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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 30 Apr '14

30 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ceace0f609c0/ Changeset: ceace0f609c0 User: devteam Date: 2014-04-30 21:35:57 Summary: Moved API tests to live under test/ rather than test/functional/. Removed test for DNAse flanked genes. Added test for UCSC table browser. Affected #: 32 files This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/c05ab2ae3a58/ Changeset: c05ab2ae3a58 User: devteam Date: 2014-04-30 21:43:21 Summary: Add options to the shell script wrappers to run the API tests. Affected #: 2 files diff -r ceace0f609c00b15a28b1737b8782beed92bd927 -r c05ab2ae3a58938e07c33193a7a52a89cbd43056 run_functional_tests.sh --- a/run_functional_tests.sh +++ b/run_functional_tests.sh @@ -10,6 +10,7 @@ echo "'run_functional_tests.sh aaa' for testing one test case of 'aaa' ('aaa' is the file name with path)" echo "'run_functional_tests.sh -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id)" echo "'run_functional_tests.sh -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')" + echo "'run_functional_tests.sh -api' for running API functional tests" echo "'run_functional_tests.sh -list' for listing all the tool ids" echo "'run_functional_tests.sh -toolshed' for running all the test scripts in the ./test/tool_shed/functional directory" echo "'run_functional_tests.sh -toolshed testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory" @@ -50,6 +51,12 @@ else python ./test/tool_shed/functional_tests.py -v --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html $2 fi +elif [ $1 = '-api' ]; then + if [ ! $2 ]; then + python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_api_tests.html ./test/api + else + python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_api_tests.html $2 + fi elif [ $1 = '-workflow' ]; then python ./scripts/functional_tests.py -v functional.workflow:WorkflowTestCase --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html -workflow $2 elif [ $1 = '-data_managers' ]; then diff -r ceace0f609c00b15a28b1737b8782beed92bd927 -r c05ab2ae3a58938e07c33193a7a52a89cbd43056 run_tests.sh --- a/run_tests.sh +++ b/run_tests.sh @@ -10,6 +10,7 @@ '${0##*/} -id bbb' for testing one tool with id 'bbb' ('bbb' is the tool id) '${0##*/} -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::') '${0##*/} -list' for listing all the tool ids +'${0##*/} -api' for running all the test scripts in the ./test/api directory '${0##*/} -toolshed' for running all the test scripts in the ./test/tool_shed/functional directory '${0##*/} -toolshed testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory '${0##*/} -workflow test.xml' for running a workflow test case as defined by supplied workflow xml test file (experimental) @@ -65,6 +66,17 @@ exit 1 fi ;; + -a|-api|--api) + test_script="./scripts/functional_tests.py" + report_file="./run_api_tests.html" + if [ $# -gt 1 ]; then + api_script=$2 + shift 2 + else + api_script="./test/api" + shift 1 + fi + ;; -t|-toolshed|--toolshed) test_script="./test/tool_shed/functional_tests.py" report_file="./test/tool_shed/run_functional_tests.html" @@ -76,7 +88,7 @@ shift 1 fi ;; - -with_framework_test_tools|--with_framework_test_tools) + -with_framework_test_tools|--with_framework_test_tools) with_framework_test_tools_arg="-with_framework_test_tools" shift ;; @@ -182,6 +194,8 @@ extra_args="functional.workflow:WorkflowTestCase $workflow_file" elif [ -n "$toolshed_script" ]; then extra_args="$toolshed_script" +elif [ -n "$api_script" ]; then + extra_args="$api_script" elif [ -n "$section_id" ]; then extra_args=`python tool_list.py $section_id` elif [ -n "$test_id" ]; then 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: Fix to 197878e: properly send in html insertions to grid_config
by commits-noreply＠bitbucket.org 30 Apr '14

30 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ff4e42dde384/ Changeset: ff4e42dde384 User: carlfeberhard Date: 2014-04-30 18:04:10 Summary: Fix to 197878e: properly send in html insertions to grid_config Affected #: 1 file diff -r a56b3687e778c308b7bf47776a4973d0a9a9040b -r ff4e42dde38421d749b431b18c5ab23d7c180e08 templates/grid_base.mako --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -73,7 +73,7 @@ // load grid viewer require(['mvc/grid/grid-view'], function(GridView) { $(function() { - gridView = new GridView( ${ h.to_json_string( self.get_grid_config() ) } ); + gridView = new GridView( ${ h.to_json_string( self.get_grid_config( embedded=embedded, insert=insert ) ) } ); }); }); </script> 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: trevorw: selected_file -> repo_file
by commits-noreply＠bitbucket.org 30 Apr '14

30 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a56b3687e778/ Changeset: a56b3687e778 User: trevorw Date: 2014-04-30 02:24:47 Summary: selected_file -> repo_file Affected #: 1 file diff -r 1e76ef6d002830675756f617b334e824abf894c4 -r a56b3687e778c308b7bf47776a4973d0a9a9040b lib/tool_shed/util/commit_util.py --- a/lib/tool_shed/util/commit_util.py +++ b/lib/tool_shed/util/commit_util.py @@ -184,10 +184,10 @@ commands.remove( repo.ui, repo, repo_file, force=True ) except Exception, e: log.debug( "Error removing files using the mercurial API, so trying a different approach, the error was: %s" % str( e )) - relative_selected_file = selected_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) + relative_selected_file = repo_file.split( 'repo_%d' % repository.id )[1].lstrip( '/' ) repo.dirstate.remove( relative_selected_file ) repo.dirstate.write() - absolute_selected_file = os.path.abspath( selected_file ) + absolute_selected_file = os.path.abspath( repo_file ) if os.path.isdir( absolute_selected_file ): try: os.rmdir( absolute_selected_file ) @@ -451,7 +451,7 @@ if last_actions_package_altered: last_actions_elem[ last_actions_elem_package_index ] = last_actions_elem_package_elem actions_group_elem[ last_actions_index ] = last_actions_elem - else: + else: # Inspect the sub elements of last_actions_elem to locate all <repository> tags and # populate them with toolshed and changeset_revision attributes if necessary. last_actions_package_altered, altered, last_actions_elem, message = \ 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: data libraries: new API for deleting LDAs, UI improvements, download router flow changes
by commits-noreply＠bitbucket.org 30 Apr '14

30 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1e76ef6d0028/ Changeset: 1e76ef6d0028 User: martenson Date: 2014-04-30 00:11:06 Summary: data libraries: new API for deleting LDAs, UI improvements, download router flow changes Affected #: 16 files diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 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 @@ -46,12 +46,48 @@ except Exception, e: raise exceptions.ObjectNotFound( 'Requested dataset was not found.' ) rval = dataset.to_dict() - - rval['id'] = trans.security.encode_id(rval['id']); - rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']); + rval['deleted'] = dataset.deleted + rval['id'] = trans.security.encode_id(rval['id']) + rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']) + rval['parent_library_id'] = trans.security.encode_id(rval['parent_library_id']) rval['folder_id'] = 'F' + trans.security.encode_id(rval['folder_id']) return rval + + @expose_api + def delete( self, trans, encoded_dataset_id, **kwd ): + """ + delete( self, trans, encoded_dataset_id, **kwd ): + * DELETE /api/libraries/datasets/{encoded_dataset_id} + Marks the dataset deleted. + """ + undelete = util.string_as_bool( kwd.get( 'undelete', False ) ) + try: + dataset = self.get_library_dataset( trans, id = encoded_dataset_id, check_ownership=False, check_accessible=False ) + except Exception, e: + raise exceptions.ObjectNotFound( 'Requested dataset was not found.' + str(e) ) + current_user_roles = trans.get_current_user_roles() + allowed = trans.app.security_agent.can_modify_library_item( current_user_roles, dataset ) + if ( not allowed ) and ( not trans.user_is_admin() ): + raise exceptions.InsufficientPermissionsException( 'You do not have proper permissions to delete this dataset.') + + if undelete: + dataset.deleted = False + else: + dataset.deleted = True + + trans.sa_session.add( dataset ) + trans.sa_session.flush() + + rval = dataset.to_dict() + rval['deleted'] = dataset.deleted + rval['id'] = trans.security.encode_id(rval['id']) + rval['ldda_id'] = trans.security.encode_id(rval['ldda_id']) + rval['parent_library_id'] = trans.security.encode_id(rval['parent_library_id']) + rval['folder_id'] = 'F' + trans.security.encode_id(rval['folder_id']) + return rval + + @web.expose def download( self, trans, format, **kwd ): """ diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -218,6 +218,12 @@ action='show', conditions=dict( method=[ "GET" ] ) ) + webapp.mapper.connect( 'delete_lda_item', + '/api/libraries/datasets/:encoded_dataset_id', + controller='lda_datasets', + action='delete', + conditions=dict( method=[ "DELETE" ] ) ) + webapp.mapper.connect( 'download_lda_items', '/api/libraries/datasets/download/:format', controller='lda_datasets', diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -78,8 +78,10 @@ }); this.library_router.on('route:download', function(folder_id, format) { - if ($('#center').find(':checked').length === 0) { + if ($('#folder_list_body').find(':checked').length === 0) { + //TODO make URL sharable mod_toastr.info('You have to select some datasets to download'); + Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: true, replace: true}); } else { Galaxy.libraries.folderToolbarView.download(folder_id, format); Galaxy.libraries.library_router.navigate('folders/' + folder_id, {trigger: false, replace: true}); diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/mvc/library/library-folderlist-view.js --- a/static/scripts/mvc/library/library-folderlist-view.js +++ b/static/scripts/mvc/library/library-folderlist-view.js @@ -104,6 +104,11 @@ }); $("#center [data-toggle]").tooltip(); this.checkEmptiness(); + $('.deleted_dataset').hover(function() { + $(this).find('.show_on_hover').show(); + }, function () { + $(this).find('.show_on_hover').hide(); + }); }, /** @@ -114,6 +119,11 @@ _.each(this.collection.models.reverse(), function(model) { that.renderOne(model); }); + $('.deleted_dataset').hover(function() { + $(this).find('.show_on_hover').show(); + }, function () { + $(this).find('.show_on_hover').hide(); + }); }, /** @@ -127,17 +137,15 @@ } var rowView = new mod_library_folderrow_view.FolderRowView(model); this.$el.find('#first_folder_item').after(rowView.el); - this.checkEmptiness(); + // this.checkEmptiness(); }, /** Checks whether the list is empty and adds/removes the message */ - // TODO needs refactor checkEmptiness : function(){ if ((this.$el.find('.dataset_row').length === 0) && (this.$el.find('.folder_row').length === 0)){ - var empty_folder_tmpl = this.templateEmptyFolder(); - this.$el.find('#folder_list_body').append(empty_folder_tmpl()); + this.$el.find('.empty-folder-message').show(); } else { - this.$el.find('#empty_folder_message').remove(); + this.$el.find('.empty-folder-message').hide(); } }, @@ -192,7 +200,7 @@ var selected = event.target.checked; that = this; // Iterate each checkbox - $(':checkbox').each(function() { + $(':checkbox', '#folder_list_body').each(function() { this.checked = selected; $row = $(this.parentElement.parentElement); // Change color of selected/unselected @@ -280,10 +288,11 @@ tmpl_array.push(' <thead>'); tmpl_array.push(' <th class="button_heading"></th>'); tmpl_array.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>'); - tmpl_array.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); + tmpl_array.push(' <th style="width:30%;"><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>'); tmpl_array.push(' <th>data type</th>'); tmpl_array.push(' <th>size</th>'); tmpl_array.push(' <th>time updated (UTC)</th>'); + tmpl_array.push(' <th style="width:15%;"></th> '); tmpl_array.push(' </thead>'); tmpl_array.push(' <tbody id="folder_list_body">'); tmpl_array.push(' <tr id="first_folder_item">'); @@ -293,27 +302,17 @@ tmpl_array.push(' <td></td>'); tmpl_array.push(' <td></td>'); tmpl_array.push(' <td></td>'); + tmpl_array.push(' <td></td>'); tmpl_array.push(' </tr>'); tmpl_array.push(' </tbody>'); tmpl_array.push('</table>'); + tmpl_array.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents.</div>'); return _.template(tmpl_array.join('')); - }, - - templateEmptyFolder: function(){ - var tmpl_array = []; - - tmpl_array.push('<tr id="empty_folder_message">'); - tmpl_array.push('<td colspan="6" style="text-align:center">'); - tmpl_array.push('This folder is either empty or you do not have proper access permissions to see the contents.'); - tmpl_array.push('</td>'); - tmpl_array.push('</tr>'); - - return _.template(tmpl_array.join('')); } - - }); + +}); return { FolderListView: FolderListView diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/mvc/library/library-folderrow-view.js --- a/static/scripts/mvc/library/library-folderrow-view.js +++ b/static/scripts/mvc/library/library-folderrow-view.js @@ -15,7 +15,8 @@ lastSelectedHistory: '', events: { - 'click .library-dataset' : 'showDatasetDetails' + 'click .library-dataset' : 'showDatasetDetails', + 'click .undelete_dataset_btn' : 'undelete_dataset' }, options: { @@ -69,14 +70,22 @@ success: function (histories){ self.renderModalAfterFetch(item, histories); }, - error: function(){ - mod_toastr.error('An error occured during fetching histories:('); + error: function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error(response.responseJSON.err_msg); + } else { + mod_toastr.error('An error occured during fetching histories:('); + } self.renderModalAfterFetch(item); } }); }, - error: function(){ - mod_toastr.error('An error occured during loading dataset details :('); + error: function(model, response){ + if (typeof response.responseJSON !