diff --git a/.ci/flake8_wrapper_docstrings.sh b/.ci/flake8_wrapper_docstrings.sh index 4fe943cdf42..fa728303331 100755 --- a/.ci/flake8_wrapper_docstrings.sh +++ b/.ci/flake8_wrapper_docstrings.sh @@ -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 diff --git a/.ci/jenkins/selenium/run_tests.sh b/.ci/jenkins/selenium/run_tests.sh index 6786d51c714..4be5c13ed70 100755 --- a/.ci/jenkins/selenium/run_tests.sh +++ b/.ci/jenkins/selenium/run_tests.sh @@ -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}" diff --git a/CITATION b/CITATION index 1e6092ee725..2151602534b 100644 --- a/CITATION +++ b/CITATION @@ -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 diff --git a/client/galaxy/scripts/apps/analysis.js b/client/galaxy/scripts/apps/analysis.js index e67e7425a1f..2ccc615ca0d 100644 --- a/client/galaxy/scripts/apps/analysis.js +++ b/client/galaxy/scripts/apps/analysis.js @@ -69,6 +69,18 @@ window.app = function app( options, bootstrapped ){ Galaxy.currHistoryPanel = historyPanel.historyView; 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 /** */ 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, }); }); -}; \ No newline at end of file +}; diff --git a/client/galaxy/scripts/mvc/citation/citation-view.js b/client/galaxy/scripts/mvc/citation/citation-view.js index 5fb36002468..baccd25a9d7 100644 --- a/client/galaxy/scripts/mvc/citation/citation-view.js +++ b/client/galaxy/scripts/mvc/citation/citation-view.js @@ -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', - ' cite Galaxy.', + ' cite Galaxy.', '', ].join(''); } else { diff --git a/client/galaxy/scripts/mvc/library/library-folderlist-view.js b/client/galaxy/scripts/mvc/library/library-folderlist-view.js index 5221125b371..644f9fdcd38 100644 --- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js +++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js @@ -386,7 +386,7 @@ var FolderListView = Backbone.View.extend({ '', '' ].join('')); diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js index ff825408d3c..d6a13549869 100644 --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -1151,7 +1151,7 @@ var FolderToolbarView = Backbone.View.extend({ ' Details', '', '', - '', + '', '', '', '', diff --git a/client/galaxy/scripts/mvc/tool/tool-form-base.js b/client/galaxy/scripts/mvc/tool/tool-form-base.js index fb1c7d9af2d..6e5fa18b3a9 100644 --- a/client/galaxy/scripts/mvc/tool/tool-form-base.js +++ b/client/galaxy/scripts/mvc/tool/tool-form-base.js @@ -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 = $( '' ).attr( 'target', '_blank' ).attr( 'href', 'https://wiki.galaxyproject.org/Tools/Requirements' ).text( 'here' ); + var requirements_link = $( '' ).attr( 'target', '_blank' ).attr( 'href', 'https://galaxyproject.org/tools/requirements/' ).text( 'here' ); return $( '' ).append( requirements_message + '. Click ' ).append( requirements_link ).append( ' for more information.' ); } return 'No requirements found.'; diff --git a/client/galaxy/scripts/mvc/user/user-preferences.js b/client/galaxy/scripts/mvc/user/user-preferences.js index 4f810bd7c87..f43bac73036 100644 --- a/client/galaxy/scripts/mvc/user/user-preferences.js +++ b/client/galaxy/scripts/mvc/user/user-preferences.js @@ -153,7 +153,7 @@ define( [ 'mvc/form/form-view', 'mvc/ui/ui-misc' ], function( Form, Ui ) { return '

' + 'You are using ' + options.nice_total_disk_usage + ' of disk space in this Galaxy instance. ' + ( Galaxy.config.enable_quotas ? 'Your disk quota is: ' + options.quota + '. ' : '' ) + - 'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.' + + 'Is your usage more than expected? See the documentation for tips on how to find all of the data in your account.' + '

'; } }); diff --git a/client/galaxy/scripts/mvc/workflow/workflow-forms.js b/client/galaxy/scripts/mvc/workflow/workflow-forms.js index 965f70db631..1aed0dd189a 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-forms.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-forms.js @@ -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 here for more information. Valid inputs are: ' + input_terminal_names.join(', ') + '.' + help : 'This action will rename the output dataset. Click here for more information. Valid inputs are: ' + input_terminal_names.join(', ') + '.' },{ action : 'ChangeDatatypeAction', pja_arg : 'newtype', diff --git a/client/galaxy/scripts/viz/phyloviz.js b/client/galaxy/scripts/viz/phyloviz.js index 15a17a0909e..4fbc8d3f1e4 100644 --- a/client/galaxy/scripts/viz/phyloviz.js +++ b/client/galaxy/scripts/viz/phyloviz.js @@ -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 } } ], diff --git a/config/galaxy.ini.sample b/config/galaxy.ini.sample index 220d64e9d83..5720c826698 100644 --- a/config/galaxy.ini.sample +++ b/config/galaxy.ini.sample @@ -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 diff --git a/config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample b/config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample index e9bf4b4aa15..e632f553ec1 100644 --- a/config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample +++ b/config/plugins/interactive_environments/jupyter/config/jupyter.ini.sample @@ -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 diff --git a/config/plugins/interactive_environments/jupyter/templates/jupyter.mako b/config/plugins/interactive_environments/jupyter/templates/jupyter.mako index 8f8490f5367..eab2674bc7a 100644 --- a/config/plugins/interactive_environments/jupyter/templates/jupyter.mako +++ b/config/plugins/interactive_environments/jupyter/templates/jupyter.mako @@ -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, } ) diff --git a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample index 695ee5c6e9f..ad4d0cf9c0c 100644 --- a/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample +++ b/config/plugins/interactive_environments/rstudio/config/rstudio.ini.sample @@ -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 diff --git a/config/plugins/interactive_environments/rstudio/templates/rstudio.mako b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako index 1277c4c34ce..cbb8485c15c 100644 --- a/config/plugins/interactive_environments/rstudio/templates/rstudio.mako +++ b/config/plugins/interactive_environments/rstudio/templates/rstudio.mako @@ -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, } ) diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index f0b6295df8a..fdc09c12b2c 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -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 ) diff --git a/lib/galaxy/managers/configuration.py b/lib/galaxy/managers/configuration.py index 805c3958df5..fc34afdd619 100644 --- a/lib/galaxy/managers/configuration.py +++ b/lib/galaxy/managers/configuration.py @@ -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 ), diff --git a/lib/galaxy/tools/data_manager/manager.py b/lib/galaxy/tools/data_manager/manager.py index 1f9a9cf81fb..bb86dfaf9ab 100644 --- a/lib/galaxy/tools/data_manager/manager.py +++ b/lib/galaxy/tools/data_manager/manager.py @@ -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: diff --git a/lib/galaxy/tools/parameters/validation.py b/lib/galaxy/tools/parameters/validation.py index 36eac3f14bf..481186e2843 100644 --- a/lib/galaxy/tools/parameters/validation.py +++ b/lib/galaxy/tools/parameters/validation.py @@ -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, ) diff --git a/lib/galaxy/tools/xsd/galaxy.xsd b/lib/galaxy/tools/xsd/galaxy.xsd index 6138f86a4e3..36e92c2226f 100644 --- a/lib/galaxy/tools/xsd/galaxy.xsd +++ b/lib/galaxy/tools/xsd/galaxy.xsd @@ -5153,6 +5153,7 @@ and ``bibtex`` are the only supported options. + diff --git a/lib/galaxy/web/base/controllers/admin.py b/lib/galaxy/web/base/controllers/admin.py index 2b8f11e0386..420b24756c8 100644 --- a/lib/galaxy/web/base/controllers/admin.py +++ b/lib/galaxy/web/base/controllers/admin.py @@ -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 Contact support 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 diff --git a/lib/galaxy/web/base/interactive_environments.py b/lib/galaxy/web/base/interactive_environments.py index 291374133fe..5a61af80d9e 100644 --- a/lib/galaxy/web/base/interactive_environments.py +++ b/lib/galaxy/web/base/interactive_environments.py @@ -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 diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py index 00f9d6025bb..d3ae2386ae3 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -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 tag is ' message += '). 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 diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index 7b103af9f53..b30692cd283 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -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 shed_tool_conf.xml ' message += 'whose <toolbox> tag is <toolbox tool_path="../shed_tools">).

