mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge remote-tracking branch 'upstream/dev' into hashtags
This commit is contained in:
Dannon Baker
@@ -7,7 +7,7 @@ set -e
|
||||
# D3XX - Quoting issues.
|
||||
# D401 - First line should be in imperative mood
|
||||
# D403 - First word of the first line should be properly capitalized
|
||||
args="--ignore=D --select=D100,D201,D202,D206,D207,D208,D209,D211,D3,D401,D403"
|
||||
args="--ignore=D --select=D100,D201,D202,D206,D207,D208,D209,D211,D3,D403"
|
||||
|
||||
# If the first argument is --include, lint the modules expected to pass. If
|
||||
# the first argument is --exclude, lint all modules the full Galaxy linter lints
|
||||
|
||||
@@ -97,6 +97,12 @@ done;
|
||||
export GALAXY_TEST_SELENIUM_REMOTE=1
|
||||
export GALAXY_TEST_SELENIUM_REMOTE_PORT="${SELENIUM_PORT}"
|
||||
|
||||
# Retry all failed Selenium tests a second time to deal
|
||||
# with transiently failing tests. Failure information for
|
||||
# first tests is still populated in database/test_errors
|
||||
# and available at the top of the Jenkins test report.
|
||||
export GALAXY_TEST_SELENIUM_RETRIES=1
|
||||
|
||||
# Access Galaxy on localhost via port $GALAXY_PORT
|
||||
export GALAXY_TEST_PORT="${GALAXY_PORT}"
|
||||
|
||||
|
||||
@@ -16,7 +16,7 @@ following publications:
|
||||
a platform for interactive large-scale genome analysis."
|
||||
Genome Research. 2005 Oct; 15(10):1451-5.
|
||||
|
||||
See also: http://wiki.galaxyproject.org/CitingGalaxy
|
||||
See also: https://galaxyproject.org/citing-galaxy
|
||||
|
||||
|
||||
|
||||
|
||||
@@ -69,6 +69,18 @@ window.app = function app( options, bootstrapped ){
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||||
Galaxy.currHistoryPanel = historyPanel.historyView;
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||||
Galaxy.currHistoryPanel.listenToGalaxy( Galaxy );
|
||||
|
||||
var routingMessage = Backbone.View.extend({
|
||||
initialize: function(options) {
|
||||
this.message = options.message || "Undefined Message";
|
||||
this.msg_status = options.type || 'info';
|
||||
this.render();
|
||||
},
|
||||
render: function(){
|
||||
this.$el.html(_.escape(this.message)).addClass(this.msg_status + "message");
|
||||
}
|
||||
});
|
||||
|
||||
|
||||
// .................................................... routes
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||||
/** */
|
||||
Galaxy.router = new ( Backbone.Router.extend({
|
||||
@@ -98,7 +110,7 @@ window.app = function app( options, bootstrapped ){
|
||||
if ( this.authenticate( args, name ) ) {
|
||||
callback.apply( this, args );
|
||||
} else {
|
||||
this.push( Galaxy.root );
|
||||
this.loginRequired();
|
||||
}
|
||||
}
|
||||
},
|
||||
@@ -117,6 +129,10 @@ window.app = function app( options, bootstrapped ){
|
||||
'show_user_form'
|
||||
],
|
||||
|
||||
loginRequired: function() {
|
||||
centerPanel.display( new routingMessage({type: 'error', message: "You must be logged in to make this request."}) );
|
||||
},
|
||||
|
||||
authenticate: function( args, name ) {
|
||||
return ( Galaxy.user && Galaxy.user.id ) || this.require_login.indexOf( name ) == -1;
|
||||
},
|
||||
@@ -209,4 +225,4 @@ window.app = function app( options, bootstrapped ){
|
||||
pushState : true,
|
||||
});
|
||||
});
|
||||
};
|
||||
};
|
||||
|
||||
@@ -151,7 +151,7 @@ var CitationListView = Backbone.View.extend({
|
||||
' citations explicitly at this time. When writing up your analysis, please manually',
|
||||
' review your histories and find all references',
|
||||
' that should be cited in order to completely describe your work. Also, please remember to',
|
||||
' <a href="https://wiki.galaxyproject.org/CitingGalaxy">cite Galaxy</a>.',
|
||||
' <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.',
|
||||
'</div>',
|
||||
].join('');
|
||||
} else {
|
||||
|
||||
@@ -386,7 +386,7 @@ var FolderListView = Backbone.View.extend({
|
||||
'</table>',
|
||||
'<div class="empty-folder-message" style="display:none;">',
|
||||
'This folder is either empty or you do not have proper access permissions to see the contents. If you expected something to show up',
|
||||
' please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a>',
|
||||
' please consult the <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',
|
||||
' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',
|
||||
'</div>'
|
||||
].join(''));
|
||||
|
||||
@@ -1151,7 +1151,7 @@ var FolderToolbarView = Backbone.View.extend({
|
||||
' Details',
|
||||
'</button>',
|
||||
'<span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki">',
|
||||
'<a href="https://wiki.galaxyproject.org/DataLibraries/screen/FolderContents" target="_blank">',
|
||||
'<a href="https://galaxyproject.org/data-libraries/screen/folder-contents/" target="_blank">',
|
||||
'<button class="primary-button" type="button">',
|
||||
'<span class="fa fa-question-circle"></span>',
|
||||
' Help',
|
||||
|
||||
@@ -232,7 +232,7 @@ var LibraryListView = Backbone.View.extend({
|
||||
'<% } else{ %>',
|
||||
'<div>',
|
||||
'There are no libraries visible to you here. If you expected some to show up please consult the',
|
||||
' <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a>',
|
||||
' <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',
|
||||
' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',
|
||||
'</div>',
|
||||
'<% }%>',
|
||||
|
||||
@@ -192,7 +192,7 @@ var LibraryToolbarView = Backbone.View.extend({
|
||||
'</span>',
|
||||
'<% } %>',
|
||||
'<span class="help-button" data-toggle="tooltip" data-placement="top" title="Visit Libraries Wiki">',
|
||||
'<a href="https://wiki.galaxyproject.org/DataLibraries/screen/ListOfLibraries" target="_blank">',
|
||||
'<a href="https://galaxyproject.org/data-libraries/screen/list-of-libraries/" target="_blank">',
|
||||
'<button class="primary-button" type="button"><span class="fa fa-question-circle"></span> Help</button>',
|
||||
'</a>',
|
||||
'</span>',
|
||||
|
||||
@@ -279,7 +279,7 @@ define( [ 'utils/utils', 'utils/deferred', 'mvc/ui/ui-misc', 'mvc/form/form-view
|
||||
_.each( options.requirements, function( req, i ) {
|
||||
requirements_message += req.name + ( req.version ? ' (Version ' + req.version + ')' : '' ) + ( i < nreq - 2 ? ', ' : ( i == nreq - 2 ? ' and ' : '' ) );
|
||||
});
|
||||
var requirements_link = $( '<a/>' ).attr( 'target', '_blank' ).attr( 'href', 'https://wiki.galaxyproject.org/Tools/Requirements' ).text( 'here' );
|
||||
var requirements_link = $( '<a/>' ).attr( 'target', '_blank' ).attr( 'href', 'https://galaxyproject.org/tools/requirements/' ).text( 'here' );
|
||||
return $( '<span/>' ).append( requirements_message + '. Click ' ).append( requirements_link ).append( ' for more information.' );
|
||||
}
|
||||
return 'No requirements found.';
|
||||
|
||||
@@ -153,7 +153,7 @@ define( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) {
|
||||
return '<p class="ui-panel-footer">' +
|
||||
'You are using <strong>' + options.nice_total_disk_usage + '</strong> of disk space in this Galaxy instance. ' +
|
||||
( Galaxy.config.enable_quotas ? 'Your disk quota is: <strong>' + options.quota + '</strong>. ' : '' ) +
|
||||
'Is your usage more than expected? See the <a href="https://wiki.galaxyproject.org/Learn/ManagingDatasets" target="_blank">documentation</a> for tips on how to find all of the data in your account.' +
|
||||
'Is your usage more than expected? See the <a href="https://galaxyproject.org/learn/managing-datasets/" target="_blank">documentation</a> for tips on how to find all of the data in your account.' +
|
||||
'</p>';
|
||||
}
|
||||
});
|
||||
|
||||
@@ -151,7 +151,7 @@ define( [ 'utils/utils', 'mvc/form/form-view', 'mvc/tool/tool-form-base' ], func
|
||||
type : 'text',
|
||||
value : '',
|
||||
ignore : '',
|
||||
help : 'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>' + input_terminal_names.join(', ') + '</strong>.'
|
||||
help : 'This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid inputs are: <strong>' + input_terminal_names.join(', ') + '</strong>.'