== "undefined"){ + mod_toastr.error(response.responseJSON.err_msg); + } else { + mod_toastr.error('An error occured during loading dataset details :('); + } } }); }, @@ -163,34 +172,38 @@ } }, - // import dataset shown currently in modal into selected history - importCurrentIntoHistory : function(){ - //disable the buttons - this.modal.disableButton('Import'); - this.modal.disableButton('Download'); + // import dataset shown currently in modal into selected history + importCurrentIntoHistory : function(){ + //disable the buttons + this.modal.disableButton('Import'); + this.modal.disableButton('Download'); - var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); - this.lastSelectedHistory = history_id; //save selected history for further use + var history_id = $(this.modal.elMain).find('select[name=dataset_import_single] option:selected').val(); + this.lastSelectedHistory = history_id; //save selected history for further use - var library_dataset_id = $('#id_row').attr('data-id'); - var historyItem = new mod_library_model.HistoryItem(); - var self = this; - historyItem.url = historyItem.urlRoot + history_id + '/contents'; + var library_dataset_id = $('#id_row').attr('data-id'); + var historyItem = new mod_library_model.HistoryItem(); + var self = this; + historyItem.url = historyItem.urlRoot + history_id + '/contents'; - // save the dataset into selected history - historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ - mod_toastr.success('Dataset imported'); - //enable the buttons - self.modal.enableButton('Import'); - self.modal.enableButton('Download'); - }, error : function(){ - mod_toastr.error('An error occured! Dataset not imported. Please try again.'); - //enable the buttons - self.modal.enableButton('Import'); - self.modal.enableButton('Download'); - } - }); - }, + // save the dataset into selected history + historyItem.save({ content : library_dataset_id, source : 'library' }, { success : function(){ + mod_toastr.success('Dataset imported'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + }, error : function(){ + mod_toastr.error('An error occured! Dataset not imported. Please try again.'); + //enable the buttons + self.modal.enableButton('Import'); + self.modal.enableButton('Download'); + } + }); + }, + + undelete_dataset : function(event){ + alert('undelete dataset'); + }, templateRowFolder: function() { tmpl_array = []; @@ -211,6 +224,7 @@ // print item count only if it is given // tmpl_array.push(' <td><% if (typeof content_item.get("item_count") !== "undefined") { _.escape(content_item.get("item_count")); print("item(s)") } %></td>'); tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated + tmpl_array.push(' <td></td>'); tmpl_array.push('</tr>'); return _.template(tmpl_array.join('')); @@ -228,6 +242,7 @@ tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated + tmpl_array.push(' <td></td>'); tmpl_array.push('</tr>'); return _.template(tmpl_array.join('')); @@ -236,7 +251,7 @@ templateRowDeletedFile: function(){ tmpl_array = []; - tmpl_array.push('<tr class="active" id="<%- content_item.id %>">'); + tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">'); tmpl_array.push(' <td>'); tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>'); tmpl_array.push(' </td>'); @@ -245,6 +260,7 @@ tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>'); // data type tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>'); // size tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>'); // time updated + tmpl_array.push(' <td class="right-center"><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button></td>'); tmpl_array.push('</tr>'); return _.template(tmpl_array.join('')); diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/mvc/library/library-foldertoolbar-view.js @@ -15,7 +15,8 @@ 'click #toolbtn_create_folder' : 'createFolderFromModal', 'click #toolbtn_bulk_import' : 'modalBulkImport', 'click .toolbtn_add_files' : 'addFilesToFolderModal', - 'click #include_deleted_datasets_chk' : 'check_include_deleted' + 'click #include_deleted_datasets_chk' : 'checkIncludeDeleted', + 'click #toolbtn_bulk_delete' : 'deleteSelectedDatasets' }, defaults: { @@ -164,7 +165,9 @@ }); }, - // import all selected datasets into history + /** + * import all selected datasets into history + */ importAllIntoHistory : function (){ // disable the button to prevent multiple submission this.modal.disableButton('Import'); @@ -393,7 +396,7 @@ /** * Handles the click on 'show deleted' checkbox */ - check_include_deleted: function(event){ + checkIncludeDeleted: function(event){ if (event.target.checked){ Galaxy.libraries.folderListView.collection = new mod_library_model.Folder(); Galaxy.libraries.folderListView.listenTo(Galaxy.libraries.folderListView.collection, 'add', Galaxy.libraries.folderListView.renderOne); @@ -405,6 +408,83 @@ } }, + /** + * Deletes the selected datasets. Atomic. One by one. + */ + deleteSelectedDatasets: function(){ + var checkedValues = $('#folder_table').find(':checked'); + if(checkedValues.length === 0){ + mod_toastr.info('You have to select some datasets first'); + } else { + var template = this.templateDeletingDatasetsProgressBar(); + this.modal = Galaxy.modal; + this.modal.show({ + closing_events : true, + title : 'Deleting selected datasets', + body : template({}), + buttons : { + 'Close' : function() {Galaxy.modal.hide();} + } + }); + // init the control counters + this.options.chain_call_control.total_number = 0; + this.options.chain_call_control.failed_number = 0; + + var dataset_ids = []; + checkedValues.each(function(){ + if (this.parentElement.parentElement.id !== '') { + dataset_ids.push(this.parentElement.parentElement.id); + } + }); + // init the progress bar + this.progressStep = 100 / dataset_ids.length; + this.progress = 0; + + // prepare the dataset items to be added + var lddas_to_delete = []; + for (var i = dataset_ids.length - 1; i >= 0; i--) { + var dataset = new mod_library_model.Item({id:dataset_ids[i]}); + lddas_to_delete.push(dataset); + } + + this.options.chain_call_control.total_number = dataset_ids.length; + // call the recursive function to call ajax one after each other (request FIFO queue) + this.chainCallDeletingHdas(lddas_to_delete); + } + }, + + chainCallDeletingHdas: function(lddas_set){ + var self = this; + this.deleted_lddas = new mod_library_model.Folder(); + var popped_item = lddas_set.pop(); + if (typeof popped_item === "undefined") { + if (this.options.chain_call_control.failed_number === 0){ + mod_toastr.success('Selected datasets deleted'); + } else if (this.options.chain_call_control.failed_number === this.options.chain_call_control.total_number){ + mod_toastr.error('There was an error and no datasets were deleted.'); + } else if (this.options.chain_call_control.failed_number < this.options.chain_call_control.total_number){ + mod_toastr.warning('Some of the datasets could not be deleted'); + } + Galaxy.modal.hide(); + return this.deleted_lddas; + } + var promise = $.when(popped_item.destroy({undelete: false})); + + promise.done(function(dataset){ + // we are fine + self.$el.find('#' + popped_item.id).remove(); + self.updateProgress(); + Galaxy.libraries.folderListView.collection.add(dataset); + self.chainCallDeletingHdas(lddas_set); + }) + .fail(function(){ + // we have a problem + self.options.chain_call_control.failed_number += 1; + self.updateProgress(); + self.chainCallDeletingHdas(lddas_set); + }); + }, + templateToolBar: function(){ tmpl_array = []; @@ -500,6 +580,21 @@ return _.template(tmpl_array.join('')); }, + templateDeletingDatasetsProgressBar : function (){ + var tmpl_array = []; + + tmpl_array.push('<div class="import_text">'); + tmpl_array.push('</div>'); + tmpl_array.push('<div class="progress">'); + tmpl_array.push(' <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">'); + tmpl_array.push(' <span class="completion_span">0% Complete</span>'); + tmpl_array.push(' </div>'); + tmpl_array.push('</div>'); + tmpl_array.push(''); + + return _.template(tmpl_array.join('')); + }, + templateAddFilesInModal : function (){ var tmpl_array = []; diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/mvc/library/library-librarylist-view.js --- a/static/scripts/mvc/library/library-librarylist-view.js +++ b/static/scripts/mvc/library/library-librarylist-view.js @@ -78,11 +78,12 @@ } // initialize the library tooltips $("#center [data-toggle]").tooltip(); - // modification of upper DOM element to show scrollbars due to the #center element inheritance + // modification of upper DOM element to show scrollbars due + // to the #center element inheritance $("#center").css('overflow','auto'); }, - /** Render all given models as rows in the library list */ + /** Renders all given models as rows in the library list */ renderRows: function(libraries_to_render){ for (var i = 0; i < libraries_to_render.length; i++) { var library = libraries_to_render[i]; @@ -91,14 +92,28 @@ cachedView.delegateEvents(); this.$el.find('#library_list_body').append(cachedView.el); } else { - var rowView = new mod_library_libraryrow_view.LibraryRowView(library); - this.$el.find('#library_list_body').append(rowView.el); - // save new rowView to cache - this.rowViews[library.get('id')] = rowView; + this.renderOne({library:library}) } } }, + /** + * Creates a view for the given model and adds it to the libraries view. + * @param {Library} model of the view that will be rendered + */ + renderOne: function(options){ + var library = options.library; + var rowView = new mod_library_libraryrow_view.LibraryRowView(library); + // we want to prepend new item + if (options.prepend){ + this.$el.find('#library_list_body').prepend(rowView.el); + } else { + this.$el.find('#library_list_body').append(rowView.el); + } + // save new rowView to cache + this.rowViews[library.get('id')] = rowView; + }, + /** Table heading was clicked, update sorting preferences and re-render */ sort_clicked : function(){ if (Galaxy.libraries.preferences.get('sort_order') === 'asc'){ @@ -148,20 +163,7 @@ return _.template(tmpl_array.join('')); }, - - templateNewLibraryInModal: 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(''); - }, redirectToHome: function(){ window.location = '../'; @@ -170,69 +172,6 @@ window.location = '/user/login'; }, - // show/hide create library modal - show_library_modal : function (event){ - event.preventDefault(); - event.stopPropagation(); - - // create modal - var self = this; - this.modal = Galaxy.modal; - this.modal.show({ - closing_events : true, - title : 'Create New Library', - body : this.templateNewLibraryInModal(), - buttons : { - 'Create' : function() {self.create_new_library_event();}, - 'Close' : function() {self.modal.hide();} - } - }); - }, - - // create the new library from modal - create_new_library_event: function(){ - var libraryDetails = this.serialize_new_library(); - if (this.validate_new_library(libraryDetails)){ - var library = new mod_library_model.Library(); - var self = this; - library.save(libraryDetails, { - success: function (library) { - self.collection.add(library); - self.modal.hide(); - self.clear_library_modal(); - self.render(); - mod_toastr.success('Library created'); - }, - error: function(){ - mod_toastr.error('An error occured :('); - } - }); - } else { - mod_toastr.error('Library\'s name is missing'); - } - return false; - }, - - // clear the library modal once saved - clear_library_modal : function(){ - $("input[name='Name']").val(''); - $("input[name='Description']").val(''); - $("input[name='Synopsis']").val(''); - }, - - // serialize data from the new library form - serialize_new_library : function(){ - return { - name: $("input[name='Name']").val(), - description: $("input[name='Description']").val(), - synopsis: $("input[name='Synopsis']").val() - }; - }, - - // validate new library info - validate_new_library: function(libraryDetails){ - return libraryDetails.name !