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commit/galaxy-central: dan: Merged in hillrunner2008/galaxy-central (pull request #367)
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/855b03513ca9/ Changeset: 855b03513ca9 User: dan Date: 2014-04-14 22:56:48 Summary: Merged in hillrunner2008/galaxy-central (pull request #367) added support for the visualization of gtf file format in IGB Affected #: 2 files diff -r c2a2ce95501c9e1a3da2550ce963376a49449481 -r 855b03513ca92f33be6d4da54afffadad294a9cc datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -99,6 +99,7 @@ <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> diff -r c2a2ce95501c9e1a3da2550ce963376a49449481 -r 855b03513ca92f33be6d4da54afffadad294a9cc display_applications/igb/gtf.xml --- /dev/null +++ b/display_applications/igb/gtf.xml @@ -0,0 +1,17 @@ +<display id="igb_gtf" version="1.0.0" name="display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="gtf_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$gtf_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + </param> + </link> +</display> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/56dee1c67384/ Changeset: 56dee1c67384 User: dcnorris Date: 2014-04-14 16:05:03 Summary: adding support for the visualization of gtf file format in IGB Affected #: 2 files diff -r 6ae3b10ec63e21b0df60f9428ab312ecad0e4e62 -r 56dee1c67384211bf4844a2798bf89dfb2e8cff8 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -99,6 +99,7 @@ <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> diff -r 6ae3b10ec63e21b0df60f9428ab312ecad0e4e62 -r 56dee1c67384211bf4844a2798bf89dfb2e8cff8 display_applications/igb/gtf.xml --- /dev/null +++ b/display_applications/igb/gtf.xml @@ -0,0 +1,17 @@ +<display id="igb_gtf" version="1.0.0" name="display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="gtf_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$gtf_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + </param> + </link> +</display> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/fe0335898665/ Changeset: fe0335898665 User: dcnorris Date: 2014-04-14 22:43:49 Summary: converted tabs to spaces Affected #: 2 files diff -r 56dee1c67384211bf4844a2798bf89dfb2e8cff8 -r fe03358986651d3e4bac287cd69e77a925d05cb3 datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -99,7 +99,7 @@ <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> - <display file="igb/gtf.xml" /> + <display file="igb/gtf.xml" /></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> diff -r 56dee1c67384211bf4844a2798bf89dfb2e8cff8 -r fe03358986651d3e4bac287cd69e77a925d05cb3 display_applications/igb/gtf.xml --- a/display_applications/igb/gtf.xml +++ b/display_applications/igb/gtf.xml @@ -1,17 +1,17 @@ <display id="igb_gtf" version="1.0.0" name="display in IGB"> - <link id="View" name="View"> - <url>$bioviz</url> - <param type="data" name="gtf_file_for_name" viewable="False"/> - <param type="template" name="niceName" viewable="False" strip="True"> - #import re - #set nm=$gtf_file_for_name.name - ${re.sub('\W',"_",nm)} - </param> - <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> - - <param type="template" name="bioviz" strip="True" > - http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="gtf_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$gtf_file_for_name.name + ${re.sub('\W',"_",nm)} </param> - </link> + <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + </param> + </link></display> \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/855b03513ca9/ Changeset: 855b03513ca9 User: dan Date: 2014-04-14 22:56:48 Summary: Merged in hillrunner2008/galaxy-central (pull request #367) added support for the visualization of gtf file format in IGB Affected #: 2 files diff -r c2a2ce95501c9e1a3da2550ce963376a49449481 -r 855b03513ca92f33be6d4da54afffadad294a9cc datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -99,6 +99,7 @@ <datatype extension="gtf" type="galaxy.datatypes.interval:Gtf" display_in_upload="true"><converter file="gff_to_interval_index_converter.xml" target_datatype="interval_index"/><converter file="bed_gff_or_vcf_to_bigwig_converter.xml" target_datatype="bigwig"/> + <display