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commit/galaxy-central: greg: Fix for testing tool dependency definitions with the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 21 Dec '13

21 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b83064c6c323/ Changeset: b83064c6c323 User: greg Date: 2013-12-21 13:49:59 Summary: Fix for testing tool dependency definitions with the tool shed's install and test framework. Affected #: 2 files diff -r 38b88dceb82e092f79c2f4b6aff745d11f77dac4 -r b83064c6c323217a6072e869afafec19ce965b0f test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -197,7 +197,6 @@ ( changeset_revision, name, owner ) ) else: tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) - # Proceed with installing repositories and testing contained tools. repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) install_and_test_statistics_dict[ 'total_repositories_processed' ] += 1 if error_message: diff -r 38b88dceb82e092f79c2f4b6aff745d11f77dac4 -r b83064c6c323217a6072e869afafec19ce965b0f test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -120,7 +120,7 @@ owner, changeset_revision, encoded_repository_metadata_id ) - if this_repository_is_in_the_exclude_list or requires_excluded: + if is_excluded: # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) @@ -142,8 +142,7 @@ log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message - params = dict( test_install_error=True, - do_not_test=False ) + params = dict( test_install_error=True ) # TODO: do something useful with response_dict response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, tool_test_results_dicts, @@ -153,6 +152,8 @@ can_update_tool_shed ) else: # The repository was successfully installed. + log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) params, install_and_test_statistics_dict, tool_test_results_dict = \ install_and_test_base_util.register_installed_and_missing_dependencies( app, repository, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: docs
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/38b88dceb82e/ Changeset: 38b88dceb82e User: martenson Date: 2013-12-21 00:53:41 Summary: docs Affected #: 2 files diff -r 11c30107da4eba80c0e76613d1da223f2af8ffe8 -r 38b88dceb82e092f79c2f4b6aff745d11f77dac4 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -64,7 +64,6 @@ @web.expose_api_anonymous def show( self, trans, id, deleted='False', **kwd ): - # oh, sphinx - you bastard """ show( trans, id, deleted='False' ) * GET /api/histories/{id}: diff -r 11c30107da4eba80c0e76613d1da223f2af8ffe8 -r 38b88dceb82e092f79c2f4b6aff745d11f77dac4 lib/galaxy/webapps/galaxy/api/lda_datasets.py --- a/lib/galaxy/webapps/galaxy/api/lda_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/lda_datasets.py @@ -30,15 +30,14 @@ """ show( self, trans, id, **kwd ) * GET /api/libraries/datasets/{encoded_dataset_id}: - Displays information about the dataset identified by the encoded id. + Displays information about the dataset identified by the encoded ID. - + :param id: the encoded id of the dataset to query :type id: an encoded id string - :param id: the encoded id of the dataset to query :rtype: dictionary - :returns: detailed dataset information from - :func:`galaxy.web.base.controller.UsesVisualizationMixin.get_library_dataset.to_dict()` + :returns: detailed dataset information from base controller + .. seealso:: :attr:`galaxy.web.base.controller.UsesLibraryMixinItems.get_library_dataset` """ # Get dataset. try: @@ -66,18 +65,16 @@ """ download( self, trans, format, **kwd ) * GET /api/libraries/datasets/download/{format} + Downloads requested datasets (identified by encoded IDs) in requested format. - .. code-block:: - example: - GET localhost:8080/api/libraries/datasets/download/tbz?ldda_ids%255B%255D=a0d84b45643a2678&ldda_ids%255B%255D=fe38c84dcd46c828 + example: ``GET localhost:8080/api/libraries/datasets/download/tbz?ldda_ids%255B%255D=a0d84b45643a2678&ldda_ids%255B%255D=fe38c84dcd46c828`` + .. note:: supported format values are: 'zip', 'tgz', 'tbz', 'uncompressed' + + :param format: string representing requested archive format :type format: string - :param format: string representing requested archive format - - .. note:: supported formats are: zip, tgz, tbz, uncompressed - + :param lddas[]: an array of encoded ids :type lddas[]: an array - :param lddas[]: an array of encoded ids :rtype: file :returns: either archive with the requested datasets packed inside or a single uncompressed dataset Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: inithello: Fix for removing generated test definitions from the global scope after a repository has been tested.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/11c30107da4e/ Changeset: 11c30107da4e User: inithello Date: 2013-12-20 18:55:49 Summary: Fix for removing generated test definitions from the global scope after a repository has been tested. Affected #: 1 file diff -r 68c080722bc7f6accf73325bdf049eb84125da27 -r 11c30107da4eba80c0e76613d1da223f2af8ffe8 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -254,8 +254,6 @@ file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) - # Remove twills' old generated test before building the new tests for the current tools. - remove_tests( app ) try: install_and_test_statistics_dict = test_repository_tools( app, repository, @@ -570,6 +568,14 @@ """ tests_to_delete = [] tools_to_delete_by_id = [] + + # Push all the toolbox tests to module level + G = globals() + + # Eliminate all previous tests from G. + for key, val in G.items(): + if key.startswith( 'TestForTool_' ): + del G[ key ] global test_toolbox # Find all tests previously generated by twill. for key in test_toolbox.__dict__: @@ -590,17 +596,6 @@ if tool_id in app.toolbox.tools_by_id: log.debug( 'Deleting tool id %s from app.toolbox[ tools_by_id ].' % str( tool_id ) ) del app.toolbox.tools_by_id[ tool_id ] - # Push all the toolbox tests to module level - for key in test_install_repositories.__dict__: - if key.startswith( 'TestInstallRepository_' ): - log.debug( 'Repository installation process test %s discovered.' % str( key ) ) - # We can't delete this test just yet, we're still iterating over __dict__. - tests_to_delete.append( key ) - # Delete the discovered twill-generated tests. - for key in tests_to_delete: - if key in test_install_repositories.__dict__: - log.debug( 'Deleting test %s from test_toolbox.' % str( key ) ) - del test_install_repositories.__dict__[ key ] def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, install_and_test_statistics_dict ): @@ -674,6 +669,8 @@ can_update_tool_shed ) log.debug( 'Revision %s of repository %s owned by %s installed successfully but did not pass functional tests.' % \ ( changeset_revision, name, owner ) ) + # Remove twills' old generated test before building the new tests for the current tools. + remove_tests( app ) return install_and_test_statistics_dict if __name__ == "__main__": Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2c62316e9a5b/ Changeset: 2c62316e9a5b User: inithello Date: 2013-12-20 18:22:01 Summary: Order repository revisions by ID, descending. Affected #: 1 file diff -r c125d7050c3b5a34305c377cd31b3a77be753d99 -r 2c62316e9a5bd985b264e7bf7d10eadc1b74cde8 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -155,7 +155,7 @@ try: query = trans.sa_session.query( trans.app.model.RepositoryMetadata ) \ .filter( and_( *clause_list ) ) \ - .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \ + .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id.desc() ) \ .all() for repository_metadata in query: repository_metadata_dict = repository_metadata.to_dict( view='collection', https://bitbucket.org/galaxy/galaxy-central/commits/68c080722bc7/ Changeset: 68c080722bc7 User: inithello Date: 2013-12-20 18:22:24 Summary: Fix for error message when resetting metadata on an installed repository. Affected #: 1 file diff -r 2c62316e9a5bd985b264e7bf7d10eadc1b74cde8 -r 68c080722bc7f6accf73325bdf049eb84125da27 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -247,12 +247,16 @@ bold_start = '' bold_end = '' message = '' + if trans.webapp.name == 'galaxy': + tip_rev = str( repository.changeset_revision ) + else: + tip_rev = str( repository.tip( trans.app ) ) if not displaying_invalid_tool: if metadata_dict: - message += "Metadata may have been defined for some items in revision '%s'. " % str( repository.tip( trans.app ) ) + message += "Metadata may have been defined for some items in revision '%s'. " % tip_rev message += "Correct the following problems if necessary and reset metadata.%s" % new_line else: - message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip( trans.app ) ) + message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % tip_rev message += "installed into a local Galaxy instance. Correct the following problems and reset metadata.%s" % new_line for itc_tup in invalid_file_tups: tool_file, exception_msg = itc_tup Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: carlfeberhard: UI: remove BaseView from base-mvc; replace with View in assoc. files
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c125d7050c3b/ Changeset: c125d7050c3b User: carlfeberhard Date: 2013-12-20 18:18:50 Summary: UI: remove BaseView from base-mvc; replace with View in assoc. files Affected #: 6 files diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/mvc/annotations.js --- a/static/scripts/mvc/annotations.js +++ b/static/scripts/mvc/annotations.js @@ -1,6 +1,6 @@ /** A view on any model that has a 'annotation' attribute */ -var AnnotationEditor = BaseView.extend( LoggableMixin ).extend( HiddenUntilActivatedViewMixin ).extend({ +var AnnotationEditor = Backbone.View.extend( LoggableMixin ).extend( HiddenUntilActivatedViewMixin ).extend({ tagName : 'div', className : 'annotation-display', diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -1,23 +1,3 @@ -/** - * Base view that handles visibility based on model's hidden attribute. - */ -var BaseView = Backbone.View.extend({ - - initialize: function() { - this.model.on("change:hidden", this.update_visible, this); - this.update_visible(); - }, - - update_visible: function() { - if( this.model.attributes.hidden ){ - this.$el.hide(); - } else { - this.$el.show(); - } - } -}); - - //============================================================================== /** @class Mixin to add logging capabilities to an object. * Designed to allow switching an objects log output off/on at one central diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/mvc/visualizations/scatterplotControlForm.js --- a/static/scripts/mvc/visualizations/scatterplotControlForm.js +++ b/static/scripts/mvc/visualizations/scatterplotControlForm.js @@ -63,7 +63,7 @@ * * initialize attributes REQUIRES a dataset and an apiDatasetsURL */ -var ScatterplotControlForm = BaseView.extend( LoggableMixin ).extend({ +var ScatterplotControlForm = Backbone.View.extend( LoggableMixin ).extend({ //logger : console, className : 'scatterplot-control-form', diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/packed/mvc/annotations.js --- a/static/scripts/packed/mvc/annotations.js +++ b/static/scripts/packed/mvc/annotations.js @@ -1,1 +1,1 @@ -var AnnotationEditor=BaseView.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(a){a=a||{};this.tooltipConfig=a.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(a.$activator,a)},render:function(){var a=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(b){a.$annotation().text(b);a.model.save({annotation:b},{silent:true}).fail(function(){a.$annotation().text(a.model.previous("annotation"))})}});return this},_template:function(){var a=this.model.get("annotation");return['<label class="prompt">',_l("Annotation"),"</label>",'<div class="annotation" title="',_l("Edit annotation"),'">',a,"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}}); \ No newline at end of file +var AnnotationEditor=Backbone.View.extend(LoggableMixin).extend(HiddenUntilActivatedViewMixin).extend({tagName:"div",className:"annotation-display",initialize:function(a){a=a||{};this.tooltipConfig=a.tooltipConfig||{placement:"bottom"};this.listenTo(this.model,"change:annotation",function(){this.render()});this.hiddenUntilActivated(a.$activator,a)},render:function(){var a=this;this.$el.html(this._template());this.$el.find("[title]").tooltip(this.tooltipConfig);this.$annotation().make_text_editable({use_textarea:true,on_finish:function(b){a.$annotation().text(b);a.model.save({annotation:b},{silent:true}).fail(function(){a.$annotation().text(a.model.previous("annotation"))})}});return this},_template:function(){var a=this.model.get("annotation");return['<label class="prompt">',_l("Annotation"),"</label>",'<div class="annotation" title="',_l("Edit annotation"),'">',a,"</div>"].join("")},$annotation:function(){return this.$el.find(".annotation")},remove:function(){this.$annotation.off();this.stopListening(this.model);Backbone.View.prototype.remove.call(this)},toString:function(){return["AnnotationEditor(",this.model+"",")"].join("")}}); \ No newline at end of file diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/packed/mvc/base-mvc.js --- a/static/scripts/packed/mvc/base-mvc.js +++ b/static/scripts/packed/mvc/base-mvc.js @@ -1,1 +1,1 @@ -var BaseView=Backbone.View.extend({initialize:function(){this.model.on("change:hidden",this.update_visible,this);this.update_visible()},update_visible:function(){if(this.model.attributes.hidden){this.$el.hide()}else{this.$el.show()}}});var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.hidden){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this);this.trigger("hiddenUntilActivated:shown",this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this);this.trigger("hiddenUntilActivated:hidden",this)}this.hidden=true}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}}; \ No newline at end of file +var LoggableMixin={logger:null,log:function(){if(this.logger){var a=this.logger.log;if(typeof this.logger.log==="object"){a=Function.prototype.bind.call(this.logger.log,this.logger)}return a.apply(this.logger,arguments)}return undefined}};var SessionStorageModel=Backbone.Model.extend({initialize:function(b){b.id=(!_.isString(b.id))?(_.uniqueId()):(b.id);this.id=b.id;var a=(!this.isNew())?(this._read(this)):({});this.clear({silent:true});this.save(_.extend({},this.defaults,a,b),{silent:true});this.on("change",function(){this.save()})},sync:function(d,b,a){if(!a.silent){b.trigger("request",b,{},a)}var c;switch(d){case"create":c=this._create(b);break;case"read":c=this._read(b);break;case"update":c=this._update(b);break;case"delete":c=this._delete(b);break}if(c!==undefined||c!==null){if(a.success){a.success()}}else{if(a.error){a.error()}}return c},_create:function(a){var b=a.toJSON(),c=sessionStorage.setItem(a.id,JSON.stringify(b));return(c===null)?(c):(b)},_read:function(a){return JSON.parse(sessionStorage.getItem(a.id))},_update:function(a){return a._create(a)},_delete:function(a){return sessionStorage.removeItem(a.id)},isNew:function(){return !sessionStorage.hasOwnProperty(this.id)},_log:function(){return JSON.stringify(this.toJSON(),null," ")},toString:function(){return"SessionStorageModel("+this.id+")"}});(function(){SessionStorageModel.prototype=_.omit(SessionStorageModel.prototype,"url","urlRoot")}());var HiddenUntilActivatedViewMixin={hiddenUntilActivated:function(a,c){c=c||{};this.HUAVOptions={$elementShown:this.$el,showFn:jQuery.prototype.toggle,showSpeed:"fast"};_.extend(this.HUAVOptions,c||{});this.HUAVOptions.hasBeenShown=this.HUAVOptions.$elementShown.is(":visible");this.hidden=this.isHidden();if(a){var b=this;a.on("click",function(d){b.toggle(b.HUAVOptions.showSpeed)})}},isHidden:function(){return(this.HUAVOptions.$elementShown.is(":hidden"))},toggle:function(){if(this.hidden){if(!this.HUAVOptions.hasBeenShown){if(_.isFunction(this.HUAVOptions.onshowFirstTime)){this.HUAVOptions.hasBeenShown=true;this.HUAVOptions.onshowFirstTime.call(this)}}if(_.isFunction(this.HUAVOptions.onshow)){this.HUAVOptions.onshow.call(this);this.trigger("hiddenUntilActivated:shown",this)}this.hidden=false}else{if(_.isFunction(this.HUAVOptions.onhide)){this.HUAVOptions.onhide.call(this);this.trigger("hiddenUntilActivated:hidden",this)}this.hidden=true}return this.HUAVOptions.showFn.apply(this.HUAVOptions.$elementShown,arguments)}}; \ No newline at end of file diff -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af -r c125d7050c3b5a34305c377cd31b3a77be753d99 static/scripts/packed/mvc/visualizations/scatterplotControlForm.js --- a/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js +++ b/static/scripts/packed/mvc/visualizations/scatterplotControlForm.js @@ -1,1 +1,1 @@ -var ScatterplotControlForm=BaseView.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_config.root+"static/images/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find("[title]").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",provider:"column_with_stats",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]}; \ No newline at end of file +var ScatterplotControlForm=Backbone.View.extend(LoggableMixin).extend({className:"scatterplot-control-form",dataLoadDelay:4000,dataLoadSize:5000,loadingIndicatorImage:"loading_small_white_bg.gif",fetchMsg:"Fetching data...",renderMsg:"Rendering...",initialize:function(a){this.log(this+".initialize, attributes:",a);this.dataset=null;this.chartConfig=null;this.chart=null;this.loader=null;this.$dataControl=null;this.$chartControl=null;this.$statsDisplay=null;this.$chartDisplay=null;this.dataFetch=null;this.initializeFromAttributes(a);this.initializeChart(a);this.initializeDataLoader(a)},initializeFromAttributes:function(a){if(!a||!a.dataset){throw ("ScatterplotView requires a dataset")}else{this.dataset=a.dataset}if(jQuery.type(this.dataset.metadata_column_types)==="string"){this.dataset.metadata_column_types=this.dataset.metadata_column_types.split(", ")}this.log("\t dataset:",this.dataset);if(this.dataset.comment_lines&&this.dataset.comment_lines.length){var b=this.dataset.comment_lines[0],c=b.split("\t");if(c.length===this.dataset.metadata_column_types.length){this.possibleHeaders=c}}if(!a.apiDatasetsURL){throw ("ScatterplotView requires a apiDatasetsURL")}else{this.dataURL=a.apiDatasetsURL+"/"+this.dataset.id+"?"}this.log("\t dataURL:",this.dataURL)},initializeChart:function(a){this.chartConfig=a.chartConfig||{};this.log("\t initial chartConfig:",this.chartConfig);this.chart=new TwoVarScatterplot(this.chartConfig);this.chartConfig=this.chart.config},initializeDataLoader:function(b){var a=this;this.loader=new LazyDataLoader({url:null,start:b.start||0,total:b.total||this.dataset.metadata_data_lines,delay:this.dataLoadDelay,size:this.dataLoadSize,buildUrl:function(d,c){return this.url+"&"+jQuery.param({start_val:d,max_vals:c})}});$(this.loader).bind("error",function(e,c,d){a.log("ERROR:",c,d);alert("ERROR fetching data:\n"+c+"\n"+d);a.hideLoadingIndicator()})},render:function(){this.log(this+".render");this.$el.append(ScatterplotControlForm.templates.mainLayout({loadingIndicatorImagePath:galaxy_config.root+"static/images/"+this.loadingIndicatorImage,message:""}));this.$dataControl=this._render_dataControl();this.$chartControl=this._render_chartControl();this.$statsDisplay=this.$el.find(".tab-pane#stats-display");this.$chartDisplay=this._render_chartDisplay();if(this.chartConfig.xColumn&&this.chartConfig.yColumn){this.renderChart()}this.$el.find("[title]").tooltip();return this},_render_dataControl:function(){var b=this,a=[],e=[],c=(this.possibleHeaders&&this.$dataControl)?(this.$dataControl.find("#first-line-header-checkbox").is(":checked")):(false);_.each(this.dataset.metadata_column_types,function(i,g){var h=g+1,f="column "+h;if(b.dataset.metadata_column_names){f=b.dataset.metadata_column_names[g]}else{if(c){f=b.possibleHeaders[g]}}a.push({index:h,name:f});if(i==="int"||i==="float"){e.push({index:h,name:f})}});var d=this.$el.find(".tab-pane#data-control");d.html(ScatterplotControlForm.templates.dataControl({allColumns:a,numericColumns:e,possibleHeaders:(this.possibleHeaders)?(this.possibleHeaders.join(", ")):(""),usePossibleHeaders:c}));if(!this.dataset.metadata_column_names&&this.possibleHeaders){d.find("#first-line-header").show()}d.find("#X-select").val(this.chartConfig.xColumn);d.find("#Y-select").val(this.chartConfig.yColumn);if(this.chartConfig.idColumn!==undefined){d.find("#include-id-checkbox").attr("checked",true).trigger("change");d.find("#ID-select").val(this.chartConfig.idColumn)}return d},_render_chartControl:function(){var a=this,b=this.$el.find(".tab-pane#chart-control"),c={datapointSize:{min:2,max:10,step:1},width:{min:200,max:800,step:20},height:{min:200,max:800,step:20}};b.append(ScatterplotControlForm.templates.chartControl(this.chartConfig));b.find(".numeric-slider-input").each(function(){var f=$(this),e=f.find(".slider-output"),g=f.find(".slider"),h=f.attr("id");function d(){var j=$(this),i=j.slider("value");e.text(i)}g.slider(_.extend(c[h],{value:a.chartConfig[h],change:d,slide:d}))});return b},_render_chartDisplay:function(){var a=this.$el.find(".tab-pane#chart-display");a.append(ScatterplotControlForm.templates.chartDisplay(this.chartConfig));return a},events:{"change #include-id-checkbox":"toggleThirdColumnSelector","change #first-line-header-checkbox":"rerenderDataControl","click #data-control #render-button":"renderChart","click #chart-control #render-button":"changeChartSettings"},toggleThirdColumnSelector:function(){this.$el.find('select[name="ID"]').parent().toggle()},rerenderDataControl:function(){this.$dataControl=this._render_dataControl()},showLoadingIndicator:function(b,c){b=b||"";var a=this.$el.find("div#loading-indicator");messageBox=a.find(".loading-message");if(a.is(":visible")){if(b){messageBox.fadeOut("fast",function(){messageBox.text(b);messageBox.fadeIn("fast",c)})}else{c()}}else{if(b){messageBox.text(b)}a.fadeIn("fast",c)}},hideLoadingIndicator:function(a){this.$el.find("div#loading-indicator").fadeOut("fast",a)},renderChart:function(){this.log(this+".renderChart");this.data=null;this.meta=null;_.extend(this.chartConfig,this.getChartSettings());this.log("\t chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);this.loader.url=this.dataURL+"&"+jQuery.param(this.getDataSettings());this.log("\t loader: total lines:",this.loader.total," url:",this.loader.url);var a=this;$(this.loader).bind("loaded.new",function(c,b){a.log(a+" loaded.new",b);a.postProcessDataFetchResponse(b);a.log("\t postprocessed data:",a.data);a.log("\t postprocessed meta:",a.meta);a.showLoadingIndicator(a.renderMsg,function(){a.chart.render(a.data,a.meta);a.renderStats(a.data,a.meta);a.hideLoadingIndicator()})});$(this.loader).bind("complete",function(b,c){a.log(a+" complete",c);$(a.loader).unbind()});a.showLoadingIndicator(a.fetchMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.loader.load()})},renderStats:function(){this.log(this+".renderStats");this.$statsDisplay.html(ScatterplotControlForm.templates.statsDisplay({stats:[{name:"Count",xval:this.meta[0].count,yval:this.meta[1].count},{name:"Min",xval:this.meta[0].min,yval:this.meta[1].min},{name:"Max",xval:this.meta[0].max,yval:this.meta[1].max},{name:"Sum",xval:this.meta[0].sum,yval:this.meta[1].sum},{name:"Mean",xval:this.meta[0].mean,yval:this.meta[1].mean},{name:"Median",xval:this.meta[0].median,yval:this.meta[1].median}]}))},changeChartSettings:function(){var a=this;newChartSettings=this.getChartSettings();_.extend(this.chartConfig,newChartSettings);this.log("this.chartConfig:",this.chartConfig);this.chart.updateConfig(this.chartConfig,false);if(a.data&&a.meta){a.showLoadingIndicator(a.renderMsg,function(){a.$el.find("ul.nav").find('a[href="#chart-display"]').tab("show");a.chart.render(a.data,a.meta);a.hideLoadingIndicator()})}else{this.renderChart()}},postProcessDataFetchResponse:function(a){this.postProcessData(a.data);this.postProcessMeta(a.meta)},postProcessData:function(b){var a=this;if(a.data){_.each(b,function(d,c){a.data[c]=a.data[c].concat(d)})}else{a.data=b}},postProcessMeta:function(c){var a=this,b=this.dataset.metadata_column_types;if(a.meta){_.each(c,function(e,d){var i=a.meta[d],g=b[d];i.count+=(e.count)?(e.count):(0);if((g==="int")||(g==="float")){i.min=Math.min(e.min,i.min);i.max=Math.max(e.max,i.max);i.sum=e.sum+i.sum;i.mean=(i.count)?(i.sum/i.count):(null);var f=a.data[d].slice().sort(),h=Math.floor(f.length/2);if(f.length%2===0){i.median=((f[h]+f[(h+1)])/2)}else{i.median=f[h]}}})}else{a.meta=c}},getDataSettings:function(){var b=this.getColumnSelections(),a=[];this.log("\t columnSelections:",b);a=[b.X.colIndex-1,b.Y.colIndex-1];if(this.$dataControl.find("#include-id-checkbox").attr("checked")){a.push(b.ID.colIndex-1)}var c={data_type:"raw_data",provider:"column_with_stats",columns:"["+a+"]"};this.log("\t data settings (url params):",c);return c},getColumnSelections:function(){var a={};this.$dataControl.find("div.column-select select").each(function(){var b=$(this),c=b.val();a[b.attr("name")]={colIndex:c,colName:b.children('[value="'+c+'"]').text()}});return a},getChartSettings:function(){var c={},d=this.getColumnSelections();c.datapointSize=this.$chartControl.find("#datapointSize.numeric-slider-input").find(".slider").slider("value");c.width=this.$chartControl.find("#width.numeric-slider-input").find(".slider").slider("value");c.height=this.$chartControl.find("#height.numeric-slider-input").find(".slider").slider("value");var b=this.$chartControl.find("input#X-axis-label").val(),a=this.$chartControl.find("input#Y-axis-label").val();c.xLabel=(b==="X")?(d.X.colName):(b);c.yLabel=(a==="Y")?(d.Y.colName):(a);c.animDuration=(this.$chartControl.find("#animate-chart").is(":checked"))?(this.chart.defaults.animDuration):(0);this.log("\t chartSettings:",c);return c},toString:function(){return"ScatterplotControlForm("+((this.dataset)?