|
||||
},{
|
||||
action : 'ChangeDatatypeAction',
|
||||
pja_arg : 'newtype',
|
||||
|
||||
@@ -741,7 +741,7 @@ var HeaderButtons = Backbone.View.extend({
|
||||
$("#nodeSelectionView").show();
|
||||
} },
|
||||
{ icon_class: 'information', title: 'Phyloviz Help', on_click: function() {
|
||||
window.open('https://wiki.galaxyproject.org/Learn/Visualization/PhylogeneticTree');
|
||||
window.open('https://galaxyproject.org/learn/visualization/phylogenetic-tree/');
|
||||
// https://docs.google.com/document/d/1AXFoJgEpxr21H3LICRs3EyMe1B1X_KFPouzIgrCz3zk/edit
|
||||
} }
|
||||
],
|
||||
|
||||
+21
-19
@@ -11,9 +11,10 @@
|
||||
# values are set to the default value. Relative paths are relative to the root
|
||||
# Galaxy directory.
|
||||
#
|
||||
# Examples of many of these options are explained in more detail in the wiki:
|
||||
# Examples of many of these options are explained in more detail in the Galaxy
|
||||
# Community Hub.
|
||||
#
|
||||
# https://wiki.galaxyproject.org/Admin/Config
|
||||
# https://galaxyproject.org/admin/config
|
||||
#
|
||||
# Config hackers are encouraged to check there before asking for help.
|
||||
|
||||
@@ -179,7 +180,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
|
||||
# Path to the directory in which tool dependencies are placed. This is used by
|
||||
# the Tool Shed to install dependencies and can also be used by administrators
|
||||
# to manually install or link to dependencies. For details, see:
|
||||
# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies
|
||||
# https://galaxyproject.org/admin/config/tool-dependencies
|
||||
# Set the string to None to explicitly disable tool dependency handling.
|
||||
# If this option is set to none or an invalid path, installing tools with dependencies
|
||||
# from the Tool Shed will fail.
|
||||
@@ -305,9 +306,9 @@ paste.app_factory = galaxy.web.buildapp:app_factory
|
||||
# applied to the ToolDataTableManager at server start up.
|
||||
#shed_tool_data_table_config = config/shed_tool_data_table_conf.xml
|
||||
|
||||
# Directory where data used by tools is located, see the samples in that
|
||||
# directory and the wiki for help:
|
||||
# https://wiki.galaxyproject.org/Admin/DataIntegration
|
||||
# Directory where data used by tools is located. See the samples in that
|
||||
# directory and the Galaxy Community Hub for help:
|
||||
# https://galaxyproject.org/admin/data-integration
|
||||
#tool_data_path = tool-data
|
||||
|
||||
# Directory where Tool Data Table related files will be placed
|
||||
@@ -483,7 +484,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
|
||||
|
||||
# URL of the support resource for the galaxy instance. Used in activation
|
||||
# emails.
|
||||
#instance_resource_url = https://wiki.galaxyproject.org/
|
||||
#instance_resource_url = https://galaxyproject.org/
|
||||
|
||||
# E-mail domains blacklist is used for filtering out users that are using
|
||||
# disposable email address during the registration. If their address domain
|
||||
@@ -544,7 +545,7 @@ paste.app_factory = galaxy.web.buildapp:app_factory
|
||||
# bypass security to display datasets. Please be aware that there are security
|
||||
# implications if this is allowed. More details (including required changes to
|
||||
# the proxy server config) are available in the Apache proxy documentation on
|
||||
# the wiki.
|
||||
# the Galaxy Community Hub.
|
||||
#
|
||||
# The list of servers in this sample config are for the UCSC Main, Test and
|
||||
# Archaea browsers, but the default if left commented is to not allow any
|
||||
@@ -615,19 +616,19 @@ nglims_config_file = tool-data/nglims.yaml
|
||||
#logo_url = /
|
||||
|
||||
# The URL linked by the "Wiki" link in the "Help" menu.
|
||||
#wiki_url = https://wiki.galaxyproject.org/
|
||||
#wiki_url = https://galaxyproject.org/
|
||||
|
||||
# The URL linked by the "Support" link in the "Help" menu.
|
||||
#support_url = https://wiki.galaxyproject.org/Support
|
||||
#support_url = https://galaxyproject.org/support
|
||||
|
||||
# The URL linked by the "How to Cite Galaxy" link in the "Help" menu.
|
||||
#citation_url = https://wiki.galaxyproject.org/CitingGalaxy
|
||||
#citation_url = https://galaxyproject.org/citing-galaxy
|
||||
|
||||
# The URL linked by the "Search" link in the "Help" menu.
|
||||
#search_url = http://galaxyproject.org/search/usegalaxy/
|
||||
#search_url = https://galaxyproject.org/search/
|
||||
|
||||
# The URL linked by the "Mailing Lists" link in the "Help" menu.
|
||||
#mailing_lists_url = https://wiki.galaxyproject.org/MailingLists
|
||||
#mailing_lists_url = https://galaxyproject.org/mailing-lists
|
||||
|
||||
# The URL linked by the "Videos" link in the "Help" menu.
|
||||
#screencasts_url = https://vimeo.com/galaxyproject
|
||||
@@ -892,8 +893,9 @@ use_interactive = True
|
||||
|
||||
# -- Data Libraries
|
||||
|
||||
# These library upload options are described in much more detail in the wiki:
|
||||
# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles
|
||||
# These library upload options are described in much more detail in the Galaxy
|
||||
# Community Hub:
|
||||
# https://galaxyproject.org/data-libraries/
|
||||
|
||||
# Add an option to the library upload form which allows administrators to
|
||||
# upload a directory of files.
|
||||
@@ -979,7 +981,7 @@ use_interactive = True
|
||||
# User authentication can be delegated to an upstream proxy server (usually
|
||||
# Apache). The upstream proxy should set a REMOTE_USER header in the request.
|
||||
# Enabling remote user disables regular logins. For more information, see:
|
||||
# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy
|
||||
# https://galaxyproject.org/admin/config/apache-proxy
|
||||
#use_remote_user = False
|
||||
|
||||
# If use_remote_user is enabled and your external authentication
|
||||
@@ -1022,7 +1024,7 @@ use_interactive = True
|
||||
# users (email addresses). These users will have access to the Admin section
|
||||
# of the server, and will have access to create users, groups, roles,
|
||||
# libraries, and more. For more information, see:
|
||||
# https://wiki.galaxyproject.org/Admin/Interface
|
||||
# https://galaxyproject.org/admin/
|
||||
#admin_users = None
|
||||
|
||||
# Force everyone to log in (disable anonymous access).
|
||||
@@ -1213,7 +1215,7 @@ use_interactive = True
|
||||
# separate Galaxy into multiple processes. There are more than one way to do
|
||||
# this, and they are explained in detail in the documentation:
|
||||
#
|
||||
# https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling
|
||||
# https://galaxyproject.org/admin/config/performance/scaling
|
||||
|
||||
# By default, Galaxy manages and executes jobs from within a single process and
|
||||
# notifies itself of new jobs via in-memory queues. Jobs are run locally on
|
||||
@@ -1302,7 +1304,7 @@ use_interactive = True
|
||||
# actual user instead of as the user running the Galaxy server process. For
|
||||
# details on these options, see the documentation at:
|
||||
#
|
||||
# https://wiki.galaxyproject.org/Admin/Config/Performance/Cluster
|
||||
# https://galaxyproject.org/admin/config/performance/cluster
|
||||
#
|
||||
#drmaa_external_runjob_script = scripts/drmaa_external_runner.py
|
||||
#drmaa_external_killjob_script = scripts/drmaa_external_killer.py
|
||||
|
||||
@@ -45,6 +45,10 @@
|
||||
# inside your container to which Galaxy should connect the UI.
|
||||
#docker_connect_port = None
|
||||
|
||||
# Set the following value to false if Docker volumes between Galaxy server and Docker
|
||||
# container cannot or should not be used.
|
||||
#use_volumes = True
|
||||
|
||||
# To run containers in Docker Swarm mode on (an existing swarm), set the
|
||||
# following option to True *and*:
|
||||
# - set docker_connect_port above. For Jupyter the # port should most likely be
|
||||
|
||||
@@ -17,19 +17,26 @@ if ie_request.attr.PASSWORD_AUTH:
|
||||
else:
|
||||
PASSWORD = "none"
|
||||
|
||||
additional_ids = trans.request.params.get('additional_dataset_ids', None)
|
||||
|
||||
## Jupyter Notbook Specific
|
||||
if hda.datatype.__class__.__name__ == "Ipynb":
|
||||
DATASET_HID = hda.hid
|
||||
else:
|
||||
DATASET_HID = None
|
||||
if not additional_ids:
|
||||
additional_ids = str(trans.security.encode_id( hda.id ) )
|
||||
else:
|
||||
additional_ids += "," + trans.security.encode_id( hda.id )
|
||||
|
||||
# Add all environment variables collected from Galaxy's IE infrastructure
|
||||
ie_request.launch(
|
||||
image=trans.request.params.get('image_tag', None),
|
||||
additional_ids=trans.request.params.get('additional_dataset_ids', None),
|
||||
additional_ids=additional_ids if ie_request.use_volumes else None,
|
||||
env_override={
|
||||
'notebook_password': PASSWORD,
|
||||
'dataset_hid': DATASET_HID,
|
||||
'additional_ids': additional_ids if not ie_request.use_volumes else None,
|
||||
}
|
||||
)