file="igb/gtf.xml" /></datatype><datatype extension="toolshed.gz" type="galaxy.datatypes.binary:Binary" mimetype="multipart/x-gzip" subclass="True" /><datatype extension="h5" type="galaxy.datatypes.binary:Binary" mimetype="application/octet-stream" subclass="True" /> diff -r c2a2ce95501c9e1a3da2550ce963376a49449481 -r 855b03513ca92f33be6d4da54afffadad294a9cc display_applications/igb/gtf.xml --- /dev/null +++ b/display_applications/igb/gtf.xml @@ -0,0 +1,17 @@ +<display id="igb_gtf" version="1.0.0" name="display in IGB"> + + <link id="View" name="View"> + <url>$bioviz</url> + <param type="data" name="gtf_file_for_name" viewable="False"/> + <param type="template" name="niceName" viewable="False" strip="True"> + #import re + #set nm=$gtf_file_for_name.name + ${re.sub('\W',"_",nm)} + </param> + <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + + <param type="template" name="bioviz" strip="True" > + http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… + </param> + </link> +</display> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: merge next stable
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c2a2ce95501c/ Changeset: c2a2ce95501c User: dan Date: 2014-04-14 22:34:16 Summary: merge next stable Affected #: 1 file diff -r 12265c0cca1f20c5c87c909a4e6faaff089c70ee -r c2a2ce95501c9e1a3da2550ce963376a49449481 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -708,14 +708,6 @@ # Enable enforcement of quotas. Quotas can be set from the Admin interface. #enable_quotas = False -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - # This option allows users to see the full path of datasets via the "View # Details" option in the history. Administrators can always see this. #expose_dataset_path = False 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: dan: Remove duplicated enable_unique_workflow_defaults from universe_wsgi.ini.sample.
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1165a5a1221a/ Changeset: 1165a5a1221a Branch: next-stable User: dan Date: 2014-04-14 22:33:57 Summary: Remove duplicated enable_unique_workflow_defaults from universe_wsgi.ini.sample. Affected #: 1 file diff -r 52f8e109315ae84a36999586d333e1758511477f -r 1165a5a1221ac538bcbfd4e046a33e5bbfb1106a universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -708,14 +708,6 @@ # Enable enforcement of quotas. Quotas can be set from the Admin interface. #enable_quotas = False -# Enable a feature when running workflows. When enabled, default datasets -# are selected for "Set at Runtime" inputs from the history such that the -# same input will not be selected twice, unless there are more inputs than -# compatible datasets in the history. -# When False, the most recently added compatible item in the history will -# be used for each "Set at Runtime" input, independent of others in the Workflow -#enable_unique_workflow_defaults = False - # This option allows users to see the full path of datasets via the "View # Details" option in the history. Administrators can always see this. #expose_dataset_path = False 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: dan: merge next stable
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/12265c0cca1f/ Changeset: 12265c0cca1f User: dan Date: 2014-04-14 22:30:29 Summary: merge next stable Affected #: 1 file diff -r a48baeee4ff4014ea42a65adc73f3e5f6184f9a4 -r 12265c0cca1f20c5c87c909a4e6faaff089c70ee lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -192,7 +192,12 @@ #This needs to be done recursively through grouping parameters def rerun_callback( input, value, prefixed_name, prefixed_label ): if isinstance( value, UnvalidatedValue ): - return str( value ) + try: + return input.to_html_value( value.value, trans.app ) + except Exception, e: + # Need to determine when (if ever) the to_html_value call could fail. + log.debug( "Failed to use input.to_html_value to determine value of unvalidated parameter, defaulting to string: %s" % ( e ) ) + return str( value ) if isinstance( input, DataToolParameter ): if isinstance(value,list): values = [] 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: dan: Fix for rerun of unvalidated parameters for multiple selects.