== ''; - } }); return { diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/mvc/library/library-libraryrow-view.js --- a/static/scripts/mvc/library/library-libraryrow-view.js +++ b/static/scripts/mvc/library/library-libraryrow-view.js @@ -222,7 +222,7 @@ tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">'); tmpl_array.push(' <% if(!edit_mode) { %>'); tmpl_array.push(' <% if(library.get("deleted")) { %>'); - tmpl_array.push(' <td style="color:grey;"><%- library.get("name") %></td>'); + tmpl_array.push(' <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>'); tmpl_array.push(' <% } else { %>'); tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>'); tmpl_array.push(' <% } %>'); @@ -234,18 +234,16 @@ tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>'); tmpl_array.push(' <% } %>'); tmpl_array.push(' <td class="right-center">'); - tmpl_array.push(' <% if(library.get("deleted")) { %>'); - tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span>'); - tmpl_array.push(' <% } else if(library.get("public")) { %>'); + tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>'); tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>'); tmpl_array.push(' <% }%>'); // tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Upload to library" class="primary-button btn-xs upload_library_btn" type="button" style="<% if(button_config.upload_library_btn === false) { print("display:none;") } %>"><span class="fa fa-upload"></span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>'); - tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>'); tmpl_array.push(' </td>'); tmpl_array.push(' </tr>'); diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/mvc/library/library-librarytoolbar-view.js @@ -1,5 +1,8 @@ -define([], -function() { +define([ + "libs/toastr", + "mvc/library/library-model"], +function(mod_toastr, + mod_library_model) { /** * This view represents the top part of the library page. * It contains the tool bar with buttons. @@ -8,7 +11,7 @@ el: '#center', events: { - 'click #create_new_library_btn' : 'delegate_modal', + 'click #create_new_library_btn' : 'show_library_modal', 'click #include_deleted_chk' : 'check_include_deleted' }, @@ -32,9 +35,66 @@ } }, - delegate_modal: function(event){ - // TODO probably should refactor to have this functionality in this view, not in the library list view - Galaxy.libraries.libraryListView.show_library_modal(event); + show_library_modal : function (event){ + event.preventDefault(); + event.stopPropagation(); + + // create modal + var self = this; + this.modal = Galaxy.modal; + this.modal.show({ + closing_events : true, + title : 'Create New Library', + body : this.templateNewLibraryInModal(), + buttons : { + 'Create' : function() {self.create_new_library_event();}, + 'Close' : function() {self.modal.hide();} + } + }); + }, + + create_new_library_event: function(){ + var libraryDetails = this.serialize_new_library(); + if (this.validate_new_library(libraryDetails)){ + var library = new mod_library_model.Library(); + var self = this; + library.save(libraryDetails, { + success: function (library) { + Galaxy.libraries.libraryListView.collection.add(library); + self.modal.hide(); + self.clear_library_modal(); + Galaxy.libraries.libraryListView.render(); + mod_toastr.success('Library created'); + }, + error: function(){ + mod_toastr.error('An error occured :('); + } + }); + } else { + mod_toastr.error('Library\'s name is missing'); + } + return false; + }, + + // clear the library modal once saved + clear_library_modal : function(){ + $("input[name='Name']").val(''); + $("input[name='Description']").val(''); + $("input[name='Synopsis']").val(''); + }, + + // serialize data from the new library form + serialize_new_library : function(){ + return { + name: $("input[name='Name']").val(), + description: $("input[name='Description']").val(), + synopsis: $("input[name='Synopsis']").val() + }; + }, + + // validate new library info + validate_new_library: function(libraryDetails){ + return libraryDetails.name !== ''; }, // include or exclude deleted libraries from the view @@ -68,6 +128,21 @@ tmpl_array.push('</div>'); return _.template(tmpl_array.join('')); + }, + + + templateNewLibraryInModal: 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(''); } }); diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/packed/galaxy.library.js --- a/static/scripts/packed/galaxy.library.js +++ b/static/scripts/packed/galaxy.library.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#center").find(":checked").length===0){g.info("You have to select some datasets to download")}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}Galaxy.libraries.folderToolbarView=new i.FolderToolbarView({id:m});Galaxy.libraries.folderListView=new a.FolderListView({id:m})});this.library_router.on("route:download",function(m,n){if($("#folder_list_body").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/packed/mvc/library/library-folderlist-view.js --- a/static/scripts/packed/mvc/library/library-folderlist-view.js +++ b/static/scripts/packed/mvc/library/library-folderlist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},initialize:function(g){this.options=_.defaults(this.options||{},g);this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},render:function(g){this.options=_.defaults(this.options,g);var i=this.templateFolder();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));var h=this.folderContainer.attributes.metadata;h.contains_file=this.options.contains_file;Galaxy.libraries.folderToolbarView.configureElements(h);$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness()},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)})},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}var g=new a.FolderRowView(h);this.$el.find("#first_folder_item").after(g.el);this.checkEmptiness()},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){var g=this.templateEmptyFolder();this.$el.find("#folder_list_body").append(g())}else{this.$el.find("#empty_folder_message").remove()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");return _.template(g.join(""))},templateEmptyFolder:function(){var g=[];g.push('<tr id="empty_folder_message">');g.push('<td colspan="6" style="text-align:center">');g.push("This folder is either empty or you do not have proper access permissions to see the contents.");g.push("</td>");g.push("</tr>");return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-folderrow-view"],function(c,e,f,d,a){var b=Backbone.View.extend({el:"#folder_items_element",defaults:{include_deleted:false},progress:0,progressStep:1,modal:null,folderContainer:null,sort:"asc",events:{"click #select-all-checkboxes":"selectAll","click .dataset_row":"selectClickedRow","click .sort-folder-link":"sort_clicked"},initialize:function(g){this.options=_.defaults(this.options||{},g);this.collection=new d.Folder();this.listenTo(this.collection,"add",this.renderOne);this.fetchFolder()},fetchFolder:function(g){var g=g||{};this.options.include_deleted=g.include_deleted;var h=this;this.folderContainer=new d.FolderContainer({id:this.options.id});this.folderContainer.url=this.folderContainer.attributes.urlRoot+this.options.id+"/contents";if(this.options.include_deleted){this.folderContainer.url=this.folderContainer.url+"?include_deleted=true"}this.folderContainer.fetch({success:function(i){h.folder_container=i;h.render();h.addAll(i.get("folder").models)},error:function(j,i){if(typeof i.responseJSON!=="undefined"){f.error(i.responseJSON.err_msg)}else{f.error("An error ocurred :(")}}})},render:function(g){this.options=_.defaults(this.options,g);var i=this.templateFolder();var j=this.folderContainer.attributes.metadata.full_path;var k;if(j.length===1){k=0}else{k=j[j.length-2][0]}this.$el.html(i({path:this.folderContainer.attributes.metadata.full_path,id:this.options.id,upper_folder_id:k,order:this.sort}));var h=this.folderContainer.attributes.metadata;h.contains_file=this.options.contains_file;Galaxy.libraries.folderToolbarView.configureElements(h);$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},addAll:function(g){_.each(g.reverse(),function(h){Galaxy.libraries.folderListView.collection.add(h)});$("#center [data-toggle]").tooltip();this.checkEmptiness();$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},renderAll:function(){var g=this;_.each(this.collection.models.reverse(),function(h){g.renderOne(h)});$(".deleted_dataset").hover(function(){$(this).find(".show_on_hover").show()},function(){$(this).find(".show_on_hover").hide()})},renderOne:function(h){if(h.get("data_type")!=="folder"){this.options.contains_file=true;h.set("readable_size",this.size_to_string(h.get("file_size")))}var g=new a.FolderRowView(h);this.$el.find("#first_folder_item").after(g.el)},checkEmptiness:function(){if((this.$el.find(".dataset_row").length===0)&&(this.$el.find(".folder_row").length===0)){this.$el.find(".empty-folder-message").show()}else{this.$el.find(".empty-folder-message").hide()}},sort_clicked:function(g){g.preventDefault();if(this.sort==="asc"){this.sortFolder("name","desc");this.sort="desc"}else{this.sortFolder("name","asc");this.sort="asc"}this.render();this.renderAll()},sortFolder:function(h,g){if(h==="name"){if(g==="asc"){return this.collection.sortByNameAsc()}else{if(g==="desc"){return this.collection.sortByNameDesc()}}}},size_to_string:function(g){var h="";if(g>=100000000000){g=g/100000000000;h="TB"}else{if(g>=100000000){g=g/100000000;h="GB"}else{if(g>=100000){g=g/100000;h="MB"}else{if(g>=100){g=g/100;h="KB"}else{g=g*10;h="b"}}}}return(Math.round(g)/10)+h},selectAll:function(h){var g=h.target.checked;that=this;$(":checkbox","#folder_list_body").each(function(){this.checked=g;$row=$(this.parentElement.parentElement);if(g){that.makeDarkRow($row)}else{that.makeWhiteRow($row)}})},selectClickedRow:function(h){var j="";var g;var i;if(h.target.localName==="input"){j=h.target;g=$(h.target.parentElement.parentElement);i="input"}else{if(h.target.localName==="td"){j=$("#"+h.target.parentElement.id).find(":checkbox")[0];g=$(h.target.parentElement);i="td"}}if(j.checked){if(i==="td"){j.checked="";this.makeWhiteRow(g)}else{if(i==="input"){this.makeDarkRow(g)}}}else{if(i==="td"){j.checked="selected";this.makeDarkRow(g)}else{if(i==="input"){this.makeWhiteRow(g)}}}},makeDarkRow:function(g){g.removeClass("light");g.find("a").removeClass("light");g.addClass("dark");g.find("a").addClass("dark");g.find("span").removeClass("fa-file-o");g.find("span").addClass("fa-file")},makeWhiteRow:function(g){g.removeClass("dark");g.find("a").removeClass("dark");g.addClass("light");g.find("a").addClass("light");g.find("span").addClass("fa-file-o");g.find("span").removeClass("fa-file")},templateFolder:function(){var g=[];g.push('<ol class="breadcrumb">');g.push(' <li><a title="Return to the list of libraries" href="#">Libraries</a></li>');g.push(" <% _.each(path, function(path_item) { %>");g.push(" <% if (path_item[0] != id) { %>");g.push(' <li><a title="Return to this folder" href="#/folders/<%- path_item[0] %>"><%- path_item[1] %></a></li> ');g.push("<% } else { %>");g.push(' <li class="active"><span title="You are in this folder"><%- path_item[1] %></span></li>');g.push(" <% } %>");g.push(" <% }); %>");g.push("</ol>");g.push('<table id="folder_table" class="grid table table-condensed">');g.push(" <thead>");g.push(' <th class="button_heading"></th>');g.push(' <th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>');g.push(' <th style="width:30%;"><a class="sort-folder-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');g.push(" <th>data type</th>");g.push(" <th>size</th>");g.push(" <th>time updated (UTC)</th>");g.push(' <th style="width:15%;"></th> ');g.push(" </thead>");g.push(' <tbody id="folder_list_body">');g.push(' <tr id="first_folder_item">');g.push(' <td><a href="#<% if (upper_folder_id !== 0){ print("folders/" + upper_folder_id)} %>" title="Go to parent folder" class="btn_open_folder btn btn-default btn-xs">..<a></td>');g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" <td></td>");g.push(" </tr>");g.push(" </tbody>");g.push("</table>");g.push('<div class="empty-folder-message" style="display:none;">This folder is either empty or you do not have proper access permissions to see the contents.</div>');return _.template(g.join(""))}});return{FolderListView:b}}); \ No newline at end of file diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/packed/mvc/library/library-folderrow-view.js --- a/static/scripts/packed/mvc/library/library-folderrow-view.js +++ b/static/scripts/packed/mvc/library/library-folderrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .library-dataset":"showDatasetDetails"},options:{type:null},initialize:function(f){this.render(f)},render:function(f){var g=null;if(f.get("type")==="folder"){this.options.type="folder";g=this.templateRowFolder()}else{this.options.type="file";if(f.get("deleted")){g=this.templateRowDeletedFile()}else{g=this.templateRowFile()}}this.setElement(g({content_item:f}));this.$el.show();return this},showDatasetDetails:function(i){i.preventDefault();var j=this.id;var h=new c.Item();var g=new c.GalaxyHistories();h.id=j;var f=this;h.fetch({success:function(k){g.fetch({success:function(l){f.renderModalAfterFetch(k,l)},error:function(){e.error("An error occured during fetching histories:(");f.renderModalAfterFetch(k)}})},error:function(){e.error("An error occured during loading dataset details :(")}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}}});$(".peek").html(k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};this.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var h=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=h;var f=$("#id_row").attr("data-id");var i=new c.HistoryItem();var g=this;i.url=i.urlRoot+h+"/contents";i.save({content:f,source:"library"},{success:function(){e.success("Dataset imported");g.modal.enableButton("Import");g.modal.enableButton("Download")},error:function(){e.error("An error occured! Dataset not imported. Please try again.");g.modal.enableButton("Import");g.modal.enableButton("Download")}})},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>');tmpl_array.push(" <span>(empty folder)</span>");tmpl_array.push(" <% } %>");tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span></td>');tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")}});return{FolderRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({lastSelectedHistory:"",events:{"click .library-dataset":"showDatasetDetails","click .undelete_dataset_btn":"undelete_dataset"},options:{type:null},initialize:function(f){this.render(f)},render:function(f){var g=null;if(f.get("type")==="folder"){this.options.type="folder";g=this.templateRowFolder()}else{this.options.type="file";if(f.get("deleted")){g=this.templateRowDeletedFile()}else{g=this.templateRowFile()}}this.setElement(g({content_item:f}));this.$el.show();return this},showDatasetDetails:function(i){i.preventDefault();var j=this.id;var h=new c.Item();var g=new c.GalaxyHistories();h.id=j;var f=this;h.fetch({success:function(k){g.fetch({success:function(l){f.renderModalAfterFetch(k,l)},error:function(m,l){if(typeof l.responseJSON!=="undefined"){e.error(l.responseJSON.err_msg)}else{e.error("An error occured during fetching histories:(")}f.renderModalAfterFetch(k)}})},error:function(l,k){if(typeof k.responseJSON!=="undefined"){e.error(k.responseJSON.err_msg)}else{e.error("An error occured during loading dataset details :(")}}})},renderModalAfterFetch:function(k,h){var i=this.size_to_string(k.get("file_size"));var j=_.template(this.templateDatasetModal(),{item:k,size:i});var g=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Dataset Details",body:j,buttons:{Import:function(){g.importCurrentIntoHistory()},Download:function(){g.downloadCurrent()},Close:function(){g.modal.hide()}}});$(".peek").html(k.get("peek"));if(typeof history.models!