(this.dataset.id):(""))+")"}});ScatterplotControlForm.templates={mainLayout:Handlebars.templates["template-visualization-scatterplotControlForm"],dataControl:Handlebars.templates["template-visualization-dataControl"],chartControl:Handlebars.templates["template-visualization-chartControl"],statsDisplay:Handlebars.templates["template-visualization-statsDisplay"],chartDisplay:Handlebars.templates["template-visualization-chartDisplay"]}; \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Eliminate the need for deactivating or uninstalling repositories in order to manage the tools loaded into app.toolbox within the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0de3c7e7d632/ Changeset: 0de3c7e7d632 User: greg Date: 2013-12-20 17:13:20 Summary: Eliminate the need for deactivating or uninstalling repositories in order to manage the tools loaded into app.toolbox within the tool shed's install and test framework. Affected #: 5 files diff -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -128,17 +128,6 @@ del( kwd[ field_name ] ) return kwd - def uninstall_repository( self, repository ): - """Uninstall a repository.""" - # A repository can be uninstalled only if no dependent repositories are installed. - url = '/admin_toolshed/deactivate_or_uninstall_repository?id=%s' % self.security.encode_id( repository.id ) - self.visit_url( url ) - tc.fv ( 1, "remove_from_disk", 'true' ) - tc.submit( 'deactivate_or_uninstall_repository_button' ) - strings_displayed = [ 'The repository named' ] - strings_displayed.append( 'has been uninstalled' ) - self.check_for_strings( strings_displayed, strings_not_displayed=[] ) - def visit_url( self, url, allowed_codes=[ 200 ] ): new_url = tc.go( url ) return_code = tc.browser.get_code() diff -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -518,8 +518,6 @@ repository_dict, params, can_update_tool_shed ) - # Uninstall this repository since it is missing dependencies. - uninstall_repository_and_repository_dependencies( app, repository_dict ) def initialize_install_and_test_statistics_dict( test_framework ): # Initialize a dictionary for the summary that will be printed to stdout. @@ -591,7 +589,7 @@ log.exception( error_message ) return repository, error_message -def is_excluded( exclude_list_dicts, name, owner, changeset_revision ): +def is_excluded( exclude_list_dicts, name, owner, changeset_revision, encoded_repository_metadata_id ): """ Return True if the repository defined by the received name, owner, changeset_revision should be excluded from testing for any reason. @@ -606,7 +604,7 @@ return True, reason # Skip this repository if it has a repository dependency that is in the exclude list. repository_dependency_dicts, error_message = \ - get_repository_dependencies_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + get_repository_dependencies_for_changeset_revision( galaxy_tool_shed_url, encoded_repository_metadata_id ) if error_message: log.debug( 'Error getting repository dependencies for revision %s of repository %s owned by %s:' % \ @@ -800,96 +798,3 @@ test_runner = plug_runner result = test_runner.run( tests ) return result, test_config.plugins._plugins - -def uninstall_repository_and_repository_dependencies( app, repository_dict ): - """Uninstall a repository and all of its repository dependencies.""" - # This method assumes that the repositor defined by the received repository_dict is not a repository - # dependency of another repository. - sa_session = app.install_model.context - # The dict contains the only repository the app should have installed at this point. - name = str( repository_dict[ 'name' ] ) - owner = str( repository_dict[ 'owner' ] ) - changeset_revision = str( repository_dict[ 'changeset_revision' ] ) - # Since this install and test framework uninstalls repositories immediately after installing and testing - # them, the values of repository.installed_changeset_revision and repository.changeset_revision should be - # the same. - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - if repository.can_uninstall( app ): - # A repository can be uninstalled only if no dependent repositories are installed. So uninstallation order - # id critical. A repository is always uninstalled first, and the each of its dependencies is checked to see - # if it can be uninstalled. - uninstall_repository_dict = dict( name=name, - owner=owner, - changeset_revision=changeset_revision ) - log.debug( 'Revision %s of repository %s owned by %s selected for uninstallation.' % ( changeset_revision, name, owner ) ) - try: - test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) - # Set up nose to run the generated uninstall method as a functional test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed - # repository and all of its repository dependencies, deleting each of them from disk. - result, _ = run_tests( test_config ) - repository_uninstall_successful = result.wasSuccessful() - except Exception, e: - repository_uninstall_successful = False - log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ - ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) - if repository_uninstall_successful: - # Now that the repository is uninstalled we can attempt to uninstall each of its repository dependencies. - # We have to do this through Twill in order to maintain app.toolbox and shed_tool_conf.xml in a state that - # is valid for future tests. Since some of the repository's repository dependencies may require other of - # the repository's repository dependencies, we'll keep track of the repositories we've been able to unistall. - processed_repository_dependency_ids = [] - while len( processed_repository_dependency_ids ) < len( repository.repository_dependencies ): - for repository_dependency in repository.repository_dependencies: - if repository_dependency.id not in processed_repository_dependency_ids and repository_dependency.can_uninstall( app ): - processed_repository_dependency_ids.append( repository_dependency.id ) - rd_name = str( repository_dependency.name ) - rd_owner = str( repository_dependency.owner ) - rd_changeset_revision = str( repository_dependency.changeset_revision ) - uninstall_repository_dict = dict( name=rd_name, - owner=rd_owner, - changeset_revision=rd_changeset_revision ) - log.debug( 'Revision %s of repository dependency %s owned by %s selected for uninstallation.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) ) - # Generate a test method to uninstall the repository dependency through the embedded Galaxy application's - # web interface. - try: - test_install_repositories.generate_uninstall_method( uninstall_repository_dict ) - # Set up nose to run the generated uninstall method as a functional test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the uninstall method. - result, _ = run_tests( test_config ) - if not result.wasSuccessful(): - # We won't set ok here because we'll continue to uninstall whatever we can. - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) ) - except Exception, e: - log.exception( 'Uninstallation of revision %s of repository %s owned by %s failed: %s.' % \ - ( rd_changeset_revision, rd_name, rd_owner, str( e ) ) ) - else: - log.debug( 'Uninstallation of revision %s of repository %s owned by %s failed.' % ( changeset_revision, name, owner ) ) - else: - log_reason_repository_cannot_be_uninstalled( app, repository ) - -def uninstall_tool_dependency( app, tool_dependency ): - """Attempt to uninstall a tool dependency.""" - sa_session = app.install_model.context - # Clean out any generated tests. This is necessary for Twill. - tool_dependency_install_path = tool_dependency.installation_directory( app ) - uninstalled, error_message = tool_dependency_util.remove_tool_dependency( app, tool_dependency ) - if error_message: - log.debug( 'Error attempting to remove directory: %s' % str( tool_dependency_install_path ) ) - log.debug( error_message ) - else: - log.debug( 'Successfully removed tool dependency installation directory: %s' % str( tool_dependency_install_path ) ) - if not uninstalled or tool_dependency.status != app.model.ToolDependency.installation_status.UNINSTALLED: - tool_dependency.status = app.model.ToolDependency.installation_status.UNINSTALLED - sa_session.add( tool_dependency ) - sa_session.flush() - if os.path.exists( tool_dependency_install_path ): - log.debug( 'Uninstallation of tool dependency succeeded, but the installation path still exists on the filesystem. It is now being explicitly deleted.') - suc.remove_dir( tool_dependency_install_path ) - diff -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py --- a/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py +++ b/test/install_and_test_tool_shed_repositories/functional/test_install_repositories.py @@ -9,21 +9,6 @@ class InstallTestRepositories( InstallTestRepository ): """Abstract test case that installs and uninstalls a predefined list of repositories.""" - def do_deactivate( self, repository_dict ): - self.logout() - self.login( email='test(a)bx.psu.edu', username='test' ) - admin_user = test_db_util.get_user( 'test(a)bx.psu.edu' ) - assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email - # Get the repository defined by the received repository_dict along with all of its repository dependencies - # from the database. - name = repository_dict[ 'name' ] - owner = repository_dict[ 'owner' ] - changeset_revision = repository_dict[ 'changeset_revision' ] - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - admin_user_private_role = test_db_util.get_private_role( admin_user ) - # Uninstall the repository through the web interface using twill. - self.deactivate_repository( repository ) - def do_install( self, repository_dict ): self.logout() self.login( email='test(a)bx.psu.edu', username='test' ) @@ -34,50 +19,6 @@ # actually install more than this singe repository because repository dependencies can be installed. self.install_repository( repository_dict ) - def do_uninstall( self, repository_dict ): - self.logout() - self.login( email='test(a)bx.psu.edu', username='test' ) - admin_user = test_db_util.get_user( 'test(a)bx.psu.edu' ) - assert admin_user is not None, 'Problem retrieving user with email %s from the database' % admin_email - # Get the repository defined by the received repository_dict along with all of its repository dependencies - # from the database. - name = repository_dict[ 'name' ] - owner = repository_dict[ 'owner' ] - changeset_revision = repository_dict[ 'changeset_revision' ] - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - admin_user_private_role = test_db_util.get_private_role( admin_user ) - # Uninstall the repository and all of its repository dependencies through the Galaxy web interface using twill. - self.uninstall_repository( repository ) - -def generate_deactivate_method( repository_dict=None ): - """Generate abstract test cases for the received repository_dict.""" - if repository_dict is None: - return - # Push all the toolbox tests to module level - G = globals() - # Eliminate all previous tests from G. - for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestForTool_' ): - del G[ key ] - # Create a new subclass with a method named install_repository_XXX that deactivates the - # repository specified by the received repository_dict. - name = "TestDeactivateRepository_%s_%s" % \ - ( str( repository_dict[ 'name' ] ), str( repository_dict[ 'changeset_revision' ] ) ) - baseclasses = ( InstallTestRepositories, ) - namespace = dict() - def make_deactivate_method( repository_dict ): - def test_deactivate_repository( self ): - self.do_deactivate( repository_dict ) - return test_deactivate_repository - test_method = make_deactivate_method( repository_dict ) - test_method.__doc__ = "Deactivate the repository %s." % str( repository_dict[ 'name' ] ) - namespace[ 'uninstall_repository_%s_%s' % ( str( repository_dict[ 'name' ] ), - str( repository_dict[ 'changeset_revision' ] ) ) ] = test_method - # The new.classobj function returns a new class object, with name name, derived - # from baseclasses (which should be a tuple of classes) and with namespace dict. - new_class_obj = new.classobj( str( name ), baseclasses, namespace ) - G[ name ] = new_class_obj - def generate_install_method( repository_dict=None ): """Generate abstract test cases for the defined list of repositories.""" if repository_dict is None: @@ -104,32 +45,3 @@ # from baseclasses (which should be a tuple of classes) and with namespace dict. new_class_obj = new.classobj( str( name ), baseclasses, namespace ) G[ name ] = new_class_obj - -def generate_uninstall_method( repository_dict=None ): - """Generate abstract test cases for the received repository_dict.""" - if repository_dict is None: - return - # Push all the toolbox tests to module level - G = globals() - # Eliminate all previous tests from G. - for key, val in G.items(): - if key.startswith( 'TestInstallRepository_' ) or key.startswith( 'TestForTool_' ): - del G[ key ] - # Create a new subclass with a method named install_repository_XXX that installs the repository - # specified by the received repository_dict. - name = "TestUninstallRepository_%s_%s" % \ - ( str( repository_dict[ 'name' ] ), str( repository_dict[ 'changeset_revision' ] ) ) - baseclasses = ( InstallTestRepositories, ) - namespace = dict() - def make_uninstall_method( repository_dict ): - def test_uninstall_repository( self ): - self.do_uninstall( repository_dict ) - return test_uninstall_repository - test_method = make_uninstall_method( repository_dict ) - test_method.__doc__ = "Uninstall the repository %s." % repository_dict[ 'name' ] - namespace[ 'uninstall_repository_%s_%s' % ( str( repository_dict[ 'name' ] ), - str( repository_dict[ 'changeset_revision' ] ) ) ] = test_method - # The new.classobj function returns a new class object, with name name, derived - # from baseclasses (which should be a tuple of classes) and with namespace dict. - new_class_obj = new.classobj( str( name ), baseclasses, namespace ) - G[ name ] = new_class_obj diff -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -76,7 +76,7 @@ can_update_tool_shed = True test_framework = install_and_test_base_util.REPOSITORIES_WITH_TOOLS - + def get_failed_test_dicts( test_result, from_tool_test=True ): """Extract any useful data from the test_result.failures and test_result.errors attributes.""" failed_test_dicts = [] @@ -177,7 +177,11 @@ log.debug( error_message ) else: tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) - is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, name, owner, changeset_revision ) + is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, + name, + owner, + changeset_revision, + encoded_repository_metadata_id ) if is_excluded: # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) @@ -193,28 +197,15 @@ ( changeset_revision, name, owner ) ) else: tool_test_results_dict = install_and_test_base_util.initialize_tool_tests_results_dict( app, tool_test_results_dict ) - # Explicitly clear tests from twill's test environment. - remove_generated_tests( app ) # Proceed with installing repositories and testing contained tools. repository, error_message = install_and_test_base_util.install_repository( app, repository_dict ) install_and_test_statistics_dict[ 'total_repositories_processed' ] += 1 if error_message: # The repository installation failed. - log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % \ - ( changeset_revision, name, owner ) ) + log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message - # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. - log.debug( 'Attempting to uninstall revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) - try: - repository = \ - test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - except Exception, e: - error_message = 'Unable to find revision %s of repository %s owned by %s: %s.' % \ - ( changeset_revision, name, owner, str( e ) ) - log.exception( error_message ) - params = dict( test_install_error=True, - do_not_test=False ) + params = dict( test_install_error=True ) # TODO: do something useful with response_dict response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, tool_test_results_dicts, @@ -222,19 +213,10 @@ repository_dict, params, can_update_tool_shed ) - try: - # We are uninstalling this repository and all of its repository dependencies. - install_and_test_base_util.uninstall_repository_and_repository_dependencies( app, repository_dict ) - except Exception, e: - log.exception( 'Error attempting to uninstall revision %s of repository %s owned by %s: %s' % \ - ( changeset_revision, name, owner, str( e ) ) ) - # Clean out any generated tests. This is necessary for Twill. - remove_generated_tests( app ) - install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) + else: + # The repository was successfully installed. log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ ( changeset_revision, name, owner ) ) - else: - # The repository was successfully installed. params, install_and_test_statistics_dict, tool_test_results_dict = \ install_and_test_base_util.register_installed_and_missing_dependencies( app, repository, @@ -257,26 +239,23 @@ tool_test_results_dict=tool_test_results_dict, params=params, can_update_tool_shed=can_update_tool_shed ) - # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. - test_toolbox.toolbox = app.toolbox else: - # This repository and all of its dependencies were successfully installed. - # Configure and run functional tests for this repository. This is equivalent to + log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) + # Generate the shed_tools_dict that specifies the location of test data contained within this repository. + # and configure and run functional tests for this repository. This is equivalent to # sh run_functional_tests.sh -installed - remove_install_tests() - log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) - # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository - # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, - # and the tools_functionally_correct flag to False, as well as updating tool_test_results. file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) + # Find the path to the test-data directory within the installed repository. has_test_data, shed_tools_dict = \ parse_tool_panel_config( galaxy_shed_tool_conf_file, from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) - # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional - # test framework can find it. + # If the repository has a test-data directory we write the generated shed_tools_dict to a temporary + # file so the functional test framework can find it. file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) + # Remove twills' old generated test before building the new tests for the current tools. + remove_tests( app ) try: install_and_test_statistics_dict = test_repository_tools( app, repository, @@ -441,6 +420,8 @@ config_items.append( config_tuple ) # Write a temporary file, based on universe_wsgi.ini.sample, using the configuration options defined above. generate_config_file( 'universe_wsgi.ini.sample', galaxy_config_file, config_items ) + # kwargs must be a list when passed to the Galaxy webapp (i.e., UniverseApplication). + # The following is used to set metadata externally. kwargs[ 'tool_config_file' ] = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ] # Set the global_conf[ '__file__' ] option to the location of the temporary .ini file, which gets passed to set_metadata.sh. kwargs[ 'global_conf' ] = install_and_test_base_util.get_webapp_global_conf() @@ -581,46 +562,45 @@ # Return a "successful" response to buildbot. return 0 -def remove_generated_tests( app ): +def remove_tests( app ): """ Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them and try to re-run the tests after uninstalling the repository, which will cause false failure reports, since the test data has been deleted from disk by now. """ tests_to_delete = [] - tools_to_delete = [] + tools_to_delete_by_id = [] global test_toolbox + # Find all tests previously generated by twill. for key in test_toolbox.__dict__: if key.startswith( 'TestForTool_' ): - log.debug( 'Tool test found in test_toolbox, deleting: %s' % str( key ) ) + log.debug( 'Tool test %s discovered in test_toolbox.' % str( key ) ) # We can't delete this test just yet, we're still iterating over __dict__. tests_to_delete.append( key ) tool_id = key.replace( 'TestForTool_', '' ) - for tool in app.toolbox.tools_by_id: - if tool.replace( '_', ' ' ) == tool_id.replace( '_', ' ' ): - tools_to_delete.append( tool ) + for app_tool_id in app.toolbox.tools_by_id: + if app_tool_id.replace( '_', ' ' ) == tool_id.replace( '_', ' ' ): + tools_to_delete_by_id.append( tool_id ) + # Delete the discovered twill-generated tests. for key in tests_to_delete: - # Now delete the tests found in the previous loop. - del test_toolbox.__dict__[ key ] - for tool in tools_to_delete: - del app.toolbox.tools_by_id[ tool ] - -def remove_install_tests(): - """ - Delete any configured repository installation tests from the test_toolbox.__dict__, otherwise nose will find them - and try to install the repository again while running tool functional tests. - """ - tests_to_delete = [] - global test_toolbox + if key in test_toolbox.__dict__: + log.debug( 'Deleting test %s from test_toolbox.' % str( key ) ) + del test_toolbox.__dict__[ key ] + for tool_id in tools_to_delete_by_id: + if tool_id in app.toolbox.tools_by_id: + log.debug( 'Deleting tool id %s from app.toolbox[ tools_by_id ].' % str( tool_id ) ) + del app.toolbox.tools_by_id[ tool_id ] # Push all the toolbox tests to module level for key in test_install_repositories.__dict__: if key.startswith( 'TestInstallRepository_' ): - log.debug( 'Repository installation process found, deleting: %s' % str( key ) ) + log.debug( 'Repository installation process test %s discovered.' % str( key ) ) # We can't delete this test just yet, we're still iterating over __dict__. tests_to_delete.append( key ) + # Delete the discovered twill-generated tests. for key in tests_to_delete: - # Now delete the tests found in the previous loop. - del test_install_repositories.__dict__[ key ] + if key in test_install_repositories.__dict__: + log.debug( 'Deleting test %s from test_toolbox.' % str( key ) ) + del test_install_repositories.__dict__[ key ] def test_repository_tools( app, repository, repository_dict, tool_test_results_dicts, tool_test_results_dict, install_and_test_statistics_dict ): @@ -629,7 +609,9 @@ owner = str( repository.owner ) changeset_revision = str( repository.changeset_revision ) repository_identifier_dict = dict( name=name, owner=owner, changeset_revision=changeset_revision ) - # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. + # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the + # appropriate test methods. At this point, app.toolbox contains the upload tool and all tools contained + # in the repository. test_toolbox.toolbox = app.toolbox # Generate the test methods for this installed repository. We need to pass in True here, or it will look # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. @@ -692,15 +674,6 @@ can_update_tool_shed ) log.debug( 'Revision %s of repository %s owned by %s installed successfully but did not pass functional tests.' % \ ( changeset_revision, name, owner ) ) - # Run the uninstall method. This removes tool functional test methods from the test_toolbox module and uninstalls the - # repository using Twill. - log.debug( 'Uninstalling changeset revision %s of repository %s' % ( str( changeset_revision ), str( name ) ) ) - # We are uninstalling this repository and all of its repository dependencies. - install_and_test_base_util.uninstall_repository_and_repository_dependencies( app, repository_dict ) - # Clean out any generated tests. This is necessary for Twill. - remove_generated_tests( app ) - # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. - test_toolbox.toolbox = app.toolbox return install_and_test_statistics_dict if __name__ == "__main__": diff -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 -r 0de3c7e7d6327e1af295fc4d81419efd8b5f41af test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -115,7 +115,11 @@ log.debug( error_message ) else: tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) - is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, name, owner, changeset_revision ) + is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, + name, + owner, + changeset_revision, + encoded_repository_metadata_id ) if this_repository_is_in_the_exclude_list or requires_excluded: # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 4 new changesets
