@ var CircsterBigWigTrackView = CircsterQuantitativeTrackView.extend({ } }) ); - return [ _.min(values), this._quantile(values, 0.98) ]; + // For max, use 98% quantile in attempt to avoid very large values. However, this max may be 0 + // for sparsely populated data, so use max in that case. + return [ _.min(values), this._quantile(values, 0.98) || _.max(values) ]; } }); @@ -967,7 +978,7 @@ var Circster = Backbone.View.extend( el : $('#center .unified-panel-body'), // gaps are difficult to set because it very dependent on chromosome size and organization. - total_gap : 2 * Math.PI * 0.1, + total_gap : 2 * Math.PI * 0.4, genome : genome, model : vis, dataset_arc_height : 25 diff --git a/static/style/Gruntfile.js b/static/style/Gruntfile.js index cf49af74613..b8d9c1fb1f6 100644 --- a/static/style/Gruntfile.js +++ b/static/style/Gruntfile.js @@ -5,11 +5,11 @@ module.exports = function(grunt) { var theme = grunt.option( 'theme', 'blue' ); - var out = 'blue' - var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster' ]; + var out = 'blue'; + var lessFiles = [ 'base', 'autocomplete_tagging', 'embed_item', 'iphone', 'masthead', 'library', 'trackster', 'circster' ]; - var _ = grunt.util._; - var fmt = _.sprintf; + var _ = grunt.util._; + var fmt = _.sprintf; // Project configuration. grunt.initConfig({ diff --git a/static/style/blue/circster.css b/static/style/blue/circster.css new file mode 100644 index 00000000000..bd94ab79130 --- /dev/null +++ b/static/style/blue/circster.css @@ -0,0 +1,2 @@ +.chrom-label{font-size:80%} +.tick{font-size:80%} diff --git a/static/style/src/less/circster.less b/static/style/src/less/circster.less new file mode 100644 index 00000000000..2578d0f18bd --- /dev/null +++ b/static/style/src/less/circster.less @@ -0,0 +1,7 @@ +.chrom-label { + font-size: 80%; +} + +.tick { + font-size: 80%; +} \ No newline at end of file From 7c64f0937449eafc35f2d257c8f7fefa20f61415 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Wed, 22 Jan 2014 11:37:15 -0600 Subject: [PATCH 0008/1033] Document recently introduced reset_password_length option. --- universe_wsgi.ini.sample | 4 ++++ 1 file changed, 4 insertions(+) diff --git a/universe_wsgi.ini.sample b/universe_wsgi.ini.sample index 50062e575b6..da5c321d7b2 100644 --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -290,6 +290,10 @@ visualization_plugins_directory = config/plugins/visualizations # If no message specified the warning box will not be shown. #registration_warning_message = Please register only one account - we provide this service free of charge and have limited computational resources. Multi-accounts are tracked and will be subjected to account termination and data deletion. +# When users opt to reset passwords, new ones are created, this option +# specifies the length of these passwords. +#reset_password_length = 15 + # -- Account activation From 7954e0e4c4e7f1c4ec823c931cc6d9b9d1c1f7ac Mon Sep 17 00:00:00 2001 From: Jeremy Goecks Date: Wed, 22 Jan 2014 14:09:09 -0500 Subject: [PATCH 0009/1033] Fix for 9bc3fa1 to allow path rewrites; old Webhelper functions stripped preceding '/' but current functions do not. --- lib/galaxy/web/framework/helpers/__init__.py | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py index 91290d35688..5f0968c2b5f 100644 --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -57,7 +57,7 @@ def css( *args ): Cache-bust with time that server started running on """ - return "\n".join( [ stylesheet_link( "/static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) + return "\n".join( [ stylesheet_link( "static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) def js_helper( prefix, *args ): """ @@ -73,14 +73,14 @@ def js( *args ): Take a prefix and list of javascript names and return appropriate string of script tags. """ - return js_helper( '/static/scripts/', *args ) + return js_helper( 'static/scripts/', *args ) def templates( *args ): """ Take a list of template names (no extension) and return appropriate string of script tags. """ - return js_helper( '/static/scripts/templates/compiled/', *args ) + return js_helper( 'static/scripts/templates/compiled/', *args ) # Hashes From b627c3d0615bc4b7e55de5535d040f26cfab1018 Mon Sep 17 00:00:00 2001 From: Galaxy Date: Wed, 27 Mar 2013 12:32:29 +1300 Subject: [PATCH 0010/1033] lower case external remote user - canonicalise email address --- lib/galaxy/web/framework/__init__.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/web/framework/__init__.py b/lib/galaxy/web/framework/__init__.py index c478c2517e7..cdffb3ded38 100644 --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -726,7 +726,7 @@ class GalaxyWebTransaction( base.DefaultWebTransaction ): #If this is an api request, and they've passed a key, we let this go. assert self.app.config.remote_user_header in self.environ, \ "use_remote_user is set but %s header was not provided" % self.app.config.remote_user_header - remote_user_email = self.environ[ self.app.config.remote_user_header ] + remote_user_email = self.environ[ self.app.config.remote_user_header ].lower() if galaxy_session: # An existing session, make sure correct association exists if galaxy_session.user is None: @@ -854,7 +854,7 @@ class GalaxyWebTransaction( base.DefaultWebTransaction ): """ if not self.app.config.use_remote_user: return None - + remote_user_email = remote_user_email.lower() user = self.sa_session.query( self.app.model.User ) \ .filter( self.app.model.User.table.c.email==remote_user_email ) \ .first() From fb01c3cc96baa56cd5305da0349817ef1f179c8a Mon Sep 17 00:00:00 2001 From: Gert Hulselmans Date: Mon, 27 May 2013 20:55:52 +0200 Subject: [PATCH 0011/1033] Avoid corruption of binary files embedded in gzip, bz2 and zip archives in the upload tool. Add an option in the upload tool to disable the conversion of universal line endings to Posix line endings. This is useful for avoiding corruption of uploaded files when a binary file is contained inside a gzip, bz2 and zip archive. This fixes bug report: https://trello.com/card/issue-with-uploaded-2bit-gz-files/506338ce32ae458f6d15e4b3/702 --- lib/galaxy/datatypes/data.py | 3 ++- lib/galaxy/tools/actions/upload_common.py | 1 + lib/galaxy/tools/parameters/grouping.py | 11 +++++++++++ tools/data_source/upload.py | 12 ++++++++---- tools/data_source/upload.xml | 5 ++++- 5 files changed, 26 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py index c65605daeb0..0b4090dbabb 100644 --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -498,13 +498,14 @@ class Data( object ): def before_setting_metadata( self, dataset ): """This function is called on the dataset before metadata is set.""" dataset.clear_associated_files( metadata_safe = True ) - def __new_composite_file( self, name, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, is_binary = False, space_to_tab = False, **kwds ): + def __new_composite_file( self, name, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, is_binary = False, to_posix_lines = True, space_to_tab = False, **kwds ): kwds[ 'name' ] = name kwds[ 'optional' ] = optional kwds[ 'mimetype' ] = mimetype kwds[ 'description' ] = description kwds[ 'substitute_name_with_metadata' ] = substitute_name_with_metadata kwds[ 'is_binary' ] = is_binary + kwds[ 'to_posix_lines' ] = to_posix_lines kwds[ 'space_to_tab' ] = space_to_tab return Bunch( **kwds ) def add_composite_file( self, name, **kwds ): diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py index a533d7cb35b..920b75d2ecc 100644 --- a/lib/galaxy/tools/actions/upload_common.py +++ b/lib/galaxy/tools/actions/upload_common.py @@ -307,6 +307,7 @@ def create_paramfile( trans, uploaded_datasets ): is_binary = is_binary, link_data_only = link_data_only, uuid = uuid_str, + to_posix_lines = uploaded_dataset.to_posix_lines, space_to_tab = uploaded_dataset.space_to_tab, in_place = trans.app.config.external_chown_script is None, path = uploaded_dataset.path ) diff --git a/lib/galaxy/tools/parameters/grouping.py b/lib/galaxy/tools/parameters/grouping.py index aaaf5fc1c9a..d8dd2376db8 100644 --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -254,6 +254,9 @@ class UploadDataset( Group ): name = context.get( 'NAME', None ) info = context.get( 'INFO', None ) warnings = [] + to_posix_lines = False + if context.get( 'to_posix_lines', None ) not in [ "None", None, False ]: + to_posix_lines = True space_to_tab = False if context.get( 'space_to_tab', None ) not in [ "None", None, False ]: space_to_tab = True @@ -286,6 +289,7 @@ class UploadDataset( Group ): break if file_bunch.path: break + file_bunch.to_posix_lines = to_posix_lines file_bunch.space_to_tab = space_to_tab return file_bunch, warnings def get_filenames( context ): @@ -295,16 +299,21 @@ class UploadDataset( Group ): ftp_files = context['ftp_files'] name = context.get( 'NAME', None ) info = context.get( 'INFO', None ) + to_posix_lines = False + if context.get( 'to_posix_lines', None ) not in [ "None", None, False ]: + to_posix_lines = True space_to_tab = False if context.get( 'space_to_tab', None ) not in [ "None", None, False ]: space_to_tab = True warnings = [] file_bunch = get_data_file_filename( data_file, override_name = name, override_info = info ) if file_bunch.path: + file_bunch.to_posix_lines = to_posix_lines file_bunch.space_to_tab = space_to_tab rval.append( file_bunch ) for file_bunch in get_url_paste_urls_or_filename( context, override_name = name, override_info = info ): if file_bunch.path: + file_bunch.to_posix_lines = to_posix_lines file_bunch.space_to_tab = space_to_tab rval.append( file_bunch ) # look for files uploaded via FTP @@ -378,11 +387,13 @@ class UploadDataset( Group ): #replace sniff here with just creating an empty file temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( d_type.generate_primary_file( dataset ) ), prefix='upload_auto_primary_file' ) dataset.primary_file = temp_name + dataset.to_posix_lines = True dataset.space_to_tab = False else: file_bunch, warnings = get_one_filename( groups_incoming[ 0 ] ) writable_files_offset = 1 dataset.primary_file = file_bunch.path + dataset.to_posix_lines = file_bunch.to_posix_lines dataset.space_to_tab = file_bunch.space_to_tab dataset.warnings.extend( warnings ) if dataset.primary_file is None:#remove this before finish, this should create an empty dataset diff --git a/tools/data_source/upload.py b/tools/data_source/upload.py index 7e76de6a7f3..69dc849eaf6 100644 --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -264,10 +264,14 @@ def add_file( dataset, registry, json_file, output_path ): if link_data_only == 'copy_files': if dataset.type in ( 'server_dir', 'path_paste' ) and data_type not in [ 'gzip', 'bz2', 'zip' ]: in_place = False - if dataset.space_to_tab: - line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place ) - else: - line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) + # Convert universal line endings to Posix line endings, but allow the user to turn it off, + # so that is becomes possible to upload gzip, bz2 or zip files with binary data without + # corrupting the content of those files. + if dataset.to_posix_lines: + if dataset.space_to_tab: + line_count, converted_path = sniff.convert_newlines_sep2tabs( dataset.path, in_place=in_place ) + else: + line_count, converted_path = sniff.convert_newlines( dataset.path, in_place=in_place ) if dataset.file_type == 'auto': ext = sniff.guess_ext( dataset.path, registry.sniff_order ) else: diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml index de02c4afd36..7bf8e1ac5d7 100644 --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -1,6 +1,6 @@ - + from your computer @@ -38,6 +38,9 @@ + + + From 7d45e11af4d7a07789d5f27321643e158723bfeb Mon Sep 17 00:00:00 2001 From: Simone Leo Date: Thu, 6 Jun 2013 17:33:46 +0200 Subject: [PATCH 0012/1033] tools/fastq/fastq_paired_end_joiner: added support for recent Illumina headers --- tools/fastq/fastq_paired_end_joiner.py | 160 +++++++++++++++++++++--- tools/fastq/fastq_paired_end_joiner.xml | 39 ++++-- 2 files changed, 174 insertions(+), 25 deletions(-) diff --git a/tools/fastq/fastq_paired_end_joiner.py b/tools/fastq/fastq_paired_end_joiner.py index da6809b737d..fe2c88979e5 100644 --- a/tools/fastq/fastq_paired_end_joiner.py +++ b/tools/fastq/fastq_paired_end_joiner.py @@ -1,38 +1,162 @@ -#Dan Blankenberg -import sys, os, shutil -from galaxy_utils.sequence.fastq import fastqReader, fastqNamedReader, fastqWriter, fastqJoiner +""" +Extended version of Dan Blankenberg's fastq joiner (adds support for +recent Illumina headers). +""" + +import sys, re +import galaxy_utils.sequence.fastq as fq + + +class IDManager(object): + + def __init__(self, sep="\t"): + """ + Recent Illumina FASTQ header format:: + + @ + COORDS = :::::: + FLAGS = ::: + + where the whitespace character between and can be + either a space or a tab. + """ + self.sep = sep + + def parse_id(self, identifier): + try: + coords, flags = identifier.strip()[1:].split(self.sep, 1) + except ValueError: + raise RuntimeError("bad identifier: %r" % (identifier,)) + return coords.split(":"), flags.split(":") + + def join_id(self, parsed_id): + coords, flags = parsed_id + return "@%s%s%s" % (":".join(coords), self.sep, ":".join(flags)) + + def get_read_number(self, parsed_id): + return int(parsed_id[1][0]) + + def set_read_number(self, parsed_id, n): + parsed_id[1][0] = "%d" % n + + def get_paired_identifier(self, read): + t = self.parse_id(read.identifier) + n = self.get_read_number(t) + if n == 1: + pn = 2 + elif n == 2: + pn = 1 + else: + raise RuntimeError("Unknown read number '%d'" % n) + self.set_read_number(t, pn) + return self.join_id(t) + + +class FastqJoiner(fq.fastqJoiner): + + def __init__(self, format, force_quality_encoding=None, sep="\t"): + super(FastqJoiner, self).__init__(format, force_quality_encoding) + self.id_manager = IDManager(sep) + + def join(self, read1, read2): + force_quality_encoding = self.force_quality_encoding + if not force_quality_encoding: + if read1.is_ascii_encoded(): + force_quality_encoding = 'ascii' + else: + force_quality_encoding = 'decimal' + read1 = read1.convert_read_to_format( + self.format, force_quality_encoding=force_quality_encoding + ) + read2 = read2.convert_read_to_format( + self.format, force_quality_encoding=force_quality_encoding + ) + #-- + t1, t2 = [ + self.id_manager.parse_id(r.identifier) for r in (read1, read2) + ] + if self.id_manager.get_read_number(t1) == 2: + if not self.id_manager.get_read_number(t2) == 1: + raise RuntimeError("input files are not from mated pairs") + read1, read2 = read2, read1 + t1, t2 = t2, t1 + #-- + rval = fq.FASTQ_FORMATS[self.format]() + rval.identifier = read1.identifier + rval.description = "+" + if len(read1.description) > 1: + rval.description += rval.identifier[1:] + if rval.sequence_space == 'color': + # convert to nuc space, join, then convert back + rval.sequence = rval.convert_base_to_color_space( + read1.convert_color_to_base_space(read1.sequence) + + read2.convert_color_to_base_space(read2.sequence) + ) + else: + rval.sequence = read1.sequence + read2.sequence + if force_quality_encoding == 'ascii': + rval.quality = read1.quality + read2.quality + else: + rval.quality = "%s %s" % ( + read1.quality.strip(), read2.quality.strip() + ) + return rval + + def get_paired_identifier(self, read): + return self.id_manager.get_paired_identifier(read) + + +def sniff_sep(fastq_fn): + header = "" + with open(fastq_fn) as f: + while header == "": + try: + header = f.next().strip() + except StopIteration: + raise RuntimeError("%r: empty file" % (fastq_fn,)) + return re.search(r"\s", header).group() + def main(): - #Read command line arguments input1_filename = sys.argv[1] input1_type = sys.argv[2] or 'sanger' input2_filename = sys.argv[3] input2_type = sys.argv[4] or 'sanger' output_filename = sys.argv[5] - + fastq_style = sys.argv[6] or 'old' + #-- if input1_type != input2_type: - print "WARNING: You are trying to join files of two different types: %s and %s." % ( input1_type, input2_type ) - - input2 = fastqNamedReader( open( input2_filename, 'rb' ), input2_type ) - joiner = fastqJoiner( input1_type ) - out = fastqWriter( open( output_filename, 'wb' ), format = input1_type ) - + print "WARNING: trying to join files of different types: %s and %s" % ( + input1_type, input2_type + ) + if fastq_style == 'new': + sep = sniff_sep(input1_filename) + joiner = FastqJoiner(input1_type, sep=sep) + else: + joiner = fq.fastqJoiner(input1_type) + #-- + input2 = fq.fastqNamedReader(open(input2_filename, 'rb'), input2_type) + out = fq.fastqWriter(open(output_filename, 'wb'), format=input1_type) i = None skip_count = 0 - for i, fastq_read in enumerate( fastqReader( open( input1_filename, 'rb' ), format = input1_type ) ): - identifier = joiner.get_paired_identifier( fastq_read ) - fastq_paired = input2.get( identifier ) + for i, fastq_read in enumerate(fq.fastqReader( + open(input1_filename, 'rb' ), format=input1_type + )): + identifier = joiner.get_paired_identifier(fastq_read) + fastq_paired = input2.get(identifier) if fastq_paired is None: skip_count += 1 else: - out.write( joiner.join( fastq_read, fastq_paired ) ) + out.write(joiner.join(fastq_read, fastq_paired)) out.close() - if i is None: - print "Your file contains no valid FASTQ reads." + print "Your file contains no valid FASTQ reads" else: print input2.has_data() - print 'Joined %s of %s read pairs (%.2f%%).' % ( i - skip_count + 1, i + 1, float( i - skip_count + 1 ) / float( i + 1 ) * 100.0 ) + print 'Joined %s of %s read pairs (%.2f%%)' % ( + i - skip_count + 1, i + 1, (i - skip_count + 1) / (i + 1) * 100.0 + ) + if __name__ == "__main__": main() diff --git a/tools/fastq/fastq_paired_end_joiner.xml b/tools/fastq/fastq_paired_end_joiner.xml index c4b6e344565..41ff32c3860 100644 --- a/tools/fastq/fastq_paired_end_joiner.xml +++ b/tools/fastq/fastq_paired_end_joiner.xml @@ -1,9 +1,13 @@ - + on paired end reads - fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file' + fastq_paired_end_joiner.py '$input1_file' '${input1_file.extension[len( 'fastq' ):]}' '$input2_file' '${input2_file.extension[len( 'fastq' ):]}' '$output_file' '$style' + + + + @@ -18,14 +22,19 @@ **What it does** -This tool joins paired end FASTQ reads from two separate files into a single read in one file. The join is performed using sequence identifiers, allowing the two files to contain differing ordering. If a sequence identifier does not appear in both files, it is excluded from the output. - -Sequence identifiers with /1 and /2 appended override the left-hand and right-hand designation; i.e. if the reads end with /1 and /2, the read containing /1 will be used as the left-hand read and the read containing /2 will be used as the right-hand read. Sequences without this designation will follow the left-hand and right-hand settings set by the user. +This tool joins paired end FASTQ reads from two separate files into a +single read in one file. The join is performed using sequence +identifiers, allowing the two files to contain differing ordering. If +a sequence identifier does not appear in both files, it is excluded +from the output. ----- **Input formats** +Both old and new (from recent Illumina software) style FASTQ headers +are supported. The following example uses the "old" style. + Left-hand Read:: @HWI-EAS91_1_30788AAXX:7:21:1542:1758/1 @@ -53,10 +62,26 @@ A multiple-fastq file, for example:: ------ -**Citation** +**The "new" style** -If you use this tool, please cite `Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ +Recent Illumina FASTQ headers are structured as follows:: + @COORDS FLAGS + COORDS = INSTRUMENT:RUN_#:FLOWCELL_ID:LANE:TILE:X:Y + FLAGS = READ:IS_FILTERED:CONTROL_NUMBER:INDEX_SEQUENCE +where the whitespace character between COORDS and FLAGS can be either +a space or a tab. + +------ + +**Credits** + +This is an extended version (adds support for "new" style FASTQ headers) +of D. Blankenberg's fastq joiner: + +`Blankenberg D, Gordon A, Von Kuster G, Coraor N, Taylor J, Nekrutenko A; Galaxy Team. Manipulation of FASTQ data with Galaxy. Bioinformatics. 2010 Jul 15;26(14):1783-5. <http://www.ncbi.nlm.nih.gov/pubmed/20562416>`_ + +New style header support added by Simone Leo <simone.leo@crs4.it> From c6c8e2b03bc36c2f43b899ce2aae7e6fd54ee430 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Tue, 6 Aug 2013 15:58:00 -0400 Subject: [PATCH 0013/1033] Close extended_metadata branch From 28c264a7c31d3178e30ec39be46486230f21856b Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Tue, 8 Oct 2013 16:41:08 -0400 Subject: [PATCH 0014/1033] start data_library branch --- .hgignore | 3 ++ .../webapps/galaxy/api/folder_contents.py | 43 ++++++++++++++++++- lib/galaxy/webapps/galaxy/api/libraries.py | 5 ++- 3 files changed, 48 insertions(+), 3 deletions(-) diff --git a/.hgignore b/.hgignore index 86a0898b2ae..a502f8c0a70 100644 --- a/.hgignore +++ b/.hgignore @@ -115,3 +115,6 @@ doc/build *.rej *~ + +syntax: regexp +^static/AAA_scratch$ \ No newline at end of file diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py index 27e6ed199ec..01fc718ddd7 100644 --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -1,5 +1,5 @@ """ -API operations on the contents of a library. +API operations on the contents of a folder. """ import logging, os, string, shutil, urllib, re, socket from cgi import escape, FieldStorage @@ -11,12 +11,17 @@ from galaxy.model.orm import * log = logging.getLogger( __name__ ) class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems ): + """ + Class controls retrieval, creation and updating of folder contents. + """ @web.expose_api def index( self, trans, folder_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/contents + Displays a collection (list) of a folder's contents (files and folders). + The /api/library_contents/{encoded_library_id}/contents lists everything in a library recursively, which is not what we want here. We could add a parameter to use the recursive @@ -25,7 +30,11 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary rval = [] current_user_roles = trans.get_current_user_roles() + def traverse( folder ): + """ + Load contents of the folder (folders and datasets). + """ admin = trans.user_is_admin() rval = [] for subfolder in folder.active_folders: @@ -50,6 +59,8 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) +# log.debug("XXXXXXXXXXXXXXXXXXXXXXXXXXX folder.parent_library" + str(folder.parent_library.id)) +# log.debug("XXXXXXXXXXXXXXXXXXXXXXXXXXX folder.parent_id" + str(folder.parent_id)) parent_library = folder.parent_library except: folder = None @@ -62,15 +73,43 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): trans.response.status = 400 return "Invalid folder id ( %s ) specified." % str( folder_id ) + # TODO MARTEN Can it be that predecessors of current folder have different access rights? aka user shouldn't see them? + + # Search the path upwards and load the whole route of names and ids for breadcrumb purposes. + path_to_library = [] + + def build_path ( folder ): +# log.debug("XXXXXXXXXXXXXXXXXXXXXXX folder.parent_id BEFORE " + str(folder.parent_id)) +# log.debug("XXXXXXXXXXXXXXXXXXXXXXX folder.parent_library.id BEFORE " + str(folder.parent_library.id)) + if ( folder.parent_id != folder.parent_library.id ) and ( folder.parent_id is not None ): + log.debug("XXXXXXXXXXXXXXXXXXXXXXX LOADING UPPER FOLDER WITH ID: " + str(folder.parent_id)) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + log.debug("XXXXXXXXXXXXXXXXXXXXXXX upper_folder.id " + str(upper_folder.id)) + log.debug("XXXXXXXXXXXXXXXXXXXXXXX upper_folder.name " + str(upper_folder.name)) + path_to_library.append( ( upper_folder.id, upper_folder.name ) ) + path_to_library.extend( build_path( upper_folder ) ) + else: + pass + return path_to_library + + full_path = build_path( folder ) for content in traverse( folder ): + return_item = {} encoded_id = trans.security.encode_id( content.id ) if content.api_type == 'folder': + encoded_parent_library_id = trans.security.encode_id( content.parent_library.id ) encoded_id = 'F' + encoded_id - rval.append( dict( id = encoded_id, + if content.parent_id is not None: # For folder return its parent's id for browsing back. + encoded_parent_id = 'F' + trans.security.encode_id( content.parent_id ) + return_item.update ( dict ( parent_id = encoded_parent_id ) ) + return_item.update( dict( id = encoded_id, type = content.api_type, name = content.name, + library_id = encoded_parent_library_id, + full_path = full_path, url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) + rval.append( return_item ) return rval @web.expose_api diff --git a/lib/galaxy/webapps/galaxy/api/libraries.py b/lib/galaxy/webapps/galaxy/api/libraries.py index fe89f39e538..ce8263cb5f7 100644 --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -49,7 +49,7 @@ class LibrariesController( BaseAPIController ): trans.model.Library.table.c.id.in_( accessible_restricted_library_ids ) ) ) rval = [] for library in query: - item = library.to_dict() + item = library.to_dict( view='element' ) item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) item['id'] = trans.security.encode_id( item['id'] ) rval.append( item ) @@ -131,6 +131,9 @@ class LibrariesController( BaseAPIController ): rval['name'] = name rval['id'] = encoded_id return rval + + def edit( self, trans, payload, **kwd ): + return "Not implemented yet" @web.expose_api def delete( self, trans, id, **kwd ): From c3ba02b4a97dc539947c91548ec4e0b4cb19f373 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 17 Oct 2013 12:56:34 -0400 Subject: [PATCH 0015/1033] working reverse traversing towards root library for every folder = good for path building --- .../webapps/galaxy/api/folder_contents.py | 64 +++++++++++-------- 1 file changed, 39 insertions(+), 25 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py index 01fc718ddd7..2c70cf601b7 100644 --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -27,11 +27,11 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary we want here. We could add a parameter to use the recursive style, but this is meant to act similar to an "ls" directory listing. """ - rval = [] + folder_contents = [] current_user_roles = trans.get_current_user_roles() - def traverse( folder ): + def load_folder_contents( folder ): """ Load contents of the folder (folders and datasets). """ @@ -76,41 +76,55 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary # TODO MARTEN Can it be that predecessors of current folder have different access rights? aka user shouldn't see them? # Search the path upwards and load the whole route of names and ids for breadcrumb purposes. - path_to_library = [] + path_to_root = [] def build_path ( folder ): -# log.debug("XXXXXXXXXXXXXXXXXXXXXXX folder.parent_id BEFORE " + str(folder.parent_id)) -# log.debug("XXXXXXXXXXXXXXXXXXXXXXX folder.parent_library.id BEFORE " + str(folder.parent_library.id)) - if ( folder.parent_id != folder.parent_library.id ) and ( folder.parent_id is not None ): - log.debug("XXXXXXXXXXXXXXXXXXXXXXX LOADING UPPER FOLDER WITH ID: " + str(folder.parent_id)) - upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) - log.debug("XXXXXXXXXXXXXXXXXXXXXXX upper_folder.id " + str(upper_folder.id)) - log.debug("XXXXXXXXXXXXXXXXXXXXXXX upper_folder.name " + str(upper_folder.name)) - path_to_library.append( ( upper_folder.id, upper_folder.name ) ) - path_to_library.extend( build_path( upper_folder ) ) + path_to_root = [] + # We are almost in root + log.debug( "XXXXXXXXXXXXXXXXXXXXXXX folder.parent_id: " + str( folder.parent_id ) ) + log.debug( "XXXXXXXXXXXXXXXXXXXXXXX folder.parent_library.id: " + str( folder.parent_library.id ) ) + if folder.parent_id is None: + log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING: " + str( folder.name ) ) + path_to_root.append( ( folder.id, folder.name ) ) +# upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_library.id ) +# path_to_root.append( ( upper_folder.id, upper_folder.name ) ) else: - pass - return path_to_library + # We add the current folder and traverse up one folder. + log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ADDING THIS FOLDER AND TRAVERSING UP: " + str( folder.name ) ) + path_to_root.append( ( folder.id, folder.name ) ) + upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) + path_to_root.extend( build_path( upper_folder ) ) +# path_to_root = path_to_root.reverse() +# return path_to_root[::-1] + return path_to_root - full_path = build_path( folder ) + # Return the reversed path so it starts with the library node. + full_path = build_path( folder )[::-1] - for content in traverse( folder ): + # Go through every item in the folder and include its meta-data. + for content_item in load_folder_contents( folder ): return_item = {} - encoded_id = trans.security.encode_id( content.id ) - if content.api_type == 'folder': - encoded_parent_library_id = trans.security.encode_id( content.parent_library.id ) + encoded_id = trans.security.encode_id( content_item.id ) + + # For folder return also hierarchy values + if content_item.api_type == 'folder': + encoded_parent_library_id = trans.security.encode_id( content_item.parent_library.id ) encoded_id = 'F' + encoded_id - if content.parent_id is not None: # For folder return its parent's id for browsing back. - encoded_parent_id = 'F' + trans.security.encode_id( content.parent_id ) + if content_item.parent_id is not None: # Return folder's parent id for browsing back. + encoded_parent_id = 'F' + trans.security.encode_id( content_item.parent_id ) return_item.update ( dict ( parent_id = encoded_parent_id ) ) + + # For every item return also the default meta-data return_item.update( dict( id = encoded_id, - type = content.api_type, - name = content.name, + type = content_item.api_type, + name = content_item.name, library_id = encoded_parent_library_id, full_path = full_path, url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) - rval.append( return_item ) - return rval + folder_contents.append( return_item ) + if len( folder_contents ) == 0: + folder_contents.append( dict( full_path = full_path ) ) + return folder_contents @web.expose_api def show( self, trans, id, library_id, **kwd ): From cf6979f3a91aa944eab1599e4f9e7e0f46e776a1 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 21 Oct 2013 12:31:38 -0400 Subject: [PATCH 0016/1033] initial frontend commit --- .../webapps/galaxy/api/folder_contents.py | 15 +- static/AAA_scratch/data_library/index.html | 265 ++++++++++++++++++ .../data_library/index_working.html | 261 +++++++++++++++++ 3 files changed, 533 insertions(+), 8 deletions(-) create mode 100644 static/AAA_scratch/data_library/index.html create mode 100644 static/AAA_scratch/data_library/index_working.html diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py index 2c70cf601b7..91b527e1a27 100644 --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -27,7 +27,7 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary we want here. We could add a parameter to use the recursive style, but this is meant to act similar to an "ls" directory listing. """ - folder_contents = [] + folder_container = [] current_user_roles = trans.get_current_user_roles() @@ -100,7 +100,8 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary # Return the reversed path so it starts with the library node. full_path = build_path( folder )[::-1] - + folder_container.append( dict( full_path = full_path ) ) + folder_contents = [] # Go through every item in the folder and include its meta-data. for content_item in load_folder_contents( folder ): return_item = {} @@ -118,13 +119,11 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary return_item.update( dict( id = encoded_id, type = content_item.api_type, name = content_item.name, - library_id = encoded_parent_library_id, - full_path = full_path, - url = url_for( 'folder_contents', folder_id=encoded_id ) ) ) + library_id = encoded_parent_library_id + ) ) folder_contents.append( return_item ) - if len( folder_contents ) == 0: - folder_contents.append( dict( full_path = full_path ) ) - return folder_contents + folder_container.append( dict( folder_contents = folder_contents ) ) + return folder_container @web.expose_api def show( self, trans, id, library_id, **kwd ): diff --git a/static/AAA_scratch/data_library/index.html b/static/AAA_scratch/data_library/index.html new file mode 100644 index 00000000000..01f7861dad0 --- /dev/null +++ b/static/AAA_scratch/data_library/index.html @@ -0,0 +1,265 @@ + + + + + Data Library + + + + + +
+

Data Library

+
+
+
+ + + + + + + + + + + + + + + + + + + + diff --git a/static/AAA_scratch/data_library/index_working.html b/static/AAA_scratch/data_library/index_working.html new file mode 100644 index 00000000000..582c31bc241 --- /dev/null +++ b/static/AAA_scratch/data_library/index_working.html @@ -0,0 +1,261 @@ + + + + + Data Library + + + + + +
+