See the ' - message += 'Installation ' + message += 'Installation ' message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance section of the Galaxy Tool ' message += 'Shed wiki for all of the details.' return trans.show_error_message( message ) diff --git a/lib/galaxy/webapps/reports/config.py b/lib/galaxy/webapps/reports/config.py index a56168425be..89289aa78e8 100644 --- a/lib/galaxy/webapps/reports/config.py +++ b/lib/galaxy/webapps/reports/config.py @@ -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 diff --git a/lib/galaxy/webapps/tool_shed/config.py b/lib/galaxy/webapps/tool_shed/config.py index d787ace36c6..2526e8dfa81 100644 --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -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 ) diff --git a/lib/tool_shed/galaxy_install/tools/data_manager.py b/lib/tool_shed/galaxy_install/tools/data_manager.py index b56fc073e53..5be2c2e220f 100644 --- a/lib/tool_shed/galaxy_install/tools/data_manager.py +++ b/lib/tool_shed/galaxy_install/tools/data_manager.py @@ -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( '\n\n' ) + if data_managers_path is not None: + fh.write( '\n\n ' % data_managers_path ) + else: + fh.write( '\n\n ' ) for elem in config_elems: fh.write( xml_util.xml_to_string( elem ) ) fh.write( '\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 ) diff --git a/run_tests.sh b/run_tests.sh index 6cf42689987..4e38521a180 100755 --- a/run_tests.sh +++ b/run_tests.sh @@ -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 diff --git a/setup.cfg b/setup.cfg index b73b6ec5ade..62ef47ece00 100644 --- a/setup.cfg +++ b/setup.cfg @@ -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 diff --git a/static/maps/mvc/citation/citation-view.js.map b/static/maps/mvc/citation/citation-view.js.map index 8454efa7beb..b67e2708532 100644 --- a/static/maps/mvc/citation/citation-view.js.map +++ b/static/maps/mvc/citation/citation-view.js.map @@ -1 +1 @@ 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"],"element");return o.extend({},r.prototype.templates,{titleBar:e})}();var h=t.DatasetListItemView.extend({className:t.DatasetListItemView.prototype.className+" dataset-collection-element",initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log("DatasetDCEListItemView.initialize:",e),t.DatasetListItemView.prototype.initialize.call(this,e)},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):l.when()},toString:function(){var e=this.model?this.model+"":"(no model)";return"DatasetDCEListItemView("+e+")"}});h.prototype.templates=function(){var e=i.wrapTemplate(['
','','
','<%- element.element_identifier %>',"
","
"],"element");return o.extend({},t.DatasetListItemView.prototype.templates,{titleBar:e})}();var u=c.extend({className:c.prototype.className+" dataset-collection-element",_swapNewRender:function(e){c.prototype._swapNewRender.call(this,e);var t=this.model.get("state")||"ok";return this.$el.addClass("state-"+t),this.$el},toString:function(){var e=this.model?this.model+"":"(no model)";return"NestedDCDCEListItemView("+e+")"}});return{DCListItemView:c,DCEListItemView:d,DatasetDCEListItemView:h,NestedDCDCEListItemView:u}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a,l){n=[i(75),i(6),i(5)],s=function(e,t,i){"use strict";var n={defaults:{model_class:"DatasetCollectionElement",element_identifier:null,element_index:null,element_type:null},_mergeObject:function(e){return o.extend(e,e.object,{element_id:e.id}),delete 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e=this.get("element_identifier");return["DatasetDCE(",e,")"].join("")}})),d=r.extend({model:c,toString:function(){return["DatasetDCECollection(",this.length,")"].join("")}}),h=a.Model.extend(t.LoggableMixin).extend(t.SearchableModelMixin).extend({_logNamespace:"collections",defaults:{collection_type:null,deleted:!1},collectionClass:r,initialize:function(e,t){this.debug(this+"(DatasetCollection).initialize:",e,t,this),this.elements=this._createElementsModel(),this.on("change:elements",function(){this.log("change:elements"),this.elements=this._createElementsModel()})},_createElementsModel:function(){this.debug(this+"._createElementsModel",this.collectionClass,this.get("elements"),this.elements);var e=this.get("elements")||[];return this.unset("elements",{silent:!0}),this.elements=new this.collectionClass(e),this.elements},toJSON:function(){var e=a.Model.prototype.toJSON.call(this);return this.elements&&(e.elements=this.elements.toJSON()),e},inReadyState:function(){var 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e=[this.get("id"),this.get("name")||this.get("element_identifier")];return"DatasetCollection("+e.join(",")+")"}}),u=h.extend({collectionClass:d,toString:function(){return"List"+h.prototype.toString.call(this)}}),p=u.extend({toString:function(){return"Pair"+h.prototype.toString.call(this)}}),f=h.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedDCDCE(",e,")"].join("")}})),g=r.extend({model:f,toString:function(){return["NestedDCDCECollection(",this.length,")"].join("")}}),m=p.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedPairDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedPairDCDCE(",e,")"].join("")}})),v=g.extend({model:m,toString:function(){return["NestedPairDCDCECollection(",this.length,")"].join("")}}),_=h.extend({collectionClass:v,toString:function(){return["ListPairedDatasetCollection(",this.get("name"),")"].join("")}}),y=u.extend(t.mixin(n,{constructor:function(e,t){this.debug("\t NestedListDCDCE.constructor:",e,t),n.constructor.call(this,e,t)},toString:function(){var e=this.object?""+this.object:this.get("element_identifier");return["NestedListDCDCE(",e,")"].join("")}})),b=g.extend({model:y,toString:function(){return["NestedListDCDCECollection(",this.length,")"].join("")}}),w=h.extend({collectionClass:b,toString:function(){return["ListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{ListDatasetCollection:u,PairDatasetCollection:p,ListPairedDatasetCollection:_,ListOfListsDatasetCollection:w}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(3),i(1))},function(e,t,i){var n,s;(function(o,a,l,r){n=[i(42),i(12),i(6),i(72),i(8),i(90),i(5),i(87)],s=function(e,t,i,n,s,c,d){"use strict";function h(e,t){var i=e.toJSON(),n=m(i,{defaultHideSourceItems:t,creationFn:function(t,i,n){return t=t.map(function(e){return{id:e.id,name:e.name,src:"dataset"===e.history_content_type?"hda":"hdca"}}),e.createHDCA(t,"list",i,n)}});return n}var u="collections",p=o.View.extend(i.LoggableMixin).extend({_logNamespace:u,tagName:"li",className:"collection-element",initialize:function(e){this.element=e.element||{},this.selected=e.selected||!1},render:function(){return this.$el.attr("data-element-id",this.element.id).attr("draggable",!0).html(this.template({element:this.element})),this.selected&&this.$el.addClass("selected"),this},template:a.template(['',"<%- element.name 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creator")},oncreate:function(){},oncancel:function(){},autoscrollDist:24,highlightClr:"rgba( 64, 255, 255, 1.0 )"},footerSettings:{".hide-originals":"hideOriginals"},initialize:function(e){this.metric("ListCollectionCreator.initialize",e);var t=this;a.each(this.defaultAttributes,function(i,n){i=e[n]||i,t[n]=i}),t.initialElements=e.elements||[],this._setUpCommonSettings(e),this._instanceSetUp(),this._elementsSetUp(),this._setUpBehaviors()},_instanceSetUp:function(){this.selectedIds={},this.$dragging=null,this.blocking=!1},_elementsSetUp:function(){this.invalidElements=[],this.workingElements=[],this.elementViews=[],this.workingElements=this.initialElements.slice(0),this._ensureElementIds(),this._validateElements(),this._mangleDuplicateNames(),this._sortElements()},_ensureElementIds:function(){return this.workingElements.forEach(function(e){e.hasOwnProperty("id")||(e.id=a.uniqueId())}),this.workingElements},_validateElements:function(){var e=this;return e.invalidElements=[],this.workingElements=this.workingElements.filter(function(t){var i=e._isElementInvalid(t);return i&&e.invalidElements.push({element:t,text:i}),!i}),this.workingElements},_isElementInvalid:function(e){if("dataset"!==e.history_content_type)return d("is not a dataset");var i=e.state===t.OK||a.contains(t.NOT_READY_STATES,e.state);return i?e.deleted||e.purged?d("has been deleted or purged"):null:d("has errored, is paused, or is not accessible")},_mangleDuplicateNames:function(){var e=900,t=1,i={};this.workingElements.forEach(function(n){for(var s=n.name;i.hasOwnProperty(s);)if(s=n.name+" ("+t+")",t+=1,t>=e)throw new Error("Safety hit in while loop - thats impressive");n.name=s,i[n.name]=!0})},_sortElements:function(e){},render:function(e,t){return this.workingElements.length .clear-selected").show():this.$(".collection-elements-controls > .clear-selected").hide()},_renderList:function(e,t){var i=this,n=r("