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/882d74715634/ Changeset: 882d74715634 Branch: ccat3 User: BjoernGruening Date: 2013-11-11 10:09:54 Summary: add dependency of type package to the ccat wrapper Affected #: 1 file diff -r ea6ff3d7224db5d218eefa91af1b08626229eae1 -r 882d7471563422315959211baf12e89ae0e94a29 tools/peak_calling/ccat_wrapper.xml --- a/tools/peak_calling/ccat_wrapper.xml +++ b/tools/peak_calling/ccat_wrapper.xml @@ -10,6 +10,7 @@ '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command><requirements><requirement type="binary" version="3.0">CCAT</requirement> + <requirement type="package" version="3.0">CCAT</requirement></requirements><inputs><param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > https://bitbucket.org/galaxy/galaxy-central/commits/446d410097fd/ Changeset: 446d410097fd Branch: ccat3 User: BjoernGruening Date: 2013-11-11 10:10:41 Summary: remove ccat_2_wrapper.xml, afaik it is not used anymore Affected #: 1 file diff -r 882d7471563422315959211baf12e89ae0e94a29 -r 446d410097fd99711d3ef3160f8fd4e74f9d1a94 tools/peak_calling/ccat_2_wrapper.xml --- a/tools/peak_calling/ccat_2_wrapper.xml +++ /dev/null @@ -1,130 +0,0 @@ -<tool id="peakcalling_ccat2" name="CCAT" version="0.0.1"> - <description>Control-based ChIP-seq Analysis Tool</description> - <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' - #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': - '$input_advanced_config_file' - #else: - '${ options_type.input_config_file.fields.path }' - #end if - 'CCAT in Galaxy' - '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> - <requirements> - <requirement type="binary">CCAT</requirement> - </requirements> - <inputs> - <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > - <validator type="unspecified_build" /> - </param> - <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" > - <validator type="unspecified_build" /> - </param> - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"> - <param name="input_config_file" type="select" label="Select a pre-defined configuration file"> - <options from_data_table="ccat_configurations"> - <validator type="no_options" message="No configurations are available"/> - </options> - </param> - </when> - <when value="advanced"> - <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/> - <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/> - <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/> - <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" > - <option value="1">Transition from sense strand to anti-sense strand</option> - <option value="0" selected="True">Local maximum of read-enrichment profile</option> - </param> - <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/> - <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/> - <param name="random_seed" type="integer" label="Random Seed" value="123456"/> - <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/> - <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> - </outputs> - <configfiles> - <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced': -fragmentSize ${options_type[ 'fragment_size' ]} -slidingWinSize ${options_type[ 'sliding_window_size' ]} -movingStep ${options_type[ 'moving_step' ]} -isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} -minCount ${options_type[ 'min_count' ]} -outputNum ${options_type[ 'output_num' ]} -randomSeed ${options_type[ 'random_seed' ]} -minScore ${options_type[ 'min_score' ]} -bootstrapPass ${options_type[ 'bootstrap_pass' ]} -#end if</configfile> - </configfiles> - <tests> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="basic" /> - <param name="input_config_file" value="ccat_2.0_histone_config" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="advanced" /> - <param name="fragment_size" value="200" /> - <param name="sliding_window_size" value="500" /> - <param name="moving_step" value="50" /> - <param name="is_strand_sensitive_mode" value="0" /> - <param name="min_count" value="4" /> - <param name="output_num" value="100000" /> - <param name="random_seed" value="123456" /> - <param name="min_score" value="3.0" /> - <param name="bootstrap_pass" value="50" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - </tests> - <help> -**What it does** - -This tool allows ChIP-seq peak/region calling using CCAT. - -View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. - ------- - -**Citation** - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - - </help> -</tool> https://bitbucket.org/galaxy/galaxy-central/commits/936b96845324/ Changeset: 936b96845324 Branch: ccat3 User: BjoernGruening Date: 2013-11-11 15:35:45 Summary: remove binary dependency Affected #: 1 file diff -r 446d410097fd99711d3ef3160f8fd4e74f9d1a94 -r 936b96845324311668e5ee82761ed18a551a9fa1 tools/peak_calling/ccat_wrapper.xml --- a/tools/peak_calling/ccat_wrapper.xml +++ b/tools/peak_calling/ccat_wrapper.xml @@ -9,7 +9,6 @@ 'CCAT in Galaxy' '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command><requirements> - <requirement type="binary" version="3.0">CCAT</requirement><requirement type="package" version="3.0">CCAT</requirement></requirements><inputs> https://bitbucket.org/galaxy/galaxy-central/commits/0fb6c5d7312a/ Changeset: 0fb6c5d7312a User: natefoo Date: 2013-12-20 16:23:16 Summary: Merged in BjoernGruening/galaxy-central-bgruening/ccat3 (pull request #257) Adding requirement tag to the ccat wrapper and remove old ccat2 wrapper. Affected #: 1 file diff -r 2fcb2c12183df5ee7ec96d0f1a253c23448e4410 -r 0fb6c5d7312aafece427c4e9b19dc5e5b991c6d8 tools/peak_calling/ccat_2_wrapper.xml --- a/tools/peak_calling/ccat_2_wrapper.xml +++ /dev/null @@ -1,130 +0,0 @@ -<tool id="peakcalling_ccat2" name="CCAT" version="0.0.1"> - <description>Control-based ChIP-seq Analysis Tool</description> - <command interpreter="python">ccat_wrapper.py '$input_tag_file' '$input_control_file' '$chromInfo' - #if str( $options_type[ 'options_type_selector' ] ) == 'advanced': - '$input_advanced_config_file' - #else: - '${ options_type.input_config_file.fields.path }' - #end if - 'CCAT in Galaxy' - '$output_peak_file' '$output_region_file' '$output_top_file' '$output_log_file'</command> - <requirements> - <requirement type="binary">CCAT</requirement> - </requirements> - <inputs> - <param name="input_tag_file" type="data" format="bed" label="ChIP-Seq Tag File" > - <validator type="unspecified_build" /> - </param> - <param name="input_control_file" type="data" format="bed" label="ChIP-Seq Control File" > - <validator type="unspecified_build" /> - </param> - <conditional name="options_type"> - <param name="options_type_selector" type="select" label="Advanced Options"> - <option value="basic" selected="True">Hide Advanced Options</option> - <option value="advanced">Show Advanced Options</option> - </param> - <when value="basic"> - <param name="input_config_file" type="select" label="Select a pre-defined configuration file"> - <options from_data_table="ccat_configurations"> - <validator type="no_options" message="No configurations are available"/> - </options> - </param> - </when> - <when value="advanced"> - <param name="fragment_size" type="integer" label="Length of DNA fragment" value="200"/> - <param name="sliding_window_size" type="integer" label="Sliding window size" value="500" help="transcription factor binding default: 300; histone modifications default: 500"/> - <param name="moving_step" type="integer" label="Step of sliding window" value="50" help="transcription factor binding default: 10; histone modifications default: 50"/> - <param name="is_strand_sensitive_mode" type="select" label="isStrandSensitiveMode" > - <option value="1">Transition from sense strand to anti-sense strand</option> - <option value="0" selected="True">Local maximum of read-enrichment profile</option> - </param> - <param name="min_count" type="integer" label="Minimum number of read counts at the peak" value="4"/> - <param name="output_num" type="integer" label="Number of peaks reported in top peak file" value="100000"/> - <param name="random_seed" type="integer" label="Random Seed" value="123456"/> - <param name="min_score" type="float" label="Minimum score of normalized difference" value="3.0"/> - <param name="bootstrap_pass" type="integer" label="Number of passes in the bootstrapping process" value="50"/> - </when> - </conditional> - </inputs> - <outputs> - <data name="output_peak_file" format="interval" label="${tool.name} on ${on_string} (peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_region_file" format="interval" label="${tool.name} on ${on_string} (regions)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_top_file" format="interval" label="${tool.name} on ${on_string} (top peaks)"> - <actions> - <action type="metadata" name="chromCol" default="1"/> - <action type="metadata" name="startCol" default="3"/> - <action type="metadata" name="endCol" default="4"/> - </actions> - </data> - <data name="output_log_file" format="txt" label="${tool.name} on ${on_string} (log)"/> - </outputs> - <configfiles> - <configfile name="input_advanced_config_file">#if str( $options_type['options_type_selector' ] ) == 'advanced': -fragmentSize ${options_type[ 'fragment_size' ]} -slidingWinSize ${options_type[ 'sliding_window_size' ]} -movingStep ${options_type[ 'moving_step' ]} -isStrandSensitiveMode ${options_type[ 'is_strand_sensitive_mode' ]} -minCount ${options_type[ 'min_count' ]} -outputNum ${options_type[ 'output_num' ]} -randomSeed ${options_type[ 'random_seed' ]} -minScore ${options_type[ 'min_score' ]} -bootstrapPass ${options_type[ 'bootstrap_pass' ]} -#end if</configfile> - </configfiles> - <tests> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="basic" /> - <param name="input_config_file" value="ccat_2.0_histone_config" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - <test> - <param name="input_tag_file" value="chipseq_enriched.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="input_control_file" value="chipseq_input.bed.gz" ftype="bed" dbkey="hg18" /> - <param name="options_type_selector" value="advanced" /> - <param name="fragment_size" value="200" /> - <param name="sliding_window_size" value="500" /> - <param name="moving_step" value="50" /> - <param name="is_strand_sensitive_mode" value="0" /> - <param name="min_count" value="4" /> - <param name="output_num" value="100000" /> - <param name="random_seed" value="123456" /> - <param name="min_score" value="3.0" /> - <param name="bootstrap_pass" value="50" /> - <output name="output_peak_file" file="peakcalling_ccat2/ccat2_test_peak_out_1.interval" /> - <output name="output_region_file" file="peakcalling_ccat2/ccat2_test_region_out_1.interval" /> - <output name="output_top_file" file="peakcalling_ccat2/ccat2_test_top_out_1.interval" /> - <output name="output_log_file" file="peakcalling_ccat2/ccat2_test_log_out_1.interval" /> - </test> - </tests> - <help> -**What it does** - -This tool allows ChIP-seq peak/region calling using CCAT. - -View the original CCAT documentation: http://cmb.gis.a-star.edu.sg/ChIPSeq/paperCCAT.htm. - ------- - -**Citation** - -If you use this tool in Galaxy, please cite Blankenberg D, et al. *In preparation.* - - </help> -</tool> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Refactor method to determine excluded repositories in the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2fcb2c12183d/ Changeset: 2fcb2c12183d User: greg Date: 2013-12-20 16:05:57 Summary: Refactor method to determine excluded repositories in the tool shed's install and test framework. Affected #: 3 files diff -r bedb1e48e5c724d817f1a695ed068e0745f066cd -r 2fcb2c12183df5ee7ec96d0f1a253c23448e4410 test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -591,6 +591,41 @@ log.exception( error_message ) return repository, error_message +def is_excluded( exclude_list_dicts, name, owner, changeset_revision ): + """ + Return True if the repository defined by the received name, owner, changeset_revision should + be excluded from testing for any reason. + """ + for exclude_dict in exclude_list_dicts: + reason = exclude_dict[ 'reason' ] + exclude_repositories = exclude_dict[ 'repositories' ] + # 'repositories': + # [( name, owner, changeset_revision if changeset_revision else None ), + # ( name, owner, changeset_revision if changeset_revision else None )] + if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: + return True, reason + # Skip this repository if it has a repository dependency that is in the exclude list. + repository_dependency_dicts, error_message = \ + get_repository_dependencies_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + encoded_repository_metadata_id ) + if error_message: + log.debug( 'Error getting repository dependencies for revision %s of repository %s owned by %s:' % \ + ( changeset_revision, name, owner ) ) + log.debug( error_message ) + else: + for repository_dependency_dict in repository_dependency_dicts: + rd_name = repository_dependency_dict[ 'name' ] + rd_owner = repository_dependency_dict[ 'owner' ] + rd_changeset_revision = repository_dependency_dict[ 'changeset_revision' ] + if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \ + ( rd_name, rd_owner, None ) in exclude_repositories: + reason = 'This repository requires revision %s of repository %s owned by %s which is excluded from testing.' % \ + ( rd_changeset_revision, rd_name, rd_owner ) + return True, reason + break + return False, None + + def is_latest_downloadable_revision( url, repository_dict ): name = str( repository_dict[ 'name' ] ) owner = str( repository_dict[ 'owner' ] ) diff -r bedb1e48e5c724d817f1a695ed068e0745f066cd -r 2fcb2c12183df5ee7ec96d0f1a253c23448e4410 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -151,33 +151,15 @@ # [{ 'reason': The default reason or the reason specified in this section, # 'repositories': [( name, owner, changeset_revision if changeset_revision else None ), # ( name, owner, changeset_revision if changeset_revision else None )]}] - exclude_list = install_and_test_base_util.parse_exclude_list( exclude_list_file ) + exclude_list_dicts = install_and_test_base_util.parse_exclude_list( exclude_list_file ) else: - exclude_list = [] + exclude_list_dicts = [] # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was # started up, installing repository and tool dependencies. Upon successful installation, generate a test case for each # functional test defined for each tool in the repository and execute the test cases. Record the result of the tests. # The traceback and captured output of the tool that was run will be recored for test failures. After all tests have # completed, the repository is uninstalled, so test cases don't interfere with the next repository's functional tests. for repository_dict in repositories_to_install: - # Each repository_dict looks something like: - # { "changeset_revision": "13fa22a258b5", - # "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", - # "deleted": false, - # "deprecated": false, - # "description": "Convert column case.", - # "downloadable": true, - # "id": "529fd61ab1c6cc36", - # "long_description": "This tool takes the specified columns and converts them to uppercase or lowercase.", - # "malicious": false, - # "name": "change_case", - # "owner": "test", - # "private": false, - # "repository_id": "529fd61ab1c6cc36", - # "times_downloaded": 0, - # "tool_shed_url": "http://toolshed.local:10001", - # "url": "/api/repository_revisions/529fd61ab1c6cc36", - # "user_id": "529fd61ab1c6cc36" } encoded_repository_metadata_id = repository_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_dict[ 'tool_shed_url' ] = install_and_test_base_util.galaxy_tool_shed_url @@ -195,43 +177,10 @@ log.debug( error_message ) else: tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) - # See if this repository should be skipped for any reason. - this_repository_is_in_the_exclude_list = False - requires_excluded = False - skip_reason = None - for exclude_dict in exclude_list: - reason = exclude_dict[ 'reason' ] - exclude_repositories = exclude_dict[ 'repositories' ] - # 'repositories': - # [( name, owner, changeset_revision if changeset_revision else None ), - # ( name, owner, changeset_revision if changeset_revision else None )] - if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: - this_repository_is_in_the_exclude_list = True - skip_reason = reason - break - if not this_repository_is_in_the_exclude_list: - # Skip this repository if it has a repository dependency that is in the exclude list. - repository_dependency_dicts, error_message = \ - install_and_test_base_util.get_repository_dependencies_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - encoded_repository_metadata_id ) - if error_message: - log.debug( 'Error getting repository dependencies for revision %s of repository %s owned by %s:' % \ - ( changeset_revision, name, owner ) ) - log.debug( error_message ) - else: - for repository_dependency_dict in repository_dependency_dicts: - rd_name = repository_dependency_dict[ 'name' ] - rd_owner = repository_dependency_dict[ 'owner' ] - rd_changeset_revision = repository_dependency_dict[ 'changeset_revision' ] - if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \ - ( rd_name, rd_owner, None ) in exclude_repositories: - skip_reason = 'This repository requires revision %s of repository %s owned by %s which is excluded from testing.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) - requires_excluded = True - break - if this_repository_is_in_the_exclude_list or requires_excluded: + is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, name, owner, changeset_revision ) + if is_excluded: # If this repository is being skipped, register the reason. - tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) + tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) # TODO: do something useful with response_dict response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, diff -r bedb1e48e5c724d817f1a695ed068e0745f066cd -r 2fcb2c12183df5ee7ec96d0f1a253c23448e4410 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -98,24 +98,6 @@ # The traceback and captured output of the tool that was run will be recored for test failures. After all tests have # completed, the repository is uninstalled, so test cases don't interfere with the next repository's functional tests. for repository_dict in repositories_to_install: - # Each repository_dict looks something like: - # { "changeset_revision": "13fa22a258b5", - # "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", - # "deleted": false, - # "deprecated": false, - # "description": "Convert column case.", - # "downloadable": true, - # "id": "529fd61ab1c6cc36", - # "long_description": "This tool takes the specified columns and converts them to uppercase or lowercase.", - # "malicious": false, - # "name": "change_case", - # "owner": "test", - # "private": false, - # "repository_id": "529fd61ab1c6cc36", - # "times_downloaded": 0, - # "tool_shed_url": "http://toolshed.local:10001", - # "url": "/api/repository_revisions/529fd61ab1c6cc36", - # "user_id": "529fd61ab1c6cc36" } encoded_repository_metadata_id = repository_dict.get( 'id', None ) # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_dict[ 'tool_shed_url' ] = install_and_test_base_util.galaxy_tool_shed_url @@ -133,43 +115,10 @@ log.debug( error_message ) else: tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) - # See if this repository should be skipped for any reason. - this_repository_is_in_the_exclude_list = False - requires_excluded = False - skip_reason = None - for exclude_dict in exclude_list_dicts: - reason = exclude_dict[ 'reason' ] - exclude_repositories = exclude_dict[ 'repositories' ] - # 'repositories': - # [( name, owner, changeset_revision if changeset_revision else None ), - # ( name, owner, changeset_revision if changeset_revision else None )] - if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: - this_repository_is_in_the_exclude_list = True - skip_reason = reason - break - if not this_repository_is_in_the_exclude_list: - # Skip this repository if it has a repository dependency that is in the exclude list. - repository_dependency_dicts, error_message = \ - install_and_test_base_util.get_repository_dependencies_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, - encoded_repository_metadata_id ) - if error_message: - log.debug( 'Error getting repository dependencies for revision %s of repository %s owned by %s:' % \ - ( changeset_revision, name, owner ) ) - log.debug( error_message ) - else: - for repository_dependency_dict in repository_dependency_dicts: - rd_name = repository_dependency_dict[ 'name' ] - rd_owner = repository_dependency_dict[ 'owner' ] - rd_changeset_revision = repository_dependency_dict[ 'changeset_revision' ] - if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \ - ( rd_name, rd_owner, None ) in exclude_repositories: - skip_reason = 'This repository requires revision %s of repository %s owned by %s which is excluded from testing.' % \ - ( rd_changeset_revision, rd_name, rd_owner ) - requires_excluded = True - break + is_excluded, reason = install_and_test_base_util.is_excluded( exclude_list_dicts, name, owner, changeset_revision ) if this_repository_is_in_the_exclude_list or requires_excluded: # If this repository is being skipped, register the reason. - tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) + tool_test_results_dict[ 'not_tested' ] = dict( reason=reason ) params = dict( do_not_test=False ) # TODO: do something useful with response_dict response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Fix for install_and_test_statistics_dict being set to None when a repository's tool dependencies were determined to be unsuccessfully installed.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/bedb1e48e5c7/ Changeset: bedb1e48e5c7 User: inithello Date: 2013-12-20 15:55:14 Summary: Fix for install_and_test_statistics_dict being set to None when a repository's tool dependencies were determined to be unsuccessfully installed. Affected #: 1 file diff -r c77a66edf25294e1743cc0a3886f8062db5c1fff -r bedb1e48e5c724d817f1a695ed068e0745f066cd test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -300,15 +300,14 @@ tool_test_results_dict[ 'missing_test_components' ] = [] missing_tool_dependencies = install_and_test_base_util.get_missing_tool_dependencies( repository ) if missing_tool_dependencies or repository.missing_repository_dependencies: - install_and_test_statistics_dict = \ - install_and_test_base_util.handle_missing_dependencies( app=app, - repository=repository, - missing_tool_dependencies=missing_tool_dependencies, - repository_dict=repository_dict, - tool_test_results_dicts=tool_test_results_dicts, - tool_test_results_dict=tool_test_results_dict, - params=params, - can_update_tool_shed=can_update_tool_shed ) + install_and_test_base_util.handle_missing_dependencies( app=app, + repository=repository, + missing_tool_dependencies=missing_tool_dependencies, + repository_dict=repository_dict, + tool_test_results_dicts=tool_test_results_dicts, + tool_test_results_dict=tool_test_results_dict, + params=params, + can_update_tool_shed=can_update_tool_shed ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Make the tool shed's install and test exclude list locally accessible rather than stored in cfengine.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c77a66edf252/ Changeset: c77a66edf252 User: greg Date: 2013-12-20 15:50:03 Summary: Make the tool shed's install and test exclude list locally accessible rather than stored in cfengine. Affected #: 4 files diff -r 3e2b61de5a2322563c1ffa49e03c118144f5068c -r c77a66edf25294e1743cc0a3886f8062db5c1fff lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py --- a/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py +++ b/lib/tool_shed/scripts/check_tool_dependency_definition_repositories.py @@ -197,7 +197,16 @@ test_environment_dict[ 'tool_shed_mercurial_version' ] = __version__.version test_environment_dict[ 'tool_shed_revision' ] = get_repository_current_revision( os.getcwd() ) tool_test_results_dict[ 'test_environment' ] = test_environment_dict - repository_metadata.tool_test_results = tool_test_results_dict + # Store only the configured number of test runs. + num_tool_test_results_saved = int( app.config.num_tool_test_results_saved ) + if len( tool_test_results_dicts ) >= num_tool_test_results_saved: + test_results_index = num_tool_test_results_saved - 1 + new_tool_test_results_dicts = tool_test_results_dicts[ :test_results_index ] + else: + new_tool_test_results_dicts = [ d for d in tool_test_results_dicts ] + # Insert the new element into the first position in the list. + new_tool_test_results_dicts.insert( 0, tool_test_results_dict ) + repository_metadata.tool_test_results = new_tool_test_results_dicts app.sa_session.add( repository_metadata ) app.sa_session.flush() stop = time.time() diff -r 3e2b61de5a2322563c1ffa49e03c118144f5068c -r c77a66edf25294e1743cc0a3886f8062db5c1fff test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -41,16 +41,6 @@ self.shed_tools_dict = {} self.home() - def deactivate_repository( self, repository ): - """Deactivate a repository.""" - url = '/admin_toolshed/deactivate_or_uninstall_repository?id=%s' % self.security.encode_id( repository.id ) - self.visit_url( url ) - tc.fv ( 1, "remove_from_disk", 'false' ) - tc.submit( 'deactivate_or_uninstall_repository_button' ) - strings_displayed = [ 'The repository named' ] - strings_displayed.append( 'has been deactivated' ) - self.check_for_strings( strings_displayed, strings_not_displayed=[] ) - def initiate_installation_process( self, install_tool_dependencies=False, install_repository_dependencies=True, diff -r 3e2b61de5a2322563c1ffa49e03c118144f5068c -r c77a66edf25294e1743cc0a3886f8062db5c1fff test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -63,12 +63,11 @@ # Here's the directory where everything happens. Temporary directories are created within this directory to contain # the database, new repositories, etc. galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' ) +# File containing information about problematic repositories to exclude from test runs. +exclude_list_file = os.path.join( test_home_directory, 'exclude.xml' ) default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir -# This file is copied to the Galaxy root directory by buildbot. -# It is managed by cfengine and is not locally available. -exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'repositories_with_tools_exclude.xml' ) # This script can be run in such a way that no Tool Shed database records should be changed. if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: @@ -138,25 +137,20 @@ return tool_id, tool_version def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): + # Initialize a dictionary for the summary that will be printed to stdout. install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict( test_framework ) error_message = '' - # Initialize a dictionary for the summary that will be printed to stdout. - total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ] repositories_to_install, error_message = \ install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework ) if error_message: return None, error_message # Handle repositories