Data Library

+
+
+
+ + + + + + + + + + + + + + + + + + + + + + From 412abc3e7a3e5da2ac683fa8f7ed45d621595476 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Thu, 24 Oct 2013 14:22:26 -0400 Subject: [PATCH 0017/1033] refactoring, modals start --- lib/galaxy/model/__init__.py | 2 +- .../webapps/galaxy/api/folder_contents.py | 96 ++++++------ lib/galaxy/webapps/galaxy/api/libraries.py | 2 +- static/AAA_scratch/data_library/index.html | 142 +++++++++--------- 4 files changed, 114 insertions(+), 128 deletions(-) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 53547daf126..36386d27d41 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1835,7 +1835,7 @@ class Library( object, Dictifiable ): return name class LibraryFolder( object, Dictifiable ): - dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build' ) + dict_element_visible_keys = ( 'id', 'parent_id', 'name', 'description', 'item_count', 'genome_build', 'update_time' ) def __init__( self, name=None, description=None, item_count=0, order_id=None ): self.name = name or "Unnamed folder" self.description = description diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py index 91b527e1a27..d8604b3ebc3 100644 --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -15,42 +15,37 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary Class controls retrieval, creation and updating of folder contents. """ + def load_folder_contents( self, trans, folder ): + """ + Loads all contents of the folder (folders and data sets) but only in the first level. + """ + current_user_roles = trans.get_current_user_roles() + is_admin = trans.user_is_admin() + content_items = [] + for subfolder in folder.active_folders: + if not is_admin: + can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) + if (is_admin or can_access) and not subfolder.deleted: + subfolder.api_type = 'folder' + content_items.append( subfolder ) + for dataset in folder.datasets: + if not is_admin: + can_access = trans.app.security_agent.can_access_dataset( current_user_roles, dataset.library_dataset_dataset_association.dataset ) + if (is_admin or can_access) and not dataset.deleted: + dataset.api_type = 'file' + content_items.append( dataset ) + return content_items + @web.expose_api def index( self, trans, folder_id, **kwd ): """ GET /api/folders/{encoded_folder_id}/contents - Displays a collection (list) of a folder's contents (files and folders). - - The /api/library_contents/{encoded_library_id}/contents - lists everything in a library recursively, which is not what - we want here. We could add a parameter to use the recursive - style, but this is meant to act similar to an "ls" directory listing. + Encoded folder ID is prepended with 'F' if it is a folder as opposed to a data set which does not have it. """ folder_container = [] current_user_roles = trans.get_current_user_roles() - - def load_folder_contents( folder ): - """ - Load contents of the folder (folders and datasets). - """ - admin = trans.user_is_admin() - rval = [] - for subfolder in folder.active_folders: - if not admin: - can_access, folder_ids = trans.app.security_agent.check_folder_contents( trans.user, current_user_roles, subfolder ) - if (admin or can_access) and not subfolder.deleted: - subfolder.api_type = 'folder' - rval.append( subfolder ) - for ld in folder.datasets: - if not admin: - can_access = trans.app.security_agent.can_access_dataset( current_user_roles, ld.library_dataset_dataset_association.dataset ) - if (admin or can_access) and not ld.deleted: - ld.api_type = 'file' - rval.append( ld ) - return rval - try: decoded_folder_id = trans.security.decode_id( folder_id[-16:] ) except TypeError: @@ -59,69 +54,68 @@ class FolderContentsController( BaseAPIController, UsesLibraryMixin, UsesLibrary try: folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( decoded_folder_id ) -# log.debug("XXXXXXXXXXXXXXXXXXXXXXXXXXX folder.parent_library" + str(folder.parent_library.id)) -# log.debug("XXXXXXXXXXXXXXXXXXXXXXXXXXX folder.parent_id" + str(folder.parent_id)) parent_library = folder.parent_library except: folder = None - log.error( "FolderContentsController.index: Unable to retrieve folder %s" - % folder_id ) + log.error( "FolderContentsController.index: Unable to retrieve folder with ID: %s" % folder_id ) - # TODO: Find the API's path to this folder if necessary. - # This was needed in recursive descent, but it's not needed - # for "ls"-style content checking: - if not folder or not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + # We didn't find the folder or user does not have an access to it. + if not folder: + trans.response.status = 400 + return "Invalid folder id ( %s ) specified." % str( folder_id ) + + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_library_item( current_user_roles, folder, trans.user ) ): + log.warning( "SECURITY: User (id: %s) without proper access rights is trying to load folder with ID of %s" % ( trans.user.id, folder.id ) ) trans.response.status = 400 return "Invalid folder id ( %s ) specified." % str( folder_id ) - # TODO MARTEN Can it be that predecessors of current folder have different access rights? aka user shouldn't see them? - # Search the path upwards and load the whole route of names and ids for breadcrumb purposes. path_to_root = [] - def build_path ( folder ): + """ + Search the path upwards recursively and load the whole route of names and ids for breadcrumb purposes. + """ path_to_root = [] # We are almost in root - log.debug( "XXXXXXXXXXXXXXXXXXXXXXX folder.parent_id: " + str( folder.parent_id ) ) - log.debug( "XXXXXXXXXXXXXXXXXXXXXXX folder.parent_library.id: " + str( folder.parent_library.id ) ) if folder.parent_id is None: log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ALMOST ROOT FOLDER! ADDING: " + str( folder.name ) ) - path_to_root.append( ( folder.id, folder.name ) ) + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) # upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_library.id ) # path_to_root.append( ( upper_folder.id, upper_folder.name ) ) else: # We add the current folder and traverse up one folder. log.debug( "XXXXXXXXXXXXXXXXXXXXXXX ADDING THIS FOLDER AND TRAVERSING UP: " + str( folder.name ) ) - path_to_root.append( ( folder.id, folder.name ) ) + path_to_root.append( ( 'F' + trans.security.encode_id( folder.id ), folder.name ) ) upper_folder = trans.sa_session.query( trans.app.model.LibraryFolder ).get( folder.parent_id ) path_to_root.extend( build_path( upper_folder ) ) -# path_to_root = path_to_root.reverse() -# return path_to_root[::-1] return path_to_root # Return the reversed path so it starts with the library node. full_path = build_path( folder )[::-1] folder_container.append( dict( full_path = full_path ) ) + folder_contents = [] # Go through every item in the folder and include its meta-data. - for content_item in load_folder_contents( folder ): + for content_item in self.load_folder_contents( trans, folder ): return_item = {} encoded_id = trans.security.encode_id( content_item.id ) # For folder return also hierarchy values if content_item.api_type == 'folder': - encoded_parent_library_id = trans.security.encode_id( content_item.parent_library.id ) +# encoded_parent_library_id = trans.security.encode_id( content_item.parent_library.id ) encoded_id = 'F' + encoded_id - if content_item.parent_id is not None: # Return folder's parent id for browsing back. - encoded_parent_id = 'F' + trans.security.encode_id( content_item.parent_id ) - return_item.update ( dict ( parent_id = encoded_parent_id ) ) +# if content_item.parent_id is not None: # Return folder's parent id for browsing back. +# encoded_parent_id = 'F' + trans.security.encode_id( content_item.parent_id ) + last_updated = content_item.update_time.strftime( "%Y-%m-%d %I:%M %p" ) + return_item.update ( dict ( item_count = content_item.item_count, last_updated = last_updated ) ) # For every item return also the default meta-data return_item.update( dict( id = encoded_id, type = content_item.api_type, - name = content_item.name, - library_id = encoded_parent_library_id + name = content_item.name + ) ) folder_contents.append( return_item ) + # Put the data in the container folder_container.append( dict( folder_contents = folder_contents ) ) return folder_container diff --git a/lib/galaxy/webapps/galaxy/api/libraries.py b/lib/galaxy/webapps/galaxy/api/libraries.py index ce8263cb5f7..fba2a74dddd 100644 --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -51,7 +51,7 @@ class LibrariesController( BaseAPIController ): for library in query: item = library.to_dict( view='element' ) item['url'] = url_for( route, id=trans.security.encode_id( library.id ) ) - item['id'] = trans.security.encode_id( item['id'] ) + item['id'] = 'F' + trans.security.encode_id( item['id'] ) rval.append( item ) return rval diff --git a/static/AAA_scratch/data_library/index.html b/static/AAA_scratch/data_library/index.html index 01f7861dad0..95b705103f9 100644 --- a/static/AAA_scratch/data_library/index.html +++ b/static/AAA_scratch/data_library/index.html @@ -1,10 +1,13 @@ - + Data Library - + + + + @@ -16,7 +19,7 @@ + + @@ -88,34 +93,27 @@ - - From b172b602ad46b4d4a9ee714bba5c002552e33a4b Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Fri, 25 Oct 2013 10:34:28 +0200 Subject: [PATCH 0018/1033] add [ and ] to mapped strings and advanced filters --- tools/stats/filtering.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/tools/stats/filtering.py b/tools/stats/filtering.py index 80b6e51d145..e0a29b2e244 100644 --- a/tools/stats/filtering.py +++ b/tools/stats/filtering.py @@ -48,6 +48,8 @@ mapped_str = { '__ge__': '>=', '__sq__': '\'', '__dq__': '"', + '__ob__': '[', + '__cb__': ']', } for key, value in mapped_str.items(): cond_text = cond_text.replace( key, value ) From def30523201e5749ac5681bbe87e08469a3d8ca7 Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Fri, 25 Oct 2013 15:32:18 -0400 Subject: [PATCH 0019/1033] Close search branch. From ad762d6978428b11b9362c5e1ed2916eff0c6091 Mon Sep 17 00:00:00 2001 From: Kyle Ellrott Date: Tue, 29 Oct 2013 12:07:45 -0700 Subject: [PATCH 0020/1033] Adding parent_library_id field to the LibraryDataset 'to_dict' call. --- lib/galaxy/model/__init__.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 44cb84871cd..8897171ce1a 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2033,6 +2033,7 @@ class LibraryDataset( object ): rval = dict( id = self.id, ldda_id = ldda.id, + parent_library_id = self.folder.parent_library.id, folder_id = self.folder_id, model_class = self.__class__.__name__, name = ldda.name, From a9cdd4e7fa2f987cdafd3fe174f122af1d4c92b0 Mon Sep 17 00:00:00 2001 From: Simon Guest Date: Thu, 31 Oct 2013 14:27:19 +1300 Subject: [PATCH 0021/1033] Fixed bug in Trackster alert message, reporting dbkey as blank when can't load chroms. --- static/scripts/packed/viz/trackster/tracks.js | 2 +- static/scripts/viz/trackster/tracks.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/static/scripts/packed/viz/trackster/tracks.js b/static/scripts/packed/viz/trackster/tracks.js index 5e52c20862f..0a8748b7147 100644 --- a/static/scripts/packed/viz/trackster/tracks.js +++ b/static/scripts/packed/viz/trackster/tracks.js @@ -1 +1 @@ -define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();var ar=n[ai.attr("id")];if(ap.offsetYah){$(this).insertAfter(ai);ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al=aq&&ap.offsetY<=ah){if(ap.offsetY-aq0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("
").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("
"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("
").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("
").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("
").addClass("track-header");ac.append($("
").addClass(this.drag_handle_class));this.name_div=$("
").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac0){this.saved_filters_managers=[];for(var ac=0;ac").addClass("top-container").appendTo(ae);this.browser_content_div=$("
").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("
").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("
").addClass("intro").appendTo(this.viewport_container).hide();var af=$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("
").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("
").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("
").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("
").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("
").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='';for(var aj=0,af=ac.chrom_data.length;aj'+ai+""}if(ag.prev_chroms){ak+='"}if(ag.next_chroms){ak+='"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey:",ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;agac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(acthis.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("
").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("
").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("
").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("
").addClass("param-row").appendTo(parent_div);var ag=$("").attr("value","Run on complete dataset").appendTo(af);var ac=$("").attr("value","Run on visible region").css("margin-left","3em").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at").appendTo(ak);az.append($("").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("
").appendTo(ay).hide(),an=$("
").appendTo(aw),al=$("
").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("
").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("
").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("
").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("
").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al").attr("id",ak).addClass("feature-popup");var au=$(""),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("").appendTo(au);$("' + - '' + - ''; - - // add file type selectore - tmpl += ''; - - // add genome selector - tmpl += ''; - - // add next row - tmpl += '' + - '' + - '' + - ''; - - // return html string - return tmpl; - } -}); - -// return -return { - GalaxyUpload: GalaxyUpload -}; - -}); diff --git a/static/scripts/mvc/upload/upload-model.js b/static/scripts/mvc/upload/upload-model.js new file mode 100644 index 00000000000..c1789141612 --- /dev/null +++ b/static/scripts/mvc/upload/upload-model.js @@ -0,0 +1,27 @@ +// dependencies +define([], function() { + +// model +var Model = Backbone.Model.extend({ + defaults: { + extension : 'auto', + genome : '?', + url_paste : '', + space_to_tabs : false, + status : 'init', + info : null + } +}); + +// collection +var Collection = Backbone.Collection.extend({ + model: Model +}); + +// return +return { + Model: Model, + Collection : Collection +}; + +}); diff --git a/static/scripts/mvc/upload/upload-row.js b/static/scripts/mvc/upload/upload-row.js new file mode 100644 index 00000000000..7c88ad72587 --- /dev/null +++ b/static/scripts/mvc/upload/upload-row.js @@ -0,0 +1,270 @@ +// dependencies +define(['mvc/upload/upload-model'], function(UploadModel) { + +// item view +return Backbone.View.extend({ + // options + options: { + padding : 8 + }, + + // states + status_classes : { + init : 'symbol fa fa-trash-o', + queued : 'symbol fa fa-spinner fa-spin', + success : 'symbol fa fa-check', + error : 'symbol fa fa-exclamation-triangle' + }, + + // render + initialize: function(app, options) { + // link app + this.app = app; + + // link this + var self = this; + + // create model + this.model = new UploadModel.Model(options); + + // add upload item + this.setElement(this._template(options)); + + // link item + var it = this.$el; + + // handle click event + it.find('#symbol').on('click', function() { + // get current status + var status = self.model.get('status'); + + // only remove from queue if not in processing line + if (status == 'init' || status == 'success' || status == 'error') + { + // remove from collection + self.app.collection.remove(self.model); + } + }); + + // handle text editing event + it.find('#text-content').on('keyup', function() { + // get properties + var $el = it.find('#text-content'); + var value = $el.val(); + var count = value.length; + + // update size string + it.find('#size').html(self._formatSize (count)); + + // update url paste content + self.model.set('url_paste', value); + }); + + // handle genome selection + it.find('#genome').on('change', function(e) { + self.model.set('genome', $(e.target).val()); + }); + + // handle extension selection + it.find('#extension').on('change', function(e) { + self.model.set('extension', $(e.target).val()); + }); + + // handle space to tabs button + it.find('#space_to_tabs').on('change', function(e) { + self.model.set('space_to_tabs', $(e.target).prop('checked')); + }); + + // events + this.model.on('change:percentage', function() { + self._refreshPercentage(); + }); + this.model.on('change:status', function() { + self._refreshStatus(); + }); + this.model.on('change:info', function() { + self._refreshInfo(); + }); + this.model.on('remove', function() { + self.remove(); + }); + this.app.collection.on('reset', function() { + self.remove(); + }); + }, + + // render + render: function() { + // read model + var file_name = this.model.get('file_name'); + var file_size = this.model.get('file_size'); + + // link item + var it = this.$el; + + // update title + it.find('#title').html(file_name); + + // update info + it.find('#size').html(this._formatSize (file_size)); + + // activate text field if file content is zero + if (file_size == -1) + { + // get text component + var text = it.find('#text'); + + // get padding + var padding = this.options.padding; + + // get dimensions + var width = it.width() - 2 * padding; + var height = it.height() - padding; + + // set dimensions + text.css('width', width + 'px'); + text.css('top', height + 'px'); + it.height(height + text.height() + 2 * padding); + + // show text field + text.show(); + } + }, + + // progress + _refreshInfo: function() + { + // write error message + var info = this.model.get('info'); + if (info) { + this.$el.find('#info').html('Failed: ' + info).show(); + } else { + this.$el.find('#info').hide(); + } + }, + + // progress + _refreshPercentage : function() + { + var percentage = parseInt(this.model.get('percentage')); + this.$el.find('.progress-bar').css({ width : percentage + '%' }); + if (percentage != 100) + this.$el.find('#percentage').html(percentage + '%'); + else + this.$el.find('#percentage').html('Adding to history...'); + }, + + // status + _refreshStatus : function() + { + // get element + var it = this.$el; + + // identify new status + var status = this.model.get('status'); + var status_class = this.status_classes[status]; + + // identify symbol and reset classes + var sy = this.$el.find('#symbol'); + sy.removeClass(); + + // set new status class + sy.addClass(status_class); + + // enable form fields + if (status == 'init') { + it.find('#text-content').attr('disabled', false); + it.find('#genome').attr('disabled', false); + it.find('#extension').attr('disabled', false); + it.find('#space_to_tabs').attr('disabled', false); + } else { + it.find('#text-content').attr('disabled', true); + it.find('#genome').attr('disabled', true); + it.find('#extension').attr('disabled', true); + it.find('#space_to_tabs').attr('disabled', true); + } + + // success + if (status == 'success') { + it.addClass('success'); + it.find('#percentage').html('100%'); + } + + // error + if (status == 'error') { + it.addClass('danger'); + it.find('.progress').remove(); + } + }, + + // to string + _formatSize : function (size) + { + // identify unit + var unit = ""; + if (size >= 100000000000) { size = size / 100000000000; unit = 'TB'; } else + if (size >= 100000000) { size = size / 100000000; unit = 'GB'; } else + if (size >= 100000) { size = size / 100000; unit = 'MB'; } else + if (size >= 100) { size = size / 100; unit = 'KB'; } else + if (size > 0) { size = size * 10; unit = 'b'; } else + return '-'; + + // return formatted string + return '' + (Math.round(size) / 10) + ' ' + unit; + }, + + // template + _template: function(options) + { + // link this + var self = this; + + // construct template + var tmpl = '' + + '' + + ''; + + // add file type selectore + tmpl += ''; + + // add genome selector + tmpl += ''; + + // add next row + tmpl += '' + + '' + + '' + + ''; + + // return html string + return tmpl; + } + +}); + +}); diff --git a/static/scripts/mvc/upload/upload-view.js b/static/scripts/mvc/upload/upload-view.js new file mode 100644 index 00000000000..ae0d0194a92 --- /dev/null +++ b/static/scripts/mvc/upload/upload-view.js @@ -0,0 +1,509 @@ +// dependencies +define(["galaxy.modal", + "galaxy.masthead", + "utils/utils", + "mvc/upload/upload-model", + "mvc/upload/upload-row", + "utils/uploadbox"], + + function( mod_modal, + mod_masthead, + mod_utils, + UploadModel, + UploadItem + ) { + +// galaxy upload +return Backbone.View.extend( +{ + // own modal + modal : null, + + // button + button_show : null, + + // jquery uploadbox plugin + uploadbox: null, + + // current history + current_history: null, + + // extension types + select_extension :[['Auto-detect', 'auto']], + + // genomes + select_genome : [['Unspecified (?)', '?']], + + // collection + collection : new UploadModel.Collection(), + + // counter + counter : { + // stats + announce : 0, + success : 0, + error : 0, + running : 0, + + // reset stats + reset : function() + { + this.announce = this.success = this.error = this.running = 0; + } + }, + + // options + options : { + nginx_upload_path : '' + }, + + // initialize + initialize : function(options) + { + // link this + var self = this; + + // wait for galaxy history panel (workaround due to the use of iframes) + if (!Galaxy.currHistoryPanel) + { + window.setTimeout(function() { self.initialize() }, 500) + return; + } + + // check if logged in + if (!Galaxy.currUser.get('id')) + return; + + // add activate icon + this.button_show = new mod_masthead.GalaxyMastheadIcon ( + { + icon : 'fa-arrow-circle-o-up', + tooltip : 'Upload Files', + on_click : function(e) { self._eventShow(e) }, + on_unload : function() { + if (self.counter.running > 0) + return "Several uploads are still processing."; + }, + with_number : true + }); + + // add to masthead + Galaxy.masthead.prepend(this.button_show); + + // load extension + var self = this; + mod_utils.jsonFromUrl(galaxy_config.root + "api/datatypes", + function(datatypes) { + for (key in datatypes) + self.select_extension.push([datatypes[key], datatypes[key]]); + }); + + // load genomes + mod_utils.jsonFromUrl(galaxy_config.root + "api/genomes", + function(genomes) { + // backup default + var def = self.select_genome[0]; + + // fill array + self.select_genome = []; + for (key in genomes) + if (genomes[key].length > 1) + if (genomes[key][1] !== def[1]) + self.select_genome.push(genomes[key]); + + // sort + self.select_genome.sort(function(a, b) { + return a[0] > b[0] ? 1 : a[0] < b[0] ? -1 : 0; + }); + + // insert default back to array + self.select_genome.unshift(def); + }); + + // read in options + if (options) { + this.options = _.defaults(options, this.options); + } + + // events + this.collection.on('remove', function(item) { + self._eventRemove(item); + }); + this.collection.on('change', function(item) { + console.log('here'); + }); + }, + + // + // event triggered by upload button + // + + // show/hide upload frame + _eventShow : function (e) + { + // prevent default + e.preventDefault(); + + // create modal + if (!this.modal) + { + // make modal + var self = this; + this.modal = new mod_modal.GalaxyModal( + { + title : 'Upload files from your local drive', + body : this._template('upload-box', 'upload-info'), + buttons : { + 'Select' : function() {self.uploadbox.select()}, + 'Create' : function() {self._eventCreate()}, + 'Upload' : function() {self._eventStart()}, + 'Pause' : function() {self._eventStop()}, + 'Reset' : function() {self._eventReset()}, + 'Close' : function() {self.modal.hide()}, + }, + height : '400', + width : '900' + }); + + // set element + this.setElement('#upload-box'); + + // file upload + var self = this; + this.uploadbox = this.$el.uploadbox( + { + announce : function(index, file, message) { self._eventAnnounce(index, file, message) }, + initialize : function(index, file, message) { return self._eventInitialize(index, file, message) }, + progress : function(index, file, message) { self._eventProgress(index, file, message) }, + success : function(index, file, message) { self._eventSuccess(index, file, message) }, + error : function(index, file, message) { self._eventError(index, file, message) }, + complete : function() { self._eventComplete() } + }); + + // setup info + this._updateScreen(); + } + + // show modal + this.modal.show(); + }, + + // + // events triggered by collection + // + + // remove item from upload list + _eventRemove : function(item) + { + // update status + var status = item.get('status'); + + // reduce counter + if (status == 'success') { + this.counter.success--; + } else if (status == 'error') { + this.counter.error--; + } else { + this.counter.announce--; + } + + // show on screen info + this._updateScreen(); + + // remove from queue + this.uploadbox.remove(item.id); + }, + + // + // events triggered by the upload box plugin + // + + // a new file has been dropped/selected through the uploadbox plugin + _eventAnnounce : function(index, file, message) + { + // update counter + this.counter.announce++; + + // update screen + this._updateScreen(); + + // create view/model + var upload_item = new UploadItem(this, { + id : index, + file_name : file.name, + file_size : file.size + }); + + // add to collection + this.collection.add(upload_item.model); + + // add upload item element to table + $(this.el).find('tbody:last').append(upload_item.$el); + + // render + upload_item.render(); + }, + + // the uploadbox plugin is initializing the upload for this file + _eventInitialize : function(index, file, message) + { + // get element + var it = this.collection.get(index); + + // update status + it.set('state', 'running'); + + // update on screen counter + this.button_show.number(this.counter.announce); + + // get configuration + var file_type = it.get('extension'); + var file_name = it.get('file_name'); + var genome = it.get('genome'); + var url_paste = it.get('url_paste'); + var space_to_tabs = it.get('space_to_tabs'); + + // validate + if (!url_paste && !(file.size > 0)) + return null; + + // configure uploadbox + this.uploadbox.configure({url : this.options.nginx_upload_path, paramname : "files_0|file_data"}); + + // configure tool + tool_input = {}; + tool_input['dbkey'] = genome; + tool_input['file_type'] = file_type; + tool_input['files_0|NAME'] = file_name; + tool_input['files_0|type'] = 'upload_dataset'; + tool_input['files_0|url_paste'] = url_paste; + tool_input['space_to_tabs'] = space_to_tabs; + + // setup data + data = {}; + data['history_id'] = this.current_history; + data['tool_id'] = 'upload1'; + data['inputs'] = JSON.stringify(tool_input); + + // return additional data to be send with file + return data; + }, + + // progress + _eventProgress : function(index, file, percentage) + { + var it = this.collection.get(index); + it.set('percentage', percentage); + }, + + // success + _eventSuccess : function(index, file, message) + { + // update status + var it = this.collection.get(index); + it.set('status', 'success'); + + // update on screen counter + this.button_show.number(''); + + // update counter + this.counter.announce--; + this.counter.success++; + + // update on screen info + this._updateScreen(); + + // update galaxy history + Galaxy.currHistoryPanel.refreshHdas(); + }, + + // error + _eventError : function(index, file, message) + { + // get element + var it = this.collection.get(index); + + // update status + it.set('status', 'error'); + it.set('info', message); + + // update on screen counter + this.button_show.number(''); + + // update counter + this.counter.announce--; + this.counter.error++; + + // update on screen info + this._updateScreen(); + }, + + // queue is done + _eventComplete: function() { + // reset queued upload to initial status + this.collection.each(function(item) { + if(item.get('status') == 'queued') { + item.set('status', 'init'); + } + }); + + // update running + this.counter.running = 0; + this._updateScreen(); + }, + + // + // events triggered by this view + // + + // create (pseudo) file + _eventCreate : function () + { + this.uploadbox.add([{ name : 'New File', size : -1 }]); + }, + + // start upload process + _eventStart : function() { + // check + if (this.counter.announce == 0 || this.counter.running > 0) { + return; + } + + // switch icons for new uploads + this.collection.each(function(item) { + if(item.get('status') == 'init') { + item.set('status', 'queued'); + } + }); + + // backup current history + this.current_history = Galaxy.currHistoryPanel.model.get('id'); + + // update running + this.counter.running = this.counter.announce; + this._updateScreen(); + + // initiate upload procedure in plugin + this.uploadbox.start(); + }, + + // pause upload process + _eventStop : function() { + // check + if (this.counter.running == 0) { + return; + } + + // request pause + this.uploadbox.stop(); + + // set html content + $('#upload-info').html('Queue will pause after completing the current file...'); + }, + + // remove all + _eventReset : function() { + // make sure queue is not running + if (this.counter.running == 0) + { + // reset collection + this.collection.reset(); + + // reset counter + this.counter.reset(); + + // show on screen info + this._updateScreen(); + + // remove from queue + this.uploadbox.reset(); + } + }, + + // set screen + _updateScreen: function () + { + /* + update on screen info + */ + + // check default message + if(this.counter.announce == 0) + { + if (this.uploadbox.compatible()) + message = 'Drag&drop files into this box or click \'Select\' to select files!'; + else + message = 'Unfortunately, your browser does not support multiple file uploads or drag&drop.
Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.' + } else { + if (this.counter.running == 0) + message = 'You added ' + this.counter.announce + ' file(s) to the queue. Add more files or click \'Upload\' to proceed.'; + else + message = 'Please wait...' + this.counter.announce + ' out of ' + this.counter.running + ' remaining.'; + } + + // set html content + $('#upload-info').html(message); + + /* + update button status + */ + + // update reset button + if (this.counter.running == 0 && this.counter.announce + this.counter.success + this.counter.error > 0) + this.modal.enableButton('Reset'); + else + this.modal.disableButton('Reset'); + + // update upload button + if (this.counter.running == 0 && this.counter.announce > 0) + this.modal.enableButton('Upload'); + else + this.modal.disableButton('Upload'); + + // pause upload button + if (this.counter.running > 0) + this.modal.enableButton('Pause'); + else + this.modal.disableButton('Pause'); + + // select upload button + if (this.counter.running == 0) + { + this.modal.enableButton('Select'); + this.modal.enableButton('Create'); + } else { + this.modal.disableButton('Select'); + this.modal.disableButton('Create'); + } + + // table visibility + if (this.counter.announce + this.counter.success + this.counter.error > 0) + $(this.el).find('table').show(); + else + $(this.el).find('table').hide(); + }, + + // load html template + _template: function(id, idInfo) + { + return '
' + + '
").appendTo(av).text(ar);$("").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("
").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:X.Dataset.findOrCreate(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("
").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='Tool: <%= track.tool.name %>
Dataset: <%= track.name %>
Region(s): ',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("
").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("
");if(this.view.editor){this.drag_div=$("
").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("
").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("
");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"
"+ag.message+"
",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ad.tiles_div.append($("").text(" "));ad.tiles_div.append($("").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("
").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("
").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height());ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("
");while(ac"+commatize(ac)+"
").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;aethis.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;adag){ag=aj}}for(ae=0;aethis.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;agI){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("
").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("
");this.tiles_div.prepend($("
").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file +define(["libs/underscore","viz/visualization","viz/trackster/util","viz/trackster/slotting","viz/trackster/painters","viz/trackster/filters","mvc/data","mvc/tools"],function(ab,y,l,u,L,i,X,R){var q=ab.extend;var n={};var k=function(ac,ad){n[ac.attr("id")]=ad};var m=function(ac,ae,ag,af){ag=".group";var ad={};n[ac.attr("id")]=af;ac.bind("drag",{handle:"."+ae,relative:true},function(ao,ap){var an=$(this),at=$(this).parent(),ak=at.children(),am=n[$(this).attr("id")],aj,ai,aq,ah,al;ai=$(this).parents(ag);if(ai.length!==0){aq=ai.position().top;ah=aq+ai.outerHeight();var ar=n[ai.attr("id")];if(ap.offsetYah){$(this).insertAfter(ai);ar.remove_drawable(am);ar.container.add_drawable(am);return}}}ai=null;for(al=0;al=aq&&ap.offsetY<=ah){if(ap.offsetY-aq0?al-1:al))}}}).bind("dragstart",function(){ad["border-top"]=ac.css("border-top");ad["border-bottom"]=ac.css("border-bottom");$(this).css({"border-top":"1px solid blue","border-bottom":"1px solid blue"})}).bind("dragend",function(){$(this).css(ad)})};var F=20,B=100,I=12000,S=400,K=5000,x=100,o="Cannot display dataset due to an error. ",J="A converter for this dataset is not installed. Please check your datatypes_conf.xml file.",G="No data for this chrom/contig.",w="Preparing data. This can take a while for a large dataset. If the visualization is saved and closed, preparation will continue in the background.",z="Tool cannot be rerun: ",b="Loading data...",U="Ready for display",Q=10,H=20,C=["Histogram","Line","Filled","Intensity"];function V(ad,ac){if(!ac){ac=0}var ae=Math.pow(10,ac);return Math.round(ad*ae)/ae}var r=function(ad,ac,af){if(!r.id_counter){r.id_counter=0}this.id=r.id_counter++;this.view=ad;this.container=ac;this.drag_handle_class=af.drag_handle_class;this.is_overview=false;this.action_icons={};this.config=new j({params:this.config_params,onchange:this.config_onchange,saved_values:af.prefs});this.prefs=this.config.get("values");if(!this.prefs.name){this.prefs.name=af.name}if(this.config_onchange){this.config.on("change:values",this.config_onchange,this)}this.container_div=this.build_container_div();this.header_div=this.build_header_div();if(this.header_div){this.container_div.append(this.header_div);this.icons_div=$("
").css("float","left").hide().appendTo(this.header_div);this.build_action_icons(this.action_icons_def);this.header_div.append($("
"));this.header_div.dblclick(function(ag){ag.stopPropagation()});var ae=this;this.container_div.hover(function(){ae.icons_div.show()},function(){ae.icons_div.hide()});$("
").appendTo(this.container_div)}};r.prototype.action_icons_def=[{name:"toggle_icon",title:"Hide/show content",css_class:"toggle",on_click_fn:function(ac){if(ac.prefs.content_visible){ac.action_icons.toggle_icon.addClass("toggle-expand").removeClass("toggle");ac.hide_contents();ac.prefs.content_visible=false}else{ac.action_icons.toggle_icon.addClass("toggle").removeClass("toggle-expand");ac.prefs.content_visible=true;ac.show_contents()}}},{name:"settings_icon",title:"Edit settings",css_class:"settings-icon",on_click_fn:function(ad){var ac=new a({model:ad.config});ac.render()}},{name:"remove_icon",title:"Remove",css_class:"remove-icon",on_click_fn:function(ac){$(".tooltip").remove();ac.remove()}}];q(r.prototype,{config_params:[{key:"name",label:"Name",type:"text",default_value:""},{key:"content_visible",type:"bool",default_value:true,hidden:true}],config_onchange:function(){this.track.set_name(this.track.config.get("values").name)},init:function(){},changed:function(){this.view.changed()},can_draw:function(){if(this.enabled&&this.prefs.content_visible){return true}return false},request_draw:function(){},_draw:function(ac){},to_dict:function(){},set_name:function(ac){this.old_name=this.prefs.name;this.prefs.name=ac;this.name_div.text(this.prefs.name)},revert_name:function(){if(this.old_name){this.prefs.name=this.old_name;this.name_div.text(this.prefs.name)}},remove:function(){this.changed();this.container.remove_drawable(this);var ac=this.view;this.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})},build_container_div:function(){},build_header_div:function(){},add_action_icon:function(ad,ai,ah,ag,ac,af){var ae=this;this.action_icons[ad]=$("").attr("title",ai).addClass("icon-button").addClass(ah).tooltip().click(function(){ag(ae)}).appendTo(this.icons_div);if(af){this.action_icons[ad].hide()}},build_action_icons:function(ac){var ae;for(var ad=0;ad").addClass("content-div").attr("id","group_"+this.id+"_content_div").appendTo(this.container_div);k(this.container_div,this);k(this.content_div,this);m(this.container_div,this.drag_handle_class,".group",this);this.filters_manager=new i.FiltersManager(this);this.header_div.after(this.filters_manager.parent_div);this.saved_filters_managers=[];if("drawables" in af){this.unpack_drawables(af.drawables)}if("filters" in af){var ae=this.filters_manager;this.filters_manager=new i.FiltersManager(this,af.filters);ae.parent_div.replaceWith(this.filters_manager.parent_div);if(af.filters.visible){this.setup_multitrack_filtering()}}};q(P.prototype,r.prototype,A.prototype,{action_icons_def:[r.prototype.action_icons_def[0],r.prototype.action_icons_def[1],{name:"composite_icon",title:"Show composite track",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_composite_track()}},{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters();ac._restore_filter_managers()}else{ac.setup_multitrack_filtering();ac.request_draw({clear_tile_cache:true})}ac.filters_manager.toggle()}},r.prototype.action_icons_def[2]],build_container_div:function(){var ac=$("
").addClass("group").attr("id","group_"+this.id);if(this.container){this.container.content_div.append(ac)}return ac},build_header_div:function(){var ac=$("
").addClass("track-header");ac.append($("
").addClass(this.drag_handle_class));this.name_div=$("
").addClass("track-name").text(this.prefs.name).appendTo(ac);return ac},hide_contents:function(){this.tiles_div.hide()},show_contents:function(){this.tiles_div.show();this.request_draw()},update_icons:function(){var ae=this.drawables.length;if(ae===0){this.action_icons.composite_icon.hide();this.action_icons.filters_icon.hide()}else{if(ae===1){if(this.drawables[0] instanceof f){this.action_icons.composite_icon.show()}this.action_icons.filters_icon.hide()}else{var al,ak,ai,ao=true,ag=this.drawables[0].get_type(),ac=0;for(al=0;al1&&ac===this.drawables.length){var ap={},ad;ai=this.drawables[0];for(ak=0;ak0){this.action_icons.filters_icon.show()}else{this.action_icons.filters_icon.hide()}}else{this.action_icons.filters_icon.hide()}}}},_restore_filter_managers:function(){for(var ac=0;ac0){this.saved_filters_managers=[];for(var ac=0;ac").addClass("top-container").appendTo(ae);this.browser_content_div=$("
").addClass("content").css("position","relative").appendTo(ae);this.bottom_container=$("
").addClass("bottom-container").appendTo(ae);this.top_labeltrack=$("
").addClass("top-labeltrack").appendTo(this.top_container);this.viewport_container=$("
").addClass("viewport-container").attr("id","viewport-container").appendTo(this.browser_content_div);this.content_div=this.viewport_container;k(this.viewport_container,ac);this.intro_div=$("
").addClass("intro").appendTo(this.viewport_container).hide();var af=$("
").text("Add Datasets to Visualization").addClass("action-button").appendTo(this.intro_div).click(function(){y.select_datasets(galaxy_config.root+"visualization/list_current_history_datasets",galaxy_config.root+"api/datasets",{"f-dbkey":ac.dbkey},function(ag){ab.each(ag,function(ah){ac.add_drawable(p(ah,ac,ac))})})});this.nav_labeltrack=$("
").addClass("nav-labeltrack").appendTo(this.bottom_container);this.nav_container=$("
").addClass("trackster-nav-container").prependTo(this.top_container);this.nav=$("
").addClass("trackster-nav").appendTo(this.nav_container);this.overview=$("
").addClass("overview").appendTo(this.bottom_container);this.overview_viewport=$("
").addClass("overview-viewport").appendTo(this.overview);this.overview_close=$("").attr("title","Close overview").addClass("icon-button overview-close tooltip").hide().appendTo(this.overview_viewport);this.overview_highlight=$("
").addClass("overview-highlight").hide().appendTo(this.overview_viewport);this.overview_box_background=$("
").addClass("overview-boxback").appendTo(this.overview_viewport);this.overview_box=$("
").addClass("overview-box").appendTo(this.overview_viewport);this.default_overview_height=this.overview_box.height();this.nav_controls=$("
").addClass("nav-controls").appendTo(this.nav);this.chrom_select=$("").addClass("nav-input").hide().bind("keyup focusout",ad).appendTo(this.nav_controls);this.location_span=$("").addClass("location").attr("original-title","Click to change location").tooltip({placement:"bottom"}).appendTo(this.nav_controls);this.location_span.click(function(){ac.location_span.hide();ac.chrom_select.hide();ac.nav_input.val(ac.chrom+":"+ac.low+"-"+ac.high);ac.nav_input.css("display","inline-block");ac.nav_input.select();ac.nav_input.focus();ac.nav_input.autocomplete({source:function(ai,ag){var aj=[],ah=$.map(ac.get_tracks(d),function(ak){return ak.data_manager.search_features(ai.term).success(function(al){aj=aj.concat(al)})});$.when.apply($,ah).done(function(){ag($.map(aj,function(ak){return{label:ak[0],value:ak[1]}}))})}})});if(this.vis_id!==undefined){this.hidden_input=$("").attr("type","hidden").val(this.vis_id).appendTo(this.nav_controls)}this.zo_link=$("").attr("id","zoom-out").attr("title","Zoom out").tooltip({placement:"bottom"}).click(function(){ac.zoom_out();ac.request_redraw()}).appendTo(this.nav_controls);this.zi_link=$("").attr("id","zoom-in").attr("title","Zoom in").tooltip({placement:"bottom"}).click(function(){ac.zoom_in();ac.request_redraw()}).appendTo(this.nav_controls);this.load_chroms_deferred=this.load_chroms({low:0});this.chrom_select.bind("change",function(){ac.change_chrom(ac.chrom_select.val())});this.browser_content_div.click(function(ag){$(this).find("input").trigger("blur")});this.browser_content_div.bind("dblclick",function(ag){ac.zoom_in(ag.pageX,this.viewport_container)});this.overview_box.bind("dragstart",function(ag,ah){this.current_x=ah.offsetX}).bind("drag",function(ag,ai){var aj=ai.offsetX-this.current_x;this.current_x=ai.offsetX;var ah=Math.round(aj/ac.viewport_container.width()*(ac.max_high-ac.max_low));ac.move_delta(-ah)});this.overview_close.click(function(){ac.reset_overview()});this.viewport_container.bind("draginit",function(ag,ah){if(ag.clientX>ac.viewport_container.width()-16){return false}}).bind("dragstart",function(ag,ah){ah.original_low=ac.low;ah.current_height=ag.clientY;ah.current_x=ah.offsetX}).bind("drag",function(ai,ak){var ag=$(this);var al=ak.offsetX-ak.current_x;var ah=ag.scrollTop()-(ai.clientY-ak.current_height);ag.scrollTop(ah);ak.current_height=ai.clientY;ak.current_x=ak.offsetX;var aj=Math.round(al/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}).bind("mousewheel",function(ai,ak,ah,ag){if(ah){ah*=50;var aj=Math.round(-ah/ac.viewport_container.width()*(ac.high-ac.low));ac.move_delta(aj)}});this.top_labeltrack.bind("dragstart",function(ag,ah){return $("
").css({height:ac.browser_content_div.height()+ac.top_labeltrack.height()+ac.nav_labeltrack.height()+1,top:"0px",position:"absolute","background-color":"#ccf",opacity:0.5,"z-index":1000}).appendTo($(this))}).bind("drag",function(ak,al){$(al.proxy).css({left:Math.min(ak.pageX,al.startX)-ac.container.offset().left,width:Math.abs(ak.pageX-al.startX)});var ah=Math.min(ak.pageX,al.startX)-ac.container.offset().left,ag=Math.max(ak.pageX,al.startX)-ac.container.offset().left,aj=(ac.high-ac.low),ai=ac.viewport_container.width();ac.update_location(Math.round(ah/ai*aj)+ac.low,Math.round(ag/ai*aj)+ac.low)}).bind("dragend",function(al,am){var ah=Math.min(al.pageX,am.startX),ag=Math.max(al.pageX,am.startX),aj=(ac.high-ac.low),ai=ac.viewport_container.width(),ak=ac.low;ac.low=Math.round(ah/ai*aj)+ak;ac.high=Math.round(ag/ai*aj)+ak;$(am.proxy).remove();ac.request_redraw()});this.add_label_track(new W(this,{content_div:this.top_labeltrack}));this.add_label_track(new W(this,{content_div:this.nav_labeltrack}));$(window).bind("resize",function(){if(this.resize_timer){clearTimeout(this.resize_timer)}this.resize_timer=setTimeout(function(){ac.resize_window()},500)});$(document).bind("redraw",function(){ac.redraw()});this.reset();$(window).trigger("resize")},get_base_color:function(ac){return this.config.get("values")[ac.toLowerCase()+"_color"]||this.config.get("values").n_color}});q(Y.prototype,A.prototype,{changed:function(){this.has_changes=true},update_intro_div:function(){if(this.drawables.length===0){this.intro_div.show()}else{this.intro_div.hide()}},trigger_navigate:function(ad,af,ac,ag){if(this.timer){clearTimeout(this.timer)}if(ag){var ae=this;this.timer=setTimeout(function(){ae.trigger("navigate",ad+":"+af+"-"+ac)},500)}else{view.trigger("navigate",ad+":"+af+"-"+ac)}},update_location:function(ac,ae){this.location_span.text(commatize(ac)+" - "+commatize(ae));this.nav_input.val(this.chrom+":"+commatize(ac)+"-"+commatize(ae));var ad=view.chrom_select.val();if(ad!==""){this.trigger_navigate(ad,view.low,view.high,true)}},load_chroms:function(ae){ae.num=x;var ac=this,ad=$.Deferred();$.ajax({url:galaxy_config.root+"api/genomes/"+this.dbkey,data:ae,dataType:"json",success:function(ag){if(ag.chrom_info.length===0){return}if(ag.reference){var ah=new D(ac);ac.add_label_track(ah);ac.reference_track=ah}ac.chrom_data=ag.chrom_info;var ak='';for(var aj=0,af=ac.chrom_data.length;aj'+ai+""}if(ag.prev_chroms){ak+='"}if(ag.next_chroms){ak+='"}ac.chrom_select.html(ak);ac.chrom_start_index=ag.start_index;ad.resolve(ag.chrom_info)},error:function(){alert("Could not load chroms for this dbkey: "+ac.dbkey)}});return ad},change_chrom:function(ah,ad,aj){var ae=this;if(!ae.chrom_data){ae.load_chroms_deferred.then(function(){ae.change_chrom(ah,ad,aj)});return}if(!ah||ah==="None"){return}if(ah==="previous"){ae.load_chroms({low:this.chrom_start_index-x});return}if(ah==="next"){ae.load_chroms({low:this.chrom_start_index+x});return}var ai=$.grep(ae.chrom_data,function(ak,al){return ak.chrom===ah})[0];if(ai===undefined){ae.load_chroms({chrom:ah},function(){ae.change_chrom(ah,ad,aj)});return}else{if(ah!==ae.chrom){ae.chrom=ah;ae.chrom_select.val(ae.chrom);ae.max_high=ai.len-1;ae.reset();for(var ag=0,ac=ae.drawables.length;agac.max_high){ac.high=ac.max_high;ac.low=ac.max_high-ae}else{ac.high-=af;ac.low-=af}}ac.request_redraw({data_fetch:false});if(this.redraw_on_move_fn){clearTimeout(this.redraw_on_move_fn)}this.redraw_on_move_fn=setTimeout(function(){ac.request_redraw()},200);var ad=ac.chrom_select.val();this.trigger_navigate(ad,ac.low,ac.high,true)},add_drawable:function(ac){A.prototype.add_drawable.call(this,ac);ac.init();this.changed();this.update_intro_div()},add_label_track:function(ac){ac.view=this;ac.init();this.label_tracks.push(ac)},remove_drawable:function(ae,ad){A.prototype.remove_drawable.call(this,ae);if(ad){var ac=this;ae.container_div.hide(0,function(){$(this).remove();ac.update_intro_div()})}},reset:function(){this.low=this.max_low;this.high=this.max_high;this.viewport_container.find(".yaxislabel").remove()},request_redraw:function(ad,ae){var ac=this,af=(ae?[ae]:ac.drawables);ab.each(af,function(ag){var ah=ab.find(ac.tracks_to_be_redrawn,function(ai){return ai[0]===ag});if(ah){ah[1]=ad}else{ac.tracks_to_be_redrawn.push([ag,ad])}});if(!this.requested_redraw){requestAnimationFrame(function(){ac._redraw()});this.requested_redraw=true}},_redraw:function(){this.requested_redraw=false;var ac=this.low,ag=this.high;if(acthis.max_high){ag=this.max_high}var ad=this.high-this.low;if(this.high!==0&&ad").addClass("param-label").text(af.get("label")).appendTo(ae);var ad=$("
").addClass("param-input").html(af.get("html")).appendTo(ae);ad.find(":input").val(af.get("value"));$("
").appendTo(ae)},update_value:function(ac){this.model.set_value($(ac.target).val())}});var aa=Backbone.View.extend({initialize:function(ac){this.model.on("change:hidden",this.set_visible,this)},render:function(){var ad=this;tool=this.model,parent_div=this.$el.addClass("dynamic-tool").hide();parent_div.bind("drag",function(ah){ah.stopPropagation()}).click(function(ah){ah.stopPropagation()}).bind("dblclick",function(ah){ah.stopPropagation()}).keydown(function(ah){ah.stopPropagation()});var ae=$("
").appendTo(parent_div).text(tool.get("name"));tool.get("inputs").each(function(ai){var ah=new v({model:ai});ah.render();parent_div.append(ah.$el)});parent_div.find("input").click(function(){$(this).select()});var af=$("
").addClass("param-row").appendTo(parent_div);var ag=$("").attr("value","Run on complete dataset").appendTo(af);var ac=$("").attr("value","Run on visible region").css("margin-left","3em").appendTo(af);ac.click(function(){ad.run_on_region()});ag.click(function(){ad.run_on_dataset()});if(tool.is_visible()){this.$el.show()}},set_visible:function(){if(this.model.is_visible()){this.$el.show()}else{this.$el.hide()}},update_params:function(){for(var ac=0;ac").keydown(function(ak){ak.stopPropagation()});var ai;function ah(ao,ak){for(var at=0;at").appendTo(ak);az.append($("").addClass("icon-button arrow-circle").appendTo(ay).attr("title","Set new random color").tooltip(),aw=$("
").appendTo(ay).hide(),an=$("
").appendTo(aw),al=$("
").appendTo(aw),ap=$.farbtastic(an,{width:100,height:100,callback:au,color:ax});ay.append($("
").css("clear","both"));(function(aA){ar.click(function(){aA.setColor(l.get_random_color())})})(ap)}else{az.append($("").attr("id",am).attr("name",am).val(ax))}}}}if(ai.help){az.append($("
").text(ai.help))}}}ah(aj.get("params"),ac);var ad=this,ag=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ae=function(){ad.update_from_form($(Galaxy.modal.el));Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},af=function(ak){if((ak.keyCode||ak.which)===27){ag()}else{if((ak.keyCode||ak.which)===13){ae()}}};$(window).bind("keypress.check_enter_esc",af);Galaxy.modal.show({title:"Configure",body:ac,buttons:{Cancel:ag,Ok:ae}})},update_from_form:function(ac){var ad=this.model;var ae=false;ab.each(ad.get("params"),function(ah,af){if(!ah.hidden){var ai="param_"+af;var ag=ac.find("#"+ai).val();if(ah.type==="bool"){ag=ac.find("#"+ai).is(":checked")}ae=ad.set_param_value(ah.key,ag)||ae}})}});var c=function(ac,af,ag,ad,ae){this.track=ac;this.region=af;this.low=af.get("start");this.high=af.get("end");this.w_scale=ag;this.canvas=ad;this.html_elt=$("
").append(ad);this.data=ae;this.stale=false};c.prototype.predisplay_actions=function(){};var M=function(ac,af,ag,ad,ae){c.call(this,ac,af,ag,ad,ae)};M.prototype.predisplay_actions=function(){};var O=function(af,am,ao,ae,ah,ai,ap,ad,al){c.call(this,af,am,ao,ae,ah);this.mode=ai;this.all_slotted=ad;this.feature_mapper=al;this.has_icons=false;if(ap){this.has_icons=true;var aj=this;ae=this.html_elt.children()[0],message_div=$("
").addClass("tile-message").css({height:F,width:ae.width}).prependTo(this.html_elt);var ak=new y.GenomeRegion({chrom:af.view.chrom,start:this.low,end:this.high}),an=ah.length,ag=$("").addClass("icon more-down").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data including depth").tooltip().appendTo(message_div),ac=$("").addClass("icon more-across").attr("title","For speed, only the first "+an+" features in this region were obtained from server. Click to get more data excluding depth").tooltip().appendTo(message_div);ag.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.DEEP_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()});ac.click(function(){aj.stale=true;af.data_manager.get_more_data(ak,af.mode,1/aj.w_scale,{},af.data_manager.BROAD_DATA_REQ);$(".tooltip").hide();af.request_draw()}).dblclick(function(aq){aq.stopPropagation()})}};q(O.prototype,c.prototype);O.prototype.predisplay_actions=function(){var ad=this,ac={};if(ad.mode!=="Pack"){return}$(this.html_elt).hover(function(){this.hovered=true;$(this).mousemove()},function(){this.hovered=false;$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()}).mousemove(function(ao){if(!this.hovered){return}var aj=$(this).offset(),an=ao.pageX-aj.left,am=ao.pageY-aj.top,at=ad.feature_mapper.get_feature_data(an,am),ak=(at?at[0]:null);$(this).parents(".track-content").children(".overlay").children(".feature-popup").each(function(){if(!ak||$(this).attr("id")!==ak.toString()){$(this).remove()}});if(at){var af=ac[ak];if(!af){var ap={name:at[3],start:at[1],end:at[2],strand:at[4]},ai=ad.track.filters_manager.filters,ah;for(var al=0;al").attr("id",ak).addClass("feature-popup");var au=$(""),ar,aq,av;for(ar in ap){aq=ap[ar];av=$("").appendTo(au);$(" - ##
").appendTo(av).text(ar);$("").attr("align","left").appendTo(av).text(typeof(aq)==="number"?V(aq,2):aq)}af.append($("
").append(au));ac[ak]=af}af.appendTo($(this).parents(".track-content").children(".overlay"));var ag=an+parseInt(ad.html_elt.css("left"),10)-af.width()/2,ae=am+parseInt(ad.html_elt.css("top"),10)+7;af.css("left",ag+"px").css("top",ae+"px")}else{if(!ao.isPropagationStopped()){ao.stopPropagation();$(this).siblings().each(function(){$(this).trigger(ao)})}}}).mouseleave(function(){$(this).parents(".track-content").children(".overlay").children(".feature-popup").remove()})};var g=function(ad,ac,ae){q(ae,{drag_handle_class:"draghandle"});r.call(this,ad,ac,ae);this.dataset=null;if(ae.dataset){this.dataset=(ae.dataset instanceof Backbone.Model?ae.dataset:X.Dataset.findOrCreate(ae.dataset))}this.dataset_check_type="converted_datasets_state";this.data_url_extra_params={};this.data_query_wait=("data_query_wait" in ae?ae.data_query_wait:K);this.data_manager=("data_manager" in ae?ae.data_manager:new y.GenomeDataManager({dataset:this.dataset,genome:new y.Genome({key:ad.dbkey,chroms_info:{chrom_info:ad.chrom_data}}),data_mode_compatible:this.data_and_mode_compatible,can_subset:this.can_subset}));this.min_height_px=16;this.max_height_px=800;this.visible_height_px=this.prefs.height;this.content_div=$("
").appendTo(this.container_div);if(this.container){this.container.content_div.append(this.container_div);if(!("resize" in ae)||ae.resize){this.add_resize_handle()}}};q(g.prototype,r.prototype,{action_icons_def:[{name:"mode_icon",title:"Set display mode",css_class:"chevron-expand",on_click_fn:function(){}},r.prototype.action_icons_def[0],{name:"overview_icon",title:"Set as overview",css_class:"overview-icon",on_click_fn:function(ac){ac.view.set_overview(ac)}},r.prototype.action_icons_def[1],{name:"filters_icon",title:"Filters",css_class:"filters-icon",on_click_fn:function(ac){if(ac.filters_manager.visible()){ac.filters_manager.clear_filters()}else{ac.filters_manager.init_filters()}ac.filters_manager.toggle()}},{name:"tools_icon",title:"Tool",css_class:"hammer",on_click_fn:function(ac){ac.tool.toggle();if(ac.tool.is_visible()){ac.set_name(ac.name+ac.tool_region_and_parameters_str())}else{ac.revert_name()}$(".tooltip").remove()}},{name:"param_space_viz_icon",title:"Tool parameter space visualization",css_class:"arrow-split",on_click_fn:function(ac){var af='Tool: <%= track.tool.name %>
Dataset: <%= track.name %>
Region(s): ',ae=ab.template(af,{track:ac});var ah=function(){Galaxy.modal.hide();$(window).unbind("keypress.check_enter_esc")},ad=function(){var aj=$('select[name="regions"] option:selected').val(),al,ai=new y.GenomeRegion({chrom:view.chrom,start:view.low,end:view.high}),ak=ab.map($(".bookmark"),function(am){return new y.GenomeRegion({from_str:$(am).children(".position").text()})});if(aj==="cur"){al=[ai]}else{if(aj==="bookmarks"){al=ak}else{al=[ai].concat(ak)}}Galaxy.modal.hide();window.location.href=galaxy_config.root+"visualization/sweepster?"+$.param({dataset_id:ac.dataset.id,hda_ldda:ac.dataset.get("hda_ldda"),regions:JSON.stringify(new Backbone.Collection(al).toJSON())})},ag=function(ai){if((ai.keyCode||ai.which)===27){ah()}else{if((ai.keyCode||ai.which)===13){ad()}}};Galaxy.modal.show({title:"Visualize tool parameter space and output from different parameter settings?",body:ae,buttons:{No:ah,Yes:ad}})}},r.prototype.action_icons_def[2]],can_draw:function(){return this.dataset&&r.prototype.can_draw.call(this)},build_container_div:function(){return $("
").addClass("track").attr("id","track_"+this.id).css("position","relative")},build_header_div:function(){var ac=$("
");if(this.view.editor){this.drag_div=$("
").addClass(this.drag_handle_class).appendTo(ac)}this.name_div=$("
").addClass("track-name").appendTo(ac).text(this.prefs.name).attr("id",this.prefs.name.replace(/\s+/g,"-").replace(/[^a-zA-Z0-9\-]/g,"").toLowerCase());return ac},set_dataset:function(ac){this.dataset=ac;this.data_manager.set("dataset",ac)},on_resize:function(){this.request_draw({clear_tile_cache:true})},add_resize_handle:function(){var ac=this;var af=false;var ae=false;var ad=$("
");$(ac.container_div).hover(function(){if(ac.prefs.content_visible){af=true;ad.show()}},function(){af=false;if(!ae){ad.hide()}});ad.hide().bind("dragstart",function(ag,ah){ae=true;ah.original_height=$(ac.content_div).height()}).bind("drag",function(ah,ai){var ag=Math.min(Math.max(ai.original_height+ai.deltaY,ac.min_height_px),ac.max_height_px);$(ac.tiles_div).css("height",ag);ac.visible_height_px=(ac.max_height_px===ag?0:ag);ac.on_resize()}).bind("dragend",function(ag,ah){ac.tile_cache.clear();ae=false;if(!af){ad.hide()}ac.config.get("values").height=ac.visible_height_px;ac.changed()}).appendTo(ac.container_div)},set_display_modes:function(af,ai){this.display_modes=af;this.mode=(ai?ai:(this.config&&this.config.get("values").mode?this.config.get("values").mode:this.display_modes[0]));this.action_icons.mode_icon.attr("title","Set display mode (now: "+this.mode+")");var ad=this,ag={};for(var ae=0,ac=ad.display_modes.length;ae").text("View error").click(function(){Galaxy.modal.show({title:"Trackster Error",body:"
"+ag.message+"
",buttons:{Close:function(){Galaxy.modal.hide()}}})}));ad.tiles_div.append($("").text(" "));ad.tiles_div.append($("").text("Try again").click(function(){ad.init(true)}))}}else{if(ag==="no converter"){ad.container_div.addClass("error");ad.tiles_div.text(J)}else{if(ag==="no data"||(ag.data!==undefined&&(ag.data===null||ag.data.length===0))){ad.container_div.addClass("nodata");ad.tiles_div.text(G)}else{if(ag==="pending"){ad.container_div.addClass("pending");ad.tiles_div.html(w);setTimeout(function(){ad.init()},ad.data_query_wait)}else{if(ag==="data"||ag.status==="data"){if(ag.valid_chroms){ad.valid_chroms=ag.valid_chroms;ad.update_icons()}ad.tiles_div.text(U);if(ad.view.chrom){ad.tiles_div.text("");ad.tiles_div.css("height",ad.visible_height_px+"px");ad.enabled=true;$.when.apply($,ad.predraw_init()).done(function(){ac.resolve();ad.container_div.removeClass("nodata error pending");ad.request_draw()})}else{ac.resolve()}}}}}}});this.update_icons();return ac},predraw_init:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){ac.container_div.addClass("line-track");var af=ad.data;if(af&&af.min&&af.max){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.config.set_param_default_value("min_value",ae);ac.config.set_param_default_value("max_value",ag);ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},get_drawables:function(){return this}});var N=function(ae,ad,ag){g.call(this,ae,ad,ag);var ac=this;m(ac.container_div,ac.drag_handle_class,".group",ac);this.filters_manager=new i.FiltersManager(this,("filters" in ag?ag.filters:null));this.data_manager.set("filters_manager",this.filters_manager);this.filters_available=false;this.tool=(ag.tool?new s(ab.extend(ag.tool,{track:this,tool_state:ag.tool_state})):null);this.tile_cache=new y.Cache(Q);this.left_offset=0;if(this.header_div){this.set_filters_manager(this.filters_manager);if(this.tool){var af=new aa({model:this.tool});af.render();this.dynamic_tool_div=af.$el;this.header_div.after(this.dynamic_tool_div)}}this.tiles_div=$("
").addClass("tiles").appendTo(this.content_div);if(!this.prefs.content_visible){this.tiles_div.hide()}this.overlay_div=$("
").addClass("overlay").appendTo(this.content_div);if(ag.mode){this.change_mode(ag.mode)}};q(N.prototype,r.prototype,g.prototype,{action_icons_def:g.prototype.action_icons_def.concat([{name:"show_more_rows_icon",title:"To minimize track height, not all feature rows are displayed. Click to display more rows.",css_class:"exclamation",on_click_fn:function(ac){$(".tooltip").remove();ac.slotters[ac.view.resolution_px_b].max_rows*=2;ac.request_draw({clear_tile_cache:true})},hide:true}]),copy:function(ac){var ad=this.to_dict();q(ad,{data_manager:this.data_manager});var ae=new this.constructor(this.view,ac,ad);ae.change_mode(this.mode);ae.enabled=this.enabled;return ae},set_filters_manager:function(ac){this.filters_manager=ac;this.header_div.after(this.filters_manager.parent_div)},to_dict:function(){return{track_type:this.get_type(),dataset:{id:this.dataset.id,hda_ldda:this.dataset.get("hda_ldda")},prefs:this.prefs,mode:this.mode,filters:this.filters_manager.to_dict(),tool_state:(this.tool?this.tool.state_dict():{})}},set_min_max:function(){var ac=this;return $.getJSON(ac.dataset.url(),{data_type:"data",stats:true,chrom:ac.view.chrom,low:0,high:ac.view.max_high,hda_ldda:ac.dataset.get("hda_ldda")},function(ad){var af=ad.data;if(isNaN(parseFloat(ac.prefs.min_value))||isNaN(parseFloat(ac.prefs.max_value))){var ae=af.min,ag=af.max;ae=Math.floor(Math.min(0,Math.max(ae,af.mean-2*af.sd)));ag=Math.ceil(Math.max(0,Math.min(ag,af.mean+2*af.sd)));ac.prefs.min_value=ae;ac.prefs.max_value=ag}})},change_mode:function(ad){var ac=this;ac.mode=ad;ac.config.get("values").mode=ad;if(ad==="Auto"){this.data_manager.clear()}ac.request_draw({clear_tile_cache:true});this.action_icons.mode_icon.attr("title","Set display mode (now: "+ac.mode+")");return ac},update_icons:function(){var ac=this;if(ac.filters_available){ac.action_icons.filters_icon.show()}else{ac.action_icons.filters_icon.hide()}if(ac.tool){ac.action_icons.tools_icon.show();ac.action_icons.param_space_viz_icon.show()}else{ac.action_icons.tools_icon.hide();ac.action_icons.param_space_viz_icon.hide()}},_gen_tile_cache_key:function(ad,ac){return ad+"_"+ac},request_draw:function(ac){if(ac&&ac.clear_tile_cache){this.tile_cache.clear()}this.view.request_redraw(ac,this)},before_draw:function(){this.max_height_px=0},_draw:function(aq){if(!this.can_draw()){return}var an=aq&&aq.clear_after,al=this.view.low,ag=this.view.high,aj=ag-al,ad=this.view.container.width(),ap=this.view.resolution_px_b,af=1/ap;if(this.is_overview){al=this.view.max_low;ag=this.view.max_high;ap=ad/(view.max_high-view.max_low);af=1/ap}this.before_draw();this.tiles_div.children().addClass("remove");var ac=Math.floor(al/(af*S)),ak,am,ah,ai=[],ao=[];while((ac*S*af)").text(ad.prefs[ac]).make_text_editable({num_cols:12,on_finish:function(aj){$(".tooltip").remove();ad.config.set_param_value(ac,aj);ah()},help_text:"Set "+ai+" value"}).addClass("yaxislabel "+ag).css("color",this.prefs.label_color);this.container_div.prepend(ae)}},postdraw_actions:function(af,ag,ai,ac){var ae=ab.filter(af,function(aj){return(aj instanceof M)});if(ae.length>0){this.max_height_px=0;var ad=this;ab.each(af,function(aj){if(!(aj instanceof M)){aj.html_elt.remove();ad.draw_helper(aj.region,ai,{force:true,mode:"Coverage"})}});ad._add_yaxis_label("max")}else{this.container_div.find(".yaxislabel").remove();var ah=ab.find(af,function(aj){return aj.has_icons});if(ah){ab.each(af,function(aj){if(!aj.has_icons){aj.html_elt.css("padding-top",F)}})}}},get_mode:function(ac){return this.mode},update_auto_mode:function(ac){},_get_drawables:function(){return[this]},draw_helper:function(al,an,ao){if(!ao){ao={}}var ad=ao.force,ai=ao.mode||this.mode,af=1/an,ae=this,ag=this._get_drawables(),am=this._gen_tile_cache_key(an,al),ah=function(ap){return(ap&&"track" in ap)};var aj=(ad?undefined:ae.tile_cache.get_elt(am));if(aj){if(ah(aj)){ae.show_tile(aj,an)}return aj}if(ao.data_fetch===false){return null}var ak=function(){var ap=(ab.find(C,function(ar){return ar===ai})?"Coverage":ai);var aq=ab.map(ag,function(ar){return ar.data_manager.get_data(al,ap,af,ae.data_url_extra_params)});if(view.reference_track){aq.push(view.reference_track.data_manager.get_data(al,ai,af,view.reference_track.data_url_extra_params))}return aq};var ac=$.Deferred();ae.tile_cache.set_elt(am,ac);$.when.apply($,ak()).then(function(){var ap=ak(),av=ap,aB;if(view.reference_track){aB=view.reference_track.data_manager.subset_entry(ap.pop(),al)}var aw=[],at=[];ab.each(ag,function(aG,aD){var aF=aG.mode,aE=av[aD];if(aF==="Auto"){aF=aG.get_mode(aE);aG.update_auto_mode(aF)}aw.push(aF);at.push(aG.get_canvas_height(aE,aF,an,aq))});var au=ae.view.canvas_manager.new_canvas(),ax=al.get("start"),aC=al.get("end"),ar=0,aq=Math.ceil((aC-ax)*an)+ae.left_offset,az=ab.max(at),ay;au.width=aq;au.height=(ao.height||az);var aA=au.getContext("2d");aA.translate(ae.left_offset,0);if(ag.length>1){aA.globalAlpha=0.5;aA.globalCompositeOperation="source-over"}ab.each(ag,function(aE,aD){ay=aE.draw_tile(av[aD],aA,aw[aD],al,an,aB)});if(ay!==undefined){ae.tile_cache.set_elt(am,ay);ae.show_tile(ay,an)}ac.resolve(ay)});return ac},get_canvas_height:function(ac,ae,af,ad){return this.visible_height_px},_draw_line_track_tile:function(ac,ae,ah,ag,ai){var af=ae.canvas,ad=new L.LinePainter(ac.data,ag.get("start"),ag.get("end"),this.prefs,ah);ad.draw(ae,af.width,af.height,ai);return new M(this,ag,ai,af,ac.data)},draw_tile:function(ac,ad,ag,af,ah,ae){},show_tile:function(ae,ah){var ad=this,ac=ae.html_elt;ae.predisplay_actions();var ag=(ae.low-(this.is_overview?this.view.max_low:this.view.low))*ah;if(this.left_offset){ag-=this.left_offset}ac.css({position:"absolute",top:0,left:ag});if(ac.hasClass("remove")){ac.removeClass("remove")}else{this.tiles_div.append(ac)}ac.css("height","auto");this.max_height_px=Math.max(this.max_height_px,ac.height());ac.parent().children().css("height",this.max_height_px+"px");var af=this.max_height_px;if(this.visible_height_px!==0){af=Math.min(this.max_height_px,this.visible_height_px)}this.tiles_div.css("height",af+"px")},tool_region_and_parameters_str:function(af){var ac=this,ae=(af!==undefined?af.toString():"all"),ad=ab.values(ac.tool.get_inputs_dict()).join(", ");return" - region=["+ae+"], parameters=["+ad+"]"},data_and_mode_compatible:function(ac,ad){if(ad==="Auto"){return true}else{if(ad==="Coverage"){return ac.dataset_type==="bigwig"}else{if(ac.dataset_type==="bigwig"||ac.extra_info==="no_detail"){return false}else{return true}}}},can_subset:function(ac){if(ac.message||ac.extra_info==="no_detail"){return false}else{if(ac.dataset_type==="bigwig"){return(ac.data[1][0]-ac.data[0][0]===1)}}return true},init_for_tool_data:function(){this.data_manager.set("data_type","raw_data");this.data_query_wait=1000;this.dataset_check_type="state"}});var W=function(ad,ac){var ae={resize:false};g.call(this,ad,ac,ae);this.container_div.addClass("label-track")};q(W.prototype,g.prototype,{build_header_div:function(){},init:function(){this.enabled=true},predraw_init:function(){},_draw:function(ag){var ae=this.view,af=ae.high-ae.low,aj=Math.floor(Math.pow(10,Math.floor(Math.log(af)/Math.log(10)))),ac=Math.floor(ae.low/aj)*aj,ah=this.view.container.width(),ad=$("
");while(ac"+commatize(ac)+"
").css({position:"absolute",left:ai-1}));ac+=aj}this.content_div.children(":first").remove();this.content_div.append(ad)}});var f=function(ad,ac,ag){N.call(this,ad,ac,ag);this.drawables=[];if("drawables" in ag){var af;for(var ae=0;aethis.left_offset){this.left_offset=af.left_offset}}this.enabled=true}ab.each(this.drawables,function(ah){if(ah instanceof d||ah instanceof T){ah.change_mode("Coverage")}});this.update_icons();this.obj_type="CompositeTrack"};q(f.prototype,N.prototype,{display_modes:C,action_icons_def:[{name:"composite_icon",title:"Show individual tracks",css_class:"layers-stack",on_click_fn:function(ac){$(".tooltip").remove();ac.show_group()}}].concat(N.prototype.action_icons_def),to_dict:A.prototype.to_dict,add_drawable:A.prototype.add_drawable,unpack_drawables:A.prototype.unpack_drawables,change_mode:function(ac){N.prototype.change_mode.call(this,ac);for(var ad=0;adag){ag=aj}}for(ae=0;aethis.view.canvas_manager.char_width_px){this.tiles_div.show();return N.prototype.draw_helper.call(this,ad,ae,ac)}else{this.tiles_div.hide();return null}},can_subset:function(ac){return true},draw_tile:function(ae,ak,af,ah,al){var ad=this.data_manager.subset_entry(ae,ah),aj=ad.data;var ac=ak.canvas;ak.font=ak.canvas.manager.default_font;ak.textAlign="center";for(var ag=0,ai=aj.length;agI){mode="Squish"}else{mode="Pack"}}return mode},get_canvas_height:function(ac,ag,ah,ad){if(ag==="Coverage"||ac.dataset_type==="bigwig"){return this.summary_draw_height}else{var af=this.incremental_slots(ah,ac.data,ag);var ae=new (this.painter)(null,null,null,this.prefs,ag);return Math.max(this.min_height_px,ae.get_required_height(af,ad))}},draw_tile:function(am,aq,ao,af,aj,ae){var ap=this,ad=aq.canvas,ax=af.get("start"),ac=af.get("end"),ag=this.left_offset;if(am.dataset_type==="bigwig"){return this._draw_line_track_tile(am,aq,ao,af,aj)}var ai=[],an=this.slotters[aj].slots;all_slotted=true;if(am.data){var ak=this.filters_manager.filters;for(var ar=0,au=am.data.length;ar1){var ac;if(this.container_div.find(".yaxislabel.variant").length===0){ac=this.prefs.summary_height/2;this.tiles_div.prepend($("
").text("Summary").addClass("yaxislabel variant top").css({"font-size":ac+"px",top:(this.prefs.summary_height-ac)/2+"px"}));if(this.prefs.show_sample_data){var ai=ae.join("
");this.tiles_div.prepend($("
").html(ai).addClass("yaxislabel variant top sample").css({top:this.prefs.summary_height+2,}))}}ac=(this.mode==="Squish"?5:10)+"px";$(this.tiles_div).find(".sample").css({"font-size":ac,"line-height":ac});$(this.tiles_div).find(".yaxislabel").css("color",this.prefs.label_color)}else{this.container_div.find(".yaxislabel.variant").remove()}}});var T=function(ad,ac,ae){d.call(this,ad,ac,ae);this.painter=(ad.reference_track?L.RefBasedReadPainter:L.ReadPainter);this.update_icons()};q(T.prototype,r.prototype,N.prototype,d.prototype,{config_params:ab.union(r.prototype.config_params,[{key:"block_color",label:"Block and sense strand color",type:"color",default_value:l.get_random_color()},{key:"reverse_strand_color",label:"Antisense strand color",type:"color",default_value:l.get_random_color()},{key:"label_color",label:"Label color",type:"color",default_value:"black"},{key:"show_insertions",label:"Show insertions",type:"bool",default_value:false},{key:"show_differences",label:"Show differences only",type:"bool",default_value:true},{key:"show_counts",label:"Show summary counts",type:"bool",default_value:true},{key:"mode",type:"string",default_value:this.mode,hidden:true},{key:"min_value",label:"Histogram minimum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"max_value",label:"Histogram maximum",type:"float",default_value:null,help:"clear value to set automatically"},{key:"height",type:"int",default_value:0,hidden:true}]),config_onchange:function(){this.set_name(this.prefs.name);this.request_draw({clear_tile_cache:true})}});var e={CompositeTrack:f,DrawableGroup:P,DiagonalHeatmapTrack:t,FeatureTrack:d,LineTrack:h,ReadTrack:T,VariantTrack:Z,VcfTrack:Z};var p=function(ae,ad,ac){if("copy" in ae){return ae.copy(ac)}else{var af=ae.obj_type;if(!af){af=ae.track_type}return new e[af](ad,ac,ae)}};return{TracksterView:Y,DrawableGroup:P,LineTrack:h,FeatureTrack:d,DiagonalHeatmapTrack:t,ReadTrack:T,VariantTrack:Z,CompositeTrack:f,object_from_template:p}}); \ No newline at end of file diff --git a/static/scripts/viz/trackster/tracks.js b/static/scripts/viz/trackster/tracks.js index 6ddb5ad7e68..d38177df985 100644 --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -1246,7 +1246,7 @@ extend( TracksterView.prototype, DrawableCollection.prototype, { chrom_data.resolve(result.chrom_info); }, error: function() { - alert("Could not load chroms for this dbkey:", view.dbkey); + alert("Could not load chroms for this dbkey: " + view.dbkey); } }); return chrom_data; From d656f2e54997f8acfec51996797279ded7bf976a Mon Sep 17 00:00:00 2001 From: Bjoern Gruening Date: Thu, 31 Oct 2013 10:45:09 +0100 Subject: [PATCH 0022/1033] allow more actions after setup_r_environment --- lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py index 72a28785d97..6d2b02099e0 100755 --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -347,6 +347,7 @@ def install_and_build_package( app, tool_dependency, actions_dict ): # # https://github.com/bgruening/download_store/raw/master/DESeq2-1_0_18/BiocGenerics_0.6.0.tar.gz # + filtered_actions = actions[ 1: ] if action_dict.get( 'env_shell_file_paths', False ): install_environment.add_env_shell_file_paths( action_dict[ 'env_shell_file_paths' ] ) From 426326a566f8d142856c32dfe1194737cc1ed720 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 4 Nov 2013 14:57:29 -0500 Subject: [PATCH 0023/1033] Close next-stable branch. From 2d350ef54c71390816fabf29a12b79ed06ef0ef8 Mon Sep 17 00:00:00 2001 From: Nate Coraor Date: Mon, 4 Nov 2013 15:04:42 -0500 Subject: [PATCH 0024/1033] Added tag release_2013.11.04 for changeset 26f58e05aa10 --- .hgtags | 1 + 1 file changed, 1 insertion(+) diff --git a/.hgtags b/.hgtags index 94361505583..c31a554f001 100644 --- a/.hgtags +++ b/.hgtags @@ -4,3 +4,4 @@ a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 +26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 From b6734f720bfc9ce40095bace9823489fa0ae0b36 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Tue, 5 Nov 2013 12:34:42 -0500 Subject: [PATCH 0025/1033] UI: Translate masthead mako code into js --- static/scripts/galaxy.frame.js | 446 ++++++++++-------- static/scripts/galaxy.master.js | 362 +++++++++++++- static/scripts/galaxy.menu.js | 330 +++++++++++++ static/scripts/mvc/dataset/hda-base.js | 8 +- static/scripts/mvc/dataset/hda-edit.js | 29 +- static/scripts/packed/galaxy.frame.js | 2 +- static/scripts/packed/galaxy.master.js | 2 +- static/scripts/packed/mvc/dataset/hda-base.js | 2 +- static/scripts/packed/mvc/dataset/hda-edit.js | 2 +- static/style/blue/base.css | 2 +- static/style/src/less/base.less | 2 +- templates/base/base_panels.mako | 9 - templates/webapps/galaxy/base_panels.mako | 240 +--------- templates/webapps/galaxy/galaxy.masthead.mako | 285 +++-------- 14 files changed, 1017 insertions(+), 704 deletions(-) create mode 100644 static/scripts/galaxy.menu.js diff --git a/static/scripts/galaxy.frame.js b/static/scripts/galaxy.frame.js index a1a4a532c51..86a29e94265 100644 --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -1,5 +1,5 @@ /* - galaxy frames v2.0 + galaxy frames */ // dependencies @@ -9,7 +9,7 @@ define(["galaxy.master", "libs/backbone/backbone-relational"], function(mod_mast var GalaxyFrameManager = Backbone.View.extend( { // base element - el_main: '#everything', + el_main: 'body', // defaults inputs options: @@ -46,7 +46,7 @@ var GalaxyFrameManager = Backbone.View.extend( // scroll/element top top: 0, - // maximum viewport + // viewport scrolling state top_max: 0, // frame z-index @@ -87,7 +87,7 @@ var GalaxyFrameManager = Backbone.View.extend( { icon : 'fa-th', tooltip : 'Enable/Disable Scratchbook', - on_click : function(e) { self.event_panel_active(e) }, + on_click : function(e) { self._event_panel_active(e) }, on_unload : function() { if (self.frame_counter > 0) return "You opened " + self.frame_counter + " frame(s) which will be lost."; @@ -102,7 +102,7 @@ var GalaxyFrameManager = Backbone.View.extend( { icon : 'fa-eye', tooltip : 'Show/Hide Scratchbook', - on_click : function(e) { self.event_panel_load(e) }, + on_click : function(e) { self._event_panel_load(e) }, with_number : true }); @@ -117,13 +117,13 @@ var GalaxyFrameManager = Backbone.View.extend( this.top = this.top_max = this.options.top_min; // create - this.setElement(this.template()); + this.setElement(this._template()); // load background - $(this.el).append(this.template_background()); + $(this.el).append(this._template_background()); // load menu buttons - $(this.el).append(this.template_menu()); + $(this.el).append(this._template_menu()); // load to main frame $(this.el_main).append($(this.el)); @@ -134,7 +134,7 @@ var GalaxyFrameManager = Backbone.View.extend( var id_shadow = '#frame-shadow'; // add shadow template - $(this.el).append(this.template_shadow(id_shadow.substring(1))); + $(this.el).append(this._template_shadow(id_shadow.substring(1))); // initialize frame this.frame_shadow = { @@ -146,23 +146,142 @@ var GalaxyFrameManager = Backbone.View.extend( }; // initialize size - this.frame_resize(this.frame_shadow, {width: 0, height: 0}); + this._frame_resize(this.frame_shadow, {width: 0, height: 0}); // add shadow to frame list this.frame_list[id_shadow] = this.frame_shadow; // initialize panel - this.panel_refresh(); + this._panel_refresh(); // catch window resize event var self = this; $(window).resize(function () { if (self.visible) - self.panel_refresh(); + self._panel_refresh(); }); }, + // adds and displays a new frame/window + frame_new: function(options) + { + // frame default options + var frameOptions = + { + title: '', + content: null, + target: '', + type: null, + scratchbook: false + } + + // read in defaults + if (options) + options = _.defaults(options, frameOptions); + else + options = frameOptions; + + // check for content + if(!options.content) + return; + + // open new tab + if (options.target == '_blank') + { + window.open(options.content); + return; + } + + // reload entire window + if (options.target == '_top' || options.target == '_parent' || options.target == '_self') + { + window.location = options.content; + return; + } + + // validate + if (!this.active) + { + // fix url if main frame is unavailable + var $galaxy_main = $(window.parent.document).find('#galaxy_main'); + if (options.target == 'galaxy_main' || options.target == 'center') + { + if ($galaxy_main.length == 0) + { + var href = options.content; + if (href.indexOf('?') == -1) + href += '?'; + else + href += '&'; + href += 'use_panels=True'; + window.location = href; + } else { + $galaxy_main.attr('src', options.content); + } + } else + window.location = options.content; + + // stop + return; + } + + // check for number of frames + if (this.frame_counter >= this.options.frame_max) + { + alert("You have reached the maximum number of allowed frames (" + this.options.frame_max + ")."); + return; + } + + // generate frame identifier + var frame_id = '#frame-' + (this.frame_counter_id++); + + // check if frame exists + if ($(frame_id).length !== 0) + { + alert("This frame already exists. This page might contain multiple frame managers."); + return; + } + + // reset top + this.top = this.options.top_min; + + // append + $(this.el).append(this._template_frame(frame_id.substring(1), options.title, options.type, options.content)); + + // construct a new frame + var frame = { + id : frame_id, + screen_location : {}, + grid_location : {}, + grid_rank : null, + grid_lock : false + }; + + // set dimensions + options.width = this._to_pixel_coord('width', this.options.frame.cols); + options.height = this._to_pixel_coord('height', this.options.frame.rows); + + // default z-index + this.frame_z = parseInt($(frame.id).css('z-index')); + + // add to frame list + this.frame_list[frame_id] = frame; + + // increase frame counter + this.frame_counter++; + + // resize + this._frame_resize(frame, {width: options.width, height: options.height}); + + // place frame + this._frame_insert(frame, {top: 0, left: 0}, true); + + // show frames if hidden + if (!this.visible) + this._panel_show_hide(); + }, + /* EVENT HANDLING */ @@ -179,23 +298,23 @@ var GalaxyFrameManager = Backbone.View.extend( events: { // global frame events - 'mousemove' : 'event_frame_mouse_move', - 'mouseup' : 'event_frame_mouse_up', - 'mouseleave' : 'event_frame_mouse_up', - 'mousewheel' : 'event_panel_scroll', - 'DOMMouseScroll' : 'event_panel_scroll', + 'mousemove' : '_event_frame_mouse_move', + 'mouseup' : '_event_frame_mouse_up', + 'mouseleave' : '_event_frame_mouse_up', + 'mousewheel' : '_event_panel_scroll', + 'DOMMouseScroll' : '_event_panel_scroll', // events fixed to elements - 'mousedown .frame' : 'event_frame_mouse_down', - 'mousedown .frame-background' : 'event_panel_load', - 'mousedown .frame-scroll-up' : 'event_panel_scroll_up', - 'mousedown .frame-scroll-down' : 'event_panel_scroll_down', - 'mousedown .f-close' : 'event_frame_close', - 'mousedown .f-pin' : 'event_frame_lock' + 'mousedown .frame' : '_event_frame_mouse_down', + 'mousedown .frame-background' : '_event_panel_load', + 'mousedown .frame-scroll-up' : '_event_panel_scroll_up', + 'mousedown .frame-scroll-down' : '_event_panel_scroll_down', + 'mousedown .f-close' : '_event_frame_close', + 'mousedown .f-pin' : '_event_frame_lock' }, // drag start - event_frame_mouse_down: function (e) + _event_frame_mouse_down: function (e) { // skip if event is already active if (this.event.type !== null) @@ -218,7 +337,7 @@ var GalaxyFrameManager = Backbone.View.extend( e.preventDefault(); // identify frame - this.event.target = this.event_get_frame(e.target); + this.event.target = this._frame_identify(e.target); // check if frame is locked if (this.event.target.grid_lock) @@ -231,11 +350,11 @@ var GalaxyFrameManager = Backbone.View.extend( this.event.xy = {x: e.originalEvent.pageX, y: e.originalEvent.pageY}; // prepare drag/resize - this.frame_drag_start(this.event.target); + this._frame_drag_start(this.event.target); }, // mouse move event - event_frame_mouse_move: function (e) + _event_frame_mouse_move: function (e) { // check if (this.event.type != 'drag' && this.event.type != 'resize') @@ -255,7 +374,7 @@ var GalaxyFrameManager = Backbone.View.extend( this.event.xy = event_xy_new; // object position / size - var p = this.frame_screen (this.event.target); + var p = this._frame_screen (this.event.target); // resize event if (this.event.type == 'resize') @@ -270,23 +389,23 @@ var GalaxyFrameManager = Backbone.View.extend( p.height = Math.max(p.height, min_dim); // apply resize to frame - this.frame_resize(this.event.target, p); + this._frame_resize(this.event.target, p); // break down to grid coordinates - p.width = this.to_grid_coord('width', p.width) + 1; - p.height = this.to_grid_coord('height', p.height) + 1; + p.width = this._to_grid_coord('width', p.width) + 1; + p.height = this._to_grid_coord('height', p.height) + 1; // transfer back to pixels - p.width = this.to_pixel_coord('width', p.width); - p.height = this.to_pixel_coord('height', p.height); + p.width = this._to_pixel_coord('width', p.width); + p.height = this._to_pixel_coord('height', p.height); // apply - this.frame_resize(this.frame_shadow, p); + this._frame_resize(this.frame_shadow, p); // fix position - this.frame_insert(this.frame_shadow, { - top : this.to_grid_coord('top', p.top), - left : this.to_grid_coord('left', p.left) + this._frame_insert(this.frame_shadow, { + top : this._to_grid_coord('top', p.top), + left : this._to_grid_coord('left', p.left) }); } @@ -298,12 +417,12 @@ var GalaxyFrameManager = Backbone.View.extend( p.top += event_xy_delta.y; // apply - this.frame_offset(this.event.target, p); + this._frame_offset(this.event.target, p); // get location of shadow var l = { - top : this.to_grid_coord('top', p.top), - left : this.to_grid_coord('left', p.left) + top : this._to_grid_coord('top', p.top), + left : this._to_grid_coord('left', p.left) }; // increase priority of current frame @@ -311,26 +430,26 @@ var GalaxyFrameManager = Backbone.View.extend( l.left++; // fix position - this.frame_insert(this.frame_shadow, l); + this._frame_insert(this.frame_shadow, l); } }, // mouse up - event_frame_mouse_up: function (e) + _event_frame_mouse_up: function (e) { // check if (this.event.type != 'drag' && this.event.type != 'resize') return; // stop - this.frame_drag_stop(this.event.target); + this._frame_drag_stop(this.event.target); // reset event this.event.type = null; }, // drag start - event_frame_close: function (e) + _event_frame_close: function (e) { // check if (this.event.type !== null) @@ -340,7 +459,7 @@ var GalaxyFrameManager = Backbone.View.extend( e.preventDefault(); // get frame - var frame = this.event_get_frame(e.target); + var frame = this._frame_identify(e.target); var self = this; // fade out @@ -356,19 +475,19 @@ var GalaxyFrameManager = Backbone.View.extend( self.frame_counter--; // reload - self.panel_refresh(true); + self._panel_refresh(true); // refresh scroll state once all animations completed - self.panel_animation_complete(); + self._panel_animation_complete(); // hide if no frames left if (self.visible && self.frame_counter == 0) - self.panel_show_hide(); + self._panel_show_hide(); }); }, // drag start - event_frame_lock: function (e) + _event_frame_lock: function (e) { // check if (this.event.type !== null) @@ -378,7 +497,7 @@ var GalaxyFrameManager = Backbone.View.extend( e.preventDefault(); // get frame - var frame = this.event_get_frame(e.target); + var frame = this._frame_identify(e.target); // check if (frame.grid_lock) @@ -406,29 +525,29 @@ var GalaxyFrameManager = Backbone.View.extend( }, // show/hide panel - event_panel_load: function (e) + _event_panel_load: function (e) { // check if (this.event.type !== null) return; // load panel - this.panel_show_hide(); + this._panel_show_hide(); }, // activate/disable panel - event_panel_active: function (e) + _event_panel_active: function (e) { // check if (this.event.type !== null) return; // load panel - this.panel_active_disable(); + this._panel_active_disable(); }, // scroll - event_panel_scroll: function(e) + _event_panel_scroll: function(e) { // check if (this.event.type !== null || !this.visible) @@ -441,11 +560,11 @@ var GalaxyFrameManager = Backbone.View.extend( var delta = e.originalEvent.detail ? e.originalEvent.detail : e.originalEvent.wheelDelta / -3; // refresh panel - this.panel_scroll(delta); + this._panel_scroll(delta); }, // scroll up - event_panel_scroll_up: function(e) + _event_panel_scroll_up: function(e) { // check if (this.event.type !== null) @@ -455,11 +574,11 @@ var GalaxyFrameManager = Backbone.View.extend( e.preventDefault(); // scroll up - this.panel_scroll(-this.options.scroll); + this._panel_scroll(-this.options.scroll); }, // scroll down - event_panel_scroll_down: function(e) + _event_panel_scroll_down: function(e) { // check if (this.event.type !== null) @@ -469,31 +588,31 @@ var GalaxyFrameManager = Backbone.View.extend( e.preventDefault(); // scroll down - this.panel_scroll(this.options.scroll); - }, - - // identify - event_get_frame: function(target) - { - return this.frame_list['#' + $(target).closest('.frame').attr('id')]; + this._panel_scroll(this.options.scroll); }, /* - FRAME EVENTS START/STOP + FRAME EVENTS SUPPORT */ + // identify + _frame_identify: function(target) + { + return this.frame_list['#' + $(target).closest('.frame').attr('id')]; + }, + // drag start - frame_drag_start : function (frame) + _frame_drag_start : function (frame) { // set focus - this.frame_focus(frame, true); + this._frame_focus(frame, true); // get current dimensions - var p = this.frame_screen (frame); + var p = this._frame_screen (frame); // initialize shadow - this.frame_resize(this.frame_shadow, p); - this.frame_grid(this.frame_shadow, frame.grid_location); + this._frame_resize(this.frame_shadow, p); + this._frame_grid(this.frame_shadow, frame.grid_location); // reset location frame.grid_location = null; @@ -506,17 +625,17 @@ var GalaxyFrameManager = Backbone.View.extend( }, // drag stop - frame_drag_stop : function (frame) + _frame_drag_stop : function (frame) { // remove focus - this.frame_focus(frame, false); + this._frame_focus(frame, false); // get new dimensions - var p = this.frame_screen(this.frame_shadow); + var p = this._frame_screen(this.frame_shadow); // update frame - this.frame_resize(frame, p); - this.frame_grid(frame, this.frame_shadow.grid_location, true); + this._frame_resize(frame, p); + this._frame_grid(frame, this.frame_shadow.grid_location, true); // reset location of shadow this.frame_shadow.grid_location = null; @@ -528,7 +647,7 @@ var GalaxyFrameManager = Backbone.View.extend( $('.f-cover').hide(); // refresh scroll state once all animations completed - this.panel_animation_complete(); + this._panel_animation_complete(); }, /* @@ -536,7 +655,7 @@ var GalaxyFrameManager = Backbone.View.extend( */ // converts a pixel coordinate to grids - to_grid_coord: function (type, px) + _to_grid_coord: function (type, px) { // determine sign var sign = (type == 'width' || type == 'height') ? 1 : -1; @@ -548,7 +667,7 @@ var GalaxyFrameManager = Backbone.View.extend( }, // converts a grid coordinate to pixels - to_pixel_coord: function (type, g) + _to_pixel_coord: function (type, g) { // determine sign var sign = (type == 'width' || type == 'height') ? 1 : -1; @@ -562,25 +681,25 @@ var GalaxyFrameManager = Backbone.View.extend( }, // get grid coordinates - to_grid: function (px) + _to_grid: function (px) { // full set return { - top : this.to_grid_coord('top', px.top), - left : this.to_grid_coord('left', px.left), - width : this.to_grid_coord('width', px.width), - height : this.to_grid_coord('height', px.height) + top : this._to_grid_coord('top', px.top), + left : this._to_grid_coord('left', px.left), + width : this._to_grid_coord('width', px.width), + height : this._to_grid_coord('height', px.height) }; }, // get pixel coordinates - to_pixel: function(g) + _to_pixel: function(g) { return { - top : this.to_pixel_coord('top', g.top), - left : this.to_pixel_coord('left', g.left), - width : this.to_pixel_coord('width', g.width), - height : this.to_pixel_coord('height', g.height) + top : this._to_pixel_coord('top', g.top), + left : this._to_pixel_coord('left', g.left), + width : this._to_pixel_coord('width', g.width), + height : this._to_pixel_coord('height', g.height) }; }, @@ -589,7 +708,7 @@ var GalaxyFrameManager = Backbone.View.extend( */ // check collision - is_collision: function(g) + _is_collision: function(g) { // is collision pair function is_collision_pair (a, b) @@ -618,7 +737,7 @@ var GalaxyFrameManager = Backbone.View.extend( }, // location/grid rank - location_rank: function(loc) + _location_rank: function(loc) { return (loc.top * this.cols) + loc.left; }, @@ -628,7 +747,7 @@ var GalaxyFrameManager = Backbone.View.extend( */ // update frame counter - menu_refresh: function() + _menu_refresh: function() { // update on screen counter this.button_load.number(this.frame_counter); @@ -657,24 +776,24 @@ var GalaxyFrameManager = Backbone.View.extend( */ // panel on animation complete / frames not moving - panel_animation_complete: function() + _panel_animation_complete: function() { var self = this; - $(".frame").promise().done(function() {self.panel_scroll(0, true)}); + $(".frame").promise().done(function() {self._panel_scroll(0, true)}); }, // refresh panel - panel_refresh: function(animate) + _panel_refresh: function(animate) { // get current size this.cols = parseInt($(window).width() / this.options.cell, 10) + 1; // recalculate frame positions - this.frame_insert(null, null, animate); + this._frame_insert(null, null, animate); }, // update scroll - panel_scroll: function(delta, animate) + _panel_scroll: function(delta, animate) { // new top value var top_new = this.top - this.options.scroll * delta; @@ -699,7 +818,7 @@ var GalaxyFrameManager = Backbone.View.extend( top : frame.screen_location.top - (this.top - top_new), left : frame.screen_location.left } - this.frame_offset(frame, screen_location, animate); + this._frame_offset(frame, screen_location, animate); } } @@ -708,11 +827,11 @@ var GalaxyFrameManager = Backbone.View.extend( } // refresh - this.menu_refresh(); + this._menu_refresh(); }, // show or hide panel - panel_show_hide: function() + _panel_show_hide: function() { // check if (this.visible) @@ -750,12 +869,12 @@ var GalaxyFrameManager = Backbone.View.extend( $(".frame-background").show(); // show panel - this.panel_refresh(); + this._panel_refresh(); } }, // show or hide panel - panel_active_disable: function() + _panel_active_disable: function() { // check if (this.active) @@ -768,7 +887,7 @@ var GalaxyFrameManager = Backbone.View.extend( // hide panel if (this.visible) - this.panel_show_hide(); + this._panel_show_hide(); } else { // activate this.active = true; @@ -781,82 +900,9 @@ var GalaxyFrameManager = Backbone.View.extend( /* FRAME FUNCTIONS */ - // adds and displays a new frame/window - frame_new: function(options) - { - // validate - if (!this.active) - { - // load frame in main window - if (options.location == 'center') - { - var galaxy_main = $( window.parent.document ).find( 'iframe#galaxy_main' ); - galaxy_main.attr( 'src', options.content ); - } else - window.location = options.content; - - // stop - return; - } - - // check for number of frames - if (this.frame_counter >= this.options.frame_max) - { - alert("You have reached the maximum number of allowed frames (" + this.options.frame_max + ")."); - return; - } - - // generate frame identifier - var frame_id = '#frame-' + (this.frame_counter_id++); - - // check if frame exists - if ($(frame_id).length !== 0) - { - alert("This frame already exists. This page might contain multiple frame managers."); - return; - } - - // reset top - this.top = this.options.top_min; - - // append - $(this.el).append(this.template_frame(frame_id.substring(1), options.title, options.type, options.content)); - - // construct a new frame - var frame = { - id : frame_id, - screen_location : {}, - grid_location : {}, - grid_rank : null, - grid_lock : false - }; - - // set dimensions - options.width = this.to_pixel_coord('width', this.options.frame.cols); - options.height = this.to_pixel_coord('height', this.options.frame.rows); - - // default z-index - this.frame_z = parseInt($(frame.id).css('z-index')); - - // add to frame list - this.frame_list[frame_id] = frame; - - // increase frame counter - this.frame_counter++; - - // resize - this.frame_resize(frame, {width: options.width, height: options.height}); - - // place frame - this.frame_insert(frame, {top: 0, left: 0}, true); - - // show frames if hidden - if (!this.visible) - this.panel_show_hide(); - }, // frame insert at given location - frame_insert: function(frame, new_loc, animate) + _frame_insert: function(frame, new_loc, animate) { // define var place_list = []; @@ -868,7 +914,7 @@ var GalaxyFrameManager = Backbone.View.extend( frame.grid_location = null; // set first one to be placed - place_list.push([frame, this.location_rank(new_loc)]); + place_list.push([frame, this._location_rank(new_loc)]); } // search @@ -899,7 +945,7 @@ var GalaxyFrameManager = Backbone.View.extend( // place for (i = 0; i < place_list.length; i++) - this.frame_place(place_list[i][0], animate); + this._frame_place(place_list[i][0], animate); // identify maximum viewport size this.top_max = 0; @@ -920,17 +966,17 @@ var GalaxyFrameManager = Backbone.View.extend( this.top_max = Math.min(this.top_max, this.options.top_min); // panel menu - this.menu_refresh(); + this._menu_refresh(); }, // naive frame place - frame_place: function(frame, animate) + _frame_place: function(frame, animate) { // reset grid location frame.grid_location = null; // grid coordinates of new frame - var g = this.to_grid(this.frame_screen(frame)); + var g = this._to_grid(this._frame_screen(frame)); // try grid coordinates var done = false; @@ -944,7 +990,7 @@ var GalaxyFrameManager = Backbone.View.extend( g.left = j; // no collision - if (!this.is_collision(g)) + if (!this._is_collision(g)) { done = true; break; @@ -958,13 +1004,13 @@ var GalaxyFrameManager = Backbone.View.extend( // check if valid spot was found if (done) - this.frame_grid(frame, g, animate); + this._frame_grid(frame, g, animate); else console.log("Grid dimensions exceeded."); }, // focus - frame_focus: function(frame, has_focus) + _frame_focus: function(frame, has_focus) { // get new z-value var z = this.frame_z + (has_focus ? 1 : 0); @@ -974,7 +1020,7 @@ var GalaxyFrameManager = Backbone.View.extend( }, // new left/top position frame - frame_offset: function(frame, p, animate) + _frame_offset: function(frame, p, animate) { // update screen location frame.screen_location.left = p.left; @@ -984,7 +1030,7 @@ var GalaxyFrameManager = Backbone.View.extend( if (animate) { // set focus on animated - this.frame_focus(frame, true); + this._frame_focus(frame, true); // prepare for callback var self = this; @@ -993,7 +1039,7 @@ var GalaxyFrameManager = Backbone.View.extend( $(frame.id).animate({top: p.top, left: p.left}, 'fast', function() { // remove focus - self.frame_focus(frame, false); + self._frame_focus(frame, false); }); } else // update css @@ -1001,7 +1047,7 @@ var GalaxyFrameManager = Backbone.View.extend( }, // resize frame - frame_resize: function(frame, p) + _frame_resize: function(frame, p) { // update css $(frame.id).css({width: p.width, height: p.height}); @@ -1012,20 +1058,20 @@ var GalaxyFrameManager = Backbone.View.extend( }, // new grid location - frame_grid: function (frame, l, animate) + _frame_grid: function (frame, l, animate) { // update grid location frame.grid_location = l; // place frame - this.frame_offset(frame, this.to_pixel(l), animate); + this._frame_offset(frame, this._to_pixel(l), animate); // update grid rank - frame.grid_rank = this.location_rank(l); + frame.grid_rank = this._location_rank(l); }, // get frame dimensions - frame_screen: function(frame) + _frame_screen: function(frame) { var p = frame.screen_location; return {top: p.top, left: p.left, width: p.width, height: p.height}; @@ -1036,13 +1082,13 @@ var GalaxyFrameManager = Backbone.View.extend( */ // main element - template: function() + _template: function() { - return '
'; + return '
'; }, // fill regular frame template - template_frame: function(id, title, type, content) + _template_frame: function(id, title, type, content) { // check title if (!title) @@ -1067,19 +1113,19 @@ var GalaxyFrameManager = Backbone.View.extend( }, // fill shadow template - template_shadow: function(id) + _template_shadow: function(id) { return '
'; }, // fill background template in order to cover underlying iframes - template_background: function() + _template_background: function() { return '
'; }, // fill menu button template - template_menu: function() + _template_menu: function() { return '
' + '
'; diff --git a/static/scripts/galaxy.master.js b/static/scripts/galaxy.master.js index fb2f27340e9..1a5c30dd2b5 100644 --- a/static/scripts/galaxy.master.js +++ b/static/scripts/galaxy.master.js @@ -3,27 +3,53 @@ */ // dependencies -define(["libs/backbone/backbone-relational"], function() { +define(["utils/galaxy.utils", "libs/backbone/backbone-relational"], function(mod_utils) { // master var GalaxyMaster = Backbone.View.extend( { // base element - el_master: '#masthead', + el_master: '#everything', + + // options + options : null, // item list - list : [], + list : {}, + + // keeps track of the last element + itemLast: null, + + // counter + itemCounter: 0, + + // background + $background: null, + + // flag indicating visibility of background + backgroundVisible: false, // initialize initialize : function(options) { + // update options + this.options = options; + + // HACK: due to body events defined in galaxy.panels.js + $("body").off(); + // define this element - this.setElement($(this.template())); + this.setElement($(this._template(options))); // append to master $(this.el_master).append($(this.el)); + // assign background + this.$background = $(this.el).find('#master-background'); + // loop through item specific unload functions + // and collect all there warning messages, regarding + // the user's attempt to unload the page var self = this; window.onbeforeunload = function() { @@ -39,38 +65,133 @@ var GalaxyMaster = Backbone.View.extend( }; }, - // prevent default + // configure events events: { - 'mousedown' : function(e) {e.preventDefault()} + 'click' : '_eventRefresh', + 'mousedown' : function(e) { e.preventDefault() } }, // adds a new item to the master append : function(item) { - $(this.el).append($(item.el)); - this.list.push(item); + return this._add(item, true); }, // adds a new item to the master prepend : function(item) { - $(this.el).prepend($(item.el)); - this.list.push(item); + return this._add(item, false); + }, + + // adds a new item to the master + _add : function(item, append) + { + var $loc = $(this.el).find('#' + item.masterLocation); + if ($loc) + { + // create frame for new item + var itemId = 'master-item-' + this.itemCounter++; + var $itemNew = $(item.el); + + // configure id and class in order to mark new items + $itemNew.attr('id', itemId); + $itemNew.addClass('master-item'); + + // append to master + if (append) + $loc.append($itemNew); + else + $loc.prepend($itemNew); + + // add to list + this.list[itemId] = item; + + // return item id + return itemId; + } + + // location not found + return null; + }, + + // handle click event + _eventRefresh: function(e) + { + // identify current item + var itemCurrent = $(e.target).closest('.master-item'); + + // get identifier + if (itemCurrent.length) + itemCurrent = itemCurrent.attr('id'); + + // check last item + if (this.itemLast && this.itemLast != itemCurrent) + { + var it = this.list[this.itemLast]; + if (it) + if (it.masterReset) + it.masterReset(); + } + + // check if current item is in active state + var useBackground = false; + if (itemCurrent) + { + var it = this.list[itemCurrent]; + if (it) + if (it.masterReset) + { + if (this.itemLast == itemCurrent) + useBackground = this.backgroundVisible ? false : true; + else + useBackground = true; + } + } + + // decide wether to show/hide background + if (useBackground) + this.$background.show(); + else + this.$background.hide(); + + // backup + this.backgroundVisible = useBackground; + this.itemLast = itemCurrent; }, /* HTML TEMPLATES */ - - // fill regular modal template - template: function() + + // template item + _templateItem: function(id) { - return '
'; + return '
'; + }, + + // fill template + _template: function(options) + { + return '
' + + '' + + '
'; } }); -// frame manager +// icon var GalaxyMasterIcon = Backbone.View.extend( { // icon options @@ -85,6 +206,9 @@ var GalaxyMasterIcon = Backbone.View.extend( visible : true }, + // location identifier for master class + masterLocation: 'iconbar', + // initialize initialize: function (options) { @@ -93,12 +217,12 @@ var GalaxyMasterIcon = Backbone.View.extend( this.options = _.defaults(options, this.options); // add template for icon - this.setElement($(this.template(this.options))); + this.setElement($(this._template(this.options))); // configure icon var self = this; $(this.el).find('.icon').tooltip({title: this.options.tooltip}) - .on('click', self.options.on_click); + .on('mouseup', self.options.on_click); // visiblity if (!this.options.visible) @@ -147,7 +271,7 @@ var GalaxyMasterIcon = Backbone.View.extend( }, // fill template icon - template: function (options) + _template: function (options) { var tmpl = '
' + '
'; @@ -160,10 +284,210 @@ var GalaxyMasterIcon = Backbone.View.extend( } }); +// tab +var GalaxyMasterTab = Backbone.View.extend( +{ + // main options + options: + { + id : '', + title : 'Title', + target : '_parent', + content : '', + type : 'url', + scratchbook : false, + on_unload : null, + visible : true + }, + + // location + masterLocation: 'navbar', + + // optional sub menu + $menu: null, + + // flag if menu is visible + menuVisible: false, + + // events + events: + { + 'click .head' : '_eventClickHead' + }, + + // initialize + initialize: function (options) + { + // read in defaults + if (options) + this.options = _.defaults(options, this.options); + + // update url + if (this.options.content && this.options.content.indexOf('//') === -1) + this.options.content = galaxy_config.root + this.options.content; + + // add template for tab + this.setElement($(this._template(this.options))); + + // visiblity + if (!this.options.visible) + this.hide(); + }, + + // show + show: function() + { + $(this.el).css({visibility : 'visible'}); + }, + + // show + hide: function() + { + $(this.el).css({visibility : 'hidden'}); + }, + + // add menu item + addMenu: function (options) + { + // menu option defaults + var menuOptions = { + title : 'Title', + content : '', + type : 'url', + target : '_parent', + scratchbook : false, + divider : false + } + + // read in defaults + if (options) + menuOptions = _.defaults(options, menuOptions); + + // update url + if (menuOptions.content && menuOptions.content.indexOf('//') === -1) + menuOptions.content = galaxy_config.root + menuOptions.content; + + // check if submenu element is available + if (!this.$menu) + { + // insert submenu element into root + $(this.el).find('.root').append(this._templateMenu()); + + // show caret + $(this.el).find('.symbol').addClass('caret'); + + // update element link + this.$menu = $(this.el).find('.menu'); + } + + // create + var $item = $(this._templateMenuItem(menuOptions)); + + // append menu + this.$menu.append($item); + + // add events + var self = this; + $item.on('click', function(e) + { + // prevent default + e.preventDefault(); + + // check for menu options + self._hideMenu(); + + // no modifications if new tab is requested + if (self.options.target === '_blank') + return true; + + // load into frame + Galaxy.frame_manager.frame_new(options); + }); + + // append divider + if (menuOptions.divider) + this.$menu.append($(this._templateDivider())); + }, + + // add reset function called by master + masterReset: function() + { + this._hideMenu(); + }, + + // hide menu + _hideMenu: function() + { + if (this.$menu && this.menuVisible) + { + this.$menu.hide(); + this.menuVisible = false; + } + }, + + // show menu on header click + _eventClickHead: function(e) + { + // prevent default + e.preventDefault(); + + // check for menu options + if (this.$menu) + { + // show/hide menu + if (!this.menuVisible) + { + this.$menu.show(); + this.menuVisible = true; + } else { + this.$menu.hide(); + this.menuVisible = false; + } + } else { + // open new frame + Galaxy.frame_manager.frame_new(this.options); + } + }, + + // fill template header + _templateMenuItem: function (options) + { + return '
  • ' + options.title + '
    • '; + }, + + // fill template header + _templateMenu: function () + { + return '
      '; + }, + + _templateDivider: function() + { + return '
    • '; + }, + + // fill template + _template: function (options) + { + // start template + var tmpl = ''; + + // return template + return tmpl; + } +}); + // return return { GalaxyMaster: GalaxyMaster, - GalaxyMasterIcon : GalaxyMasterIcon + GalaxyMasterTab: GalaxyMasterTab, + GalaxyMasterIcon: GalaxyMasterIcon }; }); diff --git a/static/scripts/galaxy.menu.js b/static/scripts/galaxy.menu.js new file mode 100644 index 00000000000..95ed6c493e0 --- /dev/null +++ b/static/scripts/galaxy.menu.js @@ -0,0 +1,330 @@ +/* + galaxy menu +*/ + +// dependencies +define(["galaxy.master", "libs/backbone/backbone-relational"], function(mod_master) { + +// frame manager +var GalaxyMenu = Backbone.Model.extend( +{ + // options + options: null, + + // link master class + master: null, + + // initialize + initialize: function(options) + { + this.options = options.config; + this.master = options.master; + this.create(); + }, + + // default menu + create: function() + { + // + // Analyze data tab. + // + var tab_analysis = new mod_master.GalaxyMasterTab({ + title : "Analyze Data", + content : "root/index" + }); + this.master.append(tab_analysis); + + // + // Workflow tab. + // + var tab_workflow = new mod_master.GalaxyMasterTab({ + title : "Workflow", + content : "workflow" + + }); + this.master.append(tab_workflow); + + // + // 'Shared Items' or Libraries tab. + // + var tab_shared = new mod_master.GalaxyMasterTab({ + title : "Shared Data", + content : "library/index" + }); + + tab_shared.addMenu({ + title : "Data Libraries", + content : "library/index", + divider : true + }); + + tab_shared.addMenu({ + title : "Published Histories", + content : "history/list_published" + }); + + tab_shared.addMenu({ + title : "Published Workflows", + content : "workflow/list_published" + + }); + + tab_shared.addMenu({ + title : "Published Visualizations", + content : "visualization/list_published" + }); + + tab_shared.addMenu({ + title : "Published Pages", + content : "page/list_published" + }); + + this.master.append(tab_shared); + + // + // Lab menu. + // + if (this.options.user.requests) + { + var tab_lab = new mod_master.GalaxyMasterTab({ + title : "Lab" + }); + tab_lab.addMenu({ + title : "Sequencing Requests", + content : "requests/index" + }); + tab_lab.addMenu({ + title : "Find Samples", + content : "requests/find_samples_index" + }); + tab_lab.addMenu({ + title : "Help", + content : this.options.lims_doc_url + }); + this.master.append(tab_lab); + } + + // + // Visualization tab. + // + var tab_visualization = new mod_master.GalaxyMasterTab({ + + title : "Visualization", + content : "visualization/list" + }); + tab_visualization.addMenu({ + title : "New Track Browser", + content : "visualization/trackster", + target : "_frame" + }); + tab_visualization.addMenu({ + title : "Saved Visualizations", + content : "visualization/list", + target : "_frame" + }); + this.master.append(tab_visualization); + + // + // Cloud menu. + // + if (this.options.enable_cloud_launch) + { + var tab_cloud = new mod_master.GalaxyMasterTab({ + title : "Cloud", + content : "cloudlaunch/index" + }); + tab_cloud.addMenu({ + title : "New Cloud Cluster", + content : "cloudlaunch/index" + }); + this.master.append(tab_cloud); + } + + // + // Admin. + // + if (this.options.is_admin_user) + { + var tab_admin = new mod_master.GalaxyMasterTab({ + title : "Admin", + content : "admin/index", + extra_class : "admin-only" + }); + this.master.append(tab_admin); + } + + // + // Help tab. + // + var tab_help = new mod_master.GalaxyMasterTab({ + title : "Help" + }); + if (this.options.biostar_url) + { + tab_help.addMenu({ + title : "Galaxy Q&A Site", + content : this.options.biostar_url_redirect, + target : "_blank" + }); + tab_help.addMenu({ + title : "Ask a question", + content : "biostar/biostar_question_redirect", + target : "_blank" + }); + } + tab_help.addMenu({ + title : "Support", + content : this.options.support_url, + target : "_blank" + }); + tab_help.addMenu({ + title : "Search", + content : this.options.search_url, + target : "_blank" + }); + tab_help.addMenu({ + title : "Mailing Lists", + content : this.options.mailing_lists, + target : "_blank" + }); + tab_help.addMenu({ + title : "Videos", + content : this.options.screencasts_url, + target : "_blank" + }); + tab_help.addMenu({ + title : "Wiki", + content : this.options.wiki_url, + target : "_blank" + }); + tab_help.addMenu({ + title : "How to Cite Galaxy", + content : this.options.citation_url, + target : "_blank" + }); + if (!this.options.terms_url) + { + tab_help.addMenu({ + title : "Terms and Conditions", + content : this.options.terms_url, + target : "_blank" + }); + } + this.master.append(tab_help); + + // + // User tab. + // + if (!this.options.user.valid) + { + var tab_user = new mod_master.GalaxyMasterTab({ + title : "User", + extra_class : "loggedout-only" + }); + + // login + if (this.options.allow_user_creation) + { + tab_user.addMenu({ + title : "Login", + content : "user/login", + target : "galaxy_main" + }); + } + + // register + if (this.options.allow_user_creation) + { + tab_user.addMenu({ + title : "Register", + content : "user/create", + target : "galaxy_main" + }); + } + + // add to master + this.master.append(tab_user); + } else { + var tab_user = new mod_master.GalaxyMasterTab({ + title : "User", + extra_class : "loggedin-only" + }); + + // show user logged in info + tab_user.addMenu({ + title : "Logged in as " + this.options.user.email + }); + + // remote user + if (this.options.use_remote_user && this.options.remote_user_logout_href) + { + tab_user.addMenu({ + title : "Logout", + content : this.options.remote_user_logout_href, + target : "_top" + }); + } else { + tab_user.addMenu({ + title : "Preferences", + content : "user?cntrller=user", + target : "galaxy_main" + }); + + tab_user.addMenu({ + title : "Custom Builds", + content : "user/dbkeys", + target : "galaxy_main" + }); + + tab_user.addMenu({ + title : "Logout", + content : "user/logout", + target : "_top", + divider : true + }); + } + + // default tabs + tab_user.addMenu({ + title : "Saved Histories", + content : "history/list", + target : "galaxy_main" + }); + tab_user.addMenu({ + title : "Saved Datasets", + content : "dataset/list", + target : "galaxy_main" + }); + tab_user.addMenu({ + title : "Saved Pages", + content : "page/list", + target : "_top" + }); + + tab_user.addMenu({ + title : "API Keys", + content : "user/api_keys?cntrller=user", + target : "galaxy_main" + }); + + if (this.options.use_remote_user) + { + tab_user.addMenu({ + title : "Public Name", + content : "user/edit_username?cntrller=user", + target : "galaxy_main" + }); + } + + // add to master + this.master.append(tab_user); + } + } +}); + +// return +return { + GalaxyMenu: GalaxyMenu +}; + +}); diff --git a/static/scripts/mvc/dataset/hda-base.js b/static/scripts/mvc/dataset/hda-base.js index dd0aaabc163..dc6aa47103f 100644 --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -173,10 +173,10 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( var self = this; displayBtnData.onclick = function(){ Galaxy.frame_manager.frame_new({ - title : "Data Viewer: " + self.model.get('name'), - type : "url", - location: "center", - content : self.urls.display + title : "Data Viewer: " + self.model.get('name'), + type : "url", + target : "galaxy_main", + content : self.urls.display }); }; } diff --git a/static/scripts/mvc/dataset/hda-edit.js b/static/scripts/mvc/dataset/hda-edit.js index 4a75ef39b37..2cf6bc162d7 100644 --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -232,9 +232,9 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( return function(){// add widget Galaxy.frame_manager.frame_new( { - title : "Visualization", - type : "url", - content : visualization_url + '/' + visualization + '?' + $.param( params ) + title : "Visualization", + type : "url", + content : visualization_url + '/' + visualization + '?' + $.param( params ) }); }; } @@ -491,10 +491,11 @@ function create_scatterplot_action_fn( url, params ){ // add widget Galaxy.frame_manager.frame_new( { - title : "Scatterplot", - type : "url", - content : url + '/scatterplot?' + $.param(params), - location : 'center' + title : "Scatterplot", + type : "url", + content : url + '/scatterplot?' + $.param(params), + target : 'galaxy_main', + scratchbook : true }); //TODO: this needs to go away @@ -553,9 +554,10 @@ function create_scatterplot_action_fn( url, params ){ // add widget parent.Galaxy.frame_manager.frame_new({ - title : "Trackster", - type : "url", - content : vis_url + "/trackster?" + $.param(dataset_params) + title : "Trackster", + type : "url", + content : vis_url + "/trackster?" + $.param(dataset_params), + scratchbook : true }); }); } @@ -570,9 +572,10 @@ function create_scatterplot_action_fn( url, params ){ // add widget parent.Galaxy.frame_manager.frame_new({ - title : "Trackster", - type : "url", - content : url + title : "Trackster", + type : "url", + content : url, + scratchbook : true }); } } diff --git a/static/scripts/packed/galaxy.frame.js b/static/scripts/packed/galaxy.frame.js index ac89da91472..e2678a0279e 100644 --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1 +1 @@ -define(["galaxy.master","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el_main:"#everything",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMasterIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",on_click:function(f){c.event_panel_active(f)},on_unload:function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}});Galaxy.master.append(this.button_active);this.button_load=new b.GalaxyMasterIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",on_click:function(f){c.event_panel_load(f)},with_number:true});Galaxy.master.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this.template());$(this.el).append(this.template_background());$(this.el).append(this.template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this.template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this.frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this.panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c.panel_refresh()}})},event:{type:null,target:null,xy:null},events:{mousemove:"event_frame_mouse_move",mouseup:"event_frame_mouse_up",mouseleave:"event_frame_mouse_up",mousewheel:"event_panel_scroll",DOMMouseScroll:"event_panel_scroll","mousedown .frame":"event_frame_mouse_down","mousedown .frame-background":"event_panel_load","mousedown .frame-scroll-up":"event_panel_scroll_up","mousedown .frame-scroll-down":"event_panel_scroll_down","mousedown .f-close":"event_frame_close","mousedown 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f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this.frame_resize(this.event.target,h);h.width=this.to_grid_coord("width",h.width)+1;h.height=this.to_grid_coord("height",h.height)+1;h.width=this.to_pixel_coord("width",h.width);h.height=this.to_pixel_coord("height",h.height);this.frame_resize(this.frame_shadow,h);this.frame_insert(this.frame_shadow,{top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this.frame_offset(this.event.target,h);var c={top:this.to_grid_coord("top",h.top),left:this.to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this.frame_insert(this.frame_shadow,c)}},event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this.frame_drag_stop(this.event.target);this.event.type=null},event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this.event_get_frame(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c.panel_refresh(true);c.panel_animation_complete();if(c.visible&&c.frame_counter==0){c.panel_show_hide()}})},event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this.event_get_frame(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},event_panel_load:function(c){if(this.event.type!==null){return}this.panel_show_hide()},event_panel_active:function(c){if(this.event.type!==null){return}this.panel_active_disable()},event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this.panel_scroll(d)},event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(-this.options.scroll)},event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this.panel_scroll(this.options.scroll)},event_get_frame:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},frame_drag_start:function(d){this.frame_focus(d,true);var c=this.frame_screen(d);this.frame_resize(this.frame_shadow,c);this.frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},frame_drag_stop:function(d){this.frame_focus(d,false);var c=this.frame_screen(this.frame_shadow);this.frame_resize(d,c);this.frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this.panel_animation_complete()},to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},to_grid:function(c){return{top:this.to_grid_coord("top",c.top),left:this.to_grid_coord("left",c.left),width:this.to_grid_coord("width",c.width),height:this.to_grid_coord("height",c.height)}},to_pixel:function(c){return{top:this.to_pixel_coord("top",c.top),left:this.to_pixel_coord("left",c.left),width:this.to_pixel_coord("width",c.width),height:this.to_pixel_coord("height",c.height)}},is_collision:function(e){function c(h,g){return 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This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this.template_frame(e.substring(1),d.title,d.type,d.content));var f={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this.to_pixel_coord("width",this.options.frame.cols);d.height=this.to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(f.id).css("z-index"));this.frame_list[e]=f;this.frame_counter++;this.frame_resize(f,{width:d.width,height:d.height});this.frame_insert(f,{top:0,left:0},true);if(!this.visible){this.panel_show_hide()}},frame_insert:function(j,c,e){var d=[];if(j){j.grid_location=null;d.push([j,this.location_rank(c)])}var g=null;for(g in this.frame_list){var h=this.frame_list[g];if(h.grid_location!==null&&!h.grid_lock){h.grid_location=null;d.push([h,h.grid_rank])}}d.sort(function(k,f){var m=k[1];var l=f[1];return ml?1:0)});for(g=0;g
      '},template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d=''}return'
      '+e+'
      '+d+'
      '},template_shadow:function(c){return'
      '},template_background:function(){return'
      '},template_menu:function(){return'
      '}});return{GalaxyFrameManager:a}}); \ No newline at end of file +define(["galaxy.master","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el_main:"body",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMasterIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",on_click:function(f){c._event_panel_active(f)},on_unload:function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}});Galaxy.master.append(this.button_active);this.button_load=new b.GalaxyMasterIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",on_click:function(f){c._event_panel_load(f)},with_number:true});Galaxy.master.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this._template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this._panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c._panel_refresh()}})},frame_new:function(d){var g={title:"",content:null,target:"",type:null,scratchbook:false};if(d){d=_.defaults(d,g)}else{d=g}if(!d.content){return}if(d.target=="_blank"){window.open(d.content);return}if(d.target=="_top"||d.target=="_parent"||d.target=="_self"){window.location=d.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(d.target=="galaxy_main"||d.target=="center"){if(f.length==0){var c=d.content;if(c.indexOf("?")==-1){c+="?"}else{c+="&"}c+="use_panels=True";window.location=c}else{f.attr("src",d.content)}}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this._template_frame(e.substring(1),d.title,d.type,d.content));var h={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this._to_pixel_coord("width",this.options.frame.cols);d.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(h.id).css("z-index"));this.frame_list[e]=h;this.frame_counter++;this._frame_resize(h,{width:d.width,height:d.height});this._frame_insert(h,{top:0,left:0},true);if(!this.visible){this._panel_show_hide()}},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_panel_load","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this._frame_identify(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this._frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this._frame_resize(this.event.target,h);h.width=this._to_grid_coord("width",h.width)+1;h.height=this._to_grid_coord("height",h.height)+1;h.width=this._to_pixel_coord("width",h.width);h.height=this._to_pixel_coord("height",h.height);this._frame_resize(this.frame_shadow,h);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this._frame_offset(this.event.target,h);var c={top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this._frame_insert(this.frame_shadow,c)}},_event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this._frame_identify(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c._panel_refresh(true);c._panel_animation_complete();if(c.visible&&c.frame_counter==0){c._panel_show_hide()}})},_event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},_event_panel_load:function(c){if(this.event.type!==null){return}this._panel_show_hide()},_event_panel_active:function(c){if(this.event.type!==null){return}this._panel_active_disable()},_event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this._panel_scroll(d)},_event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(-this.options.scroll)},_event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(this.options.scroll)},_frame_identify:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},_frame_drag_start:function(d){this._frame_focus(d,true);var c=this._frame_screen(d);this._frame_resize(this.frame_shadow,c);this._frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},_frame_drag_stop:function(d){this._frame_focus(d,false);var c=this._frame_screen(this.frame_shadow);this._frame_resize(d,c);this._frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this._panel_animation_complete()},_to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},_to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},_to_grid:function(c){return{top:this._to_grid_coord("top",c.top),left:this._to_grid_coord("left",c.left),width:this._to_grid_coord("width",c.width),height:this._to_grid_coord("height",c.height)}},_to_pixel:function(c){return{top:this._to_pixel_coord("top",c.top),left:this._to_pixel_coord("left",c.left),width:this._to_pixel_coord("width",c.width),height:this._to_pixel_coord("height",c.height)}},_is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1g.top+g.height-1||h.top+h.height-1l?1:0)});for(g=0;g
      '},_template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d=''}return'
      '+e+'
      '+d+'
      '},_template_shadow:function(c){return'
      '},_template_background:function(){return'
      '},_template_menu:function(){return'
      '}});return{GalaxyFrameManager:a}}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.master.js b/static/scripts/packed/galaxy.master.js index f863ebd05d1..721ff2e37f0 100644 --- a/static/scripts/packed/galaxy.master.js +++ b/static/scripts/packed/galaxy.master.js @@ -1 +1 @@ -define(["libs/backbone/backbone-relational"],function(){var a=Backbone.View.extend({el_master:"#masthead",list:[],initialize:function(d){this.setElement($(this.template()));$(this.el_master).append($(this.el));var c=this;window.onbeforeunload=function(){var f="";for(key in c.list){if(c.list[key].options.on_unload){var e=c.list[key].options.on_unload();if(e){f+=e+" "}}}if(f!=""){return f}}},events:{mousedown:function(c){c.preventDefault()}},append:function(c){$(this.el).append($(c.el));this.list.push(c)},prepend:function(c){$(this.el).prepend($(c.el));this.list.push(c)},template:function(){return'
      '}});var b=Backbone.View.extend({options:{id:"galaxy-icon",icon:"fa-cog",tooltip:"galaxy-icon",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}this.setElement($(this.template(this.options)));var c=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip}).on("click",c.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(c){$(this.el).find(".icon").removeClass(this.options.icon).addClass(c);this.options.icon=c},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(c){$(this.el).find(".number").text(c)},template:function(d){var c="
      ';if(d.with_number){c+='
      '}c+="
      ";return c}});return{GalaxyMaster:a,GalaxyMasterIcon:b}}); \ No newline at end of file +define(["utils/galaxy.utils","libs/backbone/backbone-relational"],function(c){var a=Backbone.View.extend({el_master:"#everything",options:null,list:{},itemLast:null,itemCounter:0,$background:null,backgroundVisible:false,initialize:function(f){this.options=f;$("body").off();this.setElement($(this._template(f)));$(this.el_master).append($(this.el));this.$background=$(this.el).find("#master-background");var e=this;window.onbeforeunload=function(){var h="";for(key in e.list){if(e.list[key].options.on_unload){var g=e.list[key].options.on_unload();if(g){h+=g+" "}}}if(h!=""){return h}}},events:{click:"_eventRefresh",mousedown:function(f){f.preventDefault()}},append:function(e){return this._add(e,true)},prepend:function(e){return this._add(e,false)},_add:function(g,f){var e=$(this.el).find("#"+g.masterLocation);if(e){var h="master-item-"+this.itemCounter++;var i=$(g.el);i.attr("id",h);i.addClass("master-item");if(f){e.append(i)}else{e.prepend(i)}this.list[h]=g;return h}return null},_eventRefresh:function(h){var i=$(h.target).closest(".master-item");if(i.length){i=i.attr("id")}if(this.itemLast&&this.itemLast!=i){var g=this.list[this.itemLast];if(g){if(g.masterReset){g.masterReset()}}}var f=false;if(i){var g=this.list[i];if(g){if(g.masterReset){if(this.itemLast==i){f=this.backgroundVisible?false:true}else{f=true}}}}if(f){this.$background.show()}else{this.$background.hide()}this.backgroundVisible=f;this.itemLast=i},_templateItem:function(e){return'
      '},_template:function(e){return''}});var d=Backbone.View.extend({options:{id:"galaxy-icon",icon:"fa-cog",tooltip:"galaxy-icon",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},masterLocation:"iconbar",initialize:function(f){if(f){this.options=_.defaults(f,this.options)}this.setElement($(this._template(this.options)));var e=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip}).on("mouseup",e.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(e){$(this.el).find(".icon").removeClass(this.options.icon).addClass(e);this.options.icon=e},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(e){$(this.el).find(".number").text(e)},_template:function(f){var e="
      ';if(f.with_number){e+='
      '}e+="
      ";return e}});var b=Backbone.View.extend({options:{id:"",title:"Title",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true},masterLocation:"navbar",$menu:null,menuVisible:false,events:{"click .head":"_eventClickHead"},initialize:function(e){if(e){this.options=_.defaults(e,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},addMenu:function(g){var h={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(g){h=_.defaults(g,h)}if(h.content&&h.content.indexOf("//")===-1){h.content=galaxy_config.root+h.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".menu")}var f=$(this._templateMenuItem(h));this.$menu.append(f);var e=this;f.on("click",function(i){i.preventDefault();e._hideMenu();if(e.options.target==="_blank"){return true}Galaxy.frame_manager.frame_new(g)});if(h.divider){this.$menu.append($(this._templateDivider()))}},masterReset:function(){this._hideMenu()},_hideMenu:function(){if(this.$menu&&this.menuVisible){this.$menu.hide();this.menuVisible=false}},_eventClickHead:function(f){f.preventDefault();if(this.$menu){if(!this.menuVisible){this.$menu.show();this.menuVisible=true}else{this.$menu.hide();this.menuVisible=false}}else{Galaxy.frame_manager.frame_new(this.options)}},_templateMenuItem:function(e){return'
    • '+e.title+"
      • "},_templateMenu:function(){return'
        '},_templateDivider:function(){return'
      • '},_template:function(f){var e='';return e}});return{GalaxyMaster:a,GalaxyMasterTab:b,GalaxyMasterIcon:d}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/dataset/hda-base.js b/static/scripts/packed/mvc/dataset/hda-base.js index 9d7c0daa49d..b8339049bf4 100644 --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1 +1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer: "+c.model.get("name"),type:"url",location:"center",content:c.urls.display})}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['','',""].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['
        ','',_l("Download Dataset"),"",""+_l("Additional Files")+"",_.map(e,function(g){return['',_l("Download")," ",g.file_type,""].join("")}).join("\n"),"
        ",'
        ','','','','',"","
        "].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",faIcon:"fa-info-circle"})},_render_body:function(){var d=$('
        Error: unknown dataset state "'+this.model.get("state")+'".
        '),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("
        "+_l("This is a new dataset and not all of its data are available yet")+"
        ")},_render_body_noPermission:function(){return this._render_stateBodyHelper("
        "+_l("You do not have permission to view this dataset")+"
        ")},_render_body_discarded:function(){return this._render_stateBodyHelper("
        "+_l("The job creating this dataset was cancelled before completion")+"
        ",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("
        "+_l("This job is waiting to run")+"
        ",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("
        "+_l("This dataset is currently uploading")+"
        ")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("
        "+_l("Metadata is being auto-detected")+"
        ")},_render_body_running:function(){return this._render_stateBodyHelper("
        "+_l("This job is currently running")+"
        ",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("
        "+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"
        ",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=_l("An error occurred with this dataset")+": "+$.trim(this.model.get("misc_info"))+"";if(!this.model.get("purged")){c="
        "+this.model.get("misc_blurb")+"
        "+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("
        "+_l("No data")+": "+this.model.get("misc_blurb")+"
        ",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('
        ').append($("").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility"},toggleBodyVisibility:function(d,c){var e=this.$el.find(".dataset-body");c=(c===undefined)?(!e.is(":visible")):(c);if(c){this.expandBody()}else{this.collapseBody()}},expandBody:function(){var c=this;function d(){c.render(false).$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer: "+c.model.get("name"),type:"url",target:"galaxy_main",content:c.urls.display})}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['','',""].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['
        ','',_l("Download Dataset"),"",""+_l("Additional Files")+"",_.map(e,function(g){return['',_l("Download")," ",g.file_type,""].join("")}).join("\n"),"
        ",'
        ','','','','',"","
        "].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",faIcon:"fa-info-circle"})},_render_body:function(){var d=$('
        Error: unknown dataset state "'+this.model.get("state")+'".
        '),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("
        "+_l("This is a new dataset and not all of its data are available yet")+"
        ")},_render_body_noPermission:function(){return this._render_stateBodyHelper("
        "+_l("You do not have permission to view this dataset")+"
        ")},_render_body_discarded:function(){return this._render_stateBodyHelper("
        "+_l("The job creating this dataset was cancelled before completion")+"
        ",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("
        "+_l("This job is waiting to run")+"
        ",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("
        "+_l("This dataset is currently uploading")+"
        ")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("
        "+_l("Metadata is being auto-detected")+"
        ")},_render_body_running:function(){return this._render_stateBodyHelper("
        "+_l("This job is currently running")+"
        ",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("
        "+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"
        ",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=_l("An error occurred with this dataset")+": "+$.trim(this.model.get("misc_info"))+"";if(!this.model.get("purged")){c="
        "+this.model.get("misc_blurb")+"
        "+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("
        "+_l("No data")+": "+this.model.get("misc_blurb")+"
        ",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('
        ').append($("").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility"},toggleBodyVisibility:function(d,c){var e=this.$el.find(".dataset-body");c=(c===undefined)?(!e.is(":visible")):(c);if(c){this.expandBody()}else{this.collapseBody()}},expandBody:function(){var c=this;function d(){c.render(false).$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/dataset/hda-edit.js b/static/scripts/packed/mvc/dataset/hda-edit.js index c511ba96a5a..15243251667 100644 --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1 +1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(g||i){h.enabled=false;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h=g.urls["delete"],i={title:_l("Delete"),href:h,icon_class:"delete",onclick:function(){g.$el.find(".menu-button.delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_tagButton:function(){if(!this.hasUser){return null}return faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"})},_render_annotateButton:function(){if(!this.hasUser){return null}return faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"})},_render_body_failed_metadata:function(){var h=$("").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);g.find(".dataset-actions .left").append(this._render_visualizationsButton());g.find(".dataset-actions .right").append([this._render_tagButton(),this._render_annotateButton()]);this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display")}).render();return g},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('?').attr("href",this.urls.edit))}},events:{"click .dataset-title-bar":"toggleBodyVisibility","click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge","click .dataset-tag-btn":"displayTags","click .dataset-annotate-btn":"loadAndDisplayAnnotation"},confirmPurge:function c(g){this.model.purge();return false},displayTags:function(g){this.$el.find(".tags-display").slideToggle(this.fxSpeed);return false},loadAndDisplayAnnotation:function(j){this.log(this+".loadAndDisplayAnnotation",j);var i=this,h=this.$el.find(".annotation-display"),g=h.find(".annotation");if(h.is(":hidden")){if(!jQuery.trim(g.html())){var k=$.ajax(this.urls.annotation.get);k.fail(function(n,l,m){i.log("Annotation failed",n,l,m);i.trigger("error",i,n,{},_l("Annotation failed"))});k.done(function(l){l=l||""+_l("Describe or add notes to dataset")+"";g.html(l);h.find("[title]").tooltip();g.make_text_editable({use_textarea:true,on_finish:function(m){g.text(m);i.model.save({annotation:m},{silent:true}).fail(function(){g.text(i.model.previous("annotation"))})}});h.slideDown(i.fxSpeed)})}else{h.slideDown(i.fxSpeed)}}else{h.slideUp(i.fxSpeed)}return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),location:"center"});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i)})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:m})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(g||i){h.enabled=false;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h=g.urls["delete"],i={title:_l("Delete"),href:h,icon_class:"delete",onclick:function(){g.$el.find(".menu-button.delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_tagButton:function(){if(!this.hasUser){return null}return faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"})},_render_annotateButton:function(){if(!this.hasUser){return null}return faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"})},_render_body_failed_metadata:function(){var h=$("").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);g.find(".dataset-actions .left").append(this._render_visualizationsButton());g.find(".dataset-actions .right").append([this._render_tagButton(),this._render_annotateButton()]);this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display")}).render();return g},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('?').attr("href",this.urls.edit))}},events:{"click .dataset-title-bar":"toggleBodyVisibility","click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge","click .dataset-tag-btn":"displayTags","click .dataset-annotate-btn":"loadAndDisplayAnnotation"},confirmPurge:function c(g){this.model.purge();return false},displayTags:function(g){this.$el.find(".tags-display").slideToggle(this.fxSpeed);return false},loadAndDisplayAnnotation:function(j){this.log(this+".loadAndDisplayAnnotation",j);var i=this,h=this.$el.find(".annotation-display"),g=h.find(".annotation");if(h.is(":hidden")){if(!jQuery.trim(g.html())){var k=$.ajax(this.urls.annotation.get);k.fail(function(n,l,m){i.log("Annotation failed",n,l,m);i.trigger("error",i,n,{},_l("Annotation failed"))});k.done(function(l){l=l||""+_l("Describe or add notes to dataset")+"";g.html(l);h.find("[title]").tooltip();g.make_text_editable({use_textarea:true,on_finish:function(m){g.text(m);i.model.save({annotation:m},{silent:true}).fail(function(){g.text(i.model.previous("annotation"))})}});h.slideDown(i.fxSpeed)})}else{h.slideDown(i.fxSpeed)}}else{h.slideUp(i.fxSpeed)}return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file diff --git a/static/style/blue/base.css b/static/style/blue/base.css index 2edc2ead307..f534ad7267e 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1312,7 +1312,7 @@ div.unified-panel-body{position:absolute;top:30px;bottom:0;width:100%} #masthead .navbar-brand{position:absolute;left:0;top:0;font-family:verdana;font-weight:bold;font-size:20px;line-height:1;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000}#masthead .navbar-brand img{display:inline;width:26px;vertical-align:top} #masthead .navbar-brand a{color:white;text-decoration:none} #masthead .iconbar{position:absolute;top:5px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 10px} -#masthead .iconbar .symbol .number{font-weight:bold;font-size:10px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;position:relative;left:23px;top:-16px} +#masthead .iconbar .symbol .number{font-weight:bold;font-size:10px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;position:relative;left:23px;top:-12px} #masthead .iconbar .toggle{color:#BCC800} .quota-meter-container{position:absolute;top:0;right:0;height:32px} .quota-meter{position:absolute;top:8px;right:8px;height:16px;width:100px;background-color:#f5f5f5} diff --git a/static/style/src/less/base.less b/static/style/src/less/base.less index d376d5ccc82..f41e839e261 100644 --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -440,7 +440,7 @@ div.unified-panel-body { font-family : @font-family-sans-serif; position : relative; left : 23px; - top : -16px; + top : -12px; } .toggle diff --git a/templates/base/base_panels.mako b/templates/base/base_panels.mako index 4be9c334053..d1cb9fb360a 100644 --- a/templates/base/base_panels.mako +++ b/templates/base/base_panels.mako @@ -93,15 +93,6 @@ "libs/backbone/backbone-relational": ["libs/backbone/backbone"] } }); - - ## load galaxy js-modules - require(['galaxy.master', 'galaxy.frame', 'galaxy.modal', 'galaxy.upload'], function(master, frame, modal, upload) - { - Galaxy.master = new master.GalaxyMaster(); - Galaxy.frame_manager = new frame.GalaxyFrameManager(); - Galaxy.modal = new modal.GalaxyModal(); - ##Galaxy.upload = new upload.GalaxyUpload(); - }); diff --git a/templates/webapps/galaxy/base_panels.mako b/templates/webapps/galaxy/base_panels.mako index 5aff4f87f8d..93c76a8e241 100644 --- a/templates/webapps/galaxy/base_panels.mako +++ b/templates/webapps/galaxy/base_panels.mako @@ -1,252 +1,18 @@ <%inherit file="/base/base_panels.mako"/> +<%namespace name="mod_masthead" file="/webapps/galaxy/galaxy.masthead.mako"/> ## Default title <%def name="title()">Galaxy <%def name="javascripts()"> ${parent.javascripts()} - - -${h.templates( "helpers-common-templates" )} -${h.js( "mvc/base-mvc", "utils/localization", "mvc/user/user-model", "mvc/user/user-quotameter" )} - - -<%def name="get_user_json()"> -<% - """Bootstrapping user API JSON""" - #TODO: move into common location (poss. BaseController) - if trans.user: - user_dict = trans.user.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, - 'total_disk_usage': float } ) - ##TODO: move these into to_dict - user_dict['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) - user_dict['tags_used'] = trans.webapp.controllers[ 'tag' ].get_user_tags_used( trans ) - else: - usage = 0 - percent = None - try: - usage = trans.app.quota_agent.get_usage( trans, history=trans.history ) - percent = trans.app.quota_agent.get_percent( trans=trans, usage=usage ) - except AssertionError, assertion: - # no history for quota_agent.get_usage assertion - pass - user_dict = { - 'total_disk_usage' : int( usage ), - 'nice_total_disk_usage' : util.nice_size( usage ), - 'quota_percent' : percent - } - -%> -${h.to_json_string( user_dict )} <%def name="late_javascripts()"> ${parent.late_javascripts()} - ## Masthead <%def name="masthead()"> - - ## Tab area, fills entire width -
        -
        - -
          - - <%def name="tab( id, display, href, onclick=False, target='_parent', visible=True, extra_class='', menu_options=None )"> - ## Create a tab at the top of the panels. menu_options is a list of 2-elements lists of [name, link] - ## that are options in the menu. - - <% - cls = "" - a_cls = "" - extra = "" - if extra_class: - cls += " " + extra_class - if self.active_view == id: - cls += " active" - if menu_options: - cls += " dropdown" - a_cls += " dropdown-toggle" - extra = "" - style = "" - if not visible: - style = "display: none;" - %> -
        • - %if href: - ${display}${extra} - %else: - ${display}${extra} - %endif - %if menu_options: -
            - %for menu_item in menu_options: - %if not menu_item: -
          • - %else: -
          • - %if len ( menu_item ) == 1: - ${menu_item[0]} - %elif len ( menu_item ) == 2: - <% name, link = menu_item %> - %if onclick: - ${name} - %else: - ${name} - %endif - %else: - <% name, link, target = menu_item %> - ${name} - %endif -
            • - %endif - %endfor -
          - %endif -
          • - - - ## Analyze data tab. - ${tab( "analysis", _("Analyze Data"), h.url_for( controller='/root', action='index' ) )} - - ## Workflow tab. - ${tab( "workflow", _("Workflow"), h.url_for( controller='/workflow', action='index' ) )} - - ## 'Shared Items' or Libraries tab. - <% - menu_options = [ - [ _('Data Libraries'), h.url_for( controller='/library', action='index') ], - None, - [ _('Published Histories'), h.url_for( controller='/history', action='list_published' ) ], - [ _('Published Workflows'), h.url_for( controller='/workflow', action='list_published' ) ], - [ _('Published Visualizations'), h.url_for( controller='/visualization', action='list_published' ) ], - [ _('Published Pages'), h.url_for( controller='/page', action='list_published' ) ] - ] - tab( "shared", _("Shared Data"), h.url_for( controller='/library', action='index'), menu_options=menu_options ) - %> - - ## Lab menu. - <% - menu_options = [ - [ _('Sequencing Requests'), h.url_for( controller='/requests', action='index' ) ], - [ _('Find Samples'), h.url_for( controller='/requests', action='find_samples_index' ) ], - [ _('Help'), app.config.get( "lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts" ), "galaxy_main" ] - ] - tab( "lab", "Lab", None, menu_options=menu_options, visible=( trans.user and ( trans.user.requests or trans.app.security_agent.get_accessible_request_types( trans, trans.user ) ) ) ) - %> - - - - ## Visualization menu. - <% - menu_options = [ - [_('New Track Browser'), h.url_for( controller='/visualization', action='trackster' )], - [_('Saved Visualizations'), h.url_for( controller='/visualization', action='list' )] - ] - tab( "visualization", _("Visualization"), h.url_for( controller='/visualization', action='list' ), menu_options=menu_options, onclick=True ) - %> - - ## Cloud menu. - %if app.config.get_bool( 'enable_cloud_launch', False ): - <% - menu_options = [ - [_('New Cloud Cluster'), h.url_for( controller='/cloudlaunch', action='index' ) ], - ] - tab( "cloud", _("Cloud"), h.url_for( controller='/cloudlaunch', action='index'), menu_options=menu_options ) - %> - %endif - - ## Admin tab. - ${tab( "admin", "Admin", h.url_for( controller='/admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - - ## Help tab. - <% - menu_options = [] - if app.config.biostar_url: - menu_options = [ [_('Galaxy Q&A Site'), h.url_for( controller='biostar', action='biostar_redirect', biostar_action='show/tag/galaxy' ), "_blank" ], - [_('Ask a question'), h.url_for( controller='biostar', action='biostar_question_redirect' ), "_blank" ] ] - menu_options.extend( [ - [_('Support'), app.config.get( "support_url", "http://wiki.galaxyproject.org/Support" ), "_blank" ], - [_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/usegalaxy/" ), "_blank" ], - [_('Mailing Lists'), app.config.get( "mailing_lists", "http://wiki.galaxyproject.org/MailingLists" ), "_blank" ], - [_('Videos'), app.config.get( "videos_url", "http://vimeo.com/galaxyproject" ), "_blank" ], - [_('Wiki'), app.config.get( "wiki_url", "http://galaxyproject.org/" ), "_blank" ], - [_('How to Cite Galaxy'), app.config.get( "citation_url", "http://wiki.galaxyproject.org/CitingGalaxy" ), "_blank" ] - ] ) - if app.config.get( 'terms_url', None ) is not None: - menu_options.append( [_('Terms and Conditions'), app.config.get( 'terms_url', None ), '_blank'] ) - tab( "help", _("Help"), None, menu_options=menu_options ) - %> - - ## User tabs. - <% - # Menu for user who is not logged in. - menu_options = [ [ _("Login"), h.url_for( controller='/user', action='login' ), "galaxy_main" ] ] - if app.config.allow_user_creation: - menu_options.append( [ _("Register"), h.url_for( controller='/user', action='create', cntrller='user' ), "galaxy_main" ] ) - extra_class = "loggedout-only" - visible = ( trans.user == None ) - tab( "user", _("User"), None, visible=visible, menu_options=menu_options ) - - # Menu for user who is logged in. - if trans.user: - email = trans.user.email - else: - email = "" - menu_options = [ [ 'Logged in as %s' % email ] ] - if app.config.use_remote_user: - if app.config.remote_user_logout_href: - menu_options.append( [ _('Logout'), app.config.remote_user_logout_href, "_top" ] ) - else: - menu_options.append( [ _('Preferences'), h.url_for( controller='/user', action='index', cntrller='user' ), "galaxy_main" ] ) - menu_options.append( [ 'Custom Builds', h.url_for( controller='/user', action='dbkeys' ), "galaxy_main" ] ) - logout_url = h.url_for( controller='/user', action='logout' ) - menu_options.append( [ 'Logout', logout_url, "_top" ] ) - menu_options.append( None ) - menu_options.append( [ _('Saved Histories'), h.url_for( controller='/history', action='list' ), "galaxy_main" ] ) - menu_options.append( [ _('Saved Datasets'), h.url_for( controller='/dataset', action='list' ), "galaxy_main" ] ) - menu_options.append( [ _('Saved Pages'), h.url_for( controller='/page', action='list' ), "_top" ] ) - menu_options.append( [ _('API Keys'), h.url_for( controller='/user', action='api_keys', cntrller='user' ), "galaxy_main" ] ) - if app.config.use_remote_user: - menu_options.append( [ _('Public Name'), h.url_for( controller='/user', action='edit_username', cntrller='user' ), "galaxy_main" ] ) - - extra_class = "loggedin-only" - visible = ( trans.user != None ) - tab( "user", "User", None, visible=visible, menu_options=menu_options ) - %> - - ##
        - - -
        -
        - - ## Logo, layered over tabs to be clickable -
        - - - Galaxy - %if app.config.brand: - / ${app.config.brand} - %endif - -
        - -
        - - + <% mod_masthead.load(); %> + \ No newline at end of file diff --git a/templates/webapps/galaxy/galaxy.masthead.mako b/templates/webapps/galaxy/galaxy.masthead.mako index f2432ee9848..11589783efe 100644 --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -21,234 +21,87 @@ 'nice_total_disk_usage' : util.nice_size( usage ), 'quota_percent' : percent } + return user_dict %> -${h.to_json_string( user_dict )} ## master head generator <%def name="load()"> + <% + ## get configuration + master_config = { + ## inject configuration + 'brand' : app.config.get("brand", ""), + 'use_remote_user' : app.config.use_remote_user, + 'remote_user_logout_href' : app.config.remote_user_logout_href, + 'enable_cloud_launch' : app.config.get_bool('enable_cloud_launch', False), + 'lims_doc_url' : app.config.get("lims_doc_url", "http://main.g2.bx.psu.edu/u/rkchak/p/sts"), + 'biostar_url' : app.config.biostar_url, + 'biostar_url_redirect' : h.url_for(controller='biostar', action='biostar_redirect', biostar_action='show/tag/galaxy'), + 'support_url' : app.config.get("support_url", "http://wiki.galaxyproject.org/Support"), + 'search_url' : app.config.get("search_url", "http://galaxyproject.org/search/usegalaxy/"), + 'mailing_lists' : app.config.get("mailing_lists", "http://wiki.galaxyproject.org/MailingLists"), + 'screencasts_url' : app.config.get("screencasts_url", "http://vimeo.com/galaxyproject"), + 'wiki_url' : app.config.get("wiki_url", "http://galaxyproject.org/"), + 'citation_url' : app.config.get("citation_url", "http://wiki.galaxyproject.org/CitingGalaxy"), + 'terms_url' : app.config.get("terms_url", ""), + 'allow_user_creation' : app.config.allow_user_creation, + 'logo_url' : h.url_for(app.config.get( 'logo_url', '/')), + 'is_admin_user' : trans.user and app.config.is_admin_user(trans.user), + + ## user details + 'user' : { + 'requests' : bool(trans.user and (trans.user.requests or trans.app.security_agent.get_accessible_request_types(trans, trans.user))), + 'email' : trans.user.email if (trans.user) else "", + 'valid' : bool(trans.user != None), + 'json' : get_user_json() + } + } + %> + + ${h.templates( "helpers-common-templates" )} + ${h.js( "mvc/base-mvc", "utils/localization", "mvc/user/user-model", "mvc/user/user-quotameter" )} + ## load the frame manager - - ## start main tag -         - From 4789f253f5096fab6f9225538c5154298ea27f49 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Tue, 5 Nov 2013 13:36:07 -0500 Subject: [PATCH 0026/1033] UI: Rename frame_manager to frame --- static/scripts/galaxy.frame.js | 6 ++-- static/scripts/galaxy.master.js | 31 +++++++++++-------- static/scripts/mvc/data.js | 4 +-- static/scripts/mvc/dataset/hda-base.js | 2 +- static/scripts/mvc/dataset/hda-edit.js | 8 ++--- static/scripts/packed/galaxy.frame.js | 2 +- static/scripts/packed/galaxy.master.js | 2 +- static/scripts/packed/mvc/data.js | 2 +- static/scripts/packed/mvc/dataset/hda-base.js | 2 +- static/scripts/packed/mvc/dataset/hda-edit.js | 2 +- templates/webapps/galaxy/galaxy.masthead.mako | 2 +- 11 files changed, 34 insertions(+), 29 deletions(-) diff --git a/static/scripts/galaxy.frame.js b/static/scripts/galaxy.frame.js index 86a29e94265..09c9fa35470 100644 --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -6,7 +6,7 @@ define(["galaxy.master", "libs/backbone/backbone-relational"], function(mod_master) { // frame manager -var GalaxyFrameManager = Backbone.View.extend( +var GalaxyFrame = Backbone.View.extend( { // base element el_main: 'body', @@ -164,7 +164,7 @@ var GalaxyFrameManager = Backbone.View.extend( }, // adds and displays a new frame/window - frame_new: function(options) + add: function(options) { // frame default options var frameOptions = @@ -1134,7 +1134,7 @@ var GalaxyFrameManager = Backbone.View.extend( // return return { - GalaxyFrameManager: GalaxyFrameManager + GalaxyFrame: GalaxyFrame }; }); diff --git a/static/scripts/galaxy.master.js b/static/scripts/galaxy.master.js index 1a5c30dd2b5..475d5926cb1 100644 --- a/static/scripts/galaxy.master.js +++ b/static/scripts/galaxy.master.js @@ -99,10 +99,11 @@ var GalaxyMaster = Backbone.View.extend( $itemNew.addClass('master-item'); // append to master - if (append) + if (append) { $loc.append($itemNew); - else + } else { $loc.prepend($itemNew); + } // add to list this.list[itemId] = item; @@ -129,9 +130,11 @@ var GalaxyMaster = Backbone.View.extend( if (this.itemLast && this.itemLast != itemCurrent) { var it = this.list[this.itemLast]; - if (it) - if (it.masterReset) + if (it) { + if (it.masterReset) { it.masterReset(); + } + } } // check if current item is in active state @@ -139,21 +142,23 @@ var GalaxyMaster = Backbone.View.extend( if (itemCurrent) { var it = this.list[itemCurrent]; - if (it) - if (it.masterReset) - { - if (this.itemLast == itemCurrent) + if (it) { + if (it.masterReset) { + if (this.itemLast == itemCurrent) { useBackground = this.backgroundVisible ? false : true; - else + } else { useBackground = true; + } } + } } // decide wether to show/hide background - if (useBackground) + if (useBackground) { this.$background.show(); - else + } else { this.$background.hide(); + } // backup this.backgroundVisible = useBackground; @@ -401,7 +406,7 @@ var GalaxyMasterTab = Backbone.View.extend( return true; // load into frame - Galaxy.frame_manager.frame_new(options); + Galaxy.frame.add(options); }); // append divider @@ -445,7 +450,7 @@ var GalaxyMasterTab = Backbone.View.extend( } } else { // open new frame - Galaxy.frame_manager.frame_new(this.options); + Galaxy.frame.add(this.options); } }, diff --git a/static/scripts/mvc/data.js b/static/scripts/mvc/data.js index ae0369865c6..decdf612dfc 100644 --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -443,7 +443,7 @@ var TabularButtonTracksterView = Backbone.View.extend( dataset_params.id = vis_id; // add widget - parent.Galaxy.frame_manager.frame_new({ + parent.Galaxy.frame.add({ title : "Trackster", type : "url", content : vis_url + "/trackster?" + $.param(dataset_params) @@ -460,7 +460,7 @@ var TabularButtonTracksterView = Backbone.View.extend( var url = vis_url + "/trackster?" + $.param(dataset_params); // add widget - parent.Galaxy.frame_manager.frame_new({ + parent.Galaxy.frame.add({ title : "Trackster", type : "url", content : url diff --git a/static/scripts/mvc/dataset/hda-base.js b/static/scripts/mvc/dataset/hda-base.js index dc6aa47103f..f4eaaa4d84c 100644 --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -172,7 +172,7 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( // add frame manager option onclick event var self = this; displayBtnData.onclick = function(){ - Galaxy.frame_manager.frame_new({ + Galaxy.frame.add({ title : "Data Viewer: " + self.model.get('name'), type : "url", target : "galaxy_main", diff --git a/static/scripts/mvc/dataset/hda-edit.js b/static/scripts/mvc/dataset/hda-edit.js index 2cf6bc162d7..d42e258fba1 100644 --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -230,7 +230,7 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( return create_scatterplot_action_fn( visualization_url, params ); default: return function(){// add widget - Galaxy.frame_manager.frame_new( + Galaxy.frame.add( { title : "Visualization", type : "url", @@ -489,7 +489,7 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( function create_scatterplot_action_fn( url, params ){ action = function() { // add widget - Galaxy.frame_manager.frame_new( + Galaxy.frame.add( { title : "Scatterplot", type : "url", @@ -553,7 +553,7 @@ function create_scatterplot_action_fn( url, params ){ dataset_params.id = vis_id; // add widget - parent.Galaxy.frame_manager.frame_new({ + parent.Galaxy.frame.add({ title : "Trackster", type : "url", content : vis_url + "/trackster?" + $.param(dataset_params), @@ -571,7 +571,7 @@ function create_scatterplot_action_fn( url, params ){ var url = vis_url + "/trackster?" + $.param(dataset_params); // add widget - parent.Galaxy.frame_manager.frame_new({ + parent.Galaxy.frame.add({ title : "Trackster", type : "url", content : url, diff --git a/static/scripts/packed/galaxy.frame.js b/static/scripts/packed/galaxy.frame.js index e2678a0279e..f42f277896b 100644 --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1 +1 @@ -define(["galaxy.master","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el_main:"body",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMasterIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",on_click:function(f){c._event_panel_active(f)},on_unload:function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}});Galaxy.master.append(this.button_active);this.button_load=new b.GalaxyMasterIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",on_click:function(f){c._event_panel_load(f)},with_number:true});Galaxy.master.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this._template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this._panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c._panel_refresh()}})},frame_new:function(d){var g={title:"",content:null,target:"",type:null,scratchbook:false};if(d){d=_.defaults(d,g)}else{d=g}if(!d.content){return}if(d.target=="_blank"){window.open(d.content);return}if(d.target=="_top"||d.target=="_parent"||d.target=="_self"){window.location=d.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(d.target=="galaxy_main"||d.target=="center"){if(f.length==0){var c=d.content;if(c.indexOf("?")==-1){c+="?"}else{c+="&"}c+="use_panels=True";window.location=c}else{f.attr("src",d.content)}}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this._template_frame(e.substring(1),d.title,d.type,d.content));var h={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this._to_pixel_coord("width",this.options.frame.cols);d.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(h.id).css("z-index"));this.frame_list[e]=h;this.frame_counter++;this._frame_resize(h,{width:d.width,height:d.height});this._frame_insert(h,{top:0,left:0},true);if(!this.visible){this._panel_show_hide()}},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_panel_load","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this._frame_identify(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this._frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this._frame_resize(this.event.target,h);h.width=this._to_grid_coord("width",h.width)+1;h.height=this._to_grid_coord("height",h.height)+1;h.width=this._to_pixel_coord("width",h.width);h.height=this._to_pixel_coord("height",h.height);this._frame_resize(this.frame_shadow,h);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this._frame_offset(this.event.target,h);var c={top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this._frame_insert(this.frame_shadow,c)}},_event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this._frame_identify(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c._panel_refresh(true);c._panel_animation_complete();if(c.visible&&c.frame_counter==0){c._panel_show_hide()}})},_event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},_event_panel_load:function(c){if(this.event.type!==null){return}this._panel_show_hide()},_event_panel_active:function(c){if(this.event.type!==null){return}this._panel_active_disable()},_event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this._panel_scroll(d)},_event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(-this.options.scroll)},_event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(this.options.scroll)},_frame_identify:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},_frame_drag_start:function(d){this._frame_focus(d,true);var c=this._frame_screen(d);this._frame_resize(this.frame_shadow,c);this._frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},_frame_drag_stop:function(d){this._frame_focus(d,false);var c=this._frame_screen(this.frame_shadow);this._frame_resize(d,c);this._frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this._panel_animation_complete()},_to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},_to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},_to_grid:function(c){return{top:this._to_grid_coord("top",c.top),left:this._to_grid_coord("left",c.left),width:this._to_grid_coord("width",c.width),height:this._to_grid_coord("height",c.height)}},_to_pixel:function(c){return{top:this._to_pixel_coord("top",c.top),left:this._to_pixel_coord("left",c.left),width:this._to_pixel_coord("width",c.width),height:this._to_pixel_coord("height",c.height)}},_is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1g.top+g.height-1||h.top+h.height-1l?1:0)});for(g=0;g
        '},_template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d=''}return'
        '+e+'
        '+d+'
        '},_template_shadow:function(c){return'
        '},_template_background:function(){return'
        '},_template_menu:function(){return'
        '}});return{GalaxyFrameManager:a}}); \ No newline at end of file +define(["galaxy.master","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el_main:"body",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMasterIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",on_click:function(f){c._event_panel_active(f)},on_unload:function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}});Galaxy.master.append(this.button_active);this.button_load=new b.GalaxyMasterIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",on_click:function(f){c._event_panel_load(f)},with_number:true});Galaxy.master.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this._template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this._panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c._panel_refresh()}})},add:function(d){var g={title:"",content:null,target:"",type:null,scratchbook:false};if(d){d=_.defaults(d,g)}else{d=g}if(!d.content){return}if(d.target=="_blank"){window.open(d.content);return}if(d.target=="_top"||d.target=="_parent"||d.target=="_self"){window.location=d.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(d.target=="galaxy_main"||d.target=="center"){if(f.length==0){var c=d.content;if(c.indexOf("?")==-1){c+="?"}else{c+="&"}c+="use_panels=True";window.location=c}else{f.attr("src",d.content)}}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this._template_frame(e.substring(1),d.title,d.type,d.content));var h={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this._to_pixel_coord("width",this.options.frame.cols);d.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(h.id).css("z-index"));this.frame_list[e]=h;this.frame_counter++;this._frame_resize(h,{width:d.width,height:d.height});this._frame_insert(h,{top:0,left:0},true);if(!this.visible){this._panel_show_hide()}},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_panel_load","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this._frame_identify(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this._frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this._frame_resize(this.event.target,h);h.width=this._to_grid_coord("width",h.width)+1;h.height=this._to_grid_coord("height",h.height)+1;h.width=this._to_pixel_coord("width",h.width);h.height=this._to_pixel_coord("height",h.height);this._frame_resize(this.frame_shadow,h);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this._frame_offset(this.event.target,h);var c={top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this._frame_insert(this.frame_shadow,c)}},_event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this._frame_identify(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c._panel_refresh(true);c._panel_animation_complete();if(c.visible&&c.frame_counter==0){c._panel_show_hide()}})},_event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},_event_panel_load:function(c){if(this.event.type!==null){return}this._panel_show_hide()},_event_panel_active:function(c){if(this.event.type!==null){return}this._panel_active_disable()},_event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this._panel_scroll(d)},_event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(-this.options.scroll)},_event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(this.options.scroll)},_frame_identify:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},_frame_drag_start:function(d){this._frame_focus(d,true);var c=this._frame_screen(d);this._frame_resize(this.frame_shadow,c);this._frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},_frame_drag_stop:function(d){this._frame_focus(d,false);var c=this._frame_screen(this.frame_shadow);this._frame_resize(d,c);this._frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this._panel_animation_complete()},_to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},_to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},_to_grid:function(c){return{top:this._to_grid_coord("top",c.top),left:this._to_grid_coord("left",c.left),width:this._to_grid_coord("width",c.width),height:this._to_grid_coord("height",c.height)}},_to_pixel:function(c){return{top:this._to_pixel_coord("top",c.top),left:this._to_pixel_coord("left",c.left),width:this._to_pixel_coord("width",c.width),height:this._to_pixel_coord("height",c.height)}},_is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1g.top+g.height-1||h.top+h.height-1l?1:0)});for(g=0;g
        '},_template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d=''}return'
        '+e+'
        '+d+'
        '},_template_shadow:function(c){return'
        '},_template_background:function(){return'
        '},_template_menu:function(){return'
        '}});return{GalaxyFrame:a}}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.master.js b/static/scripts/packed/galaxy.master.js index 721ff2e37f0..b5fba12240e 100644 --- a/static/scripts/packed/galaxy.master.js +++ b/static/scripts/packed/galaxy.master.js @@ -1 +1 @@ -define(["utils/galaxy.utils","libs/backbone/backbone-relational"],function(c){var a=Backbone.View.extend({el_master:"#everything",options:null,list:{},itemLast:null,itemCounter:0,$background:null,backgroundVisible:false,initialize:function(f){this.options=f;$("body").off();this.setElement($(this._template(f)));$(this.el_master).append($(this.el));this.$background=$(this.el).find("#master-background");var e=this;window.onbeforeunload=function(){var h="";for(key in e.list){if(e.list[key].options.on_unload){var g=e.list[key].options.on_unload();if(g){h+=g+" "}}}if(h!=""){return h}}},events:{click:"_eventRefresh",mousedown:function(f){f.preventDefault()}},append:function(e){return this._add(e,true)},prepend:function(e){return this._add(e,false)},_add:function(g,f){var e=$(this.el).find("#"+g.masterLocation);if(e){var h="master-item-"+this.itemCounter++;var i=$(g.el);i.attr("id",h);i.addClass("master-item");if(f){e.append(i)}else{e.prepend(i)}this.list[h]=g;return h}return null},_eventRefresh:function(h){var i=$(h.target).closest(".master-item");if(i.length){i=i.attr("id")}if(this.itemLast&&this.itemLast!=i){var g=this.list[this.itemLast];if(g){if(g.masterReset){g.masterReset()}}}var f=false;if(i){var g=this.list[i];if(g){if(g.masterReset){if(this.itemLast==i){f=this.backgroundVisible?false:true}else{f=true}}}}if(f){this.$background.show()}else{this.$background.hide()}this.backgroundVisible=f;this.itemLast=i},_templateItem:function(e){return'
        '},_template:function(e){return''}});var d=Backbone.View.extend({options:{id:"galaxy-icon",icon:"fa-cog",tooltip:"galaxy-icon",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},masterLocation:"iconbar",initialize:function(f){if(f){this.options=_.defaults(f,this.options)}this.setElement($(this._template(this.options)));var e=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip}).on("mouseup",e.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(e){$(this.el).find(".icon").removeClass(this.options.icon).addClass(e);this.options.icon=e},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(e){$(this.el).find(".number").text(e)},_template:function(f){var e="
        ';if(f.with_number){e+='
        '}e+="
        ";return e}});var b=Backbone.View.extend({options:{id:"",title:"Title",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true},masterLocation:"navbar",$menu:null,menuVisible:false,events:{"click .head":"_eventClickHead"},initialize:function(e){if(e){this.options=_.defaults(e,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},addMenu:function(g){var h={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(g){h=_.defaults(g,h)}if(h.content&&h.content.indexOf("//")===-1){h.content=galaxy_config.root+h.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".menu")}var f=$(this._templateMenuItem(h));this.$menu.append(f);var e=this;f.on("click",function(i){i.preventDefault();e._hideMenu();if(e.options.target==="_blank"){return true}Galaxy.frame_manager.frame_new(g)});if(h.divider){this.$menu.append($(this._templateDivider()))}},masterReset:function(){this._hideMenu()},_hideMenu:function(){if(this.$menu&&this.menuVisible){this.$menu.hide();this.menuVisible=false}},_eventClickHead:function(f){f.preventDefault();if(this.$menu){if(!this.menuVisible){this.$menu.show();this.menuVisible=true}else{this.$menu.hide();this.menuVisible=false}}else{Galaxy.frame_manager.frame_new(this.options)}},_templateMenuItem:function(e){return'
      • '+e.title+"
        • "},_templateMenu:function(){return'
          '},_templateDivider:function(){return'
        • '},_template:function(f){var e='';return e}});return{GalaxyMaster:a,GalaxyMasterTab:b,GalaxyMasterIcon:d}}); \ No newline at end of file +define(["utils/galaxy.utils","libs/backbone/backbone-relational"],function(c){var a=Backbone.View.extend({el_master:"#everything",options:null,list:{},itemLast:null,itemCounter:0,$background:null,backgroundVisible:false,initialize:function(f){this.options=f;$("body").off();this.setElement($(this._template(f)));$(this.el_master).append($(this.el));this.$background=$(this.el).find("#master-background");var e=this;window.onbeforeunload=function(){var h="";for(key in e.list){if(e.list[key].options.on_unload){var g=e.list[key].options.on_unload();if(g){h+=g+" "}}}if(h!=""){return h}}},events:{click:"_eventRefresh",mousedown:function(f){f.preventDefault()}},append:function(e){return this._add(e,true)},prepend:function(e){return this._add(e,false)},_add:function(g,f){var e=$(this.el).find("#"+g.masterLocation);if(e){var h="master-item-"+this.itemCounter++;var i=$(g.el);i.attr("id",h);i.addClass("master-item");if(f){e.append(i)}else{e.prepend(i)}this.list[h]=g;return h}return null},_eventRefresh:function(h){var i=$(h.target).closest(".master-item");if(i.length){i=i.attr("id")}if(this.itemLast&&this.itemLast!=i){var g=this.list[this.itemLast];if(g){if(g.masterReset){g.masterReset()}}}var f=false;if(i){var g=this.list[i];if(g){if(g.masterReset){if(this.itemLast==i){f=this.backgroundVisible?false:true}else{f=true}}}}if(f){this.$background.show()}else{this.$background.hide()}this.backgroundVisible=f;this.itemLast=i},_templateItem:function(e){return'
          '},_template:function(e){return''}});var d=Backbone.View.extend({options:{id:"galaxy-icon",icon:"fa-cog",tooltip:"galaxy-icon",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},masterLocation:"iconbar",initialize:function(f){if(f){this.options=_.defaults(f,this.options)}this.setElement($(this._template(this.options)));var e=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip}).on("mouseup",e.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(e){$(this.el).find(".icon").removeClass(this.options.icon).addClass(e);this.options.icon=e},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(e){$(this.el).find(".number").text(e)},_template:function(f){var e="
          ';if(f.with_number){e+='
          '}e+="