|
||||
|
||||
|
||||
@@ -47,6 +47,10 @@ password_auth = True
|
||||
# inside your container to which Galaxy should connect the UI.
|
||||
#docker_connect_port = None
|
||||
|
||||
# Set the following value to false if Docker volumes between Galaxy server and Docker
|
||||
# container cannot or should not be used.
|
||||
#use_volumes = True
|
||||
|
||||
# To run containers in Docker Swarm mode on (an existing swarm), set the
|
||||
# following option to True *and*:
|
||||
# - set docker_connect_port above. For erasche/docker-rstudio-notebook the port
|
||||
|
||||
@@ -13,16 +13,23 @@ USERNAME = "rstudio"
|
||||
# Then override it again
|
||||
ie_request.notebook_pw = "rstudio"
|
||||
|
||||
additional_ids = trans.request.params.get('additional_dataset_ids', None)
|
||||
if not additional_ids:
|
||||
additional_ids = str(trans.security.encode_id( hda.id ) )
|
||||
else:
|
||||
additional_ids += "," + trans.security.encode_id( hda.id )
|
||||
|
||||
DATASET_HID = hda.hid
|
||||
|
||||
# Add all environment variables collected from Galaxy's IE infrastructure
|
||||
ie_request.launch(
|
||||
image=trans.request.params.get('image_tag', None),
|
||||
additional_ids=trans.request.params.get('additional_dataset_ids', None),
|
||||
additional_ids=additional_ids if ie_request.use_volumes else None,
|
||||
env_override={
|
||||
'notebook_username': USERNAME,
|
||||
'notebook_password': PASSWORD,
|
||||
'dataset_hid': DATASET_HID,
|
||||
'additional_ids': additional_ids if not ie_request.use_volumes else None,
|
||||
}
|
||||
)
|
||||
|
||||
|
||||
@@ -369,8 +369,9 @@ class Configuration( object ):
|
||||
self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) )
|
||||
self.message_box_content = kwargs.get( 'message_box_content', None )
|
||||
self.message_box_class = kwargs.get( 'message_box_class', 'info' )
|
||||
self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' )
|
||||
self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' )
|
||||
self.support_url = kwargs.get( 'support_url', 'https://galaxyproject.org/support' )
|
||||
self.citation_url = kwargs.get( 'citation_url', 'https://galaxyproject.org/citing-galaxy' )
|
||||
self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' )
|
||||
self.blog_url = kwargs.get( 'blog_url', None )
|
||||
self.screencasts_url = kwargs.get( 'screencasts_url', None )
|
||||
self.library_import_dir = kwargs.get( 'library_import_dir', None )
|
||||
|
||||
@@ -41,13 +41,12 @@ class ConfigSerializer( base.ModelSerializer ):
|
||||
'logo_src' : lambda i, k, **c: self.url_for( '/static/images/galaxyIcon_noText.png' ),
|
||||
'terms_url' : _defaults_to( '' ),
|
||||
|
||||
# TODO: don't hardcode here - hardcode defaults once in config.py
|
||||
'wiki_url' : _defaults_to( "http://galaxyproject.org/" ),
|
||||
'search_url' : _defaults_to( "http://galaxyproject.org/search/usegalaxy/" ),
|
||||
'mailing_lists' : _defaults_to( "https://wiki.galaxyproject.org/MailingLists" ),
|
||||
'wiki_url' : _defaults_to( self.app.config.wiki_url ),
|
||||
'search_url' : _defaults_to( self.app.config.wiki_url.rstrip("/") + "/search/" ),
|
||||
'mailing_lists' : _defaults_to( self.app.config.wiki_url.rstrip("/") + "/mailing-lists/"),
|
||||
'screencasts_url' : _defaults_to( "https://vimeo.com/galaxyproject" ),
|
||||
'citation_url' : _defaults_to( "https://wiki.galaxyproject.org/CitingGalaxy" ),
|
||||
'support_url' : _defaults_to( "https://wiki.galaxyproject.org/Support" ),
|
||||
'citation_url' : _defaults_to( self.app.config.citation_url ),
|
||||
'support_url' : _defaults_to( self.app.config.support_url ),
|
||||
'lims_doc_url' : _defaults_to( "https://usegalaxy.org/u/rkchak/p/sts" ),
|
||||
'biostar_url' : _defaults_to( '' ),
|
||||
'biostar_url_redirect' : lambda *a, **c: self.url_for( controller='biostar', action='biostar_redirect', qualified=True ),
|
||||
|
||||
@@ -37,7 +37,7 @@ class DataManagers( object ):
|
||||
continue
|
||||
self.load_from_xml( filename )
|
||||
if self.app.config.shed_data_manager_config_file:
|
||||
self.load_from_xml( self.app.config.shed_data_manager_config_file, store_tool_path=False, replace_existing=True )
|
||||
self.load_from_xml( self.app.config.shed_data_manager_config_file, store_tool_path=True, replace_existing=True )
|
||||
|
||||
def load_from_xml( self, xml_filename, store_tool_path=True, replace_existing=False ):
|
||||
try:
|
||||
@@ -57,7 +57,7 @@ class DataManagers( object ):
|
||||
tool_path = '.'
|
||||
self.tool_path = tool_path
|
||||
for data_manager_elem in root.findall( 'data_manager' ):
|
||||
self.load_manager_from_elem( data_manager_elem, replace_existing=replace_existing )
|
||||
self.load_manager_from_elem( data_manager_elem, tool_path=self.tool_path, replace_existing=replace_existing )
|
||||
|
||||
def load_manager_from_elem( self, data_manager_elem, tool_path=None, add_manager=True, replace_existing=False ):
|
||||
try:
|
||||
|
||||
@@ -248,6 +248,23 @@ class DatasetEmptyValidator( Validator ):
|
||||
raise ValueError( self.message )
|
||||
|
||||
|
||||
class DatasetExtraFilesPathEmptyValidator( Validator ):
|
||||
"""Validator that checks if a dataset's extra_files_path exists and is not empty."""
|
||||
def __init__( self, message=None ):
|
||||
self.message = message
|
||||
|
||||
@classmethod
|
||||
def from_element( cls, param, elem ):
|
||||
return cls( elem.get( 'message', None ) )
|
||||
|
||||
def validate( self, value, trans=None ):
|
||||
if value:
|
||||
if value.get_total_size() == value.get_size():
|
||||
if self.message is None:
|
||||
self.message = "The selected dataset's extra_files_path directory is empty or does not exist, this tool expects non-empty extra_files_path directories associated with the selected input."
|
||||
raise ValueError( self.message )
|
||||
|
||||
|
||||
class MetadataValidator( Validator ):
|
||||
"""
|
||||
Validator that checks for missing metadata
|
||||
@@ -438,6 +455,7 @@ validator_types = dict( expression=ExpressionValidator,
|
||||
no_options=NoOptionsValidator,
|
||||
empty_field=EmptyTextfieldValidator,
|
||||
empty_dataset=DatasetEmptyValidator,
|
||||
empty_extra_files_path=DatasetExtraFilesPathEmptyValidator,
|
||||
dataset_metadata_in_file=MetadataInFileColumnValidator,
|
||||
dataset_metadata_in_data_table=MetadataInDataTableColumnValidator,
|
||||
dataset_ok_validator=DatasetOkValidator, )
|
||||
|
||||
@@ -5153,6 +5153,7 @@ and ``bibtex`` are the only supported options.</xs:documentation>
|
||||
</xs:annotation>
|
||||
<xs:restriction base="xs:string">
|
||||
<xs:enumeration value="empty_dataset"/>
|
||||
<xs:enumeration value="empty_extra_files_path"/>
|
||||
<xs:enumeration value="expression"/>
|
||||
<xs:enumeration value="regex"/>
|
||||
<xs:enumeration value="in_range"/>
|
||||
|
||||
@@ -1041,7 +1041,7 @@ class Admin( object ):
|
||||
stop_msg += '.'
|
||||
for job_id in job_ids:
|
||||
error_msg = "This job was stopped by an administrator: %s <a href='%s' target='_blank'>Contact support</a> for additional help." \
|
||||
% ( stop_msg, self.app.config.get("support_url", "https://wiki.galaxyproject.org/Support" ) )
|
||||
% ( stop_msg, self.app.config.get("support_url", "https://galaxyproject.org/support/" ) )
|
||||
if trans.app.config.track_jobs_in_database:
|
||||
job = trans.sa_session.query( trans.app.model.Job ).get( job_id )
|
||||
job.stderr = error_msg
|
||||
|
||||
@@ -256,7 +256,7 @@ class InteractiveEnvironmentRequest(object):
|
||||
return dict([(key.upper(), item) for key, item in conf.items()])
|
||||
|
||||
def _get_import_volume_for_run(self):
|
||||
if self.attr.import_volume:
|
||||
if self.use_volumes and self.attr.import_volume:
|
||||
return '{temp_dir}:/import/'.format(temp_dir=self.temp_dir)
|
||||
return ''
|
||||
|
||||
@@ -272,7 +272,7 @@ class InteractiveEnvironmentRequest(object):
|
||||
env = self._get_env_for_run(env_override)
|
||||
import_volume_def = self._get_import_volume_for_run()
|
||||
env_str = ' '.join(['-e "%s=%s"' % (key, item) for key, item in env.items()])
|
||||
volume_str = ' '.join(['-v "%s"' % volume for volume in volumes])
|
||||
volume_str = ' '.join(['-v "%s"' % volume for volume in volumes]) if self.use_volumes else ''
|
||||
import_volume_str = '-v "{import_volume}"'.format(import_volume=import_volume_def) if import_volume_def else ''
|
||||
name = None
|
||||
# This is the basic docker command such as "sudo -u docker docker {docker_args}"
|
||||
@@ -298,6 +298,13 @@ class InteractiveEnvironmentRequest(object):
|
||||
)
|
||||
return command
|
||||
|
||||
@property
|
||||
def use_volumes(self):
|
||||
if self.attr.viz_config.has_option("docker", "use_volumes"):
|
||||
return string_as_bool_or_none(self.attr.viz_config.get("docker", "use_volumes"))
|
||||
else:
|
||||
return True
|
||||
|
||||
def container_run_args(self, image, env_override=None, volumes=None):
|
||||
if volumes is None:
|
||||
volumes = []
|
||||
@@ -434,6 +441,8 @@ class InteractiveEnvironmentRequest(object):
|
||||
:param volumes: dictionary of docker volume mounts
|
||||
|
||||
"""
|
||||
if volumes is None:
|
||||
volumes = []
|
||||
if image is None:
|
||||
image = self.default_image
|
||||
|
||||
|
||||
@@ -33,8 +33,7 @@ def get_message_for_no_shed_tool_config():
|
||||
message += 'tag that includes a tool_path attribute value which is a directory relative to the Galaxy installation directory in order to '
|
||||
message += 'automatically install tools from a tool shed into Galaxy (e.g., the file name shed_tool_conf.xml whose <toolbox> tag is '
|
||||
message += '<toolbox tool_path="../shed_tools">). For details, see the "Installation of Galaxy tool shed repository tools into a local '
|
||||
message += 'Galaxy instance" section of the Galaxy tool shed wiki at http://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy#'
|
||||
message += 'Installing_Galaxy_tool_shed_repository_tools_into_a_local_Galaxy_instance.'
|
||||
message += 'Galaxy instance" section of the Galaxy tool shed wiki at https://galaxyproject.org/installing-repositories-to-galaxy/'
|
||||
return message
|
||||
|
||||
|
||||
|
||||
@@ -961,7 +961,7 @@ class AdminToolshed( AdminGalaxy ):
|
||||
message += 'attribute value which is a directory relative to the Galaxy installation directory in order '
|
||||
message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> '
|
||||
message += 'whose <b><toolbox></b> tag is <b><toolbox tool_path="../shed_tools"></b>).<p/>See the '
|
||||
message += '<a href="https://wiki.galaxyproject.org/InstallingRepositoriesToGalaxy" target="_blank">Installation '
|
||||
message += '<a href="https://galaxyproject.org/installing-repositories-to-galaxy/" target="_blank">Installation '
|
||||
message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool '
|
||||
message += 'Shed wiki for all of the details.'