not to be tested. if os.path.exists( exclude_list_file ): - # Entries in the exclude_list look something like this. - # { 'reason': The default reason or the reason specified in this section, - # 'repositories': - # [( name, owner, changeset revision if changeset revision else None ), - # ( name, owner, changeset revision if changeset revision else None )] } - # If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified - # revision should be skipped. - log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ - str( exclude_list_file ) ) + log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % str( exclude_list_file ) ) + # The following exclude_list will look something like this: + # [{ 'reason': The default reason or the reason specified in this section, + # 'repositories': [( name, owner, changeset_revision if changeset_revision else None ), + # ( name, owner, changeset_revision if changeset_revision else None )]}] exclude_list = install_and_test_base_util.parse_exclude_list( exclude_list_file ) else: exclude_list = [] diff -r 3e2b61de5a2322563c1ffa49e03c118144f5068c -r c77a66edf25294e1743cc0a3886f8062db5c1fff test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -61,12 +61,11 @@ # Here's the directory where everything happens. Temporary directories are created within this directory to contain # the database, new repositories, etc. galaxy_test_tmp_dir = os.path.join( test_home_directory, 'tmp' ) +# File containing information about problematic repositories to exclude from test runs. +exclude_list_file = os.path.join( test_home_directory, 'exclude.xml' ) default_galaxy_locales = 'en' default_galaxy_test_file_dir = "test-data" os.environ[ 'GALAXY_INSTALL_TEST_TMP_DIR' ] = galaxy_test_tmp_dir -# This file is copied to the Galaxy root directory by buildbot. -# It is managed by cfengine and is not locally available. -exclude_list_file = os.environ.get( 'GALAXY_INSTALL_TEST_EXCLUDE_REPOSITORIES', 'tool_dependency_definition_exclude.xml' ) # This script can be run in such a way that no Tool Shed database records should be changed. if '-info_only' in sys.argv or 'GALAXY_INSTALL_TEST_INFO_ONLY' in os.environ: @@ -77,29 +76,15 @@ test_framework = install_and_test_base_util.TOOL_DEPENDENCY_DEFINITIONS def install_and_test_repositories( app, galaxy_shed_tools_dict, galaxy_shed_tool_conf_file ): + # Initialize a dictionary for the summary that will be printed to stdout. install_and_test_statistics_dict = install_and_test_base_util.initialize_install_and_test_statistics_dict( test_framework ) error_message = '' - # Initialize a dictionary for the summary that will be printed to stdout. - total_repositories_processed = install_and_test_statistics_dict[ 'total_repositories_processed' ] repositories_to_install, error_message = \ install_and_test_base_util.get_repositories_to_install( install_and_test_base_util.galaxy_tool_shed_url, test_framework ) if error_message: return None, error_message - # Handle repositories not to be tested. if os.path.exists( exclude_list_file ): - # Entries in the exclude_list look something like this. - # { 'reason': The default reason or the reason specified in this section, - # 'repositories': - # [( name, owner, changeset revision if changeset revision else None ), - # ( name, owner, changeset revision if changeset revision else None )] } - # If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified - # revision should be skipped. - # We are testing deprecated repositories because it is possible that a deprecated repository contains valid tools that - # someone has previously installed. Deleted repositories have never been installed, so should not be tested. If they are - # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted - # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. - log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ - str( exclude_list_file ) ) + log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % str( exclude_list_file ) ) # The following exclude_list will look something like this: # [{ 'reason': The default reason or the reason specified in this section, # 'repositories': [( name, owner, changeset_revision if changeset_revision else None ), @@ -201,19 +186,9 @@ install_and_test_statistics_dict[ 'total_repositories_processed' ] += 1 if error_message: # The repository installation failed. - log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % \ - ( changeset_revision, name, owner ) ) + log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( repository_identifier_dict ) tool_test_results_dict[ 'installation_errors' ][ 'current_repository' ] = error_message - # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. - log.debug( 'Attempting to uninstall revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) - try: - repository = \ - test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) - except Exception, e: - error_message = 'Unable to find revision %s of repository %s owned by %s: %s.' % \ - ( changeset_revision, name, owner, str( e ) ) - log.exception( error_message ) params = dict( test_install_error=True, do_not_test=False ) # TODO: do something useful with response_dict @@ -223,14 +198,6 @@ repository_dict, params, can_update_tool_shed ) - try: - # We are uninstalling this repository and all of its repository dependencies. - install_and_test_base_util.uninstall_repository_and_repository_dependencies( app, repository_dict ) - except Exception, e: - log.exception( 'Error attempting to uninstall revision %s of repository %s owned by %s: %s' % \ - ( changeset_revision, name, owner, str( e ) ) ) - log.debug( 'Installation failed for revision %s of repository %s owned by %s.' % \ - ( changeset_revision, name, owner ) ) else: # The repository was successfully installed. params, install_and_test_statistics_dict, tool_test_results_dict = \ Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Fix for testing repositories with tools using the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 20 Dec '13

20 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3e2b61de5a23/ Changeset: 3e2b61de5a23 User: greg Date: 2013-12-20 03:20:57 Summary: Fix for testing repositories with tools using the tool shed's install and test framework. Affected #: 1 file diff -r 9e9746198fd8c49380d42a2b4657ef241dda8f6a -r 3e2b61de5a2322563c1ffa49e03c118144f5068c test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -155,10 +155,6 @@ # ( name, owner, changeset revision if changeset revision else None )] } # If changeset revision is None, that means the entire repository is excluded from testing, otherwise only the specified # revision should be skipped. - # We are testing deprecated repositories because it is possible that a deprecated repository contains valid tools that - # someone has previously installed. Deleted repositories have never been installed, so should not be tested. If they are - # undeleted, this script will then test them the next time it runs. We don't need to check if a repository has been deleted - # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ str( exclude_list_file ) ) exclude_list = install_and_test_base_util.parse_exclude_list( exclude_list_file ) @@ -739,7 +735,9 @@ tool_test_results_dict[ 'failed_tests' ] = failed_test_dicts failed_repository_dict = repository_identifier_dict install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( failed_repository_dict ) - set_do_not_test = not is_latest_downloadable_revision( install_and_test_base_util.galaxy_tool_shed_url, repository_dict ) + set_do_not_test = \ + not install_and_test_base_util.is_latest_downloadable_revision( install_and_test_base_util.galaxy_tool_shed_url, + repository_dict ) params = dict( tools_functionally_correct=False, test_install_error=False, do_not_test=str( set_do_not_test ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Re-add changeset_revision to the information returned from the tool shed's repository_dependencies api method.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9e9746198fd8/ Changeset: 9e9746198fd8 User: greg Date: 2013-12-19 23:30:29 Summary: Re-add changeset_revision to the information returned from the tool shed's repository_dependencies api method. Affected #: 1 file diff -r 7701d6b5e1b62f501e827a3cc6ee880e8955f036 -r 9e9746198fd8c49380d42a2b4657ef241dda8f6a lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -91,6 +91,8 @@ tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ] repository_dependency = suc.get_repository_by_name_and_owner( trans.app, name, owner ) repository_dependency_dict = repository_dependency.to_dict( view='element', value_mapper=value_mapper ) + # We have to add the changeset_revision of of the repository dependency. + repository_dependency_dict[ 'changeset_revision' ] = changeset_revision repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', action='show', id=trans.security.encode_id( repository_dependency.id ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Code cleanup for the tool shed's new repository_revisions' repository_dependencies method.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7701d6b5e1b6/ Changeset: 7701d6b5e1b6 User: greg Date: 2013-12-19 23:22:32 Summary: Code cleanup for the tool shed's new repository_revisions' repository_dependencies method. Affected #: 1 file diff -r f8e9f9f0f64d853fe6db058b6c4ffaa9e497c781 -r 7701d6b5e1b62f501e827a3cc6ee880e8955f036 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -79,6 +79,8 @@ :param id: the encoded id of the `RepositoryMetadata` object """ # Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb12… + value_mapper = { 'id' : trans.security.encode_id, + 'user_id' : trans.security.encode_id } repository_dependencies_dicts = [] try: repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) @@ -87,22 +89,12 @@ rd_tups = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] for rd_tup in rd_tups: tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ] - repository_dependencies_dict = dict( tool_shed=str( tool_shed ), - name=str( name ), - owner=str( owner ), - changeset_revision=str( changeset_revision ) ) - rd = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - encoded_rd_id = trans.security.encode_id( rd.id ) - rd_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, - encoded_rd_id, - changeset_revision ) - if rd_repository_metadata is None: - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - rd_repository_metadata = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) - repository_dependencies_dict[ 'url' ] = web.url_for( controller='repository_revisions', - action='show', - id=trans.security.encode_id( rd_repository_metadata.id ) ) - repository_dependencies_dicts.append( repository_dependencies_dict ) + repository_dependency = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + repository_dependency_dict = repository_dependency.to_dict( view='element', value_mapper=value_mapper ) + repository_dependency_dict[ 'url' ] = web.url_for( controller='repositories', + action='show', + id=trans.security.encode_id( repository_dependency.id ) ) + repository_dependencies_dicts.append( repository_dependency_dict ) return repository_dependencies_dicts except Exception, e: message = "Error in the Tool Shed repository_revisions API in repository_dependencies: %s" % str( e ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Grids: Add history refresh
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f8e9f9f0f64d/ Changeset: f8e9f9f0f64d User: guerler Date: 2013-12-19 22:30:23 Summary: Grids: Add history refresh Affected #: 3 files diff -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c -r f8e9f9f0f64d853fe6db058b6c4ffaa9e497c781 static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -158,7 +158,18 @@ .keyup(function () { $(this).css("font-style", "normal"); }); }); }, - + + // refresh frames + handle_refresh: function (refresh_frames) { + if (refresh_frames) { + if ($.inArray('history', refresh_frames) > -1) { + if( top.Galaxy && top.Galaxy.currHistoryPanel ){ + top.Galaxy.currHistoryPanel.loadCurrentHistory(); + } + } + } + }, + // Initialize init_grid: function(grid_config) { @@ -167,7 +178,10 @@ // get options var options = this.grid.attributes; - + + // handle refresh requests + this.handle_refresh(options.refresh_frames); + // strip protocol and domain var url = this.grid.get('url_base'); url = url.replace(/^.*\/\/[^\/]+/, ''); diff -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c -r f8e9f9f0f64d853fe6db058b6c4ffaa9e497c781 static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var s=$(this).find("input.grid-row-select-checkbox");var r=$(this).find("span.grid-selected-count");var t=function(){r.text($(s).filter(":checked").length)};$(s).each(function(){$(this).change(t)});t()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$("<span>"+g+"<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+e+"</span>").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$("<a href='#'>"+m+"</a>");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$("<a href='#'>"+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(m,"")}return false}if(e){this.go_to(m,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(m,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=$("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh 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value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in t.columns){var f=t.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var s=r.column_config[f.label];var l=s.link;var n=s.value;var q=s.inbound;if(jQuery.type(n)==="string"){n=n.replace(/\/\//g,"/")}var d="";var p="";if(f.attach_popup){d="grid-"+h+"-popup";p="menubutton";if(l!=""){p+=" split"}p+=" popup"}m+="<td "+e+">";if(l){if(t.operations.length!=0){m+='<div id="'+d+'" class="'+p+'" style="float: left;">'}var o="";if(q){o="use-inbound"}else{o="use-outbound"}m+='<a class="label '+o+'" href="'+l+'" onclick="return false;">'+n+"</a>";if(t.operations.length!=0){m+="</div>"}}else{m+='<div id="'+d+'" class="'+p+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+n+"</label></div>"}m+="</td>"}}m+="</tr>";u++}return m},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file +jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;this.handle_refresh(d.refresh_frames);var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var 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q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var 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selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file diff -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c -r f8e9f9f0f64d853fe6db058b6c4ffaa9e497c781 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -15,7 +15,6 @@ return '/base.mako' %><%inherit file="${inherit(context)}"/> -<%namespace file="/refresh_frames.mako" import="handle_refresh_frames" /><%namespace file="/display_common.mako" import="get_class_plural" /><%def name="load(embedded = False, insert = None)"> @@ -67,9 +66,14 @@ 'use_panels' : context.get('use_panels'), 'insert' : insert, 'default_filter_dict' : default_filter_dict, - 'advanced_search' : advanced_search + 'advanced_search' : advanced_search, + 'refresh_frames' : [] } + # add refresh frames + if refresh_frames: + self.grid_config['refresh_frames'] = refresh_frames + ## add current item if exists if current_item: self.grid_config['current_item_id'] = current_item.id @@ -243,7 +247,6 @@ }); </script> - ${handle_refresh_frames()} </%def><%def name="stylesheets()"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Enhancements and fixes for registering statistics and test results in the tool shed's install and test framework.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ac5eb19c0bd/ Changeset: 4ac5eb19c0bd User: greg Date: 2013-12-19 21:56:50 Summary: Enhancements and fixes for registering statistics and test results in the tool shed's install and test framework. Affected #: 3 files diff -r 3bbb2f8e43b109b5adc8925a52ed23d9f31cd236 -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -476,7 +476,7 @@ return global_conf def handle_missing_dependencies( app, repository, missing_tool_dependencies, repository_dict, tool_test_results_dicts, - tool_test_results_dict, can_update_tool_shed ): + tool_test_results_dict, params, can_update_tool_shed ): """Handle missing repository or tool dependencies for an installed repository.""" # If a tool dependency fails to install correctly, this should be considered an installation error, # and functional tests should be skipped, since the tool dependency needs to be correctly installed @@ -508,11 +508,9 @@ owner=owner, changeset_revision=changeset_revision, error_message=error_message ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( missing_repository_dependency_info_dict ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ]\ + .append( missing_repository_dependency_info_dict ) # Record the status of this repository in the tool shed. - params = dict( tools_functionally_correct=False, - do_not_test=False, - test_install_error=True ) # TODO: do something useful with response_dict response_dict = register_test_result( galaxy_tool_shed_url, tool_test_results_dicts, @@ -663,6 +661,73 @@ log.debug( 'Repository %s owned by %s, all revisions.' % ( str( name ), str( owner ) ) ) return exclude_list +def register_installed_and_missing_dependencies( app, repository, repository_identifier_dict, install_and_test_statistics_dict, + tool_test_results_dict ): + # The repository was successfully installed. + log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ + ( str( repository.changeset_revision ), str( repository.name ), str( repository.owner ) ) ) + install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_dict ) + tool_test_results_dict[ 'successful_installations' ][ 'current_repository' ].append( repository_identifier_dict ) + params = dict( test_install_error=False, + do_not_test=False ) + if repository.missing_repository_dependencies: + params[ 'test_install_error' ] = True + # Keep statistics for this repository's repository dependencies that resulted in installation errors. + for missing_repository_dependency in repository.missing_repository_dependencies: + tool_shed = str( missing_repository_dependency.tool_shed ) + name = str( missing_repository_dependency.name ) + owner = str( missing_repository_dependency.owner ) + changset_revision = str( missing_repository_dependency.changeset_revision ) + error_message = unicodify( missing_repository_dependency.error_message ) + missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, + name=name, + owner=owner, + changset_revision=changset_revision, + error_message=error_message ) + install_and_test_statistics_dict[ 'repositories_with_installation_error' ].append( missing_repository_dependency_dict ) + tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ].append( missing_repository_dependency_info_dict ) + if repository.missing_tool_dependencies: + params[ 'test_install_error' ] = True + # Keep statistics for this repository's tool dependencies that resulted in installation errors. + for missing_tool_dependency in repository.missing_tool_dependencies: + name = str( missing_tool_dependency.name ) + type = str( missing_tool_dependency.type ) + version = str( missing_tool_dependency.version ) + error_message = unicodify( missing_tool_dependency.error_message ) + missing_tool_dependency_info_dict = dict( type=type, + name=name, + version=version, + error_message=error_message ) + install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) + tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ].append( missing_tool_dependency_info_dict ) + if repository.installed_repository_dependencies: + # Keep statistics for this repository's tool dependencies that resulted in successful installations. + for repository_dependency in repository.installed_repository_dependencies: + tool_shed = str( repository_dependency.tool_shed ) + name = str( repository_dependency.name ) + owner = str( repository_dependency.owner ) + changeset_revision = str( repository_dependency.changeset_revision ) + repository_dependency_info_dict = dict( tool_shed=tool_shed, + name=name, + owner=owner, + changeset_revision=changeset_revision ) + install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_dependency_info_dict ) + tool_test_results_dict[ 'successful_installations' ][ 'repository_dependencies' ].append( repository_dependency_info_dict ) + if repository.installed_tool_dependencies: + # Keep statistics for this repository's tool dependencies that resulted in successful installations. + for tool_dependency in repository.installed_tool_dependencies: + name = str( tool_dependency.name ) + type = str( tool_dependency.type ) + version = str( tool_dependency.version ) + installation_directory = tool_dependency.installation_directory( app ) + tool_dependency_info_dict = dict( type=type, + name=name, + version=version, + installation_directory=installation_directory ) + install_and_test_statistics_dict[ 'successful_tool_dependency_installations' ].append( tool_dependency_info_dict ) + tool_test_results_dict[ 'successful_installations' ][ 'tool_dependencies' ].append( tool_dependency_info_dict ) + return params, install_and_test_statistics_dict, tool_test_results_dict + def register_test_result( url, tool_test_results_dicts, tool_test_results_dict, repository_dict, params, can_update_tool_shed ): """ Update the repository metadata tool_test_results and appropriate flags using the Tool SHed API. This method diff -r 3bbb2f8e43b109b5adc8925a52ed23d9f31cd236 -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -207,15 +207,40 @@ tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) # See if this repository should be skipped for any reason. this_repository_is_in_the_exclude_list = False + requires_excluded = False skip_reason = None for exclude_dict in exclude_list: reason = exclude_dict[ 'reason' ] exclude_repositories = exclude_dict[ 'repositories' ] + # 'repositories': + # [( name, owner, changeset_revision if changeset_revision else None ), + # ( name, owner, changeset_revision if changeset_revision else None )] if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: this_repository_is_in_the_exclude_list = True skip_reason = reason break - if this_repository_is_in_the_exclude_list: + if not this_repository_is_in_the_exclude_list: + # Skip this repository if it has a repository dependency that is in the exclude list. + repository_dependency_dicts, error_message = \ + install_and_test_base_util.get_repository_dependencies_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + encoded_repository_metadata_id ) + if error_message: + log.debug( 'Error getting repository dependencies for revision %s of repository %s owned by %s:' % \ + ( changeset_revision, name, owner ) ) + log.debug( error_message ) + else: + for repository_dependency_dict in repository_dependency_dicts: + rd_name = repository_dependency_dict[ 'name' ] + rd_owner = repository_dependency_dict[ 'owner' ] + rd_changeset_revision = repository_dependency_dict[ 'changeset_revision' ] + if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \ + ( rd_name, rd_owner, None ) in exclude_repositories: + skip_reason = 'This repository requires revision %s of repository %s owned by %s which is excluded from testing.' % \ + ( rd_changeset_revision, rd_name, rd_owner ) + requires_excluded = True + break + if this_repository_is_in_the_exclude_list or requires_excluded: + # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) params = dict( do_not_test=False ) # TODO: do something useful with response_dict @@ -243,7 +268,8 @@ # Even if the repository failed to install, execute the uninstall method, in case a dependency did succeed. log.debug( 'Attempting to uninstall revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) try: - repository = test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) + repository = \ + test_db_util.get_installed_repository_by_name_owner_changeset_revision( name, owner, changeset_revision ) except Exception, e: error_message = 'Unable to find revision %s of repository %s owned by %s: %s.' % \ ( changeset_revision, name, owner, str( e ) ) @@ -269,19 +295,13 @@ log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ ( changeset_revision, name, owner ) ) else: - log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ - ( changeset_revision, name, owner ) ) - # Keep statistics for this repository's tool dependencies that resulted in installation errors. - for missing_tool_dependency in repository.missing_tool_dependencies: - name = str( missing_tool_dependency.name ) - type = str( missing_tool_dependency.type ) - version = str( missing_tool_dependency.version ) - error_message = unicodify( missing_tool_dependency.error_message ) - missing_tool_dependency_info_dict = dict( type=type, - name=name, - version=version, - error_message=error_message ) - install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ].append( missing_tool_dependency_info_dict ) + # The repository was successfully installed. + params, install_and_test_statistics_dict, tool_test_results_dict = \ + install_and_test_base_util.register_installed_and_missing_dependencies( app, + repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_dict ) # Add an empty 'missing_test_results' entry if it is missing from the tool_test_results_dict. The # ~/tool_shed/scripts/check_repositories_for_functional_tests.py will have entered information in the # 'missing_test_components' entry of the tool_test_results_dict dictionary for repositories that are @@ -297,25 +317,28 @@ repository_dict=repository_dict, tool_test_results_dicts=tool_test_results_dicts, tool_test_results_dict=tool_test_results_dict, + params=params, can_update_tool_shed=can_update_tool_shed ) # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. test_toolbox.toolbox = app.toolbox else: # This repository and all of