          ";return e}});var b=Backbone.View.extend({options:{id:"",title:"Title",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true},masterLocation:"navbar",$menu:null,menuVisible:false,events:{"click .head":"_eventClickHead"},initialize:function(e){if(e){this.options=_.defaults(e,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},addMenu:function(g){var h={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(g){h=_.defaults(g,h)}if(h.content&&h.content.indexOf("//")===-1){h.content=galaxy_config.root+h.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".menu")}var f=$(this._templateMenuItem(h));this.$menu.append(f);var e=this;f.on("click",function(i){i.preventDefault();e._hideMenu();if(e.options.target==="_blank"){return true}Galaxy.frame.add(g)});if(h.divider){this.$menu.append($(this._templateDivider()))}},masterReset:function(){this._hideMenu()},_hideMenu:function(){if(this.$menu&&this.menuVisible){this.$menu.hide();this.menuVisible=false}},_eventClickHead:function(f){f.preventDefault();if(this.$menu){if(!this.menuVisible){this.$menu.show();this.menuVisible=true}else{this.$menu.hide();this.menuVisible=false}}else{Galaxy.frame.add(this.options)}},_templateMenuItem:function(e){return'
        • '+e.title+"
          • "},_templateMenu:function(){return'
            '},_templateDivider:function(){return'
          • '},_template:function(f){var e='';return e}});return{GalaxyMaster:a,GalaxyMasterTab:b,GalaxyMasterIcon:d}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/data.js b/static/scripts/packed/mvc/data.js index 93e9f1e8088..9c963ba72d6 100644 --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1 +1 @@ -define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_config.root+"api/datasets"});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){new b(i)},render:function(){var m=$("").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(l,i,m){var j=$("';e+='";e+='";e+='';return e}});return{GalaxyUpload:a}}); \ No newline at end of file diff --git a/templates/webapps/galaxy/galaxy.masthead.mako b/templates/webapps/galaxy/galaxy.masthead.mako index d21a4d9f840..960ef15e27c 100644 --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -25,11 +25,11 @@ %> -## master head generator +## masthead head generator <%def name="load()"> <% ## get configuration - master_config = { + masthead_config = { ## inject configuration 'brand' : app.config.get("brand", ""), 'use_remote_user' : app.config.use_remote_user, @@ -70,37 +70,37 @@ $('').appendTo('head'); ## load galaxy js-modules - require(['galaxy.master', 'galaxy.menu', 'galaxy.modal', 'galaxy.frame', 'galaxy.upload'], - function(mod_master, mod_menu, mod_modal, mod_frame, mod_upload) + require(['galaxy.masthead', 'galaxy.menu', 'galaxy.modal', 'galaxy.frame', 'galaxy.upload'], + function(mod_masthead, mod_menu, mod_modal, mod_frame, mod_upload) { - ## check if master is available - if (Galaxy.master) + ## check if masthead is available + if (Galaxy.masthead) return; ## get configuration - var master_config = ${ h.to_json_string( master_config ) }; + var masthead_config = ${ h.to_json_string( masthead_config ) }; ## set up the quota meter (And fetch the current user data from trans) - Galaxy.currUser = new User(master_config.user.json); + Galaxy.currUser = new User(masthead_config.user.json); ## load global galaxy objects - Galaxy.master = new mod_master.GalaxyMaster(master_config); + Galaxy.masthead = new mod_masthead.GalaxyMasthead(masthead_config); Galaxy.modal = new mod_modal.GalaxyModal(); Galaxy.frame = new mod_frame.GalaxyFrame(); ## construct default menu options Galaxy.menu = new mod_menu.GalaxyMenu({ - master: Galaxy.master, - config: master_config + masthead: Galaxy.masthead, + config: masthead_config }); ## add upload plugin ##Galaxy.upload = new mod_upload.GalaxyUpload(); - ## add quota meter to master + ## add quota meter to masthead Galaxy.quotaMeter = new UserQuotaMeter({ model : Galaxy.currUser, - el : $(Galaxy.master.el).find('.quota-meter-container') + el : $(Galaxy.masthead.el).find('.quota-meter-container') }).render(); }); From 2897607f25e34c83f785c93dde191393823230c5 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 5 Nov 2013 14:16:00 -0500 Subject: [PATCH 0028/1033] Bug fix for tool functional tests with repeat elements. --- test/base/twilltestcase.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/base/twilltestcase.py b/test/base/twilltestcase.py index 0e3a4ef9d0a..9062b15ccfd 100644 --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1320,9 +1320,12 @@ class TwillTestCase( unittest.TestCase ): self.visit_url( "%s/tool_runner/index?tool_id=%s" % (self.url, tool_id) ) if repeat_name is not None: repeat_button = '%s_add' % repeat_name + # Must click somewhere in tool_form, to disambiguate what form + # is being targetted. + tc.browser.clicked( tc.browser.get_form( 'tool_form' ), None ) # Submit the "repeat" form button to add an input) tc.submit( repeat_button ) - print "button '%s' clicked" % repeat_button + #print "button '%s' clicked" % repeat_button tc.find( 'runtool_btn' ) self.submit_form( **kwd ) From b097a37d2522fbaa47e7d322a6c535fcaa36dbc6 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 5 Nov 2013 13:46:06 -0600 Subject: [PATCH 0029/1033] Enhance GATK tools to utilize GALAXY_SLOTS configuration when available. --- tools/gatk/count_covariates.xml | 2 +- tools/gatk/realigner_target_creator.xml | 2 +- tools/gatk/unified_genotyper.xml | 2 +- tools/gatk/variant_eval.xml | 2 +- tools/gatk/variant_recalibrator.xml | 2 +- tools/gatk/variant_select.xml | 2 +- 6 files changed, 6 insertions(+), 6 deletions(-) diff --git a/tools/gatk/count_covariates.xml b/tools/gatk/count_covariates.xml index c955ce36531..658502adf59 100644 --- a/tools/gatk/count_covariates.xml +++ b/tools/gatk/count_covariates.xml @@ -17,7 +17,7 @@ -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "CountCovariates" - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": diff --git a/tools/gatk/realigner_target_creator.xml b/tools/gatk/realigner_target_creator.xml index 853ab8f24cb..58b6c86dc05 100644 --- a/tools/gatk/realigner_target_creator.xml +++ b/tools/gatk/realigner_target_creator.xml @@ -19,7 +19,7 @@ -T "RealignerTargetCreator" -o "${output_interval}" -et "NO_ET" ##ET no phone home - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": -R "${reference_source.ref_file.fields.path}" diff --git a/tools/gatk/unified_genotyper.xml b/tools/gatk/unified_genotyper.xml index 39d095cca97..c54e7b1b08b 100644 --- a/tools/gatk/unified_genotyper.xml +++ b/tools/gatk/unified_genotyper.xml @@ -19,7 +19,7 @@ -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "UnifiedGenotyper" - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} --out "${output_vcf}" --metrics_file "${output_metrics}" -et "NO_ET" ##ET no phone home diff --git a/tools/gatk/variant_eval.xml b/tools/gatk/variant_eval.xml index 5055eed3fca..bd036254a13 100644 --- a/tools/gatk/variant_eval.xml +++ b/tools/gatk/variant_eval.xml @@ -17,7 +17,7 @@ -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "VariantEval" --out "${output_report}" - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": diff --git a/tools/gatk/variant_recalibrator.xml b/tools/gatk/variant_recalibrator.xml index 7aa3c94b293..e1d2513ff7c 100644 --- a/tools/gatk/variant_recalibrator.xml +++ b/tools/gatk/variant_recalibrator.xml @@ -15,7 +15,7 @@ -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "VariantRecalibrator" - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} -et "NO_ET" ##ET no phone home ##-log "${output_log}" ##don't use this to log to file, instead directly capture stdout #if $reference_source.reference_source_selector != "history": diff --git a/tools/gatk/variant_select.xml b/tools/gatk/variant_select.xml index 973469f503c..4c14793c657 100644 --- a/tools/gatk/variant_select.xml +++ b/tools/gatk/variant_select.xml @@ -14,7 +14,7 @@ -p 'java -jar "${GALAXY_DATA_INDEX_DIR}/shared/jars/gatk/GenomeAnalysisTK.jar" -T "SelectVariants" - --num_threads 4 ##hard coded, for now + --num_threads \${GALAXY_SLOTS:-4} -et "NO_ET" ##ET no phone home -o "${output_vcf}" From cfb194f0a069e254007dd50d8e97a87309d5e52a Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 5 Nov 2013 13:46:06 -0600 Subject: [PATCH 0030/1033] Enhance megablast to utilize GALAXY_SLOTS configuration when available. --- tools/metag_tools/megablast_wrapper.py | 8 ++++++-- 1 file changed, 6 insertions(+), 2 deletions(-) diff --git a/tools/metag_tools/megablast_wrapper.py b/tools/metag_tools/megablast_wrapper.py index e7c0d286b1a..80b80ae797a 100644 --- a/tools/metag_tools/megablast_wrapper.py +++ b/tools/metag_tools/megablast_wrapper.py @@ -59,9 +59,13 @@ def __main__(): if not os.path.exists( os.path.split( options.db_build )[0] ): stop_err( 'Cannot locate the target database directory. Please check your location file.' ) + try: + threads = int( os.environ['GALAXY_SLOTS']) + except Exception: + threads = 8 # arguments for megablast - megablast_command = "blastn -task megablast -db %s -query %s -out %s -outfmt '6 qseqid sgi slen ppos length mismatch gaps qstart qend sstart send evalue bitscore' -num_threads 8 -word_size %s -perc_identity %s -evalue %s -dust %s > /dev/null" \ - % ( options.db_build, query_filename, mega_temp_output, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, options.filter_query ) + megablast_command = "blastn -task megablast -db %s -query %s -out %s -outfmt '6 qseqid sgi slen ppos length mismatch gaps qstart qend sstart send evalue bitscore' -num_threads %d -word_size %s -perc_identity %s -evalue %s -dust %s > /dev/null" \ + % ( options.db_build, query_filename, mega_temp_output, threads, mega_word_size, mega_iden_cutoff, mega_evalue_cutoff, options.filter_query ) print megablast_command From 1614f791c19e2be6339eff1cdfe9103f3bdee798 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 5 Nov 2013 13:46:06 -0600 Subject: [PATCH 0031/1033] Enhance tophats to utilize GALAXY_SLOTS configuration when available. --- tools/ngs_rna/tophat2_wrapper.xml | 2 +- tools/ngs_rna/tophat_color_wrapper.xml | 2 +- tools/ngs_rna/tophat_wrapper.xml | 3 +-- 3 files changed, 3 insertions(+), 4 deletions(-) diff --git a/tools/ngs_rna/tophat2_wrapper.xml b/tools/ngs_rna/tophat2_wrapper.xml index b9492252710..e42839567fb 100644 --- a/tools/ngs_rna/tophat2_wrapper.xml +++ b/tools/ngs_rna/tophat2_wrapper.xml @@ -28,7 +28,7 @@ tophat2 ## Change this to accommodate the number of threads you have available. - --num-threads 4 + --num-threads \${GALAXY_SLOTS:-4} ## Set params. #if $params.settingsType == "full": diff --git a/tools/ngs_rna/tophat_color_wrapper.xml b/tools/ngs_rna/tophat_color_wrapper.xml index 399d2c9c46c..8698fddc6e9 100644 --- a/tools/ngs_rna/tophat_color_wrapper.xml +++ b/tools/ngs_rna/tophat_color_wrapper.xml @@ -6,7 +6,7 @@ tophat_wrapper.py ## Change this to accommodate the number of threads you have available. - --num-threads="4" + --num-threads="\${GALAXY_SLOTS:-4}" ## base- or color-space --color-space diff --git a/tools/ngs_rna/tophat_wrapper.xml b/tools/ngs_rna/tophat_wrapper.xml index a8961fe98a4..ef4bab1fc66 100644 --- a/tools/ngs_rna/tophat_wrapper.xml +++ b/tools/ngs_rna/tophat_wrapper.xml @@ -10,8 +10,7 @@ tophat_wrapper.py ## Change this to accommodate the number of threads you have available. - --num-threads="4" - + --num-threads="\${GALAXY_SLOTS:-4}" ## Provide outputs. --junctions-output=$junctions --hits-output=$accepted_hits From 162e4de0e1a8e146a061ab15c770410007fe1b2e Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 5 Nov 2013 13:46:06 -0600 Subject: [PATCH 0032/1033] Enhance bfast to utilize GALAXY_SLOTS configuration when available. --- tools/sr_mapping/bfast_wrapper.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/tools/sr_mapping/bfast_wrapper.xml b/tools/sr_mapping/bfast_wrapper.xml index 65fa785c740..e05ab88bdba 100644 --- a/tools/sr_mapping/bfast_wrapper.xml +++ b/tools/sr_mapping/bfast_wrapper.xml @@ -1,7 +1,7 @@ bfast_wrapper.py - --numThreads="4" ##HACK: hardcode numThreads for now, should come from a location file + --numThreads="\${GALAXY_SLOTS:-4}" --fastq="$input1" #if $input1.extension.startswith( "fastqcs" ): ##if extention starts with fastqcs, then we have a color space file From bc4d6467a0a128e69a1f7ff5ba95b1ec0179f54f Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Tue, 5 Nov 2013 15:32:07 -0500 Subject: [PATCH 0033/1033] HDA API, show: remove force_history_refresh, add annotation; update: allow annotation or genome_build == None; Users API: add 'tags_used' as list of unique tags used by the user; History panel tags & annotations: into Backbone sub-views, cleanup; pack scripts --- lib/galaxy/model/__init__.py | 1 + lib/galaxy/web/base/controller.py | 10 +- lib/galaxy/webapps/galaxy/api/histories.py | 2 +- .../webapps/galaxy/api/history_contents.py | 2 +- lib/galaxy/webapps/galaxy/api/users.py | 2 + static/scripts/mvc/annotations.js | 102 ++- static/scripts/mvc/base-mvc.js | 45 ++ static/scripts/mvc/dataset/hda-base.js | 17 +- static/scripts/mvc/dataset/hda-edit.js | 180 +---- static/scripts/mvc/dataset/hda-model.js | 6 +- static/scripts/mvc/history/history-model.js | 4 +- static/scripts/mvc/history/history-panel.js | 99 +-- static/scripts/mvc/tags.js | 71 +- static/scripts/packed/mvc/annotations.js | 2 +- static/scripts/packed/mvc/base-mvc.js | 2 +- static/scripts/packed/mvc/dataset/hda-base.js | 2 +- static/scripts/packed/mvc/dataset/hda-edit.js | 2 +- .../scripts/packed/mvc/dataset/hda-model.js | 2 +- .../packed/mvc/history/history-panel.js | 2 +- static/scripts/packed/mvc/tags.js | 2 +- .../templates/compiled/history-templates.js | 2 +- .../templates/compiled/template-hda-body.js | 2 +- .../compiled/template-history-historyPanel.js | 2 +- .../templates/compiled/history-templates.js | 635 +----------------- .../templates/compiled/template-hda-body.js | 50 +- .../compiled/template-history-historyPanel.js | 43 +- static/scripts/templates/hda-templates.html | 9 +- .../scripts/templates/history-templates.html | 11 +- static/style/blue/base.css | 12 +- static/style/src/less/history.less | 47 +- templates/webapps/galaxy/galaxy.masthead.mako | 4 +- .../webapps/galaxy/history/history_panel.mako | 2 +- templates/webapps/galaxy/root/history.mako | 7 +- 33 files changed, 319 insertions(+), 1062 deletions(-) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 4445aa14c98..ae7e55c4a23 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1751,6 +1751,7 @@ class HistoryDatasetAssociation( DatasetInstance, Dictifiable, UsesAnnotations ) misc_info = hda.info, misc_blurb = hda.blurb ) + # add tags string list tags_str_list = [] for tag in self.tags: tag_str = tag.user_tname diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py index 2854d1a174e..3953d67d1d4 100644 --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -596,6 +596,8 @@ class UsesHistoryDatasetAssociationMixin: return self.get_inaccessible_hda_dict( trans, hda ) hda_dict[ 'accessible' ] = True + hda_dict[ 'annotation' ] = hda.get_item_annotation_str( trans.sa_session, trans.user, hda ) + # ---- return here if deleted AND purged OR can't access purged = ( hda.purged or hda.dataset.purged ) if ( hda.deleted and purged ): @@ -632,14 +634,6 @@ class UsesHistoryDatasetAssociationMixin: if hda.deleted and not purged: return trans.security.encode_dict_ids( hda_dict ) - # if a tool declares 'force_history_refresh' in its xml, when the hda -> ready, reload the history panel - # expensive - #if( ( hda.state in [ 'running', 'queued' ] ) - #and ( hda.creating_job and hda.creating_job.tool_id ) ): - # tool_used = trans.app.toolbox.get_tool( hda.creating_job.tool_id ) - # if tool_used and tool_used.force_history_refresh: - # hda_dict[ 'force_history_refresh' ] = True - return trans.security.encode_dict_ids( hda_dict ) def get_inaccessible_hda_dict( self, trans, hda ): diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py index e394723c0dc..2c226e4e7b7 100644 --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -361,7 +361,7 @@ class HistoriesController( BaseAPIController, UsesHistoryMixin, UsesTagsMixin ): if not isinstance( val, bool ): raise ValueError( 'published must be a boolean: %s' %( str( type( val ) ) ) ) validated_payload[ 'published' ] = val - elif key == 'genome_build': + elif key == 'genome_build' and val is not None: if not ( isinstance( val, str ) or isinstance( val, unicode ) ): raise ValueError( 'genome_build must be a string: %s' %( str( type( val ) ) ) ) validated_payload[ 'genome_build' ] = sanitize_html( val, 'utf-8' ) diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py index 335382d3982..684df5050d6 100644 --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -406,7 +406,7 @@ class HistoryContentsController( BaseAPIController, UsesHistoryDatasetAssociatio if not ( isinstance( val, str ) or isinstance( val, unicode ) ): raise ValueError( 'genome_build must be a string: %s' %( str( type( val ) ) ) ) validated_payload[ 'dbkey' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) - elif key == 'annotation': + elif key == 'annotation' and val is not None: if not ( isinstance( val, str ) or isinstance( val, unicode ) ): raise ValueError( 'annotation must be a string or unicode: %s' %( str( type( val ) ) ) ) validated_payload[ 'annotation' ] = util.sanitize_html.sanitize_html( val, 'utf-8' ) diff --git a/lib/galaxy/webapps/galaxy/api/users.py b/lib/galaxy/webapps/galaxy/api/users.py index a402695ea28..d8ec8bb9390 100644 --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -71,6 +71,8 @@ class UserAPIController( BaseAPIController, UsesTagsMixin ): raise HTTPBadRequest( detail='Invalid user id ( %s ) specified' % id ) item = user.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) + + # add a list of tags used by the user (as strings) item[ 'tags_used' ] = self.get_user_tags_used( trans, user=user ) #TODO: move into api_values (needs trans, tho - can we do that with api_keys/@property??) #TODO: works with other users (from admin)?? diff --git a/static/scripts/mvc/annotations.js b/static/scripts/mvc/annotations.js index 415fc236949..7d6256ffd13 100644 --- a/static/scripts/mvc/annotations.js +++ b/static/scripts/mvc/annotations.js @@ -1,35 +1,71 @@ -/*============================================================================== -Backbone MV for Annotations - - -TODO: - -==============================================================================*/ -/** Single Tag model +/** A view on any model that has a 'annotation' attribute */ -var Annotation = BaseModel.extend( LoggableMixin ).extend({ - - // uncomment this out see log messages - logger : console, - - toString : function(){ - return 'Annotation()'; - } +var AnnotationEditor = BaseView.extend( LoggableMixin ).extend( HiddenUntilActivatedViewMixin ).extend({ + + tagName : 'div', + className : 'annotation-display', + + /** Set up listeners, parse options */ + initialize : function( options ){ + options = options || {}; + this.tooltipConfig = options.tooltipConfig || { placement: 'bottom' }; + //console.debug( this, options ); + // only listen to the model only for changes to annotations + this.listenTo( this.model, 'change:annotation', function(){ + this.render(); + }); + this.hiddenUntilActivated( options.$activator, options ); + }, + + /** Build the DOM elements, call select to on the created input, and set up behaviors */ + render : function(){ + var view = this; + this.$el.html( this._template() ); + this.$el.find( "[title]" ).tooltip( this.tooltipConfig ); + + //TODO: handle empties better + this.$annotation().make_text_editable({ + use_textarea: true, + on_finish: function( newAnnotation ){ + view.$annotation().text( newAnnotation ); + view.model.save({ annotation: newAnnotation }, { silent: true }) + .fail( function(){ + view.$annotation().text( view.model.previous( 'annotation' ) ); + }); + } + }); + return this; + }, + + /** @returns {String} the html text used to build the view's DOM */ + _template : function(){ + var annotation = this.model.get( 'annotation' ); + //if( !annotation ){ + // //annotation = [ '', _l( 'Click to add an annotation' ), '' ].join( '' ); + // annotation = [ '' ].join( '' ); + //} + return [ + //TODO: make prompt optional + '', + // set up initial tags by adding as CSV to input vals (necc. to init select2) + '
            ', + annotation, + '
            ' + ].join( '' ); + }, + + /** @returns {jQuery} the main element for this view */ + $annotation : function(){ + return this.$el.find( '.annotation' ); + }, + + /** shut down event listeners and remove this view's DOM */ + remove : function(){ + this.$annotation.off(); + this.stopListening( this.model ); + Backbone.View.prototype.remove.call( this ); + }, + + /** string rep */ + toString : function(){ return [ 'AnnotationEditor(', this.model + '', ')' ].join(''); } }); - -//------------------------------------------------------------------------------ -/** Single Tag view - */ -var AnnotationView = BaseView.extend( LoggableMixin ).extend({ - - // uncomment this out see log messages - logger : console, - - toString : function(){ - return 'AnnotationView()'; - } -}); - -//============================================================================== -/** YAGNI? A collection of Annotations, mainView? - */ diff --git a/static/scripts/mvc/base-mvc.js b/static/scripts/mvc/base-mvc.js index 4fb31472e4a..e6f035c61a8 100644 --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -218,6 +218,51 @@ var PersistentStorage = function( storageKey, storageDefaults ){ }; +//============================================================================== +var HiddenUntilActivatedViewMixin = /** @lends hiddenUntilActivatedMixin# */{ + + /** */ + hiddenUntilActivated : function( $activator, options ){ + // call this in your view's initialize fn + options = options || {}; + this.HUAVOptions = { + $elementShown : this.$el, + showFn : jQuery.prototype.toggle, + showSpeed : 'fast' + }; + _.extend( this.HUAVOptions, options || {}); + this.HUAVOptions.hasBeenShown = this.HUAVOptions.$elementShown.is( ':visible' ); + + if( $activator ){ + var mixin = this; + $activator.on( 'click', function( ev ){ + mixin.toggle( mixin.HUAVOptions.showSpeed ); + }); + } + }, + + /** */ + toggle : function(){ + // can be called manually as well with normal toggle arguments + if( this.HUAVOptions.$elementShown.is( ':hidden' ) ){ + // fire the optional fns on the first/each showing - good for render() + if( !this.HUAVOptions.hasBeenShown ){ + if( _.isFunction( this.HUAVOptions.onshowFirstTime ) ){ + this.HUAVOptions.hasBeenShown = true; + this.HUAVOptions.onshowFirstTime.call( this ); + } + } else { + if( _.isFunction( this.HUAVOptions.onshow ) ){ + this.HUAVOptions.onshow.call( this ); + } + } + } + return this.HUAVOptions.showFn.apply( this.HUAVOptions.$elementShown, arguments ); + } +}; + + + //============================================================================== function LoadingIndicator( $where, options ){ options = options || {}; diff --git a/static/scripts/mvc/dataset/hda-base.js b/static/scripts/mvc/dataset/hda-base.js index f4eaaa4d84c..e20cbfe3e51 100644 --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -180,8 +180,6 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( }); }; } - //return new IconButtonView({ model : new IconButton( displayBtnData ) }).render().$el; - displayBtnData.faIcon = 'fa-eye'; return faIconButton( displayBtnData ); }, @@ -199,7 +197,6 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( // return either: a single download icon-button (if there are no meta files) if( _.isEmpty( meta_files ) ){ return $([ - //'' '', '', '' @@ -207,7 +204,7 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( } // or a popupmenu with links to download assoc. meta files (if there are meta files) -//TODO: Popupmenu + //TODO: Popupmenu var menuId = 'dataset-' + this.model.get( 'id' ) + '-popup', html = [ '
            ', @@ -240,12 +237,6 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( */ _render_showParamsButton : function(){ // gen. safe to show in all cases - //return new IconButtonView({ model : new IconButton({ - // title : _l( 'View details' ), - // href : this.urls.show_params, - // target : 'galaxy_main', - // icon_class : 'information' - //}) }).render().$el; return faIconButton({ title : _l( 'View details' ), href : this.urls.show_params, @@ -339,8 +330,10 @@ var HDABaseView = Backbone.View.extend( LoggableMixin ).extend( /** Render an HDA whose job has failed. */ _render_body_error : function(){ - var html = _l( 'An error occurred with this dataset' ) - + ': ' + $.trim( this.model.get( 'misc_info' ) ) + ''; + var html = [ + '', _l( 'An error occurred with this dataset' ), ':', + '
            ', $.trim( this.model.get( 'misc_info' ) ), '
            ' + ].join( '' ); if( !this.model.get( 'purged' ) ){ html = '
            ' + this.model.get( 'misc_blurb' ) + '
            ' + html; } diff --git a/static/scripts/mvc/dataset/hda-edit.js b/static/scripts/mvc/dataset/hda-edit.js index d42e258fba1..de36466b5b4 100644 --- a/static/scripts/mvc/dataset/hda-edit.js +++ b/static/scripts/mvc/dataset/hda-edit.js @@ -86,10 +86,6 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( editBtnData.disabled = true; editBtnData.title = _l( 'This dataset must finish uploading before it can be edited' ); } - - - //return new IconButtonView({ model : new IconButton( editBtnData ) }).render().$el; - editBtnData.faIcon = 'fa-pencil'; return faIconButton( editBtnData ); }, @@ -124,8 +120,6 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( enabled : false }; } - //return new IconButtonView({ model : new IconButton( deleteBtnData ) }).render().$el; - deleteBtnData.faIcon = 'fa-times'; return faIconButton( deleteBtnData ); }, @@ -138,14 +132,6 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( if( this.model.get( 'state' ) !== hdaModel.HistoryDatasetAssociation.STATES.ERROR ){ return null; } - - //return new IconButtonView({ model : new IconButton({ - // title : _l( 'View or report this error' ), - // href : this.urls.report_error, - // target : 'galaxy_main', - // icon_class : 'bug' - //})}).render().$el; - return faIconButton({ title : _l( 'View or report this error' ), href : this.urls.report_error, @@ -158,13 +144,6 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( * @returns {jQuery} rendered DOM */ _render_rerunButton : function(){ - //return new IconButtonView({ model : new IconButton({ - // title : _l( 'Run this job again' ), - // href : this.urls.rerun, - // target : 'galaxy_main', - // icon_class : 'arrow-circle' - //}) }).render().$el; - return faIconButton({ title : _l( 'Run this job again' ), href : this.urls.rerun, @@ -204,15 +183,6 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( // Add dbkey to params if it exists. if( dbkey ){ params.dbkey = dbkey; } - // render the icon from template - //var visualizationsButton = new IconButtonView({ model : new IconButton({ - // title : _l( 'Visualize' ), - // href : this.urls.visualization, - // icon_class : 'chart_curve' - //})}); - //var $icon = visualizationsButton.render().addClass( 'visualize-icon' ); // needed? - ////return visualizationsButton.render().$el; - var $icon = faIconButton({ title : _l( 'Visualize' ), href : this.urls.visualization, @@ -264,13 +234,6 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( || !( visualizations && !_.isEmpty( visualizations ) ) ){ return null; } - - // render the icon from template - //var visualizationsButton = new IconButtonView({ model : new IconButton({ - // title : _l( 'Visualize' ), - // icon_class : 'chart_curve' - //})}); - //var $icon = visualizationsButton.render().$el; var $icon = faIconButton({ title : _l( 'Visualize' ), faIcon : 'fa-bar-chart-o' @@ -293,49 +256,6 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( return $icon; }, - // ......................................................................... secondary actions - /** Render icon-button to load and display tagging html. - * @returns {jQuery} rendered DOM - */ - _render_tagButton : function(){ - if( !this.hasUser ){ - return null; - } - - //return new IconButtonView({ model : new IconButton({ - // title : _l( 'Edit dataset tags' ), - // target : 'galaxy_main', - // href : this.urls.tags.get, - // icon_class : 'tags' - //})}).render().$el; - - return faIconButton({ - title : _l( 'Edit dataset tags' ), - classes : 'dataset-tag-btn', - faIcon : 'fa-tags' - }); - }, - - /** Render icon-button to load and display annotation html. - * @returns {jQuery} rendered DOM - */ - _render_annotateButton : function(){ - if( !this.hasUser ){ - return null; - } - - //return new IconButtonView({ model : new IconButton({ - // title : _l( 'Edit dataset annotation' ), - // target : 'galaxy_main', - // icon_class : 'annotate' - //})}).render().$el; - return faIconButton({ - title : _l( 'Edit dataset annotation' ), - classes : 'dataset-annotate-btn', - faIcon : 'fa-comment' - }); - }, - // ......................................................................... state body renderers /** Render an HDA where the metadata wasn't produced correctly. * Overridden to add a link to dataset/edit @@ -375,18 +295,39 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( this.makeDbkeyEditLink( $body ); // more actions/buttons - $body.find( '.dataset-actions .left' ).append( this._render_visualizationsButton() ); - $body.find( '.dataset-actions .right' ).append([ - this._render_tagButton(), - this._render_annotateButton() - ]); - this.tagsEditor = new TagsEditor({ - model : this.model, - el : $body.find( '.tags-display' ) - }).render(); + if( this.hasUser ){ + $body.find( '.dataset-actions .left' ).append( this._render_visualizationsButton() ); + this._renderTags( $body ); + this._renderAnnotation( $body ); + } return $body; }, + _renderTags : function( $where ){ + this.tagsEditor = new TagsEditor({ + model : this.model, + el : $where.find( '.tags-display' ), + onshowFirstTime : function(){ this.render(); }, + $activator : faIconButton({ + title : _l( 'Edit dataset tags' ), + classes : 'dataset-tag-btn', + faIcon : 'fa-tags' + }).appendTo( $where.find( '.dataset-actions .right' ) ) + }); + }, + _renderAnnotation : function( $where ){ + this.annotationEditor = new AnnotationEditor({ + model : this.model, + el : $where.find( '.annotation-display' ), + onshowFirstTime : function(){ this.render(); }, + $activator : faIconButton({ + title : _l( 'Edit dataset annotation' ), + classes : 'dataset-annotate-btn', + faIcon : 'fa-comment' + }).appendTo( $where.find( '.dataset-actions .right' ) ) + }); + }, + makeDbkeyEditLink : function( $body ){ // make the dbkey a link to editing if( this.model.get( 'metadata_dbkey' ) === '?' @@ -402,73 +343,16 @@ var HDAEditView = hdaBase.HDABaseView.extend( LoggableMixin ).extend( 'click .dataset-title-bar' : 'toggleBodyVisibility', 'click .dataset-undelete' : function( ev ){ this.model.undelete(); return false; }, 'click .dataset-unhide' : function( ev ){ this.model.unhide(); return false; }, - 'click .dataset-purge' : 'confirmPurge', - - 'click .dataset-tag-btn' : 'displayTags', - 'click .dataset-annotate-btn' : 'loadAndDisplayAnnotation' + 'click .dataset-purge' : 'confirmPurge' }, /** listener for item purge */ confirmPurge : function _confirmPurge( ev ){ -//TODO: confirm dialog + //TODO: confirm dialog this.model.purge(); return false; }, - // ......................................................................... tags - /** Find the tag area and, if initial: load the html (via ajax) for displaying them; otherwise, unhide/hide - */ -//TODO: into sub-MV - displayTags : function( event ){ - this.$el.find( '.tags-display' ).slideToggle( this.fxSpeed ); - return false; - }, - - // ......................................................................... annotations - /** Find the annotation area and, if initial: load the html (via ajax) for displaying them; otherwise, unhide/hide - */ - loadAndDisplayAnnotation : function( event ){ -//TODO: this is a drop in from history.mako - should use MV as well - this.log( this + '.loadAndDisplayAnnotation', event ); - var view = this, - $annotationArea = this.$el.find( '.annotation-display' ), - $annotationElem = $annotationArea.find( '.annotation' ); - - // Show or hide annotation area; if showing annotation area and it's empty, fill it. - if ( $annotationArea.is( ":hidden" ) ){ - if( !jQuery.trim( $annotationElem.html() ) ){ - // Need to fill annotation element. - var xhr = $.ajax( this.urls.annotation.get ); - xhr.fail( function( xhr, status, error ){ - view.log( "Annotation failed", xhr, status, error ); - view.trigger( 'error', view, xhr, {}, _l( "Annotation failed" ) ); - }); - xhr.done( function( html ){ - html = html || "" + _l( "Describe or add notes to dataset" ) + ""; - $annotationElem.html( html ); - $annotationArea.find( "[title]" ).tooltip(); - - $annotationElem.make_text_editable({ - use_textarea: true, - on_finish: function( newAnnotation ){ - $annotationElem.text( newAnnotation ); - view.model.save({ annotation: newAnnotation }, { silent: true }) - .fail( function(){ - $annotationElem.text( view.model.previous( 'annotation' ) ); - }); - } - }); - $annotationArea.slideDown( view.fxSpeed ); - }); - } else { - $annotationArea.slideDown( view.fxSpeed ); - } - } else { - $annotationArea.slideUp( view.fxSpeed ); - } - return false; - }, - // ......................................................................... misc /** string rep */ toString : function(){ diff --git a/static/scripts/mvc/dataset/hda-model.js b/static/scripts/mvc/dataset/hda-model.js index b43a919dff4..83f333d618f 100644 --- a/static/scripts/mvc/dataset/hda-model.js +++ b/static/scripts/mvc/dataset/hda-model.js @@ -56,7 +56,7 @@ var HistoryDatasetAssociation = Backbone.Model.extend( LoggableMixin ).extend( }, /** fetch location of this HDA's history in the api */ - urlRoot: 'api/histories/', + urlRoot: '/api/histories/', /** full url spec. for this HDA */ url : function(){ return this.urlRoot + this.get( 'history_id' ) + '/contents/' + this.get( 'id' ); @@ -80,10 +80,6 @@ var HistoryDatasetAssociation = Backbone.Model.extend( LoggableMixin ).extend( 'annotation': { 'get': galaxy_config.root + 'dataset/get_annotation_async?id=' + id, 'set': galaxy_config.root + 'dataset/annotate_async?id=' + id }, - 'tags' : { 'get': galaxy_config.root + 'tag/get_tagging_elt_async?item_id=' - + id + '&item_class=HistoryDatasetAssociation', - 'set': galaxy_config.root + 'tag/retag?item_id=' - + id + '&item_class=HistoryDatasetAssociation' }, 'meta_download' : galaxy_config.root + 'dataset/get_metadata_file?hda_id=' + id + '&metadata_name=' }; return urls; diff --git a/static/scripts/mvc/history/history-model.js b/static/scripts/mvc/history/history-model.js index 94872cbbe2f..dfbe91175e9 100644 --- a/static/scripts/mvc/history/history-model.js +++ b/static/scripts/mvc/history/history-model.js @@ -25,8 +25,8 @@ var History = Backbone.Model.extend( LoggableMixin ).extend( name : 'Unnamed History', state : 'new', - diskSize : 0, - deleted : false + diskSize : 0, + deleted : false }, // ........................................................................ urls diff --git a/static/scripts/mvc/history/history-panel.js b/static/scripts/mvc/history/history-panel.js index 3a81c22c7a3..808b2116cb5 100644 --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -13,9 +13,6 @@ TODO: tags & annotations -> out use model.save instead of urls - meta: - convert function comments to jsDoc style, complete comments - feature creep: lineage hide button @@ -633,14 +630,8 @@ var HistoryPanel = Backbone.View.extend( LoggableMixin ).extend( } else { $newRender.append( HistoryPanel.templates.historyPanel( this.model.toJSON() ) ); - $newRender.find( '.history-secondary-actions' ).append([ - this._render_tagButton(), - this._render_annotateButton() - ]); - this.tagsEditor = new TagsEditor({ - model : this.model, - el : $newRender.find( '.history-controls .tags-display' ) - }).render(); + this._renderTags( $newRender ); + this._renderAnnotation( $newRender ); } this._setUpBehaviours( $newRender ); @@ -654,34 +645,29 @@ var HistoryPanel = Backbone.View.extend( LoggableMixin ).extend( return $newRender; }, - /** Render icon-button to load and display tagging html. - * @returns {jQuery} rendered DOM - */ - _render_tagButton : function(){ - return faIconButton({ - title : _l( 'Edit history tags' ), - classes : 'history-tag-button', - faIcon : 'fa-tags' + _renderTags : function( $where ){ + this.tagsEditor = new TagsEditor({ + model : this.model, + el : $where.find( '.history-controls .tags-display' ), + onshowFirstTime : function(){ this.render(); }, + $activator : faIconButton({ + title : _l( 'Edit history tags' ), + classes : 'history-tag-btn', + faIcon : 'fa-tags' + }).appendTo( $where.find( '.history-secondary-actions' ) ) }); - //return new IconButtonView({ model : new IconButton({ - // title : _l( 'Edit history tags' ), - // icon_class : 'tags' - //})}).render().$el; }, - - /** Render icon-button to load and display annotation html. - * @returns {jQuery} rendered DOM - */ - _render_annotateButton : function(){ - return faIconButton({ - title : _l( 'Edit history tags' ), - classes : 'history-annotate-button', - faIcon : 'fa-comment' + _renderAnnotation : function( $where ){ + this.annotationEditor = new AnnotationEditor({ + model : this.model, + el : $where.find( '.history-controls .annotation-display' ), + onshowFirstTime : function(){ this.render(); }, + $activator : faIconButton({ + title : _l( 'Edit history tags' ), + classes : 'history-annotate-btn', + faIcon : 'fa-comment' + }).appendTo( $where.find( '.history-secondary-actions' ) ) }); - //return new IconButtonView({ model : new IconButton({ - // title : _l( 'Edit history annotation' ), - // icon_class : 'annotate' - //})}).render().$el; }, /** Set up HistoryPanel js/widget behaviours @@ -694,24 +680,7 @@ var HistoryPanel = Backbone.View.extend( LoggableMixin ).extend( // anon users shouldn't have access to any of the following if( !this.model || !Galaxy.currUser || Galaxy.currUser.isAnonymous() ){ return; } - // annotation slide down - var panel = this, - // need specific selector ('annotation-display' is used in HDAs, too) - $historyAnnotationArea = $where.find( '.history-controls .annotation-display' ); - $where.find( '.history-controls .history-annotate-button' ).click( function() { - if( $historyAnnotationArea.is( ":hidden" ) ){ - //HACK: for whitespace added to annotation - var $anno = panel.$el.find( '.history-controls .annotation' ); - $anno.text( jQuery.trim( $anno.text() ) ); - $historyAnnotationArea.slideDown( panel.fxSpeed ); - - } else { - $historyAnnotationArea.slideUp( panel.fxSpeed ); - } - return false; - }); - //{{#local}}Describe or add notes to history{{/local}} - + var panel = this;//, $where.find( '.history-name' ).make_text_editable({ on_finish: function( newName ){ $where.find( '.history-name' ).text( newName ); @@ -721,17 +690,6 @@ var HistoryPanel = Backbone.View.extend( LoggableMixin ).extend( }); } }); - - $where.find( '.history-controls .annotation' ).make_text_editable({ - use_textarea : true, - on_finish: function( newAnnotation ){ - $where.find( '.history-controls .annotation' ).text( newAnnotation ); - panel.model.save({ annotation: newAnnotation }) - .fail( function(){ - $where.find( '.history-controls .annotation' ).text( panel.model.previous( 'annotation' ) ); - }); - } - }); }, /** Set up/render a view for each HDA to be shown, init with model and listeners. @@ -759,9 +717,8 @@ var HistoryPanel = Backbone.View.extend( LoggableMixin ).extend( // ------------------------------------------------------------------------ panel events /** event map */ events : { - 'click .history-tag-button' : 'displayTags', -//TODO: switch to common close (X) idiom // allow (error) messages to be clicked away + //TODO: switch to common close (X) idiom 'click .message-container' : 'clearMessages' }, @@ -802,14 +759,6 @@ var HistoryPanel = Backbone.View.extend( LoggableMixin ).extend( return this.storage.get( 'show_hidden' ); }, - /** Find the tag area and, if initial: load the html (via ajax) for displaying them; otherwise, unhide/hide - */ -//TODO: into sub-MV - displayTags : function( event ){ - this.$el.find( '.history-controls .tags-display' ).slideToggle( this.fxSpeed ); - return false; - }, - // ........................................................................ loading indicator /** hide the panel and display a loading indicator (in the panel's parent) when history model's are switched */ showLoadingIndicator : function( msg, speed, callback ){ diff --git a/static/scripts/mvc/tags.js b/static/scripts/mvc/tags.js index f7e5cfed74e..14c24fbb06a 100644 --- a/static/scripts/mvc/tags.js +++ b/static/scripts/mvc/tags.js @@ -1,74 +1,88 @@ -/** */ -var TagsEditor = Backbone.View.extend( LoggableMixin ).extend({ +/** A view on any model that has a 'tags' attribute (a list of tag strings) + * Incorporates the select2 jQuery plugin for tags display/editing: + * http://ivaynberg.github.io/select2/ + */ +var TagsEditor = Backbone.View.extend( LoggableMixin ).extend( HiddenUntilActivatedViewMixin ).extend({ tagName : 'div', className : 'tags-display', - /** */ + /** Set up listeners, parse options */ initialize : function( options ){ //console.debug( this, options ); + // only listen to the model only for changes to tags - re-render this.listenTo( this.model, 'change:tags', function(){ this.render(); }); + this.hiddenUntilActivated( options.$activator, options ); }, - /** */ + /** Build the DOM elements, call select to on the created input, and set up behaviors */ render : function(){ var view = this; + this.$el.html( this._template() ); - this.$el.html( this.template() ); - this.$el.find( '.tags-input' ).select2({ + this.$input().select2({ placeholder : 'Add tags', width : '100%', tags : function(){ // initialize possible tags in the dropdown based on all the tags the user has used so far - return view.getTagsUsed(); + return view._getTagsUsed(); } }); - this._behaviors(); + + this._setUpBehaviors(); return this; }, - /** */ - template : function(){ + /** @returns {String} the html text used to build the view's DOM */ + _template : function(){ return [ //TODO: make prompt optional '', // set up initial tags by adding as CSV to input vals (necc. to init select2) - '' + '' ].join( '' ); }, - /** */ - tagsToCSV : function( tagsArray ){ + /** @returns {String} the sorted, comma-separated tags from the model */ + tagsToCSV : function(){ + var tagsArray = this.model.get( 'tags' ); if( !_.isArray( tagsArray ) || _.isEmpty( tagsArray ) ){ return ''; } return tagsArray.sort().join( ',' ); }, - /** */ - getTagsUsed : function(){ - return _.map( Galaxy.currUser.get( 'tags_used' ), function( tag ){ - return { id: tag, text: tag }; - }); + /** @returns {jQuery} the input for this view */ + $input : function(){ + return this.$el.find( '.tags-input' ); }, - /** */ - _behaviors : function(){ + /** @returns {String[]} all tags used by the current user */ + _getTagsUsed : function(){ +//TODO: global + return Galaxy.currUser.get( 'tags_used' ); + }, + + /** set up any event listeners on the view's DOM (mostly handled by select2) */ + _setUpBehaviors : function(){ var view = this; - this.$el.find( '.tags-input' ).on( 'change', function( event ){ + this.$input().on( 'change', function( event ){ // save the model's tags in either remove or added event view.model.save({ tags: event.val }, { silent: true }); // if it's new, add the tag to the users tags if( event.added ){ - view.addNewTagToTagsUsed( event.added.text ); + view._addNewTagToTagsUsed( event.added.text ); } }); }, - /** */ - addNewTagToTagsUsed : function( newTag ){ + /** add a new tag (if not already there) to the list of all tags used by the user + * @param {String} newTag the tag to add to the list of used + */ + _addNewTagToTagsUsed : function( newTag ){ +//TODO: global var tagsUsed = Galaxy.currUser.get( 'tags_used' ); if( !_.contains( tagsUsed, newTag ) ){ tagsUsed.push( newTag ); @@ -77,12 +91,13 @@ var TagsEditor = Backbone.View.extend( LoggableMixin ).extend({ } }, - /** */ + /** shut down event listeners and remove this view's DOM */ remove : function(){ - this.$el.off(); + this.$input.off(); + this.stopListening( this.model ); Backbone.View.prototype.remove.call( this ); }, - /** */ - toString : function(){ return [ 'TagSetView(', this.model + '', ')' ].join(''); } + /** string rep */ + toString : function(){ return [ 'TagsEditor(', this.model + '', ')' ].join(''); } }); diff --git a/static/scripts/packed/mvc/annotations.js b/static/scripts/packed/mvc/annotations.js index 38d4e4dea14..316dcc35ae0 100644 --- a/static/scripts/packed/mvc/annotations.js +++ b/static/scripts/packed/mvc/annotations.js @@ -1 +1 @@ -var Annotation=BaseModel.extend(LoggableMixin).extend({logger:console,toString:function(){return"Annotation()"}});var AnnotationView=BaseView.extend(LoggableMixin).extend({logger:console,toString:function(){return"AnnotationView()"}}); \ No newline at end of file +var AnnotationEditor=BaseView.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(a){a=a||{};this.tooltipConfig=a.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(a.$activator,a)},render:function(){var a=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(b){a.$annotation().text(b);a.model.save({annotation:b},{silent:true}).fail(function(){a.$annotation().text(a.model.previous("annotation"))})}});return this},_template:function(){var a=this.model.get("annotation");return['",'
            ',a,"
            "].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/base-mvc.js b/static/scripts/packed/mvc/base-mvc.js index d1060c5af2e..ec503f67c18 100644 --- a/static/scripts/packed/mvc/base-mvc.js +++ b/static/scripts/packed/mvc/base-mvc.js @@ -1 +1 @@ -var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var PersistentStorage=function(k,g){if(!k){throw ("PersistentStorage needs storageKey argument")}g=g||{};var i=sessionStorage,c=function j(m){var n=this.getItem(m);return(n!==null)?(JSON.parse(this.getItem(m))):(null)},b=function e(m,n){return this.setItem(m,JSON.stringify(n))},d=function f(m){return this.removeItem(m)};function a(n,m){n=n||{};m=m||null;return{get:function(o){if(o===undefined){return n}else{if(n.hasOwnProperty(o)){return(jQuery.type(n[o])==="object")?(new a(n[o],this)):(n[o])}}return undefined},set:function(o,p){n[o]=p;this._save();return this},deleteKey:function(o){delete n[o];this._save();return this},_save:function(){return m._save()},toString:function(){return("StorageRecursionHelper("+n+")")}}}var l={},h=c.call(i,k);if(h===null||h===undefined){h=jQuery.extend(true,{},g);b.call(i,k,h)}l=new a(h);jQuery.extend(l,{_save:function(m){return b.call(i,k,l.get())},destroy:function(){return d.call(i,k)},toString:function(){return"PersistentStorage("+k+")"}});return l};function LoadingIndicator(a,c){c=c||{};var b=this;function d(){var e=['
            ','','loading...',"
            "].join("\n");return $(e).css(c.css||{position:"fixed",margin:"12px 0px 0px 10px",opacity:"0.85"}).hide()}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}; \ No newline at end of file +var BaseModel=Backbone.RelationalModel.extend({defaults:{name:null,hidden:false},show:function(){this.set("hidden",false)},hide:function(){this.set("hidden",true)},is_visible:function(){return !this.attributes.hidden}});var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var PersistentStorage=function(k,g){if(!k){throw ("PersistentStorage needs storageKey argument")}g=g||{};var i=sessionStorage,c=function j(m){var n=this.getItem(m);return(n!==null)?(JSON.parse(this.getItem(m))):(null)},b=function e(m,n){return this.setItem(m,JSON.stringify(n))},d=function f(m){return this.removeItem(m)};function a(n,m){n=n||{};m=m||null;return{get:function(o){if(o===undefined){return n}else{if(n.hasOwnProperty(o)){return(jQuery.type(n[o])==="object")?(new a(n[o],this)):(n[o])}}return undefined},set:function(o,p){n[o]=p;this._save();return this},deleteKey:function(o){delete n[o];this._save();return this},_save:function(){return m._save()},toString:function(){return("StorageRecursionHelper("+n+")")}}}var l={},h=c.call(i,k);if(h===null||h===undefined){h=jQuery.extend(true,{},g);b.call(i,k,h)}l=new a(h);jQuery.extend(l,{_save:function(m){return b.call(i,k,l.get())},destroy:function(){return d.call(i,k)},toString:function(){return"PersistentStorage("+k+")"}});return l};var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},toggle:function(){if(this.HUAVOptions.$elementShown.is(":hidden")){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}else{if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this)}}}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}};function LoadingIndicator(a,c){c=c||{};var b=this;function d(){var e=['
            ','','loading...',"
            "].join("\n");return $(e).css(c.css||{position:"fixed",margin:"12px 0px 0px 10px",opacity:"0.85"}).hide()}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}; \ No newline at end of file diff --git a/static/scripts/packed/mvc/dataset/hda-base.js b/static/scripts/packed/mvc/dataset/hda-base.js index af45ba08789..d03b9000d5c 100644 --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1 +1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",target:"galaxy_main",content:c.urls.display})}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['','',""].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['
            ','',_l("Download Dataset"),"",""+_l("Additional Files")+"",_.map(e,function(g){return['',_l("Download")," ",g.file_type,""].join("")}).join("\n"),"
            ",'
            ','','','','',"","
            "].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",faIcon:"fa-info-circle"})},_render_body:function(){var d=$('
            Error: unknown dataset state "'+this.model.get("state")+'".
            '),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("
            "+_l("This is a new dataset and not all of its data are available yet")+"
            ")},_render_body_noPermission:function(){return this._render_stateBodyHelper("
            "+_l("You do not have permission to view this dataset")+"
            ")},_render_body_discarded:function(){return this._render_stateBodyHelper("
            "+_l("The job creating this dataset was cancelled before completion")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("
            "+_l("This job is waiting to run")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("
            "+_l("This dataset is currently uploading")+"
            ")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("
            "+_l("Metadata is being auto-detected")+"
            ")},_render_body_running:function(){return this._render_stateBodyHelper("
            "+_l("This job is currently running")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("
            "+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=_l("An error occurred with this dataset")+": "+$.trim(this.model.get("misc_info"))+"";if(!this.model.get("purged")){c="
            "+this.model.get("misc_blurb")+"
            "+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("
            "+_l("No data")+": "+this.model.get("misc_blurb")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('
            ').append($("").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility"},toggleBodyVisibility:function(d,c){var e=this.$el.find(".dataset-body");c=(c===undefined)?(!e.is(":visible")):(c);if(c){this.expandBody()}else{this.collapseBody()}},expandBody:function(){var c=this;function d(){c.render(false).$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",target:"galaxy_main",content:c.urls.display})}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['','',""].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['
            ','',_l("Download Dataset"),"",""+_l("Additional Files")+"",_.map(e,function(g){return['',_l("Download")," ",g.file_type,""].join("")}).join("\n"),"
            ",'
            ','','','','',"","
            "].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",faIcon:"fa-info-circle"})},_render_body:function(){var d=$('
            Error: unknown dataset state "'+this.model.get("state")+'".
            '),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("
            "+_l("This is a new dataset and not all of its data are available yet")+"
            ")},_render_body_noPermission:function(){return this._render_stateBodyHelper("
            "+_l("You do not have permission to view this dataset")+"
            ")},_render_body_discarded:function(){return this._render_stateBodyHelper("
            "+_l("The job creating this dataset was cancelled before completion")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("
            "+_l("This job is waiting to run")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("
            "+_l("This dataset is currently uploading")+"
            ")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("
            "+_l("Metadata is being auto-detected")+"
            ")},_render_body_running:function(){return this._render_stateBodyHelper("
            "+_l("This job is currently running")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("
            "+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=['',_l("An error occurred with this dataset"),":",'
            ',$.trim(this.model.get("misc_info")),"
            "].join("");if(!this.model.get("purged")){c="
            "+this.model.get("misc_blurb")+"
            "+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("
            "+_l("No data")+": "+this.model.get("misc_blurb")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('
            ').append($("").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility"},toggleBodyVisibility:function(d,c){var e=this.$el.find(".dataset-body");c=(c===undefined)?(!e.is(":visible")):(c);if(c){this.expandBody()}else{this.collapseBody()}},expandBody:function(){var c=this;function d(){c.render(false).$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/dataset/hda-edit.js b/static/scripts/packed/mvc/dataset/hda-edit.js index 4dd2fa4aaa8..688c3f538b1 100644 --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1 +1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(g||i){h.enabled=false;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h=g.urls["delete"],i={title:_l("Delete"),href:h,icon_class:"delete",onclick:function(){g.$el.find(".menu-button.delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_tagButton:function(){if(!this.hasUser){return null}return faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"})},_render_annotateButton:function(){if(!this.hasUser){return null}return faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"})},_render_body_failed_metadata:function(){var h=$("").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);g.find(".dataset-actions .left").append(this._render_visualizationsButton());g.find(".dataset-actions .right").append([this._render_tagButton(),this._render_annotateButton()]);this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display")}).render();return g},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('?').attr("href",this.urls.edit))}},events:{"click .dataset-title-bar":"toggleBodyVisibility","click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge","click .dataset-tag-btn":"displayTags","click .dataset-annotate-btn":"loadAndDisplayAnnotation"},confirmPurge:function c(g){this.model.purge();return false},displayTags:function(g){this.$el.find(".tags-display").slideToggle(this.fxSpeed);return false},loadAndDisplayAnnotation:function(j){this.log(this+".loadAndDisplayAnnotation",j);var i=this,h=this.$el.find(".annotation-display"),g=h.find(".annotation");if(h.is(":hidden")){if(!jQuery.trim(g.html())){var k=$.ajax(this.urls.annotation.get);k.fail(function(n,l,m){i.log("Annotation failed",n,l,m);i.trigger("error",i,n,{},_l("Annotation failed"))});k.done(function(l){l=l||""+_l("Describe or add notes to dataset")+"";g.html(l);h.find("[title]").tooltip();g.make_text_editable({use_textarea:true,on_finish:function(m){g.text(m);i.model.save({annotation:m},{silent:true}).fail(function(){g.text(i.model.previous("annotation"))})}});h.slideDown(i.fxSpeed)})}else{h.slideDown(i.fxSpeed)}}else{h.slideUp(i.fxSpeed)}return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(g||i){h.enabled=false;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h=g.urls["delete"],i={title:_l("Delete"),href:h,icon_class:"delete",onclick:function(){g.$el.find(".menu-button.delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_body_failed_metadata:function(){var h=$("").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);if(this.hasUser){g.find(".dataset-actions .left").append(this._render_visualizationsButton());this._renderTags(g);this._renderAnnotation(g)}return g},_renderTags:function(g){this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"}).appendTo(g.find(".dataset-actions .right"))})},_renderAnnotation:function(g){this.annotationEditor=new AnnotationEditor({model:this.model,el:g.find(".annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"}).appendTo(g.find(".dataset-actions .right"))})},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('?').attr("href",this.urls.edit))}},events:{"click .dataset-title-bar":"toggleBodyVisibility","click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge"},confirmPurge:function c(g){this.model.purge();return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/dataset/hda-model.js b/static/scripts/packed/mvc/dataset/hda-model.js index 8b2f4e7f6dc..51de9d7bbbb 100644 --- a/static/scripts/packed/mvc/dataset/hda-model.js +++ b/static/scripts/packed/mvc/dataset/hda-model.js @@ -1 +1 @@ -define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:null},urlRoot:"api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},tags:{get:galaxy_config.root+"tag/get_tagging_elt_async?item_id="+i+"&item_class=HistoryDatasetAssociation",set:galaxy_config.root+"tag/retag?item_id="+i+"&item_class=HistoryDatasetAssociation"},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);h.misc_info=jQuery.trim(h.misc_info);return h},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(i,j){var h=true;if((!i)&&(this.get("deleted")||this.get("purged"))){h=false}if((!j)&&(!this.get("visible"))){h=false}return h},hidden:function(){return !this.get("visible")},inReadyState:function(){var h=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(h){return this.save({deleted:true},h)},undelete:function a(h){return this.save({deleted:false},h)},hide:function b(h){return this.save({visible:false},h)},unhide:function g(h){return this.save({visible:true},h)},purge:function f(h){h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set("purged",true)});j.fail(function(o,k,n){var l=_l("Unable to purge this dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})})},searchKeys:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],search:function(h){var i=this;h=h.toLowerCase();return _.filter(this.searchKeys,function(k){var j=i.get(k);return(_.isString(j)&&j.toLowerCase().indexOf(h)!==-1)})},matches:function(h){return !!this.search(h).length},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,i){return this.filter(function(j){return j.isVisible(h,i)})},fetchAllDetails:function(){return this.fetch({data:{details:"all"}})},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return("HDACollection()")}});return{HistoryDatasetAssociation:d,HDACollection:e}}); \ No newline at end of file +define([],function(){var d=Backbone.Model.extend(LoggableMixin).extend({defaults:{history_id:null,model_class:"HistoryDatasetAssociation",hid:0,id:null,name:"(unnamed dataset)",state:"new",deleted:false,visible:true,accessible:true,purged:false,data_type:null,file_size:0,file_ext:"",meta_files:[],misc_blurb:"",misc_info:"",tags:null},urlRoot:"/api/histories/",url:function(){return this.urlRoot+this.get("history_id")+"/contents/"+this.get("id")},urls:function(){var i=this.get("id");if(!i){return{}}var h={purge:galaxy_config.root+"datasets/"+i+"/purge_async",display:galaxy_config.root+"datasets/"+i+"/display/?preview=True",edit:galaxy_config.root+"datasets/"+i+"/edit",download:galaxy_config.root+"datasets/"+i+"/display?to_ext="+this.get("file_ext"),report_error:galaxy_config.root+"dataset/errors?id="+i,rerun:galaxy_config.root+"tool_runner/rerun?id="+i,show_params:galaxy_config.root+"datasets/"+i+"/show_params",visualization:galaxy_config.root+"visualization",annotation:{get:galaxy_config.root+"dataset/get_annotation_async?id="+i,set:galaxy_config.root+"dataset/annotate_async?id="+i},meta_download:galaxy_config.root+"dataset/get_metadata_file?hda_id="+i+"&metadata_name="};return h},initialize:function(h){this.log(this+".initialize",this.attributes);this.log("\tparent history_id: "+this.get("history_id"));if(!this.get("accessible")){this.set("state",d.STATES.NOT_VIEWABLE)}this._setUpListeners()},_setUpListeners:function(){this.on("change:state",function(i,h){this.log(this+" has changed state:",i,h);if(this.inReadyState()){this.trigger("state:ready",i,h,this.previous("state"))}})},toJSON:function(){var h=Backbone.Model.prototype.toJSON.call(this);h.misc_info=jQuery.trim(h.misc_info);return h},isDeletedOrPurged:function(){return(this.get("deleted")||this.get("purged"))},isVisible:function(i,j){var h=true;if((!i)&&(this.get("deleted")||this.get("purged"))){h=false}if((!j)&&(!this.get("visible"))){h=false}return h},hidden:function(){return !this.get("visible")},inReadyState:function(){var h=_.contains(d.READY_STATES,this.get("state"));return(this.isDeletedOrPurged()||h)},hasDetails:function(){return _.has(this.attributes,"genome_build")},hasData:function(){return(this.get("file_size")>0)},"delete":function c(h){return this.save({deleted:true},h)},undelete:function a(h){return this.save({deleted:false},h)},hide:function b(h){return this.save({visible:false},h)},unhide:function g(h){return this.save({visible:true},h)},purge:function f(h){h=h||{};h.url=galaxy_config.root+"datasets/"+this.get("id")+"/purge_async";var i=this,j=jQuery.ajax(h);j.done(function(m,k,l){i.set("purged",true)});j.fail(function(o,k,n){var l=_l("Unable to purge this dataset");var m=("Removal of datasets by users is not allowed in this Galaxy instance");if(o.responseJSON&&o.responseJSON.error){l=o.responseJSON.error}else{if(o.responseText.indexOf(m)!==-1){l=m}}o.responseText=l;i.trigger("error",i,o,h,_l(l),{error:l})})},searchKeys:["name","file_ext","genome_build","misc_blurb","misc_info","annotation","tags"],search:function(h){var i=this;h=h.toLowerCase();return _.filter(this.searchKeys,function(k){var j=i.get(k);return(_.isString(j)&&j.toLowerCase().indexOf(h)!==-1)})},matches:function(h){return !!this.search(h).length},toString:function(){var h=this.get("id")||"";if(this.get("name")){h=this.get("hid")+' :"'+this.get("name")+'",'+h}return"HDA("+h+")"}});d.STATES={UPLOAD:"upload",QUEUED:"queued",RUNNING:"running",SETTING_METADATA:"setting_metadata",NEW:"new",EMPTY:"empty",OK:"ok",PAUSED:"paused",FAILED_METADATA:"failed_metadata",NOT_VIEWABLE:"noPermission",DISCARDED:"discarded",ERROR:"error"};d.READY_STATES=[d.STATES.NEW,d.STATES.OK,d.STATES.EMPTY,d.STATES.PAUSED,d.STATES.FAILED_METADATA,d.STATES.NOT_VIEWABLE,d.STATES.DISCARDED,d.STATES.ERROR];d.NOT_READY_STATES=[d.STATES.UPLOAD,d.STATES.QUEUED,d.STATES.RUNNING,d.STATES.SETTING_METADATA];var e=Backbone.Collection.extend(LoggableMixin).extend({model:d,urlRoot:galaxy_config.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(i,h){h=h||{};this.historyId=h.historyId},ids:function(){return this.map(function(h){return h.id})},notReady:function(){return this.filter(function(h){return !h.inReadyState()})},running:function(){var h=[];this.each(function(i){if(!i.inReadyState()){h.push(i.get("id"))}});return h},getByHid:function(h){return _.first(this.filter(function(i){return i.get("hid")===h}))},getVisible:function(h,i){return this.filter(function(j){return j.isVisible(h,i)})},fetchAllDetails:function(){return this.fetch({data:{details:"all"}})},matches:function(h){return this.filter(function(i){return i.matches(h)})},set:function(j,h){var i=this;j=_.map(j,function(l){var m=i.get(l.id);if(!m){return l}var k=m.toJSON();_.extend(k,l);return k});Backbone.Collection.prototype.set.call(this,j,h)},toString:function(){return("HDACollection()")}});return{HistoryDatasetAssociation:d,HDACollection:e}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/history/history-panel.js b/static/scripts/packed/mvc/history/history-panel.js index e7a35b0b500..6e1fdf5cf08 100644 --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1 +1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(d,b,a){var c=Backbone.View.extend(LoggableMixin).extend({HDAView:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(e){e=e||{};if(e.logger){this.logger=e.logger}this.log(this+".initialize:",e);this._setUpListeners();this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);if(this.model){this._setUpWebStorage(e.initiallyExpanded,e.show_deleted,e.show_hidden);this._setUpModelEventHandlers()}if(e.onready){e.onready.call(this)}},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(e){this.log(this+"",arguments)},this)}},errorHandler:function(g,j,f,i,h){var e=this._parseErrorMessage(g,j,f,i,h);if(j&&j.status===0&&j.readyState===0){}else{if(j&&j.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",e.message,e.details)})}else{this.displayMessage("error",e.message,e.details)}}}},_parseErrorMessage:function(h,l,g,k,j){var f=Galaxy.currUser,e={message:this._bePolite(k),details:{user:(f instanceof User)?(f.toJSON()):(f+""),source:(h instanceof Backbone.Model)?(h.toJSON()):(h+""),xhr:l,options:(l)?(_.omit(g,"xhr")):(g)}};_.extend(e.details,j||{});if(l&&_.isFunction(l.getAllResponseHeaders)){var i=l.getAllResponseHeaders();i=_.compact(i.split("\n"));i=_.map(i,function(m){return m.split(": ")});e.details.xhr.responseHeaders=_.object(i)}return e},_bePolite:function(e){e=e||_l("An error occurred while getting updates from the server");return e+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(f){var e=this;return this.loadHistoryWithHDADetails("current",f).then(function(h,g){e.trigger("current-history",e)})},switchToHistory:function(h,g){var e=this,f=function(){return jQuery.post(galaxy_config.root+"api/histories/"+h+"/set_as_current")};return this.loadHistoryWithHDADetails(h,g,f).then(function(j,i){e.trigger("switched-history",e)})},createNewHistory:function(g){var e=this,f=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,g,f).then(function(i,h){e.trigger("new-history",e)})},loadHistoryWithHDADetails:function(h,g,f,j){var e=this,i=function(k){return e.getExpandedHdaIds(k.id)};return this.loadHistory(h,g,f,j,i)},loadHistory:function(h,g,f,k,i){this.trigger("loading-history",this);g=g||{};var e=this;var j=d.History.getHistoryData(h,{historyFn:f,hdaFn:k,hdaDetailIds:g.initiallyExpanded||i});return this._loadHistoryFromXHR(j,g).fail(function(n,l,m){e.trigger("error",e,n,g,_l("An error was encountered while "+l),{historyId:h,history:m||{}})}).always(function(){e.trigger("loading-done",e)})},_loadHistoryFromXHR:function(g,f){var e=this;g.then(function(h,i){e.setModel(h,i,f)});g.fail(function(i,h){e.render()});return g},setModel:function(g,e,f){f=f||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){g.user=Galaxy.currUser.toJSON()}this.model=new d.History(g,e,f);this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},refreshHdas:function(f,e){if(this.model){return this.model.refresh(f,e)}return $.when()},_setUpWebStorage:function(f,e,g){this.storage=new PersistentStorage(this._getStorageKey(this.model.get("id")),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(f){this.storage.set("exandedHdas",f)}if((e===true)||(e===false)){this.storage.set("show_deleted",e)}if((g===true)||(g===false)){this.storage.set("show_hidden",g)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},_getStorageKey:function(e){if(!e){throw new Error("_getStorageKey needs valid id: "+e)}return("history:"+e)},clearWebStorage:function(){for(var e in sessionStorage){if(e.indexOf("history:")===0){sessionStorage.removeItem(e)}}},getStoredOptions:function(f){if(!f||f==="current"){return(this.storage)?(this.storage.get()):({})}var e=sessionStorage.getItem(this._getStorageKey(f));return(e===null)?({}):(JSON.parse(e))},getExpandedHdaIds:function(e){var f=this.getStoredOptions(e).expandedHdas;return((_.isEmpty(f))?([]):(_.keys(f)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(f,h,e,g){this.errorHandler(f,h,e,g)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this);this.model.hdas.on("state:ready",function(f,g,e){if((!f.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[f.id])}},this)},addHdaView:function(h){this.log("add."+this,h);var f=this;if(!h.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function g(j){var i=f.$el.find(f.emptyMsgSelector);if(i.is(":visible")){i.fadeOut(f.fxSpeed,j)}else{j()}},function e(j){f.scrollToTop();var i=f.$el.find(f.datasetsSelector);f.createHdaView(h).$el.hide().prependTo(i).slideDown(f.fxSpeed)}])},createHdaView:function(g){var f=g.get("id"),e=this.storage.get("expandedHdas").get(f),h=new this.HDAView({model:g,expanded:e,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(h);this.hdaViews[f]=h;return h.render()},_setUpHdaListeners:function(f){var e=this;f.on("body-expanded",function(g){e.storage.get("expandedHdas").set(g,true)});f.on("body-collapsed",function(g){e.storage.get("expandedHdas").deleteKey(g)});f.on("error",function(h,j,g,i){e.errorHandler(h,j,g,i)})},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},render:function(g){var e=this,f;if(this.model){f=this.renderModel()}else{f=this.renderWithoutModel()}$(e).queue("fx",[function(h){if(e.$el.is(":visible")){e.$el.fadeOut(e.fxSpeed,h)}else{h()}},function(h){e.$el.empty();if(f){e.$el.append(f.children())}e.$el.fadeIn(e.fxSpeed,h)},function(h){if(g){g.call(this)}e.trigger("rendered",this)}]);return this},renderWithoutModel:function(){var e=$("
            "),f=$("
            ").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return e.append(f)},renderModel:function(){var e=$("
            ");if(Galaxy.currUser.isAnonymous()){e.append(c.templates.anonHistoryPanel(this.model.toJSON()))}else{e.append(c.templates.historyPanel(this.model.toJSON()));e.find(".history-secondary-actions").append([this._render_tagButton(),this._render_annotateButton()]);this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display")}).render()}this._setUpBehaviours(e);if(!this.model.hdas.length||!this.renderHdas(e.find(this.datasetsSelector))){e.find(this.emptyMsgSelector).show()}return e},_render_tagButton:function(){return faIconButton({title:_l("Edit history tags"),classes:"history-tag-button",faIcon:"fa-tags"})},_render_annotateButton:function(){return faIconButton({title:_l("Edit history tags"),classes:"history-annotate-button",faIcon:"fa-comment"})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){return}var f=this,g=e.find(".history-controls .annotation-display");e.find(".history-controls .history-annotate-button").click(function(){if(g.is(":hidden")){var h=f.$el.find(".history-controls .annotation");h.text(jQuery.trim(h.text()));g.slideDown(f.fxSpeed)}else{g.slideUp(f.fxSpeed)}return false});e.find(".history-name").make_text_editable({on_finish:function(h){e.find(".history-name").text(h);f.model.save({name:h}).fail(function(){e.find(".history-name").text(f.model.previous("name"))})}});e.find(".history-controls .annotation").make_text_editable({use_textarea:true,on_finish:function(h){e.find(".history-controls .annotation").text(h);f.model.save({annotation:h}).fail(function(){e.find(".history-controls .annotation").text(f.model.previous("annotation"))})}})},renderHdas:function(f){this.hdaViews={};var e=this,g=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(g,function(h){f.prepend(e.createHdaView(h).$el)});return g.length},events:{"click .history-tag-button":"displayTags","click .message-container":"clearMessages"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(e){e.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},displayTags:function(e){this.$el.find(".history-controls .tags-display").slideToggle(this.fxSpeed);return false},showLoadingIndicator:function(f,e,g){e=(e!==undefined)?(e):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,g)}else{this.$el.fadeOut(e);this.indicator.show(f,e,g)}},hideLoadingIndicator:function(e,f){e=(e!==undefined)?(e):(this.fxSpeed);if(this.indicator){this.indicator.hide(e,f)}},displayMessage:function(j,k,i){var g=this;this.scrollToTop();var h=this.$el.find(this.msgsSelector),e=$("
            ").addClass(j+"message").html(k);if(!_.isEmpty(i)){var f=$('Details').click(function(){Galaxy.modal.show(g.messageToModalOptions(j,k,i));return false});e.append(" ",f)}return h.html(e)},messageToModalOptions:function(i,k,h){var e=this,j=$("
            "),g={title:"Details"};function f(l){l=_.omit(l,_.functions(l));return["
            "+i.join("")+"
            ").text(l);var k=this.model.get_metadata("column_types");if(m!==undefined){j.attr("colspan",m).addClass("stringalign")}else{if(k){if(i"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($(""))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(k){var j=k.model.attributes;var m=k.model.attributes.metadata.attributes;if(typeof j.data_type!=="undefined"){this.data_type=j.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof m.chromCol!=="undefined"||typeof m.startCol!=="undefined"||typeof m.endCol!=="undefined"){this.col.chrom=m.chromCol-1;this.col.start=m.startCol-1;this.col.end=m.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function l(o,p){for(var n=0;n").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file +define(["libs/backbone/backbone-relational"],function(){var d=Backbone.RelationalModel.extend({});var e=Backbone.RelationalModel.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_config.root+"api/datasets"});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){new b(i)},render:function(){var m=$("").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(l,i,m){var j=$("';e+='";e+='";e+='';return e}});return{GalaxyUpload:a}}); \ No newline at end of file +define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,c,d){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],state:{init:"fa fa-trash-o",queued:"fa fa-spinner fa-spin",running:"__running__",success:"fa fa-check",error:"fa fa-exclamation-triangle"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}var e=this;this.button_show=new c.GalaxyMastheadIcon({icon:"fa-arrow-circle-o-up",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},on_unload:function(){if(e.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.masthead.prepend(this.button_show);var e=this;d.jsonFromUrl(galaxy_config.root+"api/datatypes",function(f){for(key in f){e.select_extension.push([f[key],f[key]])}});d.jsonFromUrl(galaxy_config.root+"api/genomes",function(f){var g=e.select_genome[0];e.select_genome=[];for(key in f){if(f[key].length>1){if(f[key][1]!==g[1]){e.select_genome.push(f[key])}}}e.select_genome.sort(function(i,h){return i[0]>h[0]?1:i[0]0)){return null}this.uploadbox.configure({url:galaxy_config.root+"api/tools",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=m;tool_input.file_type=f;tool_input["files_0|NAME"]=e.name;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=l;tool_input.space_to_tabs=h;data={};data.history_id=j;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refreshHdas()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("Failed: "+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_start:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#text-content").attr("disabled",true);$(this).find("#genome").attr("disabled",true);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.start()},event_stop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#text-content").attr("disabled",false);$(this).find("#genome").attr("disabled",false);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_create:function(){this.uploadbox.add([{name:"New File",size:-1}])},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Create:function(){f.event_create()},Upload:function(){f.event_start()},Pause:function(){f.event_stop()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()},},height:"400",width:"900"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:function(){f.event_dragover()},dragleave:function(){f.event_dragleave()},announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{if(e>0){e=e*10;f="b"}else{return"-"}}}}}return""+(Math.round(e)/10)+" "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
            Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'
            "+i.join("")+"
            ").text(l);var k=this.model.get_metadata("column_types");if(m!==undefined){j.attr("colspan",m).addClass("stringalign")}else{if(k){if(i"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($(""))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(k){var j=k.model.attributes;var m=k.model.attributes.metadata.attributes;if(typeof j.data_type!=="undefined"){this.data_type=j.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof m.chromCol!=="undefined"||typeof m.startCol!=="undefined"||typeof m.endCol!=="undefined"){this.col.chrom=m.chromCol-1;this.col.start=m.startCol-1;this.col.end=m.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function l(o,p){for(var n=0;n").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/dataset/hda-base.js b/static/scripts/packed/mvc/dataset/hda-base.js index b8339049bf4..af45ba08789 100644 --- a/static/scripts/packed/mvc/dataset/hda-base.js +++ b/static/scripts/packed/mvc/dataset/hda-base.js @@ -1 +1 @@ -define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){Galaxy.frame_manager.frame_new({title:"Data Viewer: "+c.model.get("name"),type:"url",target:"galaxy_main",content:c.urls.display})}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['','',""].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['
            ','',_l("Download Dataset"),"",""+_l("Additional Files")+"",_.map(e,function(g){return['',_l("Download")," ",g.file_type,""].join("")}).join("\n"),"
            ",'
            ','','','','',"","
            "].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",faIcon:"fa-info-circle"})},_render_body:function(){var d=$('
            Error: unknown dataset state "'+this.model.get("state")+'".
            '),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("
            "+_l("This is a new dataset and not all of its data are available yet")+"
            ")},_render_body_noPermission:function(){return this._render_stateBodyHelper("
            "+_l("You do not have permission to view this dataset")+"
            ")},_render_body_discarded:function(){return this._render_stateBodyHelper("
            "+_l("The job creating this dataset was cancelled before completion")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("
            "+_l("This job is waiting to run")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("
            "+_l("This dataset is currently uploading")+"
            ")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("
            "+_l("Metadata is being auto-detected")+"
            ")},_render_body_running:function(){return this._render_stateBodyHelper("
            "+_l("This job is currently running")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("
            "+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=_l("An error occurred with this dataset")+": "+$.trim(this.model.get("misc_info"))+"";if(!this.model.get("purged")){c="
            "+this.model.get("misc_blurb")+"
            "+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("
            "+_l("No data")+": "+this.model.get("misc_blurb")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('
            ').append($("").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility"},toggleBodyVisibility:function(d,c){var e=this.$el.find(".dataset-body");c=(c===undefined)?(!e.is(":visible")):(c);if(c){this.expandBody()}else{this.collapseBody()}},expandBody:function(){var c=this;function d(){c.render(false).$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file +define(["mvc/dataset/hda-model"],function(b){var a=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"dataset hda history-panel-hda",id:function(){return"hda-"+this.model.get("id")},fxSpeed:"fast",initialize:function(c){if(c.logger){this.logger=this.model.logger=c.logger}this.log(this+".initialize:",c);this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton];this.expanded=c.expanded||false;this._setUpListeners()},_setUpListeners:function(){this.model.on("change",function(d,c){if(this.model.changedAttributes().state&&this.model.inReadyState()&&this.expanded&&!this.model.hasDetails()){this.model.fetch()}else{this.render()}},this)},render:function(e){e=(e===undefined)?(true):(e);var c=this;this.$el.find("[title]").tooltip("destroy");this.urls=this.model.urls();var d=$(a.templates.skeleton(this.model.toJSON()));d.find(".dataset-primary-actions").append(this._render_titleButtons());d.children(".dataset-body").replaceWith(this._render_body());this._setUpBehaviors(d);if(e){$(c).queue(function(f){this.$el.fadeOut(c.fxSpeed,f)})}$(c).queue(function(f){this.$el.empty().attr("class",c.className).addClass("state-"+c.model.get("state")).append(d.children());f()});if(e){$(c).queue(function(f){this.$el.fadeIn(c.fxSpeed,f)})}$(c).queue(function(f){this.trigger("rendered",c);if(this.model.inReadyState()){this.trigger("rendered:ready",c)}f()});return this},_setUpBehaviors:function(c){c=c||this.$el;make_popup_menus(c);c.find("[title]").tooltip({placement:"bottom"})},_render_titleButtons:function(){return[this._render_displayButton()]},_render_displayButton:function(){if((this.model.get("state")===b.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===b.HistoryDatasetAssociation.STATES.NEW)||(!this.model.get("accessible"))){return null}var d={icon_class:"display",target:"galaxy_main"};if(this.model.get("purged")){d.disabled=true;d.title=_l("Cannot display datasets removed from disk")}else{if(this.model.get("state")===b.HistoryDatasetAssociation.STATES.UPLOAD){d.disabled=true;d.title=_l("This dataset must finish uploading before it can be viewed")}else{d.title=_l("View data");d.href=this.urls.display;var c=this;d.onclick=function(){Galaxy.frame.add({title:"Data Viewer: "+c.model.get("name"),type:"url",target:"galaxy_main",content:c.urls.display})}}}d.faIcon="fa-eye";return faIconButton(d)},_render_downloadButton:function(){if(this.model.get("purged")||!this.model.hasData()){return null}var d=this.urls,e=this.model.get("meta_files");if(_.isEmpty(e)){return $(['','',""].join(""))}var f="dataset-"+this.model.get("id")+"-popup",c=['
            ','',_l("Download Dataset"),"",""+_l("Additional Files")+"",_.map(e,function(g){return['',_l("Download")," ",g.file_type,""].join("")}).join("\n"),"
            ",'
            ','','','','',"","
            "].join("\n");return $(c)},_render_showParamsButton:function(){return faIconButton({title:_l("View details"),href:this.urls.show_params,target:"galaxy_main",faIcon:"fa-info-circle"})},_render_body:function(){var d=$('
            Error: unknown dataset state "'+this.model.get("state")+'".
            '),c=this["_render_body_"+this.model.get("state")];if(_.isFunction(c)){d=c.call(this)}if(this.expanded){d.show()}return d},_render_stateBodyHelper:function(c,f){f=f||[];var d=this,e=$(a.templates.body(_.extend(this.model.toJSON(),{body:c})));e.find(".dataset-actions .left").append(_.map(f,function(g){return g.call(d)}));return e},_render_body_new:function(){return this._render_stateBodyHelper("
            "+_l("This is a new dataset and not all of its data are available yet")+"
            ")},_render_body_noPermission:function(){return this._render_stateBodyHelper("
            "+_l("You do not have permission to view this dataset")+"
            ")},_render_body_discarded:function(){return this._render_stateBodyHelper("
            "+_l("The job creating this dataset was cancelled before completion")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_queued:function(){return this._render_stateBodyHelper("
            "+_l("This job is waiting to run")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_upload:function(){return this._render_stateBodyHelper("
            "+_l("This dataset is currently uploading")+"
            ")},_render_body_setting_metadata:function(){return this._render_stateBodyHelper("
            "+_l("Metadata is being auto-detected")+"
            ")},_render_body_running:function(){return this._render_stateBodyHelper("
            "+_l("This job is currently running")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_paused:function(){return this._render_stateBodyHelper("
            "+_l('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume')+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_error:function(){var c=_l("An error occurred with this dataset")+": "+$.trim(this.model.get("misc_info"))+"";if(!this.model.get("purged")){c="
            "+this.model.get("misc_blurb")+"
            "+c}return this._render_stateBodyHelper(c,this.defaultPrimaryActionButtonRenderers.concat([this._render_downloadButton]))},_render_body_empty:function(){return this._render_stateBodyHelper("
            "+_l("No data")+": "+this.model.get("misc_blurb")+"
            ",this.defaultPrimaryActionButtonRenderers)},_render_body_failed_metadata:function(){var c=$('
            ').append($("").text(_l("An error occurred setting the metadata for this dataset"))),d=this._render_body_ok();d.prepend(c);return d},_render_body_ok:function(){var c=this,e=$(a.templates.body(this.model.toJSON())),d=[this._render_downloadButton].concat(this.defaultPrimaryActionButtonRenderers);e.find(".dataset-actions .left").append(_.map(d,function(f){return f.call(c)}));if(this.model.isDeletedOrPurged()){return e}return e},events:{"click .dataset-title-bar":"toggleBodyVisibility"},toggleBodyVisibility:function(d,c){var e=this.$el.find(".dataset-body");c=(c===undefined)?(!e.is(":visible")):(c);if(c){this.expandBody()}else{this.collapseBody()}},expandBody:function(){var c=this;function d(){c.render(false).$el.children(".dataset-body").slideDown(c.fxSpeed,function(){c.expanded=true;c.trigger("body-expanded",c.model.get("id"))})}if(this.model.inReadyState()&&!this.model.hasDetails()){this.model.fetch({silent:true}).always(function(e){d()})}else{d()}},collapseBody:function(){var c=this;this.$el.children(".dataset-body").slideUp(c.fxSpeed,function(){c.expanded=false;c.trigger("body-collapsed",c.model.get("id"))})},remove:function(d){var c=this;this.$el.fadeOut(c.fxSpeed,function(){c.$el.remove();c.off();if(d){d()}})},toString:function(){var c=(this.model)?(this.model+""):("(no model)");return"HDABaseView("+c+")"}});a.templates={skeleton:Handlebars.templates["template-hda-skeleton"],body:Handlebars.templates["template-hda-body"]};return{HDABaseView:a}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/dataset/hda-edit.js b/static/scripts/packed/mvc/dataset/hda-edit.js index 15243251667..4dd2fa4aaa8 100644 --- a/static/scripts/packed/mvc/dataset/hda-edit.js +++ b/static/scripts/packed/mvc/dataset/hda-edit.js @@ -1 +1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(g||i){h.enabled=false;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h=g.urls["delete"],i={title:_l("Delete"),href:h,icon_class:"delete",onclick:function(){g.$el.find(".menu-button.delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame_manager.frame_new({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_tagButton:function(){if(!this.hasUser){return null}return faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"})},_render_annotateButton:function(){if(!this.hasUser){return null}return faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"})},_render_body_failed_metadata:function(){var h=$("").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);g.find(".dataset-actions .left").append(this._render_visualizationsButton());g.find(".dataset-actions .right").append([this._render_tagButton(),this._render_annotateButton()]);this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display")}).render();return g},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('?').attr("href",this.urls.edit))}},events:{"click .dataset-title-bar":"toggleBodyVisibility","click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge","click .dataset-tag-btn":"displayTags","click .dataset-annotate-btn":"loadAndDisplayAnnotation"},confirmPurge:function c(g){this.model.purge();return false},displayTags:function(g){this.$el.find(".tags-display").slideToggle(this.fxSpeed);return false},loadAndDisplayAnnotation:function(j){this.log(this+".loadAndDisplayAnnotation",j);var i=this,h=this.$el.find(".annotation-display"),g=h.find(".annotation");if(h.is(":hidden")){if(!jQuery.trim(g.html())){var k=$.ajax(this.urls.annotation.get);k.fail(function(n,l,m){i.log("Annotation failed",n,l,m);i.trigger("error",i,n,{},_l("Annotation failed"))});k.done(function(l){l=l||""+_l("Describe or add notes to dataset")+"";g.html(l);h.find("[title]").tooltip();g.make_text_editable({use_textarea:true,on_finish:function(m){g.text(m);i.model.save({annotation:m},{silent:true}).fail(function(){g.text(i.model.previous("annotation"))})}});h.slideDown(i.fxSpeed)})}else{h.slideDown(i.fxSpeed)}}else{h.slideUp(i.fxSpeed)}return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame_manager.frame_new({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame_manager.frame_new({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-base"],function(d,a){var f=a.HDABaseView.extend(LoggableMixin).extend({initialize:function(g){a.HDABaseView.prototype.initialize.call(this,g);this.hasUser=g.hasUser;this.defaultPrimaryActionButtonRenderers=[this._render_showParamsButton,this._render_rerunButton]},_render_titleButtons:function(){return a.HDABaseView.prototype._render_titleButtons.call(this).concat([this._render_editButton(),this._render_deleteButton()])},_render_editButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.DISCARDED)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var i=this.model.get("purged"),g=this.model.get("deleted"),h={title:_l("Edit Attributes"),href:this.urls.edit,target:"galaxy_main",icon_class:"edit"};if(g||i){h.enabled=false;if(i){h.title=_l("Cannot edit attributes of datasets removed from disk")}else{if(g){h.title=_l("Undelete dataset to edit attributes")}}}else{if(this.model.get("state")===d.HistoryDatasetAssociation.STATES.UPLOAD){h.disabled=true;h.title=_l("This dataset must finish uploading before it can be edited")}}h.faIcon="fa-pencil";return faIconButton(h)},_render_deleteButton:function(){if((this.model.get("state")===d.HistoryDatasetAssociation.STATES.NEW)||(this.model.get("state")===d.HistoryDatasetAssociation.STATES.NOT_VIEWABLE)||(!this.model.get("accessible"))){return null}var g=this,h=g.urls["delete"],i={title:_l("Delete"),href:h,icon_class:"delete",onclick:function(){g.$el.find(".menu-button.delete").trigger("mouseout");g.model["delete"]()}};if(this.model.get("deleted")||this.model.get("purged")){i={title:_l("Dataset is already deleted"),icon_class:"delete",enabled:false}}i.faIcon="fa-times";return faIconButton(i)},_render_errButton:function(){if(this.model.get("state")!==d.HistoryDatasetAssociation.STATES.ERROR){return null}return faIconButton({title:_l("View or report this error"),href:this.urls.report_error,target:"galaxy_main",faIcon:"fa-bug"})},_render_rerunButton:function(){return faIconButton({title:_l("Run this job again"),href:this.urls.rerun,target:"galaxy_main",faIcon:"fa-refresh"})},_render_visualizationsButton:function(){var g=this.model.get("visualizations");if((!this.model.hasData())||(_.isEmpty(g))){return null}if(_.isObject(g[0])){return this._render_visualizationsFrameworkButton(g)}if(!this.urls.visualization){return null}var i=this.model.get("dbkey"),l=this.urls.visualization,j={},m={dataset_id:this.model.get("id"),hda_ldda:"hda"};if(i){m.dbkey=i}var h=faIconButton({title:_l("Visualize"),href:this.urls.visualization,faIcon:"fa-bar-chart-o"});function k(n){switch(n){case"trackster":return b(l,m,i);case"scatterplot":return e(l,m);default:return function(){Galaxy.frame.add({title:"Visualization",type:"url",content:l+"/"+n+"?"+$.param(m)})}}}if(g.length===1){h.attr("title",g[0]);h.click(k(g[0]))}else{_.each(g,function(o){var n=o.charAt(0).toUpperCase()+o.slice(1);j[_l(n)]=k(o)});make_popupmenu(h,j)}return h},_render_visualizationsFrameworkButton:function(g){if(!(this.model.hasData())||!(g&&!_.isEmpty(g))){return null}var i=faIconButton({title:_l("Visualize"),faIcon:"fa-bar-chart-o"});i.addClass("visualize-icon");if(_.keys(g).length===1){i.attr("title",_.keys(g)[0]);i.attr("href",_.values(g)[0])}else{var j=[];_.each(g,function(k){j.push(k)});var h=new PopupMenu(i,j)}return i},_render_tagButton:function(){if(!this.hasUser){return null}return faIconButton({title:_l("Edit dataset tags"),classes:"dataset-tag-btn",faIcon:"fa-tags"})},_render_annotateButton:function(){if(!this.hasUser){return null}return faIconButton({title:_l("Edit dataset annotation"),classes:"dataset-annotate-btn",faIcon:"fa-comment"})},_render_body_failed_metadata:function(){var h=$("").attr({href:this.urls.edit,target:"galaxy_main"}).text(_l("set it manually or retry auto-detection")),g=$("").text(". "+_l("You may be able to")+" ").append(h),i=a.HDABaseView.prototype._render_body_failed_metadata.call(this);i.find(".warningmessagesmall strong").append(g);return i},_render_body_error:function(){var g=a.HDABaseView.prototype._render_body_error.call(this);g.find(".dataset-actions .left").prepend(this._render_errButton());return g},_render_body_ok:function(){var g=a.HDABaseView.prototype._render_body_ok.call(this);if(this.model.isDeletedOrPurged()){return g}this.makeDbkeyEditLink(g);g.find(".dataset-actions .left").append(this._render_visualizationsButton());g.find(".dataset-actions .right").append([this._render_tagButton(),this._render_annotateButton()]);this.tagsEditor=new TagsEditor({model:this.model,el:g.find(".tags-display")}).render();return g},makeDbkeyEditLink:function(g){if(this.model.get("metadata_dbkey")==="?"&&!this.model.isDeletedOrPurged()){g.find(".dataset-dbkey .value").replaceWith($('?').attr("href",this.urls.edit))}},events:{"click .dataset-title-bar":"toggleBodyVisibility","click .dataset-undelete":function(g){this.model.undelete();return false},"click .dataset-unhide":function(g){this.model.unhide();return false},"click .dataset-purge":"confirmPurge","click .dataset-tag-btn":"displayTags","click .dataset-annotate-btn":"loadAndDisplayAnnotation"},confirmPurge:function c(g){this.model.purge();return false},displayTags:function(g){this.$el.find(".tags-display").slideToggle(this.fxSpeed);return false},loadAndDisplayAnnotation:function(j){this.log(this+".loadAndDisplayAnnotation",j);var i=this,h=this.$el.find(".annotation-display"),g=h.find(".annotation");if(h.is(":hidden")){if(!jQuery.trim(g.html())){var k=$.ajax(this.urls.annotation.get);k.fail(function(n,l,m){i.log("Annotation failed",n,l,m);i.trigger("error",i,n,{},_l("Annotation failed"))});k.done(function(l){l=l||""+_l("Describe or add notes to dataset")+"";g.html(l);h.find("[title]").tooltip();g.make_text_editable({use_textarea:true,on_finish:function(m){g.text(m);i.model.save({annotation:m},{silent:true}).fail(function(){g.text(i.model.previous("annotation"))})}});h.slideDown(i.fxSpeed)})}else{h.slideDown(i.fxSpeed)}}else{h.slideUp(i.fxSpeed)}return false},toString:function(){var g=(this.model)?(this.model+""):("(no model)");return"HDAView("+g+")"}});function e(g,h){action=function(){Galaxy.frame.add({title:"Scatterplot",type:"url",content:g+"/scatterplot?"+$.param(h),target:"galaxy_main",scratchbook:true});$("div.popmenu-wrapper").remove();return false};return action}function b(g,i,h){return function(){var j={};if(h){j["f-dbkey"]=h}$.ajax({url:g+"/list_tracks?"+$.param(j),dataType:"html",error:function(){alert(("Could not add this dataset to browser")+".")},success:function(k){var l=window.parent;l.Galaxy.modal.show({title:"View Data in a New or Saved Visualization",buttons:{Cancel:function(){l.Galaxy.modal.hide()},"View in saved visualization":function(){l.Galaxy.modal.show({title:"Add Data to Saved Visualization",body:k,buttons:{Cancel:function(){l.Galaxy.modal.hide()},"Add to visualization":function(){$(l.document).find("input[name=id]:checked").each(function(){l.Galaxy.modal.hide();var m=$(this).val();i.id=m;l.Galaxy.frame.add({title:"Trackster",type:"url",content:g+"/trackster?"+$.param(i),scratchbook:true})})}}})},"View in new visualization":function(){l.Galaxy.modal.hide();var m=g+"/trackster?"+$.param(i);l.Galaxy.frame.add({title:"Trackster",type:"url",content:m,scratchbook:true})}}})}});return false}}return{HDAEditView:f}}); \ No newline at end of file diff --git a/templates/webapps/galaxy/galaxy.masthead.mako b/templates/webapps/galaxy/galaxy.masthead.mako index 11589783efe..d21a4d9f840 100644 --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -86,7 +86,7 @@ ## load global galaxy objects Galaxy.master = new mod_master.GalaxyMaster(master_config); Galaxy.modal = new mod_modal.GalaxyModal(); - Galaxy.frame_manager = new mod_frame.GalaxyFrameManager(); + Galaxy.frame = new mod_frame.GalaxyFrame(); ## construct default menu options Galaxy.menu = new mod_menu.GalaxyMenu({ From 80501157d7ebb24fd882a2020152324948614f58 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Tue, 5 Nov 2013 13:52:35 -0500 Subject: [PATCH 0027/1033] UI: Rename galaxy.master.js to galaxy.masthead.js --- static/scripts/galaxy.frame.js | 16 ++--- .../{galaxy.master.js => galaxy.masthead.js} | 60 +++++++++---------- static/scripts/galaxy.menu.js | 52 ++++++++-------- static/scripts/galaxy.upload.js | 8 +-- static/scripts/packed/galaxy.frame.js | 2 +- static/scripts/packed/galaxy.master.js | 1 - static/scripts/packed/galaxy.masthead.js | 1 + static/scripts/packed/galaxy.menu.js | 1 + static/scripts/packed/galaxy.upload.js | 2 +- templates/webapps/galaxy/galaxy.masthead.mako | 26 ++++---- 10 files changed, 85 insertions(+), 84 deletions(-) rename static/scripts/{galaxy.master.js => galaxy.masthead.js} (89%) delete mode 100644 static/scripts/packed/galaxy.master.js create mode 100644 static/scripts/packed/galaxy.masthead.js create mode 100644 static/scripts/packed/galaxy.menu.js diff --git a/static/scripts/galaxy.frame.js b/static/scripts/galaxy.frame.js index 09c9fa35470..9c611ff2b6d 100644 --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -3,7 +3,7 @@ */ // dependencies -define(["galaxy.master", "libs/backbone/backbone-relational"], function(mod_master) { +define(["galaxy.masthead", "libs/backbone/backbone-relational"], function(mod_masthead) { // frame manager var GalaxyFrame = Backbone.View.extend( @@ -79,11 +79,11 @@ var GalaxyFrame = Backbone.View.extend( // initialize initialize : function(options) { - // add to master menu + // add to masthead menu var self = this; // add activate icon - this.button_active = new mod_master.GalaxyMasterIcon ( + this.button_active = new mod_masthead.GalaxyMastheadIcon ( { icon : 'fa-th', tooltip : 'Enable/Disable Scratchbook', @@ -94,11 +94,11 @@ var GalaxyFrame = Backbone.View.extend( } }); - // add to master - Galaxy.master.append(this.button_active); + // add to masthead + Galaxy.masthead.append(this.button_active); // add load icon - this.button_load = new mod_master.GalaxyMasterIcon ( + this.button_load = new mod_masthead.GalaxyMastheadIcon ( { icon : 'fa-eye', tooltip : 'Show/Hide Scratchbook', @@ -106,8 +106,8 @@ var GalaxyFrame = Backbone.View.extend( with_number : true }); - // add to master - Galaxy.master.append(this.button_load); + // add to masthead + Galaxy.masthead.append(this.button_load); // read in defaults if (options) diff --git a/static/scripts/galaxy.master.js b/static/scripts/galaxy.masthead.js similarity index 89% rename from static/scripts/galaxy.master.js rename to static/scripts/galaxy.masthead.js index 475d5926cb1..692b6adeebc 100644 --- a/static/scripts/galaxy.master.js +++ b/static/scripts/galaxy.masthead.js @@ -1,15 +1,15 @@ /* - galaxy master + galaxy masthead */ // dependencies define(["utils/galaxy.utils", "libs/backbone/backbone-relational"], function(mod_utils) { -// master -var GalaxyMaster = Backbone.View.extend( +// masthead +var GalaxyMasthead = Backbone.View.extend( { // base element - el_master: '#everything', + el_masthead: '#everything', // options options : null, @@ -41,11 +41,11 @@ var GalaxyMaster = Backbone.View.extend( // define this element this.setElement($(this._template(options))); - // append to master - $(this.el_master).append($(this.el)); + // append to masthead + $(this.el_masthead).append($(this.el)); // assign background - this.$background = $(this.el).find('#master-background'); + this.$background = $(this.el).find('#masthead-background'); // loop through item specific unload functions // and collect all there warning messages, regarding @@ -72,33 +72,33 @@ var GalaxyMaster = Backbone.View.extend( 'mousedown' : function(e) { e.preventDefault() } }, - // adds a new item to the master + // adds a new item to the masthead append : function(item) { return this._add(item, true); }, - // adds a new item to the master + // adds a new item to the masthead prepend : function(item) { return this._add(item, false); }, - // adds a new item to the master + // adds a new item to the masthead _add : function(item, append) { - var $loc = $(this.el).find('#' + item.masterLocation); + var $loc = $(this.el).find('#' + item.mastheadLocation); if ($loc) { // create frame for new item - var itemId = 'master-item-' + this.itemCounter++; + var itemId = 'masthead-item-' + this.itemCounter++; var $itemNew = $(item.el); // configure id and class in order to mark new items $itemNew.attr('id', itemId); - $itemNew.addClass('master-item'); + $itemNew.addClass('masthead-item'); - // append to master + // append to masthead if (append) { $loc.append($itemNew); } else { @@ -120,7 +120,7 @@ var GalaxyMaster = Backbone.View.extend( _eventRefresh: function(e) { // identify current item - var itemCurrent = $(e.target).closest('.master-item'); + var itemCurrent = $(e.target).closest('.masthead-item'); // get identifier if (itemCurrent.length) @@ -131,8 +131,8 @@ var GalaxyMaster = Backbone.View.extend( { var it = this.list[this.itemLast]; if (it) { - if (it.masterReset) { - it.masterReset(); + if (it.mastheadReset) { + it.mastheadReset(); } } } @@ -143,7 +143,7 @@ var GalaxyMaster = Backbone.View.extend( { var it = this.list[itemCurrent]; if (it) { - if (it.masterReset) { + if (it.mastheadReset) { if (this.itemLast == itemCurrent) { useBackground = this.backgroundVisible ? false : true; } else { @@ -172,7 +172,7 @@ var GalaxyMaster = Backbone.View.extend( // template item _templateItem: function(id) { - return '
            '; + return '
            '; }, // fill template @@ -191,13 +191,13 @@ var GalaxyMaster = Backbone.View.extend( '
            ' + '
            ' + '' + - '' + + '' + ''; } }); // icon -var GalaxyMasterIcon = Backbone.View.extend( +var GalaxyMastheadIcon = Backbone.View.extend( { // icon options options: @@ -211,8 +211,8 @@ var GalaxyMasterIcon = Backbone.View.extend( visible : true }, - // location identifier for master class - masterLocation: 'iconbar', + // location identifier for masthead class + mastheadLocation: 'iconbar', // initialize initialize: function (options) @@ -290,7 +290,7 @@ var GalaxyMasterIcon = Backbone.View.extend( }); // tab -var GalaxyMasterTab = Backbone.View.extend( +var GalaxyMastheadTab = Backbone.View.extend( { // main options options: @@ -306,7 +306,7 @@ var GalaxyMasterTab = Backbone.View.extend( }, // location - masterLocation: 'navbar', + mastheadLocation: 'navbar', // optional sub menu $menu: null, @@ -414,8 +414,8 @@ var GalaxyMasterTab = Backbone.View.extend( this.$menu.append($(this._templateDivider())); }, - // add reset function called by master - masterReset: function() + // add reset function called by masthead + mastheadReset: function() { this._hideMenu(); }, @@ -490,9 +490,9 @@ var GalaxyMasterTab = Backbone.View.extend( // return return { - GalaxyMaster: GalaxyMaster, - GalaxyMasterTab: GalaxyMasterTab, - GalaxyMasterIcon: GalaxyMasterIcon + GalaxyMasthead: GalaxyMasthead, + GalaxyMastheadTab: GalaxyMastheadTab, + GalaxyMastheadIcon: GalaxyMastheadIcon }; }); diff --git a/static/scripts/galaxy.menu.js b/static/scripts/galaxy.menu.js index 95ed6c493e0..ad28b00a8a6 100644 --- a/static/scripts/galaxy.menu.js +++ b/static/scripts/galaxy.menu.js @@ -3,7 +3,7 @@ */ // dependencies -define(["galaxy.master", "libs/backbone/backbone-relational"], function(mod_master) { +define(["galaxy.masthead", "libs/backbone/backbone-relational"], function(mod_masthead) { // frame manager var GalaxyMenu = Backbone.Model.extend( @@ -11,14 +11,14 @@ var GalaxyMenu = Backbone.Model.extend( // options options: null, - // link master class - master: null, + // link masthead class + masthead: null, // initialize initialize: function(options) { this.options = options.config; - this.master = options.master; + this.masthead = options.masthead; this.create(); }, @@ -28,26 +28,26 @@ var GalaxyMenu = Backbone.Model.extend( // // Analyze data tab. // - var tab_analysis = new mod_master.GalaxyMasterTab({ + var tab_analysis = new mod_masthead.GalaxyMastheadTab({ title : "Analyze Data", content : "root/index" }); - this.master.append(tab_analysis); + this.masthead.append(tab_analysis); // // Workflow tab. // - var tab_workflow = new mod_master.GalaxyMasterTab({ + var tab_workflow = new mod_masthead.GalaxyMastheadTab({ title : "Workflow", content : "workflow" }); - this.master.append(tab_workflow); + this.masthead.append(tab_workflow); // // 'Shared Items' or Libraries tab. // - var tab_shared = new mod_master.GalaxyMasterTab({ + var tab_shared = new mod_masthead.GalaxyMastheadTab({ title : "Shared Data", content : "library/index" }); @@ -79,14 +79,14 @@ var GalaxyMenu = Backbone.Model.extend( content : "page/list_published" }); - this.master.append(tab_shared); + this.masthead.append(tab_shared); // // Lab menu. // if (this.options.user.requests) { - var tab_lab = new mod_master.GalaxyMasterTab({ + var tab_lab = new mod_masthead.GalaxyMastheadTab({ title : "Lab" }); tab_lab.addMenu({ @@ -101,13 +101,13 @@ var GalaxyMenu = Backbone.Model.extend( title : "Help", content : this.options.lims_doc_url }); - this.master.append(tab_lab); + this.masthead.append(tab_lab); } // // Visualization tab. // - var tab_visualization = new mod_master.GalaxyMasterTab({ + var tab_visualization = new mod_masthead.GalaxyMastheadTab({ title : "Visualization", content : "visualization/list" @@ -122,14 +122,14 @@ var GalaxyMenu = Backbone.Model.extend( content : "visualization/list", target : "_frame" }); - this.master.append(tab_visualization); + this.masthead.append(tab_visualization); // // Cloud menu. // if (this.options.enable_cloud_launch) { - var tab_cloud = new mod_master.GalaxyMasterTab({ + var tab_cloud = new mod_masthead.GalaxyMastheadTab({ title : "Cloud", content : "cloudlaunch/index" }); @@ -137,7 +137,7 @@ var GalaxyMenu = Backbone.Model.extend( title : "New Cloud Cluster", content : "cloudlaunch/index" }); - this.master.append(tab_cloud); + this.masthead.append(tab_cloud); } // @@ -145,18 +145,18 @@ var GalaxyMenu = Backbone.Model.extend( // if (this.options.is_admin_user) { - var tab_admin = new mod_master.GalaxyMasterTab({ + var tab_admin = new mod_masthead.GalaxyMastheadTab({ title : "Admin", content : "admin/index", extra_class : "admin-only" }); - this.master.append(tab_admin); + this.masthead.append(tab_admin); } // // Help tab. // - var tab_help = new mod_master.GalaxyMasterTab({ + var tab_help = new mod_masthead.GalaxyMastheadTab({ title : "Help" }); if (this.options.biostar_url) @@ -210,14 +210,14 @@ var GalaxyMenu = Backbone.Model.extend( target : "_blank" }); } - this.master.append(tab_help); + this.masthead.append(tab_help); // // User tab. // if (!this.options.user.valid) { - var tab_user = new mod_master.GalaxyMasterTab({ + var tab_user = new mod_masthead.GalaxyMastheadTab({ title : "User", extra_class : "loggedout-only" }); @@ -242,10 +242,10 @@ var GalaxyMenu = Backbone.Model.extend( }); } - // add to master - this.master.append(tab_user); + // add to masthead + this.masthead.append(tab_user); } else { - var tab_user = new mod_master.GalaxyMasterTab({ + var tab_user = new mod_masthead.GalaxyMastheadTab({ title : "User", extra_class : "loggedin-only" }); @@ -316,8 +316,8 @@ var GalaxyMenu = Backbone.Model.extend( }); } - // add to master - this.master.append(tab_user); + // add to masthead + this.masthead.append(tab_user); } } }); diff --git a/static/scripts/galaxy.upload.js b/static/scripts/galaxy.upload.js index 9ed0e2d9eeb..79076eb97e3 100644 --- a/static/scripts/galaxy.upload.js +++ b/static/scripts/galaxy.upload.js @@ -3,7 +3,7 @@ */ // dependencies -define(["galaxy.modal", "galaxy.master", "utils/galaxy.utils", "utils/galaxy.uploadbox", "libs/backbone/backbone-relational"], function(mod_modal, mod_master, mod_utils) { +define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils", "utils/galaxy.uploadbox", "libs/backbone/backbone-relational"], function(mod_modal, mod_masthead, mod_utils) { // galaxy upload var GalaxyUpload = Backbone.View.extend( @@ -64,7 +64,7 @@ var GalaxyUpload = Backbone.View.extend( // add activate icon var self = this; - this.button_show = new mod_master.GalaxyMasterIcon ( + this.button_show = new mod_masthead.GalaxyMastheadIcon ( { icon : 'fa-arrow-circle-o-up', tooltip : 'Upload Files', @@ -76,8 +76,8 @@ var GalaxyUpload = Backbone.View.extend( with_number : true }); - // add to master - Galaxy.master.prepend(this.button_show); + // add to masthead + Galaxy.masthead.prepend(this.button_show); // load extension var self = this; diff --git a/static/scripts/packed/galaxy.frame.js b/static/scripts/packed/galaxy.frame.js index f42f277896b..277d945653e 100644 --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1 +1 @@ -define(["galaxy.master","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el_main:"body",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMasterIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",on_click:function(f){c._event_panel_active(f)},on_unload:function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}});Galaxy.master.append(this.button_active);this.button_load=new b.GalaxyMasterIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",on_click:function(f){c._event_panel_load(f)},with_number:true});Galaxy.master.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this._template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this._panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c._panel_refresh()}})},add:function(d){var g={title:"",content:null,target:"",type:null,scratchbook:false};if(d){d=_.defaults(d,g)}else{d=g}if(!d.content){return}if(d.target=="_blank"){window.open(d.content);return}if(d.target=="_top"||d.target=="_parent"||d.target=="_self"){window.location=d.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(d.target=="galaxy_main"||d.target=="center"){if(f.length==0){var c=d.content;if(c.indexOf("?")==-1){c+="?"}else{c+="&"}c+="use_panels=True";window.location=c}else{f.attr("src",d.content)}}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this._template_frame(e.substring(1),d.title,d.type,d.content));var h={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this._to_pixel_coord("width",this.options.frame.cols);d.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(h.id).css("z-index"));this.frame_list[e]=h;this.frame_counter++;this._frame_resize(h,{width:d.width,height:d.height});this._frame_insert(h,{top:0,left:0},true);if(!this.visible){this._panel_show_hide()}},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_panel_load","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this._frame_identify(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this._frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this._frame_resize(this.event.target,h);h.width=this._to_grid_coord("width",h.width)+1;h.height=this._to_grid_coord("height",h.height)+1;h.width=this._to_pixel_coord("width",h.width);h.height=this._to_pixel_coord("height",h.height);this._frame_resize(this.frame_shadow,h);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this._frame_offset(this.event.target,h);var c={top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this._frame_insert(this.frame_shadow,c)}},_event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this._frame_identify(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c._panel_refresh(true);c._panel_animation_complete();if(c.visible&&c.frame_counter==0){c._panel_show_hide()}})},_event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},_event_panel_load:function(c){if(this.event.type!==null){return}this._panel_show_hide()},_event_panel_active:function(c){if(this.event.type!==null){return}this._panel_active_disable()},_event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this._panel_scroll(d)},_event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(-this.options.scroll)},_event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(this.options.scroll)},_frame_identify:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},_frame_drag_start:function(d){this._frame_focus(d,true);var c=this._frame_screen(d);this._frame_resize(this.frame_shadow,c);this._frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},_frame_drag_stop:function(d){this._frame_focus(d,false);var c=this._frame_screen(this.frame_shadow);this._frame_resize(d,c);this._frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this._panel_animation_complete()},_to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},_to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},_to_grid:function(c){return{top:this._to_grid_coord("top",c.top),left:this._to_grid_coord("left",c.left),width:this._to_grid_coord("width",c.width),height:this._to_grid_coord("height",c.height)}},_to_pixel:function(c){return{top:this._to_pixel_coord("top",c.top),left:this._to_pixel_coord("left",c.left),width:this._to_pixel_coord("width",c.width),height:this._to_pixel_coord("height",c.height)}},_is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1g.top+g.height-1||h.top+h.height-1l?1:0)});for(g=0;g'},_template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d=''}return'
            '+e+'
            '+d+'
            '},_template_shadow:function(c){return'
            '},_template_background:function(){return'
            '},_template_menu:function(){return'
            '}});return{GalaxyFrame:a}}); \ No newline at end of file +define(["galaxy.masthead","libs/backbone/backbone-relational"],function(b){var a=Backbone.View.extend({el_main:"body",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",on_click:function(f){c._event_panel_active(f)},on_unload:function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",on_click:function(f){c._event_panel_load(f)},with_number:true});Galaxy.masthead.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this._template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this._panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c._panel_refresh()}})},add:function(d){var g={title:"",content:null,target:"",type:null,scratchbook:false};if(d){d=_.defaults(d,g)}else{d=g}if(!d.content){return}if(d.target=="_blank"){window.open(d.content);return}if(d.target=="_top"||d.target=="_parent"||d.target=="_self"){window.location=d.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(d.target=="galaxy_main"||d.target=="center"){if(f.length==0){var c=d.content;if(c.indexOf("?")==-1){c+="?"}else{c+="&"}c+="use_panels=True";window.location=c}else{f.attr("src",d.content)}}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this._template_frame(e.substring(1),d.title,d.type,d.content));var h={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this._to_pixel_coord("width",this.options.frame.cols);d.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(h.id).css("z-index"));this.frame_list[e]=h;this.frame_counter++;this._frame_resize(h,{width:d.width,height:d.height});this._frame_insert(h,{top:0,left:0},true);if(!this.visible){this._panel_show_hide()}},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_panel_load","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this._frame_identify(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this._frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this._frame_resize(this.event.target,h);h.width=this._to_grid_coord("width",h.width)+1;h.height=this._to_grid_coord("height",h.height)+1;h.width=this._to_pixel_coord("width",h.width);h.height=this._to_pixel_coord("height",h.height);this._frame_resize(this.frame_shadow,h);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this._frame_offset(this.event.target,h);var c={top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this._frame_insert(this.frame_shadow,c)}},_event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this._frame_identify(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c._panel_refresh(true);c._panel_animation_complete();if(c.visible&&c.frame_counter==0){c._panel_show_hide()}})},_event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},_event_panel_load:function(c){if(this.event.type!==null){return}this._panel_show_hide()},_event_panel_active:function(c){if(this.event.type!==null){return}this._panel_active_disable()},_event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this._panel_scroll(d)},_event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(-this.options.scroll)},_event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(this.options.scroll)},_frame_identify:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},_frame_drag_start:function(d){this._frame_focus(d,true);var c=this._frame_screen(d);this._frame_resize(this.frame_shadow,c);this._frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},_frame_drag_stop:function(d){this._frame_focus(d,false);var c=this._frame_screen(this.frame_shadow);this._frame_resize(d,c);this._frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this._panel_animation_complete()},_to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},_to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},_to_grid:function(c){return{top:this._to_grid_coord("top",c.top),left:this._to_grid_coord("left",c.left),width:this._to_grid_coord("width",c.width),height:this._to_grid_coord("height",c.height)}},_to_pixel:function(c){return{top:this._to_pixel_coord("top",c.top),left:this._to_pixel_coord("left",c.left),width:this._to_pixel_coord("width",c.width),height:this._to_pixel_coord("height",c.height)}},_is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1g.top+g.height-1||h.top+h.height-1l?1:0)});for(g=0;g'},_template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d=''}return'
            '+e+'
            '+d+'
            '},_template_shadow:function(c){return'
            '},_template_background:function(){return'
            '},_template_menu:function(){return'
            '}});return{GalaxyFrame:a}}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.master.js b/static/scripts/packed/galaxy.master.js deleted file mode 100644 index b5fba12240e..00000000000 --- a/static/scripts/packed/galaxy.master.js +++ /dev/null @@ -1 +0,0 @@ -define(["utils/galaxy.utils","libs/backbone/backbone-relational"],function(c){var a=Backbone.View.extend({el_master:"#everything",options:null,list:{},itemLast:null,itemCounter:0,$background:null,backgroundVisible:false,initialize:function(f){this.options=f;$("body").off();this.setElement($(this._template(f)));$(this.el_master).append($(this.el));this.$background=$(this.el).find("#master-background");var e=this;window.onbeforeunload=function(){var h="";for(key in e.list){if(e.list[key].options.on_unload){var g=e.list[key].options.on_unload();if(g){h+=g+" "}}}if(h!=""){return h}}},events:{click:"_eventRefresh",mousedown:function(f){f.preventDefault()}},append:function(e){return this._add(e,true)},prepend:function(e){return this._add(e,false)},_add:function(g,f){var e=$(this.el).find("#"+g.masterLocation);if(e){var h="master-item-"+this.itemCounter++;var i=$(g.el);i.attr("id",h);i.addClass("master-item");if(f){e.append(i)}else{e.prepend(i)}this.list[h]=g;return h}return null},_eventRefresh:function(h){var i=$(h.target).closest(".master-item");if(i.length){i=i.attr("id")}if(this.itemLast&&this.itemLast!=i){var g=this.list[this.itemLast];if(g){if(g.masterReset){g.masterReset()}}}var f=false;if(i){var g=this.list[i];if(g){if(g.masterReset){if(this.itemLast==i){f=this.backgroundVisible?false:true}else{f=true}}}}if(f){this.$background.show()}else{this.$background.hide()}this.backgroundVisible=f;this.itemLast=i},_templateItem:function(e){return'
            '},_template:function(e){return''}});var d=Backbone.View.extend({options:{id:"galaxy-icon",icon:"fa-cog",tooltip:"galaxy-icon",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},masterLocation:"iconbar",initialize:function(f){if(f){this.options=_.defaults(f,this.options)}this.setElement($(this._template(this.options)));var e=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip}).on("mouseup",e.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(e){$(this.el).find(".icon").removeClass(this.options.icon).addClass(e);this.options.icon=e},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(e){$(this.el).find(".number").text(e)},_template:function(f){var e="
            ';if(f.with_number){e+='
            '}e+="
            ";return e}});var b=Backbone.View.extend({options:{id:"",title:"Title",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true},masterLocation:"navbar",$menu:null,menuVisible:false,events:{"click .head":"_eventClickHead"},initialize:function(e){if(e){this.options=_.defaults(e,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},addMenu:function(g){var h={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(g){h=_.defaults(g,h)}if(h.content&&h.content.indexOf("//")===-1){h.content=galaxy_config.root+h.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".menu")}var f=$(this._templateMenuItem(h));this.$menu.append(f);var e=this;f.on("click",function(i){i.preventDefault();e._hideMenu();if(e.options.target==="_blank"){return true}Galaxy.frame.add(g)});if(h.divider){this.$menu.append($(this._templateDivider()))}},masterReset:function(){this._hideMenu()},_hideMenu:function(){if(this.$menu&&this.menuVisible){this.$menu.hide();this.menuVisible=false}},_eventClickHead:function(f){f.preventDefault();if(this.$menu){if(!this.menuVisible){this.$menu.show();this.menuVisible=true}else{this.$menu.hide();this.menuVisible=false}}else{Galaxy.frame.add(this.options)}},_templateMenuItem:function(e){return'
          • '+e.title+"
            • "},_templateMenu:function(){return'
              '},_templateDivider:function(){return'
            • '},_template:function(f){var e='';return e}});return{GalaxyMaster:a,GalaxyMasterTab:b,GalaxyMasterIcon:d}}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.masthead.js b/static/scripts/packed/galaxy.masthead.js new file mode 100644 index 00000000000..a654a225559 --- /dev/null +++ b/static/scripts/packed/galaxy.masthead.js @@ -0,0 +1 @@ +define(["utils/galaxy.utils","libs/backbone/backbone-relational"],function(c){var a=Backbone.View.extend({el_masthead:"#everything",options:null,list:{},itemLast:null,itemCounter:0,$background:null,backgroundVisible:false,initialize:function(f){this.options=f;$("body").off();this.setElement($(this._template(f)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var e=this;window.onbeforeunload=function(){var h="";for(key in e.list){if(e.list[key].options.on_unload){var g=e.list[key].options.on_unload();if(g){h+=g+" "}}}if(h!=""){return h}}},events:{click:"_eventRefresh",mousedown:function(f){f.preventDefault()}},append:function(e){return this._add(e,true)},prepend:function(e){return this._add(e,false)},_add:function(g,f){var e=$(this.el).find("#"+g.mastheadLocation);if(e){var h="masthead-item-"+this.itemCounter++;var i=$(g.el);i.attr("id",h);i.addClass("masthead-item");if(f){e.append(i)}else{e.prepend(i)}this.list[h]=g;return h}return null},_eventRefresh:function(h){var i=$(h.target).closest(".masthead-item");if(i.length){i=i.attr("id")}if(this.itemLast&&this.itemLast!=i){var g=this.list[this.itemLast];if(g){if(g.mastheadReset){g.mastheadReset()}}}var f=false;if(i){var g=this.list[i];if(g){if(g.mastheadReset){if(this.itemLast==i){f=this.backgroundVisible?false:true}else{f=true}}}}if(f){this.$background.show()}else{this.$background.hide()}this.backgroundVisible=f;this.itemLast=i},_templateItem:function(e){return'
              '},_template:function(e){return''}});var b=Backbone.View.extend({options:{id:"galaxy-icon",icon:"fa-cog",tooltip:"galaxy-icon",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},mastheadLocation:"iconbar",initialize:function(f){if(f){this.options=_.defaults(f,this.options)}this.setElement($(this._template(this.options)));var e=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip}).on("mouseup",e.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(e){$(this.el).find(".icon").removeClass(this.options.icon).addClass(e);this.options.icon=e},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(e){$(this.el).find(".number").text(e)},_template:function(f){var e="
              ';if(f.with_number){e+='
              '}e+="
              ";return e}});var d=Backbone.View.extend({options:{id:"",title:"Title",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true},mastheadLocation:"navbar",$menu:null,menuVisible:false,events:{"click .head":"_eventClickHead"},initialize:function(e){if(e){this.options=_.defaults(e,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},addMenu:function(g){var h={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(g){h=_.defaults(g,h)}if(h.content&&h.content.indexOf("//")===-1){h.content=galaxy_config.root+h.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".menu")}var f=$(this._templateMenuItem(h));this.$menu.append(f);var e=this;f.on("click",function(i){i.preventDefault();e._hideMenu();if(e.options.target==="_blank"){return true}Galaxy.frame.add(g)});if(h.divider){this.$menu.append($(this._templateDivider()))}},mastheadReset:function(){this._hideMenu()},_hideMenu:function(){if(this.$menu&&this.menuVisible){this.$menu.hide();this.menuVisible=false}},_eventClickHead:function(f){f.preventDefault();if(this.$menu){if(!this.menuVisible){this.$menu.show();this.menuVisible=true}else{this.$menu.hide();this.menuVisible=false}}else{Galaxy.frame.add(this.options)}},_templateMenuItem:function(e){return'
            • '+e.title+"
              • "},_templateMenu:function(){return'
                '},_templateDivider:function(){return'
              • '},_template:function(f){var e='';return e}});return{GalaxyMasthead:a,GalaxyMastheadTab:d,GalaxyMastheadIcon:b}}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.menu.js b/static/scripts/packed/galaxy.menu.js new file mode 100644 index 00000000000..e2c6c3fa75b --- /dev/null +++ b/static/scripts/packed/galaxy.menu.js @@ -0,0 +1 @@ +define(["galaxy.masthead","libs/backbone/backbone-relational"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({title:"Shared Data",content:"library/index"});g.addMenu({title:"Data Libraries",content:"library/index",divider:true});g.addMenu({title:"Published Histories",content:"history/list_published"});g.addMenu({title:"Published Workflows",content:"workflow/list_published"});g.addMenu({title:"Published Visualizations",content:"visualization/list_published"});g.addMenu({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({title:"Lab"});h.addMenu({title:"Sequencing Requests",content:"requests/index"});h.addMenu({title:"Find Samples",content:"requests/find_samples_index"});h.addMenu({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({title:"Visualization",content:"visualization/list"});k.addMenu({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.addMenu({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({title:"Cloud",content:"cloudlaunch/index"});e.addMenu({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({title:"Help"});if(this.options.biostar_url){j.addMenu({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.addMenu({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.addMenu({title:"Support",content:this.options.support_url,target:"_blank"});j.addMenu({title:"Search",content:this.options.search_url,target:"_blank"});j.addMenu({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.addMenu({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.addMenu({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.addMenu({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.addMenu({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedout-only"});if(this.options.allow_user_creation){i.addMenu({title:"Login",content:"user/login",target:"galaxy_main"})}if(this.options.allow_user_creation){i.addMenu({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({title:"User",extra_class:"loggedin-only"});i.addMenu({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.addMenu({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.addMenu({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.addMenu({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.addMenu({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.addMenu({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.addMenu({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.addMenu({title:"Saved Pages",content:"page/list",target:"_top"});i.addMenu({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.addMenu({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}}});return{GalaxyMenu:a}}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.upload.js b/static/scripts/packed/galaxy.upload.js index 761cdf35d25..2657bd49e62 100644 --- a/static/scripts/packed/galaxy.upload.js +++ b/static/scripts/packed/galaxy.upload.js @@ -1 +1 @@ -define(["galaxy.modal","galaxy.master","utils/galaxy.utils","utils/galaxy.uploadbox","libs/backbone/backbone-relational"],function(b,d,c){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],state:{init:"fa fa-trash-o",queued:"fa fa-spinner fa-spin",running:"__running__",success:"fa fa-check",error:"fa fa-exclamation-triangle"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},initialize:function(){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}var e=this;this.button_show=new d.GalaxyMasterIcon({icon:"fa-arrow-circle-o-up",tooltip:"Upload Files",on_click:function(f){e.event_show(f)},on_unload:function(){if(e.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.master.prepend(this.button_show);var e=this;c.jsonFromUrl(galaxy_config.root+"api/datatypes",function(f){for(key in f){e.select_extension.push([f[key],f[key]])}});c.jsonFromUrl(galaxy_config.root+"api/genomes",function(f){var g=e.select_genome[0];e.select_genome=[];for(key in f){if(f[key].length>1){if(f[key][1]!==g[1]){e.select_genome.push(f[key])}}}e.select_genome.sort(function(i,h){return i[0]>h[0]?1:i[0]0)){return null}this.uploadbox.configure({url:galaxy_config.root+"api/tools",paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=m;tool_input.file_type=f;tool_input["files_0|NAME"]=e.name;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=l;tool_input.space_to_tabs=h;data={};data.history_id=j;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refreshHdas()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("Failed: "+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_start:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#text-content").attr("disabled",true);$(this).find("#genome").attr("disabled",true);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.start()},event_stop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#text-content").attr("disabled",false);$(this).find("#genome").attr("disabled",false);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_create:function(){this.uploadbox.add([{name:"New File",size:-1}])},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Create:function(){f.event_create()},Upload:function(){f.event_start()},Pause:function(){f.event_stop()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()},},height:"400",width:"900"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:function(){f.event_dragover()},dragleave:function(){f.event_dragleave()},announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{if(e>0){e=e*10;f="b"}else{return"-"}}}}}return""+(Math.round(e)/10)+" "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'
                '},template_row:function(f){var e='
                You may specify a list of URLs (one per line) or paste the contents of a file.
                0%
                '},template_row:function(f){var e='
                You may specify a list of URLs (one per line) or paste the contents of a file.
                0%
                ",_.map(l,function(n,m){n=(_.isObject(n))?(f(n)):(n);return'"}).join(""),"
                '+m+''+n+"
                "].join("")}if(_.isObject(h)){g.body=j.append(f(h))}else{g.body=j.html(h)}g.buttons={Ok:function(){Galaxy.modal.hide();e.clearMessages()}};return g},clearMessages:function(){var e=this.$el.find(this.msgsSelector);e.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(e){this.$el.parent().scrollTop(e)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(f,g){if(!g){this.$el.parent().parent().scrollTop(f);return this}var e=window,h=this.$el.parent().parent(),j=$(e).innerHeight(),i=(j/2)-(g/2);$(h).scrollTop(f-i);return this},scrollToId:function(f){if((!f)||(!this.hdaViews[f])){return this}var e=this.hdaViews[f].$el;this.scrollIntoView(e.offset().top,e.outerHeight());return this},scrollToHid:function(e){var f=this.model.hdas.getByHid(e);if(!f){return this}return this.scrollToId(f.id)},connectToQuotaMeter:function(e){if(!e){return this}this.listenTo(e,"quota:over",this.showQuotaMessage);this.listenTo(e,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(e&&e.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var e=this.$el.find(".quota-message");if(e.is(":hidden")){e.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var e=this.$el.find(".quota-message");if(!e.is(":hidden")){e.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(e){if(!e){return this}this.on("new-storage",function(g,f){if(e&&g){e.findItemByHtml(_l("Include Deleted Datasets")).checked=g.get("show_deleted");e.findItemByHtml(_l("Include Hidden Datasets")).checked=g.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});c.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:c}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-base","mvc/dataset/hda-edit"],function(d,b,a){var c=Backbone.View.extend(LoggableMixin).extend({HDAView:a.HDAEditView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",emptyMsgSelector:".empty-history-message",msgsSelector:".message-container",initialize:function(e){e=e||{};if(e.logger){this.logger=e.logger}this.log(this+".initialize:",e);this._setUpListeners();this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);if(this.model){this._setUpWebStorage(e.initiallyExpanded,e.show_deleted,e.show_hidden);this._setUpModelEventHandlers()}if(e.onready){e.onready.call(this)}},_setUpListeners:function(){this.on("error",function(f,i,e,h,g){this.errorHandler(f,i,e,h,g)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...")});this.on("loading-done",function(){this.hideLoadingIndicator()});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});this.on("switched-history current-history new-history",function(){if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});if(this.logger){this.on("all",function(e){this.log(this+"",arguments)},this)}},errorHandler:function(g,j,f,i,h){var e=this._parseErrorMessage(g,j,f,i,h);if(j&&j.status===0&&j.readyState===0){}else{if(j&&j.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",e.message,e.details)})}else{this.displayMessage("error",e.message,e.details)}}}},_parseErrorMessage:function(h,l,g,k,j){var f=Galaxy.currUser,e={message:this._bePolite(k),details:{user:(f instanceof User)?(f.toJSON()):(f+""),source:(h instanceof Backbone.Model)?(h.toJSON()):(h+""),xhr:l,options:(l)?(_.omit(g,"xhr")):(g)}};_.extend(e.details,j||{});if(l&&_.isFunction(l.getAllResponseHeaders)){var i=l.getAllResponseHeaders();i=_.compact(i.split("\n"));i=_.map(i,function(m){return m.split(": ")});e.details.xhr.responseHeaders=_.object(i)}return e},_bePolite:function(e){e=e||_l("An error occurred while getting updates from the server");return e+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadCurrentHistory:function(f){var e=this;return this.loadHistoryWithHDADetails("current",f).then(function(h,g){e.trigger("current-history",e)})},switchToHistory:function(h,g){var e=this,f=function(){return jQuery.post(galaxy_config.root+"api/histories/"+h+"/set_as_current")};return this.loadHistoryWithHDADetails(h,g,f).then(function(j,i){e.trigger("switched-history",e)})},createNewHistory:function(g){var e=this,f=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,g,f).then(function(i,h){e.trigger("new-history",e)})},loadHistoryWithHDADetails:function(h,g,f,j){var e=this,i=function(k){return e.getExpandedHdaIds(k.id)};return this.loadHistory(h,g,f,j,i)},loadHistory:function(h,g,f,k,i){this.trigger("loading-history",this);g=g||{};var e=this;var j=d.History.getHistoryData(h,{historyFn:f,hdaFn:k,hdaDetailIds:g.initiallyExpanded||i});return this._loadHistoryFromXHR(j,g).fail(function(n,l,m){e.trigger("error",e,n,g,_l("An error was encountered while "+l),{historyId:h,history:m||{}})}).always(function(){e.trigger("loading-done",e)})},_loadHistoryFromXHR:function(g,f){var e=this;g.then(function(h,i){e.setModel(h,i,f)});g.fail(function(i,h){e.render()});return g},setModel:function(g,e,f){f=f||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){g.user=Galaxy.currUser.toJSON()}this.model=new d.History(g,e,f);this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers();this.trigger("new-model",this);this.render();return this},refreshHdas:function(f,e){if(this.model){return this.model.refresh(f,e)}return $.when()},_setUpWebStorage:function(f,e,g){this.storage=new PersistentStorage(this._getStorageKey(this.model.get("id")),{expandedHdas:{},show_deleted:false,show_hidden:false});this.log(this+" (prev) storage:",JSON.stringify(this.storage.get(),null,2));if(f){this.storage.set("exandedHdas",f)}if((e===true)||(e===false)){this.storage.set("show_deleted",e)}if((g===true)||(g===false)){this.storage.set("show_hidden",g)}this.show_deleted=this.storage.get("show_deleted");this.show_hidden=this.storage.get("show_hidden");this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},_getStorageKey:function(e){if(!e){throw new Error("_getStorageKey needs valid id: "+e)}return("history:"+e)},clearWebStorage:function(){for(var e in sessionStorage){if(e.indexOf("history:")===0){sessionStorage.removeItem(e)}}},getStoredOptions:function(f){if(!f||f==="current"){return(this.storage)?(this.storage.get()):({})}var e=sessionStorage.getItem(this._getStorageKey(f));return(e===null)?({}):(JSON.parse(e))},getExpandedHdaIds:function(e){var f=this.getStoredOptions(e).expandedHdas;return((_.isEmpty(f))?([]):(_.keys(f)))},_setUpModelEventHandlers:function(){this.model.on("error error:hdas",function(f,h,e,g){this.errorHandler(f,h,e,g)},this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("add",this.addHdaView,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this);this.model.hdas.on("state:ready",function(f,g,e){if((!f.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[f.id])}},this)},addHdaView:function(h){this.log("add."+this,h);var f=this;if(!h.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function g(j){var i=f.$el.find(f.emptyMsgSelector);if(i.is(":visible")){i.fadeOut(f.fxSpeed,j)}else{j()}},function e(j){f.scrollToTop();var i=f.$el.find(f.datasetsSelector);f.createHdaView(h).$el.hide().prependTo(i).slideDown(f.fxSpeed)}])},createHdaView:function(g){var f=g.get("id"),e=this.storage.get("expandedHdas").get(f),h=new this.HDAView({model:g,expanded:e,hasUser:this.model.hasUser(),logger:this.logger});this._setUpHdaListeners(h);this.hdaViews[f]=h;return h.render()},_setUpHdaListeners:function(f){var e=this;f.on("body-expanded",function(g){e.storage.get("expandedHdas").set(g,true)});f.on("body-collapsed",function(g){e.storage.get("expandedHdas").deleteKey(g)});f.on("error",function(h,j,g,i){e.errorHandler(h,j,g,i)})},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},render:function(g){var e=this,f;if(this.model){f=this.renderModel()}else{f=this.renderWithoutModel()}$(e).queue("fx",[function(h){if(e.$el.is(":visible")){e.$el.fadeOut(e.fxSpeed,h)}else{h()}},function(h){e.$el.empty();if(f){e.$el.append(f.children())}e.$el.fadeIn(e.fxSpeed,h)},function(h){if(g){g.call(this)}e.trigger("rendered",this)}]);return this},renderWithoutModel:function(){var e=$("
                "),f=$("
                ").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return e.append(f)},renderModel:function(){var e=$("
                ");if(Galaxy.currUser.isAnonymous()){e.append(c.templates.anonHistoryPanel(this.model.toJSON()))}else{e.append(c.templates.historyPanel(this.model.toJSON()));this._renderTags(e);this._renderAnnotation(e)}this._setUpBehaviours(e);if(!this.model.hdas.length||!this.renderHdas(e.find(this.datasetsSelector))){e.find(this.emptyMsgSelector).show()}return e},_renderTags:function(e){this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){return}var f=this;e.find(".history-name").make_text_editable({on_finish:function(g){e.find(".history-name").text(g);f.model.save({name:g}).fail(function(){e.find(".history-name").text(f.model.previous("name"))})}})},renderHdas:function(f){this.hdaViews={};var e=this,g=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"));_.each(g,function(h){f.prepend(e.createHdaView(h).$el)});return g.length},events:{"click .message-container":"clearMessages"},updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(e){e.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.render();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.render();return this.storage.get("show_hidden")},showLoadingIndicator:function(f,e,g){e=(e!==undefined)?(e):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,g)}else{this.$el.fadeOut(e);this.indicator.show(f,e,g)}},hideLoadingIndicator:function(e,f){e=(e!==undefined)?(e):(this.fxSpeed);if(this.indicator){this.indicator.hide(e,f)}},displayMessage:function(j,k,i){var g=this;this.scrollToTop();var h=this.$el.find(this.msgsSelector),e=$("
                ").addClass(j+"message").html(k);if(!_.isEmpty(i)){var f=$('Details').click(function(){Galaxy.modal.show(g.messageToModalOptions(j,k,i));return false});e.append(" ",f)}return h.html(e)},messageToModalOptions:function(i,k,h){var e=this,j=$("
                "),g={title:"Details"};function f(l){l=_.omit(l,_.functions(l));return["",_.map(l,function(n,m){n=(_.isObject(n))?(f(n)):(n);return'"}).join(""),"
                '+m+''+n+"
                "].join("")}if(_.isObject(h)){g.body=j.append(f(h))}else{g.body=j.html(h)}g.buttons={Ok:function(){Galaxy.modal.hide();e.clearMessages()}};return g},clearMessages:function(){var e=this.$el.find(this.msgsSelector);e.empty()},scrollPosition:function(){return this.$el.parent().scrollTop()},scrollTo:function(e){this.$el.parent().scrollTop(e)},scrollToTop:function(){this.$el.parent().scrollTop(0);return this},scrollIntoView:function(f,g){if(!g){this.$el.parent().parent().scrollTop(f);return this}var e=window,h=this.$el.parent().parent(),j=$(e).innerHeight(),i=(j/2)-(g/2);$(h).scrollTop(f-i);return this},scrollToId:function(f){if((!f)||(!this.hdaViews[f])){return this}var e=this.hdaViews[f].$el;this.scrollIntoView(e.offset().top,e.outerHeight());return this},scrollToHid:function(e){var f=this.model.hdas.getByHid(e);if(!f){return this}return this.scrollToId(f.id)},connectToQuotaMeter:function(e){if(!e){return this}this.listenTo(e,"quota:over",this.showQuotaMessage);this.listenTo(e,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(e&&e.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var e=this.$el.find(".quota-message");if(e.is(":hidden")){e.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var e=this.$el.find(".quota-message");if(!e.is(":hidden")){e.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(e){if(!e){return this}this.on("new-storage",function(g,f){if(e&&g){e.findItemByHtml(_l("Include Deleted Datasets")).checked=g.get("show_deleted");e.findItemByHtml(_l("Include Hidden Datasets")).checked=g.get("show_hidden")}});return this},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});c.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:c}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/tags.js b/static/scripts/packed/mvc/tags.js index 4e4f6a23270..3f4570b642f 100644 --- a/static/scripts/packed/mvc/tags.js +++ b/static/scripts/packed/mvc/tags.js @@ -1 +1 @@ -var TagsEditor=Backbone.View.extend(LoggableMixin).extend({tagName:"div",className:"tags-display",initialize:function(a){this.listenTo(this.model,"change:tags",function(){this.render()})},render:function(){var a=this;this.$el.html(this.template());this.$el.find(".tags-input").select2({placeholder:"Add tags",width:"100%",tags:function(){return a.getTagsUsed()}});this._behaviors();return this},template:function(){return['",''].join("")},tagsToCSV:function(a){if(!_.isArray(a)||_.isEmpty(a)){return""}return a.sort().join(",")},getTagsUsed:function(){return _.map(Galaxy.currUser.get("tags_used"),function(a){return{id:a,text:a}})},_behaviors:function(){var a=this;this.$el.find(".tags-input").on("change",function(b){a.model.save({tags:b.val},{silent:true});if(b.added){a.addNewTagToTagsUsed(b.added.text)}})},addNewTagToTagsUsed:function(a){var b=Galaxy.currUser.get("tags_used");if(!_.contains(b,a)){b.push(a);b.sort();Galaxy.currUser.set("tags_used",b)}},remove:function(){this.$el.off();Backbone.View.prototype.remove.call(this)},toString:function(){return["TagSetView(",this.model+"",")"].join("")}}); \ No newline at end of file +var TagsEditor=Backbone.View.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(a){this.listenTo(this.model,"change:tags",function(){this.render()});this.hiddenUntilActivated(a.$activator,a)},render:function(){var a=this;this.$el.html(this._template());this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return a._getTagsUsed()}});this._setUpBehaviors();return this},_template:function(){return['",''].join("")},tagsToCSV:function(){var a=this.model.get("tags");if(!_.isArray(a)||_.isEmpty(a)){return""}return a.sort().join(",")},$input:function(){return this.$el.find(".tags-input")},_getTagsUsed:function(){return Galaxy.currUser.get("tags_used")},_setUpBehaviors:function(){var a=this;this.$input().on("change",function(b){a.model.save({tags:b.val},{silent:true});if(b.added){a._addNewTagToTagsUsed(b.added.text)}})},_addNewTagToTagsUsed:function(a){var b=Galaxy.currUser.get("tags_used");if(!_.contains(b,a)){b.push(a);b.sort();Galaxy.currUser.set("tags_used",b)}},remove:function(){this.$input.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}}); \ No newline at end of file diff --git a/static/scripts/packed/templates/compiled/history-templates.js b/static/scripts/packed/templates/compiled/history-templates.js index 2c56ae93c83..15f26912654 100644 --- a/static/scripts/packed/templates/compiled/history-templates.js +++ b/static/scripts/packed/templates/compiled/history-templates.js @@ -1 +1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-body"]=b(function(h,u,s,n,B){this.compilerInfo=[4,">= 1.0.0"];s=this.merge(s,h.helpers);B=B||{};var t="",j,e="function",d=this.escapeExpression,r=this,c=s.blockHelperMissing;function q(F,E){var C="",D;C+='\n
                \n ';if(D=s.body){D=D.call(F,{hash:{},data:E})}else{D=F.body;D=typeof D===e?D.apply(F):D}if(D||D===0){C+=D}C+='\n
                \n
                \n
                \n
                \n
                \n\n ';return C}function p(F,E){var C="",D;C+='\n
                \n ';D=s["if"].call(F,F.misc_blurb,{hash:{},inverse:r.noop,fn:r.program(4,o,E),data:E});if(D||D===0){C+=D}C+="\n\n ";D=s["if"].call(F,F.data_type,{hash:{},inverse:r.noop,fn:r.program(6,m,E),data:E});if(D||D===0){C+=D}C+="\n\n ";D=s["if"].call(F,F.metadata_dbkey,{hash:{},inverse:r.noop,fn:r.program(9,g,E),data:E});if(D||D===0){C+=D}C+="\n\n ";D=s["if"].call(F,F.misc_info,{hash:{},inverse:r.noop,fn:r.program(12,z,E),data:E});if(D||D===0){C+=D}C+='\n
                \n\n
                \n
                \n
                \n
                \n\n ';D=s.unless.call(F,F.deleted,{hash:{},inverse:r.noop,fn:r.program(14,y,E),data:E});if(D||D===0){C+=D}C+="\n\n ";return C}function o(F,E){var C="",D;C+='\n
                \n ';if(D=s.misc_blurb){D=D.call(F,{hash:{},data:E})}else{D=F.misc_blurb;D=typeof D===e?D.apply(F):D}C+=d(D)+"\n
                \n ";return C}function m(G,F){var C="",E,D;C+='\n
                \n \n ';if(E=s.data_type){E=E.call(G,{hash:{},data:F})}else{E=G.data_type;E=typeof E===e?E.apply(G):E}C+=d(E)+"\n
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                \n ";return C}function A(D,C){return"database"}function z(F,E){var C="",D;C+='\n
                \n ';if(D=s.misc_info){D=D.call(F,{hash:{},data:E})}else{D=F.misc_info;D=typeof D===e?D.apply(F):D}C+=d(D)+"\n
                \n ";return C}function y(G,F){var C="",E,D;C+='\n \n
                \n\n \n
                \n \n
                \n
                \n\n
                \n ';E=s.each.call(G,G.display_apps,{hash:{},inverse:r.noop,fn:r.program(19,v,F),data:F});if(E||E===0){C+=E}C+="\n\n ";E=s.each.call(G,G.display_types,{hash:{},inverse:r.noop,fn:r.program(19,v,F),data:F});if(E||E===0){C+=E}C+='\n
                \n\n
                \n ';E=s["if"].call(G,G.peek,{hash:{},inverse:r.noop,fn:r.program(23,f,F),data:F});if(E||E===0){C+=E}C+="\n
                \n\n ";return C}function x(D,C){return"Annotation"}function w(D,C){return"Edit dataset annotation"}function v(F,E){var C="",D;C+='\n
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                \n ";return C}function k(G,F){var C="",E,D;C+='\n ';D={hash:{},inverse:r.noop,fn:r.program(21,i,F),data:F};if(E=s.local){E=E.call(G,D)}else{E=G.local;E=typeof E===e?E.apply(G):E}if(!s.local){E=c.call(G,E,D)}if(E||E===0){C+=E}C+="\n ";return C}function i(E,D){var C;if(C=s.text){C=C.call(E,{hash:{},data:D})}else{C=E.text;C=typeof C===e?C.apply(E):C}return d(C)}function f(F,E){var C="",D;C+='\n 
                ';if(D=s.peek){D=D.call(F,{hash:{},data:E})}else{D=F.peek;D=typeof D===e?D.apply(F):D}if(D||D===0){C+=D}C+="
                \n ";return C}t+='
                \n ';j=s["if"].call(u,u.body,{hash:{},inverse:r.program(3,p,B),fn:r.program(1,q,B),data:B});if(j||j===0){t+=j}t+="\n
                ";return t})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-body"]=b(function(g,r,p,k,z){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);z=z||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(D,C){var A="",B;A+='\n
                \n ';if(B=p.body){B=B.call(D,{hash:{},data:C})}else{B=D.body;B=typeof B===e?B.apply(D):B}if(B||B===0){A+=B}A+='\n
                \n
                \n
                \n
                \n
                \n\n ';return A}function m(D,C){var A="",B;A+='\n
                \n ';B=p["if"].call(D,D.misc_blurb,{hash:{},inverse:o.noop,fn:o.program(4,l,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.data_type,{hash:{},inverse:o.noop,fn:o.program(6,j,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.metadata_dbkey,{hash:{},inverse:o.noop,fn:o.program(9,f,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.misc_info,{hash:{},inverse:o.noop,fn:o.program(12,x,C),data:C});if(B||B===0){A+=B}A+='\n
                \n\n
                \n
                \n
                \n
                \n\n ';B=p.unless.call(D,D.deleted,{hash:{},inverse:o.noop,fn:o.program(14,w,C),data:C});if(B||B===0){A+=B}A+="\n\n ";return A}function l(D,C){var A="",B;A+='\n
                \n ';if(B=p.misc_blurb){B=B.call(D,{hash:{},data:C})}else{B=D.misc_blurb;B=typeof B===e?B.apply(D):B}A+=d(B)+"\n
                \n ";return A}function j(E,D){var A="",C,B;A+='\n
                \n \n ';if(C=p.data_type){C=C.call(E,{hash:{},data:D})}else{C=E.data_type;C=typeof C===e?C.apply(E):C}A+=d(C)+"\n
                \n ";return A}function i(B,A){return"format"}function f(E,D){var A="",C,B;A+='\n
                \n \n \n ';if(C=p.metadata_dbkey){C=C.call(E,{hash:{},data:D})}else{C=E.metadata_dbkey;C=typeof C===e?C.apply(E):C}A+=d(C)+"\n \n
                \n ";return A}function y(B,A){return"database"}function x(D,C){var A="",B;A+='\n
                \n ';if(B=p.misc_info){B=B.call(D,{hash:{},data:C})}else{B=D.misc_info;B=typeof B===e?B.apply(D):B}A+=d(B)+"\n
                \n ";return A}function w(D,C){var A="",B;A+='\n
                \n
                \n\n
                \n ';B=p.each.call(D,D.display_apps,{hash:{},inverse:o.noop,fn:o.program(15,v,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p.each.call(D,D.display_types,{hash:{},inverse:o.noop,fn:o.program(15,v,C),data:C});if(B||B===0){A+=B}A+='\n
                \n\n
                \n ';B=p["if"].call(D,D.peek,{hash:{},inverse:o.noop,fn:o.program(19,s,C),data:C});if(B||B===0){A+=B}A+="\n
                \n\n ";return A}function v(D,C){var A="",B;A+='\n
                \n ';if(B=p.label){B=B.call(D,{hash:{},data:C})}else{B=D.label;B=typeof B===e?B.apply(D):B}A+=d(B)+'\n \n ';B=p.each.call(D,D.links,{hash:{},inverse:o.noop,fn:o.program(16,u,C),data:C});if(B||B===0){A+=B}A+="\n \n
                \n ";return A}function u(E,D){var A="",C,B;A+='\n ';B={hash:{},inverse:o.noop,fn:o.program(17,t,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+="\n ";return A}function t(C,B){var A;if(A=p.text){A=A.call(C,{hash:{},data:B})}else{A=C.text;A=typeof A===e?A.apply(C):A}return d(A)}function s(D,C){var A="",B;A+='\n 
                ';if(B=p.peek){B=B.call(D,{hash:{},data:C})}else{B=D.peek;B=typeof B===e?B.apply(D):B}if(B||B===0){A+=B}A+="
                \n ";return A}q+='
                \n ';h=p["if"].call(r,r.body,{hash:{},inverse:o.program(3,m,z),fn:o.program(1,n,z),data:z});if(h||h===0){q+=h}q+="\n
                ";return q})})(); \ No newline at end of file diff --git a/static/scripts/packed/templates/compiled/template-history-historyPanel.js b/static/scripts/packed/templates/compiled/template-history-historyPanel.js index 46967e279fe..39d63bc385d 100644 --- a/static/scripts/packed/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/packed/templates/compiled/template-history-historyPanel.js @@ -1 +1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(h,t,r,m,z){this.compilerInfo=[4,">= 1.0.0"];r=this.merge(r,h.helpers);z=z||{};var s="",j,f,q=this,e="function",c=r.blockHelperMissing,d=this.escapeExpression;function p(E,D){var A="",C,B;A+='\n
                \n ';if(C=r.name){C=C.call(E,{hash:{},data:D})}else{C=E.name;C=typeof C===e?C.apply(E):C}A+=d(C)+"\n
                \n ";return A}function o(B,A){return"Click to rename history"}function n(D,C){var A="",B;A+='\n
                ';if(B=r.nice_size){B=B.call(D,{hash:{},data:C})}else{B=D.nice_size;B=typeof B===e?B.apply(D):B}A+=d(B)+"
                \n ";return A}function l(E,D){var A="",C,B;A+='\n
                \n ';B={hash:{},inverse:q.noop,fn:q.program(7,k,D),data:D};if(C=r.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!r.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+="\n
                \n ";return A}function k(B,A){return"You are currently viewing a deleted history!"}function g(D,C){var A="",B;A+='\n \n
                ';if(B=r.message){B=B.call(D,{hash:{},data:C})}else{B=D.message;B=typeof B===e?B.apply(D):B}A+=d(B)+"
                \n ";return A}function y(B,A){return"You are over your disk quota"}function x(B,A){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function w(B,A){return"Annotation"}function v(B,A){return"Click to edit annotation"}function u(C,B){var A;if(A=r.annotation){A=A.call(C,{hash:{},data:B})}else{A=C.annotation;A=typeof A===e?A.apply(C):A}return d(A)}function i(B,A){return"Your history is empty. Click 'Get Data' on the left pane to start"}s+='
                \n\n
                \n ';j=r["if"].call(t,t.name,{hash:{},inverse:q.noop,fn:q.program(1,p,z),data:z});if(j||j===0){s+=j}s+='\n
                \n\n
                \n ';j=r["if"].call(t,t.nice_size,{hash:{},inverse:q.noop,fn:q.program(4,n,z),data:z});if(j||j===0){s+=j}s+='\n\n
                \n
                \n
                \n\n ';j=r["if"].call(t,t.deleted,{hash:{},inverse:q.noop,fn:q.program(6,l,z),data:z});if(j||j===0){s+=j}s+='\n\n
                \n ';j=r["if"].call(t,t.message,{hash:{},inverse:q.noop,fn:q.program(9,g,z),data:z});if(j||j===0){s+=j}s+='\n
                \n\n
                \n ';f={hash:{},inverse:q.noop,fn:q.program(11,y,z),data:z};if(j=r.local){j=j.call(t,f)}else{j=t.local;j=typeof j===e?j.apply(t):j}if(!r.local){j=c.call(t,j,f)}if(j||j===0){s+=j}s+=".\n ";f={hash:{},inverse:q.noop,fn:q.program(13,x,z),data:z};if(j=r.local){j=j.call(t,f)}else{j=t.local;j=typeof j===e?j.apply(t):j}if(!r.local){j=c.call(t,j,f)}if(j||j===0){s+=j}s+='.\n
                \n \n \n \n
                \n\n \n
                \n \n
                ';j=r["if"].call(t,t.annotation,{hash:{},inverse:q.noop,fn:q.program(19,u,z),data:z});if(j||j===0){s+=j}s+='
                \n
                \n\n
                \n\n \n
                \n\n
                \n ';f={hash:{},inverse:q.noop,fn:q.program(21,i,z),data:z};if(j=r.local){j=j.call(t,f)}else{j=t.local;j=typeof j===e?j.apply(t):j}if(!r.local){j=c.call(t,j,f)}if(j||j===0){s+=j}s+="\n
                ";return s})})(); \ No newline at end of file +(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-history-historyPanel"]=b(function(h,s,q,l,w){this.compilerInfo=[4,">= 1.0.0"];q=this.merge(q,h.helpers);w=w||{};var r="",i,f,p=this,e="function",c=q.blockHelperMissing,d=this.escapeExpression;function o(B,A){var x="",z,y;x+='\n
                \n ';if(z=q.name){z=z.call(B,{hash:{},data:A})}else{z=B.name;z=typeof z===e?z.apply(B):z}x+=d(z)+"\n
                \n ";return x}function n(y,x){return"Click to rename history"}function m(A,z){var x="",y;x+='\n
                ';if(y=q.nice_size){y=y.call(A,{hash:{},data:z})}else{y=A.nice_size;y=typeof y===e?y.apply(A):y}x+=d(y)+"
                \n ";return x}function k(B,A){var x="",z,y;x+='\n
                \n ';y={hash:{},inverse:p.noop,fn:p.program(7,j,A),data:A};if(z=q.local){z=z.call(B,y)}else{z=B.local;z=typeof z===e?z.apply(B):z}if(!q.local){z=c.call(B,z,y)}if(z||z===0){x+=z}x+="\n
                \n ";return x}function j(y,x){return"You are currently viewing a deleted history!"}function g(A,z){var x="",y;x+='\n \n
                ';if(y=q.message){y=y.call(A,{hash:{},data:z})}else{y=A.message;y=typeof y===e?y.apply(A):y}x+=d(y)+"
                \n ";return x}function v(y,x){return"You are over your disk quota"}function u(y,x){return"Tool execution is on hold until your disk usage drops below your allocated quota"}function t(y,x){return"Your history is empty. Click 'Get Data' on the left pane to start"}r+='
                \n\n
                \n ';i=q["if"].call(s,s.name,{hash:{},inverse:p.noop,fn:p.program(1,o,w),data:w});if(i||i===0){r+=i}r+='\n
                \n\n
                \n ';i=q["if"].call(s,s.nice_size,{hash:{},inverse:p.noop,fn:p.program(4,m,w),data:w});if(i||i===0){r+=i}r+='\n\n
                \n
                \n
                \n\n ';i=q["if"].call(s,s.deleted,{hash:{},inverse:p.noop,fn:p.program(6,k,w),data:w});if(i||i===0){r+=i}r+='\n\n
                \n ';i=q["if"].call(s,s.message,{hash:{},inverse:p.noop,fn:p.program(9,g,w),data:w});if(i||i===0){r+=i}r+='\n
                \n\n
                \n ';f={hash:{},inverse:p.noop,fn:p.program(11,v,w),data:w};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+=".\n ";f={hash:{},inverse:p.noop,fn:p.program(13,u,w),data:w};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='.\n
                \n \n
                \n
                \n\n
                \n\n \n
                \n\n
                \n ';f={hash:{},inverse:p.noop,fn:p.program(15,t,w),data:w};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+="\n
                ";return r})})(); \ No newline at end of file diff --git a/static/scripts/templates/compiled/history-templates.js b/static/scripts/templates/compiled/history-templates.js index bf861c2ae76..d119a8f5933 100644 --- a/static/scripts/templates/compiled/history-templates.js +++ b/static/scripts/templates/compiled/history-templates.js @@ -106,63 +106,33 @@ function program12(depth0,data) { function program14(depth0,data) { - var buffer = "", stack1, options; - buffer += "\n " - + "\n
                \n\n " - + "\n
                \n \n
                \n
                \n\n
                \n "; - stack1 = helpers.each.call(depth0, depth0.display_apps, {hash:{},inverse:self.noop,fn:self.program(19, program19, data),data:data}); + var buffer = "", stack1; + buffer += "\n
                \n
                \n\n
                \n "; + stack1 = helpers.each.call(depth0, depth0.display_apps, {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n "; - stack1 = helpers.each.call(depth0, depth0.display_types, {hash:{},inverse:self.noop,fn:self.program(19, program19, data),data:data}); + stack1 = helpers.each.call(depth0, depth0.display_types, {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n
                \n\n
                \n "; - stack1 = helpers['if'].call(depth0, depth0.peek, {hash:{},inverse:self.noop,fn:self.program(23, program23, data),data:data}); + stack1 = helpers['if'].call(depth0, depth0.peek, {hash:{},inverse:self.noop,fn:self.program(19, program19, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n
                \n\n "; return buffer; } function program15(depth0,data) { - - return "Annotation"; - } - -function program17(depth0,data) { - - - return "Edit dataset annotation"; - } - -function program19(depth0,data) { - var buffer = "", stack1; buffer += "\n
                \n "; if (stack1 = helpers.label) { stack1 = stack1.call(depth0, {hash:{},data:data}); } else { stack1 = depth0.label; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } buffer += escapeExpression(stack1) + "\n \n "; - stack1 = helpers.each.call(depth0, depth0.links, {hash:{},inverse:self.noop,fn:self.program(20, program20, data),data:data}); + stack1 = helpers.each.call(depth0, depth0.links, {hash:{},inverse:self.noop,fn:self.program(16, program16, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n \n
                \n "; return buffer; } -function program20(depth0,data) { +function program16(depth0,data) { var buffer = "", stack1, options; buffer += "\n "; - options = {hash:{},inverse:self.noop,fn:self.program(21, program21, data),data:data}; + options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } @@ -182,7 +152,7 @@ function program20(depth0,data) { buffer += "\n "; return buffer; } -function program21(depth0,data) { +function program17(depth0,data) { var stack1; if (stack1 = helpers.text) { stack1 = stack1.call(depth0, {hash:{},data:data}); } @@ -190,7 +160,7 @@ function program21(depth0,data) { return escapeExpression(stack1); } -function program23(depth0,data) { +function program19(depth0,data) { var buffer = "", stack1; buffer += "\n 
                ";
@@ -209,352 +179,6 @@ function program23(depth0,data) {
   });
 })();(function() {
   var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
-templates['template-hda-body'] = template(function (Handlebars,depth0,helpers,partials,data) {
-  this.compilerInfo = [4,'>= 1.0.0'];
-helpers = this.merge(helpers, Handlebars.helpers); data = data || {};
-  var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing;
-
-function program1(depth0,data) {
-  
-  var buffer = "", stack1;
-  buffer += "\n    
                \n        ";
-  if (stack1 = helpers.body) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.body; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n    
                \n    
                \n        
                \n        
                \n    
                \n\n    ";
-  return buffer;
-  }
-
-function program3(depth0,data) {
-  
-  var buffer = "", stack1;
-  buffer += "\n    
                \n        ";
-  stack1 = helpers['if'].call(depth0, depth0.misc_blurb, {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n\n        ";
-  stack1 = helpers['if'].call(depth0, depth0.data_type, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n\n        ";
-  stack1 = helpers['if'].call(depth0, depth0.metadata_dbkey, {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n\n        ";
-  stack1 = helpers['if'].call(depth0, depth0.misc_info, {hash:{},inverse:self.noop,fn:self.program(12, program12, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n    
                "
-    + "\n\n    
                \n        
                \n        
                \n    
                \n\n    ";
-  stack1 = helpers.unless.call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n\n    ";
-  return buffer;
-  }
-function program4(depth0,data) {
-  
-  var buffer = "", stack1;
-  buffer += "\n        
                \n            ";
-  if (stack1 = helpers.misc_blurb) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.misc_blurb; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  buffer += escapeExpression(stack1)
-    + "\n        
                \n        ";
-  return buffer;
-  }
-
-function program6(depth0,data) {
-  
-  var buffer = "", stack1, options;
-  buffer += "\n        
                \n            \n            ";
-  if (stack1 = helpers.data_type) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.data_type; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  buffer += escapeExpression(stack1)
-    + "\n        
                \n        ";
-  return buffer;
-  }
-function program7(depth0,data) {
-  
-  
-  return "format";
-  }
-
-function program9(depth0,data) {
-  
-  var buffer = "", stack1, options;
-  buffer += "\n        
                \n            \n            \n                ";
-  if (stack1 = helpers.metadata_dbkey) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.metadata_dbkey; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  buffer += escapeExpression(stack1)
-    + "\n            \n        
                \n        ";
-  return buffer;
-  }
-function program10(depth0,data) {
-  
-  
-  return "database";
-  }
-
-function program12(depth0,data) {
-  
-  var buffer = "", stack1;
-  buffer += "\n        
                \n            ";
-  if (stack1 = helpers.misc_info) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.misc_info; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  buffer += escapeExpression(stack1)
-    + "\n        
                \n        ";
-  return buffer;
-  }
-
-function program14(depth0,data) {
-  
-  var buffer = "", stack1, options;
-  buffer += "\n    "
-    + "\n    
                \n        \n        
                \n    
                \n\n    "
-    + "\n    
                \n        \n        
                \n    
                \n\n    
                \n        ";
-  stack1 = helpers.each.call(depth0, depth0.display_apps, {hash:{},inverse:self.noop,fn:self.program(21, program21, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n\n        ";
-  stack1 = helpers.each.call(depth0, depth0.display_types, {hash:{},inverse:self.noop,fn:self.program(21, program21, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n    
                \n\n    
                \n    ";
-  stack1 = helpers['if'].call(depth0, depth0.peek, {hash:{},inverse:self.noop,fn:self.program(25, program25, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n    
                \n\n    ";
-  return buffer;
-  }
-function program15(depth0,data) {
-  
-  
-  return "Tags";
-  }
-
-function program17(depth0,data) {
-  
-  
-  return "Annotation";
-  }
-
-function program19(depth0,data) {
-  
-  
-  return "Edit dataset annotation";
-  }
-
-function program21(depth0,data) {
-  
-  var buffer = "", stack1;
-  buffer += "\n        
                \n            ";
-  if (stack1 = helpers.label) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.label; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  buffer += escapeExpression(stack1)
-    + "\n            \n                ";
-  stack1 = helpers.each.call(depth0, depth0.links, {hash:{},inverse:self.noop,fn:self.program(22, program22, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n            \n        
                \n        ";
-  return buffer;
-  }
-function program22(depth0,data) {
-  
-  var buffer = "", stack1, options;
-  buffer += "\n                ";
-  options = {hash:{},inverse:self.noop,fn:self.program(23, program23, data),data:data};
-  if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); }
-  else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); }
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n                ";
-  return buffer;
-  }
-function program23(depth0,data) {
-  
-  var stack1;
-  if (stack1 = helpers.text) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.text; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  return escapeExpression(stack1);
-  }
-
-function program25(depth0,data) {
-  
-  var buffer = "", stack1;
-  buffer += "\n        
                ";
-  if (stack1 = helpers.peek) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.peek; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "
                \n    ";
-  return buffer;
-  }
-
-  buffer += "
                \n    ";
-  stack1 = helpers['if'].call(depth0, depth0.body, {hash:{},inverse:self.program(3, program3, data),fn:self.program(1, program1, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n
                ";
-  return buffer;
-  });
-})();(function() {
-  var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
-templates['template-hda-skeleton'] = template(function (Handlebars,depth0,helpers,partials,data) {
-  this.compilerInfo = [4,'>= 1.0.0'];
-helpers = this.merge(helpers, Handlebars.helpers); data = data || {};
-  var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing;
-
-function program1(depth0,data) {
-  
-  var buffer = "", stack1, options;
-  buffer += "\n        
                \n            ";
-  options = {hash:{},inverse:self.noop,fn:self.program(2, program2, data),data:data};
-  if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); }
-  else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); }
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += ":\n            ";
-  options = {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data};
-  if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); }
-  else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); }
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n        
                \n        ";
-  return buffer;
-  }
-function program2(depth0,data) {
-  
-  
-  return "There was an error getting the data for this dataset";
-  }
-
-function program4(depth0,data) {
-  
-  var stack1;
-  if (stack1 = helpers.error) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.error; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  return escapeExpression(stack1);
-  }
-
-function program6(depth0,data) {
-  
-  var buffer = "", stack1;
-  buffer += "\n            ";
-  stack1 = helpers['if'].call(depth0, depth0.purged, {hash:{},inverse:self.program(10, program10, data),fn:self.program(7, program7, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n        ";
-  return buffer;
-  }
-function program7(depth0,data) {
-  
-  var buffer = "", stack1, options;
-  buffer += "\n            
                \n                ";
-  options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data};
-  if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); }
-  else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); }
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n            
                \n\n            ";
-  return buffer;
-  }
-function program8(depth0,data) {
-  
-  
-  return "This dataset has been deleted and removed from disk.";
-  }
-
-function program10(depth0,data) {
-  
-  var buffer = "", stack1, options;
-  buffer += "\n            
                \n                ";
-  options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data};
-  if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); }
-  else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); }
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n                "
-    + "\n                "
-    + "\n                Click here to undelete it\n                or here to immediately remove it from disk\n            
                \n            ";
-  return buffer;
-  }
-function program11(depth0,data) {
-  
-  
-  return "This dataset has been deleted.";
-  }
-
-function program13(depth0,data) {
-  
-  var buffer = "", stack1, options;
-  buffer += "\n        
                \n            ";
-  options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data};
-  if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); }
-  else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); }
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n            "
-    + "\n            Click here to unhide it\n        
                \n        ";
-  return buffer;
-  }
-function program14(depth0,data) {
-  
-  
-  return "This dataset has been hidden.";
-  }
-
-  buffer += "
                \n    
                \n        ";
-  stack1 = helpers['if'].call(depth0, depth0.error, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n\n        ";
-  stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n\n        ";
-  stack1 = helpers.unless.call(depth0, depth0.visible, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data});
-  if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += "\n    
                \n\n    
                \n    
                \n        \n        
                \n            ";
-  if (stack1 = helpers.hid) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  buffer += escapeExpression(stack1)
-    + "\n            ";
-  if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  buffer += escapeExpression(stack1)
-    + "\n        
                \n    
                \n\n    
                \n
                ";
-  return buffer;
-  });
-})();(function() {
-  var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {};
 templates['template-hda-skeleton'] = template(function (Handlebars,depth0,helpers,partials,data) {
   this.compilerInfo = [4,'>= 1.0.0'];
 helpers = this.merge(helpers, Handlebars.helpers); data = data || {};
@@ -874,26 +498,6 @@ function program13(depth0,data) {
 function program15(depth0,data) {
   