|
||||
return trans.show_error_message( message )
|
||||
|
||||
@@ -45,7 +45,7 @@ class Configuration( object ):
|
||||
self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) )
|
||||
self.message_box_content = kwargs.get( 'message_box_content', None )
|
||||
self.message_box_class = kwargs.get( 'message_box_class', 'info' )
|
||||
self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' )
|
||||
self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' )
|
||||
self.blog_url = kwargs.get( 'blog_url', None )
|
||||
self.screencasts_url = kwargs.get( 'screencasts_url', None )
|
||||
self.log_events = False
|
||||
|
||||
@@ -113,8 +113,8 @@ class Configuration( object ):
|
||||
self.message_box_visible = string_as_bool( kwargs.get( 'message_box_visible', False ) )
|
||||
self.message_box_content = kwargs.get( 'message_box_content', None )
|
||||
self.message_box_class = kwargs.get( 'message_box_class', 'info' )
|
||||
self.support_url = kwargs.get( 'support_url', 'https://wiki.galaxyproject.org/Support' )
|
||||
self.wiki_url = kwargs.get( 'wiki_url', 'https://wiki.galaxyproject.org/' )
|
||||
self.support_url = kwargs.get( 'support_url', 'https://galaxyproject.org/support' )
|
||||
self.wiki_url = kwargs.get( 'wiki_url', 'https://galaxyproject.org/' )
|
||||
self.blog_url = kwargs.get( 'blog_url', None )
|
||||
self.biostar_url = kwargs.get( 'biostar_url', None )
|
||||
self.screencasts_url = kwargs.get( 'screencasts_url', None )
|
||||
|
||||
@@ -14,16 +14,28 @@ class DataManagerHandler( object ):
|
||||
def __init__( self, app ):
|
||||
self.app = app
|
||||
|
||||
@property
|
||||
def data_managers_path( self ):
|
||||
tree, error_message = xml_util.parse_xml( self.app.config.shed_data_manager_config_file )
|
||||
if tree:
|
||||
root = tree.getroot()
|
||||
return root.get( 'tool_path', None )
|
||||
return None
|
||||
|
||||
def data_manager_config_elems_to_xml_file( self, config_elems, config_filename ):
|
||||
"""
|
||||
Persist the current in-memory list of config_elems to a file named by the value
|
||||
of config_filename.
|
||||
"""
|
||||
data_managers_path = self.data_managers_path
|
||||
lock = threading.Lock()
|
||||
lock.acquire( True )
|
||||
try:
|
||||
fh = open( config_filename, 'wb' )
|
||||
fh.write( '<?xml version="1.0"?>\n<data_managers>\n' )
|
||||
if data_managers_path is not None:
|
||||
fh.write( '<?xml version="1.0"?>\n<data_managers tool_path="%s">\n ' % data_managers_path )
|
||||
else:
|
||||
fh.write( '<?xml version="1.0"?>\n<data_managers>\n ' )
|
||||
for elem in config_elems:
|
||||
fh.write( xml_util.xml_to_string( elem ) )
|
||||
fh.write( '</data_managers>\n' )
|
||||
@@ -158,4 +170,4 @@ class DataManagerHandler( object ):
|
||||
self.app.data_managers.load_manager_from_elem( elem )
|
||||
# Persist the altered shed_data_manager_config file.
|
||||
if data_manager_config_has_changes:
|
||||
self.data_manager_config_elems_to_xml_file( config_elems, shed_data_manager_conf_filename )
|
||||
self.data_manager_config_elems_to_xml_file( config_elems, shed_data_manager_conf_filename )
|
||||
|
||||
@@ -112,6 +112,20 @@ address Docker exposes localhost on to its child containers. This trick
|
||||
doesn't work on Mac OS X and so GALAXY_TEST_HOST will need to be crafted
|
||||
carefully ahead of time.
|
||||
|
||||
For Selenium test cases a stack trace is usually insufficient to diagnose
|
||||
problems. For this reason, GALAXY_TEST_ERRORS_DIRECTORY is populated with
|
||||
a new directory of information for each failing test case. This information
|
||||
includes a screenshot, a stack trace, and the DOM of the currently rendered
|
||||
Galaxy instance. The new directories are created with names that include
|
||||
information about the failed test method name and the timestamp. By default,
|
||||
GALAXY_TEST_ERRORS_DIRECTORY will be set to database/errors.
|
||||
|
||||
The Selenium tests seem to be subject to transient failures at a higher
|
||||
rate than the rest of the tests in Galaxy. Though this is unfortunate,
|
||||
they have more moving pieces so this is perhaps not surprising. One can
|
||||
set the GALAXY_TEST_SELENIUM_RETRIES to a number greater than 0 to
|
||||
automatically retry every failed test case the specified number of times.
|
||||
|
||||
External Tests:
|
||||
|
||||
A small subset of tests can be run against an existing Galaxy
|
||||
|
||||
@@ -7,7 +7,7 @@
|
||||
# 501 is line length
|
||||
# W503 is line breaks before binary operators, which has been reversed in PEP 8.
|
||||
# D** are docstring linting - which we mostly ignore except D302. (Hopefully we will solve more over time).
|
||||
ignore = E128,E201,E202,E203,E501,E402,W503,D100,D101,D102,D103,D104,D105,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403
|
||||
ignore = E128,E201,E202,E203,E501,E402,W503,D100,D101,D102,D103,D104,D105,D200,D201,D202,D204,D205,D206,D207,D208,D209,D210,D211,D300,D301,D400,D401,D402,D403,D412,D413
|
||||
exclude = lib/galaxy/util/jstree.py
|
||||
# For flake8-import-order
|
||||
# https://github.com/PyCQA/flake8-import-order/blob/master/tests/test_cases/complete_smarkets.py
|
||||
|
||||
@@ -1 +1 @@
|
||||
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define(["mvc/base-mvc","mvc/citation/citation-model","utils/localization"],function(a,b,c){var d=Backbone.View.extend({tagName:"div",className:"citations",render:function(){return this.$el.append("<p>"+this.formattedReference()+"</p>"),this},formattedReference:function(){var a=this.model,b=a.entryType(),c=a.fields(),d="",e=this._asSentence((c.author?c.author:"")+(c.year?" ("+c.year+")":""))+" ",f=c.title||"",g=c.pages?"pp. "+c.pages:"",h=c.address;if("article"==b){var i=(c.volume?c.volume:"")+(c.number?" ("+c.number+")":"")+(g?", "+g:"");d=e+this._asSentence(f)+(c.journal?"In <em>"+c.journal+", ":"")+this._asSentence(i)+this._asSentence(c.address)+"</em>"}else d="inproceedings"==b||"proceedings"==b?e+this._asSentence(f)+(c.booktitle?"In <em>"+c.booktitle+", ":"")+(g?g:"")+(h?", "+h:"")+".</em>":"mastersthesis"==b||"phdthesis"==b?e+this._asSentence(f)+(c.howpublished?c.howpublished+". ":"")+(c.note?c.note+".":""):"techreport"==b?e+this._asSentence(f)+this._asSentence(c.institution)+this._asSentence(c.number)+this._asSentence(c.type):"book"==b||"inbook"==b||"incollection"==b?e+" "+this._formatBookInfo(c):e+" "+this._asSentence(f)+this._asSentence(c.howpublished)+this._asSentence(c.note);var j="";c.doi&&(j="http://dx.doi.org/"+c.doi,d+='[<a href="'+j+'" target="_blank">doi:'+c.doi+"</a>]");var k=c.url||j;return k&&(d+='[<a href="'+k+'" target="_blank">Link</a>]'),d},_formatBookInfo:function(a){var b="";return a.chapter&&(b+=a.chapter+" in "),a.title&&(b+="<em>"+a.title+"</em>"),a.editor&&(b+=", Edited by "+a.editor+", "),a.publisher&&(b+=", "+a.publisher),a.pages&&(b+=", pp. "+a.pages),a.series&&(b+=", <em>"+a.series+"</em>"),a.volume&&(b+=", Vol."+a.volume),a.issn&&(b+=", ISBN: "+a.issn),b+"."},_asSentence:function(a){return a&&a.trim()?a+". ":""}}),e=Backbone.View.extend({el:"#citations",initialize:function(){this.listenTo(this.collection,"add",this.renderCitation)},events:{"click .citations-to-bibtex":"showBibtex","click .citations-to-formatted":"showFormatted"},renderCitation:function(a){var b=new d({model:a});this.$(".citations-formatted").append(b.render().el);var c=this.$(".citations-bibtex-text");c.val(c.val()+"\n\r"+a.attributes.content)},render:function(){this.$el.html(this.citationsElement()),this.collection.each(function(a){this.renderCitation(a)},this),this.showFormatted()},showBibtex:function(){this.$(".citations-to-formatted").show(),this.$(".citations-to-bibtex").hide(),this.$(".citations-bibtex").show(),this.$(".citations-formatted").hide(),this.$(".citations-bibtex-text").select()},showFormatted:function(){this.$(".citations-to-formatted").hide(),this.$(".citations-to-bibtex").show(),this.$(".citations-bibtex").hide(),this.$(".citations-formatted").show()},partialWarningElement:function(){return this.collection.partial?['<div style="padding:5px 10px">',"<b>Warning: This is a experimental feature.</b> Most Galaxy tools will not annotate"," citations explicitly at this time. When writing up your analysis, please manually"," review your histories and find all references"," that should be cited in order to completely describe your work. Also, please remember to",' <a href="https://galaxyproject.org/citing-galaxy">cite Galaxy</a>.',"</div>"].join(""):""},citationsElement:function(){return['<div class="toolForm">','<div class="toolFormTitle">',c("Citations"),' <button type="button" class="btn btn-xs citations-to-bibtex" title="Show all in BibTeX format."><i class="fa fa-pencil-square-o"></i> Show BibTeX</button>',' <button type="button" class="btn btn-xs citations-to-formatted" title="Return to formatted citation list."><i class="fa fa-times"></i> Hide BibTeX</button>',"</div>",'<div class="toolFormBody" style="padding:5px 10px">',this.partialWarningElement(),'<span class="citations-formatted" style="word-wrap: break-word;"></span>',"</div>",'<div class="citations-bibtex toolFormBody" style="padding:5px 10px">','<textarea style="width: 100%; height: 500px;" class="citations-bibtex-text"></textarea>',"</div>","</div>"].join("")}});return{CitationView:d,CitationListView:e}});
|
||||
//# sourceMappingURL=../../../maps/mvc/citation/citation-view.js.map
|