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/52f8e109315a/ Changeset: 52f8e109315a Branch: next-stable User: dan Date: 2014-04-14 22:29:46 Summary: Fix for rerun of unvalidated parameters for multiple selects. Affected #: 1 file diff -r 8d4ceccae2367e06bc05f93bfdc51119a962307b -r 52f8e109315ae84a36999586d333e1758511477f lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -192,7 +192,12 @@ #This needs to be done recursively through grouping parameters def rerun_callback( input, value, prefixed_name, prefixed_label ): if isinstance( value, UnvalidatedValue ): - return str( value ) + try: + return input.to_html_value( value.value, trans.app ) + except Exception, e: + # Need to determine when (if ever) the to_html_value call could fail. + log.debug( "Failed to use input.to_html_value to determine value of unvalidated parameter, defaulting to string: %s" % ( e ) ) + return str( value ) if isinstance( input, DataToolParameter ): if isinstance(value,list): values = [] 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: dan: merge next-stable
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a48baeee4ff4/ Changeset: a48baeee4ff4 User: dan Date: 2014-04-14 21:47:01 Summary: merge next-stable Affected #: 2 files diff -r eebf1cdecd19c748046526cb5351604b38332e01 -r a48baeee4ff4014ea42a65adc73f3e5f6184f9a4 lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -53,16 +53,18 @@ value = incoming_value error = None try: - if value is not None or isinstance(param, DataToolParameter): + if value is not None or isinstance( param, DataToolParameter ): # Convert value from HTML representation if source == 'html': value = param.from_html( value, trans, param_values ) else: value = param.from_json( value, trans, param_values ) - # Allow the value to be converted if neccesary - filtered_value = param.filter_value( value, trans, param_values ) - # Then do any further validation on the value - param.validate( filtered_value, trans.history ) + # Only validate if late validation is not needed + if not param.need_late_validation( trans, param_values ): + # Allow the value to be converted if necessary + filtered_value = param.filter_value( value, trans, param_values ) + # Then do any further validation on the value + param.validate( filtered_value, trans.history ) elif value is None and isinstance( param, SelectToolParameter ): # An empty select list or column list param.validate( value, trans.history ) diff -r eebf1cdecd19c748046526cb5351604b38332e01 -r a48baeee4ff4014ea42a65adc73f3e5f6184f9a4 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -183,6 +183,9 @@ for validator in self.validators: validator.validate( value, history ) + def need_late_validation( self, trans, context ): + return False + def to_dict( self, trans, view='collection', value_mapper=None ): """ to_dict tool parameter. This can be overridden by subclasses. """ tool_dict = super( ToolParameter, self ).to_dict() @@ -1774,6 +1777,11 @@ else: validator.validate( value, history ) + def need_late_validation( self, trans, context ): + if trans is None or trans.workflow_building_mode: + return True + return False + def get_dependencies( self ): """ Get the *names* of the other params this param depends on. 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: dan: Fix for workflow editor in call to check_param on input parameters that need late validation but were attempting to run validators.
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8d4ceccae236/ Changeset: 8d4ceccae236 Branch: next-stable User: dan Date: 2014-04-14 21:44:36 Summary: Fix for workflow editor in call to check_param on input parameters that need late validation but were attempting to run validators. Affected #: 2 files diff -r a0769a6caf2a073209a9249df99b40a110c0f961 -r 8d4ceccae2367e06bc05f93bfdc51119a962307b lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -53,16 +53,18 @@ value = incoming_value error = None try: - if value is not None or isinstance(param, DataToolParameter): + if value is not None or isinstance( param, DataToolParameter ): # Convert value from HTML representation if source == 'html': value = param.from_html( value, trans, param_values ) else: value = param.from_json( value, trans, param_values ) - # Allow the value to be converted if neccesary - filtered_value = param.filter_value( value, trans, param_values ) - # Then do any further validation on the value - param.validate( filtered_value, trans.history ) + # Only validate if late validation