   
-  return "Annotation";
-  }
-
-function program17(depth0,data) {
-  
-  
-  return "Click to edit annotation";
-  }
-
-function program19(depth0,data) {
-  
-  var stack1;
-  if (stack1 = helpers.annotation) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  return escapeExpression(stack1);
-  }
-
-function program21(depth0,data) {
-  
-  
   return "Your history is empty. Click 'Get Data' on the left pane to start";
   }
 
@@ -921,231 +525,14 @@ function program21(depth0,data) {
   else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
   if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); }
   if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += ".\n
                \n \n " - + "\n " - + "\n
                \n\n " - + "\n
                \n \n
                "; - stack1 = helpers['if'].call(depth0, depth0.annotation, {hash:{},inverse:self.noop,fn:self.program(19, program19, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "
                \n
                \n\n
                " + buffer += ".\n
                \n \n
                \n
                \n\n
                " + "\n\n " + "\n
                \n\n
                \n "; - options = {hash:{},inverse:self.noop,fn:self.program(21, program21, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n
                "; - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, self=this, functionType="function", blockHelperMissing=helpers.blockHelperMissing, escapeExpression=this.escapeExpression; - -function program1(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n
                \n "; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n
                \n "; - return buffer; - } -function program2(depth0,data) { - - - return "Click to rename history"; - } - -function program4(depth0,data) { - - var buffer = "", stack1; - buffer += "\n
                "; - if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "
                \n "; - return buffer; - } - -function program6(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n
                \n "; - options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n
                \n "; - return buffer; - } -function program7(depth0,data) { - - - return "You are currently viewing a deleted history!"; - } - -function program9(depth0,data) { - - var buffer = "", stack1; - buffer += "\n " - + "\n
                "; - if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "
                \n "; - return buffer; - } - -function program11(depth0,data) { - - - return "You are over your disk quota"; - } - -function program13(depth0,data) { - - - return "Tool execution is on hold until your disk usage drops below your allocated quota"; - } - -function program15(depth0,data) { - - - return "Tags"; - } - -function program17(depth0,data) { - - - return "Annotation"; - } - -function program19(depth0,data) { - - - return "Click to edit annotation"; - } - -function program21(depth0,data) { - - var buffer = "", stack1; - buffer += "\n "; - if (stack1 = helpers.annotation) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n "; - return buffer; - } - -function program23(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n "; - options = {hash:{},inverse:self.noop,fn:self.program(24, program24, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - return buffer; - } -function program24(depth0,data) { - - - return "Describe or add notes to history"; - } - -function program26(depth0,data) { - - - return "Your history is empty. Click 'Get Data' on the left pane to start"; - } - - buffer += "
                \n\n
                \n "; - stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n
                \n\n
                \n "; - stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n
                \n
                \n
                \n\n "; - stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n
                \n "; - stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n
                \n\n
                \n "; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n "; - options = {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n
                \n \n " - + "\n " - + "\n
                \n \n
                \n
                \n\n " - + "\n
                \n \n
                \n "; - stack1 = helpers['if'].call(depth0, depth0.annotation, {hash:{},inverse:self.program(23, program23, data),fn:self.program(21, program21, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n
                \n
                \n\n
                " - + "\n\n " - + "\n
                \n\n
                \n "; - options = {hash:{},inverse:self.noop,fn:self.program(26, program26, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n
                "; return buffer; }); diff --git a/static/scripts/templates/compiled/template-hda-body.js b/static/scripts/templates/compiled/template-hda-body.js index 0fd190fc8fb..388d122a09c 100644 --- a/static/scripts/templates/compiled/template-hda-body.js +++ b/static/scripts/templates/compiled/template-hda-body.js @@ -106,63 +106,33 @@ function program12(depth0,data) { function program14(depth0,data) { - var buffer = "", stack1, options; - buffer += "\n " - + "\n
                \n\n " - + "\n
                \n \n
                \n
                \n\n
                \n "; - stack1 = helpers.each.call(depth0, depth0.display_apps, {hash:{},inverse:self.noop,fn:self.program(19, program19, data),data:data}); + var buffer = "", stack1; + buffer += "\n
                \n
                \n\n
                \n "; + stack1 = helpers.each.call(depth0, depth0.display_apps, {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n "; - stack1 = helpers.each.call(depth0, depth0.display_types, {hash:{},inverse:self.noop,fn:self.program(19, program19, data),data:data}); + stack1 = helpers.each.call(depth0, depth0.display_types, {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n
                \n\n
                \n "; - stack1 = helpers['if'].call(depth0, depth0.peek, {hash:{},inverse:self.noop,fn:self.program(23, program23, data),data:data}); + stack1 = helpers['if'].call(depth0, depth0.peek, {hash:{},inverse:self.noop,fn:self.program(19, program19, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n
                \n\n "; return buffer; } function program15(depth0,data) { - - return "Annotation"; - } - -function program17(depth0,data) { - - - return "Edit dataset annotation"; - } - -function program19(depth0,data) { - var buffer = "", stack1; buffer += "\n
                \n "; if (stack1 = helpers.label) { stack1 = stack1.call(depth0, {hash:{},data:data}); } else { stack1 = depth0.label; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } buffer += escapeExpression(stack1) + "\n \n "; - stack1 = helpers.each.call(depth0, depth0.links, {hash:{},inverse:self.noop,fn:self.program(20, program20, data),data:data}); + stack1 = helpers.each.call(depth0, depth0.links, {hash:{},inverse:self.noop,fn:self.program(16, program16, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n \n
                \n "; return buffer; } -function program20(depth0,data) { +function program16(depth0,data) { var buffer = "", stack1, options; buffer += "\n "; - options = {hash:{},inverse:self.noop,fn:self.program(21, program21, data),data:data}; + options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } @@ -182,7 +152,7 @@ function program20(depth0,data) { buffer += "\n "; return buffer; } -function program21(depth0,data) { +function program17(depth0,data) { var stack1; if (stack1 = helpers.text) { stack1 = stack1.call(depth0, {hash:{},data:data}); } @@ -190,7 +160,7 @@ function program21(depth0,data) { return escapeExpression(stack1); } -function program23(depth0,data) { +function program19(depth0,data) { var buffer = "", stack1; buffer += "\n 
                ";
diff --git a/static/scripts/templates/compiled/template-history-historyPanel.js b/static/scripts/templates/compiled/template-history-historyPanel.js
index 12a80b45d07..8f93a3fe09e 100644
--- a/static/scripts/templates/compiled/template-history-historyPanel.js
+++ b/static/scripts/templates/compiled/template-history-historyPanel.js
@@ -87,26 +87,6 @@ function program13(depth0,data) {
 function program15(depth0,data) {
   
   
-  return "Annotation";
-  }
-
-function program17(depth0,data) {
-  
-  
-  return "Click to edit annotation";
-  }
-
-function program19(depth0,data) {
-  
-  var stack1;
-  if (stack1 = helpers.annotation) { stack1 = stack1.call(depth0, {hash:{},data:data}); }
-  else { stack1 = depth0.annotation; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
-  return escapeExpression(stack1);
-  }
-
-function program21(depth0,data) {
-  
-  
   return "Your history is empty. Click 'Get Data' on the left pane to start";
   }
 
@@ -134,29 +114,10 @@ function program21(depth0,data) {
   else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; }
   if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); }
   if(stack1 || stack1 === 0) { buffer += stack1; }
-  buffer += ".\n
                \n \n " - + "\n " - + "\n
                \n\n " - + "\n
                \n \n
                "; - stack1 = helpers['if'].call(depth0, depth0.annotation, {hash:{},inverse:self.noop,fn:self.program(19, program19, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "
                \n
                \n\n
                " + buffer += ".\n
                \n \n
                \n
                \n\n
                " + "\n\n " + "\n
                \n\n
                \n "; - options = {hash:{},inverse:self.noop,fn:self.program(21, program21, data),data:data}; + options = {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}; if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } diff --git a/static/scripts/templates/hda-templates.html b/static/scripts/templates/hda-templates.html index ea48b2db619..3cc41486dbd 100644 --- a/static/scripts/templates/hda-templates.html +++ b/static/scripts/templates/hda-templates.html @@ -97,15 +97,8 @@
                {{#unless deleted }} - {{! TODO: move to mvc/tag.js }}
                - - {{! TODO: move to mvc/annotations.js }} -
                - -
                -
                +
                {{#each display_apps}} diff --git a/static/scripts/templates/history-templates.html b/static/scripts/templates/history-templates.html index 9f2583ff6c5..c701e3ffbf2 100644 --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -38,17 +38,8 @@ {{#local}}Tool execution is on hold until your disk usage drops below your allocated quota{{/local}}.
                - {{! tags and annotations }} - {{! TODO: move to mvc/tag.js }}
                - - {{! TODO: move to mvc/annotations.js }} -
                - -
                {{#if annotation}}{{annotation}}{{/if}}
                -
                +
                {{! end history-controls }} diff --git a/static/style/blue/base.css b/static/style/blue/base.css index f534ad7267e..95e2cb33b7b 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1517,7 +1517,7 @@ div.permissionContainer{padding-left:20px} .history-panel .message-container [class$=message]{margin:0px} .history-panel .history-controls{margin:10px;padding:0px}.history-panel .history-controls .history-title{margin-bottom:4px} .history-panel .history-controls .history-name{word-wrap:break-word;font-weight:bold} -.history-panel .history-controls .history-title input{font-weight:bold;margin:-2px 0 -2px -4px} +.history-panel .history-controls .history-title input{font-weight:bold;width:100%;margin:-2px 0 -2px -4px} .history-panel .history-controls .history-subtitle{margin-bottom:8px} .history-panel .history-controls .history-size{float:left} .history-panel .history-controls .history-secondary-actions{float:right}.history-panel .history-controls .history-secondary-actions .icon-btn{margin-left:2px} @@ -1526,7 +1526,9 @@ div.permissionContainer{padding-left:20px} .history-panel .history-controls .tags-display label:after,.history-panel .history-controls .annotation-display label:after{content:':'} .history-panel .history-controls .tags-display .select2-container{min-width:0px}.history-panel .history-controls .tags-display .select2-container .select2-choices{border-radius:3px} .history-panel .history-controls .tags-display input{border-radius:3px} -.history-panel .history-controls .annotation-display .annotation{border-radius:3px;border:1px solid fadout(#999, 50%);padding:4px;white-space:pre-line} +.history-panel .history-controls .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.5);padding:4px;white-space:pre-line} +.history-panel .history-controls .annotation-display .annotation:empty{height:20px} +.history-panel .history-controls .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} .history-panel .history-controls .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} .history-panel .dataset{border-width:1px 0px 0px 0px} .history-panel .dataset:last-child{border-width:1px 0px 1px 0px} @@ -1536,6 +1538,7 @@ div.permissionContainer{padding-left:20px} .dataset .info-section{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px} .dataset .dataset-padding{padding:6px 10px 6px 8px} .dataset [class$=messagesmall]{margin:6px 10px 2px 8px;font-size:90%} +.dataset .help-text{font-weight:normal;font-style:italic;font-size:90%;color:#555} .dataset .dataset-title-bar{cursor:pointer;padding:6px 10px 6px 8px} .dataset .dataset-title-bar .dataset-title{display:inline;font-weight:bold;text-decoration:underline;word-break:normal;line-height:16px} .dataset .dataset-primary-actions{float:right;margin:6px 10px 0}.dataset .dataset-primary-actions .icon-btn{margin-left:2px} @@ -1545,15 +1548,18 @@ div.permissionContainer{padding-left:20px} .dataset .dataset-body .prompt:after{content:':'} .dataset .dataset-body .dataset-summary{margin-bottom:8px}.dataset .dataset-body .dataset-summary .dataset-blurb{margin-bottom:2px} .dataset .dataset-body .dataset-summary .dataset-datatype,.dataset .dataset-body .dataset-summary .dataset-dbkey{display:inline}.dataset .dataset-body .dataset-summary .dataset-datatype .value,.dataset .dataset-body .dataset-summary .dataset-dbkey .value{font-weight:bold} -.dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:','} +.dataset .dataset-body .dataset-summary .dataset-datatype .value:after{content:',';font-weight:normal;font-style:italic;font-size:90%;color:#555} .dataset .dataset-body .dataset-summary .dataset-dbkey:after{content:' ';display:block;margin-bottom:8px} .dataset .dataset-body .dataset-summary .dataset-info{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px}.dataset .dataset-body .dataset-summary .dataset-info .value{white-space:pre-line} +.dataset .dataset-body .dataset-summary .job-error-text{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;overflow:auto;white-space:pre} .dataset .dataset-body .dataset-actions .left{float:left}.dataset .dataset-body .dataset-actions .left .icon-btn{margin-right:2px} .dataset .dataset-body .dataset-actions .left .icon-btn-group{margin-right:2px}.dataset .dataset-body .dataset-actions .left .icon-btn-group .icon-btn{margin-right:0} .dataset .dataset-body .dataset-actions .left:not(:empty){margin-bottom:8px} .dataset .dataset-body .dataset-actions .right{float:right}.dataset .dataset-body .dataset-actions .right .icon-btn{margin-left:2px} .dataset .dataset-body .tags-display{display:none;margin-bottom:8px}.dataset .dataset-body .tags-display .select2-container{min-width:0px}.dataset .dataset-body .tags-display .select2-container .select2-choices{border-radius:3px} .dataset .dataset-body .annotation-display{display:none;margin-bottom:8px}.dataset .dataset-body .annotation-display .annotation{border-radius:3px;border:1px solid rgba(153,153,153,0.30000000000000004);padding:4px;white-space:pre-line} +.dataset .dataset-body .annotation-display .annotation:empty{height:20px} +.dataset .dataset-body .annotation-display .annotation:empty:after{position:relative;top:-4px;font-size:10px;font-style:italic;color:grey;content:'Click here to edit annotation'} .dataset .dataset-body .annotation-display textarea{margin:0px 0px 2px 0px;display:block;border-radius:3px;width:100%} .dataset .dataset-body .dataset-display-applications .display-application:last-child{margin-bottom:8px} .dataset .dataset-body .dataset-peek{margin-bottom:8px}.dataset .dataset-body .dataset-peek pre.peek{width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset .dataset-body .dataset-peek pre.peek th{color:white;background:#5f6990} diff --git a/static/style/src/less/history.less b/static/style/src/less/history.less index 3d6992776a4..5ee5c02106f 100644 --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -95,6 +95,7 @@ } .history-title input { font-weight: bold; + width: 100%; // keep the text in position margin: -2px 0px -2px -4px; } @@ -148,10 +149,22 @@ .annotation-display { .annotation { border-radius: 3px; - border: 1px solid fadout( @layout-border-color, 50% ); + border: 1px solid fadeout( @layout-border-color, 50% ); padding: 4px; white-space: pre-line; } + .annotation:empty { + height: @icon-btn-size; + } + // fake placeholder for editable text annotation + .annotation:empty:after { + position: relative; + top: -4px; + font-size: 10px; + font-style: italic; + color: grey; + content : 'Click here to edit annotation'; + } textarea { margin: 0px 0px 2px 0px; display: block; @@ -221,6 +234,13 @@ font-size: 90%; } + .help-text { + font-weight: normal; + font-style: italic; + font-size: 90%; + color: #555; + } + .dataset-title-bar { cursor: pointer; .dataset-padding; @@ -265,10 +285,7 @@ font-weight: normal; } .prompt { - font-weight: normal; - font-style: italic; - font-size: 90%; - color: #555; + .help-text; } .prompt:after { content: ':'; @@ -286,6 +303,7 @@ } .dataset-datatype .value:after { content: ','; + .help-text; } .dataset-dbkey:after { content: ' '; @@ -298,6 +316,13 @@ white-space: pre-line; } } + + .job-error-text { + .info-section; + overflow: auto; + white-space: pre; + } + // handle the last vertical gap in the parent as summary is used in other states as well (w/o info) .vertical-spacing; } @@ -346,6 +371,18 @@ .info-section; white-space: pre-line; } + .annotation:empty { + height: @icon-btn-size; + } + // fake placeholder for editable text annotation + .annotation:empty:after { + position: relative; + top: -4px; + font-size: 10px; + font-style: italic; + color: grey; + content : 'Click here to edit annotation'; + } textarea { margin: 0px 0px 2px 0px; display: block; diff --git a/templates/webapps/galaxy/galaxy.masthead.mako b/templates/webapps/galaxy/galaxy.masthead.mako index 960ef15e27c..3ae0a604fb8 100644 --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -6,7 +6,9 @@ if trans.user: user_dict = trans.user.to_dict( view='element', value_mapper={ 'id': trans.security.encode_id, 'total_disk_usage': float } ) - user_dict['quota_percent'] = trans.app.quota_agent.get_percent( trans=trans ) + user_dict[ 'quota_percent' ] = trans.app.quota_agent.get_percent( trans=trans ) + users_api_controller = trans.webapp.api_controllers[ 'users' ] + user_dict[ 'tags_used' ] = users_api_controller.get_user_tags_used( trans, user=trans.user ) else: usage = 0 percent = None diff --git a/templates/webapps/galaxy/history/history_panel.mako b/templates/webapps/galaxy/history/history_panel.mako index 2cdb60e2d11..9949d63b266 100644 --- a/templates/webapps/galaxy/history/history_panel.mako +++ b/templates/webapps/galaxy/history/history_panel.mako @@ -90,7 +90,7 @@ ${history_panel_javascripts()} ## ----------------------------------------------------------------------------- generic 'base' function <%def name="history_panel_javascripts()"> ${h.js( - "mvc/tags" + "mvc/tags", "mvc/annotations" )} ##TODO: concat these diff --git a/templates/webapps/galaxy/root/history.mako b/templates/webapps/galaxy/root/history.mako index 896c787cd17..73201a76a8f 100644 --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -9,11 +9,6 @@ ## ----------------------------------------------------------------------------- <%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css( - "base", - "history", - "autocomplete_tagging" - )} -## -## Custom grid methods. -## - -<%namespace file="./grid_common.mako" import="*" /> - <%def name="make_grid( grid )">
                @@ -147,7 +261,14 @@ - + @@ -157,7 +278,7 @@ <%def name="grid_title()"> -