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define(["layout/masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view","libs/underscore"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null,all_fetched:!1},initialize:function(a){this.options=g.defaults(this.options||{},a,this.defaults);var b=this;this.modal=null,this.collection=new e.Libraries,this.collection.url=this.collection.urlRoot+"?deleted=false",this.collection.fetch({success:function(){b.render()},error:function(a,b){d.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},render:function(a){this.options=g.extend(this.options,a),this.setElement("#libraries_element");var b=this.templateLibraryList(),c=null,d=null;if($(".tooltip").hide(),"undefined"!=typeof a&&(d="undefined"!=typeof a.models?a.models:null),null!==this.collection&&null===d)this.sortLibraries(),c=Galaxy.libraries.preferences.get("with_deleted")?this.collection.models:this.collection.where({deleted:!1});else if(null!==d)if(Galaxy.libraries.preferences.get("with_deleted"))c=d;else{var e=function(a){return a.get("deleted")===!1};c=g.filter(d,e)}else c=[];(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_libraries_count=c.length;var f=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&f<this.options.total_libraries_count?(c=c.slice(f,f+Galaxy.libraries.preferences.get("library_page_size")),this.options.libraries_shown=c.length,Galaxy.libraries.preferences.get("library_page_size")*this.options.show_page>this.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(c=[]),this.$el.html(b({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(c)):(this.$el.html(b({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var a=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){a.options.all_fetched=!0,a.render()},error:function(a,b){d.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}},renderRows:function(a){for(var b=0;b<a.length;b++){var c=a[b];this.renderOne({library:c})}},renderOne:function(a){var b=a.library,c=new f.LibraryRowView(b);this.$el.find("#library_list_body").append(c.el)},sort_clicked:function(){Galaxy.libraries.preferences.set("asc"===Galaxy.libraries.preferences.get("sort_order")?{sort_order:"desc"}:{sort_order:"asc"}),this.render()},sortLibraries:function(){"name"===Galaxy.libraries.preferences.get("sort_by")&&("asc"===Galaxy.libraries.preferences.get("sort_order")?this.collection.sortByNameAsc():"desc"===Galaxy.libraries.preferences.get("sort_order")&&this.collection.sortByNameDesc())},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},searchLibraries:function(a){var b=$.trim(a);if(""!==b){var c=null;c=this.collection.search(a),this.options.searching=!0,this.render({models:c})}else this.options.searching=!1,this.render()},templateLibraryList:function(){return g.template(['<div class="library_container table-responsive">',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","<div>","There are no libraries matching your search. Try different keyword.","</div>","<% } else{ %>","<div>","There are no libraries visible to you here. If you expected some to show up please consult the",' <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">library security wikipage</a>',' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',"</div>","<% }%>","<% } else{ %>",'<table class="grid table table-condensed">',"<thead>",'<th style="width:30%;">','<a class="sort-libraries-link" title="Click to reverse order" href="#">',"name","</a>",'<span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"/>',"</th>",'<th style="width:22%;">description</th>','<th style="width:22%;">synopsis</th> ','<th style="width:26%;"></th>',"</thead>",'<tbody id="library_list_body">',"</tbody>","</table>","<% }%>","</div>"].join(""))}});return{LibraryListView:h}});
|
||||
define(["layout/masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view","libs/underscore"],function(a,b,c,d,e,f,g){var h=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},defaults:{page_count:null,show_page:null,all_fetched:!1},initialize:function(a){this.options=g.defaults(this.options||{},a,this.defaults);var b=this;this.modal=null,this.collection=new e.Libraries,this.collection.url=this.collection.urlRoot+"?deleted=false",this.collection.fetch({success:function(){b.render()},error:function(a,b){d.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})},render:function(a){this.options=g.extend(this.options,a),this.setElement("#libraries_element");var b=this.templateLibraryList(),c=null,d=null;if($(".tooltip").hide(),"undefined"!=typeof a&&(d="undefined"!=typeof a.models?a.models:null),null!==this.collection&&null===d)this.sortLibraries(),c=Galaxy.libraries.preferences.get("with_deleted")?this.collection.models:this.collection.where({deleted:!1});else if(null!==d)if(Galaxy.libraries.preferences.get("with_deleted"))c=d;else{var e=function(a){return a.get("deleted")===!1};c=g.filter(d,e)}else c=[];(null===this.options.show_page||this.options.show_page<1)&&(this.options.show_page=1),this.options.total_libraries_count=c.length;var f=Galaxy.libraries.preferences.get("library_page_size")*(this.options.show_page-1);this.options.page_count=Math.ceil(this.options.total_libraries_count/Galaxy.libraries.preferences.get("library_page_size")),this.options.total_libraries_count>0&&f<this.options.total_libraries_count?(c=c.slice(f,f+Galaxy.libraries.preferences.get("library_page_size")),this.options.libraries_shown=c.length,Galaxy.libraries.preferences.get("library_page_size")*this.options.show_page>this.options.total_libraries_count+Galaxy.libraries.preferences.get("library_page_size")&&(c=[]),this.$el.html(b({length:1,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options),this.renderRows(c)):(this.$el.html(b({length:0,order:Galaxy.libraries.preferences.get("sort_order"),search_term:Galaxy.libraries.libraryToolbarView.options.search_term})),Galaxy.libraries.libraryToolbarView.renderPaginator(this.options)),$("#center [data-toggle]").tooltip(),$("#center").css("overflow","auto")},fetchDeleted:function(){if(this.options.all_fetched)this.render();else{var a=this;this.collection.url=this.collection.urlRoot+"?deleted=true",this.collection.fetch({remove:!1,success:function(){a.options.all_fetched=!0,a.render()},error:function(a,b){d.error("undefined"!=typeof b.responseJSON?b.responseJSON.err_msg:"An error ocurred.")}})}},renderRows:function(a){for(var b=0;b<a.length;b++){var c=a[b];this.renderOne({library:c})}},renderOne:function(a){var b=a.library,c=new f.LibraryRowView(b);this.$el.find("#library_list_body").append(c.el)},sort_clicked:function(){Galaxy.libraries.preferences.set("asc"===Galaxy.libraries.preferences.get("sort_order")?{sort_order:"desc"}:{sort_order:"asc"}),this.render()},sortLibraries:function(){"name"===Galaxy.libraries.preferences.get("sort_by")&&("asc"===Galaxy.libraries.preferences.get("sort_order")?this.collection.sortByNameAsc():"desc"===Galaxy.libraries.preferences.get("sort_order")&&this.collection.sortByNameDesc())},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},searchLibraries:function(a){var b=$.trim(a);if(""!==b){var c=null;c=this.collection.search(a),this.options.searching=!0,this.render({models:c})}else this.options.searching=!1,this.render()},templateLibraryList:function(){return g.template(['<div class="library_container table-responsive">',"<% if(length === 0) { %>","<% if(search_term.length > 0) { %>","<div>","There are no libraries matching your search. Try different keyword.","</div>","<% } else{ %>","<div>","There are no libraries visible to you here. If you expected some to show up please consult the",' <a href="https://galaxyproject.org/data-libraries/#permissions" target="_blank">library security wikipage</a>',' or visit the <a href="https://biostar.usegalaxy.org/" target="_blank">Galaxy support site</a>.',"</div>","<% }%>","<% } else{ %>",'<table class="grid table table-condensed">',"<thead>",'<th style="width:30%;">','<a class="sort-libraries-link" title="Click to reverse order" href="#">',"name","</a>",'<span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"/>',"</th>",'<th style="width:22%;">description</th>','<th style="width:22%;">synopsis</th> ','<th style="width:26%;"></th>',"</thead>",'<tbody id="library_list_body">',"</tbody>","</table>","<% }%>","</div>"].join(""))}});return{LibraryListView:h}});
|
||||
//# sourceMappingURL=../../../maps/mvc/library/library-librarylist-view.js.map
|
||||
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|
||||