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":content+=": "+n}t._showAlert(content,"alert-danger")},events:{"click .more-help":"_clickMoreHelp","click .less-help":"_clickLessHelp","click .main-help":"_toggleHelp","click .header .alert button":"_hideAlert","click .reset":"reset","click .clear-selected":"clearSelectedElements","click .collection-elements":"clearSelectedElements","dragover .collection-elements":"_dragoverElements","drop .collection-elements":"_dropElements","collection-element.dragstart .collection-elements":"_elementDragstart","collection-element.dragend .collection-elements":"_elementDragend","change .collection-name":"_changeName","keydown .collection-name":"_nameCheckForEnter","change .hide-originals":"_changeHideOriginals","click .cancel-create":"_cancelCreate","click .create-collection":"_clickCreate"},reset:function(){this._instanceSetUp(),this._elementsSetUp(),this.render()},clearSelectedElements:function(e){this.$(".collection-elements .collection-element").removeClass("selected"),this.$(".collection-elements-controls > .clear-selected").hide()},_dragoverElements:function(e){e.preventDefault();var t=this.$list();this._checkForAutoscroll(t,e.originalEvent.clientY);var i=this._getNearestElement(e.originalEvent.clientY);this.$(".element-drop-placeholder").remove();var n=l('
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",'
','','',"
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','',d("Start over"),"",'',d("Clear selected"),"","
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',"
"].join("")),footer:a.template(['
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','','
',d("Name"),":
","
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",'
','
','",'
','",'","
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','","
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","
    ","
  • ",d(["Rename elements in the list by clicking on ",'the existing name.'].join("")),"
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  • ",d(["Discard elements from the final created list by clicking on the ",'"Discard" button.'].join("")),"
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  • ",d(["Reorder the list by clicking and dragging elements. Select multiple elements by clicking on ",'them and you can then move those selected by dragging the ',"entire group. Deselect them by clicking them again or by clicking the ",'the "Clear selected" link.'].join("")),"
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  • ",d(['Click the "Start over" link to begin again as if you had just opened ',"the interface."].join("")),"
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  • ",d(['Click the "Cancel" button to exit the interface.'].join("")),"
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","

",d(['Once your collection is complete, enter a name and ','click "Create list".'].join("")),"

"].join("")),invalidElements:a.template([d("The following selections could not be included due to problems:"),"
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"].join("")),noElementsLeft:a.template(['
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    ','',"<% if( _.size( problems ) ){ %>",d("The following selections could not be included due to problems"),":","
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    ",'
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    ','","
    ","
    ","
    "].join(""))}),toString:function(){return"ListCollectionCreator"}}),g=function(e,t,i){var n,o=r.Deferred(),l=Galaxy.modal||new s.View;return t=a.defaults(t||{},{elements:e,oncancel:function(){l.hide(),o.reject("cancelled")},oncreate:function(e,t){l.hide(),o.resolve(t)}}),n=new i(t),l.show({title:t.title||d("Create a collection"),body:n.$el,width:"80%",height:"100%",closing_events:!0}),n.render(),window._collectionCreator=n,o},m=function(e,t){return t=t||{},t.title=d("Create a collection from a list of datasets"),g(e,t,f)};return{DatasetCollectionElementView:p,ListCollectionCreator:f,collectionCreatorModal:g,listCollectionCreatorModal:m,createListCollection:h}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2),i(1),i(1))},function(e,t,i){var n,s;(function(o,a,l,r){n=[i(45),i(12),i(18),i(6),i(5)],s=function(e,t,i,n,s){"use strict";var c="dataset",d=e.ListItemView,h=d.extend({_logNamespace:c,className:d.prototype.className+" dataset",id:function(){return["dataset",this.model.get("id")].join("-")},initialize:function(e){e.logger&&(this.logger=this.model.logger=e.logger),this.log(this+".initialize:",e),d.prototype.initialize.call(this,e),this.linkTarget=e.linkTarget||"_blank"},_setUpListeners:function(){d.prototype._setUpListeners.call(this);var e=this;return e.listenTo(e.model,{change:function(t,i){e.model.changedAttributes().state&&e.model.inReadyState()&&e.expanded&&!e.model.hasDetails()?e.model.fetch({silent:!0}).done(function(){e.render()}):o.has(t.changed,"tags")&&1===o.keys(t.changed).length?this.$("> .title-bar").replaceWith(this._renderTitleBar()):e.render()}})},_fetchModelDetails:function(){var e=this;return e.model.inReadyState()&&!e.model.hasDetails()?e.model.fetch({silent:!0}):a.when()},remove:function(e,t){var i=this;e=e||this.fxSpeed,this.$el.fadeOut(e,function(){l.View.prototype.remove.call(i),t&&t.call(i)})},_swapNewRender:function(e){return d.prototype._swapNewRender.call(this,e),this.model.has("state")&&this.$el.addClass("state-"+this.model.get("state")),this.$el},_renderPrimaryActions:function(){return[this._renderDisplayButton()]},_renderDisplayButton:function(){var e=this.model.get("state");if(e===t.NOT_VIEWABLE||e===t.DISCARDED||!this.model.get("accessible"))return null; -var n={target:this.linkTarget,classes:"display-btn"};if(this.model.get("purged"))n.disabled=!0,n.title=s("Cannot display datasets removed from disk");else if(e===t.UPLOAD)n.disabled=!0,n.title=s("This dataset must finish uploading before it can be viewed");else if(e===t.NEW)n.disabled=!0,n.title=s("This dataset is not yet viewable");else{n.title=s("View data"),n.href=this.model.urls.display;var o=this;n.onclick=function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.addDataset(o.model.get("id")),e.preventDefault())}}return n.faIcon="fa-eye",i(n)},_renderDetails:function(){if(this.model.get("state")===t.NOT_VIEWABLE)return r(this.templates.noAccess(this.model.toJSON(),this));var e=d.prototype._renderDetails.call(this);return e.find(".actions .left").empty().append(this._renderSecondaryActions()),e.find(".summary").html(this._renderSummary()).prepend(this._renderDetailMessages()),e.find(".display-applications").html(this._renderDisplayApplications()),this._setUpBehaviors(e),e},_renderSummary:function(){var e=this.model.toJSON(),t=this.templates.summaries[e.state];return(t=t||this.templates.summaries.unknown)(e,this)},_renderDetailMessages:function(){var e=this,t=r('
    '),i=e.model.toJSON();return o.each(e.templates.detailMessages,function(n){t.append(r(n(i,e)))}),t},_renderDisplayApplications:function(){return this.model.isDeletedOrPurged()?"":[this.templates.displayApplications(this.model.get("display_apps"),this),this.templates.displayApplications(this.model.get("display_types"),this)].join("")},_renderSecondaryActions:function(){switch(this.debug("_renderSecondaryActions"),this.model.get("state")){case t.NOT_VIEWABLE:return[];case t.OK:case t.FAILED_METADATA:case t.ERROR:return[this._renderDownloadButton(),this._renderShowParamsButton()]}return[this._renderShowParamsButton()]},_renderShowParamsButton:function(){return i({title:s("View details"),classes:"params-btn",href:this.model.urls.show_params,target:this.linkTarget,faIcon:"fa-info-circle",onclick:function(e){Galaxy.frame&&Galaxy.frame.active&&(Galaxy.frame.add({title:"Dataset details",url:this.href}),e.preventDefault(),e.stopPropagation())}})},_renderDownloadButton:function(){return this.model.get("purged")||!this.model.hasData()?null:o.isEmpty(this.model.get("meta_files"))?r(['','',""].join("")):this._renderMetaFileDownloadButton()},_renderMetaFileDownloadButton:function(){var e=this.model.urls;return r(['