==undefined){var f=_.template(this.templateHistorySelectInModal(),{histories:h.models});$(this.modal.elMain).find(".buttons").prepend(f);if(g.lastSelectedHistory.length>0){$(this.modal.elMain).find("#dataset_import_single").val(g.lastSelectedHistory)}}},size_to_string:function(f){var g="";if(f>=100000000000){f=f/100000000000;g="TB"}else{if(f>=100000000){f=f/100000000;g="GB"}else{if(f>=100000){f=f/100000;g="MB"}else{if(f>=100){f=f/100;g="KB"}else{f=f*10;g="b"}}}}return(Math.round(f)/10)+g},downloadCurrent:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var f=[];f.push($("#id_row").attr("data-id"));var g="/api/libraries/datasets/download/uncompressed";var h={ldda_ids:f};this.processDownload(g,h);this.modal.enableButton("Import");this.modal.enableButton("Download")},processDownload:function(g,h,i){if(g&&h){h=typeof h=="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},importCurrentIntoHistory:function(){this.modal.disableButton("Import");this.modal.disableButton("Download");var h=$(this.modal.elMain).find("select[name=dataset_import_single] option:selected").val();this.lastSelectedHistory=h;var f=$("#id_row").attr("data-id");var i=new c.HistoryItem();var g=this;i.url=i.urlRoot+h+"/contents";i.save({content:f,source:"library"},{success:function(){e.success("Dataset imported");g.modal.enableButton("Import");g.modal.enableButton("Download")},error:function(){e.error("An error occured! Dataset not imported. Please try again.");g.modal.enableButton("Import");g.modal.enableButton("Download")}})},undelete_dataset:function(f){alert("undelete dataset")},templateRowFolder:function(){tmpl_array=[];tmpl_array.push('<tr class="folder_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Folder" class="fa fa-folder-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(" <td></td>");tmpl_array.push(" <td>");tmpl_array.push(' <a href="#folders/<%- content_item.id %>"><%- content_item.get("name") %></a>');tmpl_array.push(' <% if (content_item.get("item_count") === 0) { %>');tmpl_array.push(" <span>(empty folder)</span>");tmpl_array.push(" <% } %>");tmpl_array.push(" </td>");tmpl_array.push(" <td>folder</td>");tmpl_array.push(" <td></td>");tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowFile:function(){tmpl_array=[];tmpl_array.push('<tr class="dataset_row light" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td style="text-align: center; "><input style="margin: 0;" type="checkbox"></td>');tmpl_array.push(' <td><a href="#" class="library-dataset"><%- content_item.get("name") %><a></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(" <td></td>");tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateRowDeletedFile:function(){tmpl_array=[];tmpl_array.push('<tr class="active deleted_dataset" id="<%- content_item.id %>">');tmpl_array.push(" <td>");tmpl_array.push(' <span title="Dataset" class="fa fa-file-o"></span>');tmpl_array.push(" </td>");tmpl_array.push(' <td><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"></span></td>');tmpl_array.push(' <td style="color:grey;"><%- content_item.get("name") %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("data_type")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("readable_size")) %></td>');tmpl_array.push(' <td><%= _.escape(content_item.get("update_time")) %></td>');tmpl_array.push(' <td class="right-center"><button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn show_on_hover" type="button" style="display:none;"><span class="fa fa-unlock"> Undelete</span></button></td>');tmpl_array.push("</tr>");return _.template(tmpl_array.join(""))},templateDatasetModal:function(){var f=[];f.push('<div class="modal_table">');f.push(' <table class="grid table table-striped table-condensed">');f.push(" <tr>");f.push(' <th scope="row" id="id_row" data-id="<%= _.escape(item.get("ldda_id")) %>">Name</th>');f.push(' <td><%= _.escape(item.get("name")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Data type</th>');f.push(' <td><%= _.escape(item.get("data_type")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Genome build</th>');f.push(' <td><%= _.escape(item.get("genome_build")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Size</th>');f.push(" <td><%= _.escape(size) %></td>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Date uploaded (UTC)</th>');f.push(' <td><%= _.escape(item.get("date_uploaded")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Uploaded by</th>');f.push(' <td><%= _.escape(item.get("uploaded_by")) %></td>');f.push(" </tr>");f.push(' <tr scope="row">');f.push(' <th scope="row">Data Lines</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_data_lines")) %></td>');f.push(" </tr>");f.push(' <th scope="row">Comment Lines</th>');f.push(' <% if (item.get("metadata_comment_lines") === "") { %>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_comment_lines")) %></td>');f.push(" <% } else { %>");f.push(' <td scope="row">unknown</td>');f.push(" <% } %>");f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Number of Columns</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_columns")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Column Types</th>');f.push(' <td scope="row"><%= _.escape(item.get("metadata_column_types")) %></td>');f.push(" </tr>");f.push(" <tr>");f.push(' <th scope="row">Miscellaneous information</th>');f.push(' <td scope="row"><%= _.escape(item.get("misc_blurb")) %></td>');f.push(" </tr>");f.push(" </table>");f.push(' <pre class="peek">');f.push(" </pre>");f.push("</div>");return f.join("")},templateHistorySelectInModal:function(){var f=[];f.push('<span id="history_modal_combo" style="width:100%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_single" name="dataset_import_single" style="width:40%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return f.join("")}});return{FolderRowView:a}}); \ No newline at end of file diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"check_include_deleted"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g=false;if(Galaxy.currUser){g=Galaxy.currUser.isAdmin()}this.$el.html(h({id:this.options.id,admin_user:g}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$("#toolbtn_create_folder").show();$(".toolbtn_add_files").show()}if(this.options.contains_file===true){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var j=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=j;var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(n({history_name:m}));var k=100/o.length;this.initProgress(k);var f=[];for(var g=o.length-1;g>=0;g--){var h=o[g];var l=new c.HistoryItem();l.url=l.urlRoot+j+"/contents";l.content=h;l.source="library";f.push(l)}this.options.chain_call_control.total_number=f.length;this.chainCall(f,m)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history")}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},check_include_deleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.collection=new c.Folder();Galaxy.libraries.folderListView.listenTo(Galaxy.libraries.folderListView.collection,"add",Galaxy.libraries.folderListView.renderOne);Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.collection=new c.Folder();Galaxy.libraries.folderListView.listenTo(Galaxy.libraries.folderListView.collection,"add",Galaxy.libraries.folderListView.renderOne);Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<div id="library_folder_toolbar">');tmpl_array.push('<span data-toggle="tooltip" data-placement="top" title="Include deleted datasets"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push('<div class="btn-group">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("</div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; " type="button"><span class="fa fa-book"></span> to history</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button" style="margin-left: 0.5em; " type="button"><span class="fa fa-trash-o"></span> delete</button>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_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("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click .toolbtn_add_files":"addFilesToFolderModal","click #include_deleted_datasets_chk":"checkIncludeDeleted","click #toolbtn_bulk_delete":"deleteSelectedDatasets"},defaults:{can_add_library_item:false,contains_file:false,chain_call_control:{total_number:0,failed_number:0}},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g=false;if(Galaxy.currUser){g=Galaxy.currUser.isAdmin()}this.$el.html(h({id:this.options.id,admin_user:g}))},configureElements:function(f){this.options=_.extend(this.options,f);if(this.options.can_add_library_item===true){$("#toolbtn_create_folder").show();$(".toolbtn_add_files").show()}if(this.options.contains_file===true){$("#toolbtn_bulk_import").show();$("#toolbtn_dl").show()}this.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var g=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];g.url=g.urlRoot+"/"+current_folder_id;g.save(f,{success:function(h){Galaxy.modal.hide();e.success("Folder created");h.set({type:"folder"});Galaxy.libraries.folderListView.collection.add(h)},error:function(i,h){Galaxy.modal.hide();if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("input[name='Name']").val(),description:$("input[name='Description']").val()}},validate_new_folder:function(f){return f.name!==""},modalBulkImport:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(i,h){if(typeof h.responseJSON!=="undefined"){e.error(h.responseJSON.err_msg)}else{e.error("An error ocurred :(")}}})},importAllIntoHistory:function(){this.modal.disableButton("Import");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var j=$("select[name=dataset_import_bulk] option:selected").val();this.options.last_used_history_id=j;var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateImportIntoHistoryProgressBar();this.modal.$el.find(".modal-body").html(n({history_name:m}));var k=100/o.length;this.initProgress(k);var f=[];for(var g=o.length-1;g>=0;g--){var h=o[g];var l=new c.HistoryItem();l.url=l.urlRoot+j+"/contents";l.content=h;l.source="library";f.push(l)}this.options.chain_call_control.total_number=f.length;this.chainCall(f,m)},chainCall:function(g,j){var f=this;var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets imported into history")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were imported into history.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be imported into history")}}}Galaxy.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source}));i.done(function(){f.updateProgress();f.chainCall(g,j)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCall(g,j)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".progress-bar-import").width(Math.round(this.progress)+"%");txt_representation=Math.round(this.progress)+"% Complete";$(".completion_span").text(txt_representation)},download:function(f,j){var h=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){h.push(this.parentElement.parentElement.id)}});var g="/api/libraries/datasets/download/"+j;var i={ldda_ids:h};this.processDownload(g,i,"get")},processDownload:function(g,h,i){if(g&&h){h=typeof h==="string"?h:$.param(h);var f="";$.each(h.split("&"),function(){var j=this.split("=");f+='<input type="hidden" name="'+j[0]+'" value="'+j[1]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var g=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:g({histories:f.histories.models}),buttons:{Add:function(){f.addAllDatasetsFromHistory()},Close:function(){Galaxy.modal.hide()}}});if(f.histories.models.length>0){f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})}else{e.error("An error ocurred :(")}})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("An error ocurred :(")}})},addAllDatasetsFromHistory:function(){this.modal.disableButton("Add");this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var f=[];this.modal.$el.find("#selected_history_content").find(":checked").each(function(){var i=$(this.parentElement).data("id");if(i){f.push(i)}});var l=this.options.folder_name;var k=this.templateAddingDatasetsProgressBar();this.modal.$el.find(".modal-body").html(k({folder_name:l}));this.progressStep=100/f.length;this.progress=0;var j=[];for(var h=f.length-1;h>=0;h--){history_dataset_id=f[h];var g=new c.Item();g.url="/api/folders/"+this.options.id+"/contents";g.set({from_hda_id:history_dataset_id});j.push(g)}this.options.chain_call_control.total_number=j.length;this.chainCallAddingHdas(j)},chainCallAddingHdas:function(g){var f=this;this.added_hdas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets from history added to the folder")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were added to the folder.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be added to the folder")}}}Galaxy.modal.hide();return this.added_hdas}var i=$.when(h.save({from_hda_id:h.get("from_hda_id")}));i.done(function(j){Galaxy.libraries.folderListView.collection.add(j);f.updateProgress();f.chainCallAddingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallAddingHdas(g)})},checkIncludeDeleted:function(f){if(f.target.checked){Galaxy.libraries.folderListView.collection=new c.Folder();Galaxy.libraries.folderListView.listenTo(Galaxy.libraries.folderListView.collection,"add",Galaxy.libraries.folderListView.renderOne);Galaxy.libraries.folderListView.fetchFolder({include_deleted:true})}else{Galaxy.libraries.folderListView.collection=new c.Folder();Galaxy.libraries.folderListView.listenTo(Galaxy.libraries.folderListView.collection,"add",Galaxy.libraries.folderListView.renderOne);Galaxy.libraries.folderListView.fetchFolder({include_deleted:false})}},deleteSelectedDatasets:function(){var f=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{var j=this.templateDeletingDatasetsProgressBar();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Deleting selected datasets",body:j({}),buttons:{Close:function(){Galaxy.modal.hide()}}});this.options.chain_call_control.total_number=0;this.options.chain_call_control.failed_number=0;var g=[];f.each(function(){if(this.parentElement.parentElement.id!