define(["utils/utils","mvc/form/form-view","mvc/tool/tool-form-base"],function(a,b,c){var d=Backbone.View.extend({initialize:function(a){this.form=new b(a)}}),e=Backbone.View.extend({initialize:function(b){var d=this;this.workflow=b.workflow,this.node=b.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},a.deepeach(b.inputs,function(b){b.type&&(-1!=["data","data_collection"].indexOf(b.type)?(b.type="hidden",b.info="Data input '"+b.name+"' ("+a.textify(b.extensions)+")",b.value={__class__:"RuntimeValue"}):b.fixed||(b.collapsible_value={__class__:"RuntimeValue"},b.is_workflow=b.options&&0==b.options.length||-1!=["integer","float"].indexOf(b.type)))}),a.deepeach(b.inputs,function(a){"conditional"==a.type&&(a.test_param.collapsible_value=void 0)}),this._makeSections(b),this.form=new c(a.merge(b,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,sustain_version:!0,cls:"ui-portlet-narrow",postchange:function(b,c){var e=c.model.attributes,f={tool_id:e.id,tool_version:e.version,type:"tool",inputs:$.extend(!0,{},c.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",f),a.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:f,success:function(a){c.update(a.config_form),c.errors(a.config_form),d.node.update_field_data(a),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",a),b.resolve()},error:function(a){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",a),b.reject()}})}}))):Galaxy.emit.debug("tool-form-workflow::initialize()","Node not found in workflow.")},_makeSections:function(a){var b=a.inputs,c=a.datatypes,d=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(d){b.push({name:"pja__"+d+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+d])),ignore:"false",help:"An email notification will be sent when the job has completed.",payload:{host:window.location.host}}),b.push({name:"pja__"+d+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+d])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var e in this.node.output_terminals)b.push(this._makeSection(e,c))}},_makeSection:function(a,b){function c(b,e){e=e||[],e.push(b);for(var f in b.inputs){var g=b.inputs[f],h=g.action;if(h){if(g.name="pja__"+a+"__"+g.action,g.pja_arg&&(g.name+="__"+g.pja_arg),g.payload)for(var i in g.payload){var j=g.payload[i];g.payload[g.name+"__"+i]=j,delete j}var k=d.post_job_actions[g.action+a];if(k){for(var l in e)e[l].expanded=!0;g.value=g.pja_arg?k.action_arguments&&k.action_arguments[g.pja_arg]||g.value:"true"}}g.inputs&&c(g,e.slice(0))}}var d=this,e=[],f=[];for(key in b)e.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)f.push(this.node.input_terminals[key].name);e.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),e.unshift({0:"Sequences",1:"Sequences"}),e.unshift({0:"Roadmaps",1:"Roadmaps"}),e.unshift({0:"Leave unchanged",1:"__empty__"});var g={title:"Configure Output: '"+a+"'",type:"section",flat:!0,inputs:[{label:"Label",type:"text",value:(output=this.node.getWorkflowOutput(a))&&output.label||"",help:"This will provide a short name to describe the output - this must be unique across workflows.",onchange:function(b){d.workflow.attemptUpdateOutputLabel(d.node,a,b)}},{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information. Valid inputs are: <strong>'+f.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:e,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return c(g),g}});return{Default:d,Tool:e}});
|
||||
define(["utils/utils","mvc/form/form-view","mvc/tool/tool-form-base"],function(a,b,c){var d=Backbone.View.extend({initialize:function(a){this.form=new b(a)}}),e=Backbone.View.extend({initialize:function(b){var d=this;this.workflow=b.workflow,this.node=b.node,this.node?(this.post_job_actions=this.node.post_job_actions||{},a.deepeach(b.inputs,function(b){b.type&&(-1!=["data","data_collection"].indexOf(b.type)?(b.type="hidden",b.info="Data input '"+b.name+"' ("+a.textify(b.extensions)+")",b.value={__class__:"RuntimeValue"}):b.fixed||(b.collapsible_value={__class__:"RuntimeValue"},b.is_workflow=b.options&&0==b.options.length||-1!=["integer","float"].indexOf(b.type)))}),a.deepeach(b.inputs,function(a){"conditional"==a.type&&(a.test_param.collapsible_value=void 0)}),this._makeSections(b),this.form=new c(a.merge(b,{text_enable:"Set in Advance",text_disable:"Set at Runtime",narrow:!0,initial_errors:!0,sustain_version:!0,cls:"ui-portlet-narrow",postchange:function(b,c){var e=c.model.attributes,f={tool_id:e.id,tool_version:e.version,type:"tool",inputs:$.extend(!0,{},c.data.create())};Galaxy.emit.debug("tool-form-workflow::postchange()","Sending current state.",f),a.request({type:"POST",url:Galaxy.root+"api/workflows/build_module",data:f,success:function(a){c.update(a.config_form),c.errors(a.config_form),d.node.update_field_data(a),Galaxy.emit.debug("tool-form-workflow::postchange()","Received new model.",a),b.resolve()},error:function(a){Galaxy.emit.debug("tool-form-workflow::postchange()","Refresh request failed.",a),b.reject()}})}}))):Galaxy.emit.debug("tool-form-workflow::initialize()","Node not found in workflow.")},_makeSections:function(a){var b=a.inputs,c=a.datatypes,d=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(d){b.push({name:"pja__"+d+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+d])),ignore:"false",help:"An email notification will be sent when the job has completed.",payload:{host:window.location.host}}),b.push({name:"pja__"+d+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+d])),ignore:"false",help:"Upon completion of this step, delete non-starred outputs from completed workflow steps if they are no longer required as inputs."});for(var e in this.node.output_terminals)b.push(this._makeSection(e,c))}},_makeSection:function(a,b){function c(b,e){e=e||[],e.push(b);for(var f in b.inputs){var g=b.inputs[f],h=g.action;if(h){if(g.name="pja__"+a+"__"+g.action,g.pja_arg&&(g.name+="__"+g.pja_arg),g.payload)for(var i in g.payload){var j=g.payload[i];g.payload[g.name+"__"+i]=j,delete j}var k=d.post_job_actions[g.action+a];if(k){for(var l in e)e[l].expanded=!0;g.value=g.pja_arg?k.action_arguments&&k.action_arguments[g.pja_arg]||g.value:"true"}}g.inputs&&c(g,e.slice(0))}}var d=this,e=[],f=[];for(key in b)e.push({0:b[key],1:b[key]});for(key in this.node.input_terminals)f.push(this.node.input_terminals[key].name);e.sort(function(a,b){return a.label>b.label?1:a.label<b.label?-1:0}),e.unshift({0:"Sequences",1:"Sequences"}),e.unshift({0:"Roadmaps",1:"Roadmaps"}),e.unshift({0:"Leave unchanged",1:"__empty__"});var g={title:"Configure Output: '"+a+"'",type:"section",flat:!0,inputs:[{label:"Label",type:"text",value:(output=this.node.getWorkflowOutput(a))&&output.label||"",help:"This will provide a short name to describe the output - this must be unique across workflows.",onchange:function(b){d.workflow.attemptUpdateOutputLabel(d.node,a,b)}},{action:"RenameDatasetAction",pja_arg:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the output dataset. Click <a href="https://galaxyproject.org/learn/advanced-workflow/variables/">here</a> for more information. Valid inputs are: <strong>'+f.join(", ")+"</strong>."},{action:"ChangeDatatypeAction",pja_arg:"newtype",label:"Change datatype",type:"select",ignore:"__empty__",value:"__empty__",options:e,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",pja_arg:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{title:"Assign columns",type:"section",flat:!0,inputs:[{action:"ColumnSetAction",pja_arg:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",pja_arg:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};return c(g),g}});return{Default:d,Tool:e}});
|
||||
//# sourceMappingURL=../../../maps/mvc/workflow/workflow-forms.js.map
|
||||
File diff suppressed because one or more lines are too long
@@ -51,11 +51,11 @@
|
||||
repository tools may include code that produces malicious behavior, so be aware of what you are installing.
|
||||
</p>
|
||||
<p>
|
||||
If you discover a repository that causes problems after installation, contact <a href="https://wiki.galaxyproject.org/Support" target="_blank">Galaxy support</a>,
|
||||
If you discover a repository that causes problems after installation, contact <a href="https://galaxyproject.org/support" target="_blank">Galaxy support</a>,
|
||||
sending all necessary information, and appropriate action will be taken.
|
||||
</p>
|
||||
<p>
|
||||
<a href="https://wiki.galaxyproject.org/ToolShedRepositoryFeatures#Contact_repository_owner" target="_blank">Contact the repository owner</a> for
|
||||
<a href="https://galaxyproject.org/toolshed/repository-features/#contact-repository-owner" target="_blank">Contact the repository owner</a> for
|
||||
general questions or concerns.
|
||||
</p>
|
||||
</div>
|
||||
|
||||
@@ -33,7 +33,7 @@
|
||||
%if trans.app.config.enable_quotas:
|
||||
Your disk quota is: <strong>${trans.app.quota_agent.get_quota( trans.user, nice_size=True )}</strong>.
|
||||
%endif
|
||||
Is your usage more than expected? See the <a href="https://wiki.galaxyproject.org/Learn/ManagingDatasets" target="_blank">documentation</a> for tips on how to find all of the data in your account.
|
||||
Is your usage more than expected? See the <a href="https://galaxyproject.org/learn/managing-datasets/" target="_blank">documentation</a> for tips on how to find all of the data in your account.
|
||||
</p>
|
||||
%endif
|
||||
%else:
|
||||
|
||||
@@ -4,7 +4,7 @@
|
||||
<%def name="title()">Galaxy Administration</%def>
|
||||
|
||||
<h2>Administration</h2>
|
||||
Please visit <a href="https://wiki.galaxyproject.org/Admin" target="_blank">the Galaxy administration hub</a> to learn how to keep your Galaxy in best shape.
|
||||
Please visit <a href="https://galaxyproject.org/admin" target="_blank">the Galaxy administration hub</a> to learn how to keep your Galaxy in best shape.
|
||||
%if message:
|
||||
${render_msg( message, status )}
|
||||
%else:
|
||||
@@ -28,7 +28,7 @@ Please visit <a href="https://wiki.galaxyproject.org/Admin" target="_blank">the
|
||||
<ul>
|
||||
%if trans.app.tool_shed_registry and trans.app.tool_shed_registry.tool_sheds:
|
||||
<li>
|
||||
<strong>Search Tool Shed</strong> - Search and install new tools and other Galaxy utilities from the Tool Shed. See <a href="https://wiki.galaxyproject.org/Admin/Tools/AddToolFromToolShedTutorial" target="_blank">the tutorial</a>.
|
||||
<strong>Search Tool Shed</strong> - Search and install new tools and other Galaxy utilities from the Tool Shed. See <a href="https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial" target="_blank">the tutorial</a>.
|
||||
</li>
|
||||
%endif
|
||||
%if tool_shed_repository_ids:
|
||||
@@ -84,14 +84,14 @@ Please visit <a href="https://wiki.galaxyproject.org/Admin" target="_blank">the
|
||||
<ul>
|
||||
%if trans.app.config.enable_quotas:
|
||||
<li>
|
||||
<strong>Quotas</strong> - Manage user space quotas. See <a href="https://wiki.galaxyproject.org/Admin/DiskQuotas" target="_blank">wiki</a> for details.