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    ","<% } %>"]),error:n.wrapTemplate(["<% if( model.error ){ %>",'
    ',s("There was an error getting the data for this dataset"),": <%- model.error %>","
    ","<% } %>"]),purged:n.wrapTemplate(["<% if( model.purged ){ %>",'
    ',s("This dataset has been deleted and removed from disk"),"
    ","<% } %>"]),deleted:n.wrapTemplate(["<% if( model.deleted && !model.purged ){ %>",'
    ',s("This dataset has been deleted"),"
    ","<% } %>"])}),i=n.wrapTemplate(['
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    ','
    ','
    ','
    ',"
    ","<% if( !dataset.deleted && !dataset.purged ){ %>",'
    ','
    ','
    ',"<% if( dataset.peek ){ %>",'
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    "],"dataset"),a=n.wrapTemplate(['
    ','
    ',s("You do not have permission to view this dataset"),"
    ","
    "],"dataset"),l={};l[t.OK]=l[t.FAILED_METADATA]=n.wrapTemplate(["<% if( dataset.misc_blurb ){ %>",'
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    ","<% } %>","<% if( dataset.file_ext ){ %>",'
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    ","<% } %>","<% if( dataset.misc_info ){ %>",'
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    ","<% } %>"],"dataset"),l[t.NEW]=n.wrapTemplate(["
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    "],"dataset"),l[t.NOT_VIEWABLE]=n.wrapTemplate(["
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    "],"dataset"),l[t.RUNNING]=n.wrapTemplate(["
    ",s("This job is currently running"),"
    "],"dataset"),l[t.UPLOAD]=n.wrapTemplate(["
    ",s("This dataset is currently uploading"),"
    "],"dataset"),l[t.SETTING_METADATA]=n.wrapTemplate(["
    ",s("Metadata is being auto-detected"),"
    "],"dataset"),l[t.PAUSED]=n.wrapTemplate(["
    ",s('This job is paused. Use the "Resume Paused Jobs" in the history menu to resume'),"
    "],"dataset"),l[t.ERROR]=n.wrapTemplate(["<% if( !dataset.purged ){ %>","
    <%- dataset.misc_blurb %>
    ","<% } %>",'',s("An error occurred with this dataset"),":",'
    <%- dataset.misc_info %>
    '],"dataset"),l[t.EMPTY]=n.wrapTemplate(["
    ",s("No data"),": <%- dataset.misc_blurb %>
    "],"dataset"),l.unknown=n.wrapTemplate(['
    Error: unknown dataset state: "<%- dataset.state %>"
    '],"dataset");var r={resubmitted:n.wrapTemplate(["<% if( model.resubmitted ){ %>",'
    ',s("The job creating this dataset has been resubmitted"),"
    ","<% } %>"])},c=n.wrapTemplate(["<% _.each( apps, function( app ){ %>",'
    ','<%- app.label %> ','',"<% _.each( app.links, function( link ){ %>",'',"<% print( _l( link.text ) ); %>"," ","<% }); %>","","
    ","<% }); %>"],"apps");return o.extend({},d.prototype.templates,{warnings:e,details:i,noAccess:a,summaries:l,detailMessages:r,displayApplications:c})}(),{DatasetListItemView:h}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3),i(1))},function(e,t,i){var n,s;(function(o,a,l){n=[i(4)],s=function(e){var t=o.Model.extend({initialize:function(e){this.app=e},checksum:function(){var e="",t=this;return this.app.section.$el.find(".section-row").each(function(){var i=a(this).attr("id"),n=t.app.field_list[i];n&&(e+=i+":"+JSON.stringify(n.value&&n.value())+":"+n.collapsed+";")}),e},create:function(){function e(e,t,i){n.flat_dict[e]=t,o[e]=i,n.app.element_list[t]&&n.app.element_list[t].$el.attr("tour_id",e)}function t(s,o){for(var a in o){var l=o[a];if(l.input){var r=l.input,c=s;switch(""!=s&&(c+="|"),c+=r.name,r.type){case"repeat":var d="section-",h=[],u=null;for(var p in l){var f=p.indexOf(d);f!=-1&&(f+=d.length,h.push(parseInt(p.substr(f))),u||(u=p.substr(0,f)))}h.sort(function(e,t){return e-t});var a=0;for(var g in h)t(c+"_"+a++,l[u+h[g]]);break;case"conditional":var m=n.app.field_list[r.id].value();e(c+"|"+r.test_param.name,r.id,m);var v=i(r,m);v!=-1&&t(c,o[r.id+"-section-"+v]);break;case"section":t(!r.flat&&c||"",l);break;default:var _=n.app.field_list[r.id];if(_&&_.value){var m=_.value();if((void 0===r.ignore||r.ignore!=m)&&(_.collapsed&&r.collapsible_value&&(m=r.collapsible_value),e(c,r.id,m),r.payload))for(var y in r.payload)e(y,r.id,r.payload[y])}}}}}var n=this,s={};this._iterate(this.app.section.$el,s);var o={};return this.flat_dict={},t("",s),o},match:function(e){return this.flat_dict&&this.flat_dict[e]},matchCase:function(e,t){return i(e,t)},matchModel:function(e,t){var i=this;n(e.inputs,function(e,n){i.flat_dict[n]&&t(e,i.flat_dict[n])})},matchResponse:function(e){function t(e,s){if("string"==typeof s){var o=n.flat_dict[e];o&&(i[o]=s)}else for(var a in s){var l=a;if(""!==e){var r="|";s instanceof Array&&(r="_"),l=e+r+l}t(l,s[a])}}var i={},n=this;return t("",e),i},_iterate:function(e,t){var i=this,n=a(e).children();n.each(function(){var e=this,n=a(e).attr("id");if(a(e).hasClass("section-row")){var s=i.app.input_list[n];t[n]=s&&{input:s}||{},i._iterate(e,t[n])}else i._iterate(e,t)})}}),i=function(e,t){"boolean"==e.test_param.type&&(t="true"==t?e.test_param.truevalue||"true":e.test_param.falsevalue||"false");for(var i in e.cases)if(e.cases[i].value==t)return i;return-1},n=function(e,t,s,o){o=a.extend(!0,{},o),l.each(e,function(e){e&&e.type&&e.name&&(o[e.name]=e)});for(var r in e){var c=e[r];c.name=c.name||r;var d=s?s+"|"+c.name:c.name;switch(c.type){case"repeat":l.each(c.cache,function(e,i){n(e,t,d+"_"+i,o)});break;case"conditional":if(c.test_param){t(c.test_param,d+"|"+c.test_param.name,o);var h=i(c,c.test_param.value);h!=-1?n(c.cases[h].inputs,t,d,o):Galaxy.emit.debug("form-data::visitInputs() - Invalid case for "+d+".")}else Galaxy.emit.debug("form-data::visitInputs() - Conditional test parameter missing for "+d+".");break;case"section":n(c.inputs,t,d,o);break;default:t(c,d,o)}}};return{Manager:t,visitInputs:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(i,o,a){n=[],s=function(){return i.View.extend({initialize:function(e,t){this.app=e,this.app_options=e.model?e.model.attributes:{},this.field=t&&t.field||new i.View,this.model=t&&t.model||new i.Model({text_enable:this.app_options.text_enable||"Enable",text_disable:this.app_options.text_disable||"Disable",cls_enable:this.app_options.cls_enable||"fa fa-caret-square-o-down",cls_disable:this.app_options.cls_disable||"fa fa-caret-square-o-up"}).set(t),this.setElement(this._template()),this.$field=this.$(".ui-form-field"),this.$info=this.$(".ui-form-info"),this.$preview=this.$(".ui-form-preview"),this.$collapsible=this.$(".ui-form-collapsible"),this.$collapsible_text=this.$(".ui-form-collapsible-text"),this.$collapsible_icon=this.$(".ui-form-collapsible-icon"),this.$title=this.$(".ui-form-title"),this.$title_text=this.$(".ui-form-title-text"),this.$error_text=this.$(".ui-form-error-text"),this.$error=this.$(".ui-form-error"),this.$backdrop=this.$(".ui-form-backdrop"),this.$field.prepend(this.field.$el);var n=this.model.get("collapsible_value");this.field.collapsed=void 0!==n&&JSON.stringify(this.model.get("value"))==JSON.stringify(n),this.listenTo(this.model,"change",this.render,this),this.render();var s=this;this.$collapsible.on("click",function(){s.field.collapsed=!s.field.collapsed,e.trigger&&e.trigger("change"),s.render()})},backdrop:function(){this.model.set("backdrop",!0)},error:function(e){this.model.set("error_text",e)},reset:function(){!this.model.get("fixed")&&this.model.set("error_text",null)},render:function(){o(".tooltip").hide();var e=this.model.get("help",""),t=this.model.get("argument");t&&e.indexOf("("+t+")")==-1&&(e+=" ("+t+")"),this.$info.html(e),this.$el[this.model.get("hidden")?"hide":"show"](),this.$preview[this.field.collapsed&&this.model.get("collapsible_preview")||this.model.get("disabled")?"show":"hide"]().html(a.escape(this.model.get("text_value")));var i=this.model.get("error_text");if(this.$error[i?"show":"hide"](),this.$el[i?"addClass":"removeClass"]("ui-error"),this.$error_text.html(i),this.$backdrop[this.model.get("backdrop")?"show":"hide"](),this.field.collapsed||this.model.get("disabled")?this.$field.hide():this.$field.show(),this.field.model&&this.field.model.set({color:this.model.get("color"),style:this.model.get("style")}),this.model.get("disabled")||void 0===this.model.get("collapsible_value"))this.$title_text.show().text(this.model.get("label")),this.$collapsible.hide();else{var n=this.field.collapsed?"enable":"disable";this.$title_text.hide(),this.$collapsible.show(),this.$collapsible_text.text(this.model.get("label")),this.$collapsible_icon.removeClass().addClass("icon").addClass(this.model.get("cls_"+n)).attr("data-original-title",this.model.get("text_"+n)).tooltip({placement:"bottom"})}},_template:function(){return o("