==""){g.push(this.parentElement.parentElement.id)}});this.progressStep=100/g.length;this.progress=0;var l=[];for(var h=g.length-1;h>=0;h--){var k=new c.Item({id:g[h]});l.push(k)}this.options.chain_call_control.total_number=g.length;this.chainCallDeletingHdas(l)}},chainCallDeletingHdas:function(g){var f=this;this.deleted_lddas=new c.Folder();var h=g.pop();if(typeof h==="undefined"){if(this.options.chain_call_control.failed_number===0){e.success("Selected datasets deleted")}else{if(this.options.chain_call_control.failed_number===this.options.chain_call_control.total_number){e.error("There was an error and no datasets were deleted.")}else{if(this.options.chain_call_control.failed_number<this.options.chain_call_control.total_number){e.warning("Some of the datasets could not be deleted")}}}Galaxy.modal.hide();return this.deleted_lddas}var i=$.when(h.destroy({undelete:false}));i.done(function(j){f.$el.find("#"+h.id).remove();f.updateProgress();Galaxy.libraries.folderListView.collection.add(j);f.chainCallDeletingHdas(g)}).fail(function(){f.options.chain_call_control.failed_number+=1;f.updateProgress();f.chainCallDeletingHdas(g)})},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push('<h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push('<div id="library_folder_toolbar">');tmpl_array.push('<span data-toggle="tooltip" data-placement="top" title="Include deleted datasets"><input id="include_deleted_datasets_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push('<div class="btn-group">');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="btn btn-default primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-folder"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="btn btn-default toolbtn_add_files primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');tmpl_array.push("</div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Import selected datasets into history" id="toolbtn_bulk_import" class="primary-button" style="margin-left: 0.5em; " type="button"><span class="fa fa-book"></span> to history</button>');tmpl_array.push(' <div id="toolbtn_dl" class="btn-group" style="margin-left: 0.5em; ">');tmpl_array.push(' <button title="Download selected datasets as archive" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">');tmpl_array.push(' <span class="fa fa-download"></span> download <span class="caret"></span>');tmpl_array.push(" </button>");tmpl_array.push(' <ul class="dropdown-menu" role="menu">');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tgz">.tar.gz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/tbz">.tar.bz</a></li>');tmpl_array.push(' <li id="download_archive"><a href="#/folders/<%= id %>/download/zip">.zip</a></li>');tmpl_array.push(" </ul>");tmpl_array.push(" </div>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Mark selected datasets deleted" id="toolbtn_bulk_delete" class="primary-button" style="margin-left: 0.5em; " type="button"><span class="fa fa-trash-o"></span> delete</button>');tmpl_array.push(" </div>");tmpl_array.push(' <div id="folder_items_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewFolderInModal:function(){tmpl_array=[];tmpl_array.push('<div id="new_folder_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("</form>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateBulkImportInModal:function(){var f=[];f.push('<span id="history_modal_combo_bulk" style="width:90%; margin-left: 1em; margin-right: 1em; ">');f.push("Select history: ");f.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:50%; margin-bottom: 1em; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</span>");return _.template(f.join(""))},templateImportIntoHistoryProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Importing selected datasets to history <b><%= _.escape(history_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("Adding selected datasets from history to library folder <b><%= _.escape(folder_name) %></b>");f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-import" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateDeletingDatasetsProgressBar:function(){var f=[];f.push('<div class="import_text">');f.push("</div>");f.push('<div class="progress">');f.push(' <div class="progress-bar progress-bar-delete" role="progressbar" aria-valuenow="0" aria-valuemin="0" aria-valuemax="100" style="width: 00%;">');f.push(' <span class="completion_span">0% Complete</span>');f.push(" </div>");f.push("</div>");f.push("");return _.template(f.join(""))},templateAddFilesInModal:function(){var f=[];f.push('<div id="add_files_modal">');f.push('<div id="history_modal_combo_bulk">');f.push("Select history: ");f.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> ');f.push(" <% _.each(histories, function(history) { %>");f.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>');f.push(" <% }); %>");f.push("</select>");f.push("</div>");f.push('<div id="selected_history_content">');f.push("</div>");f.push("</div>");return _.template(f.join(""))},templateHistoryContents:function(){var f=[];f.push("Choose the datasets to import:");f.push("<ul>");f.push(" <% _.each(history_contents, function(history_item) { %>");f.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">');f.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>');f.push(" </li>");f.push(" <% }); %>");f.push("</ul>");return _.template(f.join(""))}});return{FolderToolbarView:a}}); \ No newline at end of file diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/packed/mvc/library/library-librarylist-view.js --- a/static/scripts/packed/mvc/library/library-librarylist-view.js +++ b/static/scripts/packed/mvc/library/library-librarylist-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){h.render()},error:function(){e.error("An error occured. Please try again.")}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(m){for(var l=0;l<m.length;l++){var k=m[l];var j=_.findWhere(this.rowViews,{id:k.get("id")});if(j!==undefined&&this instanceof Backbone.View){j.delegateEvents();this.$el.find("#library_list_body").append(j.el)}else{var h=new a.LibraryRowView(k);this.$el.find("#library_list_body").append(h.el);this.rowViews[k.get("id")]=h}}},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal: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("")},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},show_library_modal:function(i){i.preventDefault();i.stopPropagation();var h=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){h.create_new_library_event()},Close:function(){h.modal.hide()}}})},create_new_library_event:function(){var j=this.serialize_new_library();if(this.validate_new_library(j)){var i=new c.Library();var h=this;i.save(j,{success:function(k){h.collection.add(k);h.modal.hide();h.clear_library_modal();h.render();e.success("Library created")},error:function(){e.error("An error occured :(")}})}else{e.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:$("input[name='Synopsis']").val()}},validate_new_library:function(h){return h.name!==""}});return{LibraryListView:f}}); \ No newline at end of file +define(["galaxy.masthead","mvc/base-mvc","utils/utils","libs/toastr","mvc/library/library-model","mvc/library/library-libraryrow-view"],function(b,g,d,e,c,a){var f=Backbone.View.extend({el:"#libraries_element",events:{"click .sort-libraries-link":"sort_clicked"},modal:null,collection:null,rowViews:{},initialize:function(i){this.options=_.defaults(this.options||{},i);var h=this;this.rowViews={};this.collection=new c.Libraries();this.collection.fetch({success:function(){h.render()},error:function(){e.error("An error occured. Please try again.")}})},render:function(i){var j=this.templateLibraryList();var k=null;var h=Galaxy.libraries.preferences.get("with_deleted");var l=null;if(typeof i!=="undefined"){h=typeof i.with_deleted!=="undefined"?i.with_deleted:false;l=typeof i.models!=="undefined"?i.models:null}if(this.collection!==null&&l===null){this.sortLibraries();if(h){k=this.collection.models}else{k=this.collection.where({deleted:false})}}else{if(l!==null){k=l}else{k=[]}}this.$el.html(j({length:k.length,order:Galaxy.libraries.preferences.get("sort_order")}));if(k.length>0){this.renderRows(k)}$("#center [data-toggle]").tooltip();$("#center").css("overflow","auto")},renderRows:function(l){for(var k=0;k<l.length;k++){var j=l[k];var h=_.findWhere(this.rowViews,{id:j.get("id")});if(h!==undefined&&this instanceof Backbone.View){h.delegateEvents();this.$el.find("#library_list_body").append(h.el)}else{this.renderOne({library:j})}}},renderOne:function(j){var i=j.library;var h=new a.LibraryRowView(i);if(j.prepend){this.$el.find("#library_list_body").prepend(h.el)}else{this.$el.find("#library_list_body").append(h.el)}this.rowViews[i.get("id")]=h},sort_clicked:function(){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){Galaxy.libraries.preferences.set({sort_order:"desc"})}else{Galaxy.libraries.preferences.set({sort_order:"asc"})}this.render()},sortLibraries:function(){if(Galaxy.libraries.preferences.get("sort_by")==="name"){if(Galaxy.libraries.preferences.get("sort_order")==="asc"){this.collection.sortByNameAsc()}else{if(Galaxy.libraries.preferences.get("sort_order")==="desc"){this.collection.sortByNameDesc()}}}},templateLibraryList:function(){tmpl_array=[];tmpl_array.push('<div class="library_container table-responsive">');tmpl_array.push("<% if(length === 0) { %>");tmpl_array.push('<div>There are no libraries visible to you. If you expected some to show up please consult the <a href="https://wiki.galaxyproject.org/Admin/DataLibraries/LibrarySecurity">library security wikipage</a>.</div>');tmpl_array.push("<% } else{ %>");tmpl_array.push('<table class="grid table table-condensed">');tmpl_array.push(" <thead>");tmpl_array.push(' <th style="width:30%;"><a class="sort-libraries-link" title="Click to reverse order" href="#">name</a><span title="Sorted alphabetically" class="fa fa-sort-alpha-<%- order %>"></span></th>');tmpl_array.push(' <th style="width:22%;">description</th>');tmpl_array.push(' <th style="width:22%;">synopsis</th> ');tmpl_array.push(' <th style="width:26%;"></th> ');tmpl_array.push(" </thead>");tmpl_array.push(' <tbody id="library_list_body">');tmpl_array.push(" </tbody>");tmpl_array.push("</table>");tmpl_array.push("<% }%>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},redirectToHome:function(){window.location="../"},redirectToLogin:function(){window.location="/user/login"},});return{LibraryListView:f}}); \ No newline at end of file diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/packed/mvc/library/library-libraryrow-view.js --- a/static/scripts/packed/mvc/library/library-libraryrow-view.js +++ b/static/scripts/packed/mvc/library/library-libraryrow-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .upload_library_btn":"upload_to_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true}}this.element_visibility_config=vis_config},upload_to_library:function(){d.info("Coming soon. Stay tuned.")},permissions_on_library:function(){d.info("Coming soon. Stay tuned.")},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){d.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(){d.error("An error occured during updating the library :(")}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(){d.error("An error occured during deleting the library :(")}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(){d.error("An error occured while undeleting the library :(")}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <td style="color:grey;"><%- library.get("name") %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span>');tmpl_array.push(' <% } else if(library.get("public")) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify library" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete library" class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr"],function(b,c,d){var a=Backbone.View.extend({events:{"click .edit_library_btn":"edit_button_clicked","click .cancel_library_btn":"cancel_library_modification","click .save_library_btn":"save_library_modification","click .delete_library_btn":"delete_library","click .undelete_library_btn":"undelete_library","click .upload_library_btn":"upload_to_library","click .permission_library_btn":"permissions_on_library"},edit_mode:false,element_visibility_config:{upload_library_btn:false,edit_library_btn:false,permission_library_btn:false,save_library_btn:false,cancel_library_btn:false,delete_library_btn:false,undelete_library_btn:false},initialize:function(e){this.render(e)},render:function(f){if(typeof f==="undefined"){f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"))}this.prepareButtons(f);var e=this.templateRow();this.setElement(e({library:f,button_config:this.element_visibility_config,edit_mode:this.edit_mode}));this.$el.show();return this},repaint:function(e){$(".tooltip").hide();var f=this.$el;this.render(e);f.replaceWith(this.$el);this.