its dependencies were successfully installed. - install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_dict ) - # Configure and run functional tests for this repository. This is equivalent to sh run_functional_tests.sh -installed + # Configure and run functional tests for this repository. This is equivalent to + # sh run_functional_tests.sh -installed remove_install_tests() log.debug( 'Installation of %s succeeded, running all defined functional tests.' % str( repository.name ) ) # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, # and the tools_functionally_correct flag to False, as well as updating tool_test_results. file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( {} ) ) - has_test_data, shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, - from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + has_test_data, shed_tools_dict = \ + parse_tool_panel_config( galaxy_shed_tool_conf_file, + from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) # If the repository has a test-data directory we write the generated shed_tools_dict to a file, so the functional # test framework can find it. file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) - log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), str( shed_tools_dict ) ) ) + log.debug( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( str( galaxy_shed_tools_dict ), + str( shed_tools_dict ) ) ) try: install_and_test_statistics_dict = test_repository_tools( app, repository, @@ -327,10 +350,9 @@ exception_message = 'Error executing tests for repository %s: %s' % ( name, str( e ) ) log.exception( exception_message ) tool_test_results_dict[ 'failed_tests' ].append( exception_message ) + install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) # Record the status of this repository in the tool shed. - params = dict( tools_functionally_correct=False, - do_not_test=False, - test_install_error=False ) + params[ 'tools_functionally_correct' ] = False # TODO: do something useful with response_dict response_dict = \ install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, @@ -339,7 +361,6 @@ repository_dict, params, can_update_tool_shed ) - install_and_test_statistics_dict[ 'at_least_one_test_failed' ].append( repository_identifier_dict ) return install_and_test_statistics_dict, error_message def main(): @@ -564,11 +585,12 @@ all_tests_passed = install_and_test_statistics_dict[ 'all_tests_passed' ] at_least_one_test_failed = install_and_test_statistics_dict[ 'at_least_one_test_failed' ] successful_repository_installations = install_and_test_statistics_dict[ 'successful_repository_installations' ] + successful_tool_dependency_installations = install_and_test_statistics_dict[ 'successful_tool_dependency_installations' ] repositories_with_installation_error = install_and_test_statistics_dict[ 'repositories_with_installation_error' ] tool_dependencies_with_installation_error = install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ] now = time.strftime( "%Y-%m-%d %H:%M:%S" ) print "####################################################################################" - print "# %s - installation script for repositories containing tools completed." % now + print "# %s - installation and test script for repositories containing tools completed." % now print "# Repository revisions processed: %s" % str( total_repositories_processed ) if successful_repository_installations: print "# ----------------------------------------------------------------------------------" @@ -586,6 +608,10 @@ print '# ----------------------------------------------------------------------------------' print "# The following %d revisions have installation errors:" % len( repositories_with_installation_error ) install_and_test_base_util.display_repositories_by_owner( repositories_with_installation_error ) + if successful_tool_dependency_installations: + print "# ----------------------------------------------------------------------------------" + print "# The following %d tool dependencies were successfully installed:" % len( successful_tool_dependency_installations ) + install_and_test_base_util.display_tool_dependencies_by_name( successful_tool_dependency_installations ) if tool_dependencies_with_installation_error: print "# ----------------------------------------------------------------------------------" print "# The following %d tool dependencies have installation errors:" % len( tool_dependencies_with_installation_error ) @@ -691,7 +717,7 @@ tool_test_results_dict[ 'passed_tests' ].append( test_result ) # Update the repository_metadata table in the tool shed's database to include the passed tests. passed_repository_dict = repository_identifier_dict - results_dict[ 'all_tests_passed' ].append( passed_repository_dict ) + install_and_test_statistics_dict[ 'all_tests_passed' ].append( passed_repository_dict ) params = dict( tools_functionally_correct=True, do_not_test=False, test_install_error=False ) diff -r 3bbb2f8e43b109b5adc8925a52ed23d9f31cd236 -r 4ac5eb19c0bdd45b558f1c262198009e0106f49c test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -182,8 +182,8 @@ ( rd_changeset_revision, rd_name, rd_owner ) requires_excluded = True break - # Register the reason this repository is being skipped if, in fact, it is. if this_repository_is_in_the_exclude_list or requires_excluded: + # If this repository is being skipped, register the reason. tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) params = dict( do_not_test=False ) # TODO: do something useful with response_dict @@ -233,77 +233,12 @@ ( changeset_revision, name, owner ) ) else: # The repository was successfully installed. - log.debug( 'Installation succeeded for revision %s of repository %s owned by %s.' % \ - ( changeset_revision, name, owner ) ) - install_and_test_statistics_dict[ 'successful_repository_installations' ].append( repository_identifier_dict ) - tool_test_results_dict[ 'successful_installations' ][ 'current_repository' ]\ - .append( repository_identifier_dict ) - params = dict( test_install_error=False, - do_not_test=False ) - if repository.missing_repository_dependencies: - params[ 'test_install_error' ] = True - # Keep statistics for this repository's repository dependencies that resulted in installation errors. - for missing_repository_dependency in repository.missing_repository_dependencies: - tool_shed = str( missing_repository_dependency.tool_shed ) - name = str( missing_repository_dependency.name ) - owner = str( missing_repository_dependency.owner ) - changset_revision = str( missing_repository_dependency.changeset_revision ) - error_message = unicodify( missing_repository_dependency.error_message ) - missing_repository_dependency_info_dict = dict( tool_shed=tool_shed, - name=name, - owner=owner, - changset_revision=changset_revision, - error_message=error_message ) - install_and_test_statistics_dict[ 'repositories_with_installation_error' ]\ - .append( missing_repository_dependency_dict ) - tool_test_results_dict[ 'installation_errors' ][ 'repository_dependencies' ]\ - .append( missing_repository_dependency_info_dict ) - if repository.missing_tool_dependencies: - params[ 'test_install_error' ] = True - # Keep statistics for this repository's tool dependencies that resulted in installation errors. - for missing_tool_dependency in repository.missing_tool_dependencies: - name = str( missing_tool_dependency.name ) - type = str( missing_tool_dependency.type ) - version = str( missing_tool_dependency.version ) - error_message = unicodify( missing_tool_dependency.error_message ) - missing_tool_dependency_info_dict = dict( type=type, - name=name, - version=version, - error_message=error_message ) - install_and_test_statistics_dict[ 'tool_dependencies_with_installation_error' ]\ - .append( missing_tool_dependency_info_dict ) - tool_test_results_dict[ 'installation_errors' ][ 'tool_dependencies' ]\ - .append( missing_tool_dependency_info_dict ) - if repository.installed_repository_dependencies: - # Keep statistics for this repository's tool dependencies that resulted in successful installations. - for repository_dependency in repository.installed_repository_dependencies: - tool_shed = str( repository_dependency.tool_shed ) - name = str( repository_dependency.name ) - owner = str( repository_dependency.owner ) - changeset_revision = str( repository_dependency.changeset_revision ) - repository_dependency_info_dict = dict( tool_shed=tool_shed, - name=name, - owner=owner, - changeset_revision=changeset_revision ) - install_and_test_statistics_dict[ 'successful_repository_installations' ]\ - .append( repository_dependency_info_dict ) - tool_test_results_dict[ 'successful_installations' ][ 'repository_dependencies' ]\ - .append( repository_dependency_info_dict ) - if repository.installed_tool_dependencies: - # Keep statistics for this repository's tool dependencies that resulted in successful installations. - for tool_dependency in repository.installed_tool_dependencies: - name = str( tool_dependency.name ) - type = str( tool_dependency.type ) - version = str( tool_dependency.version ) - installation_directory = tool_dependency.installation_directory( app ) - tool_dependency_info_dict = dict( type=type, - name=name, - version=version, - installation_directory=installation_directory ) - install_and_test_statistics_dict[ 'successful_tool_dependency_installations' ]\ - .append( tool_dependency_info_dict ) - tool_test_results_dict[ 'successful_installations' ][ 'tool_dependencies' ]\ - .append( tool_dependency_info_dict ) + params, install_and_test_statistics_dict, tool_test_results_dict = \ + install_and_test_base_util.register_installed_and_missing_dependencies( app, + repository, + repository_identifier_dict, + install_and_test_statistics_dict, + tool_test_results_dict ) # TODO: do something useful with response_dict response_dict = install_and_test_base_util.register_test_result( install_and_test_base_util.galaxy_tool_shed_url, tool_test_results_dicts, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: removed unnecessary class from toolshed top menu items as it started to ‘work’ with the last bootstrap dropdown plugin inclusion (didn’t do anything until now)
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3bbb2f8e43b1/ Changeset: 3bbb2f8e43b1 User: martenson Date: 2013-12-19 21:47:36 Summary: removed unnecessary class from toolshed top menu items as it started to ‘work’ with the last bootstrap dropdown plugin inclusion (didn’t do anything until now) Affected #: 1 file diff -r cf07500dd390b0daed5a266d69f3ca20e92e06e0 -r 3bbb2f8e43b109b5adc8925a52ed23d9f31cd236 templates/webapps/tool_shed/base_panels.mako --- a/templates/webapps/tool_shed/base_panels.mako +++ b/templates/webapps/tool_shed/base_panels.mako @@ -38,9 +38,9 @@ %><li class="${cls}" style="${style}"> %if href: - <a class="${a_cls}" data-toggle="dropdown" target="${target}" href="${href}">${display}${extra}</a> + <a class="${a_cls}" target="${target}" href="${href}">${display}${extra}</a> %else: - <a class="${a_cls}" data-toggle="dropdown">${display}${extra}</a> + <a class="${a_cls}" >${display}${extra}</a> %endif %if menu_options: <ul class="dropdown-menu"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix workflow import url XSS.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8411a9f30feb/ Changeset: 8411a9f30feb Branch: stable User: dannon Date: 2013-12-19 20:38:03 Summary: Fix workflow import url XSS. Affected #: 1 file diff -r a9a0ac9c1afae8dd0d662c9c800d0228c883c107 -r 8411a9f30feb3a6fd15cecc09809afe2e24b5e79 templates/webapps/galaxy/workflow/import.mako --- a/templates/webapps/galaxy/workflow/import.mako +++ b/templates/webapps/galaxy/workflow/import.mako @@ -31,7 +31,7 @@ <form name="import_workflow" id="import_workflow" action="${h.url_for( controller='workflow', action='import_workflow' )}" enctype="multipart/form-data" method="POST"><div class="form-row"><label>Galaxy workflow URL:</label> - <input type="text" name="url" value="${url}" size="40"> + <input type="text" name="url" value="${url | h}" size="40"><div class="toolParamHelp" style="clear: both;"> If the workflow is accessible via a URL, enter the URL above and click <b>Import</b>. </div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Fix workflow import url XSS.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cf07500dd390/ Changeset: cf07500dd390 User: dannon Date: 2013-12-19 20:38:03 Summary: Fix workflow import url XSS. Affected #: 1 file diff -r 235cd1515a88fc394328a636ca4f08eb5608f3bd -r cf07500dd390b0daed5a266d69f3ca20e92e06e0 templates/webapps/galaxy/workflow/import.mako --- a/templates/webapps/galaxy/workflow/import.mako +++ b/templates/webapps/galaxy/workflow/import.mako @@ -31,7 +31,7 @@ <form name="import_workflow" id="import_workflow" action="${h.url_for( controller='workflow', action='import_workflow' )}" enctype="multipart/form-data" method="POST"><div class="form-row"><label>Galaxy workflow URL:</label> - <input type="text" name="url" value="${url}" size="40"> + <input type="text" name="url" value="${url | h}" size="40"><div class="toolParamHelp" style="clear: both;"> If the workflow is accessible via a URL, enter the URL above and click <b>Import</b>. </div> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: greg: Exclude repositories that require excluded repositories from the tool shed's install and test runs.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/235cd1515a88/ Changeset: 235cd1515a88 User: greg Date: 2013-12-19 20:36:23 Summary: Exclude repositories that require excluded repositories from the tool shed's install and test runs. Affected #: 3 files diff -r 4b62b64265487834429b5337b6d3c3c9c38b072a -r 235cd1515a88fc394328a636ca4f08eb5608f3bd lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -87,10 +87,10 @@ rd_tups = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] for rd_tup in rd_tups: tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ] - repository_dependencies_dict = dict( tool_shed=tool_shed, - name=name, - owner=owner, - changeset_revision=changeset_revision ) + repository_dependencies_dict = dict( tool_shed=str( tool_shed ), + name=str( name ), + owner=str( owner ), + changeset_revision=str( changeset_revision ) ) rd = suc.get_repository_by_name_and_owner( trans.app, name, owner ) encoded_rd_id = trans.security.encode_id( rd.id ) rd_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, diff -r 4b62b64265487834429b5337b6d3c3c9c38b072a -r 235cd1515a88fc394328a636ca4f08eb5608f3bd test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -375,6 +375,19 @@ hg_id = '%d:%s' % ( ctx_rev, str( changectx ) ) return hg_id +def get_repository_dependencies_for_changeset_revision( tool_shed_url, encoded_repository_metadata_id ): + """ + Return the list of dictionaries that define all repository dependencies of the repository_metadata + record associated with the received encoded_repository_metadata_id via the Tool Shed API. + """ + error_message = '' + parts = [ 'api', 'repository_revisions', encoded_repository_metadata_id, 'repository_dependencies' ] + api_url = get_api_url( base=tool_shed_url, parts=parts ) + repository_dependency_dicts, error_message = json_from_url( api_url ) + if error_message: + return None, error_message + return repository_dependency_dicts, error_message + def get_repository_dict( url, repository_dict ): error_message = '' parts = [ 'api', 'repositories', repository_dict[ 'repository_id' ] ] @@ -613,8 +626,8 @@ # </blacklist> # A list is returned with the following structure: # [{ 'reason': The default reason or the reason specified in this section, - # 'repositories': [( name, owner, changeset revision if changeset revision else None ), - # ( name, owner, changeset revision if changeset revision else None )]}] + # 'repositories': [( name, owner, changeset_revision if changeset_revision else None ), + # ( name, owner, changeset_revision if changeset_revision else None )]}] exclude_list = [] exclude_verbose = [] xml_tree, error_message = parse_xml( xml_filename ) diff -r 4b62b64265487834429b5337b6d3c3c9c38b072a -r 235cd1515a88fc394328a636ca4f08eb5608f3bd test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -100,9 +100,13 @@ # here because our call to the Tool Shed API filters by downloadable='true', in which case deleted will always be False. log.debug( 'Loading the list of repositories excluded from testing from the file %s...' % \ str( exclude_list_file ) ) - exclude_list = install_and_test_base_util.parse_exclude_list( exclude_list_file ) + # The following exclude_list will look something like this: + # [{ 'reason': The default reason or the reason specified in this section, + # 'repositories': [( name, owner, changeset_revision if changeset_revision else None ), + # ( name, owner, changeset_revision if changeset_revision else None )]}] + exclude_list_dicts = install_and_test_base_util.parse_exclude_list( exclude_list_file ) else: - exclude_list = [] + exclude_list_dicts = [] # Generate a test method that will use Twill to install each repository into the embedded Galaxy application that was # started up, installing repository and tool dependencies. Upon successful installation, generate a test case for each # functional test defined for each tool in the repository and execute the test cases. Record the result of the tests. @@ -146,15 +150,40 @@ tool_test_results_dict = install_and_test_base_util.get_tool_test_results_dict( tool_test_results_dicts ) # See if this repository should be skipped for any reason. this_repository_is_in_the_exclude_list = False + requires_excluded = False skip_reason = None - for exclude_dict in exclude_list: + for exclude_dict in exclude_list_dicts: reason = exclude_dict[ 'reason' ] exclude_repositories = exclude_dict[ 'repositories' ] + # 'repositories': + # [( name, owner, changeset_revision if changeset_revision else None ), + # ( name, owner, changeset_revision if changeset_revision else None )] if ( name, owner, changeset_revision ) in exclude_repositories or ( name, owner, None ) in exclude_repositories: this_repository_is_in_the_exclude_list = True skip_reason = reason break - if this_repository_is_in_the_exclude_list: + if not this_repository_is_in_the_exclude_list: + # Skip this repository if it has a repository dependency that is in the exclude list. + repository_dependency_dicts, error_message = \ + install_and_test_base_util.get_repository_dependencies_for_changeset_revision( install_and_test_base_util.galaxy_tool_shed_url, + encoded_repository_metadata_id ) + if error_message: + log.debug( 'Error getting repository dependencies for revision %s of repository %s owned by %s:' % \ + ( changeset_revision, name, owner ) ) + log.debug( error_message ) + else: + for repository_dependency_dict in repository_dependency_dicts: + rd_name = repository_dependency_dict[ 'name' ] + rd_owner = repository_dependency_dict[ 'owner' ] + rd_changeset_revision = repository_dependency_dict[ 'changeset_revision' ] + if ( rd_name, rd_owner, rd_changeset_revision ) in exclude_repositories or \ + ( rd_name, rd_owner, None ) in exclude_repositories: + skip_reason = 'This repository requires revision %s of repository %s owned by %s which is excluded from testing.' % \ + ( rd_changeset_revision, rd_name, rd_owner ) + requires_excluded = True + break + # Register the reason this repository is being skipped if, in fact, it is. + if this_repository_is_in_the_exclude_list or requires_excluded: tool_test_results_dict[ 'not_tested' ] = dict( reason=skip_reason ) params = dict( do_not_test=False ) # TODO: do something useful with response_dict Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jgoecks: Workflows API, running workflows: add support for using workflow replacement parameters in postjob actions. This enables use of rename action.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4b62b6426548/ Changeset: 4b62b6426548 User: jgoecks Date: 2013-12-19 20:30:09 Summary: Workflows API, running workflows: add support for using workflow replacement parameters in postjob actions. This enables use of rename action. Affected #: 1 file diff -r 706a30b2c1a08279a1ddf3f5149f2ade03eb5f5c -r 4b62b64265487834429b5337b6d3c3c9c38b072a lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -112,8 +112,6 @@ # ------------------------------------------------------------------------------- # - - if 'workflow_id' not in payload: # create new if 'installed_repository_file' in payload: @@ -241,11 +239,15 @@ visit_input_values( tool.inputs, step.state.inputs, callback ) job, out_data = tool.execute( trans, step.state.inputs, history=history) outputs[ step.id ] = out_data + + # Do post-job actions. + replacement_params = payload.get('replacement_params', {}) for pja in step.post_job_actions: if pja.action_type in ActionBox.immediate_actions: - ActionBox.execute(self.app, trans.sa_session, pja, job, replacement_dict=None) + ActionBox.execute(trans.app, trans.sa_session, pja, job, replacement_dict=replacement_params) else: job.add_post_job_action(pja) + for v in out_data.itervalues(): rval['outputs'].append(trans.security.encode_id(v.id)) else: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: martenson: make binding ESC key and click outside of modal optional before we solve it backwards-compatible
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/706a30b2c1a0/ Changeset: 706a30b2c1a0 User: martenson Date: 2013-12-19 20:22:35 Summary: make binding ESC key and click outside of modal optional before we solve it backwards-compatible Affected #: 4 files diff -r d6be5534b0cf85da16ac412751883e855fb475a8 -r 706a30b2c1a08279a1ddf3f5149f2ade03eb5f5c static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -415,6 +415,8 @@ 'Close' : function() { self.modal.hide(); $('.modal').remove(); self.modal = null; } // TODO refill nicely modal with data } }); + this.modal.bindEvents(event, this); + $(".peek").html(item.get("peek")); var history_footer_tmpl = _.template(this.templateHistorySelectInModal(), {histories : histories.models}); $(this.modal.elMain).find('.buttons').prepend(history_footer_tmpl); diff -r d6be5534b0cf85da16ac412751883e855fb475a8 -r 706a30b2c1a08279a1ddf3f5149f2ade03eb5f5c static/scripts/galaxy.modal.js --- a/static/scripts/galaxy.modal.js +++ b/static/scripts/galaxy.modal.js @@ -27,7 +27,7 @@ this.create(options); // Bind the hiding events - this.bindEvents(event, self); + // this.bindEvents(event, self); }, // bind the click-to-hide function diff -r d6be5534b0cf85da16ac412751883e855fb475a8 -r 706a30b2c1a08279a1ddf3f5149f2ade03eb5f5c static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(j,k,g,m){var e=Backbone.Model.extend({urlRoot:"/api/libraries"});var n=Backbone.Collection.extend({url:"/api/libraries",model:e});var h=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:h});var d=Backbone.Model.extend({defaults:{folder:new c(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(q){this.full_path=q[0].full_path;this.get("folder").reset(q[1].folder_contents);return q}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var i=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:i});var p=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var l=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var q=[];q.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<div class="library_breadcrumb">');q.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');q.push("<% _.each(path, function(path_item) { %>");q.push("<% if (path_item[0] != id) { %>");q.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');q.push("<% } else { %>");q.push('<span title="You are in this folder"><%- path_item[1] %></span>');q.push("<% } %>");q.push("<% }); %>");q.push("</div>");q.push('<table id="folder_table" class="table table-condensed">');q.push(" <thead>");q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(' <th class="button_heading">view</th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date</th>");q.push(" </thead>");q.push(" <tbody>");q.push(" <td></td>");q.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" </tr>");q.push(" <% _.each(items, function(content_item) { %>");q.push(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(" <td></td>");q.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-folder-open"></span> browse</td>');q.push(' <td><%- content_item.get("name") %>');q.push(' <% if (content_item.get("item_count") === 0) { %>');q.push(' <span class="muted">(empty folder)</span>');q.push(" <% } %>");q.push(" </td>");q.push(" <td>folder</td>");q.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');q.push(" <% } else { %>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(" <td>");q.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');q.push(' <span class="fa fa-eye"></span> details');q.push(" </button>");q.push(" </td>");q.push(' <td><%- content_item.get("name") %></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(" <% } %> ");q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div id="dataset_info_modal">');q.push(' <table class="table table-striped table-condensed">');q.push(" <tr>");q.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');q.push(' <td><%= _.escape(item.get("name")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Data type</th>');q.push(' <td><%= _.escape(item.get("data_type")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Genome build</th>');q.push(' <td><%= _.escape(item.get("genome_build")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Size</th>');q.push(" <td><%= _.escape(size) %></td>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Date uploaded</th>');q.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Uploaded by</th>');q.