    ").addClass("ui-form-element").append(o("
    ").addClass("ui-form-error ui-error").append(o("").addClass("fa fa-arrow-down")).append(o("").addClass("ui-form-error-text"))).append(o("
    ").addClass("ui-form-title").append(o("
    ").addClass("ui-form-collapsible").append(o("").addClass("ui-form-collapsible-icon")).append(o("").addClass("ui-form-collapsible-text"))).append(o("").addClass("ui-form-title-text"))).append(o("
    ").addClass("ui-form-field").append(o("").addClass("ui-form-info")).append(o("
    ").addClass("ui-form-backdrop"))).append(o("
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    ").append(this.$list=a("
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    ").append(this.button_new.$el)))},size:function(){return l.size(this.list)},add:function(e){if(!e.id||this.list[e.id])return void Galaxy.emit.debug("form-repeat::add()","Duplicate or invalid repeat block id.");var n=new i.ButtonIcon({icon:"fa-trash-o",tooltip:"Delete this repeat block",cls:"ui-button-icon-plain form-repeat-delete",onclick:function(){e.ondel&&e.ondel()}}),s=new t.View({id:e.id,title:"placeholder",cls:e.cls||"ui-portlet-repeat",operations:{button_delete:n}});s.append(e.$el),s.$el.addClass("section-row").hide(),this.list[e.id]=s,this.$list.append(s.$el.fadeIn("fast")),this.options.max>0&&this.size()>=this.options.max&&this.button_new.disable(),this._refresh()},del:function(e){return this.list[e]?(this.$list.find("#"+e).remove(),delete this.list[e],this.button_new.enable(),void this._refresh()):void Galaxy.emit.debug("form-repeat::del()","Invalid repeat block id.")},delAll:function(){for(var e in this.list)this.del(e)},hideOptions:function(){this.button_new.$el.hide(),l.each(this.list,function(e){e.hideOperation("button_delete")}),l.isEmpty(this.list)&&this.$el.append(a("
    ").addClass("ui-form-info").html(this.options.empty_text))},_refresh:function(){var e=0;for(var t in this.list){var i=this.list[t];i.title(++e+": "+this.options.title),i[this.size()>this.options.min?"showOperation":"hideOperation"]("button_delete")}}});return{View:n}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2))},function(e,t,i){var n,s;(function(o,a,l,r){n=[i(4),i(7),i(9),i(40),i(38),i(39)],s=function(e,t,i,n,s,c){var d=o.View.extend({initialize:function(e,t){this.app=e,this.inputs=t.inputs,this.parameters=new c,this.setElement(a("
    ")),this.render()},render:function(){var e=this;this.$el.empty(),l.each(this.inputs,function(t){e.add(t)})},add:function(t){var i=r.extend(!0,{},t);switch(i.id=t.id=e.uid(),this.app.input_list[i.id]=i,i.type){case"conditional":this._addConditional(i);break;case"repeat":this._addRepeat(i);break;case"section":this._addSection(i);break;default:this._addRow(i)}},_addConditional:function(e){var t=this;e.test_param.id=e.id,this.app.model.get("sustain_conditionals")&&(e.test_param.disabled=!0);var i=this._addRow(e.test_param);i.model&&i.model.set("onchange",function(i){var n=t.app.data.matchCase(e,i);for(var s in e.cases){var o=e.cases[s],a=t.$("#"+e.id+"-section-"+s),l=!1;for(var r in o.inputs)if(!o.inputs[r].hidden){l=!0;break}s==n&&l?a.fadeIn("fast"):a.hide()}t.app.trigger("change")});for(var n in e.cases){var s=new d(this.app,{inputs:e.cases[n].inputs});this._append(s.$el.addClass("ui-form-section"),e.id+"-section-"+n)}i.trigger("change")},_addRepeat:function(e){function t(t){var n=e.id+"-section-"+o++,s=new d(i.app,{inputs:t});a.add({id:n,$el:s.$el,ondel:function(){a.del(n),i.app.trigger("change")}})}for(var i=this,o=0,a=new n.View({title:e.title||"Repeat",min:e.min,max:e.max,onnew:function(){t(e.inputs),i.app.trigger("change")}}),r=l.size(e.cache),c=0;c").addClass("ui-form-info").html(e.help)),this.app.on("expand",function(e){t.$("#"+e).length>0&&t.expand()}),this._append(t.$el,e.id)},_addRow:function(e){var t=this,i=e.id;e.onchange=e.onchange||function(){t.app.trigger("change",i)};var n=this.parameters.create(e);this.app.field_list[i]=n;var o=new s(this.app,{name:e.name,label:e.hide_label?"":e.label||e.name,value:e.value,text_value:e.text_value,collapsible_value:e.collapsible_value,collapsible_preview:e.collapsible_preview,help:e.help,argument:e.argument,disabled:e.disabled,color:e.color,style:e.style,backdrop:e.backdrop,hidden:e.hidden,fixed:e.fixed,field:n});return this.app.element_list[i]=o,this._append(o.$el,e.id),n},_append:function(e,t){this.$el.append(e.addClass("section-row").attr("id",t))}});return{View:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o){n=[i(34),i(79),i(5)],s=function(e,t,i){"use strict";function n(e){return function(t,i){return this.isNew()&&(i=i||{},i.url=this.urlRoot+this.get("history_id")+"/contents",t=t||{},t.type="dataset_collection"),e.call(this,t,i)}}var s=t.HistoryContentMixin,a=e.ListDatasetCollection,l=e.PairDatasetCollection,r=e.ListPairedDatasetCollection,c=e.ListOfListsDatasetCollection,d=a.extend(s).extend({defaults:o.extend(o.clone(a.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(a.prototype.save),toString:function(){return"History"+a.prototype.toString.call(this)}}),h=l.extend(s).extend({defaults:o.extend(o.clone(l.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(l.prototype.save),toString:function(){return"History"+l.prototype.toString.call(this)}}),u=r.extend(s).extend({defaults:o.extend(o.clone(r.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:paired",model_class:"HistoryDatasetCollectionAssociation"}),save:n(r.prototype.save),toString:function(){return"History"+r.prototype.toString.call(this)}}),p=c.extend(s).extend({defaults:o.extend(o.clone(c.prototype.defaults),{history_content_type:"dataset_collection",collection_type:"list:list",model_class:"HistoryDatasetCollectionAssociation"}),save:n(c.prototype.save),toString:function(){return["HistoryListOfListsDatasetCollection(",this.get("name"),")"].join("")}});return{HistoryListDatasetCollection:d,HistoryPairDatasetCollection:h,HistoryListPairedDatasetCollection:u,HistoryListOfListsDatasetCollection:p}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a,l){n=[i(71),i(77),i(42),i(44),i(6),i(136)],s=function(e,t,i,n,s,r){"use strict";var c=e.PaginatedCollection,d=c.extend(s.LoggableMixin).extend({_logNamespace:"history",model:function(e,n){if("dataset"===e.history_content_type)return new t.HistoryDatasetAssociation(e,n);if("dataset_collection"===e.history_content_type){switch(e.collection_type){case"list":return new i.HistoryListDatasetCollection(e,n);case"paired":return new i.HistoryPairDatasetCollection(e,n);case"list:paired":return new i.HistoryListPairedDatasetCollection(e,n);case"list:list":return new i.HistoryListOfListsDatasetCollection(e,n)}var s="Unknown collection_type: "+e.collection_type;return console.warn(s,e),{validationError:s}}return{validationError:"Unknown history_content_type: "+e.history_content_type}},limitPerPage:500,limitPerProgressiveFetch:500,order:"hid",urlRoot:Galaxy.root+"api/histories",url:function(){return this.urlRoot+"/"+this.historyId+"/contents"},initialize:function(e,t){t=t||{},c.prototype.initialize.call(this,e,t),this.history=t.history||null,this.setHistoryId(t.historyId||null),this.includeDeleted=t.includeDeleted||this.includeDeleted,this.includeHidden=t.includeHidden||this.includeHidden,this.model.prototype.idAttribute="type_id"},setHistoryId:function(e){this.historyId=e,this._setUpWebStorage()},_setUpWebStorage:function(e){if(this.historyId)return this.storage=new n.HistoryPrefs({id:n.HistoryPrefs.historyStorageKey(this.historyId)}),this.trigger("new-storage",this.storage,this),this.on({"include-deleted":function(e){this.storage.includeDeleted(e)},"include-hidden":function(e){this.storage.includeHidden(e)}}),this.includeDeleted=this.storage.includeDeleted()||!1,this.includeHidden=this.storage.includeHidden()||!1,this},comparators:o.extend(o.clone(c.prototype.comparators),{name:s.buildComparator("name",{ascending:!0}),"name-dsc":s.buildComparator("name",{ascending:!1}),hid:s.buildComparator("hid",{ascending:!1}),"hid-asc":s.buildComparator("hid",{ascending:!0})}),running:function(){return this.filter(function(e){return!e.inReadyState()})},runningAndActive:function(){return this.filter(function(e){return!e.inReadyState()&&e.get("visible")&&!e.get("deleted")})},getByHid:function(e){return this.findWhere({hid:e})},haveDetails:function(){return this.all(function(e){return e.hasDetails()})},hidden:function(){return this.filter(function(e){return e.hidden()})},deleted:function(){return this.filter(function(e){return e.get("deleted")})},visibleAndUndeleted:function(){return this.filter(function(e){return e.get("visible")&&!e.get("deleted")})},setIncludeDeleted:function(e,t){if(o.isBoolean(e)&&e!