is not needed + if not param.need_late_validation( trans, param_values ): + # Allow the value to be converted if necessary + filtered_value = param.filter_value( value, trans, param_values ) + # Then do any further validation on the value + param.validate( filtered_value, trans.history ) elif value is None and isinstance( param, SelectToolParameter ): # An empty select list or column list param.validate( value, trans.history ) diff -r a0769a6caf2a073209a9249df99b40a110c0f961 -r 8d4ceccae2367e06bc05f93bfdc51119a962307b lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -183,6 +183,9 @@ for validator in self.validators: validator.validate( value, history ) + def need_late_validation( self, trans, context ): + return False + def to_dict( self, trans, view='collection', value_mapper=None ): """ to_dict tool parameter. This can be overridden by subclasses. """ tool_dict = super( ToolParameter, self ).to_dict() @@ -1774,6 +1777,11 @@ else: validator.validate( value, history ) + def need_late_validation( self, trans, context ): + if trans is None or trans.workflow_building_mode: + return True + return False + def get_dependencies( self ): """ Get the *names* of the other params this param depends on. 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: initial work on importing datasets from histories: fetching history list, fetching and displaying history contents
by commits-noreply＠bitbucket.org 14 Apr '14

14 Apr '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eebf1cdecd19/ Changeset: eebf1cdecd19 User: martenson Date: 2014-04-14 20:09:36 Summary: data libraries: initial work on importing datasets from histories: fetching history list, fetching and displaying history contents repaired bug in unbinding nested views Affected #: 6 files diff -r 6a2c7661fbef8340f84721da9e17b95d3943f850 -r eebf1cdecd19c748046526cb5351604b38332e01 static/scripts/galaxy.library.js --- a/static/scripts/galaxy.library.js +++ b/static/scripts/galaxy.library.js @@ -70,6 +70,14 @@ this.library_router.on('route:folder_content', function(id) { // TODO place caching here, sessionstorage/localstorage? + if (Galaxy.libraries.folderToolbarView){ + Galaxy.libraries.folderToolbarView.$el.unbind('click'); + // Galaxy.libraries.folderToolbarView.remove(); + } + if (Galaxy.libraries.folderListView){ + // Galaxy.libraries.folderListView.$el.unbind('click'); + // Galaxy.libraries.folderListView.remove(); + } Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({id: id}); Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({id: id}); }); diff -r 6a2c7661fbef8340f84721da9e17b95d3943f850 -r eebf1cdecd19c748046526cb5351604b38332e01 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 +15,7 @@ events: { 'click #toolbtn_create_folder' : 'createFolderFromModal', 'click #toolbtn_bulk_import' : 'modalBulkImport', - 'click #toolbtn_add_files' : 'addFilesToFolderModal' + 'click .toolbtn_add_files' : 'addFilesToFolderModal' }, defaults: { @@ -44,7 +44,7 @@ this.options = _.extend(this.options, options); if (this.options.can_add_library_item === true){ $('#toolbtn_create_folder').show(); - $('#toolbtn_add_files').show(); + $('.toolbtn_add_files').show(); } if (this.options.contains_file === true){ $('#toolbtn_bulk_import').show(); @@ -258,12 +258,30 @@ 'Close' : function() {Galaxy.modal.hide();} } }); - var history_contents_template = self.templateHistoryContents(); - self.modal.$el.find('#selected_history_content').html(history_contents_template); + self.fetchAndDisplayHistoryContents(self.histories.models[0].id); + $( "#dataset_add_bulk" ).change(function(event) { + self.fetchAndDisplayHistoryContents(event.target.value); + }); }); }, + fetchAndDisplayHistoryContents: function(history_id){ + var history_contents = new mod_library_model.HistoryContents({id:history_id}); + var self = this; + history_contents.fetch({ + success: function(history_contents){ + var history_contents_template = self.templateHistoryContents(); + mod_toastr.success('history contents fetched'); + self.histories.get(history_id).set({'contents' : history_contents}); + self.modal.