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');q.push(" </tr>");q.push(' <tr scope="row">');q.push(' <th scope="row">Data Lines</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Comment Lines</th>');q.push(' <% if (item.get("metadata_comment_lines") === "") { %>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');q.push(" <% } else { %>");q.push(' <td scope="row">unknown</td>');q.push(" <% } %>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Number of Columns</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Column Types</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Miscellaneous information</th>');q.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');q.push(" </tr>");q.push(" </table>");q.push(' <pre class="peek">');q.push(" </pre>");q.push("</div>");return q.join("")},templateHistorySelectInModal:function(){var q=[];q.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateBulkImportInModal:function(){var q=[];q.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},size_to_string:function(q){var r="";if(q>=100000000000){q=q/100000000000;r="TB"}else{if(q>=100000000){q=q/100000000;r="GB"}else{if(q>=100000){q=q/100000;r="MB"}else{if(q>=100){q=q/100;r="KB"}else{q=q*10;r="b"}}}}return(Math.round(q)/10)+r},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderModal","click .btn_open_folder":"navigateToFolder"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new d({id:q.id});r.url=r.attributes.urlRoot+q.id+"/contents";r.fetch({success:function(t){for(var v=0;v<r.attributes.folder.models.length;v++){var u=r.attributes.folder.models[v];if(u.get("type")==="file"){u.set("readable_size",s.size_to_string(u.get("file_size")))}}var x=r.full_path;var y;if(x.length===1){y=0}else{y=x[x.length-2][0]}var w=_.template(s.templateFolder(),{path:r.full_path,items:r.attributes.folder.models,id:q.id,upper_folder_id:y});s.$el.html(w)}})},navigateToFolder:function(r){var q=$(r.target).attr("data-id");if(typeof q==="undefined"){return false}else{if(q==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+q,{trigger:true,replace:true})}}},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().attr("id");var s=new h();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)}})}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});this.modal=null;var r=this;this.modal=new j.GalaxyModal({title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});$(".peek").html(v.get("peek"));var q=_.template(this.templateHistorySelectInModal(),{histories:s.models});$(this.modal.elMain).find(".buttons").prepend(q);if(r.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(r.lastSelectedHistory)}this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var q=[];q.push($("#id_row").attr("data-id"));var r="/api/libraries/datasets/download/uncompressed";var s={ldda_ids:q};folderContentView.processDownload(r,s);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var s=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=s;var q=$("#id_row").attr("data-id");var t=new b();var r=this;t.url=t.urlRoot+s+"/contents";t.save({content:q,source:"library"},{success:function(){m.success("Dataset imported");r.modal.enableButton("Import");r.modal.enableButton("Download")},error:function(){m.error("An error occured! Dataset not imported. Please try again.");r.modal.enableButton("Import");r.modal.enableButton("Download")}})},selectAll:function(r){var q=r.target.checked;that=this;$(":checkbox").each(function(){this.checked=q;$row=$(this.parentElement.parentElement);(q)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(r){var t="";var q;var s;if(r.target.localName==="input"){t=r.target;q=$(r.target.parentElement.parentElement);s="input"}else{if(r.target.localName==="td"){t=$("#"+r.target.parentElement.id).find(":checkbox")[0];q=$(r.target.parentElement);s="td"}}if(t===""){r.stopPropagation();return}if(t.checked){if(s==="td"){t.checked="";this.makeWhiteRow(q)}else{if(s==="input"){this.makeDarkRow(q)}}}else{if(s==="td"){t.checked="selected";this.makeDarkRow(q)}else{if(s==="input"){this.makeWhiteRow(q)}}}this.checkTools()},makeDarkRow:function(q){q.removeClass("light");q.find("a").removeClass("light");q.addClass("dark");q.find("a").addClass("dark")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light")},checkTools:function(){var q=$("#folder_table").find(":checked");if(q.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var r=this;var q=new o();q.fetch({success:function(s){var t=_.template(r.templateBulkImportInModal(),{histories:s.models});r.modal=new j.GalaxyModal({title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});r.modal.show()}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var s=$("select[name=dataset_import_bulk] option:selected").val();var w=$("select[name=dataset_import_bulk] option:selected").text();var y=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){y.push(this.parentElement.parentElement.id)}});var x=_.template(this.templateProgressBar(),{history_name:w});$(this.modal.elMain).find(".modal-body").html(x);var t=100/y.length;this.initProgress(t);var q=[];for(var r=y.length-1;r>=0;r--){library_dataset_id=y[r];var u=new b();var v=this;u.url=u.urlRoot+s+"/contents";u.content=library_dataset_id;u.source="library";q.push(u)}this.chainCall(q)},chainCall:function(r){var q=this;var s=r.pop();if(typeof s==="undefined"){m.success("All datasets imported");this.modal.hide();q.modal.enableButton("Import");return}var t=$.when(s.save({content:s.content,source:s.source})).done(function(u){q.updateProgress();responses.push(u);q.chainCall(r)})},initProgress:function(q){this.progress=0;this.progressStep=q},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},templateProgressBar:function(){var q=[];q.push('<div class="import_text">');q.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");q.push("</div>");q.push('<div class="progress">');q.push(' <div class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');q.push(' <span class="completion_span">0% Complete</span>');q.push(" </div>");q.push("</div>");q.push("");return q.join("")},download:function(q,u){var s=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){s.push(this.parentElement.parentElement.id)}});var r="/api/libraries/datasets/download/"+u;var t={ldda_ids:s};this.processDownload(r,t,"get")},processDownload:function(r,s,t){if(r&&s){s=typeof s=="string"?s:$.param(s);var q="";$.each(s.split("&"),function(){var u=this.split("=");q+='<input type="hidden" name="'+u[0]+'" value="'+u[1]+'" />'});$('<form action="'+r+'" method="'+(t||"post")+'">'+q+"</form>").appendTo("body").submit().remove();m.info("Your download will begin soon")}},createFolderModal:function(){m.info("This will create folder...in the future")}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},template_library_list:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var q=this;libraries=new n();libraries.fetch({success:function(r){var s=_.template(q.template_library_list(),{libraries:r.models});q.$el.html(s)},error:function(s,r){if(r.statusCode().status===403){m.error("Please log in first. Redirecting to login page in 3s.");setTimeout(q.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=new j.GalaxyModal({title:"Create New Library",body:this.template_new_library(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}});this.modal.show()},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new e();var q=this;r.save(s,{success:function(t){q.modal.hide();q.clear_library_modal();q.render();m.success("Library created")},error:function(){m.error("An error occured :(")}})}else{m.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(q){return q.name!==""},template_new_library:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")}});var f=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new l();galaxyLibraryview=new a();library_router=new p();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(q){folderContentView.render({id:q})});library_router.on("route:download",function(q,r){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+q,{trigger:true,replace:true})}else{folderContentView.download(q,r);library_router.navigate("folders/"+q,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:f}}); \ No newline at end of file +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(j,k,g,m){var e=Backbone.Model.extend({urlRoot:"/api/libraries"});var n=Backbone.Collection.extend({url:"/api/libraries",model:e});var h=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:h});var d=Backbone.Model.extend({defaults:{folder:new c(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(q){this.full_path=q[0].full_path;this.get("folder").reset(q[1].folder_contents);return q}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var i=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:i});var p=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var l=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var q=[];q.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<div class="library_breadcrumb">');q.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');q.push("<% _.each(path, function(path_item) { %>");q.push("<% if (path_item[0] != id) { %>");q.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');q.push("<% } else { %>");q.push('<span title="You are in this folder"><%- path_item[1] %></span>');q.push("<% } %>");q.push("<% }); %>");q.push("</div>");q.push('<table id="folder_table" class="table table-condensed">');q.push(" <thead>");q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(' <th class="button_heading">view</th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date</th>");q.push(" </thead>");q.push(" <tbody>");q.push(" <td></td>");q.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" </tr>");q.push(" <% _.each(items, function(content_item) { %>");q.push(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(" <td></td>");q.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-folder-open"></span> browse</td>');q.push(' <td><%- content_item.get("name") %>');q.push(' <% if (content_item.get("item_count") === 0) { %>');q.push(' <span class="muted">(empty folder)</span>');q.push(" <% } %>");q.push(" </td>");q.push(" <td>folder</td>");q.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');q.push(" <% } else { %>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(" <td>");q.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');q.push(' <span class="fa fa-eye"></span> details');q.push(" </button>");q.push(" </td>");q.push(' <td><%- content_item.get("name") %></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(" <% } %> ");q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div id="dataset_info_modal">');q.push(' <table class="table table-striped table-condensed">');q.push(" <tr>");q.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');q.push(' <td><%= _.escape(item.get("name")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Data type</th>');q.push(' <td><%= _.escape(item.get("data_type")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Genome build</th>');q.push(' <td><%= _.escape(item.get("genome_build")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Size</th>');q.push(" <td><%= _.escape(size) %></td>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Date uploaded</th>');q.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Uploaded by</th>');q.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');q.push(" </tr>");q.push(' <tr scope="row">');q.push(' <th scope="row">Data Lines</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Comment Lines</th>');q.push(' <% if (item.get("metadata_comment_lines") === "") { %>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');q.push(" <% } else { %>");q.push(' <td scope="row">unknown</td>');q.push(" <% } %>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Number of Columns</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Column Types</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Miscellaneous information</th>');q.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');q.push(" </tr>");q.push(" </table>");q.push(' <pre class="peek">');q.push(" </pre>");q.push("</div>");return q.join("")},templateHistorySelectInModal:function(){var q=[];q.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateBulkImportInModal:function(){var q=[];q.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},size_to_string:function(q){var r="";if(q>=100000000000){q=q/100000000000;r="TB"}else{if(q>=100000000){q=q/100000000;r="GB"}else{if(q>=100000){q=q/100000;r="MB"}else{if(q>=100){q=q/100;r="KB"}else{q=q*10;r="b"}}}}return(Math.round(q)/10)+r},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderModal","click .btn_open_folder":"navigateToFolder"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new d({id:q.id});r.url=r.attributes.urlRoot+q.id+"/contents";r.fetch({success:function(t){for(var v=0;v<r.attributes.folder.models.length;v++){var u=r.attributes.folder.models[v];if(u.get("type")==="file"){u.set("readable_size",s.size_to_string(u.get("file_size")))}}var x=r.full_path;var y;if(x.length===1){y=0}else{y=x[x.length-2][0]}var w=_.template(s.templateFolder(),{path:r.full_path,items:r.attributes.folder.models,id:q.id,upper_folder_id:y});s.$el.html(w)}})},navigateToFolder:function(r){var q=$(r.target).attr("data-id");if(typeof q==="undefined"){return false}else{if(q==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+q,{trigger:true,replace:true})}}},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().attr("id");var s=new h();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)}})}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});this.modal=null;var r=this;this.modal=new j.GalaxyModal({title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});this.modal.bindEvents(event,this);$(".peek").html(v.get("peek"));var q=_.template(this.templateHistorySelectInModal(),{histories:s.models});$(this.modal.elMain).find(".buttons").prepend(q);if(r.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(r.lastSelectedHistory)}this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var q=[];q.push($("#id_row").attr("data-id"));var r="/api/libraries/datasets/download/uncompressed";var s={ldda_ids:q};folderContentView.processDownload(r,s);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var s=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=s;var q=$("#id_row").attr("data-id");var t=new b();var r=this;t.url=t.urlRoot+s+"/contents";t.save({content:q,source:"library"},{success:function(){m.success("Dataset imported");r.modal.enableButton("Import");r.modal.enableButton("Download")},error:function(){m.error("An error occured! Dataset not imported. Please try again.");r.modal.enableButton("Import");r.modal.enableButton("Download")}})},selectAll:function(r){var q=r.target.checked;that=this;$(":checkbox").each(function(){this.checked=q;$row=$(this.parentElement.parentElement);(q)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(r){var t="";var q;var s;if(r.target.localName==="input"){t=r.target;q=$(r.target.parentElement.parentElement);s="input"}else{if(r.target.localName==="td"){t=$("#"+r.target.parentElement.id).find(":checkbox")[0];q=$(r.target.parentElement);s="td"}}if(t===""){r.stopPropagation();return}if(t.checked){if(s==="td"){t.checked="";this.makeWhiteRow(q)}else{if(s==="input"){this.makeDarkRow(q)}}}else{if(s==="td"){t.checked="selected";this.makeDarkRow(q)}else{if(s==="input"){this.makeWhiteRow(q)}}}this.checkTools()},makeDarkRow:function(q){q.removeClass("light");q.find("a").removeClass("light");q.addClass("dark");q.find("a").addClass("dark")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light")},checkTools:function(){var q=$("#folder_table").find(":checked");if(q.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var r=this;var q=new o();q.fetch({success:function(s){var t=_.template(r.templateBulkImportInModal(),{histories:s.models});r.modal=new j.GalaxyModal({title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});r.modal.show()}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var s=$("select[name=dataset_import_bulk] option:selected").val();var w=$("select[name=dataset_import_bulk] option:selected").text();var y=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){y.push(this.parentElement.parentElement.id)}});var x=_.template(this.templateProgressBar(),{history_name:w});$(this.modal.elMain).find(".modal-body").html(x);var t=100/y.length;this.initProgress(t);var q=[];for(var r=y.length-1;r>=0;r--){library_dataset_id=y[r];var u=new b();var v=this;u.url=u.urlRoot+s+"/contents";u.content=library_dataset_id;u.source="library";q.push(u)}this.chainCall(q)},chainCall:function(r){var q=this;var s=r.pop();if(typeof s==="undefined"){m.success("All datasets imported");this.modal.hide();q.modal.enableButton("Import");return}var t=$.when(s.save({content:s.content,source:s.source})).done(function(u){q.updateProgress();responses.push(u);q.chainCall(r)})},initProgress:function(q){this.progress=0;this.progressStep=q},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},templateProgressBar:function(){var q=[];q.push('<div class="import_text">');q.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");q.push("</div>");q.push('<div class="progress">');q.push(' <div class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');q.push(' <span class="completion_span">0% Complete</span>');q.push(" </div>");q.push("</div>");q.push("");return q.join("")},download:function(q,u){var s=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){s.push(this.parentElement.parentElement.id)}});var r="/api/libraries/datasets/download/"+u;var t={ldda_ids:s};this.processDownload(r,t,"get")},processDownload:function(r,s,t){if(r&&s){s=typeof s=="string"?s:$.param(s);var q="";$.each(s.split("&"),function(){var u=this.split("=");q+='<input type="hidden" name="'+u[0]+'" value="'+u[1]+'" />'});$('<form action="'+r+'" method="'+(t||"post")+'">'+q+"</form>").appendTo("body").submit().remove();m.info("Your download will begin soon")}},createFolderModal:function(){m.info("This will create folder...in the future")}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},template_library_list:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var q=this;libraries=new n();libraries.fetch({success:function(r){var s=_.template(q.template_library_list(),{libraries:r.models});q.$el.html(s)},error:function(s,r){if(r.statusCode().status===403){m.error("Please log in first. Redirecting to login page in 3s.");setTimeout(q.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=new j.GalaxyModal({title:"Create New Library",body:this.template_new_library(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}});this.modal.show()},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new e();var q=this;r.save(s,{success:function(t){q.modal.hide();q.clear_library_modal();q.render();m.success("Library created")},error:function(){m.error("An error occured :(")}})}else{m.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(q){return q.name!==""},template_new_library:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")}});var f=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new l();galaxyLibraryview=new a();library_router=new p();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(q){folderContentView.render({id:q})});library_router.on("route:download",function(q,r){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+q,{trigger:true,replace:true})}else{folderContentView.download(q,r);library_router.navigate("folders/"+q,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:f}}); \ No newline at end of file diff -r d6be5534b0cf85da16ac412751883e855fb475a8 -r 706a30b2c1a08279a1ddf3f5149f2ade03eb5f5c static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{},initialize:function(b){self=this;if(b){this.create(b)}this.bindEvents(event,self)},bindEvents:function(c,b){$(document).on("keyup",function(d){if(d.keyCode==27){self.hide()}});$("html").on("click",function(d){b.hide()});$(".modal-content").on("click",function(d){d.stopPropagation()})},unbindEvents:function(c,b){$(document).off("keyup",function(d){if(d.keyCode==27){b.hide()}});$("html").off("click",function(d){b.hide()});$(".modal-content").off("click",function(d){d.stopPropagation()})},destroy:function(){this.hide();this.unbindEvents();$(".modal").remove()},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false;this.unbindEvents()},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},hideButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).hide()},showButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).show()},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{},initialize:function(b){self=this;if(b){this.create(b)}},bindEvents:function(c,b){$(document).on("keyup",function(d){if(d.keyCode==27){self.hide()}});$("html").on("click",function(d){b.hide()});$(".modal-content").on("click",function(d){d.stopPropagation()})},unbindEvents:function(c,b){$(document).off("keyup",function(d){if(d.keyCode==27){b.hide()}});$("html").off("click",function(d){b.hide()});$(".modal-content").off("click",function(d){d.stopPropagation()})},destroy:function(){this.hide();this.unbindEvents();$(".modal").remove()},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false;this.unbindEvents()},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},hideButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).hide()},showButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).show()},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: martenson: new packed js files for data libraries
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d6be5534b0cf/ Changeset: d6be5534b0cf User: martenson Date: 2013-12-19 20:00:41 Summary: new packed js files for data libraries Affected #: 2 files diff -r a3325216563c95e11d82aa79588ac4b125e1122b -r d6be5534b0cf85da16ac412751883e855fb475a8 static/scripts/packed/galaxy.library.js --- /dev/null +++ b/static/scripts/packed/galaxy.library.js @@ -0,0 +1,1 @@ +var view=null;var library_router=null;var responses=[];define(["galaxy.modal","galaxy.masthead","utils/galaxy.utils","libs/toastr"],function(j,k,g,m){var e=Backbone.Model.extend({urlRoot:"/api/libraries"});var n=Backbone.Collection.extend({url:"/api/libraries",model:e});var h=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:h});var d=Backbone.Model.extend({defaults:{folder:new c(),full_path:"unknown",urlRoot:"/api/folders/",id:"unknown"},parse:function(q){this.full_path=q[0].full_path;this.get("folder").reset(q[1].folder_contents);return q}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var i=Backbone.Model.extend({url:"/api/histories/"});var o=Backbone.Collection.extend({url:"/api/histories",model:i});var p=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var l=Backbone.View.extend({el:"#center",progress:0,progressStep:1,lastSelectedHistory:"",modal:null,folders:null,initialize:function(){this.folders=[];this.queue=jQuery.Deferred();this.queue.resolve()},templateFolder:function(){var q=[];q.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; ">');q.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');q.push('<div id="library_folder_toolbar" >');q.push(' <button title="Create New Folder" id="toolbtn_create_folder" class="btn btn-primary" type="button"><span class="fa fa-plus"></span><span class="fa fa-folder-close"></span> folder</button>');q.push(' <button id="toolbtn_bulk_import" class="btn btn-primary" style="display: none; margin-left: 0.5em;" type="button"><span class="fa fa-external-link"></span> to history</button>');q.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; display: none; ">');q.push(' <button id="drop_toggle" type="button" class="btn btn-primary dropdown-toggle" data-toggle="dropdown">');q.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');q.push(" </button>");q.push(' <ul class="dropdown-menu" role="menu">');q.push(' <li><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');q.push(' <li><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');q.push(" </ul>");q.push(" </div>");q.push("</div>");q.push('<div class="library_breadcrumb">');q.push('<a title="Return to the list of libraries" href="#">Libraries</a><b>|</b> ');q.push("<% _.each(path, function(path_item) { %>");q.push("<% if (path_item[0] != id) { %>");q.push('<a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a><b>|</b> ');q.push("<% } else { %>");q.push('<span title="You are in this folder"><%- path_item[1] %></span>');q.push("<% } %>");q.push("<% }); %>");q.push("</div>");q.push('<table id="folder_table" class="table table-condensed">');q.push(" <thead>");q.push(' <th style="text-align: center; width: 20px; "><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');q.push(' <th class="button_heading">view</th>');q.push(" <th>name</th>");q.push(" <th>data type</th>");q.push(" <th>size</th>");q.push(" <th>date</th>");q.push(" </thead>");q.push(" <tbody>");q.push(" <td></td>");q.push(' <td><button title="Go to parent folder" type="button" data-id="<%- upper_folder_id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-arrow-up"></span> .. go up</td>');q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" <td></td>");q.push(" </tr>");q.push(" <% _.each(items, function(content_item) { %>");q.push(' <tr class="folder_row light" id="<%- content_item.id %>">');q.push(' <% if (content_item.get("type") === "folder") { %>');q.push(" <td></td>");q.push(' <td><button title="Open this folder" type="button" data-id="<%- content_item.id %>" class="btn_open_folder btn btn-default btn-xs">');q.push(' <span class="fa fa-folder-open"></span> browse</td>');q.push(' <td><%- content_item.get("name") %>');q.push(' <% if (content_item.get("item_count") === 0) { %>');q.push(' <span class="muted">(empty folder)</span>');q.push(" <% } %>");q.push(" </td>");q.push(" <td>folder</td>");q.push(' <td><%= _.escape(content_item.get("item_count")) %> item(s)</td>');q.push(" <% } else { %>");q.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');q.push(" <td>");q.push(' <button title="See details of this dataset" type="button" class="library-dataset btn btn-default btn-xs">');q.push(' <span class="fa fa-eye"></span> details');q.push(" </button>");q.push(" </td>");q.push(' <td><%- content_item.get("name") %></td>');q.