                ${grid.title}

                +

                ${self.grid_config['title']}

                ## Render grid header. @@ -166,18 +287,18 @@ %if render_title: ${self.grid_title()} %endif - - %if grid.global_actions: + + %if self.grid_config['global_actions']:
                  - %if len( grid.global_actions ) < 3: - %for action in grid.global_actions: -
                • ${action.label}
                  • + %if len( self.grid_config['global_actions'] ) < 3: + %for action in self.grid_config['global_actions']: +
                • ${action['label']}
                  • %endfor %else:
                • Actions
                  • - %for action in grid.global_actions: - ${action.label} + %for action in self.grid_config['global_actions']: + ${action['label']} %endfor
                  %endif @@ -191,55 +312,37 @@ ## Render grid. <%def name="render_grid_table( grid, show_item_checkboxes=False)"> <% - # Set flag to indicate whether grid has operations that operate on multiple items. - multiple_item_ops_exist = False - for operation in grid.operations: - if operation.allow_multiple: - multiple_item_ops_exist = True - + # get configuration + show_item_checkboxes = self.grid_config['show_item_checkboxes'] + multiple_item_ops_exist = self.grid_config['multiple_item_ops_exist'] + sort_key = self.grid_config['sort_key'] + # Show checkboxes if flag is set or if multiple item ops exist. if show_item_checkboxes or multiple_item_ops_exist: show_item_checkboxes = True %> -
                  +
                ${render_message( message, status )} + %if message: +

                +

                ${self.grid_config['message']}
                +
                +

                + %endif +
                %if show_item_checkboxes: %endif - %for column in grid.columns: - %if column.visible: - <% - href = "" - extra = "" - if column.sortable: - if sort_key.endswith(column.key): - if not sort_key.startswith("-"): - href = url( sort=( "-" + column.key ) ) - extra = "↓" - else: - href = url( sort=( column.key ) ) - extra = "↑" - else: - href = url( sort=column.key ) - %> + %for column in self.grid_config['columns']: + %if column['visible']: 1: - colspan="${column.ncells}" - %endif + id="${column['key']}-header" > - %if href: - ${column.label} + %if column['href']: + ${column['label']} %else: - ${column.label} + ${column['label']} %endif - ${extra} + ${column['extra']} %endif %endfor @@ -259,15 +362,16 @@ ## Render grid table body contents. <%def name="render_grid_table_body_contents(grid, show_item_checkboxes=False)"> <% num_rows_rendered = 0 %> - %if query.count() == 0: + %if len(self.grid_config['items']) == 0: ## No results. <% num_rows_rendered = 1 %> %endif - %for i, item in enumerate( query ): - <% encoded_id = trans.security.encode_id( item.id ) %> + %for i, item in enumerate( self.grid_config['items'] ): + <% encoded_id = item['encode_id'] %> + <% popupmenu_id = "grid-" + str(i) + "-popup" %> @@ -278,71 +382,72 @@ %endif ## Data columns - %for column in grid.columns: - %if column.visible: + %for column in self.grid_config['columns']: + %if column['visible']: <% - # Nowrap + ## Nowrap nowrap = "" - if column.nowrap: - nowrap = 'style="white-space:nowrap;"' - # Link - link = column.get_link( trans, grid, item ) - if link: - href = url( **link ) - else: - href = None - # Value (coerced to list so we can loop) - value = column.get_value( trans, grid, item ) - if column.ncells == 1: - value = [ value ] - %> - %for cellnum, v in enumerate( value ): - <% - id = "" - # Handle non-ascii chars. - if isinstance(v, str): - v = unicode(v, 'utf-8') - # Attach popup menu? - if column.attach_popup and cellnum == 0: - id = 'grid-%d-popup' % i - # Determine appropriate class - cls = "" - if column.attach_popup: - cls = "menubutton" - if href: - cls += " split" + if column['nowrap']: + nowrap = 'style="white-space:nowrap;"' - %> - - %endfor + ${value} + %if len(self.grid_config['operations']) != 0: + + %endif + %else: +
                + %endif + %endif %endfor ## Actions column <% num_rows_rendered += 1 %> %endfor - ## Dummy rows to prevent table for moving too much. - ##%if grid.use_paging: - ## %for i in range( num_rows_rendered , grid.num_rows_per_page ): - ## - ## %endfor - ##%endif ## Render grid table footer contents. <%def name="render_grid_table_footer_contents(grid, show_item_checkboxes=False)"> - ## Row for navigating among pages. - <%namespace file="/display_common.mako" import="get_class_plural" /> - <% items_plural = get_class_plural( grid.model_class ).lower() %> - %if grid.use_paging and num_pages > 1: + <% + items_plural = self.grid_config['get_class_plural'] + num_pages = self.grid_config['num_pages'] + cur_page_num = self.grid_config['cur_page_num'] + %> + %if self.grid_config['use_paging'] and num_pages > 1: %if show_item_checkboxes: @@ -438,33 +539,29 @@ %endif - %if len([o for o in grid.operations if o.global_operation]) > 0: + %if len([o for o in self.grid_config['operations'] if o['global_operation']]) > 0: %endif - %if grid.legend: + %if self.grid_config['legend']: %endif diff --git a/templates/grid_base_async.mako b/templates/grid_base_async.mako index 4ef1792da0e..2f03c0bd673 100644 --- a/templates/grid_base_async.mako +++ b/templates/grid_base_async.mako @@ -1,6 +1,8 @@ <%namespace file="./grid_base.mako" import="*" /> <%namespace file="/display_common.mako" import="render_message" /> +${init()} + <% # Set flag to indicate whether grid has operations that operate on multiple items. multiple_item_ops_exist = False diff --git a/templates/webapps/galaxy/page/select_items_grid.mako b/templates/webapps/galaxy/page/select_items_grid.mako index 0e5cfe131af..7513cdeefc0 100644 --- a/templates/webapps/galaxy/page/select_items_grid.mako +++ b/templates/webapps/galaxy/page/select_items_grid.mako @@ -1,6 +1,6 @@ ## Template generates a grid that enables user to select items. <%namespace file="../grid_base.mako" import="*" /> - +${init()} ${grid_javascripts()} ${stylesheets()} ${render_grid_header( grid, False )} diff --git a/templates/webapps/galaxy/page/select_items_grid_async.mako b/templates/webapps/galaxy/page/select_items_grid_async.mako index cc04fd4be97..5bfacdf16c3 100644 --- a/templates/webapps/galaxy/page/select_items_grid_async.mako +++ b/templates/webapps/galaxy/page/select_items_grid_async.mako @@ -1,6 +1,6 @@ <%namespace file="../grid_base.mako" import="*" /> <%namespace file="/display_common.mako" import="render_message" /> - +${init()} ## Always show item checkboxes so that users can select items. ${render_grid_table_body_contents( grid, show_item_checkboxes=show_item_checkboxes )} ***** diff --git a/templates/webapps/galaxy/tracks/add_to_viz.mako b/templates/webapps/galaxy/tracks/add_to_viz.mako index f8288f14d63..e004b70d196 100644 --- a/templates/webapps/galaxy/tracks/add_to_viz.mako +++ b/templates/webapps/galaxy/tracks/add_to_viz.mako @@ -1,6 +1,6 @@ ## Template generates a grid that enables user to add tracks <%namespace file="../grid_base.mako" import="*" /> - +${init()} ${stylesheets()} ${grid_javascripts()} ${render_grid_header( grid, False )} diff --git a/templates/webapps/galaxy/tracks/add_tracks.mako b/templates/webapps/galaxy/tracks/add_tracks.mako index 995ac47b66d..ce8f3863c01 100644 --- a/templates/webapps/galaxy/tracks/add_tracks.mako +++ b/templates/webapps/galaxy/tracks/add_tracks.mako @@ -1,6 +1,6 @@ ## Template generates a grid that enables user to add tracks <%namespace file="../grid_base.mako" import="*" /> - +${init()} ${stylesheets()} ${grid_javascripts()} ${render_grid_header( grid, False )} diff --git a/templates/webapps/galaxy/tracks/history_select_grid.mako b/templates/webapps/galaxy/tracks/history_select_grid.mako index ac9e11390d5..53e57dc9a9a 100644 --- a/templates/webapps/galaxy/tracks/history_select_grid.mako +++ b/templates/webapps/galaxy/tracks/history_select_grid.mako @@ -4,7 +4,7 @@ ## not make it possible to easily subclass templates. ## <%namespace file="../grid_base.mako" import="*" /> - +${init()} ${stylesheets()} ${grid_javascripts()} @@ -12,18 +12,16 @@ ${grid_javascripts()} + + + + +<%def name="init()"> +<% + self.has_left_panel=False + self.has_right_panel=False + self.message_box_visible=False +%> + + +<%def name="body()"> + ${center_panel()} + + +<%def name="center_panel()"> + ## Get URL to other histories owned by user that owns this history. + <% + ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. + href_to_published_histories = h.url_for( controller='/history', action='list_published') + if history.user is not None: + href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username') + else: + href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? + %> + +
                +
                + ## Render view of history. + + + + + %if history.deleted: +
                + ${_('You are currently viewing a deleted history!')} +
                +

                + %endif + + %if not datasets: +
                + + %else: + ## Render requested datasets, ordered from newest to oldest + %for data in datasets: + %if data.visible: +
                + ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} +
                + %endif + %endfor + + +
                +
                + diff --git a/templates/webapps/galaxy/history/view.mako b/templates/webapps/galaxy/history/view.mako index 912dd566051..6521f4dd8b7 100644 --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -1,7 +1,7 @@ -<%namespace file="/display_common.mako" import="get_history_link, get_controller_name" /> -<%namespace file="/root/history_common.mako" import="render_dataset" /> -<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> +<%namespace file="/history/history_panel.mako" import="history_panel_javascripts" /> +<%namespace file="/galaxy.masthead.mako" import="get_user_json" /> +## ---------------------------------------------------------------------------- <%! def inherit(context): if context.get('use_panels'): @@ -11,90 +11,6 @@ %> <%inherit file="${inherit(context)}"/> -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jstorage" )} - - - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history", "autocomplete_tagging" )} - - - - - - <%def name="init()"> <% self.has_left_panel=False @@ -103,71 +19,171 @@ %> +<%def name="center_panel()"> + + +## ---------------------------------------------------------------------------- <%def name="body()"> ${center_panel()} +## ---------------------------------------------------------------------------- +<%def name="title()"> + ${history[ 'name' ]} + + +## ---------------------------------------------------------------------------- +<%def name="stylesheets()"> +${parent.stylesheets()} + + + +## ---------------------------------------------------------------------------- +<%def name="javascripts()"> +${parent.javascripts()} +${history_panel_javascripts()} + +%if not use_panels: + ${h.js( 'mvc/user/user-model' )} +%endif + + + + +## ---------------------------------------------------------------------------- <%def name="center_panel()"> - ## Get URL to other histories owned by user that owns this history. - <% - ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. - href_to_published_histories = h.url_for( controller='/history', action='list_published') - if history.user is not None: - href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username') - else: - href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? - %> - -
                -
                - ## Render view of history. - - - - - %if history.deleted: -
                - ${_('You are currently viewing a deleted history!')} -
                -

                - %endif - - %if not datasets: -
                - - %else: - ## Render requested datasets, ordered from newest to oldest - %for data in datasets: - %if data.visible: -
                - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} -
                - %endif - %endfor - - -
                + + +
                + + + diff --git a/templates/webapps/galaxy/root/history.mako b/templates/webapps/galaxy/root/history.mako index 16c7c8230cb..71d6a995803 100644 --- a/templates/webapps/galaxy/root/history.mako +++ b/templates/webapps/galaxy/root/history.mako @@ -21,13 +21,10 @@ ## ----------------------------------------------------------------------------- <%def name="javascripts()"> ${parent.javascripts()} +${history_panel_javascripts()} ${h.js( - "libs/require", - "mvc/base-mvc", - "utils/localization", "mvc/user/user-model" )} -${h.templates( "helpers-common-templates" )} -${history_panel_javascripts()} - ' @@ -257,23 +247,14 @@ spaceghost.historypanel.waitForHdas().then( function(){ this.test.comment( 'update should allow unicode in genome builds' ); var unicodeBuild = 'Ржевский18'; - //NOTE!: this fails on sqlite3 (with default setup) - try { - returned = this.api.hdas.update( lastHistory.id, firstHda.id, { - name : unicodeBuild - }); - //this.debug( 'returned:\n' + this.jsonStr( returned ) ); - hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); - this.test.assert( hdaShow.genome_build === unicodeBuild, - "Update accepted unicode genome_build: " + hdaShow.name ); - } catch( err ){ - //this.debug( this.jsonStr( err ) ); - if( ( err instanceof this.api.APIError ) - && ( err.status === 500 ) - && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ - this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); - } - } + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + genome_build : unicodeBuild + }); + this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.debug( 'hdaShow:\n' + this.jsonStr( hdaShow ) ); + this.test.assert( hdaShow.genome_build === unicodeBuild, + "Update accepted unicode genome_build: " + hdaShow.genome_build ); // ........................................................................................... misc_info/info this.test.comment( 'update should allow changing the misc_info' ); @@ -298,25 +279,14 @@ spaceghost.historypanel.waitForHdas().then( function(){ this.test.comment( 'update should allow unicode in misc_info' ); var unicodeInfo = '여보!'; - //NOTE!: this fails on sqlite3 (with default setup) - try { - returned = this.api.hdas.update( lastHistory.id, firstHda.id, { - misc_info : unicodeInfo - }); - //this.debug( 'returned:\n' + this.jsonStr( returned ) ); - hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); - this.test.assert( hdaShow.misc_info === unicodeInfo, - "Update accepted unicode misc_info: " + hdaShow.misc_info ); - } catch( err ){ - //this.debug( this.jsonStr( err ) ); - if( ( err instanceof this.api.APIError ) - && ( err.status === 500 ) - && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ - this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); - } - } + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + misc_info : unicodeInfo + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.misc_info === unicodeInfo, + "Update accepted unicode misc_info: " + hdaShow.misc_info ); -/* // ........................................................................................... annotation // currently fails because no annotation is returned in details this.test.comment( 'update should allow changing the annotation' ); @@ -338,25 +308,15 @@ spaceghost.historypanel.waitForHdas().then( function(){ this.test.assert( hdaShow.annotation === 'New annotation', "Update sanitized annotation: " + hdaShow.annotation ); - //NOTE!: this fails on sqlite3 (with default setup) - try { - this.test.comment( 'update should allow unicode in annotations' ); - var unicodeAnnotation = 'お願いは、それが落下させない'; - returned = this.api.hdas.update( lastHistory.id, firstHda.id, { - annotation : unicodeAnnotation - }); - //this.debug( 'returned:\n' + this.jsonStr( returned ) ); - hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); - this.test.assert( hdaShow.annotation === unicodeAnnotation, - "Update accepted unicode annotation: " + hdaShow.annotation ); - } catch( err ){ - //this.debug( this.jsonStr( err ) ); - if( ( err instanceof this.api.APIError ) - && ( err.status === 500 ) - && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ - this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); - } - } + this.test.comment( 'update should allow unicode in annotations' ); + var unicodeAnnotation = 'お願いは、それが落下させない'; + returned = this.api.hdas.update( lastHistory.id, firstHda.id, { + annotation : unicodeAnnotation + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); + this.test.assert( hdaShow.annotation === unicodeAnnotation, + "Update accepted unicode annotation: " + hdaShow.annotation ); this.test.comment( 'update should allow escaped quotations in annotations' ); var quotedAnnotation = '"Bler"'; @@ -367,8 +327,6 @@ spaceghost.historypanel.waitForHdas().then( function(){ hdaShow = this.api.hdas.show( lastHistory.id, firstHda.id ); this.test.assert( hdaShow.annotation === quotedAnnotation, "Update accepted escaped quotations in annotation: " + hdaShow.annotation ); -*/ - // ------------------------------------------------------------------------------------------- ERRORS this.test.comment( 'create should error with "Please define the source" when the param "from_ld_id" is not used' ); @@ -391,6 +349,8 @@ spaceghost.historypanel.waitForHdas().then( function(){ //var returned = this.api.hdas.update( lastHistory.id, { deleted: true, blerp: 'blerp' }); //this.debug( 'returned:' + this.jsonStr( returned ) ); //this.debug( 'page:' + this.jsonStr( this.page ) ); +/* +*/ }); // =================================================================== diff --git a/test/casperjs/api-history-tests.js b/test/casperjs/api-history-tests.js index 76ec3071416..1339e0c63b0 100644 --- a/test/casperjs/api-history-tests.js +++ b/test/casperjs/api-history-tests.js @@ -218,23 +218,14 @@ spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ this.test.assert( historyShow.name === 'New name', "Update sanitized name: " + historyShow.name ); //NOTE!: this fails on sqlite3 (with default setup) - try { - this.test.comment( 'update should allow unicode in names' ); - var unicodeName = '桜ゲノム'; - returned = this.api.histories.update( newFirstHistory.id, { - name : unicodeName - }); - //this.debug( 'returned:\n' + this.jsonStr( returned ) ); - historyShow = this.api.histories.show( newFirstHistory.id ); - this.test.assert( historyShow.name === unicodeName, "Update accepted unicode name: " + historyShow.name ); - } catch( err ){ - //this.debug( this.jsonStr( err ) ); - if( ( err instanceof this.api.APIError ) - && ( err.status === 500 ) - && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ - this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); - } - } + this.test.comment( 'update should allow unicode in names' ); + var unicodeName = '桜ゲノム'; + returned = this.api.histories.update( newFirstHistory.id, { + name : unicodeName + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.name === unicodeName, "Update accepted unicode name: " + historyShow.name ); this.test.comment( 'update should allow escaped quotations in names' ); var quotedName = '"Bler"'; @@ -294,27 +285,16 @@ spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ this.test.assert( historyShow.genome_build === 'hg18', "Update sanitized genome_build: " + historyShow.genome_build ); + // removing for now until I can determine the relationship between unicode and genome_builds this.test.comment( 'update should allow unicode in genome builds' ); var unicodeBuild = '桜12'; - //NOTE!: this fails on sqlite3 (with default setup) - try { - returned = this.api.histories.update( newFirstHistory.id, { - name : unicodeBuild - }); - //this.debug( 'returned:\n' + this.jsonStr( returned ) ); - historyShow = this.api.histories.show( newFirstHistory.id ); - this.test.assert( historyShow.genome_build === unicodeBuild, - "Update accepted unicode genome_build: " + historyShow.genome_build ); - } catch( err ){ - //this.debug( this.jsonStr( err ) ); - if( ( err instanceof this.api.APIError ) - && ( err.status === 500 ) - && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ - this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); - } else { - throw err; - } - } + returned = this.api.histories.update( newFirstHistory.id, { + genome_build : unicodeBuild + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.genome_build === unicodeBuild, + "Update accepted unicode genome_build: " + historyShow.genome_build ); // ........................................................................................... annotation @@ -337,25 +317,15 @@ spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ this.test.assert( historyShow.annotation === 'New annotation', "Update sanitized annotation: " + historyShow.annotation ); - //NOTE!: this fails on sqlite3 (with default setup) - try { - this.test.comment( 'update should allow unicode in annotations' ); - var unicodeAnnotation = 'お願いは、それが落下させない'; - returned = this.api.histories.update( newFirstHistory.id, { - annotation : unicodeAnnotation - }); - //this.debug( 'returned:\n' + this.jsonStr( returned ) ); - historyShow = this.api.histories.show( newFirstHistory.id ); - this.test.assert( historyShow.annotation === unicodeAnnotation, - "Update accepted unicode annotation: " + historyShow.annotation ); - } catch( err ){ - //this.debug( this.jsonStr( err ) ); - if( ( err instanceof this.api.APIError ) - && ( err.status === 500 ) - && ( err.message.indexOf( '(ProgrammingError) You must not use 8-bit bytestrings' ) !== -1 ) ){ - this.skipTest( 'Unicode update failed. Are you using sqlite3 as the db?' ); - } - } + this.test.comment( 'update should allow unicode in annotations' ); + var unicodeAnnotation = 'お願いは、それが落下させない'; + returned = this.api.histories.update( newFirstHistory.id, { + annotation : unicodeAnnotation + }); + //this.debug( 'returned:\n' + this.jsonStr( returned ) ); + historyShow = this.api.histories.show( newFirstHistory.id ); + this.test.assert( historyShow.annotation === unicodeAnnotation, + "Update accepted unicode annotation: " + historyShow.annotation ); this.test.comment( 'update should allow escaped quotations in annotations' ); var quotedAnnotation = '"Bler"'; @@ -371,7 +341,6 @@ spaceghost.thenOpen( spaceghost.baseUrl ).then( function(){ // ------------------------------------------------------------------------------------------- ERRORS //TODO: make sure expected errors are being passed back (but no permissions checks here - different suite) // bad ids: index, show, update, delete, undelete - /* */ //this.debug( this.jsonStr( historyShow ) ); From 03cfab563b13aea0cdd65740104b51ddc8c67ae6 Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Fri, 10 Jan 2014 13:02:26 -0500 Subject: [PATCH 0718/1033] History & HDA API: fix unicode support for tags in update --- lib/galaxy/web/base/controller.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/web/base/controller.py index 3f4e7b45550..474661cbac3 100644 --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -2469,7 +2469,7 @@ class UsesTagsMixin( object ): # based on controllers/tag retag_async: delete all old, reset to entire new trans.app.tag_handler.delete_item_tags( trans, user, item ) new_tags_str = ','.join( new_tags_list ) - trans.app.tag_handler.apply_item_tags( trans, user, item, new_tags_str.encode( 'utf-8' ) ) + trans.app.tag_handler.apply_item_tags( trans, user, item, unicode( new_tags_str.encode( 'utf-8' ), 'utf-8' ) ) trans.sa_session.flush() return item.tags From 9e5d13c430f71eb041b2679b3135ed015088c43a Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Fri, 10 Jan 2014 13:07:37 -0500 Subject: [PATCH 0719/1033] Fix refresh events for select fields in toolshed grid --- static/scripts/galaxy.base.js | 10 ++++++++-- static/scripts/galaxy.grids.js | 3 +++ static/scripts/packed/galaxy.base.js | 2 +- static/scripts/packed/galaxy.grids.js | 2 +- 4 files changed, 13 insertions(+), 4 deletions(-) diff --git a/static/scripts/galaxy.base.js b/static/scripts/galaxy.base.js index 1af2a0e565f..b0e76b667f6 100644 --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -623,8 +623,8 @@ GalaxyAsync.prototype.log_user_action = function( action, context, params ) { }); }; -$(document).ready( function() { - +// Initialize refresh events. +function init_refresh_on_change () { $("select[refresh_on_change='true']").change( function() { var select_field = $(this), select_val = select_field.val(), @@ -663,7 +663,13 @@ $(document).ready( function() { $( "a[confirm]" ).click( function() { return confirm( $(this).attr("confirm") ); }); +}; +$(document).ready( function() { + + // Refresh events for form fields. + init_refresh_on_change(); + // Tooltips if ( $.fn.tooltip ) { // Put tooltips below items in panel header so that they do not overlap masthead. diff --git a/static/scripts/galaxy.grids.js b/static/scripts/galaxy.grids.js index d33ad98ec7d..6d273696e19 100644 --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -199,6 +199,9 @@ var GridView = Backbone.View.extend({ // configure elements this.init_grid_elements(); + + // attach global event handler + init_refresh_on_change(); }, // Initialize grid controls diff --git a/static/scripts/packed/galaxy.base.js b/static/scripts/packed/galaxy.base.js index 718edffd402..d1bc10e4541 100644 --- a/static/scripts/packed/galaxy.base.js +++ b/static/scripts/packed/galaxy.base.js @@ -1 +1 @@ -(function(){var b=0;var c=["ms","moz","webkit","o"];for(var a=0;a");var f=b.data("menu_options");if(obj_length(f)<=0){$("
              • No Options.
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                ")}a.addClass("editable-text");if(b){b(m)}};var h=("cur_text" in g?g.cur_text:a.text()),k,j;if(e){k=$("").attr({rows:i,cols:c}).text($.trim(k))}else{j=$("").attr({value:$.trim(k),size:c})}j.attr("id","renaming-active");j.blur(function(){$(this).remove();l.show();if(b){b(j)}});j.keyup(function(n){if(n.keyCode===27){$(this).trigger("blur")}else{if(n.keyCode===13){var m={};m[a]=$(this).val();$(this).trigger("blur");$.ajax({url:e,data:m,error:function(){alert("Text editing for elt "+f+" failed")},success:function(o){if(o!==""){l.text(o)}else{l.html("None")}if(b){b(j)}}})}}});if(g){g(j)}l.hide();j.insertAfter(l);j.focus();j.select();return})}function init_history_items(d,a,c){var b=function(){try{var e=$.jStorage.get("history_expand_state");if(e){for(var g in e){$("#"+g+" 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h=$.jStorage.get("history_expand_state");if(!h){h={}}$("div.historyItemBody:visible").each(function(){if($.browser.mozilla){$(this).find("pre.peek").css("overflow","hidden")}$(this).slideUp("fast");if(h){delete h[$(this).parent().attr("id")]}});$.jStorage.set("history_expand_state",h)}).show()};b()}function commatize(b){b+="";var a=/(\d+)(\d{3})/;while(a.test(b)){b=b.replace(a,"$1,$2")}return b}function reset_tool_search(a){var c=$("#galaxy_tools").contents();if(c.length===0){c=$(document)}$(this).removeClass("search_active");c.find(".toolTitle").removeClass("search_match");c.find(".toolSectionBody").hide();c.find(".toolTitle").show();c.find(".toolPanelLabel").show();c.find(".toolSectionWrapper").each(function(){if($(this).attr("id")!=="recently_used_wrapper"){$(this).show()}else{if($(this).hasClass("user_pref_visible")){$(this).show()}}});c.find("#search-no-results").hide();c.find("#search-spinner").hide();if(a){var b=c.find("#tool-search-query");b.val("search tools")}}var GalaxyAsync=function(a){this.url_dict={};this.log_action=(a===undefined?false:a)};GalaxyAsync.prototype.set_func_url=function(a,b){this.url_dict[a]=b};GalaxyAsync.prototype.set_user_pref=function(a,b){var c=this.url_dict[arguments.callee];if(c===undefined){return false}$.ajax({url:c,data:{pref_name:a,pref_value:b},error:function(){return false},success:function(){return true}})};GalaxyAsync.prototype.log_user_action=function(c,b,d){if(!this.log_action){return}var a=this.url_dict[arguments.callee];if(a===undefined){return false}$.ajax({url:a,data:{action:c,context:b,params:d},error:function(){return false},success:function(){return true}})};function init_refresh_on_change(){$("select[refresh_on_change='true']").change(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");$(document).trigger("convert_to_values");a.get(0).form.submit()});$(":checkbox[refresh_on_change='true']").click(function(){var a=$(this),e=a.val(),d=false,c=a.attr("refresh_on_change_values");if(c){c=c.split(",");var b=a.attr("last_selected_value");if($.inArray(e,c)===-1&&$.inArray(b,c)===-1){return}}$(window).trigger("refresh_on_change");a.get(0).form.submit()});$("a[confirm]").click(function(){return confirm($(this).attr("confirm"))})}$(document).ready(function(){init_refresh_on_change();if($.fn.tooltip){$(".unified-panel-header [title]").tooltip({placement:"bottom"});$("[title]").tooltip({placement:"top"})}make_popup_menus();replace_big_select_inputs(20,1500);$("a").click(function(){var b=$(this);var c=(parent.frames&&parent.frames.galaxy_main);if((b.attr("target")=="galaxy_main")&&(!c)){var a=b.attr("href");if(a.indexOf("?")==-1){a+="?"}else{a+="&"}a+="use_panels=True";b.attr("href",a);b.attr("target","_self")}return b})}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.grids.js b/static/scripts/packed/galaxy.grids.js index 464c7b19a3f..aafcf61e199 100644 --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1 +1 @@ -jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;this.handle_refresh(d.refresh_frames);var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var s=$(this).find("input.grid-row-select-checkbox");var r=$(this).find("span.grid-selected-count");var t=function(){r.text($(s).filter(":checked").length)};$(s).each(function(){$(this).change(t)});t()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$(""+g+"");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$(""+e+"").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$(""+m+"");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$(""+h+"");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h
                ';u=1}for(var h in t.items){var r=t.items[h];var c=r.encode_id;var k="grid-"+h+"-popup";m+="";if(t.show_item_checkboxes){m+=''}for(j in t.columns){var f=t.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var s=r.column_config[f.label];var l=s.link;var n=s.value;var q=s.inbound;if(jQuery.type(n)==="string"){n=n.replace(/\/\//g,"/")}var d="";var p="";if(f.attach_popup){d="grid-"+h+"-popup";p="menubutton";if(l!=""){p+=" split"}p+=" popup"}m+=""}}m+="";u++}return m},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='';if(q.show_item_checkboxes){m+=""}m+=''}if(q.show_item_checkboxes){m+='"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='"}if(q.legend){m+='"}return m},template_message:function(c){return'

                '+c.message+'

                '}});return{Grid:a,GridView:b}}); \ No newline at end of file +jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;this.handle_refresh(d.refresh_frames);var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements();init_refresh_on_change()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var s=$(this).find("input.grid-row-select-checkbox");var r=$(this).find("span.grid-selected-count");var t=function(){r.text($(s).filter(":checked").length)};$(s).each(function(){$(this).change(t)});t()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$(""+g+"");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$(""+e+"").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$(""+m+"");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$(""+h+"");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h';u=1}for(var h in t.items){var r=t.items[h];var c=r.encode_id;var k="grid-"+h+"-popup";m+="";if(t.show_item_checkboxes){m+=''}for(j in t.columns){var f=t.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var s=r.column_config[f.label];var l=s.link;var n=s.value;var q=s.inbound;if(jQuery.type(n)==="string"){n=n.replace(/\/\//g,"/")}var d="";var p="";if(f.attach_popup){d="grid-"+h+"-popup";p="menubutton";if(l!=""){p+=" split"}p+=" popup"}m+=""}}m+="";u++}return m},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='';if(q.show_item_checkboxes){m+=""}m+=''}if(q.show_item_checkboxes){m+='"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='"}if(q.legend){m+='"}return m},template_message:function(c){return'

                '+c.message+'

                '}});return{Grid:a,GridView:b}}); \ No newline at end of file From d85edddba157dd1fff9d52140c34b45ce7d70e9d Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Fri, 10 Jan 2014 14:22:03 -0500 Subject: [PATCH 0720/1033] Temporarily add simplejson back until webhelpers is updated --- eggs.ini | 1 + 1 file changed, 1 insertion(+) diff --git a/eggs.ini b/eggs.ini index 4470e0c103b..1c0491984b7 100644 --- a/eggs.ini +++ b/eggs.ini @@ -26,6 +26,7 @@ pycrypto = 2.5 pysam = 0.4.2 pysqlite = 2.5.6 python_lzo = 1.08_2.03_static +simplejson = 2.1.1 threadframe = 0.2 guppy = 0.1.8 SQLAlchemy = 0.7.9 From d6ce2f475fe9b9022322a2ffcdf93478a4be62ca Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Fri, 10 Jan 2014 14:30:18 -0500 Subject: [PATCH 0721/1033] Include the changeset revision date whenever displaying the changeset revision for a repository in the tool shed per request by Ross Lazarus. --- .../tool_shed/controllers/repository.py | 16 +-- lib/tool_shed/grids/admin_grids.py | 104 +++++++++++++++++- lib/tool_shed/grids/repository_grids.py | 6 +- .../grids/repository_review_grids.py | 7 +- lib/tool_shed/grids/util.py | 8 +- lib/tool_shed/util/metadata_util.py | 9 +- lib/tool_shed/util/shed_util_common.py | 17 ++- .../common/repository_actions_menu.mako | 4 +- .../repository/manage_repository.mako | 4 +- .../preview_tools_in_changeset.mako | 2 +- .../tool_shed/repository/rate_repository.mako | 10 +- .../tool_shed/repository/view_changelog.mako | 3 +- .../tool_shed/repository/view_changeset.mako | 12 +- .../tool_shed/repository/view_repository.mako | 8 +- .../repository_review/browse_review.mako | 2 +- .../reviews_of_changeset_revision.mako | 2 +- .../reviews_of_repository.mako | 2 +- .../select_previous_review.mako | 6 +- 18 files changed, 175 insertions(+), 47 deletions(-) diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py index 454bcffa7ef..88cd5bdc531 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -2432,6 +2432,7 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ): message='Select a repository to rate', status='error' ) ) repository = suc.get_repository_in_tool_shed( trans, id ) + changeset_revision = repository.tip( trans.app ) repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) if repository.user == trans.user: return trans.response.send_redirect( web.url_for( controller='repository', @@ -2447,12 +2448,14 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ): rra = self.get_user_item_rating( trans.sa_session, trans.user, repository, webapp_model=trans.model ) metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, - repository.tip( trans.app ), + changeset_revision, metadata_only=True ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) + revision_label = suc.get_revision_label( trans, repository, changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository/rate_repository.mako', repository=repository, metadata=metadata, + revision_label=revision_label, avg_rating=avg_rating, display_reviews=display_reviews, num_ratings=num_ratings, @@ -2862,13 +2865,10 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ): has_metadata = True else: has_metadata = False - t, tz = ctx.date() - date = datetime( *gmtime( float( t ) - tz )[:6] ) - display_date = date.strftime( "%Y-%m-%d" ) change_dict = { 'ctx' : ctx, 'rev' : str( ctx.rev() ), 'date' : date, - 'display_date' : display_date, + 'display_date' : suc.get_readable_ctx_date( ctx ), 'description' : ctx.description(), 'files' : ctx.files(), 'user' : ctx.user(), @@ -2923,16 +2923,18 @@ class RepositoryController( BaseUIController, ratings_util.ItemRatings ): metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, id, ctx_str, metadata_only=True ) # For rendering the prev button. if ctx_parent: + ctx_parent_date = suc.get_readable_ctx_date( ctx_parent ) ctx_parent_rev = ctx_parent.rev() if ctx_parent_rev < 0: prev = None else: - prev = "%s:%s" % ( ctx_parent_rev, ctx_parent ) + prev = "%s:%s (%s)" % ( ctx_parent_rev, ctx_parent, ctx_parent_date ) else: prev = None if ctx_child: + ctx_child_date = suc.get_readable_ctx_date( ctx_child ) ctx_child_rev = ctx_child.rev() - next = "%s:%s" % ( ctx_child_rev, ctx_child ) + next = "%s:%s (%s)" % ( ctx_child_rev, ctx_child, ctx_child_date ) else: next = None return trans.fill_template( '/webapps/tool_shed/repository/view_changeset.mako', diff --git a/lib/tool_shed/grids/admin_grids.py b/lib/tool_shed/grids/admin_grids.py index 8714e134187..967d9328afb 100644 --- a/lib/tool_shed/grids/admin_grids.py +++ b/lib/tool_shed/grids/admin_grids.py @@ -19,48 +19,72 @@ log = logging.getLogger( __name__ ) class UserGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + + class UserLoginColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): return user.email + + class UserNameColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): if user.username: return user.username return 'not set' + + class GroupsColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): if user.groups: return len( user.groups ) return 0 + + class RolesColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): if user.roles: return len( user.roles ) return 0 + + class ExternalColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): if user.external: return 'yes' return 'no' + + class LastLoginColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): if user.galaxy_sessions: return self.format( user.galaxy_sessions[ 0 ].update_time ) return 'never' + + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): if user.purged: return "purged" elif user.deleted: return "deleted" return "" + + class EmailColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): if column_filter == 'All': return query return query.filter( and_( model.Tool.table.c.user_id == model.User.table.c.id, model.User.table.c.email == column_filter ) ) + title = "Users" model_class = model.User template='/admin/user/grid.mako' @@ -114,37 +138,56 @@ class UserGrid( grids.Grid ): num_rows_per_page = 50 preserve_state = False use_paging = True + def get_current_item( self, trans, **kwargs ): return trans.user + class RoleGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): return role.name + + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): if role.description: return role.description return '' + + class TypeColumn( grids.TextColumn ): def get_value( self, trans, grid, role ): return role.type + + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): if role.deleted: return "deleted" return "" + + class GroupsColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): if role.groups: return len( role.groups ) return 0 + + class UsersColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): if role.users: return len( role.users ) return 0 + title = "Roles" model_class = model.Role template='/admin/dataset_security/role/grid.mako' @@ -205,29 +248,43 @@ class RoleGrid( grids.Grid ): num_rows_per_page = 50 preserve_state = False use_paging = True + def apply_query_filter( self, trans, query, **kwd ): return query.filter( model.Role.type != model.Role.types.PRIVATE ) + class GroupGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, group ): return group.name + + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): if group.deleted: return "deleted" return "" + + class RolesColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): if group.roles: return len( group.roles ) return 0 + + class UsersColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): if group.members: return len( group.members ) return 0 + title = "Groups" model_class = model.Group template='/admin/dataset_security/group/grid.mako' @@ -279,6 +336,7 @@ class GroupGrid( grids.Grid ): preserve_state = False use_paging = True + class ManageCategoryGrid( CategoryGrid ): columns = [ col for col in CategoryGrid.columns ] # Override the NameColumn to include an Edit link @@ -292,12 +350,17 @@ class ManageCategoryGrid( CategoryGrid ): dict( controller='admin', action='manage_categories', operation='create' ) ) ] + class AdminRepositoryGrid( RepositoryGrid ): + + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository ): if repository.deleted: return 'yes' return '' + columns = [ RepositoryGrid.NameColumn( "Name", key="name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -326,27 +389,43 @@ class AdminRepositoryGrid( RepositoryGrid ): async_compatible=False ) ) standard_filters = [] default_filter = {} + def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.Repository ) \ .join( model.User.table ) + class RepositoryMetadataGrid( grids.Grid ): + + class IdColumn( grids.IntegerColumn ): + def get_value( self, trans, grid, repository_metadata ): return repository_metadata.id + + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): return repository_metadata.repository.name + + class OwnerColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): return repository_metadata.repository.user.username + class RevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): repository = repository_metadata.repository repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) + return suc.get_revision_label( trans, repository, repository_metadata.changeset_revision ) + + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): tools_str = '0' if repository_metadata: @@ -358,7 +437,10 @@ class RepositoryMetadataGrid( grids.Grid ): # tools_str += '%s %s
                ' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) return '%d' % len( metadata[ 'tools' ] ) return tools_str + + class DatatypesColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): datatypes_str = '0' if repository_metadata: @@ -370,7 +452,10 @@ class RepositoryMetadataGrid( grids.Grid ): # datatypes_str += '%s
                ' % datatype_metadata_dict[ 'extension' ] return '%d' % len( metadata[ 'datatypes' ] ) return datatypes_str + + class WorkflowsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): workflows_str = '0' if repository_metadata: @@ -387,21 +472,31 @@ class RepositoryMetadataGrid( grids.Grid ): # workflows_str += '%s
                ' % workflow_metadata_dict[ 'name' ] return '%d' % len( metadata[ 'workflows' ] ) return workflows_str + + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): if repository_metadata.repository.deleted: return 'yes' return '' + + class DeprecatedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): if repository_metadata.repository.deprecated: return 'yes' return '' + + class MaliciousColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): if repository_metadata.malicious: return 'yes' return '' + # Grid definition title = "Repository Metadata" model_class = model.RepositoryMetadata @@ -440,6 +535,7 @@ class RepositoryMetadataGrid( grids.Grid ): num_rows_per_page = 50 preserve_state = False use_paging = True + def build_initial_query( self, trans, **kwd ): return trans.sa_session.query( model.RepositoryMetadata ) \ .join( model.Repository.table ) diff --git a/lib/tool_shed/grids/repository_grids.py b/lib/tool_shed/grids/repository_grids.py index 4a054851f6c..dc848038cac 100644 --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -101,6 +101,10 @@ class RepositoryGrid( grids.Grid ): if len( select_field.options ) > 1: return select_field.get_html() elif len( select_field.options ) == 1: + option_items = select_field.options[ 0 ][ 0 ] + rev_label, rev_date = option_items.split( ' ' ) + rev_date = '%s' % rev_date + return '%s %s' % ( rev_label, rev_date ) return select_field.options[ 0 ][ 0 ] return '' @@ -1134,7 +1138,7 @@ class RepositoryMetadataGrid( grids.Grid ): repository = repository_metadata.repository changeset_revision = repository_metadata.changeset_revision changeset_revision_label = suc.get_revision_label( trans, repository, changeset_revision ) - return escape_html( changeset_revision_label ) + return changeset_revision_label class MaliciousColumn( grids.BooleanColumn ): diff --git a/lib/tool_shed/grids/repository_review_grids.py b/lib/tool_shed/grids/repository_review_grids.py index 99db9039b19..3a6428d3249 100644 --- a/lib/tool_shed/grids/repository_review_grids.py +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -83,9 +83,10 @@ class RepositoriesWithReviewsGrid( RepositoryGrid ): if repository_metadata_revisions: rval = '' for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, - repository_metadata, - repository=repository ) + rev, label, changeset_revision = \ + metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository ) rval += '%s
                ' % \ ( trans.security.encode_id( repository.id ), changeset_revision, label ) return rval diff --git a/lib/tool_shed/grids/util.py b/lib/tool_shed/grids/util.py index bd7450d607e..a9d036d9577 100644 --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -16,7 +16,8 @@ def build_approved_select_field( trans, name, selected_value=None, for_component select_field.add_option( option_tup[ 0 ], option_tup[ 1 ], selected=selected ) return select_field -def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, downloadable=False, reviewed=False, not_reviewed=False ): +def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, + downloadable=False, reviewed=False, not_reviewed=False ): """Build a SelectField whose options are the changeset_rev strings of certain revisions of the received repository.""" options = [] changeset_tups = [] @@ -46,7 +47,10 @@ def build_changeset_revision_select_field( trans, repository, selected_value=Non # Restrict the options to all revisions that have associated metadata. repository_metadata_revisions = repository.metadata_revisions for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=repository ) + rev, label, changeset_revision = \ + metadata_util.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository ) changeset_tups.append( ( rev, label, changeset_revision ) ) refresh_on_change_values.append( changeset_revision ) # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, diff --git a/lib/tool_shed/util/metadata_util.py b/lib/tool_shed/util/metadata_util.py index cb08a572569..c196637a699 100644 --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -1108,16 +1108,19 @@ def get_rev_label_changeset_revision_from_repository_metadata( trans, repository changeset_revision = repository_metadata.changeset_revision ctx = suc.get_changectx_for_changeset( repo, changeset_revision ) if ctx: + changeset_revision_date = suc.get_readable_ctx_date( ctx ) rev = '%04d' % ctx.rev() - label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + label = "%s:%s (%s)" % ( str( ctx.rev() ), changeset_revision, changeset_revision_date ) else: rev = '-1' label = "-1:%s" % changeset_revision return rev, label, changeset_revision -def get_sample_files_from_disk( repository_files_dir, tool_path=None, relative_install_dir=None, resetting_all_metadata_on_repository=False ): +def get_sample_files_from_disk( repository_files_dir, tool_path=None, relative_install_dir=None, + resetting_all_metadata_on_repository=False ): if resetting_all_metadata_on_repository: - # Keep track of the location where the repository is temporarily cloned so that we can strip it when setting metadata. + # Keep track of the location where the repository is temporarily cloned so that we can strip + # it when setting metadata. work_dir = repository_files_dir sample_file_metadata_paths = [] sample_file_copy_paths = [] diff --git a/lib/tool_shed/util/shed_util_common.py b/lib/tool_shed/util/shed_util_common.py index bf83152e1cc..3495ef49efe 100644 --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -924,6 +924,13 @@ def get_query_for_setting_metadata_on_repositories( trans, my_writable=False, or return trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ .filter( trans.install_model.ToolShedRepository.table.c.uninstalled == False ) +def get_readable_ctx_date( ctx ): + """Convert the date of the changeset (the received ctx) to a human-readable date.""" + t, tz = ctx.date() + date = datetime( *gmtime( float( t ) - tz )[ :6 ] ) + ctx_date = date.strftime( "%Y-%m-%d" ) + return ctx_date + def get_repo_info_tuple_contents( repo_info_tuple ): """Take care in handling the repo_info_tuple as it evolves over time as new tool shed features are introduced.""" if len( repo_info_tuple ) == 6: @@ -1206,7 +1213,8 @@ def get_revision_label( trans, repository, changeset_revision ): repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) ) ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: - return "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + return '%s:%s (%s)' % \ + ( str( ctx.rev() ), changeset_revision, str( get_readable_ctx_date( ctx ) ) ) else: return "-1:%s" % changeset_revision @@ -1215,7 +1223,8 @@ def get_rev_label_from_changeset_revision( repo, changeset_revision ): ctx = get_changectx_for_changeset( repo, changeset_revision ) if ctx: rev = '%04d' % ctx.rev() - label = "%s:%s" % ( str( ctx.rev() ), changeset_revision ) + label = '%s:%s (%s)' % \ + ( str( ctx.rev() ), changeset_revision, str( get_readable_ctx_date( ctx ) ) ) else: rev = '-1' label = "-1:%s" % changeset_revision @@ -1477,9 +1486,6 @@ def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert email_from = 'galaxy-no-reply@' + trans.request.host.split( ':' )[0] tip_changeset = repo.changelog.tip() ctx = repo.changectx( tip_changeset ) - t, tz = ctx.date() - date = datetime( *gmtime( float( t ) - tz )[:6] ) - display_date = date.strftime( "%Y-%m-%d" ) try: username = ctx.user().split()[0] except: @@ -1490,6 +1496,7 @@ def handle_email_alerts( trans, repository, content_alert_str='', new_repo_alert template = new_repo_email_alert_template else: template = email_alert_template + display_date = get_readable_ctx_date( ctx ) admin_body = string.Template( template ).safe_substitute( host=trans.request.host, sharable_link=sharable_link, repository_name=repository.name, diff --git a/templates/webapps/tool_shed/common/repository_actions_menu.mako b/templates/webapps/tool_shed/common/repository_actions_menu.mako index 129fbfe091b..93364794687 100644 --- a/templates/webapps/tool_shed/common/repository_actions_menu.mako +++ b/templates/webapps/tool_shed/common/repository_actions_menu.mako @@ -174,7 +174,9 @@ Mark repository as not deprecated %endif %if can_download: - Export this revision + %if changeset_revision is not None: + Export this revision + %endif Download as a .tar.gz file Download as a .tar.bz2 file Download as a zip file diff --git a/templates/webapps/tool_shed/repository/manage_repository.mako b/templates/webapps/tool_shed/repository/manage_repository.mako index a8a93e2b07f..a14160533b5 100644 --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -181,9 +181,9 @@ ${render_tool_shed_repository_actions( repository, metadata=metadata, changeset_
                %if can_view_change_log: - ${revision_label | h} + ${revision_label} %else: - ${revision_label | h} + ${revision_label} %endif
                diff --git a/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako b/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako index 5cc8a1f3126..8bddeafe513 100644 --- a/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako +++ b/templates/webapps/tool_shed/repository/preview_tools_in_changeset.mako @@ -51,7 +51,7 @@ ${render_galaxy_repository_actions( repository=repository )} %else:
                - ${revision_label | h} + ${revision_label}
                %endif
                diff --git a/templates/webapps/tool_shed/repository/rate_repository.mako b/templates/webapps/tool_shed/repository/rate_repository.mako index f9f209c6153..22506cc2f2b 100644 --- a/templates/webapps/tool_shed/repository/rate_repository.mako +++ b/templates/webapps/tool_shed/repository/rate_repository.mako @@ -44,16 +44,20 @@ ${render_tool_shed_repository_actions( repository, metadata=None, changeset_revi ${render_clone_str( repository )} %endif - ${render_repository_type_select_field( repository_type_select_field, render_help=False )}
                +
                + + ${repository.type | h} +
                +
                ${repository.description | h}
                - - ${repository.revision( trans.app ) | h} + + ${revision_label}
                diff --git a/templates/webapps/tool_shed/repository/view_changelog.mako b/templates/webapps/tool_shed/repository/view_changelog.mako index 77515fe2d82..b97fc79e8a7 100644 --- a/templates/webapps/tool_shed/repository/view_changelog.mako +++ b/templates/webapps/tool_shed/repository/view_changelog.mako @@ -5,7 +5,6 @@ <%namespace file="/webapps/tool_shed/common/repository_actions_menu.mako" import="render_tool_shed_repository_actions" /> <% - from galaxy.web.framework.helpers import time_ago is_new = repository.is_new( trans.app ) can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) can_download = not is_new and ( not is_malicious or can_push ) @@ -108,7 +107,7 @@ ${render_tool_shed_repository_actions( repository=repository )}
                - ${time_ago( changeset[ 'date' ] )} + ${changeset[ 'display_date' ]}
                diff --git a/templates/webapps/tool_shed/repository/view_changeset.mako b/templates/webapps/tool_shed/repository/view_changeset.mako index 14db2e83e87..0d9ac4b02d8 100644 --- a/templates/webapps/tool_shed/repository/view_changeset.mako +++ b/templates/webapps/tool_shed/repository/view_changeset.mako @@ -49,13 +49,15 @@ ${render_tool_shed_repository_actions( repository=repository )} %endif
                <% + from tool_shed.util.shed_util_common import get_readable_ctx_date + changeset_revision_date = get_readable_ctx_date( ctx ) if can_download: - title_str = 'Changeset %s:%s' % ( ctx.rev(), ctx ) + title_str = 'Changeset %s:%s (%s)' % ( ctx.rev(), ctx, changeset_revision_date ) else: - title_str = '%s changeset %s:%s' % ( repository.name, ctx.rev(), ctx ) + title_str = '%s changeset %s:%s (%s)' % ( repository.name, ctx.rev(), ctx, changeset_revision_date ) %>
                - ${title_str | h} + ${title_str}
                - %if query.count() > 0: - + %if len(self.grid_config['items']) > 0: + %endif
                No Items
                - %if href: - %if len(grid.operations) != 0: + # get column settings + column_settings = item['column_config'][column['label']] + + # load attributes + link = column_settings['link'] + value = column_settings['value'] + + # check if formatting is defined + value = str(value).replace('//', '/') + + # Attach popup menu? + id = "" + if column['attach_popup']: + id = 'grid-%d-popup' % i + endif + + # Determine appropriate class + cls = "" + if column['attach_popup']: + cls = "menubutton" + if link: + cls += " split" + endif + endif + %> + + %if link: + %if len(self.grid_config['operations']) != 0:
                - %endif - ${v} - %if len(grid.operations) != 0: -
                - %endif - %else: -
                %endif -                 		-
                - %for operation in grid.operations: - %if operation.allowed( item ) and operation.allow_popup: +
                + %for operation in self.grid_config['operations']: + <% + operation_id = operation['label'] + operation_settings = item['operation_config'][operation_id] + %> + %if operation_settings['allowed'] and operation['allow_popup']: <% target = "" - if operation.target: - target = "target='" + operation.target + "'" + if operation['target']: + target = "target='" + operation['target'] + "'" %> - %if operation.confirm: - ${operation.label} + %if operation['confirm']: + ${operation_id} %else: - ${operation.label} + ${operation_id} %endif %endif %endfor @@ -351,20 +456,16 @@
                For selected ${items_plural}: - %for operation in grid.operations: - %if operation.allow_multiple: - + %for operation in self.grid_config['operations']: + %if operation['allow_multiple']: + %endif %endfor
                - %for operation in grid.operations: - %if operation.global_operation: - <% - link = operation.global_operation() - href = url( **link ) - %> - ${operation.label} - %endif + %for operation in self.grid_config['operations']: + %if operation['global_operation']: + ${operation['label']} + %endif %endfor
                - ${grid.legend} + ${self.grid_config['legend']}
                No Items
                ";if(l){if(t.operations.length!=0){m+='
                '}var o="";if(q){o="use-inbound"}else{o="use-outbound"}m+=''+n+"";if(t.operations.length!=0){m+="
                "}}else{m+='
                "}m+="
                Page:';if(k>1){m+='1 ...'}for(var n=k;n'+n+""}else{m+=''+n+""}}if(e'+p+""}m+="";m+=' | Show All
                For selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+=' "}}m+="
                ';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+=''+d.label+""}}m+="
                '+q.legend+"
                No Items
                ";if(l){if(t.operations.length!=0){m+='
                '}var o="";if(q){o="use-inbound"}else{o="use-outbound"}m+=''+n+"";if(t.operations.length!=0){m+="
                "}}else{m+='
                "}m+="
                Page:';if(k>1){m+='1 ...'}for(var n=k;n'+n+""}else{m+=''+n+""}}if(e'+p+""}m+="";m+=' | Show All
                For selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+=' "}}m+="
                ';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+=''+d.label+""}}m+="
                '+q.legend+"
                @@ -63,10 +65,10 @@ ${render_tool_shed_repository_actions( repository=repository )} diff --git a/templates/webapps/tool_shed/repository/view_repository.mako b/templates/webapps/tool_shed/repository/view_repository.mako index 168d6638c6f..acf73943686 100644 --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -100,7 +100,11 @@ ${repository.name | h} %endif - ${render_repository_type_select_field( repository_type_select_field, render_help=False )} +
                + + ${repository.type | h} +
                +
                ${repository.description | h} @@ -113,7 +117,7 @@ %if can_view_change_log: ${revision_label} %else: - ${revision_label | h} + ${revision_label} %endif
                diff --git a/templates/webapps/tool_shed/repository_review/browse_review.mako b/templates/webapps/tool_shed/repository_review/browse_review.mako index 5d5770b66b7..2fcf92a22ff 100644 --- a/templates/webapps/tool_shed/repository_review/browse_review.mako +++ b/templates/webapps/tool_shed/repository_review/browse_review.mako @@ -34,7 +34,7 @@ ${render_tool_shed_repository_actions( repository=repository, changeset_revision
                - ${changeset_revision_label | h} + ${changeset_revision_label}
                diff --git a/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako b/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako index daa557ecf92..000dec46618 100644 --- a/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako +++ b/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako @@ -45,7 +45,7 @@ ${render_tool_shed_repository_actions( repository=repository, changeset_revision
                - ${changeset_revision_label | h} + ${changeset_revision_label}
                diff --git a/templates/webapps/tool_shed/repository_review/reviews_of_repository.mako b/templates/webapps/tool_shed/repository_review/reviews_of_repository.mako index d5f06a10f00..993e8bcba1e 100644 --- a/templates/webapps/tool_shed/repository_review/reviews_of_repository.mako +++ b/templates/webapps/tool_shed/repository_review/reviews_of_repository.mako @@ -67,7 +67,7 @@ ${render_tool_shed_repository_actions( repository=repository )}
                - + From 60094ca499c74e6b13a8202dbf1c5927bc8ce0ab Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Fri, 10 Jan 2014 15:02:20 -0500 Subject: [PATCH 0722/1033] Use class instead of substrings to identify integrated tool panel tools, sections, workflows, and section labels when saving and updating the panel. --- lib/galaxy/tools/__init__.py | 43 +++++++++++++++++---------------- lib/tool_shed/util/tool_util.py | 15 +++--------- 2 files changed, 26 insertions(+), 32 deletions(-) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index 6f5f0279e18..71d6478b60e 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -62,6 +62,7 @@ from galaxy.util.template import fill_template from galaxy.web import url_for from galaxy.web.form_builder import SelectField from galaxy.model.item_attrs import Dictifiable +from galaxy.model import Workflow from tool_shed.util import shed_util_common from .loader import load_tool, template_macro_params @@ -142,13 +143,13 @@ class ToolBox( object, Dictifiable ): # 1) adjusting init_tools() and called methods to get this right # 2) redesigning the code and/or data structure used to read/write integrated_tool_panel.xml for key, value in self.integrated_tool_panel.iteritems(): - if key.startswith( 'section_' ): + if isinstance( value, ToolSection ): for section_key, section_value in value.elems.iteritems(): if section_value is None: - if section_key.startswith( 'tool_' ): + if isinstance( section_value, Tool ): tool_id = section_key[5:] value.elems[section_key] = self.tools_by_id.get( tool_id ) - elif section_key.startswith( 'workflow_' ): + elif isinstance( section_value, Workflow ): workflow_id = section_key[9:] value.elems[section_key] = self.workflows_by_id.get( workflow_id ) @@ -252,19 +253,19 @@ class ToolBox( object, Dictifiable ): def load_tool_panel( self ): for key, val in self.integrated_tool_panel.items(): - if key.startswith( 'tool_' ): + if isinstance( val, Tool ): tool_id = key.replace( 'tool_', '', 1 ) if tool_id in self.tools_by_id: self.__add_tool_to_tool_panel( tool_id, self.tool_panel, section=False ) - elif key.startswith( 'workflow_' ): + elif isinstance( val, Workflow ): workflow_id = key.replace( 'workflow_', '', 1 ) if workflow_id in self.workflows_by_id: workflow = self.workflows_by_id[ workflow_id ] self.tool_panel[ key ] = workflow log.debug( "Loaded workflow: %s %s" % ( workflow_id, workflow.name ) ) - elif key.startswith( 'label_' ): + elif isinstance( val, ToolSectionLabel ): self.tool_panel[ key ] = val - elif key.startswith( 'section_' ): + elif isinstance( val, ToolSection ): elem = ElementTree.Element( 'section' ) elem.attrib[ 'id' ] = val.id or '' elem.attrib[ 'name' ] = val.name or '' @@ -276,13 +277,13 @@ class ToolBox( object, Dictifiable ): tool_id = section_key.replace( 'tool_', '', 1 ) if tool_id in self.tools_by_id: self.__add_tool_to_tool_panel( tool_id, section, section=True ) - elif section_key.startswith( 'workflow_' ): + elif isinstance( section_val, Workflow ): workflow_id = section_key.replace( 'workflow_', '', 1 ) if workflow_id in self.workflows_by_id: workflow = self.workflows_by_id[ workflow_id ] section.elems[ section_key ] = workflow log.debug( "Loaded workflow: %s %s" % ( workflow_id, workflow.name ) ) - elif section_key.startswith( 'label_' ): + elif isinstance( val, ToolSectionLabel ): if section_val: section.elems[ section_key ] = section_val log.debug( "Loaded label: %s" % ( section_val.text ) ) @@ -315,7 +316,7 @@ class ToolBox( object, Dictifiable ): elif section_elem.tag == 'label': key = 'label_%s' % section_elem.get( 'id' ) section.elems[ key ] = None - key = 'section_%s' % elem.get( 'id' ) + key = elem.get( 'id' ) self.integrated_tool_panel[ key ] = section elif elem.tag == 'label': key = 'label_%s' % elem.get( 'id' ) @@ -331,28 +332,28 @@ class ToolBox( object, Dictifiable ): os.write( fd, '\n' ) for key, item in self.integrated_tool_panel.items(): if item: - if key.startswith( 'tool_' ): + if isinstance( item, Tool ): os.write( fd, ' \n' % item.id ) - elif key.startswith( 'workflow_' ): + elif isinstance( item, Workflow ): os.write( fd, ' \n' % item.id ) - elif key.startswith( 'label_' ): + elif isinstance( item, ToolSectionLabel ): label_id = item.id or '' label_text = item.text or '' label_version = item.version or '' os.write( fd, ' '); + }, + + // add header cell + addHeader: function($el) { + var wrapper = $(''); + wrapper.append($el); + this.row.append(wrapper); + }, + + // header + appendHeader: function() { + // append header row + $(this.el).find('thead').append(this.row); + + // row + this.row = $(''); + }, + + // add row cell + add: function($el) { + var wrapper = $(''); + wrapper.append($el); + this.row.append(wrapper); + }, + + // append + append: function(id) { + this.commit(id); + }, + + // prepend + prepend: function(id) { + this.commit(id, true); + }, + + // commit + commit: function(id, prepend) { + // add + this.row.attr('id', id); + + // add row + if (prepend) { + $(this.el).find('tbody').prepend(this.row); + } else { + $(this.el).find('tbody').append(this.row); + } + + // row + this.row = $(''); + + // row count + this.row_count++; + this.refresh(); + }, + + // remove + remove: function(id) { + $(this.el).find('#' + id).remove(); + this.row_count--; + this.refresh(); + }, + + // remove + removeAll: function() { + $(this.el).find('tbody').html(''); + this.row_count = 0; + this.refresh(); + }, + + // value + value: function(new_value) { + // get current id/value + this.before = this.$el.find('.current').attr('id'); + + // check if new_value is defined + if (new_value !== undefined) { + this.$el.find('tr').removeClass('current'); + if (new_value) { + this.$el.find('#' + new_value).addClass('current'); + } + } + + // get current id/value + var after = this.$el.find('.current').attr('id'); + if(after === undefined) { + return null; + } else { + // fire onchange + if (after != this.before && this.options.onchange) { + this.options.onchange(new_value); + } + + // return current value + return after; + } + }, + + // cancel last change + confirm: function(new_value) { + this.value(new_value); + }, + + // onclick + onclick: function(e) { + // get values + var old_value = this.value(); + var new_value = $(e.target).closest('tr').attr('id'); + + // check equality + if (new_value && old_value != new_value) { + if (this.options.onconfirm) { + this.options.onconfirm(new_value); + } else { + this.confirm(new_value); + } + } + }, + + // onclick + ondblclick: function(e) { + var value = this.value(); + if (value && this.options.ondblclick) { + this.options.ondblclick(value); + } + }, + + // refresh + refresh: function() { + if (this.row_count == 0) { + this.$el.find('tmessage').show(); + } else { + this.$el.find('tmessage').hide(); + } + }, + + // load html template + template: function(options) + { + return '
                ' + + '
                %if prev: - Previous changeset ${prev | h} + Previous changeset ${prev} %endif %if next: - Next changeset ${next | h} + Next changeset ${next} %endif
                %if repository_reviews: diff --git a/templates/webapps/tool_shed/repository_review/select_previous_review.mako b/templates/webapps/tool_shed/repository_review/select_previous_review.mako index 285fd5b922f..8ccb9d12cf7 100644 --- a/templates/webapps/tool_shed/repository_review/select_previous_review.mako +++ b/templates/webapps/tool_shed/repository_review/select_previous_review.mako @@ -30,7 +30,7 @@ ${render_tool_shed_repository_actions( repository=repository )} %endif
                - You have elected to create a new review for revision ${changeset_revision_label | h}of this repository. Since previous revisions have been reviewed, + You have elected to create a new review for revision ${changeset_revision_label}of this repository. Since previous revisions have been reviewed, you can select a previous review to copy to your new review, or click the Create a review without copying button.
                @@ -39,7 +39,7 @@ ${render_tool_shed_repository_actions( repository=repository )}
                - ${changeset_revision_label | h} + ${changeset_revision_label}
                @@ -76,7 +76,7 @@ ${render_tool_shed_repository_actions( repository=repository )} Copy this review
                		${previous_changeset_revision_label | h}${previous_changeset_revision_label} ${render_star_rating( repository_rating_name, review.rating, disabled=True )} ${approved_str | h}
                ' + + '' + + '' + + '
                ' + + '' + options.content + '' + + '
                '; + } +}); + +}); diff --git a/config/plugins/visualizations/charts/static/library/ui.js b/config/plugins/visualizations/charts/static/library/ui.js new file mode 100644 index 00000000000..4e4e489515e --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/ui.js @@ -0,0 +1,472 @@ +// dependencies +define(['library/utils', 'library/ui.select'], function(Utils, Select) { + +// plugin +var Label = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + }, + + // template + template: function(options) { + return ''; + }, + + // value + value: function() { + return options.label; + } +}); + +// plugin +var Button = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '', + float : 'right', + cls : 'btn-default', + type : 'submit', + icon : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add event + $(this.el).on('click', options.onclick); + }, + + // element + template: function(options) { + var str = ''; + return str; + } +}); + +// plugin +var Anchor = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '' + }, + + // initialize + initialize : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add event + $(this.el).on('click', options.onclick); + }, + + // element + template: function(options) { + return ''; + } +}); + +// plugin +var Message = Backbone.View.extend( +{ + // options + optionsDefault: { + message : '', + status : 'info', + persistent : false + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement('
                '); + }, + + // update + update : function(options) { + // get options + this.options = Utils.merge(options, this.optionsDefault); + + // show message + if (options.message != '') { + this.$el.html(this.template(this.options)); + this.$el.fadeIn(); + + // check if message is persistent + if (!options.persistent) { + // set timer + var self = this; + window.setTimeout(function() { + if (self.$el.is(':visible')) { + self.$el.fadeOut(); + } else { + self.$el.hide(); + } + }, 3000); + } + } else { + this.$el.fadeOut(); + } + }, + + // element + template: function(options) { + return '
                ' + options.message + '
                '; + } +}); + +// plugin +var Searchbox = Backbone.View.extend( +{ + // options + optionsDefault: { + onclick : null, + searchword : '' + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add click event + var self = this; + if (this.options.onclick) { + this.$el.on('submit', function(e) { + var search_field = self.$el.find('#search'); + self.options.onclick(search_field.val()); + }); + } + }, + + // element + template: function(options) { + return '
                ' + + '' + + '' + + '' + + '' + + '
                '; + } +}); + +// plugin +var Title = Backbone.View.extend( +{ + // options + optionsDefault: { + label : 'Unlabeled', + body : null + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + if (this.options.body) { + this.$el.find('.body').append(this.options.body); + } + }, + + // element + template: function(options) { + return '
                ' + + options.label + ':' + + '
                '; + } +}); + +// tab +var ButtonMenu = Backbone.View.extend( +{ + // main options + options: + { + id : '', + title : '', + target : '', + href : '', + onunload : null, + onclick : null, + visible : true, + icon : null, + tag : '' + }, + + // optional sub menu + $menu: null, + + // initialize + initialize: function (options) + { + // read in defaults + if (options) + this.options = _.defaults(options, this.options); + + // add template for tab + this.setElement($(this._template(this.options))); + + // find root + var $root = $(this.el).find('.root'); + + // link head + var self = this; + $root.on('click', function(e) + { + // prevent default + e.preventDefault(); + + // add click event + if(self.options.onclick) { + self.options.onclick(); + } + }); + + // visiblity + if (!this.options.visible) + this.hide(); + }, + + // show + show: function() + { + $(this.el).show(); + }, + + // hide + hide: function() + { + $(this.el).hide(); + }, + + // add menu item + addMenu: function (options) + { + // menu option defaults + var menuOptions = { + title : '', + target : '', + href : '', + onclick : null, + divider : false, + icon : null + } + + // read in defaults + if (options) + menuOptions = _.defaults(options, menuOptions); + + // check if submenu element is available + if (!this.$menu) + { + // insert submenu element into root + $(this.el).append(this._templateMenu()); + + // update element link + this.$menu = $(this.el).find('.menu'); + } + + // create + var $item = $(this._templateMenuItem(menuOptions)); + + // add events + $item.on('click', function(e) + { + // prevent default + e.preventDefault(); + + // add click event + if(menuOptions.onclick) { + menuOptions.onclick(); + } + }); + + // append menu + this.$menu.append($item); + + // append divider + if (menuOptions.divider) + this.$menu.append($(this._templateDivider())); + }, + + // fill template header + _templateMenuItem: function (options) + { + var tmpl = '
              • ' + + ''; + + if (options.icon) + tmpl += ''; + + tmpl += ' ' + options.title + + '' + + '
                • '; + return tmpl; + }, + + // fill template header + _templateMenu: function () + { + return ''; + }, + + _templateDivider: function() + { + return '
              • '; + }, + + // fill template + _template: function (options) + { + // start template + var tmpl = '
                ' + + '' + + '
                '; + + // return template + return tmpl; + } +}); + +// plugin +var ButtonIcon = Backbone.View.extend( +{ + // options + optionsDefault: { + label : '', + float : 'right', + cls : 'icon-btn', + type : 'submit', + icon : '', + tooltip : '' + }, + + // initialize + initialize : function(options) { + // get options + if (options) + this.options = _.defaults(options, this.optionsDefault); + else + this.options = this.optionsDefault; + + // create new element + this.setElement(this.template(this.options)); + + // add event + $(this.el).on('click', options.onclick); + + // add tooltip + $(this.el).tooltip({title: options.tooltip, placement: 'bottom'}); + }, + + // element + template: function(options) { + var str = ''; + if (options.icon) { + str += ''; + } + str += options.label + + ''; + return str; + } +}); + + +// plugin +var Input = Backbone.View.extend( +{ + // options + optionsDefault: { + value : '', + type : 'text', + placeholder : '', + disabled : false + }, + + // initialize + initialize : function(options) { + // get options + if (options) + this.options = _.defaults(options, this.optionsDefault); + else + this.options = this.optionsDefault; + + // create new element + this.setElement(this.template(this.options)); + + // disable input field + if (this.options.disabled) { + this.$el.prop('disabled', true); + } + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + this.$el.val(new_val); + } + return this.$el.val(); + }, + + // element + template: function(options) { + return ''; + } +}); + +// return +return { + Label : Label, + Button : Button, + ButtonIcon : ButtonIcon, + Input : Input, + Anchor : Anchor, + Message : Message, + Searchbox : Searchbox, + Title : Title, + Select : Select, + ButtonMenu : ButtonMenu +} +}); diff --git a/config/plugins/visualizations/charts/static/library/ui.select.js b/config/plugins/visualizations/charts/static/library/ui.select.js new file mode 100644 index 00000000000..a5036ec8b4c --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/ui.select.js @@ -0,0 +1,117 @@ +// dependencies +define(['library/utils'], function(Utils) { + + +// plugin +return Backbone.View.extend( +{ + // options + optionsDefault: { + id : '', + cls : '' + }, + + // initialize + initialize : function(options) { + // configure options + this.options = Utils.merge(options, this.optionsDefault); + + // create new element + this.setElement(this.template(this.options)); + + // add change event + var self = this; + if (this.options.onchange) { + this.$el.on('change', function() { self.options.onchange(self.value()) }); + } + }, + + // value + value : function (new_val) { + if (new_val !== undefined) { + this.$el.val(new_val); + } + return this.$el.val(); + }, + + // label + label : function () { + return this.$el.find('option:selected').text(); + }, + + // disabled + disabled: function() { + return this.$el.is(':disabled'); + }, + + // render + update: function(options) { + // selected + var selected = this.$el.val(); + + // remove all options + $(this.el).find('option').remove(); + + // add new options + for (var key in options.data) { + $(this.el).append(this.templateOption(options.data[key])); + } + + // check if selected value exists + var exists = 0 != $(this.el).find('option[value=' + selected + ']').length; + + // add selected value + if (exists) + $(this.el).val(selected); + }, + + // update from url + updateUrl : function(options, callback) { + // get json + var self = this; + Utils.get(options.url, function(json) { + // write data into array + var data = []; + for (key in json) { + data.push({label: json[key].name, value: json[key].id}); + } + + // check if disabled. do not update disabled select elements. + if (!self.disabled()) { + self.update({data: data}); + } + + // callback + if (callback) { + callback(); + } + }); + }, + + // option + templateOption: function(options) { + return ''; + }, + + // element + template: function(options) { + var tmpl = ''; + return tmpl; + } +}); + +}); diff --git a/config/plugins/visualizations/charts/static/library/utils.js b/config/plugins/visualizations/charts/static/library/utils.js new file mode 100644 index 00000000000..c685872bd9c --- /dev/null +++ b/config/plugins/visualizations/charts/static/library/utils.js @@ -0,0 +1,148 @@ +// dependencies +define([], function() { + +// get +function get (url, success, error) { + request('GET', url, {}, success, error); +}; + +// delete +function del (url, success, error) { + request('DELETE', url, {}, success, error); +}; + +// post +function post (url, data, success, error) { + request('POST', url, data, success, error); +}; + +// put +function put (url, data, success, error) { + request('PUT', url, data, success, error); +}; + +// generic function to send json to url +function request (method, url, data, success, error) { + + // encode data into url + if (method == 'GET' || method == 'DELETE') { + url = url + "?" + $.param(data); + } + + // prepare request + var xhr = new XMLHttpRequest(); + xhr.open(method, url, true); + xhr.setRequestHeader('Accept', 'application/json'); + xhr.setRequestHeader('Cache-Control', 'no-cache'); + xhr.setRequestHeader('X-Requested-With', 'XMLHttpRequest'); + xhr.setRequestHeader('Content-Type', 'application/json'); + xhr.onloadend = function() { + var status = xhr.status; + if (status == 200) { + try { + response = jQuery.parseJSON(xhr.responseText); + } catch (e) { + response = xhr.responseText; + } + success && success(response); + } else { + error && error(status); + } + }; + + // make request + if (method == 'GET' || method == 'DELETE') { + xhr.send(); + } else { + xhr.send(JSON.stringify(data)); + } +}; + +// merge +function merge (options, optionsDefault) { + if (options) + return _.defaults(options, optionsDefault); + else + return optionsDefault; +}; + +// get css value +function cssGetAttribute (classnames, name) { + if (classnames.length == 0) { + console.log('cssGetAttribute() : Requires a list of classnames'); + } + + // place dummy element + var el = $('
                '); + var traverse_el = el; + for (var i in classnames) { + traverse_el.append('
                '); + traverse_el = traverse_el.find('.' + classnames[i]); + } + + // required append + el.appendTo(':eq(0)'); + + // get value + var value = el.css(name); + + // remove element + el.remove(); + + // return css value + return value; +}; + +// load css +function cssLoadFile (url) { + // check if css is already available + if (!$('link[href^="' + url + '"]').length) + $('').appendTo('head'); +}; + +// unique ide +function uuid(){ + return (new Date().getTime()).toString(36); +}; + +// wrap +function wrap($el) { + var wrapper = $('

                '); + wrapper.append($el); + return wrapper; +}; + +// time +function time() { + // get date object + var d = new Date(); + + // format items + var hours = (d.getHours() < 10 ? "0" : "") + d.getHours(); + var minutes = (d.getMinutes() < 10 ? "0" : "") + d.getMinutes() + + // format final stamp + var datetime = d.getDate() + "/" + + (d.getMonth() + 1) + "/" + + d.getFullYear() + ", " + + hours + ":" + + minutes; + return datetime; +}; + +// return +return { + cssLoadFile : cssLoadFile, + cssGetAttribute : cssGetAttribute, + merge : merge, + get : get, + post : post, + del : del, + put : put, + request: request, + uuid: uuid, + wrap : wrap, + time : time +}; + +}); diff --git a/config/plugins/visualizations/charts/static/main.js b/config/plugins/visualizations/charts/static/main.js new file mode 100644 index 00000000000..63d961fd9a0 --- /dev/null +++ b/config/plugins/visualizations/charts/static/main.js @@ -0,0 +1,150 @@ +// dependencies +define(['library/portlet', 'library/table', 'library/ui', 'library/utils'], function(Portlet, Table, Ui, Utils) { + +// widget +return Backbone.View.extend( +{ + // initialize + initialize: function(app, options) + { + // link app + this.app = app; + + // table + this.table = new Table({ + content : 'Add charts to this table.', + ondblclick : function(chart_id) { + // get chart + var chart = self.app.charts.get(chart_id); + + // show edit + self.$el.hide(); + + // update model and show create + self.app.create.setChart(chart); + self.app.create.$el.show(); + }, + onchange : function(chart_id) { + self.app.viewport.show(chart_id); + } + }); + + // add table to portlet + var self = this; + this.portlet = new Portlet({ + icon : 'fa-list', + label : 'List of created charts:', + height : 100, + operations : { + 'new' : new Ui.ButtonIcon({ + icon : 'fa-plus', + tooltip: 'Create', + onclick: function() { + self.$el.hide(); + self.app.create.reset(); + self.app.create.$el.show(); + } + }), + 'edit' : new Ui.ButtonIcon({ + icon : 'fa-pencil', + tooltip: 'Edit', + onclick: function() { + // check if element has been selected + var chart_id = self.table.value(); + if (!chart_id) { + return; + } + + // get chart + var chart = self.app.charts.get(chart_id); + + // show edit + self.$el.hide(); + self.app.create.$el.show(); + self.app.create.setChart(chart); + } + }), + 'delete' : new Ui.ButtonIcon({ + icon : 'fa-minus', + tooltip: 'Delete', + onclick: function() { + + // check if element has been selected + var chart_id = self.table.value(); + if (!chart_id) { + return; + } + + // title + var chart = self.app.charts.get(chart_id); + + // show modal + self.app.modal.show({ + title : 'Are you sure?', + body : 'The selected chart "' + chart.get('title') + '" will be irreversibly deleted.', + buttons : { + 'Cancel' : function() {self.app.modal.hide();}, + 'Delete' : function() { + // hide modal + self.app.modal.hide(); + + // remove chart + self.app.charts.remove(chart_id); + } + } + }); + } + }), + } + }); + this.portlet.append(this.table.$el); + + // append to main + this.$el.append(this.portlet.$el); + + // events + var self = this; + this.app.charts.on('add', function(chart) { + // add + self._addChart(chart); + }); + this.app.charts.on('remove', function(chart) { + // remove + self._removeChart(chart); + }); + this.app.charts.on('change', function(chart) { + // replace + self._removeChart(chart); + self._addChart(chart); + }); + }, + + // append + append : function($el) { + this.$el.append(Utils.wrap('')); + this.$el.append($el); + }, + + // add + _addChart: function(chart) { + // add title to table + this.table.add(chart.get('title')); + + // get chart type + var type = this.app.types.get(chart.get('type')); + this.table.add(type.title); + + // add additional columns + this.table.add('Last change: ' + chart.get('date')); + this.table.prepend(chart.get('id')); + this.table.value(chart.get('id')); + }, + + // remove + _removeChart: function(chart) { + // remove from to table + this.table.remove(chart.id); + } +}); + +}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/models/chart.js b/config/plugins/visualizations/charts/static/models/chart.js new file mode 100644 index 00000000000..c729ab4c5a3 --- /dev/null +++ b/config/plugins/visualizations/charts/static/models/chart.js @@ -0,0 +1,42 @@ +// dependencies +define(['models/groups'], function(Groups) { + + +// model +return Backbone.Model.extend( +{ + // defaults + defaults : { + id : null, + title : '', + type : '', + date : null + }, + + // initialize + initialize: function(options) + { + this.groups = new Groups(); + }, + + // reset + reset: function() + { + this.clear().set(this.defaults); + this.groups.reset(); + }, + + // copy + copy: function(new_chart) { + // copy chart/groups + var current = this; + current.set(new_chart.attributes); + current.groups.reset(); + new_chart.groups.each(function(group) { + current.groups.add(group.clone()); + }); + current.trigger('change', current); + } +}); + +}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/models/charts.js b/config/plugins/visualizations/charts/static/models/charts.js new file mode 100644 index 00000000000..99188856aa5 --- /dev/null +++ b/config/plugins/visualizations/charts/static/models/charts.js @@ -0,0 +1,10 @@ +// dependencies +define(['models/chart'], function(Chart) { + +// collection +return Backbone.Collection.extend( +{ + model: Chart +}); + +}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/models/datasets.js b/config/plugins/visualizations/charts/static/models/datasets.js new file mode 100644 index 00000000000..989f77e1893 --- /dev/null +++ b/config/plugins/visualizations/charts/static/models/datasets.js @@ -0,0 +1,125 @@ +// dependencies +define(['library/utils'], function(Utils) { + +// widget +return Backbone.Model.extend( +{ + // options + optionsDefault : { + limit : 20, + pace : 1000, + max : 2 + }, + + // list + list: {}, + + // initialize + initialize: function(app, options) + { + // link app + this.app = app; + + // configure options + this.options = Utils.merge(options, this.optionsDefault); + }, + + // get + get: function(options, callback) { + // check if dataset already exists + var dataset = this.list[options.id]; + if (dataset) { + if (dataset.values) { + if (dataset.values[options.column]) { + if (callback) { + callback(dataset); + } + return dataset; + } + } + } else { + this.list[options.id] = dataset = this.app.options.dataset; + } + + // initiate fetch cycle + if (options.column !== undefined) { + this._fetch(options, callback); + } else { + if (callback) { + callback(dataset); + } + return dataset; + } + + // return + return dataset; + }, + + // size + length: function() { + return this.list.length; + }, + + // request data + _fetch : function(options, callback) { + // get dataset + var dataset = this.list[options.id]; + + // initialize values for datasets + if (!dataset.values) { + dataset.values = {}; + } + if (!dataset.values[options.column]) { + dataset.values[options.column] = []; + } + + // initialize page number + if (options.page === undefined) { + options.page = 0; + } else { + options.page++; + } + + // check max page + if (options.page > this.options.max) { + return; + } + + // config limits + var limit = this.options.limit; + var offset = this.options.limit * options.page; + + // make request + var self = this; + Utils.request('GET', config.root + 'api/datasets/' + options.id, { + data_type : 'raw_data', + provider : 'dataset-column', + limit : limit, + offset : offset, + indeces : options.column + }, function(response) { + // verify if all data has been fetched + if (response.data.length > 0) { + // add values to dataset + for (var key in response.data){ + var value = response.data[key][0]; + if (value !== undefined) { + dataset.values[options.column].push(value); + } else { + return dataset; + } + } + + // update charts + if (callback) { + callback(dataset); + } + + // next call + setTimeout(function() { self._fetch(options, callback); }, self.options.pace); + } + }); + } +}); + +}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/models/group.js b/config/plugins/visualizations/charts/static/models/group.js new file mode 100644 index 00000000000..6727bbcb815 --- /dev/null +++ b/config/plugins/visualizations/charts/static/models/group.js @@ -0,0 +1,24 @@ +// dependencies +define(['library/utils'], function(Utils) { + + +// model +return Backbone.Model.extend( +{ + // defaults + defaults : { + }, + + // initialize + initialize: function(options) + { + }, + + // reset + reset: function() + { + this.clear().set(this.defaults); + } +}); + +}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/models/groups.js b/config/plugins/visualizations/charts/static/models/groups.js new file mode 100644 index 00000000000..156ada47be4 --- /dev/null +++ b/config/plugins/visualizations/charts/static/models/groups.js @@ -0,0 +1,10 @@ +// dependencies +define(['models/group'], function(Group) { + +// collection +return Backbone.Collection.extend( +{ + model: Group +}); + +}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/models/types.js b/config/plugins/visualizations/charts/static/models/types.js new file mode 100644 index 00000000000..54d03a4026c --- /dev/null +++ b/config/plugins/visualizations/charts/static/models/types.js @@ -0,0 +1,71 @@ +// dependencies +define([], function() { + +// widget +return Backbone.Model.extend( +{ + // types + defaults: { + 'bardiagram' : { + title : 'Bar diagram', + data : { + y : { + title : 'Values for y-axis' + } + } + }, + 'horizontal' : { + title : 'Bar diagram (horizontal)', + data : { + y : { + title : 'Values for y-axis' + } + } + }, + 'line' : { + title : 'Line chart', + data : { + y : { + title : 'Values for y-axis' + } + } + }, + 'linewithfocus' : { + title : 'Line chart (with focus)', + data : { + y : { + title : 'Values for y-axis' + } + } + }, + 'piechart' : { + title : 'Pie chart (under development)', + data : { + y : { + title : 'Values for y-axis' + } + } + }, + 'scatterplot' : { + title : 'Scatter plot', + data : { + x : { + title : 'Values for x-axis' + }, + y : { + title : 'Values for y-axis' + } + } + }, + 'stackedarea' : { + title : 'Stacked area', + data : { + y : { + title : 'Values for y-axis' + } + } + } + } +}); + +}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/plugins/nv.d3.css b/config/plugins/visualizations/charts/static/plugins/nv.d3.css new file mode 100644 index 00000000000..d46f7ebce24 --- /dev/null +++ b/config/plugins/visualizations/charts/static/plugins/nv.d3.css @@ -0,0 +1 @@ +.chartWrap{margin:0;padding:0;overflow:hidden}.nvtooltip.with-3d-shadow,.with-3d-shadow .nvtooltip{-moz-box-shadow:0 5px 10px rgba(0,0,0,.2);-webkit-box-shadow:0 5px 10px rgba(0,0,0,.2);box-shadow:0 5px 10px rgba(0,0,0,.2);-webkit-border-radius:6px;-moz-border-radius:6px;border-radius:6px}.nvtooltip{position:absolute;background-color:rgba(255,255,255,1);padding:1px;border:1px solid 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                "+n+" at "+t+"

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arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){"use strict";function k(e){return e.each(function(e){function U(e){var t=+(e=="e"),n=t?1:-1,r=M/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function z(){a.empty()||a.extent(w),I.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),W(),k.transitionDuration(e)}),w&&a.extent(w);var I=H.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),q=I.enter().append("g");q.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",M),q.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",M);var R=H.select(".nv-x.nv-brush").call(a);R.selectAll("rect").attr("height",M),R.selectAll(".resize").append("path").attr("d",U),W(),s.scale(g).ticks(A/100).tickSize(-M,0),H.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(H.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(M/36).tickSize(-A,0),d3.transition(H.select(".nv-context .nv-y.nv-axis")).call(o),H.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,L.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"

                "+e+"

                "+"

                "+n+" at "+t+"