$el.find('#selected_history_content').html(history_contents_template({history_contents: history_contents.models.reverse()})); + }, + error: function(){ + mod_toastr.error('history contents fetch failed'); + } + }); + }, + addFiles: function(){ alert('adding files'); }, @@ -277,7 +295,7 @@ // TOOLBAR tmpl_array.push('<div id="library_folder_toolbar" >'); tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="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="primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>'); + tmpl_array.push(' <button data-toggle="tooltip" data-placement="top" title="Add Datasets to Current Folder" id="toolbtn_add_files" class="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(' <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; display:none;" 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; display:none; ">'); tmpl_array.push(' <button title="Download selected datasets" id="drop_toggle" type="button" class="primary-button dropdown-toggle" data-toggle="dropdown">'); @@ -349,7 +367,7 @@ tmpl_array.push('<div id="add_files_modal">'); tmpl_array.push('<div id="history_modal_combo_bulk">'); tmpl_array.push('Select history: '); - tmpl_array.push('<select id="dataset_import_bulk" name="dataset_import_bulk" style="width:66%; "> '); + tmpl_array.push('<select id="dataset_add_bulk" name="dataset_add_bulk" style="width:66%; "> '); tmpl_array.push(' <% _.each(histories, function(history) { %>'); //history select box tmpl_array.push(' <option value="<%= _.escape(history.get("id")) %>"><%= _.escape(history.get("name")) %></option>'); tmpl_array.push(' <% }); %>'); @@ -366,9 +384,14 @@ templateHistoryContents : function (){ var tmpl_array = []; - tmpl_array.push('item1'); - tmpl_array.push('item2'); - tmpl_array.push('item3'); + tmpl_array.push('Choose the datasets to import:'); + tmpl_array.push('<ul>'); + tmpl_array.push(' <% _.each(history_contents, function(history_item) { %>'); + tmpl_array.push(' <li data-id="<%= _.escape(history_item.get("id")) %>">'); + tmpl_array.push(' <input style="margin: 0;" type="checkbox"><%= _.escape(history_item.get("hid")) %>: <%= _.escape(history_item.get("name")) %>'); + tmpl_array.push(' </li>'); + tmpl_array.push(' <% }); %>'); + tmpl_array.push('</ul>'); return _.template(tmpl_array.join('')); } diff -r 6a2c7661fbef8340f84721da9e17b95d3943f850 -r eebf1cdecd19c748046526cb5351604b38332e01 static/scripts/mvc/library/library-model.js --- a/static/scripts/mvc/library/library-model.js +++ b/static/scripts/mvc/library/library-model.js @@ -82,13 +82,21 @@ urlRoot : '/api/histories/' }); - // HISTORY - var GalaxyHistory = Backbone.Model.extend({ + // HISTORY CONTENTS + var HistoryContents = Backbone.Collection.extend({ urlRoot : '/api/histories/', + initialize: function(options){ + this.id = options.id; + }, url : function(){ return this.urlRoot + this.id + '/contents'; }, - model: HistoryItem + model : HistoryItem + }); + + // HISTORY + var GalaxyHistory = Backbone.Model.extend({ + urlRoot : '/api/histories/' }); // HISTORIES @@ -106,6 +114,7 @@ Folder : Folder, FolderContainer : FolderContainer, HistoryItem : HistoryItem, + HistoryContents : HistoryContents, GalaxyHistory : GalaxyHistory, GalaxyHistories : GalaxyHistories }; diff -r 6a2c7661fbef8340f84721da9e17b95d3943f850 -r eebf1cdecd19c748046526cb5351604b38332e01 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","sort/:sort_by/:order":"sort_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){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($("#center").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file +define(["galaxy.masthead","utils/utils","libs/toastr","mvc/base-mvc","mvc/library/library-model","mvc/library/library-folderlist-view","mvc/library/library-librarylist-view","mvc/library/library-librarytoolbar-view","mvc/library/library-foldertoolbar-view"],function(e,c,g,k,h,a,f,d,i){var l=Backbone.Router.extend({routes:{"":"libraries","sort/:sort_by/:order":"sort_libraries","folders/:id":"folder_content","folders/:folder_id/download/:format":"download"}});var j=k.SessionStorageModel.extend({defaults:{with_deleted:false,sort_order:"asc",sort_by:"name"}});var b=Backbone.View.extend({libraryToolbarView:null,libraryListView:null,library_router:null,folderToolbarView:null,folderListView:null,initialize:function(){Galaxy.libraries=this;this.preferences=new j({id:"global-lib-prefs"});this.library_router=new l();this.library_router.on("route:libraries",function(){Galaxy.libraries.libraryToolbarView=new d.LibraryToolbarView();Galaxy.libraries.libraryListView=new f.LibraryListView()});this.library_router.on("route:folder_content",function(m){if(Galaxy.libraries.folderToolbarView){Galaxy.libraries.folderToolbarView.