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');q.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');q.push(" <% } %> ");q.push(' <td><%= _.escape(content_item.get("time_updated")) %></td>');q.push(" </tr>");q.push(" <% }); %>");q.push(" ");q.push(" </tbody>");q.push("</table>");q.push("</div>");return q.join("")},templateDatasetModal:function(){var q=[];q.push('<div id="dataset_info_modal">');q.push(' <table class="table table-striped table-condensed">');q.push(" <tr>");q.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');q.push(' <td><%= _.escape(item.get("name")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Data type</th>');q.push(' <td><%= _.escape(item.get("data_type")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Genome build</th>');q.push(' <td><%= _.escape(item.get("genome_build")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Size</th>');q.push(" <td><%= _.escape(size) %></td>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Date uploaded</th>');q.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Uploaded by</th>');q.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');q.push(" </tr>");q.push(' <tr scope="row">');q.push(' <th scope="row">Data Lines</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');q.push(" </tr>");q.push(' <th scope="row">Comment Lines</th>');q.push(' <% if (item.get("metadata_comment_lines") === "") { %>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');q.push(" <% } else { %>");q.push(' <td scope="row">unknown</td>');q.push(" <% } %>");q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Number of Columns</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Column Types</th>');q.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');q.push(" </tr>");q.push(" <tr>");q.push(' <th scope="row">Miscellaneous information</th>');q.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');q.push(" </tr>");q.push(" </table>");q.push(' <pre class="peek">');q.push(" </pre>");q.push("</div>");return q.join("")},templateHistorySelectInModal:function(){var q=[];q.push('<span id="history_modal_combo" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_single" name="dataset_import_single" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},templateBulkImportInModal:function(){var q=[];q.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');q.push("Select history: ");q.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');q.push(" <% _.each(histories, function(history) { %>");q.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');q.push(" <% }); %>");q.push("</select>");q.push("</span>");return q.join("")},size_to_string:function(q){var r="";if(q>=100000000000){q=q/100000000000;r="TB"}else{if(q>=100000000){q=q/100000000;r="GB"}else{if(q>=100000){q=q/100000;r="MB"}else{if(q>=100){q=q/100;r="KB"}else{q=q*10;r="b"}}}}return(Math.round(q)/10)+r},events:{"click #select-all-checkboxes":"selectAll","click .folder_row":"selectClickedRow","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_dl":"bulkDownload","click .library-dataset":"showDatasetDetails","click #toolbtn_create_folder":"createFolderModal","click .btn_open_folder":"navigateToFolder"},render:function(q){$("#center").css("overflow","auto");view=this;var s=this;var r=new d({id:q.id});r.url=r.attributes.urlRoot+q.id+"/contents";r.fetch({success:function(t){for(var v=0;v<r.attributes.folder.models.length;v++){var u=r.attributes.folder.models[v];if(u.get("type")==="file"){u.set("readable_size",s.size_to_string(u.get("file_size")))}}var x=r.full_path;var y;if(x.length===1){y=0}else{y=x[x.length-2][0]}var w=_.template(s.templateFolder(),{path:r.full_path,items:r.attributes.folder.models,id:q.id,upper_folder_id:y});s.$el.html(w)}})},navigateToFolder:function(r){var q=$(r.target).attr("data-id");if(typeof q==="undefined"){return false}else{if(q==="0"){library_router.navigate("#",{trigger:true,replace:true})}else{library_router.navigate("folders/"+q,{trigger:true,replace:true})}}},showDatasetDetails:function(t){t.preventDefault();var u=$(t.target).parent().parent().attr("id");var s=new h();var r=new o();s.id=u;var q=this;s.fetch({success:function(v){r.fetch({success:function(w){q.renderModalAfterFetch(v,w)}})}})},renderModalAfterFetch:function(v,s){var t=this.size_to_string(v.get("file_size"));var u=_.template(this.templateDatasetModal(),{item:v,size:t});this.modal=null;var r=this;this.modal=new j.GalaxyModal({title:"Dataset Details",body:u,buttons:{Import:function(){r.importCurrentIntoHistory()},Download:function(){r.downloadCurrent()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});$(".peek").html(v.get("peek"));var q=_.template(this.templateHistorySelectInModal(),{histories:s.models});$(this.modal.elMain).find(".buttons").prepend(q);if(r.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(r.lastSelectedHistory)}this.modal.show()},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var q=[];q.push($("#id_row").attr("data-id"));var r="/api/libraries/datasets/download/uncompressed";var s={ldda_ids:q};folderContentView.processDownload(r,s);this.modal.enableButton("Import");this.modal.enableButton("Download")},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var s=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=s;var q=$("#id_row").attr("data-id");var t=new b();var r=this;t.url=t.urlRoot+s+"/contents";t.save({content:q,source:"library"},{success:function(){m.success("Dataset imported");r.modal.enableButton("Import");r.modal.enableButton("Download")},error:function(){m.error("An error occured! Dataset not imported. Please try again.");r.modal.enableButton("Import");r.modal.enableButton("Download")}})},selectAll:function(r){var q=r.target.checked;that=this;$(":checkbox").each(function(){this.checked=q;$row=$(this.parentElement.parentElement);(q)?that.makeDarkRow($row):that.makeWhiteRow($row)});this.checkTools()},selectClickedRow:function(r){var t="";var q;var s;if(r.target.localName==="input"){t=r.target;q=$(r.target.parentElement.parentElement);s="input"}else{if(r.target.localName==="td"){t=$("#"+r.target.parentElement.id).find(":checkbox")[0];q=$(r.target.parentElement);s="td"}}if(t===""){r.stopPropagation();return}if(t.checked){if(s==="td"){t.checked="";this.makeWhiteRow(q)}else{if(s==="input"){this.makeDarkRow(q)}}}else{if(s==="td"){t.checked="selected";this.makeDarkRow(q)}else{if(s==="input"){this.makeWhiteRow(q)}}}this.checkTools()},makeDarkRow:function(q){q.removeClass("light");q.find("a").removeClass("light");q.addClass("dark");q.find("a").addClass("dark")},makeWhiteRow:function(q){q.removeClass("dark");q.find("a").removeClass("dark");q.addClass("light");q.find("a").addClass("light")},checkTools:function(){var q=$("#folder_table").find(":checked");if(q.length>0){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}else{$("#toolbtn_bulk_import").hide();$("#toolbtn_dl").hide()}},modalBulkImport:function(){var r=this;var q=new o();q.fetch({success:function(s){var t=_.template(r.templateBulkImportInModal(),{histories:s.models});r.modal=new j.GalaxyModal({title:"Import into History",body:t,buttons:{Import:function(){r.importAllIntoHistory()},Close:function(){r.modal.hide();$(".modal").remove();r.modal=null}}});r.modal.show()}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var s=$("select[name=dataset_import_bulk] option:selected").val();var w=$("select[name=dataset_import_bulk] option:selected").text();var y=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){y.push(this.parentElement.parentElement.id)}});var x=_.template(this.templateProgressBar(),{history_name:w});$(this.modal.elMain).find(".modal-body").html(x);var t=100/y.length;this.initProgress(t);var q=[];for(var r=y.length-1;r>=0;r--){library_dataset_id=y[r];var u=new b();var v=this;u.url=u.urlRoot+s+"/contents";u.content=library_dataset_id;u.source="library";q.push(u)}this.chainCall(q)},chainCall:function(r){var q=this;var s=r.pop();if(typeof s==="undefined"){m.success("All datasets imported");this.modal.hide();q.modal.enableButton("Import");return}var t=$.when(s.save({content:s.content,source:s.source})).done(function(u){q.updateProgress();responses.push(u);q.chainCall(r)})},initProgress:function(q){this.progress=0;this.progressStep=q},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},templateProgressBar:function(){var q=[];q.push('<div class="import_text">');q.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");q.push("</div>");q.push('<div class="progress">');q.push(' <div class="progress-bar" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');q.push(' <span class="completion_span">0% Complete</span>');q.push(" </div>");q.push("</div>");q.push("");return q.join("")},download:function(q,u){var s=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!=""){s.push(this.parentElement.parentElement.id)}});var r="/api/libraries/datasets/download/"+u;var t={ldda_ids:s};this.processDownload(r,t,"get")},processDownload:function(r,s,t){if(r&&s){s=typeof s=="string"?s:$.param(s);var q="";$.each(s.split("&"),function(){var u=this.split("=");q+='<input type="hidden" name="'+u[0]+'" value="'+u[1]+'" />'});$('<form action="'+r+'" method="'+(t||"post")+'">'+q+"</form>").appendTo("body").submit().remove();m.info("Your download will begin soon")}},createFolderModal:function(){m.info("This will create folder...in the future")}});var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal"},initialize:function(){},template_library_list:function(){tmpl_array=[];tmpl_array.push('<div id="library_container" style="width: 90%; margin: auto; margin-top: 2em; overflow: auto !important; ">');tmpl_array.push("");tmpl_array.push('<h3>New Data Libraries. This is work in progress. Report problems & ideas to <a href="mailto:marten@bx.psu.edu?Subject=DataLibraries_Feedback" target="_blank">Marten</a>.</h3>');tmpl_array.push('<a href="" id="create_new_library_btn" class="btn btn-primary file ">New Library</a>');tmpl_array.push('<table class="table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th class="button_heading"></th>');tmpl_array.push(" <th>name</th>");tmpl_array.push(" <th>description</th>");tmpl_array.push(" <th>synopsis</th> ");tmpl_array.push(" <th>model type</th> ");tmpl_array.push(" </thead>");tmpl_array.push(" <tbody>");tmpl_array.push(" <% _.each(libraries, function(library) { %>");tmpl_array.push(" <tr>");tmpl_array.push(' <td><button title="Open this library" type="button" data-id="<%- library.get("root_folder_id") %>" class="btn_open_folder btn btn-default btn-xs">');tmpl_array.push(' <span class="fa fa-folder-open"></span> browse</td>');tmpl_array.push(' <td><%- library.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("model_class")) %></td>');tmpl_array.push(" </tr>");tmpl_array.push(" <% }); %>");tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("</div>");return tmpl_array.join("")},render:function(){$("#center").css("overflow","auto");var q=this;libraries=new n();libraries.fetch({success:function(r){var s=_.template(q.template_library_list(),{libraries:r.models});q.$el.html(s)},error:function(s,r){if(r.statusCode().status===403){m.error("Please log in first. Redirecting to login page in 3s.");setTimeout(q.redirectToLogin,3000)}else{m.error("An error occured. Please try again.")}}})},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},modal:null,show_library_modal:function(r){r.preventDefault();r.stopPropagation();var q=this;this.modal=new j.GalaxyModal({title:"Create New Library",body:this.template_new_library(),buttons:{Create:function(){q.create_new_library_event()},Close:function(){q.modal.hide()}}});this.modal.show()},create_new_library_event:function(){var s=this.serialize_new_library();if(this.validate_new_library(s)){var r=new e();var q=this;r.save(s,{success:function(t){q.modal.hide();q.clear_library_modal();q.render();m.success("Library created")},error:function(){m.error("An error occured :(")}})}else{m.error("Library's name is missing")}return false},clear_library_modal:function(){$("input[name='Name']").val("");$("input[name='Description']").val("");$("input[name='Synopsis']").val("")},serialize_new_library:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val(),synopsis:$("input[name='Synopsis']").val()}},validate_new_library:function(q){return q.name!==""},template_new_library:function(){tmpl_array=[];tmpl_array.push('<div id="new_library_modal">');tmpl_array.push("<form>");tmpl_array.push('<input type="text" name="Name" value="" placeholder="Name">');tmpl_array.push('<input type="text" name="Description" value="" placeholder="Description">');tmpl_array.push('<input type="text" name="Synopsis" value="" placeholder="Synopsis">');tmpl_array.push("</form>");tmpl_array.push("</div>");return tmpl_array.join("")}});var f=Backbone.View.extend({folderContentView:null,galaxyLibraryview:null,initialize:function(){folderContentView=new l();galaxyLibraryview=new a();library_router=new p();library_router.on("route:libraries",function(){galaxyLibraryview.render()});library_router.on("route:folder_content",function(q){folderContentView.render({id:q})});library_router.on("route:download",function(q,r){if($("#center").find(":checked").length===0){library_router.navigate("folders/"+q,{trigger:true,replace:true})}else{folderContentView.download(q,r);library_router.navigate("folders/"+q,{trigger:false,replace:true})}});Backbone.history.start();return this}});return{GalaxyApp:f}}); \ No newline at end of file diff -r a3325216563c95e11d82aa79588ac4b125e1122b -r d6be5534b0cf85da16ac412751883e855fb475a8 static/scripts/packed/libs/toastr.js --- /dev/null +++ b/static/scripts/packed/libs/toastr.js @@ -0,0 +1,1 @@ +(function(a){a([],function(){var b=jQuery;return(function(){var d="2.0.1";var m;var e;var t=0;var c={error:"error",info:"info",success:"success",warning:"warning"};var s={clear:l,error:o,getContainer:p,info:r,options:{},subscribe:g,success:f,version:d,warning:n};return s;function o(v,w,u){return k({type:c.error,iconClass:i().iconClasses.error,message:v,optionsOverride:u,title:w})}function r(v,w,u){return k({type:c.info,iconClass:i().iconClasses.info,message:v,optionsOverride:u,title:w})}function g(u){e=u}function f(v,w,u){return k({type:c.success,iconClass:i().iconClasses.success,message:v,optionsOverride:u,title:w})}function n(v,w,u){return k({type:c.warning,iconClass:i().iconClasses.warning,message:v,optionsOverride:u,title:w})}function l(u){var v=i();if(!m){p(v)}if(u&&b(":focus",u).length===0){u[v.hideMethod]({duration:v.hideDuration,easing:v.hideEasing,complete:function(){j(u)}});return}if(m.children().length){m[v.hideMethod]({duration:v.hideDuration,easing:v.hideEasing,complete:function(){m.remove()}})}}function h(){return{tapToDismiss:true,toastClass:"toast",containerId:"toast-container",debug:false,showMethod:"fadeIn",showDuration:300,showEasing:"swing",onShown:undefined,hideMethod:"fadeOut",hideDuration:1000,hideEasing:"swing",onHidden:undefined,extendedTimeOut:1000,iconClasses:{error:"toast-error",info:"toast-info",success:"toast-success",warning:"toast-warning"},iconClass:"toast-info",positionClass:"toast-top-right",timeOut:5000,titleClass:"toast-title",messageClass:"toast-message",target:"body",closeHtml:"<button>×</button>",newestOnTop:true}}function q(u){if(!e){return}e(u)}function k(v){var F=i(),D=v.iconClass||F.iconClass;if(typeof(v.optionsOverride)!=="undefined"){F=b.extend(F,v.optionsOverride);D=v.optionsOverride.iconClass||D}t++;m=p(F);var E=null,y=b("<div/>"),A=b("<div/>"),u=b("<div/>"),B=b(F.closeHtml),z={toastId:t,state:"visible",startTime:new Date(),options:F,map:v};if(v.iconClass){y.addClass(F.toastClass).addClass(D)}if(v.title){A.append(v.title).addClass(F.titleClass);y.append(A)}if(v.message){u.append(v.message).addClass(F.messageClass);y.append(u)}if(F.closeButton){B.addClass("toast-close-button");y.prepend(B)}y.hide();if(F.newestOnTop){m.prepend(y)}else{m.append(y)}y[F.showMethod]({duration:F.showDuration,easing:F.showEasing,complete:F.onShown});if(F.timeOut>0){E=setTimeout(x,F.timeOut)}y.hover(w,C);if(!F.onclick&&F.tapToDismiss){y.click(x)}if(F.closeButton&&B){B.click(function(G){G.stopPropagation();x(true)})}if(F.onclick){y.click(function(){F.onclick();x()})}q(z);if(F.debug&&console){console.log(z)}return y;function x(G){if(b(":focus",y).length&&!G){return}return y[F.hideMethod]({duration:F.hideDuration,easing:F.hideEasing,complete:function(){j(y);if(F.onHidden){F.onHidden()}z.state="hidden";z.endTime=new Date(),q(z)}})}function C(){if(F.timeOut>0||F.extendedTimeOut>0){E=setTimeout(x,F.extendedTimeOut)}}function w(){clearTimeout(E);y.stop(true,true)[F.showMethod]({duration:F.showDuration,easing:F.showEasing})}}function p(u){if(!u){u=i()}m=b("#"+u.containerId);if(m.length){return m}m=b("<div/>").attr("id",u.containerId).addClass(u.positionClass);m.appendTo(b(u.target));return m}function i(){return b.extend({},h(),s.options)}function j(u){if(!m){m=p()}if(u.is(":visible")){return}u.remove();u=null;if(m.children().length===0){m.remove()}}})()})}(typeof define==="function"&&define.amd?define:function(b,a){if(typeof module!=="undefined"&&module.exports){module.exports=a(require(b[0]))}else{window.toastr=a(window.jQuery)}})); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Enhance the tool shed's api to deliver repository dependencies defined for a specific repository revision.
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a3325216563c/ Changeset: a3325216563c User: greg Date: 2013-12-19 19:42:45 Summary: Enhance the tool shed's api to deliver repository dependencies defined for a specific repository revision. Affected #: 2 files diff -r 52a25164775e815eb3e5c8ae053c6ab4caa350ff -r a3325216563c95e11d82aa79588ac4b125e1122b lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -9,6 +9,11 @@ from tool_shed.util import export_util import tool_shed.util.shed_util_common as suc +from galaxy import eggs +eggs.require( 'mercurial' ) + +from mercurial import hg + log = logging.getLogger( __name__ ) @@ -66,6 +71,46 @@ return message @web.expose_api_anonymous + def repository_dependencies( self, trans, id, **kwd ): + """ + GET /api/repository_revisions/{encoded repository_metadata id}/repository_dependencies + Displays information about a repository_metadata record in the Tool Shed. + + :param id: the encoded id of the `RepositoryMetadata` object + """ + # Example URL: http://localhost:9009/api/repository_revisions/repository_dependencies/bb12… + repository_dependencies_dicts = [] + try: + repository_metadata = metadata_util.get_repository_metadata_by_id( trans, id ) + metadata = repository_metadata.metadata + if metadata and 'repository_dependencies' in metadata: + rd_tups = metadata[ 'repository_dependencies' ][ 'repository_dependencies' ] + for rd_tup in rd_tups: + tool_shed, name, owner, changeset_revision = rd_tup[ 0:4 ] + repository_dependencies_dict = dict( tool_shed=tool_shed, + name=name, + owner=owner, + changeset_revision=changeset_revision ) + rd = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + encoded_rd_id = trans.security.encode_id( rd.id ) + rd_repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, + encoded_rd_id, + changeset_revision ) + if rd_repository_metadata is None: + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + rd_repository_metadata = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) + repository_dependencies_dict[ 'url' ] = web.url_for( controller='repository_revisions', + action='show', + id=trans.security.encode_id( rd_repository_metadata.id ) ) + repository_dependencies_dicts.append( repository_dependencies_dict ) + return repository_dependencies_dicts + except Exception, e: + message = "Error in the Tool Shed repository_revisions API in repository_dependencies: %s" % str( e ) + log.error( message, exc_info=True ) + trans.response.status = 500 + return message + + @web.expose_api_anonymous def index( self, trans, **kwd ): """ GET /api/repository_revisions diff -r 52a25164775e815eb3e5c8ae053c6ab4caa350ff -r a3325216563c95e11d82aa79588ac4b125e1122b lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -94,7 +94,8 @@ parent_resources=dict( member_name='repository', collection_name='repositories' ) ) webapp.mapper.resource( 'repository_revision', 'repository_revisions', - member={ 'export' : 'POST' }, + member={ 'repository_dependencies' : 'GET', + 'export' : 'POST' }, controller='repository_revisions', name_prefix='repository_revision_', path_prefix='/api', Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/630c98ab700f/ Changeset: 630c98ab700f User: guerler Date: 2013-12-19 19:29:33 Summary: Grids: Attempt to fix toolshed issues Affected #: 5 files diff -r a0e80a712c37754d2d33260919469a7dccb2f1b1 -r 630c98ab700fe05dea8e36c6653f68f2cf0eb0d0 static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -313,17 +313,26 @@ }); }); + // empty grid? + var items_length = options.items.length; + if (items_length == 0) { + return; + } + // // add operation popup menus // - for (var i in options['items']) + for (var i in options.items) { + // get items + var item = options.items[i]; + // get identifiers var button = $('#grid-' + i + '-popup'); button.off(); var popup = new PopupMenu(button); + // load details - var item = options['items'][i]; for (var j in options['operations']) { // get operation details @@ -715,7 +724,7 @@ } // create rows - for (i in options.items) { + for (var i in options.items) { // encode ids var item = options.items[i]; diff -r a0e80a712c37754d2d33260919469a7dccb2f1b1 -r 630c98ab700fe05dea8e36c6653f68f2cf0eb0d0 static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var r=$(this).find("input.grid-row-select-checkbox");var q=$(this).find("span.grid-selected-count");var s=function(){q.text($(r).filter(":checked").length)};$(r).each(function(){$(this).change(s)});s()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var p=this.grid.attributes;var o=this;$(".page-link > a").each(function(){$(this).click(function(){o.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(q){o.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(q){o.execute({href:$(this).attr("href")});return false})});for(var h in p.items){var k=$("#grid-"+h+"-popup");k.off();var d=new PopupMenu(k);var n=p.items[h];for(var g in p.operations){var e=p.operations[g];var l=e.label;var c=n.operation_config[l];var f=n.encode_id;if(c.allowed&&e.allow_popup){var m={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};m.func=function(s){s.preventDefault();var r=$(s.target).html();var q=this.findItemByHtml(r);o.execute(q)};d.addItem(m)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$("<span>"+g+"<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+e+"</span>").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$("<a href='#'>"+m+"</a>");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$("<a href='#'>"+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(m,"")}return false}if(e){this.go_to(m,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(m,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=$("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){c.init_grid($.parseJSON(e));$(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},template_body:function(s){var l="";var t=0;var g=s.items.length;if(g==0){l+='<tr><td colspan="100"><em>No Items</em></td></tr>';t=1}for(i in s.items){var q=s.items[i];var c=q.encode_id;var h="grid-"+i+"-popup";l+="<tr ";if(s.current_item_id==q.id){l+='class="current"'}l+=">";if(s.show_item_checkboxes){l+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in s.columns){var f=s.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var r=q.column_config[f.label];var k=r.link;var m=r.value;var p=r.inbound;if(jQuery.type(m)==="string"){m=m.replace(/\/\//g,"/")}var d="";var o="";if(f.attach_popup){d="grid-"+i+"-popup";o="menubutton";if(k!=""){o+=" split"}o+=" popup"}l+="<td "+e+">";if(k){if(s.operations.length!=0){l+='<div id="'+d+'" class="'+o+'" style="float: left;">'}var n="";if(p){n="use-inbound"}else{n="use-outbound"}l+='<a class="label '+n+'" href="'+k+'" onclick="return false;">'+m+"</a>";if(s.operations.length!=0){l+="</div>"}}else{l+='<div id="'+d+'" class="'+o+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+m+"</label></div>"}l+="</td>"}}l+="</tr>";t++}return l},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file +jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));setTimeout(function(){$("#grid-message").html("")},5000)}this.init_grid_elements()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var s=$(this).find("input.grid-row-select-checkbox");var r=$(this).find("span.grid-selected-count");var t=function(){r.text($(s).filter(":checked").length)};$(s).each(function(){$(this).change(t)});t()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$("<span>"+g+"<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+e+"</span>").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$("<a href='#'>"+m+"</a>");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$("<a href='#'>"+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(m,"")}return false}if(e){this.go_to(m,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(m,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=$("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){c.init_grid($.parseJSON(e));$(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},template_body:function(t){var m="";var u=0;var g=t.items.length;if(g==0){m+='<tr><td colspan="100"><em>No Items</em></td></tr>';u=1}for(var h in t.items){var r=t.items[h];var c=r.encode_id;var k="grid-"+h+"-popup";m+="<tr ";if(t.current_item_id==r.id){m+='class="current"'}m+=">";if(t.show_item_checkboxes){m+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in t.columns){var f=t.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var s=r.column_config[f.label];var l=s.link;var n=s.value;var q=s.inbound;if(jQuery.type(n)==="string"){n=n.replace(/\/\//g,"/")}var d="";var p="";if(f.attach_popup){d="grid-"+h+"-popup";p="menubutton";if(l!