                "},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=250;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return 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\ No newline at end of file diff --git a/config/plugins/visualizations/charts/static/viewport.js b/config/plugins/visualizations/charts/static/viewport.js new file mode 100644 index 00000000000..a2c83c1c1d1 --- /dev/null +++ b/config/plugins/visualizations/charts/static/viewport.js @@ -0,0 +1,202 @@ +// dependencies +define(['library/portlet', 'library/ui', 'library/utils'], + function(Portlet, Ui, Utils) { + +// widget +return Backbone.View.extend( +{ + // list + list: {}, + + // options + optionsDefault : + { + height : 300 + }, + + // initialize + initialize: function(app, options) + { + // link app + this.app = app; + + // link options + this.options = Utils.merge(options, this.optionsDefault); + + // add table to portlet + this.portlet = new Portlet({ + height : this.options.height, + overflow : 'hidden' + }); + + // set this element + this.setElement(this.portlet.$el); + + // events + var self = this; + + // add + this.app.charts.on('add', function(chart) { + self._addChart(chart); + }); + + // remove + this.app.charts.on('remove', function(chart) { + self._removeChart(chart.id); + }); + + // replace + this.app.charts.on('change', function(chart) { + self._removeChart(chart.id); + self._addChart(chart); + }); + }, + + // show + show: function(id) { + // hide all + this.$el.find('svg').hide(); + + var item = this.list[id]; + if (item) { + // show selected chart + this.$el.find(item.svg_id).show(); + + // this trigger d3 update events + $(window).trigger('resize'); + } + }, + + // add + _addChart: function(chart) { + // make sure that svg does not exist already + this._removeChart(chart.id); + + // create id + var svg_id = '#svg_' + chart.id; + + // create element + var chart_el = $(this._template({id: svg_id, height : this.options.height})); + + // add to portlet + this.portlet.append(chart_el); + + // backup id + this.list[chart.id] = { + svg_id : svg_id + } + + // identify chart type + var chart_type = chart.get('type'); + var chart_settings = this.app.types.get(chart_type); + + // create chart view + var self = this; + require(['charts/' + chart_type], function(ChartView) { + // create chart + var view = new ChartView(self.app, {svg_id : svg_id, chart : chart}); + + // reset chart data + var chart_data = []; + + // request data + var chart_index = 0; + chart.groups.each(function(group) { + + // add group data + chart_data.push({ + key : (chart_index + 1) + ':' + group.get('label'), + values : [] + }); + + // get data + for (var key in chart_settings.data) { + // configure request + var data_options = { + view : view, + data : chart_data, + index : chart_index, + dataset_id : group.get('dataset_id'), + column : group.get(key), + column_key : key + } + + // make request + self._data(data_options); + } + + // count + chart_index++; + }); + + // add view + self.list[chart.id].view = view; + }); + }, + + // data + _data: function(options) { + // gather objects + var view = options.view; + var data = options.data; + + // gather parameters + var index = options.index; + var column = options.column; + var dataset_id = options.dataset_id; + var column_key = options.column_key; + var group_data = data[options.index]; + + // send request + self.app.datasets.get({id : dataset_id, column: column}, function(dataset) { + // select column + var values = dataset.values[column]; + var n_values = values.length; + + // read column values + var column_values = []; + for (var i = 0; i < n_values; i++) { + var value = values[i]; + if(!isNaN(value)) { + column_values.push(value); + } else { + column_values.push(0) + } + } + + // write column values + for (var i = 0; i < n_values; i++) { + // make sure dictionary exists + if (group_data.values[i] === undefined) { + group_data.values[i] = { + x : i, + y : 0 + } + } + + // write data + group_data.values[i][column_key] = column_values[i]; + } + + // refresh view + view.refresh(data); + }); + + }, + + // remove + _removeChart: function(id) { + var item = this.list[id]; + if (item) { + d3.select(item.svg_id).remove(); + $(item.svg_id).remove(); + } + }, + + // template + _template: function(options) { + return ''; + } +}); + +}); \ No newline at end of file diff --git a/config/plugins/visualizations/charts/templates/charts.mako b/config/plugins/visualizations/charts/templates/charts.mako new file mode 100644 index 00000000000..5f50efa337e --- /dev/null +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -0,0 +1,78 @@ +<% + scripts = [ 'jquery/jquery.js', + 'bootstrap.js', + 'require.js', + 'underscore.js', + 'backbone/backbone.js', + 'd3.js'] +%> + + + + + + + ${hda.name} | ${visualization_name} + + %for v in scripts: + + %endfor + + ## css + + + ## install nv.d3 module + + + + + + + + + From 4edc5cc240419d9a2dc4946c93d21d530e6833ac Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Mon, 13 Jan 2014 06:14:39 -0500 Subject: [PATCH 0737/1033] Sample data for visualization plugin --- config/plugins/visualizations/charts/sample.txt | 1 + 1 file changed, 1 insertion(+) create mode 100644 config/plugins/visualizations/charts/sample.txt diff --git a/config/plugins/visualizations/charts/sample.txt b/config/plugins/visualizations/charts/sample.txt new file mode 100644 index 00000000000..b9d792d6f84 --- /dev/null +++ b/config/plugins/visualizations/charts/sample.txt @@ -0,0 +1 @@ +43 55 63 99 28 85 20 31 47 14 1 63 94 83 94 74 7 73 51 7 8 34 2 94 87 21 72 51 3 84 5 50 40 30 59 43 19 77 30 80 22 55 69 43 77 72 12 54 53 56 36 34 81 28 59 64 54 29 57 69 57 90 93 32 45 98 40 16 52 83 6 17 39 86 10 11 38 69 19 50 67 51 47 22 58 27 65 49 92 96 \ No newline at end of file From aa08c20912c1643b1a2594a7b37be84e41e24a59 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Mon, 13 Jan 2014 06:17:24 -0500 Subject: [PATCH 0738/1033] Update sample data for visualization plugin --- config/plugins/visualizations/charts/sample.txt | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/config/plugins/visualizations/charts/sample.txt b/config/plugins/visualizations/charts/sample.txt index b9d792d6f84..a75b7f2aa9c 100644 --- a/config/plugins/visualizations/charts/sample.txt +++ b/config/plugins/visualizations/charts/sample.txt @@ -1 +1,9 @@ -43 55 63 99 28 85 20 31 47 14 1 63 94 83 94 74 7 73 51 7 8 34 2 94 87 21 72 51 3 84 5 50 40 30 59 43 19 77 30 80 22 55 69 43 77 72 12 54 53 56 36 34 81 28 59 64 54 29 57 69 57 90 93 32 45 98 40 16 52 83 6 17 39 86 10 11 38 69 19 50 67 51 47 22 58 27 65 49 92 96 \ No newline at end of file +43 55 63 99 28 85 20 31 47 14 +1 63 94 83 94 74 7 73 51 7 +8 34 2 94 87 21 72 51 3 84 +5 50 40 30 59 43 19 77 30 80 +22 55 69 43 77 72 12 54 53 56 +36 34 81 28 59 64 54 29 57 69 +57 90 93 32 45 98 40 16 52 83 +6 17 39 86 10 11 38 69 19 50 +67 51 47 22 58 27 65 49 92 96 \ No newline at end of file From 5f91eb4fd1707e262e11579ee976932c594d5765 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 13 Jan 2014 08:58:22 -0600 Subject: [PATCH 0739/1033] Non-exhaustive tools related PEP-8 fixes. Fixes for api/tools.py, tools/__init__.py, and tools/parameters/{__init__.py,basic.py}. --- lib/galaxy/tools/__init__.py | 176 ++++++++++++++++-------- lib/galaxy/tools/parameters/__init__.py | 14 +- lib/galaxy/tools/parameters/basic.py | 60 ++++---- lib/galaxy/webapps/galaxy/api/tools.py | 25 ++-- 4 files changed, 176 insertions(+), 99 deletions(-) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index ecb79c182b5..14e3ded2ae6 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -20,7 +20,7 @@ import urllib from math import isinf from galaxy import eggs -eggs.require( "MarkupSafe" ) #MarkupSafe must load before mako +eggs.require( "MarkupSafe" ) # MarkupSafe must load before mako eggs.require( "Mako" ) eggs.require( "elementtree" ) eggs.require( "Paste" ) @@ -69,11 +69,13 @@ from .loader import load_tool, template_macro_params log = logging.getLogger( __name__ ) -WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile( '''\$\{.+?\}''' ) +WORKFLOW_PARAMETER_REGULAR_EXPRESSION = re.compile( '''\$\{.+?\}''' ) + class ToolNotFoundException( Exception ): pass + def to_dict_helper( obj, kwargs ): """ Helper function that provides the appropriate kwargs to to_dict an object. """ @@ -83,6 +85,7 @@ def to_dict_helper( obj, kwargs ): return obj.to_dict( **kwargs ) + class ToolBox( object, Dictifiable ): """Container for a collection of tools""" @@ -421,6 +424,7 @@ class ToolBox( object, Dictifiable ): return self.app.install_model.context.query( self.app.install_model.ToolVersion ) \ .filter( self.app.install_model.ToolVersion.table.c.tool_id == tool_id ) \ .first() + def __get_tool_shed_repository( self, tool_shed, name, owner, installed_changeset_revision ): return self.app.install_model.context.query( self.app.install_model.ToolShedRepository ) \ .filter( and_( self.app.install_model.ToolShedRepository.table.c.tool_shed == tool_shed, @@ -730,8 +734,8 @@ class ToolBox( object, Dictifiable ): # Produce panel. rval = [] kwargs = dict( - trans = trans, - link_details = True + trans=trans, + link_details=True ) for elt in panel_elts: rval.append( to_dict_helper( elt, kwargs ) ) @@ -798,7 +802,6 @@ def _filter_for_panel( item, filters, context ): return None - class ToolSection( object, Dictifiable ): """ A group of tools with similar type/purpose that will be displayed as a @@ -828,8 +831,8 @@ class ToolSection( object, Dictifiable ): section_dict = super( ToolSection, self ).to_dict() section_elts = [] kwargs = dict( - trans = trans, - link_details = link_details + trans=trans, + link_details=link_details ) for elt in self.elems.values(): section_elts.append( to_dict_helper( elt, kwargs ) ) @@ -837,6 +840,7 @@ class ToolSection( object, Dictifiable ): return section_dict + class ToolSectionLabel( object, Dictifiable ): """ A label for a set of tools that can be displayed above groups of tools @@ -850,6 +854,7 @@ class ToolSectionLabel( object, Dictifiable ): self.id = elem.get( "id" ) self.version = elem.get( "version" ) or '' + class DefaultToolState( object ): """ Keeps track of the state of a users interaction with a tool between @@ -860,6 +865,7 @@ class DefaultToolState( object ): self.page = 0 self.rerun_remap_job_id = None self.inputs = None + def encode( self, tool, app, secure=True ): """ Convert the data to a string @@ -877,6 +883,7 @@ class DefaultToolState( object ): return "%s:%s" % ( a, b ) else: return value + def decode( self, value, tool, app, secure=True ): """ Restore the state from a string @@ -896,6 +903,7 @@ class DefaultToolState( object ): self.rerun_remap_job_id = None self.inputs = params_from_strings( tool.inputs, values, app, ignore_errors=True ) + class ToolOutput( object, Dictifiable ): """ Represents an output datasets produced by a tool. For backward @@ -907,7 +915,7 @@ class ToolOutput( object, Dictifiable ): dict_collection_visible_keys = ( 'name', 'format', 'label', 'hidden' ) def __init__( self, name, format=None, format_source=None, metadata_source=None, - parent=None, label=None, filters = None, actions = None, hidden=False ): + parent=None, label=None, filters=None, actions=None, hidden=False ): self.name = name self.format = format self.format_source = format_source @@ -993,16 +1001,19 @@ class Tool( object, Dictifiable ): # Parse XML element containing configuration self.parse( root, guid=guid ) self.external_runJob_script = app.config.drmaa_external_runjob_script + @property def sa_session( self ): """Returns a SQLAlchemy session""" return self.app.model.context + @property def tool_version( self ): """Return a ToolVersion if one exists for our id""" return self.app.install_model.context.query( self.app.install_model.ToolVersion ) \ .filter( self.app.install_model.ToolVersion.table.c.tool_id == self.id ) \ .first() + @property def tool_versions( self ): # If we have versions, return them. @@ -1010,6 +1021,7 @@ class Tool( object, Dictifiable ): if tool_version: return tool_version.get_versions( self.app ) return [] + @property def tool_version_ids( self ): # If we have versions, return a list of their tool_ids. @@ -1017,6 +1029,7 @@ class Tool( object, Dictifiable ): if tool_version: return tool_version.get_version_ids( self.app ) return [] + @property def tool_shed_repository( self ): # If this tool is included in an installed tool shed repository, return it. @@ -1075,7 +1088,7 @@ class Tool( object, Dictifiable ): :returns: galaxy.jobs.JobDestination -- The destination definition and runner parameters. """ return self.app.job_config.get_destination(self.__get_job_tool_configuration(job_params=job_params).destination) - + def get_panel_section( self ): for key, item in self.app.toolbox.integrated_tool_panel.items(): if item: @@ -1099,7 +1112,7 @@ class Tool( object, Dictifiable ): # Get the (user visible) name of the tool self.name = root.get( "name" ) if not self.name: - raise Exception, "Missing tool 'name'" + raise Exception( "Missing tool 'name'" ) # Get the UNIQUE id for the tool self.old_id = root.get( "id" ) if guid is None: @@ -1107,7 +1120,7 @@ class Tool( object, Dictifiable ): else: self.id = guid if not self.id: - raise Exception, "Missing tool 'id'" + raise Exception( "Missing tool 'id'" ) self.version = root.get( "version" ) if not self.version: # For backward compatibility, some tools may not have versions yet. @@ -1127,7 +1140,7 @@ class Tool( object, Dictifiable ): # Command line (template). Optional for tools that do not invoke a local program command = root.find("command") if command is not None and command.text is not None: - self.command = command.text.lstrip() # get rid of leading whitespace + self.command = command.text.lstrip() # get rid of leading whitespace # Must pre-pend this AFTER processing the cheetah command template self.interpreter = command.get( "interpreter", None ) else: @@ -1169,14 +1182,15 @@ class Tool( object, Dictifiable ): self_ids = [ self.id.lower() ] if self.old_id != self.id: # Handle toolshed guids - self_ids = [ self.id.lower(), self.id.lower().rsplit('/',1)[0], self.old_id.lower() ] + self_ids = [ self.id.lower(), self.id.lower().rsplit('/', 1)[0], self.old_id.lower() ] self.all_ids = self_ids # In the toolshed context, there is no job config. if 'job_config' in dir(self.app): self.job_tool_configurations = self.app.job_config.get_job_tool_configurations(self_ids) # Is this a 'hidden' tool (hidden in tool menu) self.hidden = xml_text(root, "hidden") - if self.hidden: self.hidden = string_as_bool(self.hidden) + if self.hidden: + self.hidden = string_as_bool(self.hidden) # Load any tool specific code (optional) Edit: INS 5/29/2007, # allow code files to have access to the individual tool's # "module" if it has one. Allows us to reuse code files, etc. @@ -1186,7 +1200,7 @@ class Tool( object, Dictifiable ): for hook_elem in code_elem.findall("hook"): for key, value in hook_elem.items(): # map hook to function - self.hook_map[key]=value + self.hook_map[key] = value file_name = code_elem.get("file") code_path = os.path.join( self.tool_dir, file_name ) execfile( code_path, self.code_namespace ) @@ -1308,7 +1322,7 @@ class Tool( object, Dictifiable ): elif len( enctypes ) == 1: self.enctype = enctypes.pop() else: - raise Exception, "Conflicting required enctypes: %s" % str( enctypes ) + raise Exception( "Conflicting required enctypes: %s" % str( enctypes ) ) # Check if the tool either has no parameters or only hidden (and # thus hardcoded) FIXME: hidden parameters aren't # parameters at all really, and should be passed in a different @@ -1318,6 +1332,7 @@ class Tool( object, Dictifiable ): if not isinstance( param, ( HiddenToolParameter, BaseURLToolParameter ) ): self.input_required = True break + def parse_help( self, root ): """ Parse the help text for the tool. Formatted in reStructuredText, but @@ -1365,6 +1380,7 @@ class Tool( object, Dictifiable ): # Pad out help pages to match npages ... could this be done better? while len( self.help_by_page ) < self.npages: self.help_by_page.append( self.help ) + def parse_outputs( self, root ): """ Parse elements and fill in self.outputs (keyed by name) @@ -1601,6 +1617,7 @@ class Tool( object, Dictifiable ): else: display = None return display, inputs + def parse_input_elem( self, parent_elem, enctypes, context=None ): """ Parse a parent element whose children are inputs -- these could be @@ -1653,7 +1670,7 @@ class Tool( object, Dictifiable ): input_elem = elem.find( "param" ) assert input_elem is not None, " must have a child " group.test_param = self.parse_param_elem( input_elem, enctypes, context ) - possible_cases = list( group.test_param.legal_values ) #store possible cases, undefined whens will have no inputs + possible_cases = list( group.test_param.legal_values ) # store possible cases, undefined whens will have no inputs # Must refresh when test_param changes group.test_param.refresh_on_change = True # And a set of possible cases @@ -1694,6 +1711,7 @@ class Tool( object, Dictifiable ): param.ref_input = context[ param.data_ref ] self.input_params.append( param ) return rval + def parse_param_elem( self, input_elem, enctypes, context ): """ Parse a single "" element and return a ToolParameter instance. @@ -1777,12 +1795,14 @@ class Tool( object, Dictifiable ): raise Exception( "'get_param_html_map' only supported for simple paramters" ) rval[key] = param.get_html( trans, other_values=other_values ) return rval + def get_param( self, key ): """ Returns the parameter named `key` or None if there is no such parameter. """ return self.inputs.get( key, None ) + def get_hook(self, name): """ Returns an object from the code file referenced by `code_namespace` @@ -1795,6 +1815,7 @@ class Tool( object, Dictifiable ): elif name in self.code_namespace: return self.code_namespace[name] return None + def visit_inputs( self, value, callback ): """ Call the function `callback` on each parameter of this tool. Visits @@ -1811,6 +1832,7 @@ class Tool( object, Dictifiable ): callback( "", input, value[input.name] ) else: input.visit_inputs( "", value[input.name], callback ) + def handle_input( self, trans, incoming, history=None, old_errors=None, process_state='update', source='html' ): """ Process incoming parameters for this tool from the dict `incoming`, @@ -1955,6 +1977,7 @@ class Tool( object, Dictifiable ): [ self.find_fieldstorage( y ) for y in x.values() ] elif type( x ) is types.ListType: [ self.find_fieldstorage( y ) for y in x ] + def handle_interrupted( self, trans, inputs ): """ Upon handling inputs, if it appears that we have received an incomplete @@ -2320,6 +2343,7 @@ class Tool( object, Dictifiable ): errors[ input.name ] = error state[ input.name ] = value return errors + @property def params_with_missing_data_table_entry( self ): """ @@ -2333,6 +2357,7 @@ class Tool( object, Dictifiable ): if options and options.missing_tool_data_table_name and input_param not in params: params.append( input_param ) return params + @property def params_with_missing_index_file( self ): """ @@ -2346,6 +2371,7 @@ class Tool( object, Dictifiable ): if options and options.missing_index_file and input_param not in params: params.append( input_param ) return params + def get_static_param_values( self, trans ): """ Returns a map of parameter names and values if the tool does not @@ -2361,6 +2387,7 @@ class Tool( object, Dictifiable ): else: raise Exception( "Unexpected parameter type" ) return args + def execute( self, trans, incoming={}, set_output_hid=True, history=None, **kwargs ): """ Execute the tool using parameter values in `incoming`. This just @@ -2369,10 +2396,13 @@ class Tool( object, Dictifiable ): when run will build the tool's outputs, e.g. `DefaultToolAction`. """ return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) + def params_to_strings( self, params, app ): return params_to_strings( self.inputs, params, app ) + def params_from_strings( self, params, app, ignore_errors=False ): return params_from_strings( self.inputs, params, app, ignore_errors ) + def check_and_update_param_values( self, values, trans, update_values=True, allow_workflow_parameters=False ): """ Check that all parameters have values, and fill in with default @@ -2382,6 +2412,7 @@ class Tool( object, Dictifiable ): messages = {} self.check_and_update_param_values_helper( self.inputs, values, trans, messages, update_values=update_values, allow_workflow_parameters=allow_workflow_parameters ) return messages + def check_and_update_param_values_helper( self, inputs, values, trans, messages, context=None, prefix="", update_values=True, allow_workflow_parameters=False ): """ Recursive helper for `check_and_update_param_values_helper` @@ -2438,6 +2469,7 @@ class Tool( object, Dictifiable ): messages[ input.name ] = "Value no longer valid for '%s%s', replaced with default" % ( prefix, input.label ) if update_values: values[ input.name ] = input.get_initial_value( trans, context ) + def handle_unvalidated_param_values( self, input_values, app ): """ Find any instances of `UnvalidatedValue` within input_values and @@ -2448,6 +2480,7 @@ class Tool( object, Dictifiable ): if not self.check_values: return self.handle_unvalidated_param_values_helper( self.inputs, input_values, app ) + def handle_unvalidated_param_values_helper( self, inputs, input_values, app, context=None, prefix="" ): """ Recursive helper for `handle_unvalidated_param_values` @@ -2488,6 +2521,7 @@ class Tool( object, Dictifiable ): % ( prefix, input.label, e ) raise LateValidationError( message ) input_values[ input.name ] = value + def handle_job_failure_exception( self, e ): """ Called by job.fail when an exception is generated to allow generation @@ -2499,6 +2533,7 @@ class Tool( object, Dictifiable ): if isinstance( e, LateValidationError ): message = e.message return message + def build_param_dict( self, incoming, input_datasets, output_datasets, output_paths, job_working_directory ): """ Build the dictionary of parameters for substituting into the command @@ -2754,6 +2789,7 @@ class Tool( object, Dictifiable ): # Remove newlines redirect_url_params = redirect_url_params.replace( "\n", " " ).replace( "\r", " " ) return redirect_url_params + def parse_redirect_url( self, data, param_dict ): """ Parse the REDIRECT_URL tool param. Tools that send data to an external @@ -2793,6 +2829,7 @@ class Tool( object, Dictifiable ): USERNAME = 'Anonymous' redirect_url += "&USERNAME=%s" % USERNAME return redirect_url + def call_hook( self, hook_name, *args, **kwargs ): """ Call the custom code hook function identified by 'hook_name' if any, @@ -2808,15 +2845,19 @@ class Tool( object, Dictifiable ): original_message = e.args[0] e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, original_message ), ) raise + def exec_before_job( self, app, inp_data, out_data, param_dict={} ): pass - def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ): + + def exec_after_process( self, app, inp_data, out_data, param_dict, job=None ): pass - def job_failed( self, job_wrapper, message, exception = False ): + + def job_failed( self, job_wrapper, message, exception=False ): """ Called when a job has failed """ pass + def collect_associated_files( self, output, job_working_directory ): """ Find extra files in the job working directory and move them into @@ -2835,10 +2876,11 @@ class Tool( object, Dictifiable ): for f in files: self.app.object_store.update_from_file(hda.dataset, extra_dir=extra_dir, - alt_name = f, - file_name = os.path.join(root, f), - create = True, - preserve_symlinks = True ) + alt_name=f, + file_name=os.path.join(root, f), + create=True, + preserve_symlinks=True + ) # Clean up after being handled by object store. # FIXME: If the object (e.g., S3) becomes async, this will # cause issues so add it to the object store functionality? @@ -2848,6 +2890,7 @@ class Tool( object, Dictifiable ): except Exception, e: log.debug( "Error in collect_associated_files: %s" % ( e ) ) continue + def collect_child_datasets( self, output, job_working_directory ): """ Look for child dataset files, create HDA and attach to parent. @@ -2858,9 +2901,9 @@ class Tool( object, Dictifiable ): for name, outdata in output.items(): filenames = [] if 'new_file_path' in self.app.config.collect_outputs_from: - filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path,"child_%i_*" % outdata.id) ) ) + filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path, "child_%i_*" % outdata.id) ) ) if 'job_working_directory' in self.app.config.collect_outputs_from: - filenames.extend( glob.glob(os.path.join(job_working_directory,"child_%i_*" % outdata.id) ) ) + filenames.extend( glob.glob(os.path.join(job_working_directory, "child_%i_*" % outdata.id) ) ) for filename in filenames: if not name in children: children[name] = {} @@ -2909,12 +2952,14 @@ class Tool( object, Dictifiable ): # Need to update all associated output hdas, i.e. history was # shared with job running for dataset in outdata.dataset.history_associations: - if outdata == dataset: continue + if outdata == dataset: + continue # Create new child dataset - child_data = child_dataset.copy( parent_id = dataset.id ) + child_data = child_dataset.copy( parent_id=dataset.id ) self.sa_session.add( child_data ) self.sa_session.flush() return children + def collect_primary_datasets( self, output, job_working_directory ): """ Find any additional datasets generated by a tool and attach (for @@ -2937,9 +2982,9 @@ class Tool( object, Dictifiable ): for name, outdata in output.items(): filenames = [] if 'new_file_path' in self.app.config.collect_outputs_from: - filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path,"primary_%i_*" % outdata.id) ) ) + filenames.extend( glob.glob(os.path.join(self.app.config.new_file_path, "primary_%i_*" % outdata.id) ) ) if 'job_working_directory' in self.app.config.collect_outputs_from: - filenames.extend( glob.glob(os.path.join(job_working_directory,"primary_%i_*" % outdata.id) ) ) + filenames.extend( glob.glob(os.path.join(job_working_directory, "primary_%i_*" % outdata.id) ) ) for filename in filenames: if not name in primary_datasets: primary_datasets[name] = {} @@ -2948,8 +2993,10 @@ class Tool( object, Dictifiable ): parent_id = int(fields.pop(0)) designation = fields.pop(0) visible = fields.pop(0).lower() - if visible == "visible": visible = True - else: visible = False + if visible == "visible": + visible = True + else: + visible = False ext = fields.pop(0).lower() dbkey = outdata.dbkey if fields: @@ -2999,7 +3046,8 @@ class Tool( object, Dictifiable ): # Need to update all associated output hdas, i.e. history was # shared with job running for dataset in outdata.dataset.history_associations: - if outdata == dataset: continue + if outdata == dataset: + continue new_data = primary_data.copy() dataset.history.add( new_data ) self.sa_session.add( new_data ) @@ -3029,7 +3077,7 @@ class Tool( object, Dictifiable ): if io_details: tool_dict[ 'inputs' ] = [ input.to_dict( trans ) for input in self.inputs.values() ] tool_dict[ 'outputs' ] = [ output.to_dict() for output in self.outputs.values() ] - + tool_dict[ 'panel_section_id' ], tool_dict[ 'panel_section_name' ] = self.get_panel_section() return tool_dict @@ -3044,6 +3092,7 @@ class OutputParameterJSONTool( Tool ): JSONified within the contents of an output dataset """ tool_type = 'output_parameter_json' + def _prepare_json_list( self, param_list ): rval = [] for value in param_list: @@ -3054,6 +3103,7 @@ class OutputParameterJSONTool( Tool ): else: rval.append( str( value ) ) return rval + def _prepare_json_param_dict( self, param_dict ): rval = {} for key, value in param_dict.iteritems(): @@ -3064,11 +3114,12 @@ class OutputParameterJSONTool( Tool ): else: rval[ key ] = str( value ) return rval + def exec_before_job( self, app, inp_data, out_data, param_dict=None ): if param_dict is None: param_dict = {} json_params = {} - json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? + json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) # it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? json_params[ 'output_data' ] = [] json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) json_filename = None @@ -3078,12 +3129,12 @@ class OutputParameterJSONTool( Tool ): #allow multiple files to be created file_name = str( wrapped_data ) extra_files_path = str( wrapped_data.files_path ) - data_dict = dict( out_data_name = out_name, - ext = data.ext, - dataset_id = data.dataset.id, - hda_id = data.id, - file_name = file_name, - extra_files_path = extra_files_path ) + data_dict = dict( out_data_name=out_name, + ext=data.ext, + dataset_id=data.dataset.id, + hda_id=data.id, + file_name=file_name, + extra_files_path=extra_files_path ) json_params[ 'output_data' ].append( data_dict ) if json_filename is None: json_filename = file_name @@ -3091,6 +3142,7 @@ class OutputParameterJSONTool( Tool ): out.write( json.dumps( json_params ) ) out.close() + class DataSourceTool( OutputParameterJSONTool ): """ Alternate implementation of Tool for data_source tools -- those that @@ -3101,11 +3153,13 @@ class DataSourceTool( OutputParameterJSONTool ): def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '' % self.id ) ) + def parse_inputs( self, root ): super( DataSourceTool, self ).parse_inputs( root ) if 'GALAXY_URL' not in self.inputs: self.inputs[ 'GALAXY_URL' ] = self._build_GALAXY_URL_parameter() self.inputs_by_page[0][ 'GALAXY_URL' ] = self.inputs[ 'GALAXY_URL' ] + def exec_before_job( self, app, inp_data, out_data, param_dict=None ): if param_dict is None: param_dict = {} @@ -3115,7 +3169,7 @@ class DataSourceTool( OutputParameterJSONTool ): name = param_dict.get( 'name' ) json_params = {} - json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? + json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) # it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? json_params[ 'output_data' ] = [] json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) json_filename = None @@ -3138,12 +3192,12 @@ class DataSourceTool( OutputParameterJSONTool ): data.extension = cur_data_type file_name = str( wrapped_data ) extra_files_path = str( wrapped_data.files_path ) - data_dict = dict( out_data_name = out_name, - ext = data.ext, - dataset_id = data.dataset.id, - hda_id = data.id, - file_name = file_name, - extra_files_path = extra_files_path ) + data_dict = dict( out_data_name=out_name, + ext=data.ext, + dataset_id=data.dataset.id, + hda_id=data.id, + file_name=file_name, + extra_files_path=extra_files_path ) json_params[ 'output_data' ].append( data_dict ) if json_filename is None: json_filename = file_name @@ -3151,15 +3205,18 @@ class DataSourceTool( OutputParameterJSONTool ): out.write( json.dumps( json_params ) ) out.close() + class AsyncDataSourceTool( DataSourceTool ): tool_type = 'data_source_async' def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '' % self.id ) ) + class DataDestinationTool( Tool ): tool_type = 'data_destination' + class SetMetadataTool( Tool ): """ Tool implementation for special tool that sets metadata on an existing @@ -3167,8 +3224,8 @@ class SetMetadataTool( Tool ): """ tool_type = 'set_metadata' requires_setting_metadata = False - - def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ): + + def exec_after_process( self, app, inp_data, out_data, param_dict, job=None ): for name, dataset in inp_data.iteritems(): external_metadata = JobExternalOutputMetadataWrapper( job ) if external_metadata.external_metadata_set_successfully( dataset, app.model.context ): @@ -3191,23 +3248,28 @@ class SetMetadataTool( Tool ): dataset.set_peek() self.sa_session.add( dataset ) self.sa_session.flush() - def job_failed( self, job_wrapper, message, exception = False ): + + def job_failed( self, job_wrapper, message, exception=False ): job = job_wrapper.sa_session.query( model.Job ).get( job_wrapper.job_id ) if job: inp_data = {} for dataset_assoc in job.input_datasets: inp_data[dataset_assoc.name] = dataset_assoc.dataset - return self.exec_after_process( job_wrapper.app, inp_data, {}, job_wrapper.get_param_dict(), job = job ) + return self.exec_after_process( job_wrapper.app, inp_data, {}, job_wrapper.get_param_dict(), job=job ) + class ExportHistoryTool( Tool ): tool_type = 'export_history' + class ImportHistoryTool( Tool ): tool_type = 'import_history' + class GenomeIndexTool( Tool ): tool_type = 'index_genome' + class DataManagerTool( OutputParameterJSONTool ): tool_type = 'manage_data' default_tool_action = DataManagerToolAction @@ -3218,9 +3280,9 @@ class DataManagerTool( OutputParameterJSONTool ): if self.data_manager_id is None: self.data_manager_id = self.id - def exec_after_process( self, app, inp_data, out_data, param_dict, job = None, **kwds ): + def exec_after_process( self, app, inp_data, out_data, param_dict, job=None, **kwds ): #run original exec_after_process - super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job = job, **kwds ) + super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job=job, **kwds ) #process results of tool if job and job.state == job.states.ERROR: return @@ -3267,8 +3329,8 @@ tool_types = {} for tool_class in [ Tool, DataDestinationTool, SetMetadataTool, DataSourceTool, AsyncDataSourceTool, DataManagerTool ]: tool_types[ tool_class.tool_type ] = tool_class -# ---- Utility classes to be factored out ----------------------------------- +# ---- Utility classes to be factored out ----------------------------------- class TracksterConfig: """ Trackster configuration encapsulation. """ @@ -3282,6 +3344,7 @@ class TracksterConfig: actions.append( SetParamAction.parse( action_elt ) ) return TracksterConfig( actions ) + class SetParamAction: """ Set parameter action. """ @@ -3294,10 +3357,12 @@ class SetParamAction: """ Parse action from element. """ return SetParamAction( elt.get( "name" ), elt.get( "output_name" ) ) + class BadValue( object ): def __init__( self, value ): self.value = value + class ToolStdioRegex( object ): """ This is a container for the element's regex subelement. @@ -3313,6 +3378,7 @@ class ToolStdioRegex( object ): self.error_level = "fatal" self.desc = "" + class ToolStdioExitCode( object ): """ This is a container for the element's subelement. @@ -3532,6 +3598,6 @@ def get_incoming_value( incoming, key, default ): else: return incoming.get( key, default ) + class InterruptedUpload( Exception ): pass - diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py index 3a41460a355..3b65ce53717 100644 --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -6,6 +6,7 @@ from basic import * from grouping import * from galaxy.util.json import * + def visit_input_values( inputs, input_values, callback, name_prefix="", label_prefix="" ): """ Given a tools parameter definition (`inputs`) and a specific set of @@ -35,11 +36,12 @@ def visit_input_values( inputs, input_values, callback, name_prefix="", label_pr else: new_value = callback( input, input_values[input.name], - prefixed_name = name_prefix + input.name, - prefixed_label = label_prefix + input.label ) + prefixed_name=name_prefix + input.name, + prefixed_label=label_prefix + input.label ) if new_value: input_values[input.name] = new_value + def check_param( trans, param, incoming_value, param_values, source='html' ): """ Check the value of a single parameter `param`. The value in @@ -62,12 +64,13 @@ def check_param( trans, param, incoming_value, param_values, source='html' ): # Then do any further validation on the value param.validate( filtered_value, trans.history ) elif value is None and isinstance( param, SelectToolParameter ): - # An empty select list or column list - param.validate( value, trans.history ) + # An empty select list or column list + param.validate( value, trans.history ) except ValueError, e: error = str( e ) return value, error + def params_to_strings( params, param_values, app ): """ Convert a dictionary of parameter values to a dictionary of strings @@ -83,6 +86,7 @@ def params_to_strings( params, param_values, app ): rval[ key ] = str( to_json_string( value ) ) return rval + def params_from_strings( params, param_values, app, ignore_errors=False ): """ Convert a dictionary of strings as produced by `params_to_strings` @@ -98,6 +102,7 @@ def params_from_strings( params, param_values, app, ignore_errors=False ): rval[ key ] = value return rval + def params_to_incoming( incoming, inputs, input_values, app, name_prefix="" ): """ Given a tool's parameter definition (`inputs`) and a specific set of @@ -119,4 +124,3 @@ def params_to_incoming( incoming, inputs, input_values, app, name_prefix="" ): params_to_incoming( incoming, input.cases[current].inputs, values, app, new_name_prefix ) else: incoming[ name_prefix + input.name ] = input.to_html_value( input_values.get( input.name ), app ) - diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index c5300eb6040..efe2935aec2 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1441,10 +1441,11 @@ class DrillDownSelectToolParameter( SelectToolParameter ): for opt in option['options']: recurse_option( option_list, opt ) rval = [] - recurse_option( rval, get_base_option( value, self.get_options( other_values = other_values ) ) ) + recurse_option( rval, get_base_option( value, self.get_options( other_values=other_values ) ) ) return rval or [value] - if value is None: return "None" + if value is None: + return "None" rval = [] if self.hierarchy == "exact": rval = value @@ -1483,8 +1484,9 @@ class DrillDownSelectToolParameter( SelectToolParameter ): if value == option['value']: return option['name'] rval = get_option_display( value, option['options'] ) - if rval: return rval - return None #not found + if rval: + return rval + return None # not found if isinstance( value, UnvalidatedValue ): suffix = "\n(value not yet validated)" @@ -1524,12 +1526,12 @@ class DrillDownSelectToolParameter( SelectToolParameter ): options = [] try: options = self.get_options( trans, {} ) - except KeyError, key_err: + except KeyError: # will sometimes error if self.is_dynamic and self.filtered # bc we dont/cant fill out other_values above ({}) pass - d[ 'options' ] = options; + d[ 'options' ] = options return d @@ -1762,7 +1764,7 @@ class DataToolParameter( ToolParameter ): if v: if v.deleted: raise ValueError( "The previously selected dataset has been previously deleted" ) - if v.dataset.state in [galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED ]: + if v.dataset.state in [ galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED ]: raise ValueError( "The previously selected dataset has entered an unusable state" ) return rval @@ -1794,7 +1796,8 @@ class DataToolParameter( ToolParameter ): return app.model.context.query( app.model.HistoryDatasetAssociation ).get( int( value ) ) def to_param_dict_string( self, value, other_values={} ): - if value is None: return "None" + if value is None: + return "None" return value.file_name def value_to_display_text( self, value, app ): @@ -1828,12 +1831,13 @@ class DataToolParameter( ToolParameter ): if self.tool is None or self.tool.has_multiple_pages or not hasattr( trans, 'workflow_building_mode' ) or trans.workflow_building_mode: return False if other_values is None: - return True # we don't know other values, so we can't check, assume ok + return True # we don't know other values, so we can't check, assume ok converter_safe = [True] - def visitor( prefix, input, value, parent = None ): + + def visitor( prefix, input, value, parent=None ): if isinstance( input, SelectToolParameter ) and self.name in input.get_dependencies(): if input.is_dynamic and ( input.dynamic_options or ( not input.dynamic_options and not input.options ) or not input.options.converter_safe ): - converter_safe[0] = False #This option does not allow for conversion, i.e. uses contents of dataset file to generate options + converter_safe[0] = False # This option does not allow for conversion, i.e. uses contents of dataset file to generate options self.tool.visit_inputs( other_values, visitor ) return False not in converter_safe @@ -1960,21 +1964,24 @@ class LibraryDatasetToolParameter( ToolParameter ): # self.html = form_builder.HiddenField( self.name, trans.history.id ).get_html() # return self.html -parameter_types = dict( text = TextToolParameter, - integer = IntegerToolParameter, - float = FloatToolParameter, - boolean = BooleanToolParameter, - genomebuild = GenomeBuildParameter, - select = SelectToolParameter, - data_column = ColumnListParameter, - hidden = HiddenToolParameter, - hidden_data = HiddenDataToolParameter, - baseurl = BaseURLToolParameter, - file = FileToolParameter, - ftpfile = FTPFileToolParameter, - data = DataToolParameter, - library_data = LibraryDatasetToolParameter, - drill_down = DrillDownSelectToolParameter ) +parameter_types = dict( + text=TextToolParameter, + integer=IntegerToolParameter, + float=FloatToolParameter, + boolean=BooleanToolParameter, + genomebuild=GenomeBuildParameter, + select=SelectToolParameter, + data_column=ColumnListParameter, + hidden=HiddenToolParameter, + hidden_data=HiddenDataToolParameter, + baseurl=BaseURLToolParameter, + file=FileToolParameter, + ftpfile=FTPFileToolParameter, + data=DataToolParameter, + library_data=LibraryDatasetToolParameter, + drill_down=DrillDownSelectToolParameter +) + class UnvalidatedValue( object ): """ @@ -1993,4 +2000,3 @@ class RuntimeValue( object ): runtime. """ pass - diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index ca07a28903c..063d1566b24 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,9 +1,11 @@ import urllib from galaxy import web, util -from galaxy.web.base.controller import BaseAPIController, UsesHistoryDatasetAssociationMixin, UsesVisualizationMixin, UsesHistoryMixin +from galaxy.web.base.controller import BaseAPIController +from galaxy.web.base.controller import UsesVisualizationMixin +from galaxy.web.base.controller import UsesHistoryMixin from galaxy.visualization.genomes import GenomeRegion -from galaxy.util.json import to_json_string, from_json_string +from galaxy.util.json import to_json_string from galaxy.visualization.data_providers.genome import * import logging @@ -47,7 +49,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix GET /api/tools/{tool_id} Returns tool information, including parameters and inputs. """ - io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) + io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) link_details = util.string_as_bool( kwd.get( 'link_details', False ) ) try: id = urllib.unquote_plus( id ) @@ -96,7 +98,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix for k, v in payload.iteritems(): if k.startswith("files_") or k.startswith("__files_"): inputs[k] = v - + #for inputs that are coming from the Library, copy them into the history input_patch = {} for k, v in inputs.iteritems(): @@ -112,7 +114,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix inputs['runtool_btn'] = 'Execute' # TODO: encode data ids and decode ids. # TODO: handle dbkeys - params = util.Params( inputs, sanitize = False ) + params = util.Params( inputs, sanitize=False ) # process_state will be 'populate' or 'update'. When no tool # state is specified in input - it will be 'populate', and # tool will fully expand repeat and conditionals when building @@ -140,8 +142,8 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix for output_name, output in output_datasets: output_dict = output.to_dict() #add the output name back into the output data structure - #so it's possible to figure out which newly created elements - #correspond with which tool file outputs + #so it's possible to figure out which newly created elements + #correspond with which tool file outputs output_dict['output_name'] = output_name outputs.append( trans.security.encode_dict_ids( output_dict ) ) return rval @@ -185,14 +187,13 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix # HACK: add run button so that tool.handle_input will run tool. kwargs['runtool_btn'] = 'Execute' - params = util.Params( kwargs, sanitize = False ) + params = util.Params( kwargs, sanitize=False ) template, vars = tool.handle_input( trans, params.__dict__, history=target_history ) # TODO: check for errors and ensure that output dataset is available. output_datasets = vars[ 'out_data' ].values() return self.add_track_async( trans, output_datasets[0].id ) - def _rerun_tool( self, trans, payload, **kwargs ): """ Rerun a tool to produce a new output dataset that corresponds to a @@ -363,7 +364,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix continue input_dataset = jida.dataset - if input_dataset is None: #optional dataset and dataset wasn't selected + if input_dataset is None: # optional dataset and dataset wasn't selected tool_params[ jida.name ] = None elif run_on_regions and 'data' in input_dataset.datatype.data_sources: # Dataset is indexed and hence a subset can be extracted and used @@ -407,7 +408,7 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix # Set metadata. # TODO: set meta internally if dataset is small enough? trans.app.datatypes_registry.set_external_metadata_tool.tool_action.execute( trans.app.datatypes_registry.set_external_metadata_tool, - trans, incoming = { 'input1':new_dataset }, + trans, incoming={ 'input1': new_dataset }, overwrite=False, job_params={ "source" : "trackster" } ) # Add HDA subset association. subset_association = trans.app.model.HistoryDatasetAssociationSubset( hda=input_dataset, subset=new_dataset, location=regions_str ) @@ -450,5 +451,5 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMix dataset_dict = output_dataset.to_dict() dataset_dict[ 'id' ] = trans.security.encode_id( dataset_dict[ 'id' ] ) - dataset_dict[ 'track_config' ] = self.get_new_track_config( trans, output_dataset ); + dataset_dict[ 'track_config' ] = self.get_new_track_config( trans, output_dataset ) return dataset_dict From fbcf068e81cd7cb18980003d84d67e4230e21822 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 13 Jan 2014 08:58:22 -0600 Subject: [PATCH 0740/1033] Initial work on tool execution unit tests. Going to be doing some more work on tool state stuff so it will be good to have a way to test that. This also brings in test/unit/tools_support.py from Pull Request #287 (would be overkill for just these tests, but it is useful for future tests coming down the pipe.) --- test/unit/tools/__init__.py | 0 test/unit/tools/test_execution.py | 104 ++++++++++++++++++++++++++++++ test/unit/tools_support.py | 51 +++++++++++++++ 3 files changed, 155 insertions(+) create mode 100644 test/unit/tools/__init__.py create mode 100644 test/unit/tools/test_execution.py create mode 100644 test/unit/tools_support.py diff --git a/test/unit/tools/__init__.py b/test/unit/tools/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/test/unit/tools/test_execution.py b/test/unit/tools/test_execution.py new file mode 100644 index 00000000000..3bb8b81fb77 --- /dev/null +++ b/test/unit/tools/test_execution.py @@ -0,0 +1,104 @@ +""" Test Tool execution and state handling logic. +""" +import os + +from unittest import TestCase + +import galaxy.model +from galaxy.tools import Tool +from galaxy.tools import DefaultToolState +from galaxy.util import parse_xml +from galaxy.util import string_to_object +from galaxy.util import object_to_string +from galaxy.util.odict import odict +from tools_support import UsesApp + +EXAMPLE_TOOL_CONTENTS = ''' + echo "$text" < $out1 + + + + + + +''' + + +class ToolExecutionTestCase( TestCase, UsesApp ): + + def setUp(self): + self.setup_app() + self.app.job_config["get_job_tool_configurations"] = lambda ids: None + self.app.config.drmaa_external_runjob_script = "" + self.app.config.tool_secret = "testsecret" + self.trans = MockTrans( self.app ) + self.tool_action = MockAction( self.trans ) + self.tool_file = os.path.join( self.test_directory, "tool.xml" ) + + def tearDown(self): + self.tear_down_app() + + def test_state_new( self ): + self.__write_tool( EXAMPLE_TOOL_CONTENTS ) + self.__setup_tool( ) + template, template_vars = self.tool.handle_input( + trans=self.trans, + incoming=dict( param1="moo" ) + # no runtool_btn, just rerenders the form mako with tool + # state populated. + ) + assert template == "tool_form.mako" + assert not template_vars[ "errors" ] + state = template_vars[ "tool_state" ] + assert state.inputs[ "param1" ] == "moo" + + def test_execute( self ): + self.__write_tool( EXAMPLE_TOOL_CONTENTS ) + self.__setup_tool( ) + template, template_vars = self.tool.handle_input( + trans=self.trans, + incoming=dict( param1="moo", runtool_btn="dummy" ) + ) + assert template == "tool_executed.mako" + + def __setup_tool( self ): + tree = parse_xml( self.tool_file ) + self.tool = Tool( self.tool_file, tree.getroot(), self.app ) + self.tool.tool_action = self.tool_action + + def __write_tool( self, contents ): + open( self.tool_file, "w" ).write( contents ) + + def __string_to_state( self, state_string ): + encoded_state = string_to_object( state_string ) + state = DefaultToolState() + state.decode( encoded_state, self.tool, self.app ) + return state + + def __inputs_to_state( self, inputs ): + tool_state = DefaultToolState() + tool_state.inputs = inputs + return tool_state + + def __inputs_to_state_string( self, inputs ): + tool_state = self.__inputs_to_state( inputs ) + return object_to_string( tool_state.encode( self.tool, self.app ) ) + + +class MockAction( object ): + + def __init__( self, expected_trans ): + self.expected_trans = expected_trans + self.execution_call_args = [] + + def execute( self, tool, trans, **kwds ): + assert self.expected_trans == trans + self.execution_call_args.append( kwds ) + return None, odict(dict(out1="1")) + + +class MockTrans( object ): + + def __init__( self, app ): + self.app = app + self.history = galaxy.model.History() diff --git a/test/unit/tools_support.py b/test/unit/tools_support.py new file mode 100644 index 00000000000..9d839a4106a --- /dev/null +++ b/test/unit/tools_support.py @@ -0,0 +1,51 @@ +""" Module contains test fixtures meant to aide in the testing of jobs and +tool evaluation. Such extensive "fixtures" are something of an anti-pattern +so use of this should be limitted to tests of very 'extensive' classes. +""" + +import os.path +import tempfile +import shutil + +from galaxy.util.bunch import Bunch +from galaxy.model import mapping + + +class UsesApp( object ): + + def setup_app( self ): + # The following line is needed in order to create + # HistoryDatasetAssociations - ideally the model classes would be + # usable without the ORM infrastructure in place. + mapping.init( "/tmp", "sqlite:///:memory:", create_tables=True ) + self.test_directory = tempfile.mkdtemp() + self.app = MockApp(self.test_directory) + + def tear_down_app( self ): + shutil.rmtree( self.test_directory ) + + +class MockApp( object ): + + def __init__( self, test_directory ): + + self.datatypes_registry = Bunch( + integrated_datatypes_configs='/galaxy/integrated_datatypes_configs.xml', + get_datatype_by_extension=lambda ext: Bunch(), + ) + + self.config = Bunch( + outputs_to_working_directory=False, + new_file_path=os.path.join(test_directory, "new_files"), + tool_data_path=os.path.join(test_directory, "tools"), + root=os.path.join(test_directory, "galaxy"), + admin_users="mary@example.com", + ) + + # Setup some attributes for downstream extension by specific tests. + self.job_config = Bunch() + self.model = Bunch() + self.toolbox = None + self.object_store = None + +__all__ = [ UsesApp ] From 4de7fb7b1bb475a3be62df63abce478abcfe57ff Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 13 Jan 2014 08:58:22 -0600 Subject: [PATCH 0741/1033] Initial work on tools API functional tests. Just tests some simple indexing and tool execution. Tons more one can and should test. --- test/functional/api/test_tools.py | 102 ++++++++++++++++++++++++++++++ 1 file changed, 102 insertions(+) create mode 100644 test/functional/api/test_tools.py diff --git a/test/functional/api/test_tools.py b/test/functional/api/test_tools.py new file mode 100644 index 00000000000..fdef6d59aa4 --- /dev/null +++ b/test/functional/api/test_tools.py @@ -0,0 +1,102 @@ +# Test tools API. +from itertools import chain +from json import dumps +import time + +from base import api +from operator import itemgetter + + +class ToolsTestCase( api.ApiTestCase ): + + def test_index( self ): + index = self._get( "tools" ) + tools_index = index.json() + # In panels by default, so flatten out sections... + tools = list( chain( *map( itemgetter( "elems" ), tools_index ) ) ) + tool_ids = map( itemgetter( "id" ), tools ) + assert "upload1" in tool_ids + assert "cat1" in tool_ids + + def test_no_panel_index( self ): + index = self._get( "tools", data=dict(in_panel="false") ) + tools_index = index.json() + # No need to flatten out sections, with in_panel=False, only tools are + # returned. + tool_ids = map( itemgetter( "id" ), tools_index ) + assert "upload1" in tool_ids + assert "cat1" in tool_ids + + def test_upload1_paste( self ): + history_id = self._new_history() + payload = self._upload_payload( history_id, 'Hello World' ) + create_response = self._post( "tools", data=payload ) + self._assert_has_keys( create_response.json(), 'outputs' ) + + def test_run_cat1( self ): + history_id = self._new_history() + new_dataset = self._new_dataset( history_id ) + dataset_id = new_dataset[ 'id' ] + payload = self._run_tool_payload( + tool_id='cat1', + inputs=dict( + input1=dict( + src='hda', + id=dataset_id + ), + ), + history_id=history_id, + ) + create_response = self._post( "tools", data=payload ) + self._assert_status_code_is( create_response, 200 ) + self._assert_has_keys( create_response.json(), 'outputs' ) + self._wait_for_history( history_id, assert_ok=True ) + + def _new_dataset( self, history_id, content='TestData123', **kwds ): + payload = self._upload_payload( history_id, content, **kwds ) + run_response = self._post( "tools", data=payload ) + self._assert_status_code_is( run_response, 200 ) + return run_response.json()["outputs"][0] + + def _wait_for_history( self, history_id, assert_ok=False ): + while True: + history_details_response = self._get( "histories/%s" % history_id ) + self._assert_status_code_is( history_details_response, 200 ) + history_state = history_details_response.json()[ "state" ] + if history_state not in [ "running", "queued" ]: + break + time.sleep( .1 ) + if assert_ok: + self.assertEquals( history_state, 'ok' ) + + def _new_history( self, **kwds ): + name = kwds.get( "name", "API Test History" ) + create_history_response = self._post( "histories", data=dict( name=name ) ) + self._assert_status_code_is( create_history_response, 200 ) + history_id = create_history_response.json()[ "id" ] + return history_id + + def _upload_payload( self, history_id, content, **kwds ): + name = kwds.get( "name", "Test Dataset" ) + dbkey = kwds.get( "dbkey", "?" ) + file_type = kwds.get( "file_type", 'txt' ) + upload_params = { + 'files_0|NAME': name, + 'files_0|url_paste': content, + 'dbkey': dbkey, + 'file_type': file_type, + } + return self._run_tool_payload( + tool_id='upload1', + inputs=upload_params, + history_id=history_id, + upload_type='upload_dataset' + ) + + def _run_tool_payload( self, tool_id, inputs, history_id, **kwds ): + return dict( + tool_id=tool_id, + inputs=dumps(inputs), + history_id=history_id, + **kwds + ) From 2d68dd7c60f89599ab4756b728f60173387d2e49 Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Mon, 13 Jan 2014 10:35:44 -0500 Subject: [PATCH 0742/1033] Update create_applet_tag_peekcreate_applet_tag_peek of images.py (used for e.g. GMAJ) to display an error message is Java is not installed/enabled for the browser. --- lib/galaxy/datatypes/images.py | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/lib/galaxy/datatypes/images.py b/lib/galaxy/datatypes/images.py index f2fc663a9f8..f1a4b95efe5 100644 --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -213,7 +213,6 @@ Binary.register_sniffable_binary_format("pdf", "pdf", Pdf) def create_applet_tag_peek( class_name, archive, params ): text = """ - @@ -221,17 +220,14 @@ def create_applet_tag_peek( class_name, archive, params ): for name, value in params.iteritems(): text += """""" % ( name, value ) text += """ - """ % ( class_name, archive ) for name, value in params.iteritems(): text += """""" % ( name, value ) - text += """ - + text += """
                You must install and enable Java in your browser in order to access this applet.
                 - """ return """

                %s

                """ % text From 2c7b758b32c5f714d6f046a83181f559b9b9036d Mon Sep 17 00:00:00 2001 From: Dannon Baker Date: Mon, 13 Jan 2014 10:54:20 -0500 Subject: [PATCH 0743/1033] Eliminate simplejson for real this time. Update WebHelpers to v 1.3 (no longer requires simplejson), fix deprecated methods. --- eggs.ini | 3 +-- lib/galaxy/web/framework/helpers/__init__.py | 28 +++++++++++++------- 2 files changed, 19 insertions(+), 12 deletions(-) diff --git a/eggs.ini b/eggs.ini index 1c0491984b7..27a2a45b644 100644 --- a/eggs.ini +++ b/eggs.ini @@ -26,7 +26,6 @@ pycrypto = 2.5 pysam = 0.4.2 pysqlite = 2.5.6 python_lzo = 1.08_2.03_static -simplejson = 2.1.1 threadframe = 0.2 guppy = 0.1.8 SQLAlchemy = 0.7.9 @@ -61,7 +60,7 @@ SVGFig = 1.1.6 Tempita = 0.5.1 twill = 0.9 WebError = 0.8a -WebHelpers = 0.2 +WebHelpers = 1.3 WebOb = 0.8.5 wsgiref = 0.1.2 Babel = 0.9.4 diff --git a/lib/galaxy/web/framework/helpers/__init__.py b/lib/galaxy/web/framework/helpers/__init__.py index 3d28eb951d2..1b53f98343b 100644 --- a/lib/galaxy/web/framework/helpers/__init__.py +++ b/lib/galaxy/web/framework/helpers/__init__.py @@ -1,14 +1,19 @@ -import pkg_resources +""" +Galaxy web framework helpers +""" -pkg_resources.require( "WebHelpers" ) -from webhelpers import date, stylesheet_link_tag, javascript_include_tag, url_for - -from galaxy.util.json import to_json_string -from galaxy.util import hash_util -from datetime import datetime, timedelta import time - from cgi import escape +from datetime import datetime, timedelta +from galaxy import eggs +from galaxy.util import hash_util +from galaxy.util.json import to_json_string +eggs.require( "WebHelpers" ) +from webhelpers import date +from webhelpers.html.tags import stylesheet_link, javascript_link + +eggs.require( "Routes" ) +from routes import url_for server_starttime = int(time.time()) @@ -25,6 +30,9 @@ def time_ago( x ): return date.distance_of_time_in_words( x, datetime.utcnow() ).replace("about", "~") + " ago" def iff( a, b, c ): + """ + Ternary shortcut + """ if a: return b else: @@ -48,7 +56,7 @@ def css( *args ): Cache-bust with time that server started running on """ - return "\n".join( [ stylesheet_link_tag( "/static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) + return "\n".join( [ stylesheet_link( "/static/style/" + name + ".css?v=%s" % server_starttime ) for name in args ] ) def js_helper( prefix, *args ): """ @@ -57,7 +65,7 @@ def js_helper( prefix, *args ): Cache-bust with time that server started running on """ - return "\n".join( [ javascript_include_tag( prefix + name + ".js?v=%s" % server_starttime ) for name in args ] ) + return "\n".join( [ javascript_link( prefix + name + ".js?v=%s" % server_starttime ) for name in args ] ) def js( *args ): """ From f573f18371936d1e19cbd2b213aa065923423ff5 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Mon, 13 Jan 2014 11:18:56 -0500 Subject: [PATCH 0744/1033] Charts: Increase chart data volume limit --- config/plugins/visualizations/charts/static/models/datasets.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/plugins/visualizations/charts/static/models/datasets.js b/config/plugins/visualizations/charts/static/models/datasets.js index 989f77e1893..f6dc78ffaf7 100644 --- a/config/plugins/visualizations/charts/static/models/datasets.js +++ b/config/plugins/visualizations/charts/static/models/datasets.js @@ -8,7 +8,7 @@ return Backbone.Model.extend( optionsDefault : { limit : 20, pace : 1000, - max : 2 + max : 10 }, // list From 5ce8b0eb0676bbfe4031a80bee7c51e87fe73832 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Mon, 13 Jan 2014 11:54:52 -0500 Subject: [PATCH 0745/1033] Charts: Adjust chart data volume --- config/plugins/visualizations/charts/static/models/datasets.js | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/plugins/visualizations/charts/static/models/datasets.js b/config/plugins/visualizations/charts/static/models/datasets.js index f6dc78ffaf7..03f92fcaae8 100644 --- a/config/plugins/visualizations/charts/static/models/datasets.js +++ b/config/plugins/visualizations/charts/static/models/datasets.js @@ -8,7 +8,7 @@ return Backbone.Model.extend( optionsDefault : { limit : 20, pace : 1000, - max : 10 + max : 5 }, // list From e9dc530655b68c8eb7ae2c2a4be3ef6930804fdd Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 13 Jan 2014 12:26:30 -0500 Subject: [PATCH 0746/1033] =?UTF-8?q?disable=20visualization=20and=20workf?= =?UTF-8?q?lows=20menu=20items=20for=20anonymous=20users=20that=20can?= =?UTF-8?q?=E2=80=99t=20use=20them,=20show=20notification=20of=20clicked,?= =?UTF-8?q?=20also=20add=20possibility=20to=20use=20titles=20in=20menu=20(?= =?UTF-8?q?shown=20by=20default=20on=20hoover)?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- static/scripts/galaxy.masthead.js | 21 ++++++++-- static/scripts/galaxy.menu.js | 53 +++++++++++++++++------- static/scripts/packed/galaxy.masthead.js | 2 +- static/scripts/packed/galaxy.menu.js | 2 +- static/style/blue/base.css | 4 +- static/style/src/less/toastr.less | 6 +-- 6 files changed, 61 insertions(+), 27 deletions(-) diff --git a/static/scripts/galaxy.masthead.js b/static/scripts/galaxy.masthead.js index 2bf3b42b1e9..9ed389fa263 100644 --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -3,7 +3,7 @@ */ // dependencies -define(["utils/galaxy.utils"], function(mod_utils) { +define(["utils/galaxy.utils", "libs/toastr"], function(mod_utils, mod_toastr) { // masthead var GalaxyMasthead = Backbone.View.extend( @@ -259,7 +259,9 @@ var GalaxyMastheadTab = Backbone.View.extend( type : 'url', scratchbook : false, on_unload : null, - visible : true + visible : true, + disabled : false, + title_attribute : '' }, // location @@ -288,6 +290,12 @@ var GalaxyMastheadTab = Backbone.View.extend( // add template for tab this.setElement($(this._template(this.options))); + // disable menu items that are not available to anonymous user + // also show title to explain why they are disabled + if (this.options.disabled){ + $(this.el).find('.root').addClass('disabled'); + } + // visiblity if (!this.options.visible) this.hide(); @@ -371,9 +379,14 @@ var GalaxyMastheadTab = Backbone.View.extend( // prevent default e.preventDefault(); + if (this.options.disabled){ + mod_toastr.info('Please register to use this feature'); + return + } + // check for menu options if (!this.$menu) { - Galaxy.frame.add(this.options); + Galaxy.frame.add(this.options); } }, @@ -400,7 +413,7 @@ var GalaxyMastheadTab = Backbone.View.extend( // start template var tmpl = '
                '});b.prototype=c.extend({},c.fn.tooltip.Constructor.prototype);b.prototype.constructor=b;b.prototype.getDefaults=function(){return b.DEFAULTS};b.prototype.setContent=function(){var f=this.tip();var e=this.getTitle();var d=this.getContent();f.find(".popover-title")[this.options.html?"html":"text"](e);f.find(".popover-content")[this.options.html?"html":"text"](d);f.removeClass("fade top bottom left right in");if(!f.find(".popover-title").html()){f.find(".popover-title").hide()}};b.prototype.hasContent=function(){return this.getTitle()||this.getContent()};b.prototype.getContent=function(){var d=this.$element;var e=this.options;return d.attr("data-content")||(typeof e.content=="function"?e.content.call(d[0]):e.content)};b.prototype.arrow=function(){return this.$arrow=this.$arrow||this.tip().find(".arrow")};b.prototype.tip=function(){if(!this.$tip){this.$tip=c(this.options.template)}return this.$tip};var a=c.fn.popover;c.fn.popover=function(d){return this.each(function(){var g=c(this);var f=g.data("bs.popover");var e=typeof d=="object"&&d;if(!f){g.data("bs.popover",(f=new b(this,e)))}if(typeof d=="string"){f[d]()}})};c.fn.popover.Constructor=b;c.fn.popover.noConflict=function(){c.fn.popover=a;return this}}(jQuery); \ No newline at end of file From 42c0119d939f6d89b3978a1b6fc23eac12c8ba0d Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Mon, 13 Jan 2014 16:54:40 -0500 Subject: [PATCH 0757/1033] Fixes for mapping values in the Galaxy tool shed install methods. --- .../webapps/galaxy/api/tool_shed_repositories.py | 13 +++++++------ 1 file changed, 7 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py index 795183b562e..707ad945733 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -66,8 +66,9 @@ class ToolShedRepositoriesController( BaseAPIController ): exported_workflows.append( display_dict ) return exported_workflows - def __get_value_mapper( self, trans ): - value_mapper = { 'id' : trans.security.encode_id } + def __get_value_mapper( self, trans, tool_shed_repository ): + value_mapper={ 'id' : trans.security.encode_id( tool_shed_repository.id ), + 'error_message' : tool_shed_repository.error_message or '' } return value_mapper @web.expose_api @@ -142,7 +143,7 @@ class ToolShedRepositoriesController( BaseAPIController ): for tool_shed_repository in trans.install_model.context.query( trans.app.install_model.ToolShedRepository ) \ .order_by( trans.app.install_model.ToolShedRepository.table.c.name ): tool_shed_repository_dict = \ - tool_shed_repository.to_dict( value_mapper=self.__get_value_mapper( trans ) ) + tool_shed_repository.to_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) ) tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) @@ -336,7 +337,7 @@ class ToolShedRepositoriesController( BaseAPIController ): tool_path, install_tool_dependencies, reinstalling=False ) - tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans ) ) + tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) ) tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) @@ -471,7 +472,7 @@ class ToolShedRepositoriesController( BaseAPIController ): repair_dict = repository_util.repair_tool_shed_repository( trans, repository, encoding_util.tool_shed_encode( repo_info_dict ) ) - repository_dict = repository.to_dict( value_mapper=self.__get_value_mapper( trans ) ) + repository_dict = repository.to_dict( value_mapper=self.__get_value_mapper( trans, repository ) ) repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( repository.id ) ) @@ -538,7 +539,7 @@ class ToolShedRepositoriesController( BaseAPIController ): if tool_shed_repository is None: log.debug( "Unable to locate tool_shed_repository record for id %s." % ( str( id ) ) ) return {} - tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans ) ) + tool_shed_repository_dict = tool_shed_repository.as_dict( value_mapper=self.__get_value_mapper( trans, tool_shed_repository ) ) tool_shed_repository_dict[ 'url' ] = web.url_for( controller='tool_shed_repositories', action='show', id=trans.security.encode_id( tool_shed_repository.id ) ) From d969394856ec4dcc678ab9ed98b50398ca1a1185 Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 13 Jan 2014 18:04:48 -0500 Subject: [PATCH 0758/1033] =?UTF-8?q?galaxy=20top=20menu=20disabled=20item?= =?UTF-8?q?s=20lighter=20grey=E2=80=A6.?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- static/style/blue/base.css | 4 ++-- static/style/src/less/galaxy_bootstrap/variables.less | 2 +- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/static/style/blue/base.css b/static/style/blue/base.css index c1071ff6d69..a784bd63ad9 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -581,7 +581,7 @@ textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon .navbar-inverse .navbar-text{color:#999} .navbar-inverse .navbar-nav>li>a{color:#999}.navbar-inverse .navbar-nav>li>a:hover,.navbar-inverse .navbar-nav>li>a:focus{color:#fff;background-color:transparent} .navbar-inverse .navbar-nav>.active>a,.navbar-inverse .navbar-nav>.active>a:hover,.navbar-inverse .navbar-nav>.active>a:focus{color:#fff;background-color:#181a24} -.navbar-inverse .navbar-nav>.disabled>a,.navbar-inverse .navbar-nav>.disabled>a:hover,.navbar-inverse .navbar-nav>.disabled>a:focus{color:#444;background-color:transparent} +.navbar-inverse .navbar-nav>.disabled>a,.navbar-inverse .navbar-nav>.disabled>a:hover,.navbar-inverse .navbar-nav>.disabled>a:focus{color:#666;background-color:transparent} .navbar-inverse .navbar-toggle{border-color:#333}.navbar-inverse .navbar-toggle:hover,.navbar-inverse .navbar-toggle:focus{background-color:#333} .navbar-inverse .navbar-toggle .icon-bar{background-color:#fff} .navbar-inverse .navbar-collapse,.navbar-inverse .navbar-form{border-color:#1e212d} @@ -589,7 +589,7 @@ textarea.input-group-sm>.form-control,textarea.input-group-sm>.input-group-addon .navbar-inverse .navbar-nav>.dropdown>a:hover .caret{border-top-color:#fff;border-bottom-color:#fff} .navbar-inverse .navbar-nav>.dropdown>a .caret{border-top-color:#999;border-bottom-color:#999} .navbar-inverse .navbar-nav>.open>a .caret,.navbar-inverse .navbar-nav>.open>a:hover .caret,.navbar-inverse .navbar-nav>.open>a:focus .caret{border-top-color:#fff;border-bottom-color:#fff} -@media (max-width:767px){.navbar-inverse .navbar-nav .open .dropdown-menu>.dropdown-header{border-color:#181a24} .navbar-inverse .navbar-nav .open .dropdown-menu>li>a{color:#999}.navbar-inverse .navbar-nav .open .dropdown-menu>li>a:hover,.navbar-inverse .navbar-nav .open .dropdown-menu>li>a:focus{color:#fff;background-color:transparent} .navbar-inverse .navbar-nav .open .dropdown-menu>.active>a,.navbar-inverse .navbar-nav .open .dropdown-menu>.active>a:hover,.navbar-inverse .navbar-nav .open .dropdown-menu>.active>a:focus{color:#fff;background-color:#181a24} .navbar-inverse .navbar-nav .open .dropdown-menu>.disabled>a,.navbar-inverse .navbar-nav .open .dropdown-menu>.disabled>a:hover,.navbar-inverse .navbar-nav .open .dropdown-menu>.disabled>a:focus{color:#444;background-color:transparent}} +@media (max-width:767px){.navbar-inverse .navbar-nav .open .dropdown-menu>.dropdown-header{border-color:#181a24} .navbar-inverse .navbar-nav .open .dropdown-menu>li>a{color:#999}.navbar-inverse .navbar-nav .open .dropdown-menu>li>a:hover,.navbar-inverse .navbar-nav .open .dropdown-menu>li>a:focus{color:#fff;background-color:transparent} .navbar-inverse .navbar-nav .open .dropdown-menu>.active>a,.navbar-inverse .navbar-nav .open .dropdown-menu>.active>a:hover,.navbar-inverse .navbar-nav .open .dropdown-menu>.active>a:focus{color:#fff;background-color:#181a24} .navbar-inverse .navbar-nav .open .dropdown-menu>.disabled>a,.navbar-inverse .navbar-nav .open .dropdown-menu>.disabled>a:hover,.navbar-inverse .navbar-nav .open .dropdown-menu>.disabled>a:focus{color:#666;background-color:transparent}} .navbar-inverse .navbar-link{color:#999}.navbar-inverse .navbar-link:hover{color:#fff} .breadcrumb{padding:8px 15px;margin-bottom:17px;list-style:none;background-color:#f5f5f5;border-radius:3px}.breadcrumb>li{display:inline-block}.breadcrumb>li+li:before{content:"/\00a0";padding:0 5px;color:#ccc} .breadcrumb>.active{color:#999} diff --git a/static/style/src/less/galaxy_bootstrap/variables.less b/static/style/src/less/galaxy_bootstrap/variables.less index 587008f24e5..38860942b26 100644 --- a/static/style/src/less/galaxy_bootstrap/variables.less +++ b/static/style/src/less/galaxy_bootstrap/variables.less @@ -344,7 +344,7 @@ @navbar-inverse-link-hover-bg: transparent; @navbar-inverse-link-active-color: @navbar-inverse-link-hover-color; @navbar-inverse-link-active-bg: darken(@navbar-inverse-bg, 10%); -@navbar-inverse-link-disabled-color: #444; +@navbar-inverse-link-disabled-color: #666; @navbar-inverse-link-disabled-bg: transparent; // Inverted navbar brand label From 906ac9bfef9779f6c776b5016828fbc84e7ed46e Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Mon, 13 Jan 2014 18:06:51 -0500 Subject: [PATCH 0759/1033] toaster removal form masthead --- static/scripts/galaxy.masthead.js | 2 +- static/scripts/packed/galaxy.masthead.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/static/scripts/galaxy.masthead.js b/static/scripts/galaxy.masthead.js index 838a22d0b60..da3e2d5a7ff 100644 --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -3,7 +3,7 @@ */ // dependencies -define(["utils/galaxy.utils", "libs/toastr"], function(mod_utils, mod_toastr) { +define(["utils/galaxy.utils"], function(mod_utils) { // masthead var GalaxyMasthead = Backbone.View.extend( diff --git a/static/scripts/packed/galaxy.masthead.js b/static/scripts/packed/galaxy.masthead.js index 19d7fb799c8..e77d72ecfa6 100644 --- a/static/scripts/packed/galaxy.masthead.js +++ b/static/scripts/packed/galaxy.masthead.js @@ -1 +1 @@ -define(["utils/galaxy.utils","libs/toastr"],function(c,e){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(g){this.options=g;$("body").off();this.setElement($(this._template(g)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var f=this;window.onbeforeunload=function(){var i="";for(key in f.list){if(f.list[key].options.on_unload){var h=f.list[key].options.on_unload();if(h){i+=h+" "}}}if(i!=""){return i}}},events:{click:"_click",mousedown:function(f){f.preventDefault()}},append:function(f){return this._add(f,true)},prepend:function(f){return this._add(f,false)},highlight:function(g){var f=$(this.el).find("#"+g+"> li");if(f){f.addClass("active")}},_add:function(i,g){var f=$(this.el).find("#"+i.location);if(f){var h=$(i.el);h.addClass("masthead-item");if(g){f.append(h)}else{f.prepend(h)}this.list.push(i)}return null},_click:function(h){var g=$(this.el).find(".popup");if(g){g.hide()}var f=$(h.target).closest(".masthead-item").find(".popup");if($(h.target).hasClass("head")){f.show();this.$background.show()}else{this.$background.hide()}},_template:function(f){return''}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},location:"iconbar",initialize:function(g){if(g){this.options=_.defaults(g,this.options)}this.setElement($(this._template(this.options)));var f=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",f.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(f){$(this.el).find(".icon").removeClass(this.options.icon).addClass(f);this.options.icon=f},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(f){$(this.el).find(".number").text(f)},_template:function(g){var f='
                ';if(g.with_number){f+='
                '}f+="
                ";return f}});var d=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(f){if(f){this.options=_.defaults(f,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(h){var i={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(h){i=_.defaults(h,i)}if(i.content&&i.content.indexOf("//")===-1){i.content=galaxy_config.root+i.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var g=$(this._templateMenuItem(i));this.$menu.append(g);var f=this;g.on("click",function(j){j.preventDefault();if(f.options.target==="_blank"){return true}Galaxy.frame.add(h)});if(i.divider){this.$menu.append($(this._templateDivider()))}},_head:function(f){f.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var f=$(this.el).find(".head");f.popover({html:true,content:'Please log in or register to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){f.popover("hide")},5000)})},_templateMenuItem:function(f){return'
              • '+f.title+"
                • "},_templateMenu:function(){return'
                  '},_templateDivider:function(){return'
                • '},_template:function(g){var f='';return f}});return{GalaxyMasthead:a,GalaxyMastheadTab:d,GalaxyMastheadIcon:b}}); \ No newline at end of file +define(["utils/galaxy.utils"],function(c){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(f){this.options=f;$("body").off();this.setElement($(this._template(f)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var e=this;window.onbeforeunload=function(){var h="";for(key in e.list){if(e.list[key].options.on_unload){var g=e.list[key].options.on_unload();if(g){h+=g+" "}}}if(h!=""){return h}}},events:{click:"_click",mousedown:function(f){f.preventDefault()}},append:function(e){return this._add(e,true)},prepend:function(e){return this._add(e,false)},highlight:function(f){var e=$(this.el).find("#"+f+"> li");if(e){e.addClass("active")}},_add:function(h,f){var e=$(this.el).find("#"+h.location);if(e){var g=$(h.el);g.addClass("masthead-item");if(f){e.append(g)}else{e.prepend(g)}this.list.push(h)}return null},_click:function(h){var g=$(this.el).find(".popup");if(g){g.hide()}var f=$(h.target).closest(".masthead-item").find(".popup");if($(h.target).hasClass("head")){f.show();this.$background.show()}else{this.$background.hide()}},_template:function(e){return''}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},location:"iconbar",initialize:function(f){if(f){this.options=_.defaults(f,this.options)}this.setElement($(this._template(this.options)));var e=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",e.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(e){$(this.el).find(".icon").removeClass(this.options.icon).addClass(e);this.options.icon=e},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(e){$(this.el).find(".number").text(e)},_template:function(f){var e='
                  ';if(f.with_number){e+='
                  '}e+="
                  ";return e}});var d=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(e){if(e){this.options=_.defaults(e,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(g){var h={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(g){h=_.defaults(g,h)}if(h.content&&h.content.indexOf("//")===-1){h.content=galaxy_config.root+h.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var f=$(this._templateMenuItem(h));this.$menu.append(f);var e=this;f.on("click",function(i){i.preventDefault();if(e.options.target==="_blank"){return true}Galaxy.frame.add(g)});if(h.divider){this.$menu.append($(this._templateDivider()))}},_head:function(f){f.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var e=$(this.el).find(".head");e.popover({html:true,content:'Please log in or register to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){e.popover("hide")},5000)})},_templateMenuItem:function(e){return'
                • '+e.title+"
                  • "},_templateMenu:function(){return'
                    '},_templateDivider:function(){return'
                  • '},_template:function(f){var e='';return e}});return{GalaxyMasthead:a,GalaxyMastheadTab:d,GalaxyMastheadIcon:b}}); \ No newline at end of file From 7bb726c80bd5d8e1047db2fca9910a9c0a3f1e6a Mon Sep 17 00:00:00 2001 From: John Chilton Date: Tue, 14 Jan 2014 08:00:57 -0600 Subject: [PATCH 0760/1033] Add data parameter tests to tool execution unit tests. --- test/unit/tools/test_execution.py | 62 +++++++++++++++++++++++++++++-- test/unit/tools_support.py | 43 ++++++++++++++++++++- 2 files changed, 101 insertions(+), 4 deletions(-) diff --git a/test/unit/tools/test_execution.py b/test/unit/tools/test_execution.py index 4396fcf138e..360935e1e7c 100644 --- a/test/unit/tools/test_execution.py +++ b/test/unit/tools/test_execution.py @@ -9,6 +9,7 @@ from galaxy.tools import Tool from galaxy.tools import DefaultToolState from galaxy.tools.parameters import params_to_incoming from galaxy.util import parse_xml +from galaxy.util.bunch import Bunch from galaxy.util import string_to_object from galaxy.util import object_to_string from galaxy.util.odict import odict @@ -40,15 +41,31 @@ REPEAT_TOOL_CONTENTS = ''' ''' +# A tool with data parameters (kind of like cat1) my favorite test tool :) +SIMPLE_CAT_TOOL_CONTENTS = ''' + cat "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1 + + + + + + + + + + +''' + class ToolExecutionTestCase( TestCase, UsesApp ): def setUp(self): self.setup_app() + self.history = galaxy.model.History() self.app.job_config["get_job_tool_configurations"] = lambda ids: None self.app.config.drmaa_external_runjob_script = "" self.app.config.tool_secret = "testsecret" - self.trans = MockTrans( self.app ) + self.trans = MockTrans( self.app, self.history ) self.tool_action = MockAction( self.trans ) self.tool_file = os.path.join( self.test_directory, "tool.xml" ) @@ -102,6 +119,29 @@ class ToolExecutionTestCase( TestCase, UsesApp ): state = self.__assert_rerenders_tool_without_errors( template, template_vars ) assert len( state.inputs[ "repeat1" ] ) == 1 + def test_data_param_execute( self ): + self.__init_tool( SIMPLE_CAT_TOOL_CONTENTS ) + hda = self.__add_dataset(1) + # Execute tool action + template, template_vars = self.__handle_with_incoming( + param1=1, + runtool_btn="dummy", + ) + assert template == "tool_executed.mako" + # Tool 'executed' once, with hda as param1 + assert len( self.tool_action.execution_call_args ) == 1 + assert self.tool_action.execution_call_args[ 0 ][ "incoming" ][ "param1" ] == hda + + def test_data_param_state_update( self ): + self.__init_tool( SIMPLE_CAT_TOOL_CONTENTS ) + hda = self.__add_dataset( 1 ) + # Update state + template, template_vars = self.__handle_with_incoming( + param1=1, + ) + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert hda == state.inputs[ "param1" ] + def __handle_with_incoming( self, previous_state=None, **kwds ): """ Execute tool.handle_input with incoming specified by kwds (optionally extending a previous state). @@ -122,12 +162,21 @@ class ToolExecutionTestCase( TestCase, UsesApp ): new_incoming.update( kwds ) return new_incoming + def __add_dataset( self, id, state='ok' ): + hda = galaxy.model.HistoryDatasetAssociation() + hda.id = id + hda.dataset = galaxy.model.Dataset() + hda.dataset.state = 'ok' + + self.trans.sa_session.model_objects[ galaxy.model.HistoryDatasetAssociation ][ id ] = hda + self.history.datasets.append( hda ) + return hda + def __assert_rerenders_tool_without_errors( self, template, template_vars ): assert template == "tool_form.mako" assert not template_vars[ "errors" ] state = template_vars[ "tool_state" ] return state - assert state.inputs[ "param1" ] == "moo" def __init_tool( self, tool_contents ): self.__write_tool( tool_contents ) @@ -174,6 +223,13 @@ class MockAction( object ): class MockTrans( object ): - def __init__( self, app ): + def __init__( self, app, history ): self.app = app + self.history = history self.history = galaxy.model.History() + self.workflow_building_mode = False + self.webapp = Bunch( name="galaxy" ) + self.sa_session = self.app.model.context + + def get_history( self ): + return self.history diff --git a/test/unit/tools_support.py b/test/unit/tools_support.py index 9d839a4106a..59cd404770f 100644 --- a/test/unit/tools_support.py +++ b/test/unit/tools_support.py @@ -3,11 +3,13 @@ tool evaluation. Such extensive "fixtures" are something of an anti-pattern so use of this should be limitted to tests of very 'extensive' classes. """ +from collections import defaultdict import os.path import tempfile import shutil from galaxy.util.bunch import Bunch +import galaxy.model from galaxy.model import mapping @@ -44,8 +46,47 @@ class MockApp( object ): # Setup some attributes for downstream extension by specific tests. self.job_config = Bunch() - self.model = Bunch() + # Create self.model to mimic app.model. + self.model = Bunch( context=MockContext() ) + for module_member_name in dir( galaxy.model ): + module_member = getattr(galaxy.model, module_member_name) + if type( module_member ) == type: + self.model[ module_member_name ] = module_member self.toolbox = None self.object_store = None + +class MockContext(object): + + def __init__(self, model_objects=None): + self.expunged_all = False + self.flushed = False + self.model_objects = model_objects or defaultdict( lambda: {} ) + self.created_objects = [] + + def expunge_all(self): + self.expunged_all = True + + def query(self, clazz): + return MockQuery(self.model_objects.get(clazz)) + + def flush(self): + self.flushed = True + + def add(self, object): + self.created_objects.append(object) + + +class MockQuery(object): + + def __init__(self, class_objects): + self.class_objects = class_objects + + def filter_by(self, **kwds): + return Bunch(first=lambda: None) + + def get(self, id): + return self.class_objects.get(id, None) + + __all__ = [ UsesApp ] From d4aa83f35f68b6aa1a5aa5edce545aee348f6f56 Mon Sep 17 00:00:00 2001 From: Carl Eberhard Date: Tue, 14 Jan 2014 10:04:20 -0500 Subject: [PATCH 0761/1033] Visualizations Registry: default to on --- .../scatterplot/config/scatterplot.xml | 6 + .../src/scatterplot-config-editor.js | 20 ++- .../scatterplot/static/scatterplot-edit.js | 2 +- .../scatterplot/templates/scatterplot.mako | 51 ++++-- lib/galaxy/app.py | 4 +- lib/galaxy/config.py | 2 +- lib/galaxy/visualization/registry.py | 118 ++++++++++++- static/scripts/mvc/dataset/hda-edit.js | 15 +- static/scripts/mvc/ui.js | 4 + .../scatterplotControlForm.js | 0 .../mvc/visualization/visualization-model.js | 158 ++++++++++++++++++ static/scripts/packed/mvc/dataset/hda-edit.js | 2 +- static/scripts/packed/mvc/ui.js | 2 +- .../galaxy/visualization/scatterplot.mako | 2 +- universe_wsgi.ini.sample | 2 +- 15 files changed, 349 insertions(+), 39 deletions(-) rename static/scripts/mvc/{visualizations => visualization}/scatterplotControlForm.js (100%) create mode 100644 static/scripts/mvc/visualization/visualization-model.js diff --git a/config/plugins/visualizations/scatterplot/config/scatterplot.xml b/config/plugins/visualizations/scatterplot/config/scatterplot.xml index d206f46b2a1..5895f43d2db 100644 --- a/config/plugins/visualizations/scatterplot/config/scatterplot.xml +++ b/config/plugins/visualizations/scatterplot/config/scatterplot.xml @@ -7,9 +7,15 @@ tabular.Tabular dataset_id + + Visualization + scatterplot + visualization_id + dataset_id + visualization_id diff --git a/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js b/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js index 01d0eb8025f..204deefeb90 100644 --- a/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js +++ b/config/plugins/visualizations/scatterplot/src/scatterplot-config-editor.js @@ -10,6 +10,7 @@ todo: Allow setting perPage of config Auto render if given data and/or config Allow option to auto set width/height based on screen real estate avail. + Handle large number of pages better (Known genes hg19) Use d3.nest to allow grouping, pagination/filtration by group (e.g. chromCol) Semantic HTML (figure, caption) Save as visualization, load from visualization @@ -29,26 +30,28 @@ todo: * configuring which data will be used * configuring the plot display */ -var ScatterplotConfigEditor = BaseView.extend( LoggableMixin ).extend({ +var ScatterplotConfigEditor = Backbone.View.extend( LoggableMixin ).extend({ //TODO: !should be a view on a visualization model //logger : console, className : 'scatterplot-control-form', /** initialize requires a configuration Object containing a dataset Object */ initialize : function( attributes ){ - //console.log( this + '.initialize, attributes:', attributes ); - if( !attributes || !attributes.config || !attributes.dataset ){ - throw new Error( "ScatterplotView requires a configuration and dataset" ); + if( !this.model ){ + this.model = new Visualization({ type: 'scatterplot' }); } - //console.log( 'config:', attributes.config ); + console.log( this + '.initialize, attributes:', attributes ); + if( !attributes || !attributes.dataset ){ + throw new Error( "ScatterplotConfigEditor requires a dataset" ); + } this.dataset = attributes.dataset; - //console.log( 'dataset:', this.dataset ); + console.log( 'dataset:', this.dataset ); //TODO: ScatterplotView -> ScatterplotDisplay, this.plotView -> this.display this.plotView = new ScatterplotView({ dataset : attributes.dataset, - config : attributes.config + model : this.model //TODO: if data }); }, @@ -58,8 +61,7 @@ var ScatterplotConfigEditor = BaseView.extend( LoggableMixin ).extend({ //console.log( this + '.render' ); // render the tab controls, areas and loading indicator - this.$el.append( ScatterplotConfigEditor.templates.mainLayout({ - })); + this.$el.append( ScatterplotConfigEditor.templates.mainLayout({})); // render the tab content this.$el.find( '#data-control' ).append( this._render_dataControl() ); diff --git a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js index 1d8558e84f5..b8b804c3a75 100644 --- a/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js +++ b/config/plugins/visualizations/scatterplot/static/scatterplot-edit.js @@ -1 +1 @@ -function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){q.redraw(),e(),s=d(),$(".chart-info-box").remove(),$(o.node()).trigger("zoom.scatterplot",[])}function g(a,c,d){return c+=8,$(['
                    ',b.idColumn?"
                    "+d[b.idColumn]+"
                    ":"","
                    ",j(d),"
                    ","
                    ",k(d),"
                    ","
                    "].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,10]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.x.ticks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.y.ticks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=4;q.x.label=o.append("text").attr("class","axis-label").text(b.x.label).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("class","axis-label").text(b.y.label).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",b.height).attr("r",0);t.transition().duration(b.animDuration).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",b.datapointSize),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='

                    \n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n

                    \n\n
                    \n \n
                    ',(f=c.datapointSize)?f=f.call(b,{hash:{},data:e}):(f=b.datapointSize,f=typeof f===h?f.apply(b):f),g+=i(f)+'
                    \n
                    \n

                    \n Size of the graphic representation of each data point\n

                    \n
                    \n\n
                    \n \n
                    ',(f=c.width)?f=f.call(b,{hash:{},data:e}):(f=b.width,f=typeof f===h?f.apply(b):f),g+=i(f)+'
                    \n
                    \n

                    \n (not including chart margins and axes)\n

                    \n
                    \n\n
                    \n \n
                    ',(f=c.height)?f=f.call(b,{hash:{},data:e}):(f=b.height,f=typeof f===h?f.apply(b):f),g+=i(f)+'
                    \n
                    \n

                    \n (not including chart margins and axes)\n

                    \n
                    \n\n
                    \n \n \n

                    \n
                    \n\n
                    \n \n \n

                    \n
                    \n\n\n'}),this.Templates.datacontrol=Handlebars.template(function(a,b,c,d,e){function f(a,b){var d,e="";return e+='\n \n "}function g(){return'checked="true"'}this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var h,i="",j="function",k=this.escapeExpression,l=this;return i+='

                    \n Use the following controls to change the data used by the chart.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n

                    \n\n\n
                    \n \n \n
                    \n
                    \n \n \n
                    \n\n\n
                    \n \n \n

                    \n These will be displayed (along with the x and y values) when you hover over\n a data point.\n

                    \n
                    \n\n\n\n\n\n\n'}),this.Templates.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='
                    \n \n \n\n \n
                    \n \n
                    \n \n
                    \n \n \n
                    \n \n
                    \n\n \n
                    \n\n
                    \n
                    \n'});var ScatterplotConfigEditor=BaseView.extend(LoggableMixin).extend({className:"scatterplot-control-form",initialize:function(a){if(!a||!a.config||!a.dataset)throw new Error("ScatterplotView requires a configuration and dataset");this.dataset=a.dataset,this.plotView=new ScatterplotView({dataset:a.dataset,config:a.config})},render:function(){return this.$el.append(ScatterplotConfigEditor.templates.mainLayout({})),this.$el.find("#data-control").append(this._render_dataControl()),this._render_chartControls(this.$el.find("#chart-control")),this._render_chartDisplay(),this.$el.find("[title]").tooltip(),this},_render_dataControl:function(){var a=this.dataset,b=_.map(a.metadata_column_types,function(b,c){var d={index:c,type:b,name:"column "+(c+1)};return a.metadata_column_names&&a.metadata_column_names[c]&&(d.name=a.metadata_column_names[c]),d}),c=_.filter(b,function(a){return"int"===a.type||"float"===a.type});2>c&&(c=b);var d=this.$el.find(".tab-pane#data-control");return d.html(ScatterplotConfigEditor.templates.dataControl({allColumns:b,numericColumns:c})),d.find('[name="xColumn"]').val(this.plotView.config.xColumn||c[0].index),d.find('[name="yColumn"]').val(this.plotView.config.yColumn||c[1].index),void 0!==this.plotView.config.idColumn&&(d.find("#include-id-checkbox").prop("checked",!0).trigger("change"),d.find('select[name="idColumn"]').val(this.plotView.config.idColumn)),d},_render_chartControls:function(a){function b(){var a=$(this);a.siblings(".slider-output").text(a.slider("value"))}a.html(ScatterplotConfigEditor.templates.chartControl(this.plotView.config));var c=this,d={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};return a.find(".numeric-slider-input").each(function(){var a=$(this),e=a.attr("data-config-key"),f=_.extend(d[e],{value:c.plotView.config[e],change:b,slide:b});a.find(".slider").slider(f)}),this.dataset.metadata_column_names,a},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");return this.plotView.setElement(a),this.plotView.render(),a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart"},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.updateConfigWithDataSettings(),this.updateConfigWithChartSettings(),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.plotView.fetchData()},updateConfigWithDataSettings:function(){var a=this.$el.find("#data-control"),b={xColumn:Number(a.find('[name="xColumn"]').val()),yColumn:Number(a.find('[name="yColumn"]').val())};return a.find("#include-id-checkbox").prop("checked")&&(b.idColumn=a.find('[name="idColumn"]').val()),_.extend(this.plotView.config,b)},updateConfigWithChartSettings:function(){var a=this.plotView,b=this.$el.find("#chart-control");return["datapointSize","width","height"].forEach(function(c){a.config[c]=b.find('.numeric-slider-input[data-config-key="'+c+'"]').find(".slider").slider("value")}),a.config.x.label=b.find('input[name="X-axis-label"]').val(),a.config.y.label=b.find('input[name="Y-axis-label"]').val(),a.config},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:Templates.editor,dataControl:Templates.datacontrol,chartControl:Templates.chartcontrol};var ScatterplotView=Backbone.View.extend({defaults:{metadata:{dataLines:void 0},pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},x:{ticks:10,label:"X"},y:{ticks:10,label:"Y"},datapointSize:4,animDuration:500},initialize:function(a){this.config=_.extend(_.clone(this.defaults),a.config||{}),this.dataset=a.dataset},updateConfig:function(a){this.config=this.config||{},_.extend(this.config,a)},fetchData:function(){this.showLoadingIndicator("getting data");var a=this;return xhr=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:this.config.pagination.perPage,offset:this.config.pagination.currPage*this.config.pagination.perPage}),xhr.done(function(b){a.renderData(b.data)}),xhr.fail(function(a,b,c){alert("Error loading data:\n"+a.responseText),console.error(a,b,c)}),xhr.always(function(){a.hideLoadingIndicator()}),xhr},render:function(a){return this.$el.addClass("scatterplot-display").html(['
                    ','
                    ','','',"
                    ","",'
                    '].join("")),this.$el.children().hide(),a&&this.renderData(a),this},showLoadingIndicator:function(a,b){a=a||"",b=b||"fast";var c=this.$el.find(".loading-indicator");a&&c.find(".loading-indicator-message").text(a),c.is(":visible")||(this.toggleStats(!1),c.css({left:this.config.width/2,top:this.config.height/2}).show())},hideLoadingIndicator:function(a){a=a||"fast",this.$el.find(".loading-indicator").hide()},renderData:function(a){this.$el.find(".controls").empty().append(this.renderControls(a)).show(),this.renderPlot(a),this.getStats(a)},renderControls:function(a){var b=this,c=$('
                    '),d=$('
                    ');return c.append([this.renderPrevNext(a),this.renderPagination(a)]),d.append([this.renderLineInfo(a),$("").addClass("stats-toggle-btn").click(function(){b.toggleStats()}),$("").addClass("rerender-btn").click(function(){b.renderPlot(a)})]),[c,d]},renderLineInfo:function(a){var b=this.dataset.metadata_data_lines||"an unknown number of",c=this.config.pagination.currPage*this.config.pagination.perPage,d=c+a.length;return $("

                    ").addClass("scatterplot-data-info").text(["Displaying lines",c+1,"to",d,"of",b,"lines"].join(" "))},renderPrevNext:function(a){function b(a){return $(['

                  • ',a,"
                    • "].join(""))}if(!a||0===this.config.pagination.currPage&&a.length0&&(c.config.pagination.currPage-=1,c.fetchData())}),g=b("Next").click(function(){(!e||c.config.pagination.currPage").addClass("pagination data-prev-next").append([f,g]);return 0===c.config.pagination.currPage&&f.addClass("disabled"),e&&c.config.pagination.currPage===e-1&&g.addClass("disabled"),h},renderPagination:function(a){function b(a){return $(['
                  • ',a,"
                    • "].join(""))}function c(){d.config.pagination.currPage=$(this).data("page"),d.fetchData()}if(!a||0===this.config.pagination.currPage&&a.length").addClass("pagination data-pages"),h=0;f>h;h+=1){var i=b(h+1).attr("data-page",h).click(c);h===this.config.pagination.currPage&&i.addClass("active"),g.append(i)}return g},renderPlot:function(a){this.toggleStats(!1);var b=this.$el.find("svg");b.off().empty().show(),scatterplot(b.get(0),this.config,a)},getStats:function(a){var b=this;meanWorker=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js"),meanWorker.postMessage({data:a,keys:[this.config.xColumn,this.config.yColumn]}),meanWorker.onerror=function(){meanWorker.terminate()},meanWorker.onmessage=function(a){b.renderStats(a.data)}},renderStats:function(a){var b=this.$el.find(".stats-display"),c=this.config.x.label,d=this.config.y.label,e=$("").addClass("table").append([""].join("")).append(_.map(a,function(a,b){return $([""].join(""))}));b.empty().append(e)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}); \ No newline at end of file +function scatterplot(a,b,c){function d(){var a={v:{},h:{}};return a.v.lines=p.selectAll("line.v-grid-line").data(m.x.ticks(q.x.fn.ticks()[0])),a.v.lines.enter().append("svg:line").classed("grid-line v-grid-line",!0),a.v.lines.attr("x1",m.x).attr("x2",m.x).attr("y1",0).attr("y2",b.height),a.v.lines.exit().remove(),a.h.lines=p.selectAll("line.h-grid-line").data(m.y.ticks(q.y.fn.ticks()[0])),a.h.lines.enter().append("svg:line").classed("grid-line h-grid-line",!0),a.h.lines.attr("x1",0).attr("x2",b.width).attr("y1",m.y).attr("y2",m.y),a.h.lines.exit().remove(),a}function e(){return t.attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",function(a,b){return m.y(k(a,b))}).style("display","block").filter(function(){var a=d3.select(this).attr("cx"),c=d3.select(this).attr("cy");return 0>a||a>b.width?!0:0>c||c>b.height?!0:!1}).style("display","none")}function f(){q.redraw(),e(),s=d(),$(".chart-info-box").remove(),$(o.node()).trigger("zoom.scatterplot",[])}function g(a,c,d){return c+=8,$(['
                    ',b.idColumn?"
                    "+d[b.idColumn]+"
                    ":"","
                    ",j(d),"
                    ","
                    ",k(d),"
                    ","
                    "].join("")).css({top:a,left:c,"z-index":2})}var h=function(a,b){return"translate("+a+","+b+")"},i=function(a,b,c){return"rotate("+a+","+b+","+c+")"},j=function(a){return a[b.xColumn]},k=function(a){return a[b.yColumn]},l={x:{extent:d3.extent(c,j)},y:{extent:d3.extent(c,k)}},m={x:d3.scale.linear().domain(l.x.extent).range([0,b.width]),y:d3.scale.linear().domain(l.y.extent).range([b.height,0])},n=d3.behavior.zoom().x(m.x).y(m.y).scaleExtent([1,10]),o=d3.select(a).attr("class","scatterplot").attr("width","100%").attr("height",b.height+(b.margin.top+b.margin.bottom)),p=o.append("g").attr("class","content").attr("transform",h(b.margin.left,b.margin.top)).call(n);p.append("rect").attr("class","zoom-rect").attr("width",b.width).attr("height",b.height).style("fill","transparent");var q={x:{},y:{}};q.x.fn=d3.svg.axis().orient("bottom").scale(m.x).ticks(b.x.ticks).tickFormat(d3.format("s")),q.y.fn=d3.svg.axis().orient("left").scale(m.y).ticks(b.y.ticks).tickFormat(d3.format("s")),q.x.g=p.append("g").attr("class","x axis").attr("transform",h(0,b.height)).call(q.x.fn),q.y.g=p.append("g").attr("class","y axis").call(q.y.fn);var r=4;q.x.label=o.append("text").attr("class","axis-label").text(b.x.label).attr("text-anchor","middle").attr("dominant-baseline","text-after-edge").attr("x",b.width/2+b.margin.left).attr("y",b.height+b.margin.bottom+b.margin.top-r),q.y.label=o.append("text").attr("class","axis-label").text(b.y.label).attr("text-anchor","middle").attr("dominant-baseline","text-before-edge").attr("x",r).attr("y",b.height/2).attr("transform",i(-90,r,b.height/2)),q.redraw=function(){o.select(".x.axis").call(q.x.fn),o.select(".y.axis").call(q.y.fn)};var s=d(),t=p.selectAll(".glyph").data(c).enter().append("svg:circle").classed("glyph",!0).attr("cx",function(a,b){return m.x(j(a,b))}).attr("cy",b.height).attr("r",0);t.transition().duration(b.animDuration).attr("cy",function(a,b){return m.y(k(a,b))}).attr("r",b.datapointSize),n.on("zoom",f),t.on("mouseover",function(a,c){var d=d3.select(this);d.style("fill","red").style("fill-opacity",1),p.append("line").attr("stroke","red").attr("stroke-width",1).attr("x1",d.attr("cx")-b.datapointSize).attr("y1",d.attr("cy")).attr("x2",0).attr("y2",d.attr("cy")).classed("hoverline",!0),d.attr("cy")= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f,g="",h="function",i=this.escapeExpression;return g+='

                    \n Use the following controls to how the chart is displayed.\n The slide controls can be moved by the mouse or, if the \'handle\' is in focus, your keyboard\'s arrow keys.\n Move the focus between controls by using the tab or shift+tab keys on your keyboard.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n

                    \n\n
                    \n \n
                    ',(f=c.datapointSize)?f=f.call(b,{hash:{},data:e}):(f=b.datapointSize,f=typeof f===h?f.apply(b):f),g+=i(f)+'
                    \n
                    \n

                    \n Size of the graphic representation of each data point\n

                    \n
                    \n\n
                    \n \n
                    ',(f=c.width)?f=f.call(b,{hash:{},data:e}):(f=b.width,f=typeof f===h?f.apply(b):f),g+=i(f)+'
                    \n
                    \n

                    \n (not including chart margins and axes)\n

                    \n
                    \n\n
                    \n \n
                    ',(f=c.height)?f=f.call(b,{hash:{},data:e}):(f=b.height,f=typeof f===h?f.apply(b):f),g+=i(f)+'
                    \n
                    \n

                    \n (not including chart margins and axes)\n

                    \n
                    \n\n
                    \n \n \n

                    \n
                    \n\n
                    \n \n \n

                    \n
                    \n\n\n'}),this.scatterplot.datacontrol=Handlebars.template(function(a,b,c,d,e){function f(a,b){var d,e="";return e+='\n \n "}function g(){return'checked="true"'}this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var h,i="",j="function",k=this.escapeExpression,l=this;return i+='

                    \n Use the following controls to change the data used by the chart.\n Use the \'Draw\' button to render (or re-render) the chart with the current settings.\n

                    \n\n\n
                    \n \n \n
                    \n
                    \n \n \n
                    \n\n\n
                    \n \n \n

                    \n These will be displayed (along with the x and y values) when you hover over\n a data point.\n

                    \n
                    \n\n\n\n\n\n\n'}),this.scatterplot.editor=Handlebars.template(function(a,b,c,d,e){this.compilerInfo=[4,">= 1.0.0"],c=this.merge(c,a.helpers),e=e||{};var f="";return f+='
                    \n \n \n\n \n
                    \n \n
                    \n \n
                    \n \n \n
                    \n \n
                    \n\n \n
                    \n\n
                    \n
                    \n'});var ScatterplotConfigEditor=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",initialize:function(a){if(this.model||(this.model=new Visualization({type:"scatterplot"})),console.log(this+".initialize, attributes:",a),!a||!a.dataset)throw new Error("ScatterplotConfigEditor requires a dataset");this.dataset=a.dataset,console.log("dataset:",this.dataset),this.plotView=new ScatterplotView({dataset:a.dataset,model:this.model})},render:function(){return this.$el.append(ScatterplotConfigEditor.templates.mainLayout({})),this.$el.find("#data-control").append(this._render_dataControl()),this._render_chartControls(this.$el.find("#chart-control")),this._render_chartDisplay(),this.$el.find("[title]").tooltip(),this},_render_dataControl:function(){var a=this.dataset,b=_.map(a.metadata_column_types,function(b,c){var d={index:c,type:b,name:"column "+(c+1)};return a.metadata_column_names&&a.metadata_column_names[c]&&(d.name=a.metadata_column_names[c]),d}),c=_.filter(b,function(a){return"int"===a.type||"float"===a.type});2>c&&(c=b);var d=this.$el.find(".tab-pane#data-control");return d.html(ScatterplotConfigEditor.templates.dataControl({allColumns:b,numericColumns:c})),d.find('[name="xColumn"]').val(this.plotView.config.xColumn||c[0].index),d.find('[name="yColumn"]').val(this.plotView.config.yColumn||c[1].index),void 0!==this.plotView.config.idColumn&&(d.find("#include-id-checkbox").prop("checked",!0).trigger("change"),d.find('select[name="idColumn"]').val(this.plotView.config.idColumn)),d},_render_chartControls:function(a){function b(){var a=$(this);a.siblings(".slider-output").text(a.slider("value"))}a.html(ScatterplotConfigEditor.templates.chartControl(this.plotView.config));var c=this,d={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};return a.find(".numeric-slider-input").each(function(){var a=$(this),e=a.attr("data-config-key"),f=_.extend(d[e],{value:c.plotView.config[e],change:b,slide:b});a.find(".slider").slider(f)}),this.dataset.metadata_column_names,a},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");return this.plotView.setElement(a),this.plotView.render(),a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","click #data-control .render-button":"renderChart","click #chart-control .render-button":"renderChart"},toggleThirdColumnSelector:function(){this.$el.find('select[name="idColumn"]').parent().toggle()},renderChart:function(){this.$el.find(".nav li.disabled").removeClass("disabled"),this.updateConfigWithDataSettings(),this.updateConfigWithChartSettings(),this.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show"),this.plotView.fetchData()},updateConfigWithDataSettings:function(){var a=this.$el.find("#data-control"),b={xColumn:Number(a.find('[name="xColumn"]').val()),yColumn:Number(a.find('[name="yColumn"]').val())};return a.find("#include-id-checkbox").prop("checked")&&(b.idColumn=a.find('[name="idColumn"]').val()),_.extend(this.plotView.config,b)},updateConfigWithChartSettings:function(){var a=this.plotView,b=this.$el.find("#chart-control");return["datapointSize","width","height"].forEach(function(c){a.config[c]=b.find('.numeric-slider-input[data-config-key="'+c+'"]').find(".slider").slider("value")}),a.config.x.label=b.find('input[name="X-axis-label"]').val(),a.config.y.label=b.find('input[name="Y-axis-label"]').val(),a.config},toString:function(){return"ScatterplotConfigEditor("+(this.dataset?this.dataset.id:"")+")"}});ScatterplotConfigEditor.templates={mainLayout:scatterplot.editor,dataControl:scatterplot.datacontrol,chartControl:scatterplot.chartcontrol};var ScatterplotView=Backbone.View.extend({defaults:{metadata:{dataLines:void 0},pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},x:{ticks:10,label:"X"},y:{ticks:10,label:"Y"},datapointSize:4,animDuration:500},initialize:function(a){this.config=_.extend(_.clone(this.defaults),a.config||{}),this.dataset=a.dataset},updateConfig:function(a){this.config=this.config||{},_.extend(this.config,a)},fetchData:function(){this.showLoadingIndicator("getting data");var a=this;return xhr=jQuery.getJSON("/api/datasets/"+this.dataset.id,{data_type:"raw_data",provider:"dataset-column",limit:this.config.pagination.perPage,offset:this.config.pagination.currPage*this.config.pagination.perPage}),xhr.done(function(b){a.renderData(b.data)}),xhr.fail(function(a,b,c){alert("Error loading data:\n"+a.responseText),console.error(a,b,c)}),xhr.always(function(){a.hideLoadingIndicator()}),xhr},render:function(a){return this.$el.addClass("scatterplot-display").html(['
                    ','
                    ','','',"
                    ","",'
                    '].join("")),this.$el.children().hide(),a&&this.renderData(a),this},showLoadingIndicator:function(a,b){a=a||"",b=b||"fast";var c=this.$el.find(".loading-indicator");a&&c.find(".loading-indicator-message").text(a),c.is(":visible")||(this.toggleStats(!1),c.css({left:this.config.width/2,top:this.config.height/2}).show())},hideLoadingIndicator:function(a){a=a||"fast",this.$el.find(".loading-indicator").hide()},renderData:function(a){this.$el.find(".controls").empty().append(this.renderControls(a)).show(),this.renderPlot(a),this.getStats(a)},renderControls:function(a){var b=this,c=$('
                    '),d=$('
                    ');return c.append([this.renderPrevNext(a),this.renderPagination(a)]),d.append([this.renderLineInfo(a),$("").addClass("stats-toggle-btn").click(function(){b.toggleStats()}),$("").addClass("rerender-btn").click(function(){b.renderPlot(a)})]),[c,d]},renderLineInfo:function(a){var b=this.dataset.metadata_data_lines||"an unknown number of",c=this.config.pagination.currPage*this.config.pagination.perPage,d=c+a.length;return $("

                    ").addClass("scatterplot-data-info").text(["Displaying lines",c+1,"to",d,"of",b,"lines"].join(" "))},renderPrevNext:function(a){function b(a){return $(['

                  • ',a,"
                    • "].join(""))}if(!a||0===this.config.pagination.currPage&&a.length0&&(c.config.pagination.currPage-=1,c.fetchData())}),g=b("Next").click(function(){(!e||c.config.pagination.currPage").addClass("pagination data-prev-next").append([f,g]);return 0===c.config.pagination.currPage&&f.addClass("disabled"),e&&c.config.pagination.currPage===e-1&&g.addClass("disabled"),h},renderPagination:function(a){function b(a){return $(['
                  • ',a,"
                    • "].join(""))}function c(){d.config.pagination.currPage=$(this).data("page"),d.fetchData()}if(!a||0===this.config.pagination.currPage&&a.length").addClass("pagination data-pages"),h=0;f>h;h+=1){var i=b(h+1).attr("data-page",h).click(c);h===this.config.pagination.currPage&&i.addClass("active"),g.append(i)}return g},renderPlot:function(a){this.toggleStats(!1);var b=this.$el.find("svg");b.off().empty().show(),scatterplot(b.get(0),this.config,a)},getStats:function(a){var b=this;meanWorker=new Worker("/plugins/visualizations/scatterplot/static/worker-stats.js"),meanWorker.postMessage({data:a,keys:[this.config.xColumn,this.config.yColumn]}),meanWorker.onerror=function(){meanWorker.terminate()},meanWorker.onmessage=function(a){b.renderStats(a.data)}},renderStats:function(a){var b=this.$el.find(".stats-display"),c=this.config.x.label,d=this.config.y.label,e=$("
                    ",c,"",d,"
                    ",b,"",a[0],"",a[1],"
                    ").addClass("table").append([""].join("")).append(_.map(a,function(a,b){return $([""].join(""))}));b.empty().append(e)},toggleStats:function(a){var b=this.$el.find(".stats-display");a=void 0===a?b.is(":hidden"):a,a?(this.$el.find("svg").hide(),b.show(),this.$el.find(".controls .stats-toggle-btn").text("Plot")):(b.hide(),this.$el.find("svg").show(),this.$el.find(".controls .stats-toggle-btn").text("Stats"))},toString:function(){return"ScatterplotView()"}}),ScatterplotModel=Visualization.extend({defaults:{type:"scatterplot",config:{metadata:{dataLines:void 0},pagination:{currPage:0,perPage:3e3},width:400,height:400,margin:{top:16,right:16,bottom:40,left:54},x:{ticks:10,label:"X"},y:{ticks:10,label:"Y"},datapointSize:4,animDuration:500}}}); \ No newline at end of file diff --git a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako index 9c074f502d0..a6a1a182106 100644 --- a/config/plugins/visualizations/scatterplot/templates/scatterplot.mako +++ b/config/plugins/visualizations/scatterplot/templates/scatterplot.mako @@ -1,3 +1,24 @@ +<% + hda_dict = trans.security.encode_dict_ids( hda.to_dict() ) + + config = query_args + title = "Scatterplot of '" + hda.name + "'" + info = hda.info + + visualization = context.get( 'visualization' ) + if visualization is not None: + config = visualization.latest_revision.config + config.update( query_args ) + title = visualization.title + info = config.get( 'description', info ) + + config[ 'type' ] = 'scatterplot' + + # optionally bootstrap data from dprov + ##data = list( hda.datatype.dataset_column_dataprovider( hda, limit=10000 ) ) +%> +## ---------------------------------------------------------------------------- + @@ -13,14 +34,15 @@ ## ---------------------------------------------------------------------------- + + - - - + + @@ -30,25 +52,20 @@ %if not embedded: ## dataset info: only show if on own page
                    -

                    Scatterplot of '${hda.name}'

                    -

                    ${hda.info}

                    +

                    ${title}

                    +

                    ${info}

                    +<%def name="render_deprecated_repository_dependencies_message( deprecated_repository_dependency_tups )"> +
                    + <% + from tool_shed.util.common_util import parse_repository_dependency_tuple + msg = '
                      ' + for deprecated_repository_dependency_tup in deprecated_repository_dependency_tups: + toolshed, name, owner, changeset_revision, pir, oicct = \ + parse_repository_dependency_tuple( deprecated_repository_dependency_tup ) + msg += '
                    • Revision %s of repository %s owned by %s
                      • ' % \ + ( changeset_revision, name, owner ) + msg += '
                    ' + %> + This repository depends upon the following deprecated repositories
                    + ${msg} +
                    + + <%def name="render_star_rating( name, rating, disabled=False )"> <% if disabled: @@ -87,6 +104,20 @@ +<%def name="render_multiple_heads_message( heads )"> +
                    + <% + from tool_shed.util.shed_util_common import get_revision_label_from_ctx + heads_str = '' + for ctx in heads: + heads_str += '%s
                    ' % get_revision_label_from_ctx( ctx, include_date=True ) + %> + Contact the administrator of this Tool Shed as soon as possible and let them know that + this repository has the following multiple heads which must be merged.
                    + ${heads_str} +
                    + + <%def name="render_review_comment( comment_text )"> @@ -353,7 +386,19 @@ if wf_parms: ${p_text} %else: - ${param.value_to_display_text( value, app )} + + + ${param.value_to_display_text( value, app )} + + + + ${param.get_html_field( t, value, other_values).get_html( str(step.id) + "|" + "editable" + "|"+ prefix )} + + + + + %endif %endif From ae96c90894d95f0cf0fa580215d8afe0158b4740 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 17 Jan 2014 09:48:17 -0600 Subject: [PATCH 0820/1033] Provide item style access to runner params. --- lib/galaxy/jobs/runners/__init__.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/lib/galaxy/jobs/runners/__init__.py b/lib/galaxy/jobs/runners/__init__.py index 334b20c4850..65a2a9b1f4f 100644 --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -41,6 +41,8 @@ class RunnerParams( object ): def __getattr__( self, name ): return self.params.get( name, self.specs[ name ][ 'default' ] ) + __getitem__ = __getattr__ + class BaseJobRunner( object ): def __init__( self, app, nworkers, **kwargs ): From 766fbee77b7e082a3f8e08502b271366313eb368 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Fri, 17 Jan 2014 09:48:17 -0600 Subject: [PATCH 0821/1033] Handle subclassed DRMAA exceptions properly. No clue if this was a problem, but realized it might be. --- lib/galaxy/jobs/runners/drmaa.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/jobs/runners/drmaa.py b/lib/galaxy/jobs/runners/drmaa.py index dfda8b23f25..57b335ef64a 100644 --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -231,7 +231,10 @@ class DRMAAJobRunner( AsynchronousJobRunner ): assert external_job_id not in ( None, 'None' ), '(%s/%s) Invalid job id' % ( galaxy_id_tag, external_job_id ) state = self.ds.jobStatus( external_job_id ) except ( drmaa.InternalException, drmaa.InvalidJobException ), e: - ecn = e.__class__.__name__ + if isinstance( e , drmaa.InvalidJobException ): + ecn = "InvalidJobException".lower() + else: + ecn = "InternalException".lower() retry_param = ecn.lower() + '_retries' state_param = ecn.lower() + '_state' retries = getattr( ajs, retry_param, 0 ) From 513717662661bb7b533eb8d268c78cb6752b0e2c Mon Sep 17 00:00:00 2001 From: Martin Cech Date: Fri, 17 Jan 2014 12:19:04 -0500 Subject: [PATCH 0822/1033] =?UTF-8?q?library=20history=20=E2=80=98back?= =?UTF-8?q?=E2=80=99=20button=20bug=20removal?= MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit --- lib/galaxy/webapps/galaxy/api/authenticate.py | 15 +++++++++++++-- static/scripts/galaxy.library.js | 8 ++++---- static/scripts/packed/galaxy.library.js | 2 +- 3 files changed, 18 insertions(+), 7 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/api/authenticate.py b/lib/galaxy/webapps/galaxy/api/authenticate.py index b463058b139..d982c24aceb 100644 --- a/lib/galaxy/webapps/galaxy/api/authenticate.py +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -22,8 +22,8 @@ class AuthenticationController( BaseAPIController ): * GET /api/authenticate/baseauth returns an API key for authenticated user based on BaseAuth headers - :rtype: dict :returns: api_key in json format + :rtype: dict :raises: ObjectNotFound, HTTPBadRequest """ @@ -48,9 +48,20 @@ class AuthenticationController( BaseAPIController ): return dict( api_key= api_key_row.key ) def _decode_baseauth( self, encoded_str ): - """Decode an encrypted HTTP basic authentication string. Returns a tuple of + """ + Decode an encrypted HTTP basic authentication string. Returns a tuple of the form (email, password), and raises a HTTPBadRequest exception if nothing could be decoded. + + :param encoded_str: BaseAuth string encoded base64 + :type encoded_str: string + + :returns: email of the user + :rtype: string + :returns: password of the user + :rtype: string + + :raises: HTTPBadRequest """ split = encoded_str.strip().split( ' ' ) diff --git a/static/scripts/galaxy.library.js b/static/scripts/galaxy.library.js index 40f89acb12d..9a571536cde 100644 --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -406,9 +406,9 @@ var FolderContentView = Backbone.View.extend({ if (typeof folder_id === 'undefined') { return false; } else if (folder_id === '0'){ - library_router.navigate('#', {trigger: true, replace: true}); + library_router.navigate('/', {trigger: true, replace: false}); } else { - library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); + library_router.navigate('folders/' + folder_id, {trigger: true, replace: false}); } }, @@ -984,9 +984,9 @@ var GalaxyLibrary = Backbone.View.extend({ } }); -Backbone.history.start(); +Backbone.history.start({pushState: false}); -return this +// return this } }); diff --git a/static/scripts/packed/galaxy.library.js b/static/scripts/packed/galaxy.library.js index 61fb82dcc1d..e895978471c 100644 --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1 +1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('
                    ');r.push('

                    Data Libraries Beta Test. This is work in progress. Please report problems & ideas via email and Trello.