$el.find("[data-toggle]").tooltip()},prepareButtons:function(e){vis_config=this.element_visibility_config;if(this.edit_mode===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.delete_library_btn=false;if(e.get("deleted")===true){vis_config.undelete_library_btn=true;vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false}else{if(e.get("deleted")===false){vis_config.save_library_btn=false;vis_config.cancel_library_btn=false;vis_config.undelete_library_btn=false;if(e.get("can_user_add")===true){vis_config.upload_library_btn=true}if(e.get("can_user_modify")===true){vis_config.edit_library_btn=true}if(e.get("can_user_manage")===true){vis_config.permission_library_btn=true}}}}else{if(this.edit_mode===true){vis_config.upload_library_btn=false;vis_config.edit_library_btn=false;vis_config.permission_library_btn=false;vis_config.save_library_btn=true;vis_config.cancel_library_btn=true;vis_config.delete_library_btn=true}}this.element_visibility_config=vis_config},upload_to_library:function(){d.info("Coming soon. Stay tuned.")},permissions_on_library:function(){d.info("Coming soon. Stay tuned.")},edit_button_clicked:function(){this.edit_mode=true;this.repaint()},cancel_library_modification:function(){d.info("Modifications canceled");this.edit_mode=false;this.repaint()},save_library_modification:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var g=false;var i=this.$el.find(".input_library_name").val();if(typeof i!=="undefined"&&i!==f.get("name")){if(i.length>2){f.set("name",i);g=true}else{d.warning("Library name has to be at least 3 characters long");return}}var h=this.$el.find(".input_library_description").val();if(typeof h!=="undefined"&&h!==f.get("description")){f.set("description",h);g=true}var j=this.$el.find(".input_library_synopsis").val();if(typeof j!=="undefined"&&j!==f.get("synopsis")){f.set("synopsis",j);g=true}if(g){var e=this;f.save(null,{patch:true,success:function(k){e.edit_mode=false;e.repaint(k);d.success("Changes to library saved")},error:function(){d.error("An error occured during updating the library :(")}})}else{this.edit_mode=false;this.repaint(f);d.info("Nothing has changed")}},delete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.destroy({success:function(g){g.set("deleted",true);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;if(Galaxy.libraries.preferences.get("with_deleted")===false){$(".tooltip").hide();e.$el.remove()}else{if(Galaxy.libraries.preferences.get("with_deleted")===true){e.repaint(g)}}d.success("Library has been marked deleted")},error:function(){d.error("An error occured during deleting the library :(")}})},undelete_library:function(){var f=Galaxy.libraries.libraryListView.collection.get(this.$el.data("id"));var e=this;f.url=f.urlRoot+f.id+"?undelete=true";f.destroy({success:function(g){g.set("deleted",false);Galaxy.libraries.libraryListView.collection.add(g);e.edit_mode=false;e.repaint(g);d.success("Library has been undeleted")},error:function(){d.error("An error occured while undeleting the library :(")}})},templateRow:function(){tmpl_array=[];tmpl_array.push(' <tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">');tmpl_array.push(" <% if(!edit_mode) { %>");tmpl_array.push(' <% if(library.get("deleted")) { %>');tmpl_array.push(' <td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"></span><%- library.get("name") %></td>');tmpl_array.push(" <% } else { %>");tmpl_array.push(' <td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td><%= _.escape(library.get("description")) %></td>');tmpl_array.push(' <td><%= _.escape(library.get("synopsis")) %></td>');tmpl_array.push(" <% } else if(edit_mode){ %>");tmpl_array.push(' <td><input type="text" class="form-control input_library_name" placeholder="name" value="<%- library.get("name") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_description" placeholder="description" value="<%- library.get("description") %>"></td>');tmpl_array.push(' <td><input type="text" class="form-control input_library_synopsis" placeholder="synopsis" value="<%- library.get("synopsis") %>"></td>');tmpl_array.push(" <% } %>");tmpl_array.push(' <td class="right-center">');tmpl_array.push(' <% if( (library.get("public")) && (library.get("deleted") === false) ) { %>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Public" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"></span>');tmpl_array.push(" <% }%>");tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify <%- library.get("name") %>" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Modify permissions" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Delete library (can be undeleted later)" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>');tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>');tmpl_array.push(" </td>");tmpl_array.push(" </tr>");return _.template(tmpl_array.join(""))}});return{LibraryRowView:a}}); \ No newline at end of file diff -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 -r 1e76ef6d002830675756f617b334e824abf894c4 static/scripts/packed/mvc/library/library-librarytoolbar-view.js --- a/static/scripts/packed/mvc/library/library-librarytoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-librarytoolbar-view.js @@ -1,1 +1,1 @@ -define([],function(){var a=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"delegate_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var d=this.templateToolBar();var c=false;var b=false;if(Galaxy.currUser){c=Galaxy.currUser.isAdmin();b=Galaxy.currUser.isAnonymous()}else{b=true}this.$el.html(d({admin_user:c,anon_user:b}));if(c){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},delegate_modal:function(b){Galaxy.libraries.libraryListView.show_library_modal(b)},check_include_deleted:function(b){if(b.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');tmpl_array.push(" </div>");tmpl_array.push(" <% } %>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))}});return{LibraryToolbarView:a}}); \ No newline at end of file +define(["libs/toastr","mvc/library/library-model"],function(b,a){var c=Backbone.View.extend({el:"#center",events:{"click #create_new_library_btn":"show_library_modal","click #include_deleted_chk":"check_include_deleted"},initialize:function(){this.render()},render:function(){var f=this.templateToolBar();var e=false;var d=false;if(Galaxy.currUser){e=Galaxy.currUser.isAdmin();d=Galaxy.currUser.isAnonymous()}else{d=true}this.$el.html(f({admin_user:e,anon_user:d}));if(e){this.$el.find("#include_deleted_chk")[0].checked=Galaxy.libraries.preferences.get("with_deleted")}},show_library_modal:function(e){e.preventDefault();e.stopPropagation();var d=this;this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Library",body:this.templateNewLibraryInModal(),buttons:{Create:function(){d.create_new_library_event()},Close:function(){d.modal.hide()}}})},create_new_library_event:function(){var f=this.serialize_new_library();if(this.validate_new_library(f)){var e=new a.Library();var d=this;e.save(f,{success:function(g){Galaxy.libraries.libraryListView.collection.add(g);d.modal.hide();d.clear_library_modal();Galaxy.libraries.libraryListView.render();b.success("Library created")},error:function(){b.error("An error occured :(")}})}else{b.error("Library's name is missing")}return false},clear_library_modal:function(){$("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(d){return d.name!==""},check_include_deleted:function(d){if(d.target.checked){Galaxy.libraries.preferences.set({with_deleted:true});Galaxy.libraries.libraryListView.render()}else{Galaxy.libraries.preferences.set({with_deleted:false});Galaxy.libraries.libraryListView.render()}},templateToolBar:function(){tmpl_array=[];tmpl_array.push('<div class="library_style_container">');tmpl_array.push(' <div id="toolbar_form" margin-top:0.5em; ">');tmpl_array.push(' <h3>Data Libraries Beta Test. This is work in progress. Please report problems & ideas via <a href="mailto:galaxy-bugs@bx.psu.edu?Subject=DataLibrariesBeta_Feedback" target="_blank">email</a> and <a href="https://trello.com/c/nwYQNFPK/56-data-library-ui-progressive-display-of-fol…" target="_blank">Trello</a>.</h3>');tmpl_array.push(" <% if(admin_user === true) { %>");tmpl_array.push(' <div id="library_toolbar">');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Include deleted libraries"><input id="include_deleted_chk" style="margin: 0;" type="checkbox"><span class="fa fa-trash-o fa-lg"></span></input></span>');tmpl_array.push(' <span data-toggle="tooltip" data-placement="top" title="Create New Library"><button id="create_new_library_btn" class="primary-button btn-xs" type="button"><span class="fa fa-plus"></span> New Library</button><span>');tmpl_array.push(" </div>");tmpl_array.push(" <% } %>");tmpl_array.push(" </div>");tmpl_array.push(' <div id="libraries_element">');tmpl_array.push(" </div>");tmpl_array.push("</div>");return _.template(tmpl_array.join(""))},templateNewLibraryInModal: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("")}});return{LibraryToolbarView:c}}); \ 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: davebgx: Fix admin and library feature functional tests. Improve handling of checkbox parameters and multi-select inputs in functional tests.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2ff24ef0746f/ Changeset: 2ff24ef0746f User: davebgx Date: 2014-04-29 21:39:43 Summary: Fix admin and library feature functional tests. Improve handling of checkbox parameters and multi-select inputs in functional tests. Affected #: 4 files diff -r b34eaa5eaa3176bc7498adcda597e7fa58996a2b -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1312,7 +1312,7 @@ # Submit for refresh tc.submit( '___refresh_grouping___' ) - def visit_url( self, url, params=None, checkbox_params=None, allowed_codes=[ 200 ] ): + def visit_url( self, url, params=None, doseq=False, allowed_codes=[ 200 ] ): if params is None: params = dict() parsed_url = urlparse( url ) @@ -1325,26 +1325,7 @@ key, value = query_parameter.split( '=' ) params[ key ] = value if params: - url += '?%s' % urllib.urlencode( params ) - checked_boxes = dict() - unchecked_boxes = dict() - if checkbox_params is not None: - for checkbox_field in checkbox_params: - if checkbox_field in checked_boxes or checkbox_field in unchecked_boxes: - continue - if asbool( checkbox_params[ checkbox_field ] ): - checked_boxes[ checkbox_field ] = True - else: - unchecked_boxes[ checkbox_field ] = False - # Any checkbox field that is found twice in the controller's incoming parameters is considered checked, - # while any field that only appears once is considered unchecked. - checkbox_params = '&'.join( [ urllib.urlencode( checked_boxes ), - urllib.urlencode( checked_boxes ), - urllib.urlencode( unchecked_boxes ) ] ) - if params or parsed_url.query: - url += '&%s' % checkbox_params - else: - url += '?%s' % checkbox_params + url += '?%s' % urllib.urlencode( params, doseq=doseq ) new_url = tc.go( url ) return_code = tc.browser.get_code() assert return_code in allowed_codes, 'Invalid HTTP return code %s, allowed codes: %s' % \ @@ -1506,10 +1487,11 @@ if in_group_ids: url_params[ 'in_groups' ] = ','.join( in_group_ids ) if create_group_for_role == 'yes': - checkbox_params = dict( create_group_for_role='yes' ) + url_params[ 'create_group_for_role' ] = [ 'yes', 'yes' ] + doseq = True else: - checkbox_params = None - self.visit_url( url, url_params, checkbox_params=checkbox_params ) + doseq=False + self.visit_url( url, params=url_params, doseq=doseq ) for check_str in strings_displayed: self.check_page_for_string( check_str ) if private_role: @@ -1561,7 +1543,7 @@ self.check_page_for_string( check_str ) # Tests associated with groups - def create_group( self, name='Group One', in_user_ids=[], in_role_ids=[], create_role_for_group='', strings_displayed=[] ): + def create_group( self, name='Group One', in_user_ids=[], in_role_ids=[], create_role_for_group=False, strings_displayed=[] ): """Create a new group""" url = "/admin/groups" params = dict( operation='create', create_group_button='Save', name=name ) @@ -1569,11 +1551,13 @@ params [ 'in_users' ] = ','.join( in_user_ids ) if in_role_ids: params[ 'in_roles' ] = ','.join( in_role_ids ) - if create_role_for_group == 'yes': - checkbox_params = dict( create_role_for_group='yes' ) + if create_role_for_group: + params[ 'create_role_for_group' ] = [ 'yes', 'yes' ] + doseq = True else: - checkbox_params = None - self.visit_url( url, params=params, checkbox_params=checkbox_params ) + params[ 'create_role_for_group' ] = 'no' + doseq = False + self.visit_url( url, params=params, doseq=doseq ) for check_str in strings_displayed: self.check_page_for_string( check_str ) self.visit_url( "/admin/groups" ) @@ -2398,11 +2382,9 @@ #tc.fv( "1", "do_action", format ) #tc.submit( "action_on_datasets_button" ) # Here's the new approach... - url = "%s/library_common/act_on_multiple_datasets?cntrller=%s&library_id=%s&do_action=%s" \ - % ( self.url, cntrller, library_id, format ) - for ldda_id in ldda_ids: - url += "&ldda_ids=%s" % ldda_id - self.visit_url( url ) + params = dict( cntrller=cntrller, library_id=library_id, do_action=format, ldda_ids=ldda_ids ) + url = "/library_common/act_on_multiple_datasets" + self.visit_url( url, params, doseq=True ) tc.code( 200 ) archive = self.write_temp_file( self.last_page(), suffix='.' + format ) return archive diff -r b34eaa5eaa3176bc7498adcda597e7fa58996a2b -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 test/functional/test_admin_features.py --- a/test/functional/test_admin_features.py +++ b/test/functional/test_admin_features.py @@ -209,7 +209,7 @@ self.create_group( name=name, in_user_ids=in_user_ids, in_role_ids=in_role_ids, - create_role_for_group='yes', + create_role_for_group=True, strings_displayed=[ "Group '%s' has been created with %d associated users and %d associated roles." % ( name, len( in_user_ids ), num_gras ), "One of the roles associated with this group is the newly created role with the same name." ] ) # Get the group object for later tests diff -r b34eaa5eaa3176bc7498adcda597e7fa58996a2b -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 test/functional/test_library_features.py --- a/test/functional/test_library_features.py +++ b/test/functional/test_library_features.py @@ -69,7 +69,7 @@ self.library_info( 'library_admin', self.security.encode_id( library1.id ), library1.name, - new_name=name, + new_name='library1', new_description='library1 description', new_synopsis='library1 synopsis' ) refresh( library1 ) diff -r b34eaa5eaa3176bc7498adcda597e7fa58996a2b -r 2ff24ef0746f3ef874d817052d48bf2278b10a33 test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -1053,10 +1053,19 @@ # form doesn't get parsed correctly. encoded_repository_id = self.security.encode_id( installed_repository.id ) params = dict( id=encoded_repository_id, no_changes=no_changes, new_tool_panel_section_label=new_tool_panel_section_label ) - checkbox_params = dict( install_repository_dependencies=install_repository_dependencies, - install_tool_dependencies=install_tool_dependencies ) + doseq = False + if install_repository_dependencies: + params[ 'install_repository_dependencies' ] = [ 'True', 'True' ] + doseq = True + else: + params[ 'install_repository_dependencies' ] = False + if install_tool_dependencies: + params[ 'install_tool_dependencies' ] = [ 'True', 'True' ] + doseq = True + else: + params[ 'install_tool_dependencies' ] = False url = '/admin_toolshed/reinstall_repository' - self.visit_galaxy_url( url, params=params, checkbox_params=checkbox_params ) + self.visit_galaxy_url( url, params=params, doseq=doseq ) # Manually initiate the install process, as with installing a repository. See comments in the # initiate_installation_process method for details. repository_ids = self.initiate_installation_process( install_tool_dependencies, @@ -1435,9 +1444,9 @@ self.visit_galaxy_url( url ) self.check_for_strings( strings, strings_not_displayed ) - def visit_galaxy_url( self, url, params=None, checkbox_params=None ): + def visit_galaxy_url( self, url, params=None, doseq=False ): url = '%s%s' % ( self.galaxy_url, url ) - self.visit_url( url, params=params, checkbox_params=checkbox_params ) + self.visit_url( url, params=params, doseq=doseq ) def wait_for_repository_installation( self, repository_ids ): final_states = [ galaxy_model.ToolShedRepository.installation_status.ERROR, 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: Add a Tool Shed API script that can be used to retrieve the current set of categories from a Tool Shed (e.g. the test Tool Shed) and create each of them in a local development Tool Shed. This script can be used to streamline the process of creating a new development Tool Shed, populating it with categories expected in a public Tool Shed, and creating a new repository hierarchy that can be exported into a capsule and imported into the public Tool Shed.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b34eaa5eaa31/ Changeset: b34eaa5eaa31 User: greg Date: 2014-04-29 21:11:46 Summary: Add a Tool Shed API script that can be used to retrieve the current set of categories from a Tool Shed (e.g. the test Tool Shed) and create each of them in a local development Tool Shed. This script can be used to streamline the process of creating a new development Tool Shed, populating it with categories expected in a public Tool Shed, and creating a new repository hierarchy that can be exported into a capsule and imported into the public Tool Shed. Affected #: 1 file diff -r 87bf6a0324f3182ccf16ad18b662f80272f187bc -r b34eaa5eaa3176bc7498adcda597e7fa58996a2b lib/tool_shed/scripts/api/create_categories.py --- /dev/null +++ b/lib/tool_shed/scripts/api/create_categories.py @@ -0,0 +1,57 @@ +#!/usr/bin/env python +""" +This script will retrieve a list of dictionaries (one for each category) from the Tool Shed defined +by the --from_tool_shed parameter, which should be a base Tool Shed URL. It will retrieve the category +name and description from each dictionary and create a new category with that name and description in +the Tool Shed defined by the --to_tool_shed parameter (a different base Tool Shed URL). Categories +that already exist with a specified name in the Tool Shed in which the categories are being created +will not be affected. + +This script is very useful for populating a new development Tool Shed with the set of categories that +currently exist in either the test or main public Galaxy Tool Sheds. This will streamline building +new repository hierarchies in the development Tool Shed and exportin gthem into a capsule that can be +imported into one of the public Tool Sheds. + +Here is a working example of how to use this script to retrieve the current set of repositories that are +available in the test public Tool Shed and create each of them in a local development Tool Shed. + +./create_categories.py -a <api key> -f http://testtoolshed.g2.bx.psu.edu -t http://localhost:9009 +""" + +import os +import sys +import argparse +sys.path.insert( 0, os.path.dirname( __file__ ) ) +from common import get +from common import submit + +def main( options ): + api_key = options.api + from_tool_shed = options.from_tool_shed.rstrip( '/' ) + to_tool_shed = options.to_tool_shed.rstrip( '/' ) + # Get the categories from the specified Tool Shed. + url = '%s/api/categories' % from_tool_shed + category_dicts = get( url ) + create_response_dicts = [] + for category_dict in category_dicts: + name = category_dict.get( 'name', None ) + description = category_dict.get( 'description', None ) + if name is not None and description is not None: + data = dict( name=name, + description=description ) + url = '%s/api/categories/new/create_category' % to_tool_shed + try: + response = submit( url, data, api_key ) + except Exception, e: + response = str( e ) + log.exception( str( e ) ) + create_response_dict = dict( response=response ) + create_response_dicts.append( create_response_dict ) + +if __name__ == '__main__': + parser = argparse.ArgumentParser( description='Retrieve a list of categories from a Tool Shed and create them in another Tool Shed.' ) + parser.add_argument( "-a", "--api", dest="api", required=True, help="API Key for Tool Shed in which categories will be created" ) + parser.add_argument( "-f", "--from_tool_shed", dest="from_tool_shed", required=True, help="URL of Tool Shed from which to retrieve the categories" ) + parser.add_argument( "-t", "--to_tool_shed", dest="to_tool_shed", required=True, help="URL of Tool Shed in which to create the categories" ) + options = parser.parse_args() + main( options ) 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: Enhance the Tool Shed API to provide functions for retrieving and creating categories.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/87bf6a0324f3/ Changeset: 87bf6a0324f3 User: greg Date: 2014-04-29 20:58:21 Summary: Enhance the Tool Shed API to provide functions for retrieving and creating categories. Affected #: 3 files diff -r 0fee9a84cec6dd78774f30bd60ab7d41d2efc619 -r 87bf6a0324f3182ccf16ad18b662f80272f187bc lib/galaxy/webapps/tool_shed/api/categories.py --- /dev/null +++ b/lib/galaxy/webapps/tool_shed/api/categories.py @@ -0,0 +1,103 @@ +import logging +import os + +from galaxy import util +from galaxy import web +from galaxy.web.base.controller import BaseAPIController +import tool_shed.util.shed_util_common as suc + +log = logging.getLogger( __name__ ) + + +class CategoriesController( BaseAPIController ): + """RESTful controller for interactions with categories in the Tool Shed.""" + + def __get_value_mapper( self, trans ): + value_mapper = { 'id' : trans.security.encode_id } + return value_mapper + + @web.expose_api + def create_category( self, trans, payload, **kwd ): + """ + POST /api/categories/create_category + Returns a dictionary of information about the created category. + +: param key: the current Galaxy admin user's API key + + The following parameters are included in the payload. + :param name (required): the name of the category + :param description (optional): the description of the category (if not provided, the name will be used) + """ + category_dict = dict( message = '', + status = 'ok' ) + # Make sure the current user's API key proves he is an admin user in this Tool Shed. + if trans.user_is_admin(): + # Get the information about the category to be created from the payload. + name = payload.get( 'name', '' ) + if name: + description = payload.get( 'description', '' ) + if not description: + # Default the description to the name. + description = name + if suc.get_category_by_name( trans, name ): + category_dict[ 'message' ] = 'A category with that name already exists' + category_dict[ 'status' ] = 'error' + else: + # Create the category + category = trans.app.model.Category( name=name, description=description ) + trans.sa_session.add( category ) + trans.sa_session.flush() + category_dict = category.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans ) ) + category_dict[ 'message' ] = "Category '%s' has been created" % str( category.name ) + category_dict[ 'url' ] = web.url_for( controller='categories', + action='show', + id=trans.security.encode_id( category.id ) ) + else: + category_dict[ 'message' ] = "Missing required parameter 'name'." + category_dict[ 'status' ] = 'error' + else: + category_dict[ 'message' ] = 'You are not authorized to create a category in this Tool Shed.' + category_dict[ 'status' ] = 'error' + return category_dict + + @web.expose_api_anonymous + def index( self, trans, deleted=False, **kwd ): + """ + GET /api/categories + Returns a list of dictionaries that contain information about each category. + """ + # Example URL: http://localhost:9009/api/categories + category_dicts = [] + deleted = util.asbool( deleted ) + for category in trans.sa_session.query( trans.app.model.Category ) \ + .filter( trans.app.model.Category.table.c.deleted == deleted ) \ + .order_by( trans.app.model.Category.table.c.name ): + category_dict = category.to_dict( view='collection', + value_mapper=self.__get_value_mapper( trans ) ) + category_dict[ 'url' ] = web.url_for( controller='categories', + action='show', + id=trans.security.encode_id( category.id ) ) + category_dicts.append( category_dict ) + return category_dicts + + @web.expose_api_anonymous + def show( self, trans, id, **kwd ): + """ + GET /api/categories/{encoded_category_id} + Returns a dictionary of information about a category. + + :param id: the encoded id of the Repository object + """ + # Example URL: http://localhost:9009/api/categories/f9cad7b01a472135 + category = suc.get_category( trans, id ) + if category is None: + category_dict = dict( message = 'Unable to locate category record for id %s.' % ( str( id ) ), + status = 'error' ) + return category_dict + category_dict = category.to_dict( view='element', + value_mapper=self.__get_value_mapper( trans ) ) + category_dict[ 'url' ] = web.url_for( controller='categories', + action='show', + id=trans.security.encode_id( category.id ) ) + return category_dict diff -r 0fee9a84cec6dd78774f30bd60ab7d41d2efc619 -r 87bf6a0324f3182ccf16ad18b662f80272f187bc lib/galaxy/webapps/tool_shed/buildapp.py --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -80,6 +80,13 @@ webapp.add_route( '/repos/*path_info', controller='hg', action='handle_request', path_info='/' ) # Add the web API. # A good resource for RESTful services - http://routes.readthedocs.org/en/latest/restful.html webapp.add_api_controllers( 'galaxy.webapps.tool_shed.api', app ) + webapp.mapper.resource( 'category', + 'categories', + controller='categories', + name_prefix='category_', + path_prefix='/api', + new={ 'create_category' : 'POST' }, + parent_resources=dict( member_name='category', collection_name='categories' ) ) webapp.mapper.resource( 'repository', 'repositories', controller='repositories', diff -r 0fee9a84cec6dd78774f30bd60ab7d41d2efc619 -r 87bf6a0324f3182ccf16ad18b662f80272f187bc lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -470,9 +470,9 @@ # lists of discovered repository dependencies, but these lists will be empty in the # required_repo_info_dict since dependency discovery has not yet been performed for these # dictionaries. - required_repo_infor_dict_key = required_repo_info_dict.keys()[ 0 ] + required_repo_info_dict_key = required_repo_info_dict.keys()[ 0 ] all_repo_info_dicts_keys = [ d.keys()[ 0 ] for d in all_repo_info_dicts ] - if required_repo_infor_dict_key not in all_repo_info_dicts_keys: + if required_repo_info_dict_key not in all_repo_info_dicts_keys: all_repo_info_dicts.append( required_repo_info_dict ) all_required_repo_info_dict[ 'all_repo_info_dicts' ] = all_repo_info_dicts return all_required_repo_info_dict Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: jmchilton: More refactoring of tools API test case.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0fee9a84cec6/ Changeset: 0fee9a84cec6 User: jmchilton Date: 2014-04-29 20:53:06 Summary: More refactoring of tools API test case. Affected #: 1 file diff -r 43cf1476a77405f9890a6b97fe9993c2936650a5 -r 0fee9a84cec6dd78774f30bd60ab7d41d2efc619 test/functional/api/test_tools.py --- a/test/functional/api/test_tools.py +++ b/test/functional/api/test_tools.py @@ -82,15 +82,23 @@ self.assertEqual( output1_content.strip(), "Cat1Test\nCat2Test" ) def _cat1_outputs( self, history_id, inputs ): - create_response = self._run_cat1( history_id, inputs ) + return self._run_outputs( self._run_cat1( history_id, inputs ) ) + + def _run_and_get_outputs( self, tool_id, history_id, inputs ): + return self._run_outputs( self._run( tool_id, history_id, inputs ) ) + + def _run_outputs( self, create_response ): self._assert_status_code_is( create_response, 200 ) create = create_response.json() self._assert_has_keys( create, 'outputs' ) return create[ 'outputs' ] def _run_cat1( self, history_id, inputs ): + return self._run( 'cat1', history_id, inputs ) + + def _run( self, tool_id, history_id, inputs ): payload = self.dataset_populator.run_tool_payload( - tool_id='cat1', + tool_id=tool_id, inputs=inputs, history_id=history_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: davebgx: Fix sample tracking functional tests.