$el.unbind("click")}if(Galaxy.libraries.folderListView){}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($("#center").find(":checked").length===0){g.info("You have to select some datasets to download");Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:true,replace:true})}else{Galaxy.libraries.folderToolbarView.download(m,n);Galaxy.libraries.library_router.navigate("folders/"+m,{trigger:false,replace:true})}});Backbone.history.start({pushState:false})}});return{GalaxyApp:b}}); \ No newline at end of file diff -r 6a2c7661fbef8340f84721da9e17b95d3943f850 -r eebf1cdecd19c748046526cb5351604b38332e01 static/scripts/packed/mvc/library/library-foldertoolbar-view.js --- a/static/scripts/packed/mvc/library/library-foldertoolbar-view.js +++ b/static/scripts/packed/mvc/library/library-foldertoolbar-view.js @@ -1,1 +1,1 @@ -define(["galaxy.masthead","utils/utils","libs/toastr","mvc/library/library-model"],function(b,d,e,c){var a=Backbone.View.extend({el:"#center",events:{"click #toolbtn_create_folder":"createFolderFromModal","click #toolbtn_bulk_import":"modalBulkImport","click #toolbtn_add_files":"addFilesToFolderModal"},defaults:{can_add_library_item:false,contains_file:false},modal:null,histories:null,initialize:function(f){this.options=_.defaults(f||{},this.defaults);this.render()},render:function(f){this.options=_.extend(this.options,f);var h=this.templateToolBar();var g=Galaxy.currUser.isAdmin();this.$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.$el.find("[data-toggle]").tooltip()},createFolderFromModal:function(){event.preventDefault();event.stopPropagation();var f=this;var g=this.templateNewFolderInModal();this.modal=Galaxy.modal;this.modal.show({closing_events:true,title:"Create New Folder",body:g(),buttons:{Create:function(){f.create_new_folder_event()},Close:function(){Galaxy.modal.hide()}}})},create_new_folder_event:function(){var f=this.serialize_new_folder();if(this.validate_new_folder(f)){var h=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;var g=this;h.save(f,{success:function(i){g.modal.hide();e.success("Folder created");i.set({type:"folder"});Galaxy.libraries.folderListView.folderContainer.attributes.folder.add(i);Galaxy.libraries.folderListView.render({id:current_folder_id})},error:function(){e.error("An error occured :(")}})}else{e.error("Folder's name is missing")}return false},serialize_new_folder:function(){return{name:$("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(){}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var h=$("select[name=dataset_import_bulk] option:selected").val();var m=$("select[name=dataset_import_bulk] option:selected").text();var o=[];$("#folder_table").find(":checked").each(function(){if(this.parentElement.parentElement.id!==""){o.push(this.parentElement.parentElement.id)}});var n=this.templateProgressBar();$(this.modal.elMain).find(".modal-body").html(n({history_name:m}));var j=100/o.length;this.initProgress(j);var f=[];for(var g=o.length-1;g>=0;g--){library_dataset_id=o[g];var k=new c.HistoryItem();var l=this;k.url=k.urlRoot+h+"/contents";k.content=library_dataset_id;k.source="library";f.push(k)}this.chainCall(f)},chainCall:function(g){var f=this;var h=g.pop();if(typeof h==="undefined"){e.success("All datasets imported");this.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source})).done(function(j){f.updateProgress();f.chainCall(g)})},initProgress:function(f){this.progress=0;this.progressStep=f},updateProgress:function(){this.progress+=this.progressStep;$(".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]+'" />'});$('<form action="'+g+'" method="'+(i||"post")+'">'+f+"</form>").appendTo("body").submit().remove();e.info("Your download will begin soon")}},addFilesToFolderModal:function(){this.refreshUserHistoriesList(function(f){f.modal=Galaxy.modal;var h=f.templateAddFilesInModal();f.modal.show({closing_events:true,title:"Add datasets from history to "+f.options.folder_name,body:h({histories:f.histories.models}),buttons:{Add:function(){f.addFiles()},Close:function(){Galaxy.modal.hide()}}});var g=f.templateHistoryContents();f.modal.