                    ');r.push('
                    ');r.push(' ');r.push(' ');r.push(' ");r.push("
                    ");r.push('
                    ');r.push('Libraries | ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<%- path_item[1] %> | ');r.push("<% } else { %>");r.push('<%- path_item[1] %>');r.push("<% } %>");r.push("<% }); %>");r.push("
                    ");r.push('
                    ",c,"",d,"
                    ",b,"",a[0],"",a[1],"
                    ');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" <% _.each(items, function(content_item) { %>");r.push(' ');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" ");r.push(' ');r.push(' ");r.push(" ");r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" <% } %> ");r.push(' ');r.push(" ");r.push(" <% }); %>");r.push(" ");r.push(" ");r.push("
                    viewnamedata typesizedate (UTC)
                    <%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' (empty folder)');r.push(" <% } %>");r.push(" folder<%= _.escape(content_item.get("item_count")) %> item(s)");r.push(' ");r.push(" <%- content_item.get("name") %><%= _.escape(content_item.get("data_type")) %><%= _.escape(content_item.get("readable_size")) %><%= _.escape(content_item.get("time_updated")) %>
                    ");r.push("
                    ");return r.join("")},templateDatasetModal:function(){var r=[];r.push('
                    ');r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" <% } %>");r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push("
                    ">Name<%= _.escape(item.get("name")) %>
                    Data type<%= _.escape(item.get("data_type")) %>
                    Genome build<%= _.escape(item.get("genome_build")) %>
                    Size<%= _.escape(size) %>
                    Date uploaded (UTC)<%= _.escape(item.get("date_uploaded")) %>
                    Uploaded by<%= _.escape(item.get("uploaded_by")) %>
                    Data Lines<%= _.escape(item.get("metadata_data_lines")) %>
                    Comment Lines<%= _.escape(item.get("metadata_comment_lines")) %>unknown
                    Number of Columns<%= _.escape(item.get("metadata_columns")) %>
                    Column Types<%= _.escape(item.get("metadata_column_types")) %>
                    Miscellaneous information<%= _.escape(item.get("misc_blurb")) %>
                    ");r.push(' 
                    ');r.push("
                    ");r.push("
                    ");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('');r.push("Select history: ");r.push('");r.push("");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('');r.push("Select history: ");r.push('");r.push("");return r.join("")},templateProgressBar:function(){var r=[];r.push('
                    ');r.push("Importing selected datasets to history <%= _.escape(history_name) %>");r.push("
                    ");r.push('
                    ');r.push('
                    ');r.push(' 0% Complete');r.push("
                    ");r.push("
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                    ');tmpl_array.push("
                    ");tmpl_array.push('');tmpl_array.push('');tmpl_array.push("
                    ");tmpl_array.push("
                    ");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+r,{trigger:true,replace:true})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hideOrDestroy()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! 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Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hideOrDestroy()}}});s.modal.show()},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hideOrDestroy();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+=''});$('
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                    ');tmpl_array.push("");tmpl_array.push('

                    Data Libraries Beta Test. This is work in progress. Please report problems & ideas via email and Trello.

                    ');tmpl_array.push('New Library');tmpl_array.push('');tmpl_array.push(" ");tmpl_array.push(' ');tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" ");tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(" ");tmpl_array.push(" <% }); %>");tmpl_array.push(" ");tmpl_array.push("
                    namedescriptionsynopsismodel type
                    <%- library.get("name") %><%= _.escape(library.get("description")) %><%= _.escape(library.get("synopsis")) %><%= _.escape(library.get("model_class")) %>
                    ");tmpl_array.push("
                    ");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('
                    ');tmpl_array.push("
                    ");tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push("
                    ");tmpl_array.push("
                    ");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.info("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('
                    ');r.push('

                    Data Libraries Beta Test. This is work in progress. Please report problems & ideas via email and Trello.

                    ');r.push('
                    ');r.push(' ');r.push(' ');r.push(' ");r.push("
                    ");r.push('
                    ');r.push('Libraries | ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<%- path_item[1] %> | ');r.push("<% } else { %>");r.push('<%- path_item[1] %>');r.push("<% } %>");r.push("<% }); %>");r.push("
                    ");r.push('');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" <% _.each(items, function(content_item) { %>");r.push(' ');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" ");r.push(' ');r.push(' ");r.push(" ");r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" <% } %> ");r.push(' ');r.push(" ");r.push(" <% }); %>");r.push(" ");r.push(" ");r.push("
                    viewnamedata typesizedate (UTC)
                    <%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' (empty folder)');r.push(" <% } %>");r.push(" folder<%= _.escape(content_item.get("item_count")) %> item(s)");r.push(' ");r.push(" <%- content_item.get("name") %><%= _.escape(content_item.get("data_type")) %><%= _.escape(content_item.get("readable_size")) %><%= _.escape(content_item.get("time_updated")) %>
                    ");r.push("
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There - # are currently only two supported processes; download_by_url and clone via a "shell_command" action type. + # are currently three supported processes; download_binary, download_by_url and clone via a "shell_command" + # action type. action_type, action_dict = actions[ 0 ] if action_type == 'download_binary': url = action_dict[ 'url' ] @@ -316,11 +317,13 @@ def install_and_build_package( app, tool_dependency, actions_dict ): downloaded_filename = td_common_util.download_binary( url, work_dir ) # Filter out any actions that are not download_binary, chmod, or set_environment. filtered_actions = filter_actions_after_binary_installation( actions[ 1: ] ) - # Set actions to the same, so that the current download_binary doesn't get re-run in the filtered actions below. + # Set actions to the same, so that the current download_binary doesn't get re-run in the + # filtered actions below. actions = filtered_actions except Exception, e: log.exception( str( e ) ) - # No binary exists, or there was an error downloading the binary from the generated URL. Proceed with the remaining actions. + # No binary exists, or there was an error downloading the binary from the generated URL. + # Proceed with the remaining actions. filtered_actions = actions[ 1: ] action_type, action_dict = filtered_actions[ 0 ] # If the downloaded file exists, move it to $INSTALL_DIR. Put this outside the try/catch above so that @@ -345,8 +348,9 @@ def install_and_build_package( app, tool_dependency, actions_dict ): is_binary = action_dict.get( 'is_binary', False ) log.debug( 'Attempting to download via url: %s', url ) if 'target_filename' in action_dict: - # Sometimes compressed archives extract their content to a folder other than the default defined file name. Using this - # attribute will ensure that the file name is set appropriately and can be located after download, decompression and extraction. + # Sometimes compressed archives extract their content to a folder other than the default + # defined file name. Using this attribute will ensure that the file name is set appropriately + # and can be located after download, decompression and extraction. downloaded_filename = action_dict[ 'target_filename' ] else: downloaded_filename = os.path.split( url )[ -1 ] @@ -374,8 +378,9 @@ def install_and_build_package( app, tool_dependency, actions_dict ): filtered_actions = actions[ 1: ] url = action_dict[ 'url' ] if 'target_filename' in action_dict: - # Sometimes compressed archives extracts their content to a folder other than the default defined file name. Using this - # attribute will ensure that the file name is set appropriately and can be located after download, decompression and extraction. + # Sometimes compressed archives extracts their content to a folder other than the default + # defined file name. Using this attribute will ensure that the file name is set appropriately + # and can be located after download, decompression and extraction. filename = action_dict[ 'target_filename' ] else: filename = url.split( '/' )[ -1 ] diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py index a160bbdd644..dcc4931c833 100755 --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -324,31 +324,37 @@ def move_file( current_dir, source, destination, rename_to=None ): def parse_package_elem( package_elem, platform_info_dict=None, include_after_install_actions=True ): """ - Parse a element within a tool dependency definition and return a list of action tuples. This method is called when setting - metadata on a repository that includes a tool_dependencies.xml file or when installing a repository that includes a tool_dependencies.xml - file. If installing, platform_info_dict must be a valid dictionary and include_after_install_actions must be True. + Parse a element within a tool dependency definition and return a list of action tuples. + This method is called when setting metadata on a repository that includes a tool_dependencies.xml + file or when installing a repository that includes a tool_dependencies.xml file. If installing, + platform_info_dict must be a valid dictionary and include_after_install_actions must be True. """ - # The actions_elem_tuples list contains tag sets (possibly inside of an tag set) to be processed in the order - # they are defined in the tool_dependencies.xml file. + # The actions_elem_tuples list contains tag sets (possibly inside of an + # tag set) to be processed in the order they are defined in the tool_dependencies.xml file. actions_elem_tuples = [] - # The tag sets that will go into the actions_elem_list are those that install a compiled binary if the architecture and operating system - # match it's defined attributes. If compiled binary is not installed, the first tag set [following those that have the os and - # architecture attributes] that does not have os or architecture attributes will be processed. This tag set must contain the recipe for - # downloading and compiling source. + # The tag sets that will go into the actions_elem_list are those that install a compiled binary if + # the architecture and operating system match it's defined attributes. If compiled binary is not + # installed, the first tag set [following those that have the os and architecture attributes] + # that does not have os or architecture attributes will be processed. This tag set must contain the + # recipe for downloading and compiling source. actions_elem_list = [] for elem in package_elem: if elem.tag == 'actions': - # We have an tag that should not be matched against a specific combination of architecture and operating system. + # We have an tag that should not be matched against a specific combination of + # architecture and operating system. in_actions_group = False actions_elem_tuples.append( ( in_actions_group, elem ) ) elif elem.tag == 'actions_group': - # We have an actions_group element, and its child elements should therefore be compared with the current operating system + # We have an actions_group element, and its child elements should therefore be compared + # with the current operating system # and processor architecture. in_actions_group = True - # Record the number of elements so we can filter out any elements that precede elements. + # Record the number of elements so we can filter out any elements that precede + # elements. actions_elem_count = len( elem.findall( 'actions' ) ) - # Record the number of elements that have both architecture and os specified, in order to filter out any - # platform-independent elements that come before platform-specific elements. + # Record the number of elements that have both architecture and os specified, in order + # to filter out any platform-independent elements that come before platform-specific + # elements. platform_actions_elements = [] for actions_elem in elem.findall( 'actions' ): if actions_elem.get( 'architecture' ) is not None and actions_elem.get( 'os' ) is not None: @@ -356,8 +362,9 @@ def parse_package_elem( package_elem, platform_info_dict=None, include_after_ins platform_actions_element_count = len( platform_actions_elements ) platform_actions_elements_processed = 0 actions_elems_processed = 0 - # The tag sets that will go into the after_install_actions list are tags instead of tags. These will be processed - # only if they are at the very end of the tag set (after all tag sets). See below for details. + # The tag sets that will go into the after_install_actions list are tags instead of + # tags. These will be processed only if they are at the very end of the tag set (after + # all tag sets). See below for details. after_install_actions = [] # Inspect the element and build the actions_elem_list and the after_install_actions list. for child_element in elem: @@ -365,60 +372,71 @@ def parse_package_elem( package_elem, platform_info_dict=None, include_after_ins actions_elems_processed += 1 system = child_element.get( 'os' ) architecture = child_element.get( 'architecture' ) - # Skip tags that have only one of architecture or os specified, in order for the count in - # platform_actions_elements_processed to remain accurate. + # Skip tags that have only one of architecture or os specified, in order for the + # count in platform_actions_elements_processed to remain accurate. if ( system and not architecture ) or ( architecture and not system ): log.debug( 'Error: Both architecture and os attributes must be specified in an tag.' ) continue - # Since we are inside an tag set, compare it with our current platform information and filter the - # tag sets that don't match. Require both the os and architecture attributes to be defined in order to find a match. + # Since we are inside an tag set, compare it with our current platform information + # and filter the tag sets that don't match. Require both the os and architecture attributes + # to be defined in order to find a match. if system and architecture: platform_actions_elements_processed += 1 - # If either the os or architecture do not match the platform, this tag will not be considered a match. Skip - # it and proceed with checking the next one. + # If either the os or architecture do not match the platform, this tag will not be + # considered a match. Skip it and proceed with checking the next one. if platform_info_dict: if platform_info_dict[ 'os' ] != system or platform_info_dict[ 'architecture' ] != architecture: continue else: - # We must not be installing a repository into Galaxy, so determining if we can install a binary is not necessary. + # We must not be installing a repository into Galaxy, so determining if we can install a + # binary is not necessary. continue else: - # tags without both os and architecture attributes are only allowed to be specified after platform-specific - # tags. If we find a platform-independent tag before all platform-specific tags have been - # processed. + # tags without both os and architecture attributes are only allowed to be specified + # after platform-specific tags. If we find a platform-independent tag before + # all platform-specific tags have been processed. if platform_actions_elements_processed < platform_actions_element_count: - message = 'Error: tags without os and architecture attributes are only allowed after all tags with ' - message += 'os and architecture attributes have been defined. Skipping the tag set with no os or architecture ' - message += 'attributes that has been defined between two tag sets that have these attributes defined. ' - log.debug( message ) + debug_msg = 'Error: tags without os and architecture attributes are only allowed ' + debug_msg += 'after all tags with os and architecture attributes have been defined. ' + debug_msg += 'Skipping the tag set with no os or architecture attributes that has ' + debug_msg += 'been defined between two tag sets that have these attributes defined. ' + log.debug( debug_msg ) continue - # If we reach this point, it means one of two things: 1) The system and architecture attributes are not defined in this - # tag, or 2) The system and architecture attributes are defined, and they are an exact match for the current - # platform. Append the child element to the list of elements to process. + # If we reach this point, it means one of two things: 1) The system and architecture attributes are + # not defined in this tag, or 2) The system and architecture attributes are defined, and + # they are an exact match for the current platform. Append the child element to the list of elements + # to process. actions_elem_list.append( child_element ) elif child_element.tag == 'action': # Any tags within an tag set must come after all tags. if actions_elems_processed == actions_elem_count: - # If all elements have been processed, then this element can be appended to the list of actions to - # execute within this group. + # If all elements have been processed, then this element can be appended to the + # list of actions to execute within this group. after_install_actions.append( child_element ) else: - # If any elements remain to be processed, then log a message stating that elements are not allowed - # to precede any elements within an tag set. - message = 'Error: tags are only allowed at the end of an tag set after all tags. ' - message += 'Skipping <%s> element with type %s.' % ( child_element.tag, child_element.get( 'type' ) ) - log.debug( message ) + # If any elements remain to be processed, then log a message stating that + # elements are not allowed to precede any elements within an tag set. + debug_msg = 'Error: tags are only allowed at the end of an tag set after ' + debug_msg += 'all tags. Skipping <%s> element with type %s.' % \ + ( child_element.tag, child_element.get( 'type', 'unknown' ) ) + log.debug( debug_msg ) continue if platform_info_dict is None and not include_after_install_actions: # We must be setting metadata on a repository. - actions_elem_tuples.append( ( in_actions_group, actions_elem_list[ 0 ] ) ) + if len( actions_elem_list ) >= 1: + actions_elem_tuples.append( ( in_actions_group, actions_elem_list[ 0 ] ) ) + else: + # We are processing a recipe that contains only an tag set for installing a binary, + # but does not include an additional recipe for installing and compiling from source. + actions_elem_tuples.append( ( in_actions_group, [] ) ) elif platform_info_dict is not None and include_after_install_actions: # We must be installing a repository. if after_install_actions: actions_elem_list.extend( after_install_actions ) actions_elem_tuples.append( ( in_actions_group, actions_elem_list ) ) else: - # Skip any element that is not or - this will skip comments, tags and tags. + # Skip any element that is not or - this will skip comments, tags + # and tags. in_actions_group = False continue return actions_elem_tuples diff --git a/lib/tool_shed/util/metadata_util.py b/lib/tool_shed/util/metadata_util.py index c196637a699..1ada2889d44 100644 --- a/lib/tool_shed/util/metadata_util.py +++ b/lib/tool_shed/util/metadata_util.py @@ -791,26 +791,30 @@ def generate_package_dependency_metadata( app, elem, valid_tool_dependencies_dic if sub_elem.tag == 'readme': requirements_dict[ 'readme' ] = sub_elem.text elif sub_elem.tag == 'repository': - # We have a complex repository dependency. If the returned value of repository_dependency_is_valid is True, the tool - # dependency definition will be set as invalid. This is currently the only case where a tool dependency definition is - # considered invalid. - repository_dependency_tup, repository_dependency_is_valid, error_message = handle_repository_elem( app=app, - repository_elem=sub_elem, - only_if_compiling_contained_td=False ) + # We have a complex repository dependency. If the returned value of repository_dependency_is_valid + # is True, the tool dependency definition will be set as invalid. This is currently the only case + # where a tool dependency definition is considered invalid. + repository_dependency_tup, repository_dependency_is_valid, error_message = \ + handle_repository_elem( app=app, repository_elem=sub_elem, only_if_compiling_contained_td=False ) elif sub_elem.tag == 'install': package_install_version = sub_elem.get( 'version', '1.0' ) if package_install_version == '1.0': - # Complex repository dependencies can be defined within the last tag set contained in an tag set. - # Comments, tag sets and tag sets will be skipped in td_common_util.parse_package_elem(). - actions_elem_tuples = td_common_util.parse_package_elem( sub_elem, platform_info_dict=None, include_after_install_actions=False ) + # Complex repository dependencies can be defined within the last tag set contained in an + # tag set. Comments, tag sets and tag sets will be skipped + # in td_common_util.parse_package_elem(). + actions_elem_tuples = td_common_util.parse_package_elem( sub_elem, + platform_info_dict=None, + include_after_install_actions=False ) if actions_elem_tuples: - # We now have a list of a single tuple that looks something like: [(True, )] + # We now have a list of a single tuple that looks something like: + # [(True, )] actions_elem_tuple = actions_elem_tuples[ 0 ] in_actions_group, actions_elem = actions_elem_tuple if in_actions_group: - # Since we're inside an tag set, inspect the actions_elem to see if a complex repository dependency - # is defined. By definition, complex repository dependency definitions contained within the last tag set - # within an tag set will have the value of "only_if_compiling_contained_td" set to True in + # Since we're inside an tag set, inspect the actions_elem to see if a complex + # repository dependency is defined. By definition, complex repository dependency definitions + # contained within the last tag set within an tag set will have the + # value of "only_if_compiling_contained_td" set to True in for action_elem in actions_elem: if action_elem.tag == 'package': # @@ -834,7 +838,8 @@ def generate_package_dependency_metadata( app, elem, valid_tool_dependencies_dic # Append the error message to the requirements_dict. requirements_dict[ 'error' ] = error_message invalid_tool_dependencies_dict[ dependency_key ] = requirements_dict - return valid_tool_dependencies_dict, invalid_tool_dependencies_dict, repository_dependency_tup, repository_dependency_is_valid, error_message + return valid_tool_dependencies_dict, invalid_tool_dependencies_dict, repository_dependency_tup, \ + repository_dependency_is_valid, error_message def generate_repository_dependency_metadata( app, repository_dependencies_config, metadata_dict ): """ @@ -1986,7 +1991,8 @@ def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str content_alert_str=content_alert_str, **kwd ) if error_message: - # FIXME: This probably should not redirect since this method is called from the upload controller as well as the repository controller. + # FIXME: This probably should not redirect since this method is called from the upload controller as well + # as the repository controller. # If there is an error, display it. return trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', From ca07eb79e9e59f7dca365c7290d71509b0e8d10e Mon Sep 17 00:00:00 2001 From: Daniel Blankenberg Date: Fri, 17 Jan 2014 15:45:04 -0500 Subject: [PATCH 0824/1033] Change log.error to log.debug. --- lib/galaxy/tools/data/__init__.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/tools/data/__init__.py b/lib/galaxy/tools/data/__init__.py index 009aab2d2b8..4879724a0d1 100644 --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -400,7 +400,7 @@ class TabularToolDataTable( ToolDataTable ): if fields not in self.data or allow_duplicates: self.data.append( fields ) else: - log.error( "Attempted to add fields (%s) to data table '%s', but this entry already exists and allow_duplicates is False.", fields, self.name ) + log.debug( "Attempted to add fields (%s) to data table '%s', but this entry already exists and allow_duplicates is False.", fields, self.name ) is_error = True else: log.error( "Attempted to add fields (%s) to data table '%s', but there were not enough fields specified ( %i < %i ).", fields, self.name, len( fields ), self.largest_index + 1 ) From ac120fb0d1c219f53a655a909a5ca2fa8a680f7b Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Fri, 17 Jan 2014 16:35:05 -0500 Subject: [PATCH 0825/1033] Dict url entry changes and improved logging for the Tool Shed api. --- .../tool_shed/api/repository_revisions.py | 19 +++++++++++++------ 1 file changed, 13 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py index ab1adf3456f..73f1a100757 100644 --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -186,9 +186,9 @@ class RepositoryRevisionsController( BaseAPIController ): value_mapper=self.__get_value_mapper( trans ) ) # We have to add the changeset_revision of of the repository dependency. repository_dependency_dict[ 'changeset_revision' ] = changeset_revision - repository_dependency_dict[ 'url' ] = web.url_for( controller='repository_revisions', + repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', action='show', - id=repository_dependency_repository_metadata_id ) + id=repository_dependency_id ) repository_dependencies_dicts.append( repository_dependency_dict ) return repository_dependencies_dicts @@ -205,11 +205,13 @@ class RepositoryRevisionsController( BaseAPIController ): if repository_metadata is None: log.debug( 'Cannot locate repository_metadata with id %s' % str( id ) ) return {} + encoded_repository_id = trans.security.encode_id( repository_metadata.repository_id ) + repository = suc.get_repository_by_id( trans, encoded_repository_id ) repository_metadata_dict = repository_metadata.to_dict( view='element', value_mapper=self.__get_value_mapper( trans ) ) - repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', + repository_metadata_dict[ 'url' ] = web.url_for( controller='repositories', action='show', - id=trans.security.encode_id( repository_metadata.id ) ) + id=encoded_repository_id ) return repository_metadata_dict @web.expose_api @@ -223,8 +225,11 @@ class RepositoryRevisionsController( BaseAPIController ): raise HTTPBadRequest( detail="Missing required parameter 'id'." ) repository_metadata = metadata_util.get_repository_metadata_by_id( trans, repository_metadata_id ) if repository_metadata is None: - log.debug( 'Cannot locate repository_metadata with id %s' % str( repository_metadata_id ) ) + decoded_repository_metadata_id = trans.security.decode_id( repository_metadata_id ) + log.debug( 'Cannot locate repository_metadata with id %s' % str( decoded_repository_metadata_id ) ) return {} + else: + decoded_repository_metadata_id = repository_metadata.id flush_needed = False for key, new_value in payload.items(): if key == 'time_last_tested': @@ -239,6 +244,8 @@ class RepositoryRevisionsController( BaseAPIController ): setattr( repository_metadata, key, new_value ) flush_needed = True if flush_needed: + log.debug( 'Updating repository_metadata record with id %s and changeset_revision %s.' % \ + ( str( decoded_repository_metadata_id ), str( repository_metadata.changeset_revision ) ) ) trans.sa_session.add( repository_metadata ) trans.sa_session.flush() trans.sa_session.refresh( repository_metadata ) @@ -246,5 +253,5 @@ class RepositoryRevisionsController( BaseAPIController ): value_mapper=self.__get_value_mapper( trans ) ) repository_metadata_dict[ 'url' ] = web.url_for( controller='repository_revisions', action='show', - id=trans.security.encode_id( repository_metadata.id ) ) + id=repository_metadata_id ) return repository_metadata_dict From 2bcaebf46b34535e52b68fe4c4713654c771ce4f Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Fri, 17 Jan 2014 16:57:18 -0500 Subject: [PATCH 0826/1033] Improved logging in the tool shed's install and test framework. --- test/install_and_test_tool_shed_repositories/base/util.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/test/install_and_test_tool_shed_repositories/base/util.py b/test/install_and_test_tool_shed_repositories/base/util.py index 873afd5898b..293a8110adb 100644 --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -402,10 +402,13 @@ def get_repositories_to_install( tool_shed_url, test_framework ): log.debug( "...retrieved %d repository revisions for installation and possible testing." % len( repository_dicts ) ) log.debug( "Repository revisions for testing:" ) for repository_dict in repository_dicts: + repository_id = str( repository_dict.get( 'repository_id', None ) ) + repository_metadata_id = str( repository_dict.get( 'id', None ) ) name = str( repository_dict.get( 'name', None ) ) owner = str( repository_dict.get( 'owner', None ) ) changeset_revision = str( repository_dict.get( 'changeset_revision', None ) ) - log.debug( "Revision %s of repository %s owned by %s" % ( changeset_revision, name, owner ) ) + log.debug( "Revision %s of repository %s owned by %s with repository_id %s, (repository_metadata) id %s" % \ + ( changeset_revision, name, owner, repository_id, repository_metadata_id ) ) return repository_dicts, error_message def get_repository( name, owner, changeset_revision ): From 30186d6b87595b55a3978deac595408b8818f2aa Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Fri, 17 Jan 2014 17:55:15 -0500 Subject: [PATCH 0827/1033] Separate upload javascript into files and place into mvc directory --- .../visualizations/charts/static/app.js | 17 +- static/scripts/galaxy.library.js | 2 +- static/scripts/galaxy.masthead.js | 6 +- static/scripts/galaxy.upload.js | 703 ------------------ static/scripts/mvc/upload/upload-model.js | 27 + static/scripts/mvc/upload/upload-row.js | 270 +++++++ static/scripts/mvc/upload/upload-view.js | 509 +++++++++++++ static/scripts/packed/galaxy.library.js | 2 +- static/scripts/packed/galaxy.masthead.js | 2 +- static/scripts/packed/galaxy.upload.js | 1 - .../scripts/packed/mvc/upload/upload-model.js | 1 + .../scripts/packed/mvc/upload/upload-row.js | 1 + .../scripts/packed/mvc/upload/upload-view.js | 1 + .../{galaxy.uploadbox.js => uploadbox.js} | 0 .../utils/{galaxy.utils.js => utils.js} | 0 .../{galaxy.uploadbox.js => uploadbox.js} | 0 .../utils/{galaxy.utils.js => utils.js} | 0 templates/webapps/galaxy/galaxy.masthead.mako | 6 +- 18 files changed, 830 insertions(+), 718 deletions(-) delete mode 100644 static/scripts/galaxy.upload.js create mode 100644 static/scripts/mvc/upload/upload-model.js create mode 100644 static/scripts/mvc/upload/upload-row.js create mode 100644 static/scripts/mvc/upload/upload-view.js delete mode 100644 static/scripts/packed/galaxy.upload.js create mode 100644 static/scripts/packed/mvc/upload/upload-model.js create mode 100644 static/scripts/packed/mvc/upload/upload-row.js create mode 100644 static/scripts/packed/mvc/upload/upload-view.js rename static/scripts/packed/utils/{galaxy.uploadbox.js => uploadbox.js} (100%) rename static/scripts/packed/utils/{galaxy.utils.js => utils.js} (100%) rename static/scripts/utils/{galaxy.uploadbox.js => uploadbox.js} (100%) rename static/scripts/utils/{galaxy.utils.js => utils.js} (100%) diff --git a/config/plugins/visualizations/charts/static/app.js b/config/plugins/visualizations/charts/static/app.js index 3c95349c926..c50978f41b8 100644 --- a/config/plugins/visualizations/charts/static/app.js +++ b/config/plugins/visualizations/charts/static/app.js @@ -46,12 +46,23 @@ return Backbone.View.extend( // append main this.charts_view.append(this.viewport_view.$el); - // create + // set elements + this.setElement(this.portlet.$el); + + // hide views this.group_view.$el.hide(); this.charts_view.$el.hide(); - // set elements - this.setElement(this.portlet.$el); + // events + var self = this; + this.config.on('change:current_view', function() { + self._showCurrent(); + }); + }, + + // current view + _showCurrent: function() { + }, // execute command diff --git a/static/scripts/galaxy.library.js b/static/scripts/galaxy.library.js index 9a571536cde..1973a0c9e8c 100644 --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -11,7 +11,7 @@ var responses = []; define([ "galaxy.modal", "galaxy.masthead", - "utils/galaxy.utils", + "utils/utils", "libs/toastr"], function(mod_modal, mod_masthead, mod_utils, mod_toastr) { // MMMMMMMMMMMMMMM diff --git a/static/scripts/galaxy.masthead.js b/static/scripts/galaxy.masthead.js index da3e2d5a7ff..9e36e58578d 100644 --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -1,9 +1,5 @@ -/* - galaxy masthead -*/ - // dependencies -define(["utils/galaxy.utils"], function(mod_utils) { +define([], function() { // masthead var GalaxyMasthead = Backbone.View.extend( diff --git a/static/scripts/galaxy.upload.js b/static/scripts/galaxy.upload.js deleted file mode 100644 index 6cc0e6ff007..00000000000 --- a/static/scripts/galaxy.upload.js +++ /dev/null @@ -1,703 +0,0 @@ -/* - galaxy upload -*/ - -// dependencies -define(["galaxy.modal", "galaxy.masthead", "utils/galaxy.utils", "utils/galaxy.uploadbox"], function(mod_modal, mod_masthead, mod_utils) { - -// galaxy upload -var GalaxyUpload = Backbone.View.extend( -{ - // own modal - modal : null, - - // button - button_show : null, - - // upload mod - uploadbox: null, - - // current history - current_history: null, - - // extension types - select_extension :[['Auto-detect', 'auto']], - - // genomes - select_genome : [['Unspecified (?)', '?']], - - // states - state : { - init : 'fa fa-trash-o', - queued : 'fa fa-spinner fa-spin', - running : '__running__', - success : 'fa fa-check', - error : 'fa fa-exclamation-triangle' - }, - - // counter - counter : { - // stats - announce : 0, - success : 0, - error : 0, - running : 0, - - // reset stats - reset : function() - { - this.announce = this.success = this.error = this.running = 0; - } - }, - - // options - options : { - nginx_upload_path : '' - }, - - // initialize - initialize : function(options) - { - // wait for galaxy history panel (workaround due to the use of iframes) - if (!Galaxy.currHistoryPanel) - { - var self = this; - window.setTimeout(function() { self.initialize() }, 500) - return; - } - - // check if logged in - if (!Galaxy.currUser.get('id')) - return; - - // add activate icon - var self = this; - this.button_show = new mod_masthead.GalaxyMastheadIcon ( - { - icon : 'fa-arrow-circle-o-up', - tooltip : 'Upload Files', - on_click : function(e) { self.event_show(e) }, - on_unload : function() { - if (self.counter.running > 0) - return "Several uploads are still processing."; - }, - with_number : true - }); - - // add to masthead - Galaxy.masthead.prepend(this.button_show); - - // load extension - var self = this; - mod_utils.jsonFromUrl(galaxy_config.root + "api/datatypes", - function(datatypes) { - for (key in datatypes) - self.select_extension.push([datatypes[key], datatypes[key]]); - }); - - // load genomes - mod_utils.jsonFromUrl(galaxy_config.root + "api/genomes", - function(genomes) { - // backup default - var def = self.select_genome[0]; - - // fill array - self.select_genome = []; - for (key in genomes) - if (genomes[key].length > 1) - if (genomes[key][1] !== def[1]) - self.select_genome.push(genomes[key]); - - // sort - self.select_genome.sort(function(a, b) { - return a[0] > b[0] ? 1 : a[0] < b[0] ? -1 : 0; - }); - - // insert default back to array - self.select_genome.unshift(def); - }); - - // read in options - if (options) { - this.options = _.defaults(options, this.options); - } - }, - - // mouse over - event_dragover : function (e) - { - }, - - // mouse left - event_dragleave : function (e) - { - }, - - // start - event_announce : function(index, file, message) - { - // make id - var id = '#upload-' + index; - - // add upload item - $(this.el).find('tbody:last').append(this.template_row(id)); - - // access upload item - var it = this.get_upload_item(index); - - // fade in - it.fadeIn(); - - // update title - it.find('#title').html(file.name); - - // update info - it.find('#size').html(this.size_to_string (file.size)); - - // add functionality to new row elements - var self = this; - - // handle click event - it.find('#symbol').on('click', function() { self.event_remove (index) }); - - // handle text editing event - it.find('#text-content').on('keyup', function() { - var count = it.find('#text-content').val().length; - it.find('#size').html(self.size_to_string (count)); - }); - - // handle genome selection event - var self = this; - it.find('#genome').on('change', function(e) { - // identify selected genome - var selected_genome = $(e.target).val(); - - // update genome - var items = $(self.el).find('.upload-item'); - items.each(function() - { - var symbol = $(this).find('#symbol'); - var genome = $(this).find('#genome'); - if(symbol.hasClass(self.state.init) && genome.val() == '?') { - genome.val(selected_genome); - } - }); - }); - - // initialize progress - this.event_progress(index, file, 0); - - // update counter - this.counter.announce++; - - // update screen - this.update_screen(); - - // activate text field if file content is zero - if (file.size == -1) - { - // get text component - var text = it.find('#text'); - - // get padding - var padding = 8; - - // get dimensions - var width = it.width() - 2 * padding; - var height = it.height() - padding; - - // set dimensions - text.css('width', width + 'px'); - text.css('top', height + 'px'); - it.height(height + text.height() + 2 * padding); - - // show text field - text.show(); - } - }, - - // start - event_initialize : function(index, file, message) - { - // update on screen counter - this.button_show.number(this.counter.announce); - - // get element - var it = this.get_upload_item(index); - - // update status - var sy = it.find('#symbol'); - sy.addClass(this.state.running); - - // get configuration - var file_type = it.find('#extension').val(); - var genome = it.find('#genome').val(); - var url_paste = it.find('#text-content').val(); - var space_to_tabs = it.find('#space_to_tabs').is(':checked'); - - // validate - if (!url_paste && !(file.size > 0)) - return null; - - // configure uploadbox - this.uploadbox.configure({url : this.options.nginx_upload_path, paramname : "files_0|file_data"}); - - // configure tool - tool_input = {}; - tool_input['dbkey'] = genome; - tool_input['file_type'] = file_type; - tool_input['files_0|NAME'] = file.name; - tool_input['files_0|type'] = 'upload_dataset'; - tool_input['files_0|url_paste'] = url_paste; - tool_input['space_to_tabs'] = space_to_tabs; - - // setup data - data = {}; - data['history_id'] = this.current_history; - data['tool_id'] = 'upload1'; - data['inputs'] = JSON.stringify(tool_input); - - // return additional data to be send with file - return data; - }, - - // progress - event_progress : function(index, file, message) - { - // get element - var it = this.get_upload_item(index); - - // get value - var percentage = parseInt(message); - - // update progress - it.find('.progress-bar').css({ width : percentage + '%' }); - - // update value - if (percentage != 100) - it.find('#percentage').html(percentage + '%'); - else - it.find('#percentage').html('Adding to history...'); - }, - - // success - event_success : function(index, file, message) - { - // make sure progress is shown correctly - this.event_progress(index, file, 100); - - // update on screen counter - this.button_show.number(''); - - // update counter - this.counter.announce--; - this.counter.success++; - - // update on screen info - this.update_screen(); - - // get element - var it = this.get_upload_item(index); - - // update progress frame - it.addClass('success'); - - // update text - it.find('#percentage').html('100%'); - - // update icon - var sy = it.find('#symbol'); - sy.removeClass(this.state.running); - sy.removeClass(this.state.queued); - sy.addClass(this.state.success); - - // update galaxy history - Galaxy.currHistoryPanel.refreshHdas(); - }, - - // error - event_error : function(index, file, message) - { - // make sure progress is shown correctly - this.event_progress(index, file, 0); - - // update on screen counter - this.button_show.number(''); - - // update counter - this.counter.announce--; - this.counter.error++; - - // update on screen info - this.update_screen(); - - // get element - var it = this.get_upload_item(index); - - // update progress frame - it.addClass('danger'); - - // remove progress bar - it.find('.progress').remove(); - - // write error message - it.find('#info').html('Failed: ' + message).show(); - - // update icon - var sy = it.find('#symbol'); - sy.removeClass(this.state.running); - sy.removeClass(this.state.queued); - sy.addClass(this.state.error); - }, - - // start upload process - event_start : function() - { - // check - if (this.counter.announce == 0 || this.counter.running > 0) - return; - - // switch icons for new uploads - var items = $(this.el).find('.upload-item'); - var self = this; - items.each(function() - { - var symbol = $(this).find('#symbol'); - if(symbol.hasClass(self.state.init)) - { - // set status - symbol.removeClass(self.state.init); - symbol.addClass(self.state.queued); - - // disable options - $(this).find('#text-content').attr('disabled', true); - $(this).find('#genome').attr('disabled', true); - $(this).find('#extension').attr('disabled', true); - $(this).find('#space_to_tabs').attr('disabled', true); - } - }); - - // backup current history - this.current_history = Galaxy.currHistoryPanel.model.get('id'); - - // update running - this.counter.running = this.counter.announce; - this.update_screen(); - - // initiate upload procedure in plugin - this.uploadbox.start(); - }, - - // pause upload process - event_stop : function() - { - // check - if (this.counter.running == 0) - return; - - // request pause - this.uploadbox.stop(); - - // set html content - $('#upload-info').html('Queue will pause after completing the current file...'); - }, - - // queue is done - event_complete: function() - { - // update running - this.counter.running = 0; - this.update_screen(); - - // switch icons for new uploads - var items = $(this.el).find('.upload-item'); - var self = this; - items.each(function() - { - var symbol = $(this).find('#symbol'); - if(symbol.hasClass(self.state.queued) && !symbol.hasClass(self.state.running)) - { - // update status - symbol.removeClass(self.state.queued); - symbol.addClass(self.state.init); - - // disable options - $(this).find('#text-content').attr('disabled', false); - $(this).find('#genome').attr('disabled', false); - $(this).find('#extension').attr('disabled', false); - $(this).find('#space_to_tabs').attr('disabled', false); - } - }); - }, - - // remove all - event_reset : function() - { - // make sure queue is not running - if (this.counter.running == 0) - { - // remove from screen - var items = $(this.el).find('.upload-item'); - $(this.el).find('table').fadeOut({ complete : function() { items.remove(); }}); - - // reset counter - this.counter.reset(); - - // show on screen info - this.update_screen(); - - // remove from queue - this.uploadbox.reset(); - } - }, - - // remove item from upload list - event_remove : function(index) - { - // get item - var it = this.get_upload_item(index); - var sy = it.find('#symbol'); - - // only remove from queue if not in processing line - if (sy.hasClass(this.state.init) || sy.hasClass(this.state.success) || sy.hasClass(this.state.error)) - { - // reduce counter - if (it.hasClass('success')) - this.counter.success--; - else if (it.hasClass('danger')) - this.counter.error--; - else - this.counter.announce--; - - // show on screen info - this.update_screen(); - - // remove from queue - this.uploadbox.remove(index); - - // remove element - it.remove(); - } - }, - - // create (pseudo) file - event_create : function () - { - this.uploadbox.add([{ name : 'New File', size : -1 }]); - }, - - // show/hide upload frame - event_show : function (e) - { - // prevent default - e.preventDefault(); - - // create modal - if (!this.modal) - { - // make modal - var self = this; - this.modal = new mod_modal.GalaxyModal( - { - title : 'Upload files from your local drive', - body : this.template('upload-box', 'upload-info'), - buttons : { - 'Select' : function() {self.uploadbox.select()}, - 'Create' : function() {self.event_create()}, - 'Upload' : function() {self.event_start()}, - 'Pause' : function() {self.event_stop()}, - 'Reset' : function() {self.event_reset()}, - 'Close' : function() {self.modal.hide()}, - }, - height : '400', - width : '900' - }); - - // set element - this.setElement('#upload-box'); - - // file upload - var self = this; - this.uploadbox = this.$el.uploadbox( - { - dragover : function() { self.event_dragover() }, - dragleave : function() { self.event_dragleave() }, - announce : function(index, file, message) { self.event_announce(index, file, message) }, - initialize : function(index, file, message) { return self.event_initialize(index, file, message) }, - success : function(index, file, message) { self.event_success(index, file, message) }, - progress : function(index, file, message) { self.event_progress(index, file, message) }, - error : function(index, file, message) { self.event_error(index, file, message) }, - complete : function() { self.event_complete() }, - }); - - // setup info - this.update_screen(); - } - - // show modal - this.modal.show(); - }, - - // get upload item - get_upload_item: function(index) - { - // get element - return $(this.el).find('#upload-' + index); - }, - - // to string - size_to_string : function (size) - { - // identify unit - var unit = ""; - if (size >= 100000000000) { size = size / 100000000000; unit = 'TB'; } else - if (size >= 100000000) { size = size / 100000000; unit = 'GB'; } else - if (size >= 100000) { size = size / 100000; unit = 'MB'; } else - if (size >= 100) { size = size / 100; unit = 'KB'; } else - if (size > 0) { size = size * 10; unit = 'b'; } else - return '-'; - - // return formatted string - return '' + (Math.round(size) / 10) + ' ' + unit; - }, - - // set screen - update_screen: function () - { - /* - update on screen info - */ - - // check default message - if(this.counter.announce == 0) - { - if (this.uploadbox.compatible()) - message = 'Drag&drop files into this box or click \'Select\' to select files!'; - else - message = 'Unfortunately, your browser does not support multiple file uploads or drag&drop.
                    Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+.' - } else { - if (this.counter.running == 0) - message = 'You added ' + this.counter.announce + ' file(s) to the queue. Add more files or click \'Upload\' to proceed.'; - else - message = 'Please wait...' + this.counter.announce + ' out of ' + this.counter.running + ' remaining.'; - } - - // set html content - $('#upload-info').html(message); - - /* - update button status - */ - - // update reset button - if (this.counter.running == 0 && this.counter.announce + this.counter.success + this.counter.error > 0) - this.modal.enableButton('Reset'); - else - this.modal.disableButton('Reset'); - - // update upload button - if (this.counter.running == 0 && this.counter.announce > 0) - this.modal.enableButton('Upload'); - else - this.modal.disableButton('Upload'); - - // pause upload button - if (this.counter.running > 0) - this.modal.enableButton('Pause'); - else - this.modal.disableButton('Pause'); - - // select upload button - if (this.counter.running == 0) - { - this.modal.enableButton('Select'); - this.modal.enableButton('Create'); - } else { - this.modal.disableButton('Select'); - this.modal.disableButton('Create'); - } - - // table visibility - if (this.counter.announce + this.counter.success + this.counter.error > 0) - $(this.el).find('table').show(); - else - $(this.el).find('table').hide(); - }, - - // load html template - template: function(id, idInfo) - { - return '
                    ' + - '' + - '' + - '' + - '' + - '' + - '' + - '' + - '' + - '' + - '' + - '' + - '' + - '' + - '' + - '
                    ' + - '
                    '; - }, - - template_row: function(id) - { - // construct template - var tmpl = '
                    ' + - '
                    ' + - '
                    ' + - '
                    ' + - '
                    You may specify a list of URLs (one per line) or paste the contents of a file.
                    ' + - '' + - '
                    ' + - '
                    ' + - '
                    		' + - '' + - '' + - '' + - '' + - '
                    ' + - '
                    ' + - '
                    ' + - '
                    0%
                    ' + - '
                    ' + - '
                    ' + - '
                    ' + + '
                    ' + + '
                    ' + + '
                    ' + + '
                    You may specify a list of URLs (one per line) or paste the contents of a file.
                    ' + + '' + + '
                    ' + + '
                    ' + + '
                    		' + + '' + + '' + + '' + + '' + + '
                    ' + + '
                    ' + + '
                    ' + + '
                    0%
                    ' + + '
                    ' + + '
                    ' + + '
                    ' + + '' + + '' + + '' + + '' + + '' + + '' + + '' + + '' + + '' + + '' + + '' + + '' + + '' + + '
                    ' + + '
                    '; + } +}); + +}); diff --git a/static/scripts/packed/galaxy.library.js b/static/scripts/packed/galaxy.library.js index e895978471c..9f490a0b24c 100644 --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1 +1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('
                    ');r.push('

                    Data Libraries Beta Test. This is work in progress. Please report problems & ideas via email and Trello.

                    ');r.push('                    ");r.push('
                    ');r.push('Libraries | ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<%- path_item[1] %> | ');r.push("<% } else { %>");r.push('<%- path_item[1] %>');r.push("<% } %>");r.push("<% }); %>");r.push("
                    ");r.push('');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" <% _.each(items, function(content_item) { %>");r.push(' ');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" ");r.push(' ');r.push(' ");r.push(" ");r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" <% } %> ");r.push(' ');r.push(" ");r.push(" <% }); %>");r.push(" ");r.push(" ");r.push("
                    viewnamedata typesizedate (UTC)
                    <%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' (empty folder)');r.push(" <% } %>");r.push(" folder<%= _.escape(content_item.get("item_count")) %> item(s)");r.push(' ");r.push(" <%- content_item.get("name") %><%= _.escape(content_item.get("data_type")) %><%= _.escape(content_item.get("readable_size")) %><%= _.escape(content_item.get("time_updated")) %>
                    ");r.push("
                    ");return r.join("")},templateDatasetModal:function(){var r=[];r.push('
                    ');r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" <% } %>");r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push("
                    ">Name<%= _.escape(item.get("name")) %>
                    Data type<%= _.escape(item.get("data_type")) %>
                    Genome build<%= _.escape(item.get("genome_build")) %>
                    Size<%= _.escape(size) %>
                    Date uploaded (UTC)<%= _.escape(item.get("date_uploaded")) %>
                    Uploaded by<%= _.escape(item.get("uploaded_by")) %>
                    Data Lines<%= _.escape(item.get("metadata_data_lines")) %>
                    Comment Lines<%= _.escape(item.get("metadata_comment_lines")) %>unknown
                    Number of Columns<%= _.escape(item.get("metadata_columns")) %>
                    Column Types<%= _.escape(item.get("metadata_column_types")) %>
                    Miscellaneous information<%= _.escape(item.get("misc_blurb")) %>
                    ");r.push(' 
                    ');r.push("
                    ");r.push("
                    ");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('');r.push("Select history: ");r.push('");r.push("");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('');r.push("Select history: ");r.push('");r.push("");return r.join("")},templateProgressBar:function(){var r=[];r.push('
                    ');r.push("Importing selected datasets to history <%= _.escape(history_name) %>");r.push("
                    ");r.push('
                    ');r.push('
                    ');r.push(' 0% Complete');r.push("
                    ");r.push("
                    ");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('
                    ');tmpl_array.push("
                    ");tmpl_array.push('');tmpl_array.push('');tmpl_array.push("
                    ");tmpl_array.push("
                    ");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("/",{trigger:true,replace:false})}else{library_router.navigate("folders/"+r,{trigger:true,replace:false})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hideOrDestroy()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hideOrDestroy()}}});s.modal.show()},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hideOrDestroy();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+=''});$('
                    '+r+"
                    ").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hideOrDestroy();r.modal=null}}});this.modal.show()},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hideOrDestroy();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('
                    ');tmpl_array.push("");tmpl_array.push('

                    Data Libraries Beta Test. This is work in progress. Please report problems & ideas via email and Trello.

                    ');tmpl_array.push('New Library');tmpl_array.push('');tmpl_array.push(" ");tmpl_array.push(' ');tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" ");tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(" ");tmpl_array.push(" <% }); %>");tmpl_array.push(" ");tmpl_array.push("
                    namedescriptionsynopsismodel type
                    <%- library.get("name") %><%= _.escape(library.get("description")) %><%= _.escape(library.get("synopsis")) %><%= _.escape(library.get("model_class")) %>
                    ");tmpl_array.push("
                    ");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('
                    ');tmpl_array.push("
                    ");tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push("
                    ");tmpl_array.push("
                    ");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.info("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/utils","libs/toastr"],function(k,l,h,n){var f=Backbone.Model.extend({urlRoot:"/api/libraries"});var c=Backbone.Model.extend({urlRoot:"/api/folders"});var o=Backbone.Collection.extend({url:"/api/libraries",model:f});var i=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var d=Backbone.Collection.extend({model:i});var e=Backbone.Model.extend({defaults:{folder:new d(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(r){this.full_path=r[0].full_path;this.get("folder").reset(r[1].folder_contents);return r}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Model.extend({url:"/api/histories/"});var p=Backbone.Collection.extend({url:"/api/histories",model:j});var q=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var m=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var r=[];r.push('
                    ');r.push('

                    Data Libraries Beta Test. This is work in progress. Please report problems & ideas via email and Trello.

                    ');r.push('
                    ');r.push(' ');r.push(' ');r.push(' ");r.push("
                    ");r.push('
                    ');r.push('Libraries | ');r.push("<% _.each(path, function(path_item) { %>");r.push("<% if (path_item[0] != id) { %>");r.push('<%- path_item[1] %> | ');r.push("<% } else { %>");r.push('<%- path_item[1] %>');r.push("<% } %>");r.push("<% }); %>");r.push("
                    ");r.push('');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" ");r.push(" <% _.each(items, function(content_item) { %>");r.push(' ');r.push(' <% if (content_item.get("type") === "folder") { %>');r.push(" ");r.push(' ');r.push(' ");r.push(" ");r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" <% } %> ");r.push(' ');r.push(" ");r.push(" <% }); %>");r.push(" ");r.push(" ");r.push("
                    viewnamedata typesizedate (UTC)
                    <%- content_item.get("name") %>');r.push(' <% if (content_item.get("item_count") === 0) { %>');r.push(' (empty folder)');r.push(" <% } %>");r.push(" folder<%= _.escape(content_item.get("item_count")) %> item(s)");r.push(' ");r.push(" <%- content_item.get("name") %><%= _.escape(content_item.get("data_type")) %><%= _.escape(content_item.get("readable_size")) %><%= _.escape(content_item.get("time_updated")) %>
                    ");r.push("
                    ");return r.join("")},templateDatasetModal:function(){var r=[];r.push('
                    ');r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(" ");r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(' ');r.push(' ');r.push(" ");r.push(' ');r.push(' <% if (item.get("metadata_comment_lines") === "") { %>');r.push(' ');r.push(" <% } else { %>");r.push(' ');r.push(" <% } %>");r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push(" ");r.push(' ');r.push(' ');r.push(" ");r.push("
                    ">Name<%= _.escape(item.get("name")) %>
                    Data type<%= _.escape(item.get("data_type")) %>
                    Genome build<%= _.escape(item.get("genome_build")) %>
                    Size<%= _.escape(size) %>
                    Date uploaded (UTC)<%= _.escape(item.get("date_uploaded")) %>
                    Uploaded by<%= _.escape(item.get("uploaded_by")) %>
                    Data Lines<%= _.escape(item.get("metadata_data_lines")) %>
                    Comment Lines<%= _.escape(item.get("metadata_comment_lines")) %>unknown
                    Number of Columns<%= _.escape(item.get("metadata_columns")) %>
                    Column Types<%= _.escape(item.get("metadata_column_types")) %>
                    Miscellaneous information<%= _.escape(item.get("misc_blurb")) %>
                    ");r.push(' 
                    ');r.push("
                    ");r.push("
                    ");return r.join("")},templateHistorySelectInModal:function(){var r=[];r.push('');r.push("Select history: ");r.push('");r.push("");return r.join("")},templateBulkImportInModal:function(){var r=[];r.push('');r.push("Select history: ");r.push('");r.push("");return r.join("")},templateProgressBar:function(){var r=[];r.push('
                    ');r.push("Importing selected datasets to history <%= _.escape(history_name) %>");r.push("
                    ");r.push('
                    ');r.push('
                    ');r.push(' 0% Complete');r.push("
                    ");r.push("
                    ");r.push("");return r.join("")},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('
                    ');tmpl_array.push("
                    ");tmpl_array.push('');tmpl_array.push('');tmpl_array.push("
                    ");tmpl_array.push("
                    ");return tmpl_array.join("")},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderFromModal","click .btn_open_folder":"navigateToFolder"},render:function(r){$("#center").css("overflow","auto");view=this;var t=this;var s=new e({id:r.id});s.url=s.attributes.urlRoot+r.id+"/contents";s.fetch({success:function(u){for(var w=0;w=100000000000){r=r/100000000000;s="TB"}else{if(r>=100000000){r=r/100000000;s="GB"}else{if(r>=100000){r=r/100000;s="MB"}else{if(r>=100){r=r/100;s="KB"}else{r=r*10;s="b"}}}}return(Math.round(r)/10)+s},navigateToFolder:function(s){var r=$(s.target).attr("data-id");if(typeof r==="undefined"){return false}else{if(r==="0"){library_router.navigate("/",{trigger:true,replace:false})}else{library_router.navigate("folders/"+r,{trigger:true,replace:false})}}},showDatasetDetails:function(u){u.preventDefault();var v=$(u.target).parent().parent().attr("id");var t=new i();var s=new p();t.id=v;var r=this;t.fetch({success:function(w){s.fetch({success:function(x){r.renderModalAfterFetch(w,x)},error:function(){n.error("An error occured during fetching histories:(");r.renderModalAfterFetch(w)}})},error:function(){n.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(w,t){var u=this.size_to_string(w.get("file_size"));var v=_.template(this.templateDatasetModal(),{item:w,size:u});var s=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Dataset Details",body:v,buttons:{Import:function(){s.importCurrentIntoHistory()},Download:function(){s.downloadCurrent()},Close:function(){s.modal.hideOrDestroy()}}});$(".peek").html(w.get("peek"));if(typeof history.models!==undefined){var r=_.template(this.templateHistorySelectInModal(),{histories:t.models});$(this.modal.elMain).find(".buttons").prepend(r);if(s.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(s.lastSelectedHistory)}}this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var r=[];r.push($("#id_row").attr("data-id"));var s="/api/libraries/datasets/download/uncompressed";var t={ldda_ids:r};folderContentView.processDownload(s,t);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var t=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=t;var r=$("#id_row").attr("data-id");var u=new b();var s=this;u.url=u.urlRoot+t+"/contents";u.save({content:r,source:"library"},{success:function(){n.success("Dataset imported");s.modal.enableButton("Import");s.modal.enableButton("Download")},error:function(){n.error("An error occured! Dataset not imported. Please try again.");s.modal.enableButton("Import");s.modal.enableButton("Download")}})},selectAll:function(s){var r=s.target.checked;that=this;$(":checkbox").each(function(){this.checked=r;$row=$(this.parentElement.parentElement);(r)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(s){var u="";var r;var t;if(s.target.localName==="input"){u=s.target;r=$(s.target.parentElement.parentElement);t="input"}else{if(s.target.localName==="td"){u=$("#"+s.target.parentElement.id).find(":checkbox")[0];r=$(s.target.parentElement);t="td"}}if(u===""){s.stopPropagation();return}if(u===undefined){s.stopPropagation();return}if(u.checked){if(t==="td"){u.checked="";this.makeWhiteRow(r)}else{if(t==="input"){this.makeDarkRow(r)}}}else{if(t==="td"){u.checked="selected";this.makeDarkRow(r)}else{if(t==="input"){this.makeWhiteRow(r)}}}this.checkTools()},makeDarkRow:function(r){r.removeClass("light");r.find("a").removeClass("light");r.addClass("dark");r.find("a").addClass("dark")},makeWhiteRow:function(r){r.removeClass("dark");r.find("a").removeClass("dark");r.addClass("light");r.find("a").addClass("light")},checkTools:function(){var r=$("#folder_table").find(":checked");if(r.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var s=this;var r=new p();r.fetch({success:function(t){var u=_.template(s.templateBulkImportInModal(),{histories:t.models});s.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Import into History",body:u,buttons:{Import:function(){s.importAllIntoHistory()},Close:function(){s.modal.hideOrDestroy()}}});s.modal.show()},error:function(){n.error("An error occured :(")}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var t=$("select[name=dataset_import_bulk] option:selected").val();var x=$("select[name=dataset_import_bulk] option:selected").text();var z=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){z.push(this.parentElement.parentElement.id)}});var y=_.template(this.templateProgressBar(),{history_name:x});$(this.modal.elMain).find(".modal-body").html(y);var u=100/z.length;this.initProgress(u);var r=[];for(var s=z.length-1;s>=0;s--){library_dataset_id=z[s];var v=new b();var w=this;v.url=v.urlRoot+t+"/contents";v.content=library_dataset_id;v.source="library";r.push(v)}this.chainCall(r)},chainCall:function(s){var r=this;var t=s.pop();if(typeof t==="undefined"){n.success("All datasets imported");this.modal.hideOrDestroy();return}var u=$.when(t.save({content:t.content,source:t.source})).done(function(v){r.updateProgress();responses.push(v);r.chainCall(s)})},initProgress:function(r){this.progress=0;this.progressStep=r},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(r,v){var t=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){t.push(this.parentElement.parentElement.id)}});var s="/api/libraries/datasets/download/"+v;var u={ldda_ids:t};this.processDownload(s,u,"get")},processDownload:function(s,t,u){if(s&&t){t=typeof t=="string"?t:$.param(t);var r="";$.each(t.split("&"),function(){var v=this.split("=");r+=''});$('
                    '+r+"
                    ").appendTo("body").submit().remove();n.info("Your download will begin soon")}},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Create New Folder",body:this.templateNewFolderInModal(),buttons:{Create:function(){r.create_new_folder_event()},Close:function(){r.modal.hideOrDestroy();r.modal=null}}});this.modal.show()},create_new_folder_event:function(){var r=this.serialize_new_folder();if(this.validate_new_folder(r)){var t=new c();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];t.url=t.urlRoot+"/"+current_folder_id;var s=this;t.save(r,{success:function(u){s.modal.hideOrDestroy();n.success("Folder created");s.render({id:current_folder_id})},error:function(){n.error("An error occured :(")}})}else{n.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(r){return r.name!==""}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('
                    ');tmpl_array.push("");tmpl_array.push('

                    Data Libraries Beta Test. This is work in progress. Please report problems & ideas via email and Trello.