|
||||
<strong>Quotas</strong> - Manage user space quotas. See <a href="https://galaxyproject.org/admin/disk-quotas" target="_blank">wiki</a> for details.
|
||||
</li>
|
||||
%endif
|
||||
<li>
|
||||
<strong>Data libraries</strong> - Data libraries enable authorized Galaxy users to share datasets with other groups or users. Only administrators can create data libraries. See <a href="https://wiki.galaxyproject.org/DataLibraries" target="_blank">wiki</a> for details and <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity" target="_blank">this page</a> for security description.
|
||||
<strong>Data libraries</strong> - Data libraries enable authorized Galaxy users to share datasets with other groups or users. Only administrators can create data libraries. See <a href="https://galaxyproject.org/data-libraries" target="_blank">wiki</a> for details.
|
||||
</li>
|
||||
<li>
|
||||
<strong>Local data</strong> - Manage the reference (and other) data that is stored within Tool Data Tables. See <a href="https://wiki.galaxyproject.org/Admin/Tools/DataManagers" target="_blank">wiki</a> for details.
|
||||
<strong>Local data</strong> - Manage the reference (and other) data that is stored within Tool Data Tables. See <a href="https://galaxyproject.org/admin/tools/data-managers" target="_blank">wiki</a> for details.
|
||||
</li>
|
||||
</ul>
|
||||
<h4>Form definitions</h4>
|
||||
@@ -104,7 +104,7 @@ Please visit <a href="https://wiki.galaxyproject.org/Admin" target="_blank">the
|
||||
<h4>Sample tracking</h4>
|
||||
<ul>
|
||||
<li>
|
||||
Please see the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySampleTracking" target="_blank">sample tracking tutorial</a>.
|
||||
Please see the <a href="https://galaxyproject.org/archive/library-sample-tracking" target="_blank">sample tracking tutorial</a>.
|
||||
</li>
|
||||
</ul>
|
||||
%endif
|
||||
|
||||
@@ -67,4 +67,4 @@
|
||||
<br/>
|
||||
%endif
|
||||
|
||||
${render_msg( 'To find out more information about Data Managers, please visit the <a href="https://wiki.galaxyproject.org/Admin/Tools/DataManagers" target="_blank">wiki.</a>', "info" ) }
|
||||
${render_msg( 'To find out more information about Data Managers, please visit the <a href="https://galaxyproject.org/admin/tools/data-managers/" target="_blank">wiki.</a>', "info" ) }
|
||||
|
||||
@@ -15,12 +15,12 @@
|
||||
'lims_doc_url' : app.config.get("lims_doc_url", "https://usegalaxy.org/u/rkchak/p/sts"),
|
||||
'biostar_url' : app.config.biostar_url,
|
||||
'biostar_url_redirect' : h.url_for( controller='biostar', action='biostar_redirect', qualified=True ),
|
||||
'support_url' : app.config.get("support_url", "https://wiki.galaxyproject.org/Support"),
|
||||
'search_url' : app.config.get("search_url", "http://galaxyproject.org/search/usegalaxy/"),
|
||||
'mailing_lists' : app.config.get("mailing_lists", "https://wiki.galaxyproject.org/MailingLists"),
|
||||
'support_url' : app.config.get("support_url", "https://galaxyproject.org/support"),
|
||||
'search_url' : app.config.get("search_url", "http://galaxyproject.org/search/"),
|
||||
'mailing_lists' : app.config.get("mailing_lists", "https://galaxyproject.org/mailing-lists"),
|
||||
'screencasts_url' : app.config.get("screencasts_url", "https://vimeo.com/galaxyproject"),
|
||||
'wiki_url' : app.config.get("wiki_url", "https://wiki.galaxyproject.org/"),
|
||||
'citation_url' : app.config.get("citation_url", "https://wiki.galaxyproject.org/CitingGalaxy"),
|
||||
'wiki_url' : app.config.get("wiki_url", "https://galaxyproject.org/"),
|
||||
'citation_url' : app.config.get("citation_url", "https://galaxyproject.org/citing-galaxy"),
|
||||
'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', '/')),
|
||||
@@ -78,4 +78,4 @@
|
||||
});
|
||||
});
|
||||
</script>
|
||||
</%def>
|
||||
</%def>
|
||||
|
||||
@@ -115,13 +115,13 @@
|
||||
if qa_url:
|
||||
menu_options = [ [_('Galaxy Q&A'), qa_url, "_blank" ] ]
|
||||
menu_options.extend( [
|
||||
[_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://wiki.galaxyproject.org/ToolShed" ), "_blank" ],
|
||||
[_('Support'), app.config.get( "support_url", "https://wiki.galaxyproject.org/Support" ), "_blank" ],
|
||||
[_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/usegalaxy/" ), "_blank" ],
|
||||
[_('Mailing Lists'), app.config.get( "mailing_lists_url", "https://wiki.galaxyproject.org/MailingLists" ), "_blank" ],
|
||||
[_('Tool Shed Wiki'), app.config.get( "wiki_url", "https://galaxyproject.org/toolshed" ), "_blank" ],
|
||||
[_('Support'), app.config.get( "support_url", "https://galaxyproject.org/support" ), "_blank" ],
|
||||
[_('Search'), app.config.get( "search_url", "http://galaxyproject.org/search/" ), "_blank" ],
|
||||
[_('Mailing Lists'), app.config.get( "mailing_lists_url", "https://galaxyproject.org/mailing-lists" ), "_blank" ],
|
||||
[_('Videos'), app.config.get( "screencasts_url", "https://vimeo.com/galaxyproject" ), "_blank" ],
|
||||
[_('Wiki'), app.config.get( "wiki_url", "http://galaxyproject.org/" ), "_blank" ],
|
||||
[_('How to Cite Galaxy'), app.config.get( "citation_url", "https://wiki.galaxyproject.org/CitingGalaxy" ), "_blank" ]
|
||||
[_('How to Cite Galaxy'), app.config.get( "citation_url", "https://galaxyproject.org/citing-galaxy" ), "_blank" ]
|
||||
] )
|
||||
tab( "help", _("Help"), None, menu_options=menu_options )
|
||||
%>
|
||||
|
||||
@@ -131,7 +131,7 @@ class JobsApiTestCase( api.ApiTestCase ):
|
||||
self._assert_has_keys( show_jobs_response.json(), "command_line", "external_id" )
|
||||
|
||||
def test_deleting_output_keep_running_until_all_deleted( self ):
|
||||
history_id, job_state, outputs = self._setup_running_two_output_job( 60 )
|
||||
history_id, job_state, outputs = self._setup_running_two_output_job( 120 )
|
||||
|
||||
# Delete one of the two outputs and make sure the job is still running.
|
||||
self._raw_update_history_item( history_id, outputs[0]["id"], {"deleted": True} )
|
||||
@@ -145,7 +145,7 @@ class JobsApiTestCase( api.ApiTestCase ):
|
||||
assert final_state in ["deleted_new", "deleted"], final_state
|
||||
|
||||
def test_purging_output_keep_running_until_all_purged( self ):
|
||||
history_id, job_state, outputs = self._setup_running_two_output_job( 60 )
|
||||
history_id, job_state, outputs = self._setup_running_two_output_job( 120 )
|
||||
|
||||
# Pretty much right away after the job is running, these paths should be populated -
|
||||
# if they are grab them and make sure they are deleted at the end of the job.
|
||||
|
||||
@@ -13,6 +13,7 @@ from base.populators import (
|
||||
DatasetCollectionPopulator,
|
||||
DatasetPopulator,
|
||||
skip_without_tool,
|
||||
wait_on,
|
||||
WorkflowPopulator
|
||||
)
|
||||
from galaxy.exceptions import error_codes
|
||||
@@ -259,6 +260,10 @@ class BaseWorkflowsApiTestCase( api.ApiTestCase ):
|
||||
def _history_jobs( self, history_id ):
|
||||
return self._get("jobs", { "history_id": history_id, "order_by": "create_time" } ).json()
|
||||
|
||||
def _assert_history_job_count( self, history_id, n ):
|
||||
jobs = self._history_jobs( history_id )
|
||||
self.assertEqual( len( jobs ), n )
|
||||
|
||||
|
||||
# Workflow API TODO:
|
||||
# - Allow history_id as param to workflow run action. (hist_id)
|
||||
@@ -1104,20 +1109,21 @@ steps:
|
||||
test_data:
|
||||
test_input: "hello world"
|
||||
""", history_id=history_id, wait=False)
|
||||
time.sleep( 2 )
|
||||
history_id = run_summary.history_id
|
||||
workflow_id = run_summary.workflow_id
|
||||
invocation_id = run_summary.invocation_id
|
||||
# Wait for first two jobs to be scheduled - upload and first cat.
|
||||
wait_on( lambda: len( self._history_jobs( history_id ) ) >= 2 or None, "history jobs" )
|
||||
self.dataset_populator.wait_for_history( history_id, assert_ok=True )
|
||||
invocation = self._invocation_details( workflow_id, invocation_id )
|
||||
assert invocation[ 'state' ] != 'scheduled'
|
||||
assert invocation[ 'state' ] != 'scheduled', invocation
|
||||
# Expect two jobs - the upload and first cat. randomlines shouldn't run
|
||||
# it is implicitly dependent on second cat.
|
||||
assert len( self._history_jobs( history_id ) ) == 2
|
||||
self._assert_history_job_count( history_id, 2 )
|
||||
|
||||
self.__review_paused_steps( workflow_id, invocation_id, order_index=2, action=True )
|
||||
self.wait_for_invocation_and_jobs( history_id, workflow_id, invocation_id )
|
||||
assert len( self._history_jobs( history_id ) ) == 4
|
||||
self._assert_history_job_count( history_id, 4 )
|
||||
|
||||
def test_run_with_validated_parameter_connection_valid( self ):
|
||||
history_id = self.dataset_populator.new_history()
|
||||
|
||||
@@ -79,7 +79,7 @@ class NavigatesGalaxy(HasDriver):
|
||||
self.switch_to_main_panel()
|
||||
yield
|
||||
finally:
|
||||
self.driver.switch_to.default_content
|
||||
self.driver.switch_to.default_content()
|
||||
|
||||
def api_get(self, endpoint, data={}, raw=False):
|
||||
full_url = self.build_url("api/" + endpoint, for_selenium=False)
|
||||
@@ -148,7 +148,14 @@ class NavigatesGalaxy(HasDriver):
|
||||
contents = self.api_get("histories/%s/contents" % current_history_id)
|
||||
history_item = [d for d in contents if d["hid"] == hid][0]
|
||||
history_item_selector = "#%s-%s" % (history_item["history_content_type"], history_item["id"])
|
||||
self.wait_for_selector_visible(history_item_selector)
|
||||
try:
|
||||
self.wait_for_selector_visible(history_item_selector)
|
||||
except self.TimeoutException as e:
|
||||
dataset_elements = self.driver.find_elements_by_css_selector("#current-history-panel .list-items div")
|
||||
div_ids = [d.get_attribute('id') for d in dataset_elements]
|
||||
template = "Failed waiting on history item %d to become visible, visible datasets include [%s]."