$el.find("#selected_history_content").html(g)})},addFiles:function(){alert("adding files")},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(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="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="primary-button" type="button" style="display:none;"><span class="fa fa-plus"></span><span class="fa fa-file"></span></span></button>');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; display:none;" 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; display:none; ">');tmpl_array.push(' <button title="Download selected datasets" 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(" </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(""))},templateProgressBar: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(""))},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_import_bulk" name="dataset_import_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("item1");f.push("item2");f.push("item3");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"},defaults:{can_add_library_item:false,contains_file:false},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=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 h=new c.FolderAsModel();url_items=Backbone.history.fragment.split("/");current_folder_id=url_items[url_items.length-1];h.url=h.urlRoot+"/"+current_folder_id;var g=this;h.save(f,{success:function(i){g.modal.hide();e.success("Folder created");i.set({type:"folder"});Galaxy.libraries.folderListView.folderContainer.attributes.folder.add(i);Galaxy.libraries.folderListView.render({id:current_folder_id})},error:function(){e.error("An error occured :(")}})}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=$("#folder_table").find(":checked");if(f.length===0){e.info("You have to select some datasets first")}else{this.refreshUserHistoriesList(function(g){var h=g.templateBulkImportInModal();g.modal=Galaxy.modal;g.modal.show({closing_events:true,title:"Import into History",body:h({histories:g.histories.models}),buttons:{Import:function(){g.importAllIntoHistory()},Close:function(){Galaxy.modal.hide()}}})})}},refreshUserHistoriesList:function(g){var f=this;this.histories=new c.GalaxyHistories();this.histories.fetch({success:function(){g(f)},error:function(){}})},importAllIntoHistory:function(){this.modal.disableButton("Import");var h=$("select[name=dataset_import_bulk] option:selected").val();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.templateProgressBar();$(this.modal.elMain).find(".modal-body").html(n({history_name:m}));var j=100/o.length;this.initProgress(j);var f=[];for(var g=o.length-1;g>=0;g--){library_dataset_id=o[g];var k=new c.HistoryItem();var l=this;k.url=k.urlRoot+h+"/contents";k.content=library_dataset_id;k.source="library";f.push(k)}this.chainCall(f)},chainCall:function(g){var f=this;var h=g.pop();if(typeof h==="undefined"){e.success("All datasets imported");this.modal.hide();return}var i=$.when(h.save({content:h.content,source:h.source})).done(function(j){f.updateProgress();f.chainCall(g)})},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.addFiles()},Close:function(){Galaxy.modal.hide()}}});f.fetchAndDisplayHistoryContents(f.histories.models[0].id);$("#dataset_add_bulk").change(function(h){f.fetchAndDisplayHistoryContents(h.target.value)})})},fetchAndDisplayHistoryContents:function(h){var g=new c.HistoryContents({id:h});var f=this;g.fetch({success:function(j){var i=f.templateHistoryContents();e.success("history contents fetched");f.histories.get(h).set({contents:j});f.modal.$el.find("#selected_history_content").html(i({history_contents:j.models.reverse()}))},error:function(){e.error("history contents fetch failed")}})},addFiles:function(){alert("adding files")},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(' <button data-toggle="tooltip" data-placement="top" title="Create New Folder" id="toolbtn_create_folder" class="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="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(' <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; display:none;" 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; display:none; ">');tmpl_array.push(' <button title="Download selected datasets" 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(" </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(""))},templateProgressBar: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(""))},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 6a2c7661fbef8340f84721da9e17b95d3943f850 -r eebf1cdecd19c748046526cb5351604b38332e01 static/scripts/packed/mvc/library/library-model.js --- a/static/scripts/packed/mvc/library/library-model.js +++ b/static/scripts/packed/mvc/library/library-model.js @@ -1,1 +1,1 @@ -define([],function(){var e=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(k){var j=true;if((!show_delete)&&(this.get("deleted"))){j=false}return j}});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var