                    ');tmpl_array.push('New Library');tmpl_array.push('');tmpl_array.push(" ");tmpl_array.push(' ');tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" ");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" ");tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(" ");tmpl_array.push(" <% }); %>");tmpl_array.push(" ");tmpl_array.push("
                    namedescriptionsynopsismodel type
                    <%- library.get("name") %><%= _.escape(library.get("description")) %><%= _.escape(library.get("synopsis")) %><%= _.escape(library.get("model_class")) %>
                    ");tmpl_array.push("
                    ");return tmpl_array.join("")},templateNewLibraryInModal:function(){tmpl_array=[];tmpl_array.push('
                    ');tmpl_array.push("
                    ");tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push(' ');tmpl_array.push("
                    ");tmpl_array.push("
                    ");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var r=this;libraries=new o();libraries.fetch({success:function(s){var t=_.template(r.templateLibraryList(),{libraries:s.models});r.$el.html(t)},error:function(t,s){if(s.statusCode().status===403){n.info("Please log in first. Redirecting to login page in 3s.");setTimeout(r.redirectToLogin,3000)}else{n.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(s){s.preventDefault();s.stopPropagation();var r=this;this.modal=new k.GalaxyModal({destructible:true,bindClosingEvents:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){r.create_new_library_event()},Close:function(){r.modal.hideOrDestroy()}}});this.modal.show()},create_new_library_event:function(){var t=this.serialize_new_library();if(this.validate_new_library(t)){var s=new f();var r=this;s.save(t,{success:function(u){r.modal.hideOrDestroy();r.clear_library_modal();r.render();n.success("Library created")},error:function(){n.error("An error occured :(")}})}else{n.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(r){return r.name!==""}});var g=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new m();galaxyLibraryview=new a();library_router=new q();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(r){folderContentView.render({id:r})});library_router.on("route:download",function(r,s){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+r,{trigger:true,replace:true})}else{folderContentView.download(r,s);library_router.navigate("folders/"+r,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:g}}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.masthead.js b/static/scripts/packed/galaxy.masthead.js index e77d72ecfa6..a95706b1eb7 100644 --- a/static/scripts/packed/galaxy.masthead.js +++ b/static/scripts/packed/galaxy.masthead.js @@ -1 +1 @@ -define(["utils/galaxy.utils"],function(c){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(f){this.options=f;$("body").off();this.setElement($(this._template(f)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var e=this;window.onbeforeunload=function(){var h="";for(key in e.list){if(e.list[key].options.on_unload){var g=e.list[key].options.on_unload();if(g){h+=g+" "}}}if(h!=""){return h}}},events:{click:"_click",mousedown:function(f){f.preventDefault()}},append:function(e){return this._add(e,true)},prepend:function(e){return this._add(e,false)},highlight:function(f){var e=$(this.el).find("#"+f+"> li");if(e){e.addClass("active")}},_add:function(h,f){var e=$(this.el).find("#"+h.location);if(e){var g=$(h.el);g.addClass("masthead-item");if(f){e.append(g)}else{e.prepend(g)}this.list.push(h)}return null},_click:function(h){var g=$(this.el).find(".popup");if(g){g.hide()}var f=$(h.target).closest(".masthead-item").find(".popup");if($(h.target).hasClass("head")){f.show();this.$background.show()}else{this.$background.hide()}},_template:function(e){return''}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},location:"iconbar",initialize:function(f){if(f){this.options=_.defaults(f,this.options)}this.setElement($(this._template(this.options)));var e=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",e.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(e){$(this.el).find(".icon").removeClass(this.options.icon).addClass(e);this.options.icon=e},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(e){$(this.el).find(".number").text(e)},_template:function(f){var e='
                    ';if(f.with_number){e+='
                    '}e+="
                    ";return e}});var d=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(e){if(e){this.options=_.defaults(e,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(g){var h={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(g){h=_.defaults(g,h)}if(h.content&&h.content.indexOf("//")===-1){h.content=galaxy_config.root+h.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var f=$(this._templateMenuItem(h));this.$menu.append(f);var e=this;f.on("click",function(i){i.preventDefault();if(e.options.target==="_blank"){return true}Galaxy.frame.add(g)});if(h.divider){this.$menu.append($(this._templateDivider()))}},_head:function(f){f.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var e=$(this.el).find(".head");e.popover({html:true,content:'Please log in or register to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){e.popover("hide")},5000)})},_templateMenuItem:function(e){return'
                  • '+e.title+"
                    • "},_templateMenu:function(){return'
                      '},_templateDivider:function(){return'
                    • '},_template:function(f){var e='';return e}});return{GalaxyMasthead:a,GalaxyMastheadTab:d,GalaxyMastheadIcon:b}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;window.onbeforeunload=function(){var g="";for(key in d.list){if(d.list[key].options.on_unload){var f=d.list[key].options.on_unload();if(f){g+=f+" "}}}if(g!=""){return g}}},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){return''}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='
                      ';if(e.with_number){d+='
                      '}d+="
                      ";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please log in or register to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'
                    • '+d.title+"
                      • "},_templateMenu:function(){return'
                        '},_templateDivider:function(){return'
                      • '},_template:function(e){var d='';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.upload.js b/static/scripts/packed/galaxy.upload.js deleted file mode 100644 index af140100f64..00000000000 --- a/static/scripts/packed/galaxy.upload.js +++ /dev/null @@ -1 +0,0 @@ -define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","utils/galaxy.uploadbox"],function(b,c,d){var a=Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],state:{init:"fa fa-trash-o",queued:"fa fa-spinner fa-spin",running:"__running__",success:"fa fa-check",error:"fa fa-exclamation-triangle"},counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(f){if(!Galaxy.currHistoryPanel){var e=this;window.setTimeout(function(){e.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}var e=this;this.button_show=new c.GalaxyMastheadIcon({icon:"fa-arrow-circle-o-up",tooltip:"Upload Files",on_click:function(g){e.event_show(g)},on_unload:function(){if(e.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.masthead.prepend(this.button_show);var e=this;d.jsonFromUrl(galaxy_config.root+"api/datatypes",function(g){for(key in g){e.select_extension.push([g[key],g[key]])}});d.jsonFromUrl(galaxy_config.root+"api/genomes",function(g){var h=e.select_genome[0];e.select_genome=[];for(key in g){if(g[key].length>1){if(g[key][1]!==h[1]){e.select_genome.push(g[key])}}}e.select_genome.sort(function(j,i){return j[0]>i[0]?1:j[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=l;tool_input.file_type=f;tool_input["files_0|NAME"]=e.name;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=k;tool_input.space_to_tabs=h;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},event_progress:function(f,g,i){var h=this.get_upload_item(f);var e=parseInt(i);h.find(".progress-bar").css({width:e+"%"});if(e!=100){h.find("#percentage").html(e+"%")}else{h.find("#percentage").html("Adding to history...")}},event_success:function(e,f,h){this.event_progress(e,f,100);this.button_show.number("");this.counter.announce--;this.counter.success++;this.update_screen();var g=this.get_upload_item(e);g.addClass("success");g.find("#percentage").html("100%");var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.success);Galaxy.currHistoryPanel.refreshHdas()},event_error:function(e,f,h){this.event_progress(e,f,0);this.button_show.number("");this.counter.announce--;this.counter.error++;this.update_screen();var g=this.get_upload_item(e);g.addClass("danger");g.find(".progress").remove();g.find("#info").html("Failed: "+h).show();var i=g.find("#symbol");i.removeClass(this.state.running);i.removeClass(this.state.queued);i.addClass(this.state.error)},event_start:function(){if(this.counter.announce==0||this.counter.running>0){return}var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.init)){g.removeClass(e.state.init);g.addClass(e.state.queued);$(this).find("#text-content").attr("disabled",true);$(this).find("#genome").attr("disabled",true);$(this).find("#extension").attr("disabled",true);$(this).find("#space_to_tabs").attr("disabled",true)}});this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this.update_screen();this.uploadbox.start()},event_stop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},event_complete:function(){this.counter.running=0;this.update_screen();var f=$(this.el).find(".upload-item");var e=this;f.each(function(){var g=$(this).find("#symbol");if(g.hasClass(e.state.queued)&&!g.hasClass(e.state.running)){g.removeClass(e.state.queued);g.addClass(e.state.init);$(this).find("#text-content").attr("disabled",false);$(this).find("#genome").attr("disabled",false);$(this).find("#extension").attr("disabled",false);$(this).find("#space_to_tabs").attr("disabled",false)}})},event_reset:function(){if(this.counter.running==0){var e=$(this.el).find(".upload-item");$(this.el).find("table").fadeOut({complete:function(){e.remove()}});this.counter.reset();this.update_screen();this.uploadbox.reset()}},event_remove:function(e){var f=this.get_upload_item(e);var g=f.find("#symbol");if(g.hasClass(this.state.init)||g.hasClass(this.state.success)||g.hasClass(this.state.error)){if(f.hasClass("success")){this.counter.success--}else{if(f.hasClass("danger")){this.counter.error--}else{this.counter.announce--}}this.update_screen();this.uploadbox.remove(e);f.remove()}},event_create:function(){this.uploadbox.add([{name:"New File",size:-1}])},event_show:function(g){g.preventDefault();if(!this.modal){var f=this;this.modal=new b.GalaxyModal({title:"Upload files from your local drive",body:this.template("upload-box","upload-info"),buttons:{Select:function(){f.uploadbox.select()},Create:function(){f.event_create()},Upload:function(){f.event_start()},Pause:function(){f.event_stop()},Reset:function(){f.event_reset()},Close:function(){f.modal.hide()},},height:"400",width:"900"});this.setElement("#upload-box");var f=this;this.uploadbox=this.$el.uploadbox({dragover:function(){f.event_dragover()},dragleave:function(){f.event_dragleave()},announce:function(e,h,i){f.event_announce(e,h,i)},initialize:function(e,h,i){return f.event_initialize(e,h,i)},success:function(e,h,i){f.event_success(e,h,i)},progress:function(e,h,i){f.event_progress(e,h,i)},error:function(e,h,i){f.event_error(e,h,i)},complete:function(){f.event_complete()},});this.update_screen()}this.modal.show()},get_upload_item:function(e){return $(this.el).find("#upload-"+e)},size_to_string:function(e){var f="";if(e>=100000000000){e=e/100000000000;f="TB"}else{if(e>=100000000){e=e/100000000;f="GB"}else{if(e>=100000){e=e/100000;f="MB"}else{if(e>=100){e=e/100;f="KB"}else{if(e>0){e=e*10;f="b"}else{return"-"}}}}}return""+(Math.round(e)/10)+" "+f},update_screen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                        Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},template:function(f,e){return'
                        '},template_row:function(f){var e='
                        You may specify a list of URLs (one per line) or paste the contents of a file.
                        ';e+='";e+='";e+='
                        0%
                        ';return e}});return{GalaxyUpload:a}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/upload/upload-model.js b/static/scripts/packed/mvc/upload/upload-model.js new file mode 100644 index 00000000000..952fa5301eb --- /dev/null +++ b/static/scripts/packed/mvc/upload/upload-model.js @@ -0,0 +1 @@ +define([],function(){var b=Backbone.Model.extend({defaults:{extension:"auto",genome:"?",url_paste:"",space_to_tabs:false,status:"init",info:null}});var a=Backbone.Collection.extend({model:b});return{Model:b,Collection:a}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/upload/upload-row.js b/static/scripts/packed/mvc/upload/upload-row.js new file mode 100644 index 00000000000..2b7a790d1c7 --- /dev/null +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -0,0 +1 @@ +define(["mvc/upload/upload-model"],function(a){return Backbone.View.extend({options:{padding:8},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(e,c){this.app=e;var b=this;this.model=new a.Model(c);this.setElement(this._template(c));var d=this.$el;d.find("#symbol").on("click",function(){var f=b.model.get("status");if(f=="init"||f=="success"||f=="error"){b.app.collection.remove(b.model)}});d.find("#text-content").on("keyup",function(){var f=d.find("#text-content");var h=f.val();var g=h.length;d.find("#size").html(b._formatSize(g));b.model.set("url_paste",h)});d.find("#genome").on("change",function(f){b.model.set("genome",$(f.target).val())});d.find("#extension").on("change",function(f){b.model.set("extension",$(f.target).val())});d.find("#space_to_tabs").on("change",function(f){b.model.set("space_to_tabs",$(f.target).prop("checked"))});this.model.on("change:percentage",function(){b._refreshPercentage()});this.model.on("change:status",function(){b._refreshStatus()});this.model.on("change:info",function(){b._refreshInfo()});this.model.on("remove",function(){b.remove()});this.app.collection.on("reset",function(){b.remove()})},render:function(){var h=this.model.get("file_name");var c=this.model.get("file_size");var e=this.$el;e.find("#title").html(h);e.find("#size").html(this._formatSize(c));if(c==-1){var g=e.find("#text");var f=this.options.padding;var d=e.width()-2*f;var b=e.height()-f;g.css("width",d+"px");g.css("top",b+"px");e.height(b+g.height()+2*f);g.show()}},_refreshInfo:function(){var b=this.model.get("info");if(b){this.$el.find("#info").html("Failed: "+b).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var b=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:b+"%"});if(b!=100){this.$el.find("#percentage").html(b+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var c=this.$el;var b=this.model.get("status");var e=this.status_classes[b];var d=this.$el.find("#symbol");d.removeClass();d.addClass(e);if(b=="init"){c.find("#text-content").attr("disabled",false);c.find("#genome").attr("disabled",false);c.find("#extension").attr("disabled",false);c.find("#space_to_tabs").attr("disabled",false)}else{c.find("#text-content").attr("disabled",true);c.find("#genome").attr("disabled",true);c.find("#extension").attr("disabled",true);c.find("#space_to_tabs").attr("disabled",true)}if(b=="success"){c.addClass("success");c.find("#percentage").html("100%")}if(b=="error"){c.addClass("danger");c.find(".progress").remove()}},_formatSize:function(b){var c="";if(b>=100000000000){b=b/100000000000;c="TB"}else{if(b>=100000000){b=b/100000000;c="GB"}else{if(b>=100000){b=b/100000;c="MB"}else{if(b>=100){b=b/100;c="KB"}else{if(b>0){b=b*10;c="b"}else{return"-"}}}}}return""+(Math.round(b)/10)+" "+c},_template:function(d){var c=this;var b='
                        You may specify a list of URLs (one per line) or paste the contents of a file.
                        ';b+='";b+='";b+='
                        0%
                        ';return b}})}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/upload/upload-view.js b/static/scripts/packed/mvc/upload/upload-view.js new file mode 100644 index 00000000000..f9badaec927 --- /dev/null +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -0,0 +1 @@ +define(["galaxy.modal","galaxy.masthead","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","utils/uploadbox"],function(a,d,e,c,b){return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(g){var f=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){f.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new d.GalaxyMastheadIcon({icon:"fa-arrow-circle-o-up",tooltip:"Upload Files",on_click:function(h){f._eventShow(h)},on_unload:function(){if(f.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.masthead.prepend(this.button_show);var f=this;e.jsonFromUrl(galaxy_config.root+"api/datatypes",function(h){for(key in h){f.select_extension.push([h[key],h[key]])}});e.jsonFromUrl(galaxy_config.root+"api/genomes",function(h){var i=f.select_genome[0];f.select_genome=[];for(key in h){if(h[key].length>1){if(h[key][1]!==i[1]){f.select_genome.push(h[key])}}}f.select_genome.sort(function(k,j){return k[0]>j[0]?1:k[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=m;tool_input.file_type=g;tool_input["files_0|NAME"]=k;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=l;tool_input.space_to_tabs=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(g,h,f){var i=this.collection.get(g);i.set("percentage",f)},_eventSuccess:function(f,g,i){var h=this.collection.get(f);h.set("status","success");this.button_show.number("");this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(f,g,i){var h=this.collection.get(f);h.set("status","error");h.set("info",i);this.button_show.number("");this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(f){if(f.get("status")=="queued"){f.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}this.collection.each(function(f){if(f.get("status")=="init"){f.set("status","queued")}});this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset()}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                        Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_template:function(g,f){return'
                        '}})}); \ No newline at end of file diff --git a/static/scripts/packed/utils/galaxy.uploadbox.js b/static/scripts/packed/utils/uploadbox.js similarity index 100% rename from static/scripts/packed/utils/galaxy.uploadbox.js rename to static/scripts/packed/utils/uploadbox.js diff --git a/static/scripts/packed/utils/galaxy.utils.js b/static/scripts/packed/utils/utils.js similarity index 100% rename from static/scripts/packed/utils/galaxy.utils.js rename to static/scripts/packed/utils/utils.js diff --git a/static/scripts/utils/galaxy.uploadbox.js b/static/scripts/utils/uploadbox.js similarity index 100% rename from static/scripts/utils/galaxy.uploadbox.js rename to static/scripts/utils/uploadbox.js diff --git a/static/scripts/utils/galaxy.utils.js b/static/scripts/utils/utils.js similarity index 100% rename from static/scripts/utils/galaxy.utils.js rename to static/scripts/utils/utils.js diff --git a/templates/webapps/galaxy/galaxy.masthead.mako b/templates/webapps/galaxy/galaxy.masthead.mako index be27046e52f..8d8c1f2394c 100644 --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -80,8 +80,8 @@ ## load galaxy js-modules $(function() { - require(['galaxy.masthead', 'galaxy.menu', 'galaxy.modal', 'galaxy.frame', 'galaxy.upload'], - function(mod_masthead, mod_menu, mod_modal, mod_frame, mod_upload) + require(['galaxy.masthead', 'galaxy.menu', 'galaxy.modal', 'galaxy.frame', 'mvc/upload/upload-view'], + function(mod_masthead, mod_menu, mod_modal, mod_frame, GalaxyUpload) { ## check if masthead is available if (Galaxy.masthead) @@ -102,7 +102,7 @@ }); ## add upload plugin - ##Galaxy.upload = new mod_upload.GalaxyUpload(masthead_config); + ##Galaxy.upload = new GalaxyUpload(masthead_config); ## set up the quota meter (And fetch the current user data from trans) ## add quota meter to masthead From 720bbdf41fce7d51062f81d5dbebb86bacfc424a Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Fri, 17 Jan 2014 18:13:55 -0500 Subject: [PATCH 0828/1033] Upload: Add automated genome selection --- static/scripts/mvc/upload/upload-row.js | 13 ++++++++++++- static/scripts/mvc/upload/upload-view.js | 9 +++++++-- static/scripts/packed/mvc/upload/upload-row.js | 2 +- static/scripts/packed/mvc/upload/upload-view.js | 2 +- 4 files changed, 21 insertions(+), 5 deletions(-) diff --git a/static/scripts/mvc/upload/upload-row.js b/static/scripts/mvc/upload/upload-row.js index 7c88ad72587..217b7b5a75b 100644 --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -85,6 +85,9 @@ return Backbone.View.extend({ this.model.on('change:info', function() { self._refreshInfo(); }); + this.model.on('change:genome', function() { + self._refreshGenome(); + }); this.model.on('remove', function() { self.remove(); }); @@ -130,7 +133,15 @@ return Backbone.View.extend({ text.show(); } }, - + + // genome + _refreshGenome: function() + { + // write error message + var genome = this.model.get('genome'); + this.$el.find('#genome').val(genome); + }, + // progress _refreshInfo: function() { diff --git a/static/scripts/mvc/upload/upload-view.js b/static/scripts/mvc/upload/upload-view.js index ae0d0194a92..ae29d5303a5 100644 --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -129,8 +129,13 @@ return Backbone.View.extend( this.collection.on('remove', function(item) { self._eventRemove(item); }); - this.collection.on('change', function(item) { - console.log('here'); + this.collection.on('change:genome', function(item) { + var genome = item.get('genome'); + self.collection.each(function(item) { + if (item.get('status') == 'init' && item.get('genome') == '?') { + item.set('genome', genome); + } + }); }); }, diff --git a/static/scripts/packed/mvc/upload/upload-row.js b/static/scripts/packed/mvc/upload/upload-row.js index 2b7a790d1c7..4ff4b0cdeaf 100644 --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1 +1 @@ -define(["mvc/upload/upload-model"],function(a){return Backbone.View.extend({options:{padding:8},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(e,c){this.app=e;var b=this;this.model=new a.Model(c);this.setElement(this._template(c));var d=this.$el;d.find("#symbol").on("click",function(){var f=b.model.get("status");if(f=="init"||f=="success"||f=="error"){b.app.collection.remove(b.model)}});d.find("#text-content").on("keyup",function(){var f=d.find("#text-content");var h=f.val();var g=h.length;d.find("#size").html(b._formatSize(g));b.model.set("url_paste",h)});d.find("#genome").on("change",function(f){b.model.set("genome",$(f.target).val())});d.find("#extension").on("change",function(f){b.model.set("extension",$(f.target).val())});d.find("#space_to_tabs").on("change",function(f){b.model.set("space_to_tabs",$(f.target).prop("checked"))});this.model.on("change:percentage",function(){b._refreshPercentage()});this.model.on("change:status",function(){b._refreshStatus()});this.model.on("change:info",function(){b._refreshInfo()});this.model.on("remove",function(){b.remove()});this.app.collection.on("reset",function(){b.remove()})},render:function(){var h=this.model.get("file_name");var c=this.model.get("file_size");var e=this.$el;e.find("#title").html(h);e.find("#size").html(this._formatSize(c));if(c==-1){var g=e.find("#text");var f=this.options.padding;var d=e.width()-2*f;var b=e.height()-f;g.css("width",d+"px");g.css("top",b+"px");e.height(b+g.height()+2*f);g.show()}},_refreshInfo:function(){var b=this.model.get("info");if(b){this.$el.find("#info").html("Failed: "+b).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var b=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:b+"%"});if(b!=100){this.$el.find("#percentage").html(b+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var c=this.$el;var b=this.model.get("status");var e=this.status_classes[b];var d=this.$el.find("#symbol");d.removeClass();d.addClass(e);if(b=="init"){c.find("#text-content").attr("disabled",false);c.find("#genome").attr("disabled",false);c.find("#extension").attr("disabled",false);c.find("#space_to_tabs").attr("disabled",false)}else{c.find("#text-content").attr("disabled",true);c.find("#genome").attr("disabled",true);c.find("#extension").attr("disabled",true);c.find("#space_to_tabs").attr("disabled",true)}if(b=="success"){c.addClass("success");c.find("#percentage").html("100%")}if(b=="error"){c.addClass("danger");c.find(".progress").remove()}},_formatSize:function(b){var c="";if(b>=100000000000){b=b/100000000000;c="TB"}else{if(b>=100000000){b=b/100000000;c="GB"}else{if(b>=100000){b=b/100000;c="MB"}else{if(b>=100){b=b/100;c="KB"}else{if(b>0){b=b*10;c="b"}else{return"-"}}}}}return""+(Math.round(b)/10)+" "+c},_template:function(d){var c=this;var b='
                        You may specify a list of URLs (one per line) or paste the contents of a file.
                        ';b+='";b+='";b+='
                        0%
                        ';return b}})}); \ No newline at end of file +define(["mvc/upload/upload-model"],function(a){return Backbone.View.extend({options:{padding:8},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(e,c){this.app=e;var b=this;this.model=new a.Model(c);this.setElement(this._template(c));var d=this.$el;d.find("#symbol").on("click",function(){var f=b.model.get("status");if(f=="init"||f=="success"||f=="error"){b.app.collection.remove(b.model)}});d.find("#text-content").on("keyup",function(){var f=d.find("#text-content");var h=f.val();var g=h.length;d.find("#size").html(b._formatSize(g));b.model.set("url_paste",h)});d.find("#genome").on("change",function(f){b.model.set("genome",$(f.target).val())});d.find("#extension").on("change",function(f){b.model.set("extension",$(f.target).val())});d.find("#space_to_tabs").on("change",function(f){b.model.set("space_to_tabs",$(f.target).prop("checked"))});this.model.on("change:percentage",function(){b._refreshPercentage()});this.model.on("change:status",function(){b._refreshStatus()});this.model.on("change:info",function(){b._refreshInfo()});this.model.on("change:genome",function(){b._refreshGenome()});this.model.on("remove",function(){b.remove()});this.app.collection.on("reset",function(){b.remove()})},render:function(){var h=this.model.get("file_name");var c=this.model.get("file_size");var e=this.$el;e.find("#title").html(h);e.find("#size").html(this._formatSize(c));if(c==-1){var g=e.find("#text");var f=this.options.padding;var d=e.width()-2*f;var b=e.height()-f;g.css("width",d+"px");g.css("top",b+"px");e.height(b+g.height()+2*f);g.show()}},_refreshGenome:function(){var b=this.model.get("genome");this.$el.find("#genome").val(b)},_refreshInfo:function(){var b=this.model.get("info");if(b){this.$el.find("#info").html("Failed: "+b).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var b=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:b+"%"});if(b!=100){this.$el.find("#percentage").html(b+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var c=this.$el;var b=this.model.get("status");var e=this.status_classes[b];var d=this.$el.find("#symbol");d.removeClass();d.addClass(e);if(b=="init"){c.find("#text-content").attr("disabled",false);c.find("#genome").attr("disabled",false);c.find("#extension").attr("disabled",false);c.find("#space_to_tabs").attr("disabled",false)}else{c.find("#text-content").attr("disabled",true);c.find("#genome").attr("disabled",true);c.find("#extension").attr("disabled",true);c.find("#space_to_tabs").attr("disabled",true)}if(b=="success"){c.addClass("success");c.find("#percentage").html("100%")}if(b=="error"){c.addClass("danger");c.find(".progress").remove()}},_formatSize:function(b){var c="";if(b>=100000000000){b=b/100000000000;c="TB"}else{if(b>=100000000){b=b/100000000;c="GB"}else{if(b>=100000){b=b/100000;c="MB"}else{if(b>=100){b=b/100;c="KB"}else{if(b>0){b=b*10;c="b"}else{return"-"}}}}}return""+(Math.round(b)/10)+" "+c},_template:function(d){var c=this;var b='
                        You may specify a list of URLs (one per line) or paste the contents of a file.
                        ';b+='";b+='";b+='
                        0%
                        ';return b}})}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/upload/upload-view.js b/static/scripts/packed/mvc/upload/upload-view.js index f9badaec927..85765d6328d 100644 --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1 +1 @@ -define(["galaxy.modal","galaxy.masthead","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","utils/uploadbox"],function(a,d,e,c,b){return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(g){var f=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){f.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new d.GalaxyMastheadIcon({icon:"fa-arrow-circle-o-up",tooltip:"Upload Files",on_click:function(h){f._eventShow(h)},on_unload:function(){if(f.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.masthead.prepend(this.button_show);var f=this;e.jsonFromUrl(galaxy_config.root+"api/datatypes",function(h){for(key in h){f.select_extension.push([h[key],h[key]])}});e.jsonFromUrl(galaxy_config.root+"api/genomes",function(h){var i=f.select_genome[0];f.select_genome=[];for(key in h){if(h[key].length>1){if(h[key][1]!==i[1]){f.select_genome.push(h[key])}}}f.select_genome.sort(function(k,j){return k[0]>j[0]?1:k[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=m;tool_input.file_type=g;tool_input["files_0|NAME"]=k;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=l;tool_input.space_to_tabs=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(g,h,f){var i=this.collection.get(g);i.set("percentage",f)},_eventSuccess:function(f,g,i){var h=this.collection.get(f);h.set("status","success");this.button_show.number("");this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(f,g,i){var h=this.collection.get(f);h.set("status","error");h.set("info",i);this.button_show.number("");this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(f){if(f.get("status")=="queued"){f.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}this.collection.each(function(f){if(f.get("status")=="init"){f.set("status","queued")}});this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset()}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                        Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_template:function(g,f){return'
                        '}})}); \ No newline at end of file +define(["galaxy.modal","galaxy.masthead","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","utils/uploadbox"],function(a,d,e,c,b){return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(g){var f=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){f.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new d.GalaxyMastheadIcon({icon:"fa-arrow-circle-o-up",tooltip:"Upload Files",on_click:function(h){f._eventShow(h)},on_unload:function(){if(f.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.masthead.prepend(this.button_show);var f=this;e.jsonFromUrl(galaxy_config.root+"api/datatypes",function(h){for(key in h){f.select_extension.push([h[key],h[key]])}});e.jsonFromUrl(galaxy_config.root+"api/genomes",function(h){var i=f.select_genome[0];f.select_genome=[];for(key in h){if(h[key].length>1){if(h[key][1]!==i[1]){f.select_genome.push(h[key])}}}f.select_genome.sort(function(k,j){return k[0]>j[0]?1:k[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=m;tool_input.file_type=g;tool_input["files_0|NAME"]=k;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=l;tool_input.space_to_tabs=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(g,h,f){var i=this.collection.get(g);i.set("percentage",f)},_eventSuccess:function(f,g,i){var h=this.collection.get(f);h.set("status","success");this.button_show.number("");this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(f,g,i){var h=this.collection.get(f);h.set("status","error");h.set("info",i);this.button_show.number("");this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(f){if(f.get("status")=="queued"){f.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}this.collection.each(function(f){if(f.get("status")=="init"){f.set("status","queued")}});this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset()}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                        Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_template:function(g,f){return'
                        '}})}); \ No newline at end of file From 2f711d1a9fea58fbaa8ed34c747fb988af3459e2 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Fri, 17 Jan 2014 18:17:35 -0500 Subject: [PATCH 0829/1033] DataViewer: Remove console output --- static/scripts/mvc/data.js | 17 +++++++++-------- static/scripts/packed/mvc/data.js | 2 +- 2 files changed, 10 insertions(+), 9 deletions(-) diff --git a/static/scripts/mvc/data.js b/static/scripts/mvc/data.js index 5df675de9dc..23882e0fc8a 100644 --- a/static/scripts/mvc/data.js +++ b/static/scripts/mvc/data.js @@ -304,27 +304,28 @@ var TabularButtonTracksterView = Backbone.View.extend( } // check - if(this.col.chrom === null) - { - console.log("TabularButtonTrackster : Chromosome column undefined."); + if(this.col.chrom === null) { return; } // get dataset id - if (typeof options.model.attributes.id === "undefined") + if (typeof options.model.attributes.id === "undefined") { console.log("TabularButtonTrackster : Dataset identification is missing."); - else + } else { this.dataset_id = options.model.attributes.id; + } // get url - if (typeof options.model.attributes.url_viz === "undefined") + if (typeof options.model.attributes.url_viz === "undefined") { console.log("TabularButtonTrackster : Url for visualization controller is missing."); - else + } else { this.url_viz = options.model.attributes.url_viz; + } // get genome_build / database key - if (typeof options.model.attributes.genome_build !== "undefined") + if (typeof options.model.attributes.genome_build !== "undefined") { this.genome_build = options.model.attributes.genome_build; + } // render the icon from template var btn_viz = new IconButtonView({ model : new IconButton({ diff --git a/static/scripts/packed/mvc/data.js b/static/scripts/packed/mvc/data.js index abe3c45d631..50af2b8436b 100644 --- a/static/scripts/packed/mvc/data.js +++ b/static/scripts/packed/mvc/data.js @@ -1 +1 @@ -define([],function(){var d=Backbone.Model.extend({});var e=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_config.root+"api/datasets"});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){new b(i)},render:function(){var m=$("").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(l,i,m){var j=$("';b+='";b+='";b+='';return b}})}); \ No newline at end of file +define(["mvc/upload/upload-model"],function(a){return Backbone.View.extend({options:{padding:8},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",running:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(e,c){this.app=e;var b=this;this.model=new a.Model(c);this.setElement(this._template(c));var d=this.$el;d.find("#symbol").on("click",function(){var f=b.model.get("status");if(f=="init"||f=="success"||f=="error"){b.app.collection.remove(b.model)}});d.find("#text-content").on("keyup",function(){var f=d.find("#text-content");var h=f.val();var g=h.length;d.find("#size").html(b._formatSize(g));b.model.set("url_paste",h);b.model.set("file_size",g)});d.find("#genome").on("change",function(f){b.model.set("genome",$(f.target).val())});d.find("#extension").on("change",function(f){b.model.set("extension",$(f.target).val())});d.find("#space_to_tabs").on("change",function(f){b.model.set("space_to_tabs",$(f.target).prop("checked"))});this.model.on("change:percentage",function(){b._refreshPercentage()});this.model.on("change:status",function(){b._refreshStatus()});this.model.on("change:info",function(){b._refreshInfo()});this.model.on("change:genome",function(){b._refreshGenome()});this.model.on("remove",function(){b.remove()});this.app.collection.on("reset",function(){b.remove()})},render:function(){var h=this.model.get("file_name");var c=this.model.get("file_size");var e=this.$el;e.find("#title").html(h);e.find("#size").html(this._formatSize(c));if(c==-1){var g=e.find("#text");var f=this.options.padding;var d=e.width()-2*f;var b=e.height()-f;g.css("width",d+"px");g.css("top",b+"px");e.height(b+g.height()+2*f);g.show()}},_refreshGenome:function(){var b=this.model.get("genome");this.$el.find("#genome").val(b)},_refreshInfo:function(){var b=this.model.get("info");if(b){this.$el.find("#info").html("Failed: "+b).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var b=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:b+"%"});if(b!=100){this.$el.find("#percentage").html(b+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var c=this.$el;var b=this.model.get("status");var e=this.status_classes[b];var d=this.$el.find("#symbol");d.removeClass();d.addClass(e);if(b=="init"){c.find("#text-content").attr("disabled",false);c.find("#genome").attr("disabled",false);c.find("#extension").attr("disabled",false);c.find("#space_to_tabs").attr("disabled",false)}else{c.find("#text-content").attr("disabled",true);c.find("#genome").attr("disabled",true);c.find("#extension").attr("disabled",true);c.find("#space_to_tabs").attr("disabled",true)}if(b=="success"){c.addClass("success");c.find("#percentage").html("100%")}if(b=="error"){c.addClass("danger");c.find(".progress").remove()}},_formatSize:function(b){var c="";if(b>=100000000000){b=b/100000000000;c="TB"}else{if(b>=100000000){b=b/100000000;c="GB"}else{if(b>=100000){b=b/100000;c="MB"}else{if(b>=100){b=b/100;c="KB"}else{if(b>0){b=b*10;c="b"}else{return"-"}}}}}return""+(Math.round(b)/10)+" "+c},_template:function(d){var c=this;var b='';b+='";b+='";b+='';return b}})}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/upload/upload-view.js b/static/scripts/packed/mvc/upload/upload-view.js index 14b4ca3fb27..4ea6842e80b 100644 --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1 +1 @@ -define(["galaxy.modal","galaxy.masthead","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,g,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(i){var h=this;this.model=i;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){h._percentage(h.model.get("percentage"))});this.model.on("change:status",function(){h._status(h.model.get("status"))})},_status:function(i){var h=this.$el.find(".progress-bar");if(i!=""){h.addClass("progress-bar-"+i)}else{h.removeClass();h.addClass("progress-bar")}},_percentage:function(h){this.$el.find(".progress-bar").css({width:h+"%"})},_template:function(h){return'
                         '+h.label+"
                        "}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Upload Files",label:"Upload",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(j){for(key in j){h.select_extension.push([j[key],j[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){var k=h.select_genome[0];h.select_genome=[];for(key in j){if(j[key].length>1){if(j[key][1]!==k[1]){h.select_genome.push(j[key])}}}h.select_genome.sort(function(m,l){return m[0]>l[0]?1:m[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=o;tool_input.file_type=i;tool_input["files_0|NAME"]=m;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=n;tool_input.space_to_tabs=k;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.button_show.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("status","success");var h=k.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("status","error");j.set("info",k);this.button_show.set("percentage",this._upload_percentage(100,i.size));this.button_show.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.button_show.set("progress",0);this.button_show.set("status","");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset()}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                        Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'
                        "+i.join("")+"
                        ").text(l);var k=this.model.get_metadata("column_types");if(m!==undefined){j.attr("colspan",m).addClass("stringalign")}else{if(k){if(i"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($(""))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(k){var j=k.model.attributes;var m=k.model.attributes.metadata.attributes;if(typeof j.data_type!=="undefined"){this.data_type=j.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof m.chromCol!=="undefined"||typeof m.startCol!=="undefined"||typeof m.endCol!=="undefined"){this.col.chrom=m.chromCol-1;this.col.start=m.startCol-1;this.col.end=m.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function l(o,p){for(var n=0;n").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file +define([],function(){var d=Backbone.Model.extend({});var e=Backbone.Model.extend({defaults:{id:"",type:"",name:"",hda_ldda:"hda",metadata:null},initialize:function(){this._set_metadata();this.on("change",this._set_metadata,this)},_set_metadata:function(){var i=new d();_.each(_.keys(this.attributes),function(j){if(j.indexOf("metadata_")===0){var l=j.split("metadata_")[1];i.set(l,this.attributes[j]);delete this.attributes[j]}},this);this.set("metadata",i,{silent:true})},get_metadata:function(i){return this.attributes.metadata.get(i)},urlRoot:galaxy_config.root+"api/datasets"});var c=e.extend({defaults:_.extend({},e.prototype.defaults,{chunk_url:null,first_data_chunk:null,chunk_index:-1,at_eof:false}),initialize:function(i){e.prototype.initialize.call(this);this.attributes.chunk_index=(this.attributes.first_data_chunk?1:0)},get_next_chunk:function(){if(this.attributes.at_eof){return null}var i=this,j=$.Deferred();$.getJSON(this.attributes.chunk_url,{chunk:i.attributes.chunk_index++}).success(function(k){var l;if(k.ck_data!==""){l=k}else{i.attributes.at_eof=true;l=null}j.resolve(l)});return j}});var g=Backbone.Collection.extend({model:e});var f=Backbone.View.extend({initialize:function(i){new b(i)},render:function(){var m=$("").attr({id:"content_table",cellpadding:0});this.$el.append(m);var i=this.model.get_metadata("column_names");if(i){m.append("")}var k=this.model.get("first_data_chunk");if(k){this._renderChunk(k)}var j=this,n=_.find(this.$el.parents(),function(o){return $(o).css("overflow")==="auto"}),l=false;if(!n){n=window}n=$(n);n.scroll(function(){if(!l&&(j.$el.height()-n.scrollTop()-n.height()<=0)){l=true;$.when(j.model.get_next_chunk()).then(function(o){if(o){j._renderChunk(o);l=false}})}});$("#loading_indicator").ajaxStart(function(){$(this).show()}).ajaxStop(function(){$(this).hide()})},_renderCell:function(l,i,m){var j=$("';b+='";b+='";b+='';return b}})}); \ No newline at end of file +define(["mvc/upload/upload-model"],function(a){return Backbone.View.extend({options:{padding:8},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(e,c){this.app=e;var b=this;this.model=new a.Model(c);this.setElement(this._template(c));var d=this.$el;d.find("#symbol").on("click",function(){var f=b.model.get("status");if(f=="init"||f=="success"||f=="error"){b.app.collection.remove(b.model)}});d.find("#text-content").on("keyup",function(){var f=d.find("#text-content");var h=f.val();var g=h.length;d.find("#size").html(b._formatSize(g));b.model.set("url_paste",h);b.model.set("file_size",g)});d.find("#genome").on("change",function(f){b.model.set("genome",$(f.target).val())});d.find("#extension").on("change",function(f){b.model.set("extension",$(f.target).val())});d.find("#space_to_tabs").on("change",function(f){b.model.set("space_to_tabs",$(f.target).prop("checked"))});this.model.on("change:percentage",function(){b._refreshPercentage()});this.model.on("change:status",function(){b._refreshStatus()});this.model.on("change:info",function(){b._refreshInfo()});this.model.on("change:genome",function(){b._refreshGenome()});this.model.on("remove",function(){b.remove()});this.app.collection.on("reset",function(){b.remove()})},render:function(){var h=this.model.get("file_name");var c=this.model.get("file_size");var e=this.$el;e.find("#title").html(h);e.find("#size").html(this._formatSize(c));if(c==-1){var g=e.find("#text");var f=this.options.padding;var d=e.width()-2*f;var b=e.height()-f;g.css("width",d+"px");g.css("top",b+"px");e.height(b+g.height()+2*f);g.show()}},_refreshGenome:function(){var b=this.model.get("genome");this.$el.find("#genome").val(b)},_refreshInfo:function(){var b=this.model.get("info");if(b){this.$el.find("#info").html("Failed: "+b).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var b=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:b+"%"});if(b!=100){this.$el.find("#percentage").html(b+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var c=this.$el;var b=this.model.get("status");var e=this.status_classes[b];var d=this.$el.find("#symbol");d.removeClass();d.addClass(e);if(b=="init"){c.find("#text-content").attr("disabled",false);c.find("#genome").attr("disabled",false);c.find("#extension").attr("disabled",false);c.find("#space_to_tabs").attr("disabled",false)}else{c.find("#text-content").attr("disabled",true);c.find("#genome").attr("disabled",true);c.find("#extension").attr("disabled",true);c.find("#space_to_tabs").attr("disabled",true)}if(b=="success"){c.addClass("success");c.find("#percentage").html("100%")}if(b=="error"){c.addClass("danger");c.find(".progress").remove()}},_formatSize:function(b){var c="";if(b>=100000000000){b=b/100000000000;c="TB"}else{if(b>=100000000){b=b/100000000;c="GB"}else{if(b>=100000){b=b/100000;c="MB"}else{if(b>=100){b=b/100;c="KB"}else{if(b>0){b=b*10;c="b"}else{return"-"}}}}}return""+(Math.round(b)/10)+" "+c},_template:function(d){var c=this;var b='';b+='";b+='";b+='';return b}})}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/upload/upload-view.js b/static/scripts/packed/mvc/upload/upload-view.js index 85765d6328d..14b4ca3fb27 100644 --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1 +1 @@ -define(["galaxy.modal","galaxy.masthead","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","utils/uploadbox"],function(a,d,e,c,b){return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new c.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(g){var f=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){f.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new d.GalaxyMastheadIcon({icon:"fa-arrow-circle-o-up",tooltip:"Upload Files",on_click:function(h){f._eventShow(h)},on_unload:function(){if(f.counter.running>0){return"Several uploads are still processing."}},with_number:true});Galaxy.masthead.prepend(this.button_show);var f=this;e.jsonFromUrl(galaxy_config.root+"api/datatypes",function(h){for(key in h){f.select_extension.push([h[key],h[key]])}});e.jsonFromUrl(galaxy_config.root+"api/genomes",function(h){var i=f.select_genome[0];f.select_genome=[];for(key in h){if(h[key].length>1){if(h[key][1]!==i[1]){f.select_genome.push(h[key])}}}f.select_genome.sort(function(k,j){return k[0]>j[0]?1:k[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=m;tool_input.file_type=g;tool_input["files_0|NAME"]=k;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=l;tool_input.space_to_tabs=i;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(g,h,f){var i=this.collection.get(g);i.set("percentage",f)},_eventSuccess:function(f,g,i){var h=this.collection.get(f);h.set("status","success");this.button_show.number("");this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(f,g,i){var h=this.collection.get(f);h.set("status","error");h.set("info",i);this.button_show.number("");this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(f){if(f.get("status")=="queued"){f.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}this.collection.each(function(f){if(f.get("status")=="init"){f.set("status","queued")}});this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset()}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                        Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_template:function(g,f){return'
                        "+i.join("")+"
                        ").text(l);var k=this.model.get_metadata("column_types");if(m!==undefined){j.attr("colspan",m).addClass("stringalign")}else{if(k){if(i"),k=this.model.get_metadata("columns");if(j.length===k){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this)}else{if(j.length>k){_.each(j.slice(0,k-1),function(n,m){l.append(this._renderCell(n,m))},this);l.append(this._renderCell(j.slice(k-1).join("\t"),k-1))}else{if(k>5&&j.length===k-1){_.each(j,function(n,m){l.append(this._renderCell(n,m))},this);l.append($(""))}else{l.append(this._renderCell(i,0,k))}}}return l},_renderChunk:function(i){var j=this.$el.find("table");_.each(i.ck_data.split("\n"),function(k,l){j.append(this._renderRow(k))},this)}});var b=Backbone.View.extend({col:{chrom:null,start:null,end:null},url_viz:null,dataset_id:null,genome_build:null,data_type:null,initialize:function(k){var j=k.model.attributes;var m=k.model.attributes.metadata.attributes;if(typeof j.data_type!=="undefined"){this.data_type=j.data_type}else{console.log("TabularButtonTrackster : Data type missing.")}if(this.data_type=="bed"){if(typeof m.chromCol!=="undefined"||typeof m.startCol!=="undefined"||typeof m.endCol!=="undefined"){this.col.chrom=m.chromCol-1;this.col.start=m.startCol-1;this.col.end=m.endCol-1}else{console.log("TabularButtonTrackster : Bed-file metadata incomplete.")}}if(this.data_type=="vcf"){function l(o,p){for(var n=0;n").appendTo(i);return new f({el:j,model:new c(k)}).render()};return{Dataset:e,TabularDataset:c,DatasetCollection:g,TabularDatasetChunkedView:f,createTabularDatasetChunkedView:h}}); \ No newline at end of file From 4154e5e9465bd7919c8fb579de1a5a12334ecdf2 Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Fri, 17 Jan 2014 20:31:47 -0500 Subject: [PATCH 0830/1033] Improved logging in the tool shed's install and test framework. --- test/install_and_test_tool_shed_repositories/base/util.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/install_and_test_tool_shed_repositories/base/util.py b/test/install_and_test_tool_shed_repositories/base/util.py index 293a8110adb..79b582d4b99 100644 --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -1001,6 +1001,8 @@ def save_test_results_for_changeset_revision( url, tool_test_results_dicts, tool # Set the time_last_tested entry so that the repository_metadata.time_last_tested will be set in the tool shed. params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) + log.debug( 'url: %s' % str( url ) ) + log.degug( 'params: %s' % str( params ) ) try: return update( tool_shed_api_key, url, params, return_formatted=False ) except Exception, e: From b67781ebdaee5f449d04f42121331dbd8ec482e9 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Sat, 18 Jan 2014 14:48:10 -0500 Subject: [PATCH 0831/1033] Upload: Introduce progress button --- static/scripts/mvc/upload/upload-row.js | 1 + static/scripts/mvc/upload/upload-view.js | 155 +++++++++++++++--- .../scripts/packed/mvc/upload/upload-row.js | 2 +- .../scripts/packed/mvc/upload/upload-view.js | 2 +- static/scripts/packed/utils/utils.js | 2 +- static/scripts/packed/viz/trackster.js | 2 +- static/scripts/utils/utils.js | 11 +- static/scripts/viz/trackster.js | 2 +- 8 files changed, 146 insertions(+), 31 deletions(-) diff --git a/static/scripts/mvc/upload/upload-row.js b/static/scripts/mvc/upload/upload-row.js index 217b7b5a75b..03a9139580c 100644 --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -58,6 +58,7 @@ return Backbone.View.extend({ // update url paste content self.model.set('url_paste', value); + self.model.set('file_size', count); }); // handle genome selection diff --git a/static/scripts/mvc/upload/upload-view.js b/static/scripts/mvc/upload/upload-view.js index ae29d5303a5..51f039f846c 100644 --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -4,15 +4,89 @@ define(["galaxy.modal", "utils/utils", "mvc/upload/upload-model", "mvc/upload/upload-row", + "mvc/ui", "utils/uploadbox"], - function( mod_modal, - mod_masthead, - mod_utils, + function( Modal, + Masthead, + Utils, UploadModel, UploadItem ) { +// create model +var ProgressButtonModel = Backbone.Model.extend({ + defaults: { + percentage : 0, + icon : 'fa-circle', + label : '', + status : '' + } +}); + +// progress bar button on ui +var ProgressButton = Backbone.View.extend({ + // model + model : null, + + // initialize + initialize : function(model) { + // link this + var self = this; + + // create model + this.model = model; + + // get options + this.options = this.model.attributes; + + // create new element + this.setElement(this._template(this.options)); + + // add event + $(this.el).on('click', this.options.onclick); + + // add tooltip + if (this.options.tooltip) { + $(this.el).tooltip({title: this.options.tooltip, placement: 'bottom'}); + } + + // events + this.model.on('change:percentage', function() { + self._percentage(self.model.get('percentage')); + }); + this.model.on('change:status', function() { + self._status(self.model.get('status')); + }); + }, + + // set status + _status: function(value) { + var $el = this.$el.find('.progress-bar'); + if (value != '') { + $el.addClass('progress-bar-' + value); + } else { + $el.removeClass(); + $el.addClass('progress-bar'); + } + }, + + // set percentage + _percentage: function(value) { + this.$el.find('.progress-bar').css({ width : value + '%' }); + }, + + // template + _template: function(options) { + return '
                        ' + + '
                        ' + + '
                        ' + + '
                        ' + + '
                         ' + options.label + '
                        ' + + '
                        '; + } +}); + // galaxy upload return Backbone.View.extend( { @@ -28,6 +102,9 @@ return Backbone.View.extend( // current history current_history: null, + // current upload size + upload_size: 0, + // extension types select_extension :[['Auto-detect', 'auto']], @@ -74,32 +151,35 @@ return Backbone.View.extend( if (!Galaxy.currUser.get('id')) return; - // add activate icon - this.button_show = new mod_masthead.GalaxyMastheadIcon ( - { - icon : 'fa-arrow-circle-o-up', + // create model + this.button_show = new ProgressButtonModel({ + icon : 'fa-upload', tooltip : 'Upload Files', - on_click : function(e) { self._eventShow(e) }, - on_unload : function() { + label : 'Upload', + onclick : function(e) { + if (e) { + self._eventShow(e) + } + }, + onunload : function() { if (self.counter.running > 0) return "Several uploads are still processing."; - }, - with_number : true + } }); - // add to masthead - Galaxy.masthead.prepend(this.button_show); + // define location + $('#left .unified-panel-header-inner').append((new ProgressButton(this.button_show)).$el); // load extension var self = this; - mod_utils.jsonFromUrl(galaxy_config.root + "api/datatypes", + Utils.jsonFromUrl(galaxy_config.root + "api/datatypes", function(datatypes) { for (key in datatypes) self.select_extension.push([datatypes[key], datatypes[key]]); }); // load genomes - mod_utils.jsonFromUrl(galaxy_config.root + "api/genomes", + Utils.jsonFromUrl(galaxy_config.root + "api/genomes", function(genomes) { // backup default var def = self.select_genome[0]; @@ -154,7 +234,7 @@ return Backbone.View.extend( { // make modal var self = this; - this.modal = new mod_modal.GalaxyModal( + this.modal = new Modal.GalaxyModal( { title : 'Upload files from your local drive', body : this._template('upload-box', 'upload-info'), @@ -257,9 +337,6 @@ return Backbone.View.extend( // update status it.set('state', 'running'); - - // update on screen counter - this.button_show.number(this.counter.announce); // get configuration var file_type = it.get('extension'); @@ -297,8 +374,12 @@ return Backbone.View.extend( // progress _eventProgress : function(index, file, percentage) { + // set progress for row var it = this.collection.get(index); it.set('percentage', percentage); + + // update ui button + this.button_show.set('percentage', this._upload_percentage(percentage, file.size)); }, // success @@ -308,8 +389,14 @@ return Backbone.View.extend( var it = this.collection.get(index); it.set('status', 'success'); - // update on screen counter - this.button_show.number(''); + // file size + var file_size = it.get('file_size'); + + // update ui button + this.button_show.set('percentage', this._upload_percentage(100, file_size)); + + // update completed + this.upload_completed += file_size * 100; // update counter this.counter.announce--; @@ -332,8 +419,12 @@ return Backbone.View.extend( it.set('status', 'error'); it.set('info', message); - // update on screen counter - this.button_show.number(''); + // update ui button + this.button_show.set('percentage', this._upload_percentage(100, file.size)); + this.button_show.set('status', 'danger'); + + // update completed + this.upload_completed += file.size * 100; // update counter this.counter.announce--; @@ -373,14 +464,23 @@ return Backbone.View.extend( if (this.counter.announce == 0 || this.counter.running > 0) { return; } - + + // reset current size + var self = this; + this.upload_size = 0; + this.upload_completed = 0; // switch icons for new uploads this.collection.each(function(item) { if(item.get('status') == 'init') { item.set('status', 'queued'); + self.upload_size += item.get('file_size'); } }); + // reset progress + this.button_show.set('progress', 0); + this.button_show.set('status', ''); + // backup current history this.current_history = Galaxy.currHistoryPanel.model.get('id'); @@ -398,7 +498,7 @@ return Backbone.View.extend( if (this.counter.running == 0) { return; } - + // request pause this.uploadbox.stop(); @@ -488,6 +588,11 @@ return Backbone.View.extend( $(this.el).find('table').hide(); }, + // calculate percentage of all queued uploads + _upload_percentage: function(percentage, size) { + return (this.upload_completed + (percentage * size)) / this.upload_size; + }, + // load html template _template: function(id, idInfo) { diff --git a/static/scripts/packed/mvc/upload/upload-row.js b/static/scripts/packed/mvc/upload/upload-row.js index 4ff4b0cdeaf..f9967a33030 100644 --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1 +1 @@ -define(["mvc/upload/upload-model"],function(a){return Backbone.View.extend({options:{padding:8},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(e,c){this.app=e;var b=this;this.model=new a.Model(c);this.setElement(this._template(c));var d=this.$el;d.find("#symbol").on("click",function(){var f=b.model.get("status");if(f=="init"||f=="success"||f=="error"){b.app.collection.remove(b.model)}});d.find("#text-content").on("keyup",function(){var f=d.find("#text-content");var h=f.val();var g=h.length;d.find("#size").html(b._formatSize(g));b.model.set("url_paste",h)});d.find("#genome").on("change",function(f){b.model.set("genome",$(f.target).val())});d.find("#extension").on("change",function(f){b.model.set("extension",$(f.target).val())});d.find("#space_to_tabs").on("change",function(f){b.model.set("space_to_tabs",$(f.target).prop("checked"))});this.model.on("change:percentage",function(){b._refreshPercentage()});this.model.on("change:status",function(){b._refreshStatus()});this.model.on("change:info",function(){b._refreshInfo()});this.model.on("change:genome",function(){b._refreshGenome()});this.model.on("remove",function(){b.remove()});this.app.collection.on("reset",function(){b.remove()})},render:function(){var h=this.model.get("file_name");var c=this.model.get("file_size");var e=this.$el;e.find("#title").html(h);e.find("#size").html(this._formatSize(c));if(c==-1){var g=e.find("#text");var f=this.options.padding;var d=e.width()-2*f;var b=e.height()-f;g.css("width",d+"px");g.css("top",b+"px");e.height(b+g.height()+2*f);g.show()}},_refreshGenome:function(){var b=this.model.get("genome");this.$el.find("#genome").val(b)},_refreshInfo:function(){var b=this.model.get("info");if(b){this.$el.find("#info").html("Failed: "+b).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var b=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:b+"%"});if(b!=100){this.$el.find("#percentage").html(b+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var c=this.$el;var b=this.model.get("status");var e=this.status_classes[b];var d=this.$el.find("#symbol");d.removeClass();d.addClass(e);if(b=="init"){c.find("#text-content").attr("disabled",false);c.find("#genome").attr("disabled",false);c.find("#extension").attr("disabled",false);c.find("#space_to_tabs").attr("disabled",false)}else{c.find("#text-content").attr("disabled",true);c.find("#genome").attr("disabled",true);c.find("#extension").attr("disabled",true);c.find("#space_to_tabs").attr("disabled",true)}if(b=="success"){c.addClass("success");c.find("#percentage").html("100%")}if(b=="error"){c.addClass("danger");c.find(".progress").remove()}},_formatSize:function(b){var c="";if(b>=100000000000){b=b/100000000000;c="TB"}else{if(b>=100000000){b=b/100000000;c="GB"}else{if(b>=100000){b=b/100000;c="MB"}else{if(b>=100){b=b/100;c="KB"}else{if(b>0){b=b*10;c="b"}else{return"-"}}}}}return""+(Math.round(b)/10)+" "+c},_template:function(d){var c=this;var b='
                        You may specify a list of URLs (one per line) or paste the contents of a file.
                        0%
                        You may specify a list of URLs (one per line) or paste the contents of a file.
                        0%
                        '}})}); \ No newline at end of file +define(["galaxy.modal","galaxy.masthead","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,g,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(i){var h=this;this.model=i;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){h._percentage(h.model.get("percentage"))});this.model.on("change:status",function(){h._status(h.model.get("status"))})},_status:function(i){var h=this.$el.find(".progress-bar");if(i!=""){h.addClass("progress-bar-"+i)}else{h.removeClass();h.addClass("progress-bar")}},_percentage:function(h){this.$el.find(".progress-bar").css({width:h+"%"})},_template:function(h){return'
                         '+h.label+"
                        "}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(i){var h=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){h.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Upload Files",label:"Upload",onclick:function(j){if(j){h._eventShow(j)}},onunload:function(){if(h.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var h=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(j){for(key in j){h.select_extension.push([j[key],j[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(j){var k=h.select_genome[0];h.select_genome=[];for(key in j){if(j[key].length>1){if(j[key][1]!==k[1]){h.select_genome.push(j[key])}}}h.select_genome.sort(function(m,l){return m[0]>l[0]?1:m[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=o;tool_input.file_type=i;tool_input["files_0|NAME"]=m;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=n;tool_input.space_to_tabs=k;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(i,j,h){var k=this.collection.get(i);k.set("percentage",h);this.button_show.set("percentage",this._upload_percentage(h,j.size))},_eventSuccess:function(i,j,l){var k=this.collection.get(i);k.set("status","success");var h=k.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,h));this.upload_completed+=h*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(h,i,k){var j=this.collection.get(h);j.set("status","error");j.set("info",k);this.button_show.set("percentage",this._upload_percentage(100,i.size));this.button_show.set("status","danger");this.upload_completed+=i.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(h){if(h.get("status")=="queued"){h.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var h=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(i){if(i.get("status")=="init"){i.set("status","queued");h.upload_size+=i.get("file_size")}});this.button_show.set("progress",0);this.button_show.set("status","");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset()}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                        Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(h,i){return(this.upload_completed+(h*i))/this.upload_size},_template:function(i,h){return'
                        '}})}); \ No newline at end of file diff --git a/static/scripts/packed/utils/utils.js b/static/scripts/packed/utils/utils.js index 9dfe097ab5a..c0f130945c7 100644 --- a/static/scripts/packed/utils/utils.js +++ b/static/scripts/packed/utils/utils.js @@ -1 +1 @@ -define(["libs/underscore"],function(c){function d(g,f,e){var h=new XMLHttpRequest();h.open("GET",g,true);h.setRequestHeader("Accept","application/json");h.setRequestHeader("Cache-Control","no-cache");h.setRequestHeader("X-Requested-With","XMLHttpRequest");h.onloadend=function(){var i=h.status;if(i==200){try{response=jQuery.parseJSON(h.responseText)}catch(j){response=h.responseText}f&&f(response)}else{e&&e(i)}};h.send()}function b(h,e){var f=$('
                        ');f.appendTo(":eq(0)");var g=f.css(e);f.remove();return g}function a(e){if(!$('link[href^="'+e+'"]').length){$('').appendTo("head")}}return{cssLoadFile:a,cssGetAttribute:b,jsonFromUrl:d}}); \ No newline at end of file +define(["libs/underscore"],function(c){function d(h,g,f){var i=new XMLHttpRequest();i.open("GET",h,true);i.setRequestHeader("Accept","application/json");i.setRequestHeader("Cache-Control","no-cache");i.setRequestHeader("X-Requested-With","XMLHttpRequest");i.onloadend=function(){var j=i.status;if(j==200){try{response=jQuery.parseJSON(i.responseText)}catch(k){response=i.responseText}g&&g(response)}else{f&&f(j)}};i.send()}function b(i,f){var g=$('
                        ');g.appendTo(":eq(0)");var h=g.css(f);g.remove();return h}function a(f){if(!$('link[href^="'+f+'"]').length){$('').appendTo("head")}}function e(f,g){if(f){return c.defaults(f,g)}else{return g}}return{cssLoadFile:a,cssGetAttribute:b,jsonFromUrl:d,merge:e}}); \ No newline at end of file diff --git a/static/scripts/packed/viz/trackster.js b/static/scripts/packed/viz/trackster.js index 5875a5504e4..63953c09557 100644 --- a/static/scripts/packed/viz/trackster.js +++ b/static/scripts/packed/viz/trackster.js @@ -1 +1 @@ -var ui=null;var view=null;var browser_router=null;require(["utils/galaxy.utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/backbone/backbone","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey").val(galaxy_config.app.default_dbkey)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='
                        Is the build not listed here? Add a Custom Build
                        ';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.prefs.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file +var ui=null;var view=null;var browser_router=null;require(["utils/utils","libs/jquery/jstorage","libs/jquery/jquery.event.drag","libs/jquery/jquery.event.hover","libs/jquery/jquery.mousewheel","libs/jquery/jquery-ui","libs/jquery/select2","libs/farbtastic","libs/jquery/jquery.form","libs/jquery/jquery.rating","mvc/ui"],function(a){a.cssLoadFile("static/style/jquery.rating.css");a.cssLoadFile("static/style/autocomplete_tagging.css");a.cssLoadFile("static/style/jquery-ui/smoothness/jquery-ui.css");a.cssLoadFile("static/style/library.css");a.cssLoadFile("static/style/trackster.css")});define(["libs/backbone/backbone","viz/visualization","viz/trackster_ui"],function(c,a,b){var d=Backbone.View.extend({initialize:function(){ui=new b.TracksterUI(galaxy_config.root);ui.createButtonMenu();ui.buttonMenu.$el.attr("style","float: right");$("#center .unified-panel-header-inner").append(ui.buttonMenu.$el);$("#right .unified-panel-title").append("Bookmarks");$("#right .unified-panel-icons").append("");$("#right-border").click(function(){view.resize_window()});force_right_panel("hide");if(galaxy_config.app.id){this.view_existing()}else{this.view_new()}},set_up_router:function(e){browser_router=new a.TrackBrowserRouter(e);Backbone.history.start()},view_existing:function(){var e=galaxy_config.app.viz_config;view=ui.create_visualization({container:$("#center .unified-panel-body"),name:e.title,vis_id:e.vis_id,dbkey:e.dbkey},e.viewport,e.tracks,e.bookmarks,true);this.init_editor()},view_new:function(){var e=this;$.ajax({url:galaxy_config.root+"api/genomes?chrom_info=True",data:{},error:function(){alert("Couldn't create new browser.")},success:function(f){Galaxy.modal.show({title:"New Visualization",body:e.template_view_new(f),buttons:{Cancel:function(){window.location=galaxy_config.root+"visualization/list"},Create:function(){e.create_browser($("#new-title").val(),$("#new-dbkey").val());Galaxy.modal.hide()}}});if(galaxy_config.app.default_dbkey){$("#new-dbkey").val(galaxy_config.app.default_dbkey)}$("#new-title").focus();$("select[name='dbkey']").select2();$("#overlay").css("overflow","auto")}})},template_view_new:function(e){var g='
                        Is the build not listed here? Add a Custom Build
                        ';return g},create_browser:function(f,e){$(document).trigger("convert_to_values");view=ui.create_visualization({container:$("#center .unified-panel-body"),name:f,dbkey:e},galaxy_config.app.gene_region);this.init_editor();view.editor=true},init_editor:function(){$("#center .unified-panel-title").text(view.prefs.name+" ("+view.dbkey+")");if(galaxy_config.app.add_dataset){$.ajax({url:galaxy_config.root+"api/datasets/"+galaxy_config.app.add_dataset,data:{hda_ldda:"hda",data_type:"track_config"},dataType:"json",success:function(e){view.add_drawable(b.object_from_template(e,view,view))}})}$("#add-bookmark-button").click(function(){var f=view.chrom+":"+view.low+"-"+view.high,e="Bookmark description";return ui.add_bookmark(f,e,true)});ui.init_keyboard_nav(view);this.set_up_router({view:view})}});return{GalaxyApp:d}}); \ No newline at end of file diff --git a/static/scripts/utils/utils.js b/static/scripts/utils/utils.js index 67e4e88366f..b242ff66ff3 100644 --- a/static/scripts/utils/utils.js +++ b/static/scripts/utils/utils.js @@ -63,11 +63,20 @@ function cssLoadFile (url) { $('').appendTo('head'); }; +// merge +function merge (options, optionsDefault) { + if (options) + return _.defaults(options, optionsDefault); + else + return optionsDefault; +}; + // return return { cssLoadFile : cssLoadFile, cssGetAttribute : cssGetAttribute, - jsonFromUrl : jsonFromUrl + jsonFromUrl : jsonFromUrl, + merge : merge }; }); diff --git a/static/scripts/viz/trackster.js b/static/scripts/viz/trackster.js index 6d15095eff4..e7965bff1a7 100644 --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -7,7 +7,7 @@ var browser_router = null; require( [ // load js libraries - 'utils/galaxy.utils', + 'utils/utils', 'libs/jquery/jstorage', 'libs/jquery/jquery.event.drag', 'libs/jquery/jquery.event.hover', From a25d3792cba309fd040946db2c65669099607baf Mon Sep 17 00:00:00 2001 From: Greg Von Kuster Date: Sat, 18 Jan 2014 15:46:36 -0500 Subject: [PATCH 0832/1033] Debug fix. --- test/install_and_test_tool_shed_repositories/base/util.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/test/install_and_test_tool_shed_repositories/base/util.py b/test/install_and_test_tool_shed_repositories/base/util.py index 79b582d4b99..3f639c78360 100644 --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -1002,7 +1002,7 @@ def save_test_results_for_changeset_revision( url, tool_test_results_dicts, tool params[ 'time_last_tested' ] = 'This entry will result in this value being set via the Tool Shed API.' url = '%s' % ( suc.url_join( galaxy_tool_shed_url,'api', 'repository_revisions', str( metadata_revision_id ) ) ) log.debug( 'url: %s' % str( url ) ) - log.degug( 'params: %s' % str( params ) ) + log.debug( 'params: %s' % str( params ) ) try: return update( tool_shed_api_key, url, params, return_formatted=False ) except Exception, e: From 3b6b4ec2c15f49099dfe14687868ed8a58731f9d Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Sun, 19 Jan 2014 09:11:52 -0500 Subject: [PATCH 0833/1033] Upload: Finalize Progress button, fix icon size --- static/scripts/mvc/upload/upload-row.js | 1 + static/scripts/mvc/upload/upload-view.js | 49 ++++++++++++++----- .../scripts/packed/mvc/upload/upload-row.js | 2 +- .../scripts/packed/mvc/upload/upload-view.js | 2 +- static/style/blue/base.css | 6 ++- static/style/src/less/upload.less | 35 +++++++++++++ templates/webapps/galaxy/galaxy.masthead.mako | 2 +- 7 files changed, 80 insertions(+), 17 deletions(-) diff --git a/static/scripts/mvc/upload/upload-row.js b/static/scripts/mvc/upload/upload-row.js index 03a9139580c..bb5a1b48b24 100644 --- a/static/scripts/mvc/upload/upload-row.js +++ b/static/scripts/mvc/upload/upload-row.js @@ -12,6 +12,7 @@ return Backbone.View.extend({ status_classes : { init : 'symbol fa fa-trash-o', queued : 'symbol fa fa-spinner fa-spin', + running : 'symbol fa fa-spinner fa-spin', success : 'symbol fa fa-check', error : 'symbol fa fa-exclamation-triangle' }, diff --git a/static/scripts/mvc/upload/upload-view.js b/static/scripts/mvc/upload/upload-view.js index 51f039f846c..2f3c3e72bab 100644 --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -1,6 +1,5 @@ // dependencies define(["galaxy.modal", - "galaxy.masthead", "utils/utils", "mvc/upload/upload-model", "mvc/upload/upload-row", @@ -8,7 +7,6 @@ define(["galaxy.modal", "utils/uploadbox"], function( Modal, - Masthead, Utils, UploadModel, UploadItem @@ -58,27 +56,45 @@ var ProgressButton = Backbone.View.extend({ this.model.on('change:status', function() { self._status(self.model.get('status')); }); + + // unload event + var self = this; + window.onbeforeunload = function() { + var text = ""; + if (self.options.onunload) { + text = self.options.onunload(); + } + if (text != "") + return text; + }; }, // set status _status: function(value) { var $el = this.$el.find('.progress-bar'); + $el.removeClass(); + $el.addClass('progress-bar'); + $el.addClass('progress-bar-notransition'); if (value != '') { $el.addClass('progress-bar-' + value); - } else { - $el.removeClass(); - $el.addClass('progress-bar'); } }, // set percentage _percentage: function(value) { - this.$el.find('.progress-bar').css({ width : value + '%' }); + var $el = this.$el.find('.progress-bar'); + if (value) { + // change to new percentage + $el.css({ width : value + '%' }); + } else { + // reset without transition + $el.css({ width : '0%' }); + } }, // template _template: function(options) { - return '
                        ' + + return '
                        ' + '
                        ' + '
                        ' + '
                        ' + @@ -154,7 +170,7 @@ return Backbone.View.extend( // create model this.button_show = new ProgressButtonModel({ icon : 'fa-upload', - tooltip : 'Upload Files', + tooltip : 'upload files', label : 'Upload', onclick : function(e) { if (e) { @@ -162,8 +178,9 @@ return Backbone.View.extend( } }, onunload : function() { - if (self.counter.running > 0) + if (self.counter.running > 0) { return "Several uploads are still processing."; + } } }); @@ -336,7 +353,7 @@ return Backbone.View.extend( var it = this.collection.get(index); // update status - it.set('state', 'running'); + it.set('status', 'running'); // get configuration var file_type = it.get('extension'); @@ -478,8 +495,8 @@ return Backbone.View.extend( }); // reset progress - this.button_show.set('progress', 0); - this.button_show.set('status', ''); + this.button_show.set('percentage', 0); + this.button_show.set('status', 'success'); // backup current history this.current_history = Galaxy.currHistoryPanel.model.get('id'); @@ -498,7 +515,10 @@ return Backbone.View.extend( if (this.counter.running == 0) { return; } - + + // show upload has paused + this.button_show.set('status', 'info'); + // request pause this.uploadbox.stop(); @@ -522,6 +542,9 @@ return Backbone.View.extend( // remove from queue this.uploadbox.reset(); + + // reset button + this.button_show.set('percentage', 0); } }, diff --git a/static/scripts/packed/mvc/upload/upload-row.js b/static/scripts/packed/mvc/upload/upload-row.js index f9967a33030..52c448f7f80 100644 --- a/static/scripts/packed/mvc/upload/upload-row.js +++ b/static/scripts/packed/mvc/upload/upload-row.js @@ -1 +1 @@ -define(["mvc/upload/upload-model"],function(a){return Backbone.View.extend({options:{padding:8},status_classes:{init:"symbol fa fa-trash-o",queued:"symbol fa fa-spinner fa-spin",success:"symbol fa fa-check",error:"symbol fa fa-exclamation-triangle"},initialize:function(e,c){this.app=e;var b=this;this.model=new a.Model(c);this.setElement(this._template(c));var d=this.$el;d.find("#symbol").on("click",function(){var f=b.model.get("status");if(f=="init"||f=="success"||f=="error"){b.app.collection.remove(b.model)}});d.find("#text-content").on("keyup",function(){var f=d.find("#text-content");var h=f.val();var g=h.length;d.find("#size").html(b._formatSize(g));b.model.set("url_paste",h);b.model.set("file_size",g)});d.find("#genome").on("change",function(f){b.model.set("genome",$(f.target).val())});d.find("#extension").on("change",function(f){b.model.set("extension",$(f.target).val())});d.find("#space_to_tabs").on("change",function(f){b.model.set("space_to_tabs",$(f.target).prop("checked"))});this.model.on("change:percentage",function(){b._refreshPercentage()});this.model.on("change:status",function(){b._refreshStatus()});this.model.on("change:info",function(){b._refreshInfo()});this.model.on("change:genome",function(){b._refreshGenome()});this.model.on("remove",function(){b.remove()});this.app.collection.on("reset",function(){b.remove()})},render:function(){var h=this.model.get("file_name");var c=this.model.get("file_size");var e=this.$el;e.find("#title").html(h);e.find("#size").html(this._formatSize(c));if(c==-1){var g=e.find("#text");var f=this.options.padding;var d=e.width()-2*f;var b=e.height()-f;g.css("width",d+"px");g.css("top",b+"px");e.height(b+g.height()+2*f);g.show()}},_refreshGenome:function(){var b=this.model.get("genome");this.$el.find("#genome").val(b)},_refreshInfo:function(){var b=this.model.get("info");if(b){this.$el.find("#info").html("Failed: "+b).show()}else{this.$el.find("#info").hide()}},_refreshPercentage:function(){var b=parseInt(this.model.get("percentage"));this.$el.find(".progress-bar").css({width:b+"%"});if(b!=100){this.$el.find("#percentage").html(b+"%")}else{this.$el.find("#percentage").html("Adding to history...")}},_refreshStatus:function(){var c=this.$el;var b=this.model.get("status");var e=this.status_classes[b];var d=this.$el.find("#symbol");d.removeClass();d.addClass(e);if(b=="init"){c.find("#text-content").attr("disabled",false);c.find("#genome").attr("disabled",false);c.find("#extension").attr("disabled",false);c.find("#space_to_tabs").attr("disabled",false)}else{c.find("#text-content").attr("disabled",true);c.find("#genome").attr("disabled",true);c.find("#extension").attr("disabled",true);c.find("#space_to_tabs").attr("disabled",true)}if(b=="success"){c.addClass("success");c.find("#percentage").html("100%")}if(b=="error"){c.addClass("danger");c.find(".progress").remove()}},_formatSize:function(b){var c="";if(b>=100000000000){b=b/100000000000;c="TB"}else{if(b>=100000000){b=b/100000000;c="GB"}else{if(b>=100000){b=b/100000;c="MB"}else{if(b>=100){b=b/100;c="KB"}else{if(b>0){b=b*10;c="b"}else{return"-"}}}}}return""+(Math.round(b)/10)+" "+c},_template:function(d){var c=this;var b='
                        You may specify a list of URLs (one per line) or paste the contents of a file.
                        0%
                        You may specify a list of URLs (one per line) or paste the contents of a file.
                        0%
                        '}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;window.onbeforeunload=function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}}},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");if(h){g.css({width:h+"%"})}else{g.css({width:"0%"})}},_template:function(g){return'
                         '+g.label+"
                        "}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"upload files",label:"Upload",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|NAME"]=l;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                        Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'
                        '}})}); \ No newline at end of file diff --git a/static/style/blue/base.css b/static/style/blue/base.css index a784bd63ad9..45811c86bf3 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1250,6 +1250,10 @@ label{font-weight:normal} .galaxy-frame .frame .f-close{right:5px;top:3px} .galaxy-frame .frame .f-pin{left:6px;top:3px} .galaxy-frame .frame .f-resize{background:#fff;width:16px;height:16px;color:#2c3143;right:0px;bottom:0px;text-align:center;line-height:16px;border:0px} +.progress-button{position:absolute;width:100px;right:10px;top:6px;cursor:pointer;height:19px;border:1px solid #aaa;-moz-border-radius:3px;border-radius:3px}.progress-button .progress-bar-danger{background:#f9c7c5} +.progress-button .progress-bar-success{background:#aff1af;border:0px} +.progress-button .progress-bar-info{background:#ffc} +.progress-button .progress-bar-notransition{-webkit-transition:none;-moz-transition:none;-ms-transition:none;-o-transition:none;transition:none} .upload-info{font-weight:normal;text-align:center} .upload-box{width:100%;height:95%;text-align:center;overflow:scroll;font-size:12px;line-height:1.33;-moz-border-radius:5px;border-radius:5px;border:1px dashed #bfbfbf;padding:10px;overflow-x:hidden;-ms-overflow-style:none}.upload-box .table{width:100%} .upload-box .table th{text-align:center;white-space:nowrap} @@ -1262,7 +1266,7 @@ label{font-weight:normal} .upload-box .size{width:60px;white-space:nowrap} .upload-box .info{width:130px;font-size:11px}.upload-box .info .progress{top:1px;position:relative;width:100%;padding:0px;margin:0px}.upload-box .info .progress .progress-bar{border-radius:inherit;-moz-border-radius:inherit} .upload-box .info .progress .percentage{position:absolute;text-align:center;width:100%;color:#fff} -.upload-box .symbol{cursor:pointer} +.upload-box .symbol{font-size:1.2em;cursor:pointer} .libraryRow{background-color:#ebd9b2} .datasetHighlighted{background-color:#f9f9f9} .libraryItemDeleted-True{font-style:italic} diff --git a/static/style/src/less/upload.less b/static/style/src/less/upload.less index 628183008af..6475afae0aa 100644 --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -1,3 +1,37 @@ +.progress-button { + position: absolute; + width: 100px; + right: 10px; + top: 6px; + cursor: pointer; + height: 19px; + border: 1px solid @input-border; + -moz-border-radius: @border-radius-base; + border-radius: @border-radius-base; + + .progress-bar-danger { + background: @state-danger-bg; + } + + .progress-bar-success { + background: @state-success-bg; + + border : 0px; + } + + .progress-bar-info { + background: @state-running-bg; + } + + .progress-bar-notransition { + -webkit-transition: none; + -moz-transition: none; + -ms-transition: none; + -o-transition: none; + transition: none; + } +} + .upload-info { font-weight: normal; @@ -99,6 +133,7 @@ } .symbol { + font-size: 1.2em; cursor: pointer; } } \ No newline at end of file diff --git a/templates/webapps/galaxy/galaxy.masthead.mako b/templates/webapps/galaxy/galaxy.masthead.mako index 8d8c1f2394c..726aa0adb91 100644 --- a/templates/webapps/galaxy/galaxy.masthead.mako +++ b/templates/webapps/galaxy/galaxy.masthead.mako @@ -102,7 +102,7 @@ }); ## add upload plugin - ##Galaxy.upload = new GalaxyUpload(masthead_config); + Galaxy.upload = new GalaxyUpload(masthead_config); ## set up the quota meter (And fetch the current user data from trans) ## add quota meter to masthead From 751b5b99f104ce83d46551412a7e07fc9691b748 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Sun, 19 Jan 2014 09:17:01 -0500 Subject: [PATCH 0834/1033] Upload: Fix tooltip text --- static/scripts/mvc/upload/upload-view.js | 2 +- static/scripts/packed/mvc/upload/upload-view.js | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/static/scripts/mvc/upload/upload-view.js b/static/scripts/mvc/upload/upload-view.js index 2f3c3e72bab..dc6690e8ef7 100644 --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -170,7 +170,7 @@ return Backbone.View.extend( // create model this.button_show = new ProgressButtonModel({ icon : 'fa-upload', - tooltip : 'upload files', + tooltip : 'Upload files', label : 'Upload', onclick : function(e) { if (e) { diff --git a/static/scripts/packed/mvc/upload/upload-view.js b/static/scripts/packed/mvc/upload/upload-view.js index 4ea6842e80b..a03c17ef7e0 100644 --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1 +1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;window.onbeforeunload=function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}}},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");if(h){g.css({width:h+"%"})}else{g.css({width:"0%"})}},_template:function(g){return'
                         '+g.label+"
                        "}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"upload files",label:"Upload",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|NAME"]=l;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                        Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'
                        '}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;window.onbeforeunload=function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}}},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");if(h){g.css({width:h+"%"})}else{g.css({width:"0%"})}},_template:function(g){return'
                         '+g.label+"
                        "}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Upload files",label:"Upload",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|NAME"]=l;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                        Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'
                        '}})}); \ No newline at end of file From 09fd8c7ae04e9878e1c5b0391cd80e04bd673c10 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Sun, 19 Jan 2014 10:05:53 -0500 Subject: [PATCH 0835/1033] UI: Enable multiple onbeforeunload events --- static/scripts/galaxy.frame.js | 9 +++---- static/scripts/galaxy.masthead.js | 24 +++++++++---------- static/scripts/mvc/upload/upload-view.js | 7 +++--- static/scripts/packed/galaxy.frame.js | 2 +- static/scripts/packed/galaxy.masthead.js | 2 +- .../scripts/packed/mvc/upload/upload-view.js | 2 +- 6 files changed, 24 insertions(+), 22 deletions(-) diff --git a/static/scripts/galaxy.frame.js b/static/scripts/galaxy.frame.js index df174c3fed4..9c90e6192be 100644 --- a/static/scripts/galaxy.frame.js +++ b/static/scripts/galaxy.frame.js @@ -87,10 +87,11 @@ var GalaxyFrame = Backbone.View.extend( { icon : 'fa-th', tooltip : 'Enable/Disable Scratchbook', - on_click : function(e) { self._event_panel_active(e) }, - on_unload : function() { - if (self.frame_counter > 0) + onclick : function(e) { self._event_panel_active(e) }, + onunload : function() { + if (self.frame_counter > 0) { return "You opened " + self.frame_counter + " frame(s) which will be lost."; + } } }); @@ -102,7 +103,7 @@ var GalaxyFrame = Backbone.View.extend( { icon : 'fa-eye', tooltip : 'Show/Hide Scratchbook', - on_click : function(e) { self._event_panel_load(e) }, + onclick : function(e) { self._event_panel_load(e) }, with_number : true }); diff --git a/static/scripts/galaxy.masthead.js b/static/scripts/galaxy.masthead.js index 9e36e58578d..748b0d87b79 100644 --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -36,18 +36,18 @@ var GalaxyMasthead = Backbone.View.extend( // loop through unload functions if the user attempts to unload the page var self = this; - window.onbeforeunload = function() - { + $(window).on('beforeunload', function() { var text = ""; - for (key in self.list) - if (self.list[key].options.on_unload) - { - var q = self.list[key].options.on_unload(); + for (key in self.list) { + if (self.list[key].options.onunload) { + var q = self.list[key].options.onunload(); if (q) text += q + " "; } - if (text != "") + } + if (text != "") { return text; - }; + } + }); }, // configure events @@ -159,8 +159,8 @@ var GalaxyMastheadIcon = Backbone.View.extend( icon : 'fa-cog', tooltip : '', with_number : false, - on_click : function() { alert ('clicked') }, - on_unload : null, + onclick : function() { alert ('clicked') }, + onunload : null, visible : true }, @@ -180,7 +180,7 @@ var GalaxyMastheadIcon = Backbone.View.extend( // configure icon var self = this; $(this.el).find('.icon').tooltip({title: this.options.tooltip, placement: 'bottom'}) - .on('mouseup', self.options.on_click); + .on('mouseup', self.options.onclick); // visiblity if (!this.options.visible) @@ -254,7 +254,7 @@ var GalaxyMastheadTab = Backbone.View.extend( content : '', type : 'url', scratchbook : false, - on_unload : null, + onunload : null, visible : true, disabled : false, title_attribute : '' diff --git a/static/scripts/mvc/upload/upload-view.js b/static/scripts/mvc/upload/upload-view.js index dc6690e8ef7..5f108c6da1a 100644 --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -59,14 +59,15 @@ var ProgressButton = Backbone.View.extend({ // unload event var self = this; - window.onbeforeunload = function() { + $(window).on('beforeunload', function() { var text = ""; if (self.options.onunload) { text = self.options.onunload(); } - if (text != "") + if (text != "") { return text; - }; + } + }); }, // set status diff --git a/static/scripts/packed/galaxy.frame.js b/static/scripts/packed/galaxy.frame.js index bfffd210e7a..0240d4b35c0 100644 --- a/static/scripts/packed/galaxy.frame.js +++ b/static/scripts/packed/galaxy.frame.js @@ -1 +1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.View.extend({el_main:"body",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",on_click:function(f){c._event_panel_active(f)},on_unload:function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",on_click:function(f){c._event_panel_load(f)},with_number:true});Galaxy.masthead.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this._template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this._panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c._panel_refresh()}})},add:function(d){var g={title:"",content:null,target:"",type:null,scratchbook:false};if(d){d=_.defaults(d,g)}else{d=g}if(!d.content){return}if(d.target=="_blank"){window.open(d.content);return}if(d.target=="_top"||d.target=="_parent"||d.target=="_self"){window.location=d.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(d.target=="galaxy_main"||d.target=="center"){if(f.length==0){var c=d.content;if(c.indexOf("?")==-1){c+="?"}else{c+="&"}c+="use_panels=True";window.location=c}else{f.attr("src",d.content)}}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this._template_frame(e.substring(1),d.title,d.type,d.content));var h={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this._to_pixel_coord("width",this.options.frame.cols);d.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(h.id).css("z-index"));this.frame_list[e]=h;this.frame_counter++;this._frame_resize(h,{width:d.width,height:d.height});this._frame_insert(h,{top:0,left:0},true);if(!this.visible){this._panel_show_hide()}},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_panel_load","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this._frame_identify(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this._frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this._frame_resize(this.event.target,h);h.width=this._to_grid_coord("width",h.width)+1;h.height=this._to_grid_coord("height",h.height)+1;h.width=this._to_pixel_coord("width",h.width);h.height=this._to_pixel_coord("height",h.height);this._frame_resize(this.frame_shadow,h);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this._frame_offset(this.event.target,h);var c={top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this._frame_insert(this.frame_shadow,c)}},_event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this._frame_identify(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c._panel_refresh(true);c._panel_animation_complete();if(c.visible&&c.frame_counter==0){c._panel_show_hide()}})},_event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},_event_panel_load:function(c){if(this.event.type!==null){return}this._panel_show_hide()},_event_panel_active:function(c){if(this.event.type!==null){return}this._panel_active_disable()},_event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this._panel_scroll(d)},_event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(-this.options.scroll)},_event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(this.options.scroll)},_frame_identify:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},_frame_drag_start:function(d){this._frame_focus(d,true);var c=this._frame_screen(d);this._frame_resize(this.frame_shadow,c);this._frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},_frame_drag_stop:function(d){this._frame_focus(d,false);var c=this._frame_screen(this.frame_shadow);this._frame_resize(d,c);this._frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this._panel_animation_complete()},_to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},_to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},_to_grid:function(c){return{top:this._to_grid_coord("top",c.top),left:this._to_grid_coord("left",c.left),width:this._to_grid_coord("width",c.width),height:this._to_grid_coord("height",c.height)}},_to_pixel:function(c){return{top:this._to_pixel_coord("top",c.top),left:this._to_pixel_coord("left",c.left),width:this._to_pixel_coord("width",c.width),height:this._to_pixel_coord("height",c.height)}},_is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1g.top+g.height-1||h.top+h.height-1l?1:0)});for(g=0;g
                        '},_template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d=''}return'
                        '+e+'
                        '+d+'
                        '},_template_shadow:function(c){return'
                        '},_template_background:function(){return'
                        '},_template_menu:function(){return'
                        '}});return{GalaxyFrame:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.View.extend({el_main:"body",options:{frame:{cols:6,rows:3},rows:1000,cell:130,margin:5,scroll:5,top_min:40,frame_max:9},cols:0,top:0,top_max:0,frame_z:0,frame_counter:0,frame_counter_id:0,frame_list:[],frame_shadow:null,visible:false,active:false,button_active:null,button_load:null,initialize:function(d){var c=this;this.button_active=new b.GalaxyMastheadIcon({icon:"fa-th",tooltip:"Enable/Disable Scratchbook",onclick:function(f){c._event_panel_active(f)},onunload:function(){if(c.frame_counter>0){return"You opened "+c.frame_counter+" frame(s) which will be lost."}}});Galaxy.masthead.append(this.button_active);this.button_load=new b.GalaxyMastheadIcon({icon:"fa-eye",tooltip:"Show/Hide Scratchbook",onclick:function(f){c._event_panel_load(f)},with_number:true});Galaxy.masthead.append(this.button_load);if(d){this.options=_.defaults(d,this.options)}this.top=this.top_max=this.options.top_min;this.setElement(this._template());$(this.el).append(this._template_background());$(this.el).append(this._template_menu());$(this.el_main).append($(this.el));var e="#frame-shadow";$(this.el).append(this._template_shadow(e.substring(1)));this.frame_shadow={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};this._frame_resize(this.frame_shadow,{width:0,height:0});this.frame_list[e]=this.frame_shadow;this._panel_refresh();var c=this;$(window).resize(function(){if(c.visible){c._panel_refresh()}})},add:function(d){var g={title:"",content:null,target:"",type:null,scratchbook:false};if(d){d=_.defaults(d,g)}else{d=g}if(!d.content){return}if(d.target=="_blank"){window.open(d.content);return}if(d.target=="_top"||d.target=="_parent"||d.target=="_self"){window.location=d.content;return}if(!this.active){var f=$(window.parent.document).find("#galaxy_main");if(d.target=="galaxy_main"||d.target=="center"){if(f.length==0){var c=d.content;if(c.indexOf("?")==-1){c+="?"}else{c+="&"}c+="use_panels=True";window.location=c}else{f.attr("src",d.content)}}else{window.location=d.content}return}if(this.frame_counter>=this.options.frame_max){alert("You have reached the maximum number of allowed frames ("+this.options.frame_max+").");return}var e="#frame-"+(this.frame_counter_id++);if($(e).length!==0){alert("This frame already exists. This page might contain multiple frame managers.");return}this.top=this.options.top_min;$(this.el).append(this._template_frame(e.substring(1),d.title,d.type,d.content));var h={id:e,screen_location:{},grid_location:{},grid_rank:null,grid_lock:false};d.width=this._to_pixel_coord("width",this.options.frame.cols);d.height=this._to_pixel_coord("height",this.options.frame.rows);this.frame_z=parseInt($(h.id).css("z-index"));this.frame_list[e]=h;this.frame_counter++;this._frame_resize(h,{width:d.width,height:d.height});this._frame_insert(h,{top:0,left:0},true);if(!this.visible){this._panel_show_hide()}},event:{type:null,target:null,xy:null},events:{mousemove:"_event_frame_mouse_move",mouseup:"_event_frame_mouse_up",mouseleave:"_event_frame_mouse_up",mousewheel:"_event_panel_scroll",DOMMouseScroll:"_event_panel_scroll","mousedown .frame":"_event_frame_mouse_down","mousedown .frame-background":"_event_panel_load","mousedown .frame-scroll-up":"_event_panel_scroll_up","mousedown .frame-scroll-down":"_event_panel_scroll_down","mousedown .f-close":"_event_frame_close","mousedown .f-pin":"_event_frame_lock"},_event_frame_mouse_down:function(c){if(this.event.type!==null){return}if($(c.target).hasClass("f-header")||$(c.target).hasClass("f-title")){this.event.type="drag"}if($(c.target).hasClass("f-resize")){this.event.type="resize"}if(this.event.type===null){return}c.preventDefault();this.event.target=this._frame_identify(c.target);if(this.event.target.grid_lock){this.event.type=null;return}this.event.xy={x:c.originalEvent.pageX,y:c.originalEvent.pageY};this._frame_drag_start(this.event.target)},_event_frame_mouse_move:function(i){if(this.event.type!="drag"&&this.event.type!="resize"){return}var g={x:i.originalEvent.pageX,y:i.originalEvent.pageY};var d={x:g.x-this.event.xy.x,y:g.y-this.event.xy.y};this.event.xy=g;var h=this._frame_screen(this.event.target);if(this.event.type=="resize"){h.width+=d.x;h.height+=d.y;var f=this.options.cell-this.options.margin-1;h.width=Math.max(h.width,f);h.height=Math.max(h.height,f);this._frame_resize(this.event.target,h);h.width=this._to_grid_coord("width",h.width)+1;h.height=this._to_grid_coord("height",h.height)+1;h.width=this._to_pixel_coord("width",h.width);h.height=this._to_pixel_coord("height",h.height);this._frame_resize(this.frame_shadow,h);this._frame_insert(this.frame_shadow,{top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)})}if(this.event.type=="drag"){h.left+=d.x;h.top+=d.y;this._frame_offset(this.event.target,h);var c={top:this._to_grid_coord("top",h.top),left:this._to_grid_coord("left",h.left)};if(c.left!==0){c.left++}this._frame_insert(this.frame_shadow,c)}},_event_frame_mouse_up:function(c){if(this.event.type!="drag"&&this.event.type!="resize"){return}this._frame_drag_stop(this.event.target);this.event.type=null},_event_frame_close:function(d){if(this.event.type!==null){return}d.preventDefault();var f=this._frame_identify(d.target);var c=this;$(f.id).fadeOut("fast",function(){$(f.id).remove();delete c.frame_list[f.id];c.frame_counter--;c._panel_refresh(true);c._panel_animation_complete();if(c.visible&&c.frame_counter==0){c._panel_show_hide()}})},_event_frame_lock:function(c){if(this.event.type!==null){return}c.preventDefault();var d=this._frame_identify(c.target);if(d.grid_lock){d.grid_lock=false;$(d.id).find(".f-pin").removeClass("toggle");$(d.id).find(".f-header").removeClass("f-not-allowed");$(d.id).find(".f-title").removeClass("f-not-allowed");$(d.id).find(".f-resize").show();$(d.id).find(".f-close").show()}else{d.grid_lock=true;$(d.id).find(".f-pin").addClass("toggle");$(d.id).find(".f-header").addClass("f-not-allowed");$(d.id).find(".f-title").addClass("f-not-allowed");$(d.id).find(".f-resize").hide();$(d.id).find(".f-close").hide()}},_event_panel_load:function(c){if(this.event.type!==null){return}this._panel_show_hide()},_event_panel_active:function(c){if(this.event.type!==null){return}this._panel_active_disable()},_event_panel_scroll:function(c){if(this.event.type!==null||!this.visible){return}c.preventDefault();var d=c.originalEvent.detail?c.originalEvent.detail:c.originalEvent.wheelDelta/-3;this._panel_scroll(d)},_event_panel_scroll_up:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(-this.options.scroll)},_event_panel_scroll_down:function(c){if(this.event.type!==null){return}c.preventDefault();this._panel_scroll(this.options.scroll)},_frame_identify:function(c){return this.frame_list["#"+$(c).closest(".frame").attr("id")]},_frame_drag_start:function(d){this._frame_focus(d,true);var c=this._frame_screen(d);this._frame_resize(this.frame_shadow,c);this._frame_grid(this.frame_shadow,d.grid_location);d.grid_location=null;$(this.frame_shadow.id).show();$(".f-cover").show()},_frame_drag_stop:function(d){this._frame_focus(d,false);var c=this._frame_screen(this.frame_shadow);this._frame_resize(d,c);this._frame_grid(d,this.frame_shadow.grid_location,true);this.frame_shadow.grid_location=null;$(this.frame_shadow.id).hide();$(".f-cover").hide();this._panel_animation_complete()},_to_grid_coord:function(e,d){var c=(e=="width"||e=="height")?1:-1;if(e=="top"){d-=this.top}return parseInt((d+c*this.options.margin)/this.options.cell,10)},_to_pixel_coord:function(e,f){var c=(e=="width"||e=="height")?1:-1;var d=(f*this.options.cell)-c*this.options.margin;if(e=="top"){d+=this.top}return d},_to_grid:function(c){return{top:this._to_grid_coord("top",c.top),left:this._to_grid_coord("left",c.left),width:this._to_grid_coord("width",c.width),height:this._to_grid_coord("height",c.height)}},_to_pixel:function(c){return{top:this._to_pixel_coord("top",c.top),left:this._to_pixel_coord("left",c.left),width:this._to_pixel_coord("width",c.width),height:this._to_pixel_coord("height",c.height)}},_is_collision:function(e){function c(h,g){return !(h.left>g.left+g.width-1||h.left+h.width-1g.top+g.height-1||h.top+h.height-1l?1:0)});for(g=0;g
                        '},_template_frame:function(f,e,c,d){if(!e){e=""}if(c=="url"){d=''}return'
                        '+e+'
                        '+d+'
                        '},_template_shadow:function(c){return'
                        '},_template_background:function(){return'
                        '},_template_menu:function(){return'
                        '}});return{GalaxyFrame:a}}); \ No newline at end of file diff --git a/static/scripts/packed/galaxy.masthead.js b/static/scripts/packed/galaxy.masthead.js index a95706b1eb7..721a60a67ba 100644 --- a/static/scripts/packed/galaxy.masthead.js +++ b/static/scripts/packed/galaxy.masthead.js @@ -1 +1 @@ -define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;window.onbeforeunload=function(){var g="";for(key in d.list){if(d.list[key].options.on_unload){var f=d.list[key].options.on_unload();if(f){g+=f+" "}}}if(g!=""){return g}}},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){return''}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,on_click:function(){alert("clicked")},on_unload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.on_click);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='
                        ';if(e.with_number){d+='
                        '}d+="
                        ";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,on_unload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please log in or register to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'
                      • '+d.title+"
                        • "},_templateMenu:function(){return'
                          '},_templateDivider:function(){return'
                        • '},_template:function(e){var d='';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({el_masthead:"#everything",options:null,$background:null,list:[],initialize:function(e){this.options=e;$("body").off();this.setElement($(this._template(e)));$(this.el_masthead).append($(this.el));this.$background=$(this.el).find("#masthead-background");var d=this;$(window).on("beforeunload",function(){var g="";for(key in d.list){if(d.list[key].options.onunload){var f=d.list[key].options.onunload();if(f){g+=f+" "}}}if(g!=""){return g}})},events:{click:"_click",mousedown:function(d){d.preventDefault()}},append:function(d){return this._add(d,true)},prepend:function(d){return this._add(d,false)},highlight:function(e){var d=$(this.el).find("#"+e+"> li");if(d){d.addClass("active")}},_add:function(g,e){var d=$(this.el).find("#"+g.location);if(d){var f=$(g.el);f.addClass("masthead-item");if(e){d.append(f)}else{d.prepend(f)}this.list.push(g)}return null},_click:function(g){var f=$(this.el).find(".popup");if(f){f.hide()}var d=$(g.target).closest(".masthead-item").find(".popup");if($(g.target).hasClass("head")){d.show();this.$background.show()}else{this.$background.hide()}},_template:function(d){return''}});var b=Backbone.View.extend({options:{id:"",icon:"fa-cog",tooltip:"",with_number:false,onclick:function(){alert("clicked")},onunload:null,visible:true},location:"iconbar",initialize:function(e){if(e){this.options=_.defaults(e,this.options)}this.setElement($(this._template(this.options)));var d=this;$(this.el).find(".icon").tooltip({title:this.options.tooltip,placement:"bottom"}).on("mouseup",d.options.onclick);if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},icon:function(d){$(this.el).find(".icon").removeClass(this.options.icon).addClass(d);this.options.icon=d},toggle:function(){$(this.el).addClass("toggle")},untoggle:function(){$(this.el).removeClass("toggle")},number:function(d){$(this.el).find(".number").text(d)},_template:function(e){var d='
                          ';if(e.with_number){d+='
                          '}d+="
                          ";return d}});var c=Backbone.View.extend({options:{id:"",title:"",target:"_parent",content:"",type:"url",scratchbook:false,onunload:null,visible:true,disabled:false,title_attribute:""},location:"navbar",$menu:null,events:{"click .head":"_head"},initialize:function(d){if(d){this.options=_.defaults(d,this.options)}if(this.options.content&&this.options.content.indexOf("//")===-1){this.options.content=galaxy_config.root+this.options.content}this.setElement($(this._template(this.options)));if(this.options.disabled){$(this.el).find(".root").addClass("disabled");this._attachPopover()}if(!this.options.visible){this.hide()}},show:function(){$(this.el).css({visibility:"visible"})},hide:function(){$(this.el).css({visibility:"hidden"})},add:function(f){var g={title:"Title",content:"",type:"url",target:"_parent",scratchbook:false,divider:false};if(f){g=_.defaults(f,g)}if(g.content&&g.content.indexOf("//")===-1){g.content=galaxy_config.root+g.content}if(!this.$menu){$(this.el).find(".root").append(this._templateMenu());$(this.el).find(".symbol").addClass("caret");this.$menu=$(this.el).find(".popup")}var e=$(this._templateMenuItem(g));this.$menu.append(e);var d=this;e.on("click",function(h){h.preventDefault();if(d.options.target==="_blank"){return true}Galaxy.frame.add(f)});if(g.divider){this.$menu.append($(this._templateDivider()))}},_head:function(d){d.preventDefault();if(this.options.disabled){return}if(!this.$menu){Galaxy.frame.add(this.options)}},_attachPopover:function(){var d=$(this.el).find(".head");d.popover({html:true,content:'Please log in or register to use this feature.',placement:"bottom"}).on("shown.bs.popover",function(){setTimeout(function(){d.popover("hide")},5000)})},_templateMenuItem:function(d){return'
                        • '+d.title+"
                          • "},_templateMenu:function(){return'
                            '},_templateDivider:function(){return'
                          • '},_template:function(e){var d='';return d}});return{GalaxyMasthead:a,GalaxyMastheadTab:c,GalaxyMastheadIcon:b}}); \ No newline at end of file diff --git a/static/scripts/packed/mvc/upload/upload-view.js b/static/scripts/packed/mvc/upload/upload-view.js index a03c17ef7e0..9df9ece6a00 100644 --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1 +1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;window.onbeforeunload=function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}}},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");if(h){g.css({width:h+"%"})}else{g.css({width:"0%"})}},_template:function(g){return'
                             '+g.label+"
                            "}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Upload files",label:"Upload",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|NAME"]=l;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                            Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'
                            '}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;$(window).on("beforeunload",function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}})},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");if(h){g.css({width:h+"%"})}else{g.css({width:"0%"})}},_template:function(g){return'
                             '+g.label+"
                            "}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Upload files",label:"Upload",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|NAME"]=l;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                            Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'
                            '}})}); \ No newline at end of file From b14682397ee1c3c90da76808070e607d94ca93ee Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Sun, 19 Jan 2014 12:22:38 -0500 Subject: [PATCH 0836/1033] Upload: Update progress button --- static/scripts/mvc/upload/upload-view.js | 8 +------- static/scripts/packed/mvc/upload/upload-view.js | 2 +- 2 files changed, 2 insertions(+), 8 deletions(-) diff --git a/static/scripts/mvc/upload/upload-view.js b/static/scripts/mvc/upload/upload-view.js index 5f108c6da1a..f384fef9ef9 100644 --- a/static/scripts/mvc/upload/upload-view.js +++ b/static/scripts/mvc/upload/upload-view.js @@ -84,13 +84,7 @@ var ProgressButton = Backbone.View.extend({ // set percentage _percentage: function(value) { var $el = this.$el.find('.progress-bar'); - if (value) { - // change to new percentage - $el.css({ width : value + '%' }); - } else { - // reset without transition - $el.css({ width : '0%' }); - } + $el.css({ width : value + '%' }); }, // template diff --git a/static/scripts/packed/mvc/upload/upload-view.js b/static/scripts/packed/mvc/upload/upload-view.js index 9df9ece6a00..921ed615b2b 100644 --- a/static/scripts/packed/mvc/upload/upload-view.js +++ b/static/scripts/packed/mvc/upload/upload-view.js @@ -1 +1 @@ -define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;$(window).on("beforeunload",function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}})},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");if(h){g.css({width:h+"%"})}else{g.css({width:"0%"})}},_template:function(g){return'
                             '+g.label+"
                            "}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Upload files",label:"Upload",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|NAME"]=l;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                            Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'
                            '}})}); \ No newline at end of file +define(["galaxy.modal","utils/utils","mvc/upload/upload-model","mvc/upload/upload-row","mvc/ui","utils/uploadbox"],function(c,f,e,d){var b=Backbone.Model.extend({defaults:{percentage:0,icon:"fa-circle",label:"",status:""}});var a=Backbone.View.extend({model:null,initialize:function(h){var g=this;this.model=h;this.options=this.model.attributes;this.setElement(this._template(this.options));$(this.el).on("click",this.options.onclick);if(this.options.tooltip){$(this.el).tooltip({title:this.options.tooltip,placement:"bottom"})}this.model.on("change:percentage",function(){g._percentage(g.model.get("percentage"))});this.model.on("change:status",function(){g._status(g.model.get("status"))});var g=this;$(window).on("beforeunload",function(){var i="";if(g.options.onunload){i=g.options.onunload()}if(i!=""){return i}})},_status:function(h){var g=this.$el.find(".progress-bar");g.removeClass();g.addClass("progress-bar");g.addClass("progress-bar-notransition");if(h!=""){g.addClass("progress-bar-"+h)}},_percentage:function(h){var g=this.$el.find(".progress-bar");g.css({width:h+"%"})},_template:function(g){return'
                             '+g.label+"
                            "}});return Backbone.View.extend({modal:null,button_show:null,uploadbox:null,current_history:null,upload_size:0,select_extension:[["Auto-detect","auto"]],select_genome:[["Unspecified (?)","?"]],collection:new e.Collection(),counter:{announce:0,success:0,error:0,running:0,reset:function(){this.announce=this.success=this.error=this.running=0}},options:{nginx_upload_path:""},initialize:function(h){var g=this;if(!Galaxy.currHistoryPanel){window.setTimeout(function(){g.initialize()},500);return}if(!Galaxy.currUser.get("id")){return}this.button_show=new b({icon:"fa-upload",tooltip:"Upload files",label:"Upload",onclick:function(i){if(i){g._eventShow(i)}},onunload:function(){if(g.counter.running>0){return"Several uploads are still processing."}}});$("#left .unified-panel-header-inner").append((new a(this.button_show)).$el);var g=this;f.jsonFromUrl(galaxy_config.root+"api/datatypes",function(i){for(key in i){g.select_extension.push([i[key],i[key]])}});f.jsonFromUrl(galaxy_config.root+"api/genomes",function(i){var j=g.select_genome[0];g.select_genome=[];for(key in i){if(i[key].length>1){if(i[key][1]!==j[1]){g.select_genome.push(i[key])}}}g.select_genome.sort(function(l,k){return l[0]>k[0]?1:l[0]0)){return null}this.uploadbox.configure({url:this.options.nginx_upload_path,paramname:"files_0|file_data"});tool_input={};tool_input.dbkey=n;tool_input.file_type=h;tool_input["files_0|NAME"]=l;tool_input["files_0|type"]="upload_dataset";tool_input["files_0|url_paste"]=m;tool_input.space_to_tabs=j;data={};data.history_id=this.current_history;data.tool_id="upload1";data.inputs=JSON.stringify(tool_input);return data},_eventProgress:function(h,i,g){var j=this.collection.get(h);j.set("percentage",g);this.button_show.set("percentage",this._upload_percentage(g,i.size))},_eventSuccess:function(h,i,k){var j=this.collection.get(h);j.set("status","success");var g=j.get("file_size");this.button_show.set("percentage",this._upload_percentage(100,g));this.upload_completed+=g*100;this.counter.announce--;this.counter.success++;this._updateScreen();Galaxy.currHistoryPanel.refreshHdas()},_eventError:function(g,h,j){var i=this.collection.get(g);i.set("status","error");i.set("info",j);this.button_show.set("percentage",this._upload_percentage(100,h.size));this.button_show.set("status","danger");this.upload_completed+=h.size*100;this.counter.announce--;this.counter.error++;this._updateScreen()},_eventComplete:function(){this.collection.each(function(g){if(g.get("status")=="queued"){g.set("status","init")}});this.counter.running=0;this._updateScreen()},_eventCreate:function(){this.uploadbox.add([{name:"New File",size:-1}])},_eventStart:function(){if(this.counter.announce==0||this.counter.running>0){return}var g=this;this.upload_size=0;this.upload_completed=0;this.collection.each(function(h){if(h.get("status")=="init"){h.set("status","queued");g.upload_size+=h.get("file_size")}});this.button_show.set("percentage",0);this.button_show.set("status","success");this.current_history=Galaxy.currHistoryPanel.model.get("id");this.counter.running=this.counter.announce;this._updateScreen();this.uploadbox.start()},_eventStop:function(){if(this.counter.running==0){return}this.button_show.set("status","info");this.uploadbox.stop();$("#upload-info").html("Queue will pause after completing the current file...")},_eventReset:function(){if(this.counter.running==0){this.collection.reset();this.counter.reset();this._updateScreen();this.uploadbox.reset();this.button_show.set("percentage",0)}},_updateScreen:function(){if(this.counter.announce==0){if(this.uploadbox.compatible()){message="Drag&drop files into this box or click 'Select' to select files!"}else{message="Unfortunately, your browser does not support multiple file uploads or drag&drop.
                            Please upgrade to i.e. Firefox 4+, Chrome 7+, IE 10+, Opera 12+ or Safari 6+."}}else{if(this.counter.running==0){message="You added "+this.counter.announce+" file(s) to the queue. Add more files or click 'Upload' to proceed."}else{message="Please wait..."+this.counter.announce+" out of "+this.counter.running+" remaining."}}$("#upload-info").html(message);if(this.counter.running==0&&this.counter.announce+this.counter.success+this.counter.error>0){this.modal.enableButton("Reset")}else{this.modal.disableButton("Reset")}if(this.counter.running==0&&this.counter.announce>0){this.modal.enableButton("Upload")}else{this.modal.disableButton("Upload")}if(this.counter.running>0){this.modal.enableButton("Pause")}else{this.modal.disableButton("Pause")}if(this.counter.running==0){this.modal.enableButton("Select");this.modal.enableButton("Create")}else{this.modal.disableButton("Select");this.modal.disableButton("Create")}if(this.counter.announce+this.counter.success+this.counter.error>0){$(this.el).find("table").show()}else{$(this.el).find("table").hide()}},_upload_percentage:function(g,h){return(this.upload_completed+(g*h))/this.upload_size},_template:function(h,g){return'
                            '}})}); \ No newline at end of file From 7427cf16cd960f57b8376aca48bc1c10a2c4c233 Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Sun, 19 Jan 2014 13:11:46 -0500 Subject: [PATCH 0837/1033] UI: Unifiy icon button toggle color --- static/style/blue/base.css | 6 +++--- static/style/src/less/base.less | 2 +- static/style/src/less/frame.less | 4 ++-- static/style/src/less/upload.less | 7 ++----- 4 files changed, 8 insertions(+), 11 deletions(-) diff --git a/static/style/blue/base.css b/static/style/blue/base.css index 45811c86bf3..66cf83b16e6 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1234,10 +1234,10 @@ label{font-weight:normal} .select2-measure-scrollbar{position:absolute;top:-10000px;left:-10000px;width:100px;height:100px;overflow:scroll} @media only screen and (-webkit-min-device-pixel-ratio:1.5),only screen and (min-resolution:144dpi){.select2-search input,.select2-search-choice-close,.select2-container .select2-choice abbr,.select2-container .select2-choice .select2-arrow b{background-image:url('../images/select2x2.png') !important;background-repeat:no-repeat !important;background-size:60px 40px !important} .select2-search input{background-position:100% -21px !important}}.select2-container{min-width:256px} .galaxy-frame{}.galaxy-frame .corner{-moz-border-radius:5px;border-radius:5px} -.galaxy-frame .toggle{color:#BCC800} +.galaxy-frame .toggle{color:gold} .galaxy-frame .frame-background{z-index:1000;position:absolute;display:none;top:0px;left:0px;height:100%;width:100%;opacity:0.6;background:#000;overflow:auto} .galaxy-frame .frame-shadow{z-index:1001;position:absolute;display:none;top:0px;left:0px;opacity:0.5;background:#2c3143;border:1px solid #888} -.galaxy-frame .frame-menu{z-index:1005;position:absolute;cursor:pointer;color:#BCC800;right:10px} +.galaxy-frame .frame-menu{z-index:1005;position:absolute;cursor:pointer;color:gold;right:10px} .galaxy-frame .frame-scroll-up{top:50px} .galaxy-frame .frame-scroll-down{bottom:20px} .galaxy-frame .frame{z-index:1002;overflow:hidden;position:absolute;background:#fff;border:1px solid #888;-webkit-box-shadow:0 0 5px rgba(0,0,0,0.3);}.galaxy-frame .frame .f-content{position:absolute;overflow:hidden;background:#fff;border:none;top:24px;bottom:3px;left:3px;right:3px} @@ -1370,7 +1370,7 @@ div.unified-panel-body{position:absolute;top:30px;bottom:0;width:100%} #masthead .navbar-brand a{color:white;text-decoration:none} #masthead .iconbar{position:absolute;top:5px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 10px;height:26px} #masthead .iconbar .symbol .number{font-weight:bold;font-size:10px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;position:relative;left:23px;top:-12px} -#masthead .iconbar .toggle{color:#BCC800} +#masthead .iconbar .toggle{color:gold} .quota-meter-container{position:absolute;top:0;right:0;height:32px} .quota-meter{position:absolute;top:8px;right:8px;height:16px;width:100px;background-color:#f5f5f5} .quota-meter-bar{position:absolute;top:0;left:0;height:16px;background-color:#5f6990} diff --git a/static/style/src/less/base.less b/static/style/src/less/base.less index ad6f34a3f3f..5bf71cf9bf3 100644 --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -448,7 +448,7 @@ div.unified-panel-body { .toggle { - color : #BCC800; + color : gold; } } } diff --git a/static/style/src/less/frame.less b/static/style/src/less/frame.less index 63777a3a0ed..453fffefa76 100644 --- a/static/style/src/less/frame.less +++ b/static/style/src/less/frame.less @@ -8,7 +8,7 @@ .toggle { - color: #BCC800; + color: gold; } .frame-background @@ -45,7 +45,7 @@ z-index : @zindex-navbar + 5; position : absolute; cursor : pointer; - color : #BCC800; + color : gold; right : 10px; } diff --git a/static/style/src/less/upload.less b/static/style/src/less/upload.less index 6475afae0aa..6a1f43d519d 100644 --- a/static/style/src/less/upload.less +++ b/static/style/src/less/upload.less @@ -15,7 +15,6 @@ .progress-bar-success { background: @state-success-bg; - border : 0px; } @@ -32,14 +31,12 @@ } } -.upload-info -{ +.upload-info { font-weight: normal; text-align: center; } -.upload-box -{ +.upload-box { width : 100%; height : 95%; text-align : center; From 164d6093632302cc3dd7e97c840ffba2d723d17c Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Mon, 20 Jan 2014 10:28:59 -0500 Subject: [PATCH 0838/1033] Scratchbook: Make UI buttons smaller --- .../plugins/visualizations/charts/static/charts/bardiagram.js | 3 +-- static/style/blue/base.css | 2 +- static/style/src/less/base.less | 3 ++- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/config/plugins/visualizations/charts/static/charts/bardiagram.js b/config/plugins/visualizations/charts/static/charts/bardiagram.js index 9c3dd545d99..06dbd7eeeea 100644 --- a/config/plugins/visualizations/charts/static/charts/bardiagram.js +++ b/config/plugins/visualizations/charts/static/charts/bardiagram.js @@ -1,5 +1,5 @@ // dependencies -define(['library/utils'], function(Utils) { +define([], function() { // widget return Backbone.View.extend( @@ -8,7 +8,6 @@ return Backbone.View.extend( initialize: function(app, options) { this.app = app; this.options = options; - this.chart = options.chart; }, // render diff --git a/static/style/blue/base.css b/static/style/blue/base.css index 66cf83b16e6..15989e42b7e 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1368,7 +1368,7 @@ div.unified-panel-body{position:absolute;top:30px;bottom:0;width:100%} #masthead li.dropdown>a:hover .caret{border-top-color:gold;border-bottom-color:gold} #masthead .navbar-brand{position:absolute;left:0;top:0;font-family:verdana;font-weight:bold;font-size:20px;line-height:1;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000}#masthead .navbar-brand img{display:inline;width:26px;vertical-align:top} #masthead .navbar-brand a{color:white;text-decoration:none} -#masthead .iconbar{position:absolute;top:5px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 10px;height:26px} +#masthead .iconbar{position:absolute;top:7px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 10px;height:26px;font-size:11px} #masthead .iconbar .symbol .number{font-weight:bold;font-size:10px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;position:relative;left:23px;top:-12px} #masthead .iconbar .toggle{color:gold} .quota-meter-container{position:absolute;top:0;right:0;height:32px} diff --git a/static/style/src/less/base.less b/static/style/src/less/base.less index 5bf71cf9bf3..1cc8ec30166 100644 --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -423,7 +423,7 @@ div.unified-panel-body { .iconbar { position : absolute; - top : 5px; + top : 7px; right : 110px; cursor : pointer; color : @gray-light; @@ -434,6 +434,7 @@ div.unified-panel-body { float : left; margin : 0px 10px; height : 26px; + font-size : 11px; } .symbol .number From 323a7c57c718b5c753203cfc6fa4a7f7ceb0ccd9 Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 20 Jan 2014 08:35:50 -0600 Subject: [PATCH 0839/1033] Fix for b1121a315205e8152d9c59199443c492340e9f0b. That did not work in Bjoern's setup for reasons that still are eluding me - but this variant works and is less hacky, more readable anyway. --- tools/data_source/upload.xml | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/tools/data_source/upload.xml b/tools/data_source/upload.xml index a0520d5a225..f9aea6df629 100644 --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -38,12 +38,15 @@ - - + + + From 969c3bbfd65d8bd2a6d650c1e7d6acc45ab507a6 Mon Sep 17 00:00:00 2001 From: Dave Bouvier Date: Mon, 20 Jan 2014 10:58:28 -0500 Subject: [PATCH 0840/1033] Correctly specify the location for the check file that indicates completion of stage 1. --- install_and_test_tool_shed_repositories.sh | 15 ++++++++++----- 1 file changed, 10 insertions(+), 5 deletions(-) diff --git a/install_and_test_tool_shed_repositories.sh b/install_and_test_tool_shed_repositories.sh index 0f29f715cb8..9273ec3c6f2 100644 --- a/install_and_test_tool_shed_repositories.sh +++ b/install_and_test_tool_shed_repositories.sh @@ -22,6 +22,11 @@ if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY ] ; then exit 1 fi +if [ -z $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR ] ; then + echo "This script requires the GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR environment variable to be set to your configured tool dependency path." + exit 1 +fi + if [ -z $GALAXY_INSTALL_TEST_TOOL_SHED_URL ] ; then echo "This script requires the GALAXY_INSTALL_TEST_TOOL_SHED_URL environment variable to be set and non-empty." exit 1 @@ -45,8 +50,8 @@ fi test_tool_dependency_definitions () { # Test installation of repositories of type tool_dependency_definition. - if [ -f /ToolDepsTest/stage_1_complete ] ; then - rm /ToolDepsTest/stage_1_complete + if [ -f $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR/stage_1_complete ] ; then + rm $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR/stage_1_complete fi echo "Starting stage 1, tool dependency definitions." python test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py $* -v --with-nosehtml --html-report-file \ @@ -54,11 +59,11 @@ test_tool_dependency_definitions () { test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ test/functional/test_toolbox.py echo "Stage 1 complete, exit code $?" - touch /ToolDepsTest/stage_1_complete + touch $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR/stage_1_complete } test_repositories_with_tools () { - if [ ! -f /ToolDepsTest/stage_1_complete ] ; then + if [ ! -f $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR/stage_1_complete ] ; then echo 'Stage 1 did not complete its run, exiting.' exit 1 fi @@ -69,7 +74,7 @@ test_repositories_with_tools () { test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py \ test/functional/test_toolbox.py echo "Stage 2 complete, exit code $?" - rm /ToolDepsTest/stage_1_complete + rm $GALAXY_INSTALL_TEST_TOOL_DEPENDENCY_DIR/stage_1_complete } which='both' From 02e2a9979d6020cb572fc2c36bf0634df283a97b Mon Sep 17 00:00:00 2001 From: Aysam Guerler Date: Mon, 20 Jan 2014 11:00:47 -0500 Subject: [PATCH 0841/1033] Masthead: Adjust icon bar --- static/style/blue/base.css | 2 +- static/style/src/less/base.less | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/static/style/blue/base.css b/static/style/blue/base.css index 15989e42b7e..af80526cc43 100644 --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1368,7 +1368,7 @@ div.unified-panel-body{position:absolute;top:30px;bottom:0;width:100%} #masthead li.dropdown>a:hover .caret{border-top-color:gold;border-bottom-color:gold} #masthead .navbar-brand{position:absolute;left:0;top:0;font-family:verdana;font-weight:bold;font-size:20px;line-height:1;color:white;padding:5px 20px 12px;margin-left:-15px;z-index:2000}#masthead .navbar-brand img{display:inline;width:26px;vertical-align:top} #masthead .navbar-brand a{color:white;text-decoration:none} -#masthead .iconbar{position:absolute;top:7px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 10px;height:26px;font-size:11px} +#masthead .iconbar{position:absolute;top:6px;right:110px;cursor:pointer;color:#999;overflow:hidden}#masthead .iconbar .symbol{float:left;margin:0px 10px;height:26px;font-size:11px} #masthead .iconbar .symbol .number{font-weight:bold;font-size:10px;font-family:"Lucida Grande",verdana,arial,helvetica,sans-serif;position:relative;left:23px;top:-12px} #masthead .iconbar .toggle{color:gold} .quota-meter-container{position:absolute;top:0;right:0;height:32px} diff --git a/static/style/src/less/base.less b/static/style/src/less/base.less index 1cc8ec30166..4d13f788892 100644 --- a/static/style/src/less/base.less +++ b/static/style/src/less/base.less @@ -423,7 +423,7 @@ div.unified-panel-body { .iconbar { position : absolute; - top : 7px; + top : 6px; right : 110px; cursor : pointer; color : @gray-light; From 957e529b2aa18bab6d25dcdd2d46c0d7543f4c5b Mon Sep 17 00:00:00 2001 From: John Chilton Date: Mon, 20 Jan 2014 09:39:12 -0600 Subject: [PATCH 0842/1033] Fix small bug in handling of 'brand' text. This was changed in 5828950834e3c888683dbeb567e10bcaf335c94f, after that commit the brand was no longer preceeded by a / in the masthead the way it is in the title. I assume this was an oversite and not intentional, if intentional feel free to backout of this commit. --- static/scripts/galaxy.masthead.js | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/static/scripts/galaxy.masthead.js b/static/scripts/galaxy.masthead.js index 748b0d87b79..99243410c01 100644 --- a/static/scripts/galaxy.masthead.js +++ b/static/scripts/galaxy.masthead.js @@ -131,6 +131,7 @@ var GalaxyMasthead = Backbone.View.extend( // fill template _template: function(options) { + var brand_text = options.brand ? ("/ " + options.brand) : "" ; return '