|
||||
message = template % (hid, ",".join(div_ids))
|
||||
raise self.prepend_timeout_message(e, message)
|
||||
return history_item_selector
|
||||
|
||||
def history_panel_wait_for_hid_hidden(self, hid, timeout=60):
|
||||
|
||||
@@ -29,7 +29,7 @@ define([ 'test-app', 'mvc/form/form-input', 'mvc/ui/ui-misc', 'mvc/form/form-dat
|
||||
ok( dropdown.children().length == 2, 'Found two menu items' );
|
||||
dropdown.find( '.fa-info-circle' ).parent().click();
|
||||
this.clock.tick ( window.WAIT_FADE );
|
||||
ok( form.$( '.ui-message' ).html() === '<span>This tool requires req_name_a (Version req_version_a) and req_name_b (Version req_version_b). Click <a target="_blank" href="https://wiki.galaxyproject.org/Tools/Requirements">here</a> for more information.</span>', 'Check requirements message' );
|
||||
ok( form.$( '.ui-message' ).html() === '<span>This tool requires req_name_a (Version req_version_a) and req_name_b (Version req_version_b). Click <a target="_blank" href="https://galaxyproject.org/tools/requirements/">here</a> for more information.</span>', 'Check requirements message' );
|
||||
ok( form.$( '.form-repeat-delete' ).css( 'display' ) == 'none', 'Delete button disabled' );
|
||||
var $add = form.$( '.form-repeat-add' );
|
||||
ok( !$add.attr( 'disabled' ), 'Adding new repeat possible' );
|
||||
@@ -101,4 +101,4 @@ define([ 'test-app', 'mvc/form/form-input', 'mvc/ui/ui-misc', 'mvc/form/form-dat
|
||||
input.model.set( 'help', '_help (_argument)' );
|
||||
ok( input.$info.html() == '_help (_argument)', 'Correct help text with argument from help' );
|
||||
} );
|
||||
});
|
||||
});
|
||||
|
||||
@@ -6,6 +6,7 @@ import datetime
|
||||
import json
|
||||
import os
|
||||
import time
|
||||
import traceback
|
||||
|
||||
from functools import wraps
|
||||
|
||||
@@ -49,6 +50,8 @@ GALAXY_TEST_SELENIUM_REMOTE_PORT = os.environ.get("GALAXY_TEST_SELENIUM_REMOTE_P
|
||||
GALAXY_TEST_SELENIUM_REMOTE_HOST = os.environ.get("GALAXY_TEST_SELENIUM_REMOTE_HOST", DEFAULT_SELENIUM_REMOTE_HOST)
|
||||
GALAXY_TEST_SELENIUM_HEADLESS = os.environ.get("GALAXY_TEST_SELENIUM_HEADLESS", DEFAULT_SELENIUM_HEADLESS)
|
||||
GALAXY_TEST_EXTERNAL_FROM_SELENIUM = os.environ.get("GALAXY_TEST_EXTERNAL_FROM_SELENIUM", None)
|
||||
# Auto-retry selenium tests this many times.
|
||||
GALAXY_TEST_SELENIUM_RETRIES = int(os.environ.get("GALAXY_TEST_SELENIUM_RETRIES", "0"))
|
||||
|
||||
# Test case data
|
||||
DEFAULT_PASSWORD = '123456'
|
||||
@@ -66,32 +69,38 @@ def selenium_test(f):
|
||||
|
||||
@wraps(f)
|
||||
def func_wrapper(self, *args, **kwds):
|
||||
try:
|
||||
return f(self, *args, **kwds)
|
||||
except Exception:
|
||||
if GALAXY_TEST_ERRORS_DIRECTORY and GALAXY_TEST_ERRORS_DIRECTORY != "0":
|
||||
if not os.path.exists(GALAXY_TEST_ERRORS_DIRECTORY):
|
||||
os.makedirs(GALAXY_TEST_ERRORS_DIRECTORY)
|
||||
result_name = f.__name__ + datetime.datetime.now().strftime("%Y%m%d%H%M%s")
|
||||
target_directory = os.path.join(GALAXY_TEST_ERRORS_DIRECTORY, result_name)
|
||||
retry_attempts = 0
|
||||
while True:
|
||||
try:
|
||||
return f(self, *args, **kwds)
|
||||
except Exception:
|
||||
if GALAXY_TEST_ERRORS_DIRECTORY and GALAXY_TEST_ERRORS_DIRECTORY != "0":
|
||||
if not os.path.exists(GALAXY_TEST_ERRORS_DIRECTORY):
|
||||
os.makedirs(GALAXY_TEST_ERRORS_DIRECTORY)
|
||||
result_name = f.__name__ + datetime.datetime.now().strftime("%Y%m%d%H%M%s")
|
||||
target_directory = os.path.join(GALAXY_TEST_ERRORS_DIRECTORY, result_name)
|
||||
|
||||
def write_file(name, content):
|
||||
with open(os.path.join(target_directory, name), "wb") as buf:
|
||||
buf.write(content.encode("utf-8"))
|
||||
def write_file(name, content):
|
||||
with open(os.path.join(target_directory, name), "wb") as buf:
|
||||
buf.write(content.encode("utf-8"))
|
||||
|
||||
os.makedirs(target_directory)
|
||||
self.driver.save_screenshot(os.path.join(target_directory, "last.png"))
|
||||
write_file("page_source.txt", self.driver.page_source)
|
||||
write_file("DOM.txt", self.driver.execute_script("return document.documentElement.outerHTML"))
|
||||
iframes = self.driver.find_elements_by_css_selector("iframe")
|
||||
for iframe in iframes:
|
||||
pass
|
||||
# TODO: Dump content out for debugging in the future.
|
||||
# iframe_id = iframe.get_attribute("id")
|
||||
# if iframe_id:
|
||||
# write_file("iframe_%s" % iframe_id, "My content")
|
||||
os.makedirs(target_directory)
|
||||
self.driver.save_screenshot(os.path.join(target_directory, "last.png"))
|
||||
write_file("page_source.txt", self.driver.page_source)
|
||||
write_file("DOM.txt", self.driver.execute_script("return document.documentElement.outerHTML"))
|
||||
write_file("stacktrace.txt", traceback.format_exc())
|
||||
iframes = self.driver.find_elements_by_css_selector("iframe")
|
||||
for iframe in iframes:
|
||||
pass
|
||||
# TODO: Dump content out for debugging in the future.
|
||||
# iframe_id = iframe.get_attribute("id")
|
||||
# if iframe_id:
|
||||
# write_file("iframe_%s" % iframe_id, "My content")
|
||||
|
||||
raise
|
||||
if retry_attempts < GALAXY_TEST_SELENIUM_RETRIES:
|
||||
retry_attempts += 1
|
||||
else:
|
||||
raise
|
||||
|
||||
return func_wrapper
|
||||
|
||||
|
||||
@@ -29,10 +29,8 @@ class WorkflowRunTestCase(SeleniumTestCase, UsesHistoryItemAssertions):
|
||||
with self.main_panel():
|
||||
self.workflow_run_submit()
|
||||
|
||||
time.sleep(.5)
|
||||
self.wait_for_history()
|
||||
self.home()
|
||||
self.history_panel_wait_for_hid_ok(2)
|
||||
self.history_panel_wait_for_hid_ok(3)
|
||||
self.history_panel_click_item_title(hid=2, wait=True)
|
||||
self.assert_item_summary_includes(2, "2 sequences")
|
||||
|
||||
|
||||
@@ -7,9 +7,7 @@ commands = bash .ci/flake8_wrapper.sh
|
||||
whitelist_externals = bash
|
||||
deps =
|
||||
flake8
|
||||
flake8-docstrings
|
||||
# The next dep can be removed when https://gitlab.com/pycqa/flake8-docstrings/issues/19 is fixed
|
||||
pydocstyle<2
|
||||
flake8-docstrings>=1.1.0
|
||||
|
||||
[testenv:py33-lint]
|
||||
commands = bash .ci/flake8_py3_wrapper.sh
|
||||
@@ -81,9 +79,8 @@ whitelist_externals = bash
|
||||
skip_install = True
|
||||
deps =
|
||||
flake8
|
||||
flake8-docstrings
|
||||
# The next dep can be removed when https://gitlab.com/pycqa/flake8-docstrings/issues/19 is fixed
|
||||
pydocstyle<2
|
||||
flake8-docstrings>=1.1.0
|
||||
|
||||
|
||||
[testenv:py27-lint-docstring-include-list]
|
||||
commands = bash .ci/flake8_wrapper_docstrings.sh --include
|
||||
@@ -91,6 +88,4 @@ whitelist_externals = bash
|
||||
skip_install = True
|
||||
deps =
|
||||
flake8
|
||||
flake8-docstrings
|
||||
# The next dep can be removed when https://gitlab.com/pycqa/flake8-docstrings/issues/19 is fixed
|
||||
pydocstyle<2
|
||||
flake8-docstrings>=1.1.0
|
||||
|
||||
Reference in New Issue
Block a user