h=Backbone.Collection.extend({url:"/api/libraries",model:e,sort_key:"name",sort_order:null,initialize:function(j){j=j||{}},getVisible:function(k,l){l=l||[];var j=new h(this.filter(function(m){return m.isVisible(k)}));return j}});var f=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:f});var d=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(j){this.get("folder").reset(j.folder_contents);return j}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var g=Backbone.Model.extend({urlRoot:"/api/histories/",url:function(){return this.urlRoot+this.id+"/contents"},model:b});var i=Backbone.Collection.extend({url:"/api/histories",model:g});return{Library:e,FolderAsModel:a,Libraries:h,Item:f,Folder:c,FolderContainer:d,HistoryItem:b,GalaxyHistory:g,GalaxyHistories:i}}); \ No newline at end of file +define([],function(){var f=Backbone.Model.extend({urlRoot:"/api/libraries/",isVisible:function(l){var k=true;if((!show_delete)&&(this.get("deleted"))){k=false}return k}});var a=Backbone.Model.extend({urlRoot:"/api/folders"});var i=Backbone.Collection.extend({url:"/api/libraries",model:f,sort_key:"name",sort_order:null,initialize:function(k){k=k||{}},getVisible:function(l,m){m=m||[];var k=new i(this.filter(function(n){return n.isVisible(l)}));return k}});var g=Backbone.Model.extend({urlRoot:"/api/libraries/datasets"});var c=Backbone.Collection.extend({model:g});var e=Backbone.Model.extend({defaults:{folder:new c(),urlRoot:"/api/folders/",id:"unknown"},parse:function(k){this.get("folder").reset(k.folder_contents);return k}});var b=Backbone.Model.extend({urlRoot:"/api/histories/"});var d=Backbone.Collection.extend({urlRoot:"/api/histories/",initialize:function(k){this.id=k.id},url:function(){return this.urlRoot+this.id+"/contents"},model:b});var h=Backbone.Model.extend({urlRoot:"/api/histories/"});var j=Backbone.Collection.extend({url:"/api/histories",model:h});return{Library:f,FolderAsModel:a,Libraries:i,Item:g,Folder:c,FolderContainer:e,HistoryItem:b,HistoryContents:d,GalaxyHistory:h,GalaxyHistories:j}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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

14 Apr '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a0769a6caf2a/ Changeset: a0769a6caf2a Branch: next-stable User: davebgx Date: 2014-04-14 19:17:12 Summary: Fixed tool help image for gops complement. Affected #: 1 file diff -r 2e1b1227509d83d646b54f32b01bc4fbb26bb3ad -r a0769a6caf2a073209a9249df99b40a110c0f961 scripts/migrate_tools/0010_tools.xml --- a/scripts/migrate_tools/0010_tools.xml +++ b/scripts/migrate_tools/0010_tools.xml @@ -12,7 +12,7 @@ <repository owner="devteam" name="cluster" changeset_revision="520de69b107a" description="Cluster"><tool id="gops_cluster_1" version="1.0.0" file="new_operations/cluster.xml" /></repository> - <repository owner="devteam" name="complement" changeset_revision="67c4ed724bfd" description="Complement intervals of a dataset"> + <repository owner="devteam" name="complement" changeset_revision="2221cf5f59aa" description="Complement intervals of a dataset"><tool id="gops_complement_1" version="1.0.0" file="new_operations/complement.xml" /></repository><repository owner="devteam" name="compute_q_values" changeset_revision="63abfc350814" description="Compute q-values based on multiple simultaneous tests p-values"> https://bitbucket.org/galaxy/galaxy-central/commits/6a2c7661fbef/ Changeset: 6a2c7661fbef User: davebgx Date: 2014-04-14 19:18:47 Summary: Merge in fix from next-stable. Affected #: 1 file diff -r 4131de825802f46ff97194d02b25739a20856b17 -r 6a2c7661fbef8340f84721da9e17b95d3943f850 scripts/migrate_tools/0010_tools.xml --- a/scripts/migrate_tools/0010_tools.xml +++ b/scripts/migrate_tools/0010_tools.xml @@ -12,7 +12,7 @@ <repository owner="devteam" name="cluster" changeset_revision="520de69b107a" description="Cluster"><tool id="gops_cluster_1" version="1.0.0" file="new_operations/cluster.xml" /></repository> - <repository owner="devteam" name="complement" changeset_revision="67c4ed724bfd" description="Complement intervals of a dataset"> + <repository owner="devteam" name="complement" changeset_revision="2221cf5f59aa" description="Complement intervals of a dataset"><tool id="gops_complement_1" version="1.0.0" file="new_operations/complement.xml" /></repository><repository owner="devteam" name="compute_q_values" changeset_revision="63abfc350814" description="Compute q-values based on multiple simultaneous tests p-values"> 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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