==this.includeDeleted){if(this.includeDeleted=e,o.result(t,"silent"))return;this.trigger("include-deleted",e,this)}},setIncludeHidden:function(e,t){if(o.isBoolean(e)&&e!==this.includeHidden){if(this.includeHidden=e,t=t||{},o.result(t,"silent"))return;this.trigger("include-hidden",e,this)}},fetch:function(e){if(e=e||{},this.historyId&&!e.details){var t=n.HistoryPrefs.get(this.historyId).toJSON();o.isEmpty(t.expandedIds)||(e.details=o.values(t.expandedIds).join(","))}return c.prototype.fetch.call(this,e)},_buildFetchData:function(e){return o.extend(c.prototype._buildFetchData.call(this,e),{v:"dev"})},_fetchParams:c.prototype._fetchParams.concat(["v","details"]),_buildFetchFilters:function(e){var t=c.prototype._buildFetchFilters.call(this,e)||{},i={};return this.includeDeleted||(i.deleted=!1,i.purged=!1),this.includeHidden||(i.visible=!0),o.defaults(t,i)},getTotalItemCount:function(){return this.history.contentsShown()},fetchUpdated:function(e,t){return e&&(t=t||{filters:{}},t.remove=!1,t.filters={"update_time-ge":e.toISOString(),visible:""}),this.fetch(t)},fetchDeleted:function(e){e=e||{};var t=this;return e.filters=o.extend(e.filters,{deleted:!0,purged:void 0}),e.remove=!1,t.trigger("fetching-deleted",t),t.fetch(e).always(function(){t.trigger("fetching-deleted-done",t)})},fetchHidden:function(e){e=e||{};var t=this;return e.filters=o.extend(e.filters,{visible:!1}),e.remove=!1,t.trigger("fetching-hidden",t),t.fetch(e).always(function(){t.trigger("fetching-hidden-done",t)})},fetchAllDetails:function(e){e=e||{};var t={details:"all"};return e.data=o.extend(e.data||{},t),this.fetch(e)},fetchCollectionCounts:function(e){return e=e||{},e.keys=["type_id","element_count"].join(","),e.filters=o.extend(e.filters||{},{history_content_type:"dataset_collection"}),e.remove=!1,this.fetch(e)},_filterAndUpdate:function(e,t){var i=this,n=i.model.prototype.idAttribute,s=[t];return i.fetch({filters:e,remove:!1}).then(function(e){return e=e.reduce(function(e,t,s){var o=i.get(t[n]);return o?e.concat(o):e},[]),i.ajaxQueue("save",s,e)})},ajaxQueue:function(e,t,i){return i=i||this.models,new r.AjaxQueue(i.slice().reverse().map(function(i,n){var s=o.isString(e)?i[e]:e;return function(){return s.apply(i,t)}})).deferred},progressivelyFetchDetails:function(e){function i(t){t=t||0;var a=o.extend(o.clone(e),{view:"summary",keys:c,limit:l,offset:t,reset:0===t,remove:!1});o.defer(function(){s.fetch.call(s,a).fail(n.reject).done(function(e){n.notify(e,l,t),e.length!==l?(s.allFetched=!0,n.resolve(e,l,t)):i(t+l)})})}e=e||{};var n=a.Deferred(),s=this,l=e.limitPerCall||s.limitPerProgressiveFetch,r=t.HistoryDatasetAssociation.prototype.searchAttributes,c=r.join(",");return i(),n},isCopyable:function(e){var t=["HistoryDatasetAssociation","HistoryDatasetCollectionAssociation"];return o.isObject(e)&&e.id&&o.contains(t,e.model_class)},copy:function(e){var t,i,n;o.isString(e)?(t=e,n="hda",i="dataset"):(t=e.id,n={HistoryDatasetAssociation:"hda",LibraryDatasetDatasetAssociation:"ldda",HistoryDatasetCollectionAssociation:"hdca"}[e.model_class]||"hda",i="hdca"===n?"dataset_collection":"dataset");var s=this,l=a.ajax(this.url(),{method:"POST",contentType:"application/json",data:JSON.stringify({content:t,source:n,type:i})}).done(function(e){s.add([e],{parse:!0})}).fail(function(e,o,a){s.trigger("error",s,l,{},"Error copying contents",{type:i,id:t,source:n})});return l},createHDCA:function(e,t,i,n,s){var o=this.model({history_content_type:"dataset_collection",collection_type:t,history_id:this.historyId,name:i,hide_source_items:n||!1,element_identifiers:e});return o.save(s)},haveSearchDetails:function(){return this.allFetched&&this.all(function(e){return o.has(e.attributes,"annotation")})},matches:function(e){return this.filter(function(t){return t.matches(e)})},clone:function(){var e=l.Collection.prototype.clone.call(this);return e.historyId=this.historyId,e},toString:function(){return["HistoryContents(",[this.historyId,this.length].join(),")"].join("")}});return{HistoryContents:d}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2),i(1),i(3))},function(e,t,i){var n,s;(function(o){n=[i(6)],s=function(e){"use strict";var t=e.SessionStorageModel.extend({defaults:{expandedIds:{},show_deleted:!1,show_hidden:!1},addExpanded:function(e){var t=this.get("expandedIds");t[e.id]=e.get("id"),this.save("expandedIds",t)},removeExpanded:function(e){var t=this.get("expandedIds");delete t[e.id],this.save("expandedIds",t)},isExpanded:function(e){return o.result(this.get("expandedIds"),e,!1)},allExpanded:function(){return o.values(this.get("expandedIds"))},clearExpanded:function(){this.set("expandedIds",{})},includeDeleted:function(e){return o.isUndefined(e)||this.set("show_deleted",e),this.get("show_deleted")},includeHidden:function(e){return o.isUndefined(e)||this.set("show_hidden",e),this.get("show_hidden")},toString:function(){return"HistoryPrefs("+this.id+")"}},{storageKeyPrefix:"history:",historyStorageKey:function(e){if(!e)throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+e);return t.storageKeyPrefix+e},get:function(e){return new t({id:t.historyStorageKey(e)})},clearAll:function(e){for(var i in sessionStorage)0===i.indexOf(t.storageKeyPrefix)&&sessionStorage.removeItem(i)}});return{HistoryPrefs:t}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(2))},function(e,t,i){var n,s;(function(o,a,l,r){n=[i(6),i(5)],s=function(e,t){"use strict";var i="list",n=o.View.extend(e.LoggableMixin).extend({_logNamespace:i,initialize:function(e){this.expanded=e.expanded||!1,this.log("\t expanded:",this.expanded), -this.fxSpeed=void 0!==e.fxSpeed?e.fxSpeed:this.fxSpeed},fxSpeed:"fast",render:function(e){var t=this._buildNewRender();return this._setUpBehaviors(t),this._queueNewRender(t,e),this},_buildNewRender:function(){var e=a(this.templates.el(this.model.toJSON(),this));return this.expanded&&this.$details(e).replaceWith(this._renderDetails().show()),e},_queueNewRender:function(e,t){t=void 0===t?this.fxSpeed:t;var i=this;0===t?(i._swapNewRender(e),i.trigger("rendered",i)):a(i).queue("fx",[function(e){i.$el.fadeOut(t,e)},function(t){i._swapNewRender(e),t()},function(e){i.$el.fadeIn(t,e)},function(e){i.trigger("rendered",i),e()}])},_swapNewRender:function(e){return this.$el.empty().attr("class",l.isFunction(this.className)?this.className():this.className).append(e.children())},_setUpBehaviors:function(e){e=e||this.$el,e.find("[title]").tooltip({placement:"bottom"})},$details:function(e){return e=e||this.$el,e.find("> .details")},_renderDetails:function(){var e=a(this.templates.details(this.model.toJSON(),this));return this._setUpBehaviors(e),e},toggleExpanded:function(e){return e=void 0===e?!this.expanded:e,e?this.expand():this.collapse(),this},expand:function(){var e=this;return e._fetchModelDetails().always(function(){e._expand()})},_fetchModelDetails:function(){return this.model.hasDetails()?r.when():this.model.fetch()},_expand:function(){var e=this,t=e._renderDetails();e.$details().replaceWith(t),e.expanded=!0,e.$details().slideDown(e.fxSpeed,function(){e.trigger("expanded",e)})},collapse:function(){this.debug(this+"(ExpandableView).collapse");var e=this;e.expanded=!1,this.$details().slideUp(e.fxSpeed,function(){e.trigger("collapsed",e)})}}),s=n.extend(e.mixin(e.SelectableViewMixin,e.DraggableViewMixin,{tagName:"div",className:"list-item",initialize:function(t){n.prototype.initialize.call(this,t),e.SelectableViewMixin.initialize.call(this,t),e.DraggableViewMixin.initialize.call(this,t),this._setUpListeners()},_setUpListeners:function(){return this.on("selectable",function(e){e?this.$(".primary-actions").hide():this.$(".primary-actions").show()},this),this},_buildNewRender:function(){var e=n.prototype._buildNewRender.call(this);return e.children(".warnings").replaceWith(this._renderWarnings()),e.children(".title-bar").replaceWith(this._renderTitleBar()),e.children(".primary-actions").append(this._renderPrimaryActions()),e.find("> .title-bar .subtitle").replaceWith(this._renderSubtitle()),e},_swapNewRender:function(e){return n.prototype._swapNewRender.call(this,e),this.selectable&&this.showSelector(0),this.draggable&&this.draggableOn(),this.$el},_renderWarnings:function(){var e=this,t=a('