=""){p+=" split"}p+=" popup"}m+="<td "+e+">";if(l){if(t.operations.length!=0){m+='<div id="'+d+'" class="'+p+'" style="float: left;">'}var o="";if(q){o="use-inbound"}else{o="use-outbound"}m+='<a class="label '+o+'" href="'+l+'" onclick="return false;">'+n+"</a>";if(t.operations.length!=0){m+="</div>"}}else{m+='<div id="'+d+'" class="'+p+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+n+"</label></div>"}m+="</td>"}}m+="</tr>";u++}return m},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file diff -r a0e80a712c37754d2d33260919469a7dccb2f1b1 -r 630c98ab700fe05dea8e36c6653f68f2cf0eb0d0 static/scripts/packed/galaxy.menu.js --- a/static/scripts/packed/galaxy.menu.js +++ b/static/scripts/packed/galaxy.menu.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({id:"workflow",title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index"});g.add({title:"Data Libraries",content:"library/index",divider:true});g.add({title:"Published Histories",content:"history/list_published"});g.add({title:"Published Workflows",content:"workflow/list_published"});g.add({title:"Published Visualizations",content:"visualization/list_published"});g.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});h.add({title:"Sequencing Requests",content:"requests/index"});h.add({title:"Find Samples",content:"requests/find_samples_index"});h.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({id:"visualization",title:"Visualization",content:"visualization/list"});k.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});e.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({id:"help",title:"Help"});if(this.options.biostar_url){j.add({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.add({title:"Support",content:this.options.support_url,target:"_blank"});j.add({title:"Search",content:this.options.search_url,target:"_blank"});j.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only"});i.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){i.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only"});i.add({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.add({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.add({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.add({title:"Saved Pages",content:"page/list",target:"_top"});i.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({id:"workflow",title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index"});g.add({title:"Data Libraries",content:"library/index"});g.add({title:"New Libraries",content:"library/list",divider:true});g.add({title:"Published Histories",content:"history/list_published"});g.add({title:"Published Workflows",content:"workflow/list_published"});g.add({title:"Published Visualizations",content:"visualization/list_published"});g.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});h.add({title:"Sequencing Requests",content:"requests/index"});h.add({title:"Find Samples",content:"requests/find_samples_index"});h.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({id:"visualization",title:"Visualization",content:"visualization/list"});k.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});e.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({id:"help",title:"Help"});if(this.options.biostar_url){j.add({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.add({title:"Support",content:this.options.support_url,target:"_blank"});j.add({title:"Search",content:this.options.search_url,target:"_blank"});j.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only"});i.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){i.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only"});i.add({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.add({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.add({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.add({title:"Saved Pages",content:"page/list",target:"_top"});i.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file diff -r a0e80a712c37754d2d33260919469a7dccb2f1b1 -r 630c98ab700fe05dea8e36c6653f68f2cf0eb0d0 static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{},initialize:function(b){if(b){this.create(b)}},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{},initialize:function(b){self=this;if(b){this.create(b)}this.bindEvents(event,self)},bindEvents:function(c,b){$(document).on("keyup",function(d){if(d.keyCode==27){self.hide()}});$("html").on("click",function(d){b.hide()});$(".modal-content").on("click",function(d){d.stopPropagation()})},unbindEvents:function(c,b){$(document).off("keyup",function(d){if(d.keyCode==27){b.hide()}});$("html").off("click",function(d){b.hide()});$(".modal-content").off("click",function(d){d.stopPropagation()})},destroy:function(){this.hide();this.unbindEvents();$(".modal").remove()},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false;this.unbindEvents()},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},hideButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).hide()},showButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).show()},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file diff -r a0e80a712c37754d2d33260919469a7dccb2f1b1 -r 630c98ab700fe05dea8e36c6653f68f2cf0eb0d0 static/scripts/packed/libs/bootstrap.js --- a/static/scripts/packed/libs/bootstrap.js +++ b/static/scripts/packed/libs/bootstrap.js @@ -1,1 +1,1 @@ -+function(b){function a(){var e=document.createElement("bootstrap");var d={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"};for(var c in d){if(e.style[c]!==undefined){return{end:d[c]}}}}b.fn.emulateTransitionEnd=function(e){var d=false,c=this;b(this).one(b.support.transition.end,function(){d=true});var f=function(){if(!d){b(c).trigger(b.support.transition.end)}};setTimeout(f,e);return this};b(function(){b.support.transition=a()})}(window.jQuery);+function(c){var b=function(d){this.element=c(d)};b.prototype.show=function(){var j=this.element;var g=j.closest("ul:not(.dropdown-menu)");var 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form",function(h){h.stopPropagation()}).on("click.bs.dropdown.data-api",b,a.prototype.toggle).on("keydown.bs.dropdown.data-api",b+", [role=menu]",a.prototype.keydown)}(window.jQuery); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/52a25164775e/ Changeset: 52a25164775e User: guerler Date: 2013-12-19 19:30:31 Summary: Merge Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: martenson: packed version of data_library updated js files
by commits-noreply＠bitbucket.org 19 Dec '13

19 Dec '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e45e1b5bd2eb/ Changeset: e45e1b5bd2eb User: martenson Date: 2013-12-19 19:28:37 Summary: packed version of data_library updated js files Affected #: 3 files diff -r a0e80a712c37754d2d33260919469a7dccb2f1b1 -r e45e1b5bd2eb1cac02e90bedaf8b035dd5601b20 static/scripts/packed/galaxy.menu.js --- a/static/scripts/packed/galaxy.menu.js +++ b/static/scripts/packed/galaxy.menu.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({id:"workflow",title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index"});g.add({title:"Data Libraries",content:"library/index",divider:true});g.add({title:"Published Histories",content:"history/list_published"});g.add({title:"Published Workflows",content:"workflow/list_published"});g.add({title:"Published Visualizations",content:"visualization/list_published"});g.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});h.add({title:"Sequencing Requests",content:"requests/index"});h.add({title:"Find Samples",content:"requests/find_samples_index"});h.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({id:"visualization",title:"Visualization",content:"visualization/list"});k.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});e.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({id:"help",title:"Help"});if(this.options.biostar_url){j.add({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.add({title:"Support",content:this.options.support_url,target:"_blank"});j.add({title:"Search",content:this.options.search_url,target:"_blank"});j.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only"});i.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){i.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only"});i.add({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.add({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.add({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.add({title:"Saved Pages",content:"page/list",target:"_top"});i.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file +define(["galaxy.masthead"],function(b){var a=Backbone.Model.extend({options:null,masthead:null,initialize:function(c){this.options=c.config;this.masthead=c.masthead;this.create()},create:function(){var d=new b.GalaxyMastheadTab({id:"analysis",title:"Analyze Data",content:"root/index"});this.masthead.append(d);var c=new b.GalaxyMastheadTab({id:"workflow",title:"Workflow",content:"workflow"});this.masthead.append(c);var g=new b.GalaxyMastheadTab({id:"shared",title:"Shared Data",content:"library/index"});g.add({title:"Data Libraries",content:"library/index"});g.add({title:"New Libraries",content:"library/list",divider:true});g.add({title:"Published Histories",content:"history/list_published"});g.add({title:"Published Workflows",content:"workflow/list_published"});g.add({title:"Published Visualizations",content:"visualization/list_published"});g.add({title:"Published Pages",content:"page/list_published"});this.masthead.append(g);if(this.options.user.requests){var h=new b.GalaxyMastheadTab({id:"lab",title:"Lab"});h.add({title:"Sequencing Requests",content:"requests/index"});h.add({title:"Find Samples",content:"requests/find_samples_index"});h.add({title:"Help",content:this.options.lims_doc_url});this.masthead.append(h)}var k=new b.GalaxyMastheadTab({id:"visualization",title:"Visualization",content:"visualization/list"});k.add({title:"New Track Browser",content:"visualization/trackster",target:"_frame"});k.add({title:"Saved Visualizations",content:"visualization/list",target:"_frame"});this.masthead.append(k);if(this.options.enable_cloud_launch){var e=new b.GalaxyMastheadTab({id:"cloud",title:"Cloud",content:"cloudlaunch/index"});e.add({title:"New Cloud Cluster",content:"cloudlaunch/index"});this.masthead.append(e)}if(this.options.is_admin_user){var f=new b.GalaxyMastheadTab({id:"admin",title:"Admin",content:"admin/index",extra_class:"admin-only"});this.masthead.append(f)}var j=new b.GalaxyMastheadTab({id:"help",title:"Help"});if(this.options.biostar_url){j.add({title:"Galaxy Q&A Site",content:this.options.biostar_url_redirect,target:"_blank"});j.add({title:"Ask a question",content:"biostar/biostar_question_redirect",target:"_blank"})}j.add({title:"Support",content:this.options.support_url,target:"_blank"});j.add({title:"Search",content:this.options.search_url,target:"_blank"});j.add({title:"Mailing Lists",content:this.options.mailing_lists,target:"_blank"});j.add({title:"Videos",content:this.options.screencasts_url,target:"_blank"});j.add({title:"Wiki",content:this.options.wiki_url,target:"_blank"});j.add({title:"How to Cite Galaxy",content:this.options.citation_url,target:"_blank"});if(!this.options.terms_url){j.add({title:"Terms and Conditions",content:this.options.terms_url,target:"_blank"})}this.masthead.append(j);if(!this.options.user.valid){var i=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedout-only"});i.add({title:"Login",content:"user/login",target:"galaxy_main"});if(this.options.allow_user_creation){i.add({title:"Register",content:"user/create",target:"galaxy_main"})}this.masthead.append(i)}else{var i=new b.GalaxyMastheadTab({id:"user",title:"User",extra_class:"loggedin-only"});i.add({title:"Logged in as "+this.options.user.email});if(this.options.use_remote_user&&this.options.remote_user_logout_href){i.add({title:"Logout",content:this.options.remote_user_logout_href,target:"_top"})}else{i.add({title:"Preferences",content:"user?cntrller=user",target:"galaxy_main"});i.add({title:"Custom Builds",content:"user/dbkeys",target:"galaxy_main"});i.add({title:"Logout",content:"user/logout",target:"_top",divider:true})}i.add({title:"Saved Histories",content:"history/list",target:"galaxy_main"});i.add({title:"Saved Datasets",content:"dataset/list",target:"galaxy_main"});i.add({title:"Saved Pages",content:"page/list",target:"_top"});i.add({title:"API Keys",content:"user/api_keys?cntrller=user",target:"galaxy_main"});if(this.options.use_remote_user){i.add({title:"Public Name",content:"user/edit_username?cntrller=user",target:"galaxy_main"})}this.masthead.append(i)}if(this.options.active_view){this.masthead.highlight(this.options.active_view)}}});return{GalaxyMenu:a}}); \ No newline at end of file diff -r a0e80a712c37754d2d33260919469a7dccb2f1b1 -r e45e1b5bd2eb1cac02e90bedaf8b035dd5601b20 static/scripts/packed/galaxy.modal.js --- a/static/scripts/packed/galaxy.modal.js +++ b/static/scripts/packed/galaxy.modal.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{},initialize:function(b){if(b){this.create(b)}},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file +define([],function(){var a=Backbone.View.extend({elMain:"#everything",optionsDefault:{title:"galaxy-modal",body:"",backdrop:true,height:null,width:null},options:{},initialize:function(b){self=this;if(b){this.create(b)}this.bindEvents(event,self)},bindEvents:function(c,b){$(document).on("keyup",function(d){if(d.keyCode==27){self.hide()}});$("html").on("click",function(d){b.hide()});$(".modal-content").on("click",function(d){d.stopPropagation()})},unbindEvents:function(c,b){$(document).off("keyup",function(d){if(d.keyCode==27){b.hide()}});$("html").off("click",function(d){b.hide()});$(".modal-content").off("click",function(d){d.stopPropagation()})},destroy:function(){this.hide();this.unbindEvents();$(".modal").remove()},show:function(b){this.initialize(b);if(this.options.height){this.$body.css("height",this.options.height);this.$body.css("overflow","hidden")}else{this.$body.css("max-height",$(window).height()/2)}if(this.options.width){this.$dialog.css("width",this.options.width)}if(this.visible){this.$el.show()}else{this.$el.fadeIn("fast")}this.visible=true},hide:function(){this.$el.fadeOut("fast");this.visible=false;this.unbindEvents()},create:function(c){this.options=_.defaults(c,this.optionsDefault);if(this.options.body=="progress"){this.options.body=$('<div class="progress progress-striped active"><div class="progress-bar progress-bar-info" style="width:100%"></div></div>')}if(this.$el){this.$el.remove()}this.setElement(this.template(this.options.title));this.$dialog=(this.$el).find(".modal-dialog");this.$body=(this.$el).find(".modal-body");this.$footer=(this.$el).find(".modal-footer");this.$buttons=(this.$el).find(".buttons");this.$backdrop=(this.$el).find(".modal-backdrop");this.$body.html(this.options.body);if(!this.options.backdrop){this.$backdrop.removeClass("in")}if(this.options.buttons){var b=this;$.each(this.options.buttons,function(d,e){b.$buttons.append($('<button id="'+String(d).toLowerCase()+'"></button>').text(d).click(e)).append(" ")})}else{this.$footer.hide()}$(this.elMain).append($(this.el))},enableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",false)},disableButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).prop("disabled",true)},hideButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).hide()},showButton:function(b){this.$buttons.find("#"+String(b).toLowerCase()).show()},scrollTop:function(){return this.$body.scrollTop()},template:function(b){return'<div class="modal"><div class="modal-backdrop fade in" style="z-index: -1;"></div><div class="modal-dialog"><div class="modal-content"><div class="modal-header"><button type="button" class="close" style="display: none;">×</button><h4 class="title">'+b+'</h4></div><div class="modal-body"></div><div class="modal-footer"><div class="buttons" style="float: right;"></div></div></div</div></div>'}});return{GalaxyModal:a}}); \ No newline at end of file diff -r a0e80a712c37754d2d33260919469a7dccb2f1b1 -r e45e1b5bd2eb1cac02e90bedaf8b035dd5601b20 static/scripts/packed/libs/bootstrap.js --- a/static/scripts/packed/libs/bootstrap.js +++ b/static/scripts/packed/libs/bootstrap.js @@ -1,1 +1,1 @@ -+function(b){function a(){var e=document.createElement("bootstrap");var d={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"};for(var c in d){if(e.style[c]!==undefined){return{end:d[c]}}}}b.fn.emulateTransitionEnd=function(e){var d=false,c=this;b(this).one(b.support.transition.end,function(){d=true});var f=function(){if(!d){b(c).trigger(b.support.transition.end)}};setTimeout(f,e);return this};b(function(){b.support.transition=a()})}(window.jQuery);+function(c){var b=function(d){this.element=c(d)};b.prototype.show=function(){var j=this.element;var g=j.closest("ul:not(.dropdown-menu)");var f=j.attr("data-target");if(!f){f=j.attr("href");f=f&&f.replace(/.*(?=#[^\s]*$)/,"")}if(j.parent("li").hasClass("active")){return}var h=g.find(".active:last a")[0];var i=c.Event("show.bs.tab",{relatedTarget:h});j.trigger(i);if(i.isDefaultPrevented()){return}var d=c(f);this.activate(j.parent("li"),g);this.activate(d,d.parent(),function(){j.trigger({type:"shown.bs.tab",relatedTarget:h})})};b.prototype.activate=function(f,e,i){var d=e.find("> .active");var h=i&&c.support.transition&&d.hasClass("fade");function g(){d.removeClass("active").find("> .dropdown-menu > .active").removeClass("active");f.addClass("active");if(h){f[0].offsetWidth;f.addClass("in")}else{f.removeClass("fade")}if(f.parent(".dropdown-menu")){f.closest("li.dropdown").addClass("active")}i&&i()}h?d.one(c.support.transition.end,g).emulateTransitionEnd(150):g();d.removeClass("in")};var a=c.fn.tab;c.fn.tab=function(d){return this.each(function(){var f=c(this);var e=f.data("bs.tab");if(!e){f.data("bs.tab",(e=new b(this)))}if(typeof d=="string"){e[d]()}})};c.fn.tab.Constructor=b;c.fn.tab.noConflict=function(){c.fn.tab=a;return this};c(document).on("click.bs.tab.data-api",'[data-toggle="tab"], [data-toggle="pill"]',function(d){d.preventDefault();c(this).tab("show")})}(window.jQuery);+function(c){var b=function(e,d){this.type=this.options=this.enabled=this.timeout=this.hoverState=this.$element=null;this.init("tooltip",e,d)};b.DEFAULTS={animation:true,placement:"top",selector:false,template:'<div class="tooltip"><div class="tooltip-arrow"></div><div class="tooltip-inner"></div></div>',trigger:"hover focus",title:"",delay:0,html:false,container:"body"};b.prototype.init=function(k,h,f){this.enabled=true;this.type=k;this.$element=c(h);this.options=this.getOptions(f);var j=this.options.trigger.split(" ");for(var g=j.length;g--;){var e=j[g];if(e=="click"){this.$element.on("click."+this.type,this.options.selector,c.proxy(this.toggle,this))}else{if(e!="manual"){var l=e=="hover"?"mouseenter":"focus";var d=e=="hover"?"mouseleave":"blur";this.$element.on(l+"."+this.type,this.options.selector,c.proxy(this.enter,this));this.$element.on(d+"."+this.type,this.options.selector,c.proxy(this.leave,this))}}}this.options.selector?(this._options=c.extend({},this.options,{trigger:"manual",selector:""})):this.fixTitle()};b.prototype.getDefaults=function(){return b.DEFAULTS};b.prototype.getOptions=function(d){d=c.extend({},this.getDefaults(),this.$element.data(),d);if(d.delay&&typeof d.delay=="number"){d.delay={show:d.delay,hide:d.delay}}return d};b.prototype.getDelegateOptions=function(){var d={};var e=this.getDefaults();this._options&&c.each(this._options,function(f,g){if(e[f]!=g){d[f]=g}});return d};b.prototype.enter=function(e){var d=e instanceof this.constructor?e:c(e.currentTarget)[this.type](this.getDelegateOptions()).data("bs."+this.type);clearTimeout(d.timeout);d.hoverState="in";if(!d.options.delay||!d.options.delay.show){return d.show()}d.timeout=setTimeout(function(){if(d.hoverState=="in"){d.show()}},d.options.delay.show)};b.prototype.leave=function(e){var d=e instanceof this.constructor?e:c(e.currentTarget)[this.type](this.getDelegateOptions()).data("bs."+this.type);clearTimeout(d.timeout);d.hoverState="out";if(!d.options.delay||!d.options.delay.hide){return d.hide()}d.timeout=setTimeout(function(){if(d.hoverState=="out"){d.hide()}},d.options.delay.hide)};b.prototype.show=function(){var n=c.Event("show.bs."+this.type);if(this.hasContent()&&this.enabled){this.$element.trigger(n);if(n.isDefaultPrevented()){return}var j=this.tip();this.setContent();if(this.options.animation){j.addClass("fade")}var i=typeof this.options.placement=="function"?this.options.placement.call(this,j[0],this.$element[0]):this.options.placement;var r=/\s?auto?\s?/i;var s=r.test(i);if(s){i=i.replace(r,"")||"top"}j.detach().css({top:0,left:0,display:"block"}).addClass(i);this.options.container?j.appendTo(this.options.container):j.insertAfter(this.$element);var o=this.getPosition();var d=j[0].offsetWidth;var l=j[0].offsetHeight;if(s){var h=this.$element.parent();var g=i;var p=document.documentElement.scrollTop||document.body.scrollTop;var q=this.options.container=="body"?window.innerWidth:h.outerWidth();var m=this.options.container=="body"?window.innerHeight:h.outerHeight();var k=this.options.container=="body"?0:h.offset().left;i=i=="bottom"&&o.top+o.height+l-p>m?"top":i=="top"&&o.top-p-l<0?"bottom":i=="right"&&o.right+d>q?"left":i=="left"&&o.left-d<k?"right":i;j.removeClass(g).addClass(i)}var f=this.getCalculatedOffset(i,o,d,l);this.applyPlacement(f,i);this.$element.trigger("shown.bs."+this.type)}};b.prototype.applyPlacement=function(i,j){var g;var k=this.tip();var f=k[0].offsetWidth;var n=k[0].offsetHeight;var e=parseInt(k.css("margin-top"),10);var h=parseInt(k.css("margin-left"),10);if(isNaN(e)){e=0}if(isNaN(h)){h=0}i.top=i.top+e;i.left=i.left+h;k.offset(i).addClass("in");var d=k[0].offsetWidth;var l=k[0].offsetHeight;if(j=="top"&&l!=n){g=true;i.top=i.top+n-l}if(/bottom|top/.test(j)){var m=0;if(i.left<0){m=i.left*-2;i.left=0;k.offset(i);d=k[0].offsetWidth;l=k[0].offsetHeight}this.replaceArrow(m-f+d,d,"left")}else{this.replaceArrow(l-n,l,"top")}if(g){k.offset(i)}};b.prototype.replaceArrow=function(f,e,d){this.arrow().css(d,f?(50*(1-f/e)+"%"):"")};b.prototype.setContent=function(){var e=this.tip();var d=this.getTitle();e.find(".tooltip-inner")[this.options.html?"html":"text"](d);e.removeClass("fade in top bottom left right")};b.prototype.hide=function(){var f=this;var h=this.tip();var g=c.Event("hide.bs."+this.type);function d(){if(f.hoverState!="in"){h.detach()}}this.$element.trigger(g);if(g.isDefaultPrevented()){return}h.removeClass("in");c.support.transition&&this.$tip.hasClass("fade")?h.one(c.support.transition.end,d).emulateTransitionEnd(150):d();this.$element.trigger("hidden.bs."+this.type);return this};b.prototype.fixTitle=function(){var d=this.$element;if(d.attr("title")||typeof(d.attr("data-original-title"))!="string"){d.attr("data-original-title",d.attr("title")||"").attr("title","")}};b.prototype.hasContent=function(){return this.getTitle()};b.prototype.getPosition=function(){var d=this.$element[0];return c.extend({},(typeof d.getBoundingClientRect=="function")?d.getBoundingClientRect():{width:d.offsetWidth,height:d.offsetHeight},this.$element.offset())};b.prototype.getCalculatedOffset=function(d,g,e,f){return d=="bottom"?{top:g.top+g.height,left:g.left+g.width/2-e/2}:d=="top"?{top:g.top-f,left:g.left+g.width/2-e/2}:d=="left"?{top:g.top+g.height/2-f/2,left:g.left-e}:{top:g.top+g.height/2-f/2,left:g.left+g.width}};b.prototype.getTitle=function(){var f;var d=this.$element;var e=this.options;f=d.attr("data-original-title")||(typeof e.title=="function"?e.title.call(d[0]):e.title);return f};b.prototype.tip=function(){return this.$tip=this.$tip||c(this.options.template)};b.prototype.arrow=function(){return this.$arrow=this.$arrow||this.tip().find(".tooltip-arrow")};b.prototype.validate=function(){if(!this.$element[0].parentNode){this.hide();this.$element=null;this.options=null}};b.prototype.enable=function(){this.enabled=true};b.prototype.disable=function(){this.enabled=false};b.prototype.toggleEnabled=function(){this.enabled=!this.enabled};b.prototype.toggle=function(f){var d=f?c(f.currentTarget)[this.type](this.getDelegateOptions()).data("bs."+this.type):this;d.tip().hasClass("in")?d.leave(d):d.enter(d)};b.prototype.destroy=function(){this.hide().$element.off("."+this.type).removeData("bs."+this.type)};var a=c.fn.tooltip;c.fn.tooltip=function(d){return this.each(function(){var g=c(this);var f=g.data("bs.tooltip");var e=typeof d=="object"&&d;if(!f){g.data("bs.tooltip",(f=new b(this,e)))}if(typeof d=="string"){f[d]()}})};c.fn.tooltip.Constructor=b;c.fn.tooltip.noConflict=function(){c.fn.tooltip=a;return this}}(window.jQuery); \ No newline at end of file ++function(b){function a(){var e=document.createElement("bootstrap");var d={WebkitTransition:"webkitTransitionEnd",MozTransition:"transitionend",OTransition:"oTransitionEnd otransitionend",transition:"transitionend"};for(var c in d){if(e.style[c]!==undefined){return{end:d[c]}}}}b.fn.emulateTransitionEnd=function(e){var d=false,c=this;b(this).one(b.support.transition.end,function(){d=true});var f=function(){if(!d){b(c).trigger(b.support.transition.end)}};setTimeout(f,e);return this};b(function(){b.support.transition=a()})}(window.jQuery);+function(c){var b=function(d){this.element=c(d)};b.prototype.show=function(){var j=this.element;var g=j.closest("ul:not(.dropdown-menu)");var f=j.attr("data-target");if(!f){f=j.attr("href");f=f&&f.replace(/.*(?=#[^\s]*$)/,"")}if(j.parent("li").hasClass("active")){return}var h=g.find(".active:last a")[0];var i=c.Event("show.bs.tab",{relatedTarget:h});j.trigger(i);if(i.isDefaultPrevented()){return}var d=c(f);this.activate(j.parent("li"),g);this.activate(d,d.parent(),function(){j.trigger({type:"shown.bs.tab",relatedTarget:h})})};b.prototype.activate=function(f,e,i){var d=e.find("> .active");var h=i&&c.support.transition&&d.hasClass("fade");function g(){d.removeClass("active").find("> .dropdown-menu > 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