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/43cf1476a774/ Changeset: 43cf1476a774 User: davebgx Date: 2014-04-29 19:21:28 Summary: Fix sample tracking functional tests. Affected #: 3 files diff -r b67a59a2beca5072eb19ad7c7e20beb40adda8da -r 43cf1476a77405f9890a6b97fe9993c2936650a5 templates/webapps/galaxy/requests/common/edit_samples.mako --- a/templates/webapps/galaxy/requests/common/edit_samples.mako +++ b/templates/webapps/galaxy/requests/common/edit_samples.mako @@ -78,7 +78,7 @@ grid_header = '<h3>Edit Current Samples of Sequencing Request "%s"</h3>' % request.name %> ${render_samples_grid( cntrller, request, displayable_sample_widgets, action='edit_samples', encoded_selected_sample_ids=encoded_selected_sample_ids, render_buttons=False, grid_header=grid_header )} - %if len( sample_operation_select_field.options ) > 1 and not is_unsubmitted: + %if len( sample_operation_select_field.options ) >= 1 and not is_unsubmitted: <div class="form-row" style="background-color:#FAFAFA;"> For selected samples: ${sample_operation_select_field.get_html()} diff -r b67a59a2beca5072eb19ad7c7e20beb40adda8da -r 43cf1476a77405f9890a6b97fe9993c2936650a5 test/base/twilltestcase.py --- a/test/base/twilltestcase.py +++ b/test/base/twilltestcase.py @@ -1633,7 +1633,7 @@ tc.submit( "create_form_button" ) if form_type == "Sequencing Sample Form": tc.submit( "add_layout_grid" ) - tc.fv( "create_form_definition", "grid_layout0", form_layout_name ) + tc.fv( "edit_form_definition", "grid_layout0", form_layout_name ) # if not adding any fields at this time, remove the default empty field if num_fields == 0: tc.submit( "remove_button" ) @@ -1677,9 +1677,9 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) if new_form_name: - tc.fv( "1", "name", new_form_name ) + tc.fv( "edit_form_definition", "name", new_form_name ) if new_form_desc: - tc.fv( "1", "description", new_form_desc ) + tc.fv( "edit_form_definition", "description", new_form_desc ) for i, field_dict in enumerate( field_dicts ): index = i + field_index tc.submit( "add_field_button" ) @@ -1693,18 +1693,18 @@ field_required_value = field_dict[ 'required' ] field_name = "field_name_%i" % index field_name_value = field_dict.get( 'name', '%i_field_name' % index ) - tc.fv( "1", field_label, field_label_value ) - tc.fv( "1", field_help, field_help_value ) - tc.fv( "1", field_required, field_required_value ) - tc.fv( "1", field_name, field_name_value ) + tc.fv( "edit_form_definition", field_label, field_label_value ) + tc.fv( "edit_form_definition", field_help, field_help_value ) + tc.fv( "edit_form_definition", field_required, field_required_value ) + tc.fv( "edit_form_definition", field_name, field_name_value ) if field_type_value.lower() == 'selectfield': # SelectFields require a refresh_on_change self.refresh_form( field_type, field_type_value ) for option_index, option in enumerate( field_dict[ 'selectlist' ] ): tc.submit( "addoption_%i" % index ) - tc.fv( "1", "field_%i_option_%i" % ( index, option_index ), option ) + tc.fv( "edit_form_definition", "field_%i_option_%i" % ( index, option_index ), option ) else: - tc.fv( "1", field_type, field_type_value ) + tc.fv( "edit_form_definition", field_type, field_type_value ) tc.submit( "save_changes_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) @@ -1892,20 +1892,22 @@ for check_str in strings_displayed: self.check_page_for_string( check_str ) for sample_index, ( sample_name, target_library_info, sample_field_values ) in enumerate( sample_value_tuples ): - tc.fv( "1", "sample_%i_name" % sample_index, sample_name ) - tc.fv( "1", "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) - self.refresh_form( "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) + tc.fv( "add_samples", "sample_%i_name" % sample_index, sample_name ) + if target_library_info[ 'library' ] is not None: + tc.fv( "add_samples", "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) + self.refresh_form( "sample_%i_library_id" % sample_index, target_library_info[ 'library' ] ) # check if the folder selectfield has been correctly populated for check_str in folder_options: self.check_page_for_string( check_str ) - tc.fv( "1", "sample_%i_folder_id" % sample_index, target_library_info[ 'folder' ] ) + if target_library_info[ 'folder' ] is not None: + tc.fv( "add_samples", "sample_%i_folder_id" % sample_index, target_library_info[ 'folder' ] ) for field_index, field_value in enumerate( sample_field_values ): - tc.fv( "1", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) + tc.fv( "add_samples", "sample_%i_field_%i" % ( sample_index, field_index ), field_value ) # Do not click on Add sample button when all the sample have been added if sample_index < len( sample_value_tuples ) - 1: tc.submit( "add_sample_button" ) # select the correct form before submitting it - tc.fv( "1", "copy_sample_index", "-1" ) + tc.fv( "add_samples", "copy_sample_index", "-1" ) tc.submit( "save_samples_button" ) for check_str in strings_displayed_after_submit: self.check_page_for_string( check_str ) diff -r b67a59a2beca5072eb19ad7c7e20beb40adda8da -r 43cf1476a77405f9890a6b97fe9993c2936650a5 test/functional/test_sample_tracking.py --- a/test/functional/test_sample_tracking.py +++ b/test/functional/test_sample_tracking.py @@ -722,7 +722,7 @@ % ( request2.name, request2.states.NEW ) def test_0100_add_samples_to_request( self ): - target_library_info = dict( library='none', folder='none' ) + target_library_info = dict( library=None, folder=None ) # Sample fields - the tuple represents a sample name and a list of sample form field values sample_value_tuples = \ [ ( 'Sample1', target_library_info, [ 'option1', 'sample1 field2 value', 'sample1 field3 value' ] ), @@ -741,12 +741,10 @@ '<input type="text" name="sample_0_name" value="Sample_1" size="10"/>' ], # sample name input field strings_displayed_after_submit=strings_displayed_after_submit ) # Submit the request - select_target_library_message = "Select a target data library and folder for a sample before selecting its datasets to transfer from the external service" self.submit_request( cntrller='requests_admin', request_id=self.security.encode_id( request2.id ), request_name=request2.name, - strings_displayed_after_submit=[ select_target_library_message, - 'The sequencing request has been submitted.' ] ) + strings_displayed_after_submit=[ 'The sequencing request has been submitted.' ] ) refresh( request2 ) # Make sure the request is showing in the 'submitted' filter self.check_request_grid( cntrller='requests_admin', @@ -776,7 +774,8 @@ strings_displayed_count = [] strings_displayed_count.append( ( library2.name, len( request1.samples ) ) ) strings_displayed_count.append( ( library2_folder1.name, len( request1.samples ) ) ) - strings_displayed = [ 'Sequencing request "%s"' % name, regular_user1.email, request2.states.SUBMITTED ] + strings_displayed = [ 'Sequencing request "%s"' % request2.name, regular_user1.email, request2.states.SUBMITTED ] + select_target_library_message = "Select a target data library and folder for a sample before selecting its datasets to transfer from the external service" self.view_request( cntrller='requests', request_id=self.security.encode_id( request2.id ), strings_displayed=strings_displayed, Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History options: have 'Purge deleted datasets' update the user disk size
by commits-noreply＠bitbucket.org 29 Apr '14

29 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b67a59a2beca/ Changeset: b67a59a2beca User: carlfeberhard Date: 2014-04-29 19:21:56 Summary: History options: have 'Purge deleted datasets' update the user disk size Affected #: 1 file diff -r b526afe822e53ce530fabe94dff683818a33b29a -r b67a59a2beca5072eb19ad7c7e20beb40adda8da templates/webapps/galaxy/root/index.mako --- a/templates/webapps/galaxy/root/index.mako +++ b/templates/webapps/galaxy/root/index.mako @@ -17,9 +17,6 @@ <%def name="javascripts()"> ${parent.javascripts()} ${tool_menu_javascripts()} - ${h.js( - "utils/LazyDataLoader" - )} </%def><%def name="late_javascripts()"> @@ -95,6 +92,10 @@ "${_("Purge Deleted Datasets")}": function() { if ( confirm( "Really delete all deleted datasets permanently? This cannot be undone." ) ) { galaxy_main.location = "${h.url_for( controller='history', action='purge_deleted_datasets' )}"; + // update the user disk size when the purge page loads + $( '#galaxy_main' ).load( function(){ + Galaxy.user.fetch(); + }) } }, "${_("Show Structure")}": function() { 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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