    '),i=e.model.toJSON();return l.each(e.templates.warnings,function(n){t.append(a(n(i,e)))}),t},_renderTitleBar:function(){return a(this.templates.titleBar(this.model.toJSON(),this))},_renderPrimaryActions:function(){return[]},_renderSubtitle:function(){return a(this.templates.subtitle(this.model.toJSON(),this))},events:{"click .title-bar":"_clickTitleBar","keydown .title-bar":"_keyDownTitleBar","click .selector":"toggleSelect"},_clickTitleBar:function(e){e.stopPropagation(),e.altKey?(this.toggleSelect(e),this.selectable||this.showSelector()):this.toggleExpanded()},_keyDownTitleBar:function(e){var t=32,i=13;return!e||"keydown"!==e.type||e.keyCode!==t&&e.keyCode!==i||(this.toggleExpanded(),e.stopPropagation(),!1)},toString:function(){var e=this.model?this.model+"":"(no model)";return"ListItemView("+e+")"}}));s.prototype.templates=function(){var t=e.wrapTemplate(['
    ','
    ','
    ','',"
    ",'
    ','
    ','
    ',"
    "]),i={},n=e.wrapTemplate(['
    ','','
    ','<%- element.name %>',"
    ",'
    ',"
    "],"element"),s=e.wrapTemplate(['
    ']),o=e.wrapTemplate(['
    ']);return{el:t,warnings:i,titleBar:n,subtitle:s,details:o}}();var c=s.extend({foldoutStyle:"foldout",foldoutPanelClass:null,initialize:function(e){"drilldown"===this.foldoutStyle&&(this.expanded=!1),this.foldoutStyle=e.foldoutStyle||this.foldoutStyle,this.foldoutPanelClass=e.foldoutPanelClass||this.foldoutPanelClass,s.prototype.initialize.call(this,e),this.foldout=this._createFoldoutPanel()},_renderDetails:function(){if("drilldown"===this.foldoutStyle)return a();var e=s.prototype._renderDetails.call(this);return this._attachFoldout(this.foldout,e)},_createFoldoutPanel:function(){var e=this.model,t=this._getFoldoutPanelClass(e),i=this._getFoldoutPanelOptions(e),n=new t(l.extend(i,{model:e}));return n},_getFoldoutPanelClass:function(){return this.foldoutPanelClass},_getFoldoutPanelOptions:function(){return{foldoutStyle:this.foldoutStyle,fxSpeed:this.fxSpeed}},_attachFoldout:function(e,t){return t=t||this.$("> .details"),this.foldout=e.render(0),e.$("> .controls").hide(),t.append(e.$el)},expand:function(){var e=this;return e._fetchModelDetails().always(function(){"foldout"===e.foldoutStyle?e._expand():"drilldown"===e.foldoutStyle&&e._expandByDrilldown()})},_expandByDrilldown:function(){var e=this;e.listenTo(e.foldout,"close",function(){e.trigger("collapsed:drilldown",e,e.foldout)}),e.trigger("expanded:drilldown",e,e.foldout)}});return c.prototype.templates=function(){var t=e.wrapTemplate(['
    ',"
    "],"collection");return l.extend({},s.prototype.templates,{details:t})}(),{ExpandableView:n,ListItemView:s,FoldoutListItemView:c}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(1),i(2),i(1))},function(e,t,i){var n,s;(function(o,a){n=[i(6),i(5)],s=function(e,t){var i=o.View.extend(e.LoggableMixin).extend(e.HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"tags-display",initialize:function(e){e.usePrompt===!1?this.label="":this.label='",this.hiddenUntilActivated(e.$activator,e)},render:function(){var e=this;return this.$el.html(this._template()),this.$input().select2({placeholder:"Add tags",width:"100%",tags:function(){return e._getTagsUsed()}}),this._setUpBehaviors(),this},_hashToName:function(e){return e.startsWith("#")?"name:"+e.slice(1):e},_nameToHash:function(e){return e.startsWith("name:")&&(e="#"+e.slice(5)),e},_template:function(){return[this.label,''].join("")},tagsToCSV:function(){var e=this,t=this.model.get("tags");return!a.isArray(t)||a.isEmpty(t)?"":t.map(function(t){return a.escape(e._nameToHash(t))}).sort().join(",")},$input:function(){return this.$el.find("input.tags-input")},_getTagsUsed:function(){var e=this;return a.map(Galaxy.user.get("tags_used"),e._nameToHash)},_setUpBehaviors:function(){var e=this;this.$input().on("change",function(t){t.val=a.map(t.val,e._hashToName),e.model.save({tags:t.val}),t.added&&e._addNewTagToTagsUsed(t.added.text+"")})},_addNewTagToTagsUsed:function(e){var t=Galaxy.user.get("tags_used");a.contains(t,e)||(t.push(e),t.sort(),Galaxy.user.set("tags_used",t))},remove:function(){this.$input.off(),this.stopListening(this.model),o.View.prototype.remove.call(this)},toString:function(){return["TagsEditor(",this.model+"",")"].join("")}});return{TagsEditor:i}}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(3),i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(4),i(58),i(7),i(21),i(20),i(32)],s=function(e,t,i,n,s,l){return n.extend({initialize:function(e){var i=this;this.deferred=new t,n.prototype.initialize.call(this,e),this.model.get("inputs")?this._buildForm(this.model.attributes):this.deferred.execute(function(e){i._buildModel(e,i.model.attributes,!0)}),this.model.get("listen_to_history")&&parent.Galaxy&&parent.Galaxy.currHistoryPanel&&this.listenTo(parent.Galaxy.currHistoryPanel.collection,"change",function(){i.model.get("onchange")()}),this.$el.on("remove",function(){i.remove()})},remove:function(){var e=this;this.$el.hide(),this.deferred.execute(function(){n.prototype.remove.call(e),Galaxy.emit.debug("tool-form-base::remove()","Destroy view.")})},_buildForm:function(e){var t=this;this.model.set(e),this.model.set({title:e.title||""+e.name+" "+e.description+" (Galaxy Version "+e.version+")",operations:!this.model.get("hide_operations")&&this._operations(),onchange:function(){t.deferred.reset(),t.deferred.execute(function(e){t.model.get("postchange")(e,t)})}}),this.model.get("customize")&&this.model.get("customize")(this),this.render(),this.model.get("collapsible")||this.$el.append(o("
    ").addClass("ui-margin-top-large").append(this._footer()))},_buildModel:function(t,n,s){var a=this,l=this.model.attributes;l.version=n.version,l.id=n.id;var r="",c={};l.job_id?r=Galaxy.root+"api/jobs/"+l.job_id+"/build_for_rerun":(r=Galaxy.root+"api/tools/"+l.id+"/build",Galaxy.params&&Galaxy.params.tool_id==l.id&&(c=o.extend({},Galaxy.params),l.version&&(c.tool_version=l.version))),e.get({url:r,data:c,success:function(e){return e.display?(a._buildForm(e),!s&&a.message.update({status:"success",message:"Now you are using '"+l.name+"' version "+l.version+", id '"+l.id+"'.",persistent:!1}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model ready.",e),void t.resolve()):void(window.location=Galaxy.root)},error:function(e,n){var s=e&&e.err_msg||"Uncaught error.";401==n?window.location=Galaxy.root+"user/login?"+o.param({redirect:Galaxy.root+"?tool_id="+l.id}):a.$el.is(":empty")?a.$el.prepend(new i.Message({message:s,status:"danger",persistent:!0,large:!0}).$el):Galaxy.modal&&Galaxy.modal.show({title:"Tool request failed",body:s,buttons:{Close:function(){Galaxy.modal.hide()}}}),Galaxy.emit.debug("tool-form-base::_buildModel()","Initial tool model request failed.",e),t.reject()}})},_operations:function(){var t=this,n=this.model.attributes,s=new i.ButtonMenu({icon:"fa-cubes",title:!n.narrow&&"Versions"||null,tooltip:"Select another tool version"});if(!n.sustain_version&&n.versions&&n.versions.length>1)for(var o in n.versions){var a=n.versions[o];a!=n.version&&s.addMenu({title:"Switch to "+a,version:a,icon:"fa-cube",onclick:function(){var e=n.id.replace(n.version,this.version),i=this.version;t.deferred.reset(),t.deferred.execute(function(n){t._buildModel(n,{id:e,version:i})})}})}else s.$el.hide();var l=new i.ButtonMenu({icon:"fa-caret-down",title:!n.narrow&&"Options"||null,tooltip:"View available options"});return n.biostar_url&&(l.addMenu({icon:"fa-question-circle",title:"Question?",onclick:function(){window.open(n.biostar_url+"/p/new/post/")}}),l.addMenu({icon:"fa-search",title:"Search",onclick:function(){window.open(n.biostar_url+"/local/search/page/?q="+n.name)}})),l.addMenu({icon:"fa-share",title:"Share",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+Galaxy.root+"root?tool_id="+n.id)}}),Galaxy.user&&Galaxy.user.get("is_admin")&&(l.addMenu({icon:"fa-download",title:"Download",onclick:function(){window.location.href=Galaxy.root+"api/tools/"+n.id+"/download"}}),l.addMenu({icon:"fa-refresh",title:"Reload XML",onclick:function(){e.get({url:Galaxy.root+"api/tools/"+n.id+"/reload",success:function(e){t.message.update({persistent:!1,message:"Tool XML has been reloaded.",status:"success"})},error:function(e){t.message.update({persistent:!1,message:e.err_msg,status:"danger"})}})}})),n.requirements&&n.requirements.length>0&&l.addMenu({icon:"fa-info-circle",title:"Requirements",onclick:function(){!this.requirements_visible||t.portlet.collapsed?(this.requirements_visible=!0,t.portlet.expand(),t.message.update({persistent:!0,message:t._templateRequirements(n),status:"info"})):(this.requirements_visible=!1,t.message.update({message:""}))}}),n.sharable_url&&l.addMenu({icon:"fa-external-link",title:"See in Tool Shed",onclick:function(){window.open(n.sharable_url)}}),{menu:l,versions:s}},_footer:function(){var e=this.model.attributes,t=o("
    ").append(this._templateHelp(e));if(e.citations){var i=o("
    "),n=new s.ToolCitationCollection;n.tool_id=e.id;var a=new l.CitationListView({el:i,collection:n});a.render(),n.fetch(),t.append(i)}return t},_templateHelp:function(e){var t=o("
    ").addClass("ui-form-help").append(e.help);return t.find("a").attr("target","_blank"),t},_templateRequirements:function(e){var t=e.requirements.length;if(t>0){var i="This tool requires ";a.each(e.requirements,function(e,n){i+=e.name+(e.version?" (Version "+e.version+")":"")+(n").attr("target","_blank").attr("href","https://wiki.galaxyproject.org/Tools/Requirements").text("here");return o("").append(i+". Click ").append(n).append(" for more information.")}return"No requirements found."}})}.apply(t,n),!(void 0!==s&&(e.exports=s))}).call(t,i(1),i(2))},function(e,t,i){var n,s;(function(o,a){n=[i(2),i(19),i(11),i(26)],s=function(e,t,i,n){"use strict";var s={hidden:!1,show:function(){this.set("hidden",!1)},hide:function(){this.set("hidden",!0)},toggle:function(){this.set("hidden",!this.get("hidden"))},is_visible:function(){return!this.attributes.hidden}},l=o.Model.extend({defaults:{name:null,label:null,type:null,value:null,html:null,num_samples:5},initialize:function(e){this.attributes.html=unescape(this.attributes.html)},copy:function(){return new l(this.toJSON())},set_value:function(e){this.set("value",e||"")}}),r=o.Collection.extend({model:l}),c=l.extend({}),d=l.extend({set_value:function(e){this.set("value",parseInt(e,10))},get_samples:function(){return d3.scale.linear().domain([this.get("min"),this.get("max")]).ticks(this.get("num_samples"))}}),h=d.extend({set_value:function(e){this.set("value",parseFloat(e))}}),u=l.extend({get_samples:function(){return e.map(this.get("options"),function(e){return e[0]})}});l.subModelTypes={integer:d,float:h,data:c,select:u};var p=o.Model.extend({defaults:{id:null,name:null,description:null,target:null,inputs:[],outputs:[]},urlRoot:Galaxy.root+"api/tools",initialize:function(t){this.set("inputs",new r(e.map(t.inputs,function(e){var t=l.subModelTypes[e.type]||l;return new t(e)})))},toJSON:function(){var e=o.Model.prototype.toJSON.call(this);return e.inputs=this.get("inputs").map(function(e){return e.toJSON()}),e},remove_inputs:function(e){var t=this,i=t.get("inputs").filter(function(t){return e.indexOf(t.get("type"))!==-1});t.get("inputs").remove(i)},copy:function(e){var t=new p(this.toJSON());if(e){var i=new o.Collection;t.get("inputs").each(function(e){e.get_samples()&&i.push(e)}),t.set("inputs",i)}return t},apply_search_results:function(t){return e.indexOf(t,this.attributes.id)!==-1?this.show():this.hide(),this.is_visible()},set_input_value:function(e,t){this.get("inputs").find(function(t){return t.get("name")===e}).set("value",t)},set_input_values:function(t){var i=this;e.each(e.keys(t),function(e){i.set_input_value(e,t[e])})},run:function(){return this._run()},rerun:function(e,t){return this._run({action:"rerun",target_dataset_id:e.id,regions:t})},get_inputs_dict:function(){var e={};return this.get("inputs").each(function(t){e[t.get("name")]=t.get("value")}),e},_run:function(n){var s=e.extend({tool_id:this.id,inputs:this.get_inputs_dict()},n),o=a.Deferred(),l=new t.ServerStateDeferred({ajax_settings:{url:this.urlRoot,data:JSON.stringify(s),dataType:"json",contentType:"application/json",type:"POST"},interval:2e3,success_fn:function(e){return"pending"!==e}});return a.when(l.go()).then(function(e){o.resolve(new i.DatasetCollection(e))}),o}});e.extend(p.prototype,s);var f=(o.View.extend({}),o.Collection.extend({model:p})),g=o.Model.extend(s),m=o.Model.extend({defaults:{elems:[],open:!1},clear_search_results:function(){e.each(this.attributes.elems,function(e){e.show()}),this.show(),this.set("open",!1)},apply_search_results:function(t){var i,n=!0;e.each(this.attributes.elems,function(e){e instanceof g?(i=e,i.hide()):e instanceof p&&e.apply_search_results(t)&&(n=!1,i&&i.show())}),n?this.hide():(this.show(),this.set("open",!0))}});e.extend(m.prototype,s);var v=o.Model.extend({defaults:{search_hint_string:"search tools",min_chars_for_search:3,clear_btn_url:"",visible:!0,query:"",results:null,clear_key:27},urlRoot:Galaxy.root+"api/tools",initialize:function(){this.on("change:query",this.do_search)},do_search:function(){var e=this.attributes.query;if(e.length");e.append(S.tool_link(this.model.toJSON()));var t=this.model.get("form_style",null);if("upload1"===this.model.id)e.find("a").on("click",function(e){e.preventDefault(),Galaxy.upload.show()});else if("regular"===t){var i=this;e.find("a").on("click",function(e){e.preventDefault(),Galaxy.router.push("/",{tool_id:i.model.id,version:i.model.get("version")})})}return this.$el.append(e),this}}),w=y.extend({tagName:"div",className:"toolPanelLabel",render:function(){return this.$el.append(a("").text(this.model.attributes.text)),this}}),x=y.extend({tagName:"div",className:"toolSectionWrapper",initialize:function(){y.prototype.initialize.call(this),this.model.on("change:open",this.update_open,this)},render:function(){this.$el.append(S.panel_section(this.model.toJSON()));var t=this.$el.find(".toolSectionBody");return e.each(this.model.attributes.elems,function(e){if(e instanceof p){var i=new b({model:e,className:"toolTitle"});i.render(),t.append(i.$el)}else if(e instanceof g){var n=new w({model:e});n.render(),t.append(n.$el)}}),this},events:{"click .toolSectionTitle > a":"toggle"},toggle:function(){this.model.set("open",!this.model.attributes.open)},update_open:function(){this.model.attributes.open?this.$el.children(".toolSectionBody").slideDown("fast"):this.$el.children(".toolSectionBody").slideUp("fast")}}),C=o.View.extend({tagName:"div",id:"tool-search",className:"bar",events:{click:"focus_and_select","keyup :input":"query_changed","change :input":"query_changed","click #search-clear-btn":"clear"},render:function(){return this.$el.append(S.tool_search(this.model.toJSON())),this.model.is_visible()||this.$el.hide(),a("#messagebox").is(":visible")&&this.$el.css("top","95px"),this.$el.find("[title]").tooltip(),this},focus_and_select:function(){this.$el.find(":input").focus().select()},clear:function(){return this.model.clear_search(),this.$el.find(":input").val(""),this.focus_and_select(),!1},query_changed:function(e){return this.model.attributes.clear_key&&this.model.attributes.clear_key===e.which?(this.clear(),!1):void this.model.set("query",this.$el.find(":input").val())}}),$=o.View.extend({tagName:"div",className:"toolMenu",initialize:function(){this.model.get("tool_search").on("change:results",this.handle_search_results,this)},render:function(){var e=this,t=new C({model:this.model.get("tool_search")});return t.render(),e.$el.append(t.$el),this.model.get("layout").each(function(t){if(t instanceof m){var i=new x({model:t});i.render(),e.$el.append(i.$el)}else if(t instanceof p){var n=new b({model:t,className:"toolTitleNoSection"});n.render(),e.$el.append(n.$el)}else if(t instanceof g){var s=new w({model:t});s.render(),e.$el.append(s.$el)}}),e.$el.find("a.tool-link").click(function(t){var i=a(this).attr("class").split(/\s+/)[0],n=e.model.get("tools").get(i);e.trigger("tool_link_click",t,n)}),this},handle_search_results:function(){var e=this.model.get("tool_search").get("results");e&&0===e.length?a("#search-no-results").show():a("#search-no-results").hide()}}),E=o.View.extend({className:"toolForm",render:function(){this.$el.children().remove(),this.$el.append(S.tool_form(this.model.toJSON()))}}),S=(o.View.extend({className:"toolMenuAndView",initialize:function(){this.tool_panel_view=new $({collection:this.collection}),this.tool_form_view=new E},render:function(){this.tool_panel_view.render(),this.tool_panel_view.$el.css("float","left"),this.$el.append(this.tool_panel_view.$el),this.tool_form_view.$el.hide(),this.$el.append(this.tool_form_view.$el);var e=this;this.tool_panel_view.on("tool_link_click",function(t,i){t.preventDefault(),e.show_tool(i)})},show_tool:function(e){var t=this;e.fetch().done(function(){t.tool_form_view.model=e,t.tool_form_view.render(),t.tool_form_view.$el.show(),a("#left").width("650px")})}}),{tool_search:e.template(['',' ',''].join("")),panel_section:e.template(['
    ','<%- name %>',"
    ",'