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commit/galaxy-central: jgoecks: Create and use mixin method for getting dataset's genome data.
by Bitbucket 10 Oct '12

10 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/220b6683e8da/ changeset: 220b6683e8da user: jgoecks date: 2012-10-10 05:49:01 summary: Create and use mixin method for getting dataset's genome data. affected #: 4 files diff -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 lib/galaxy/visualization/data_providers/genome.py --- a/lib/galaxy/visualization/data_providers/genome.py +++ b/lib/galaxy/visualization/data_providers/genome.py @@ -186,7 +186,6 @@ chrom_data = self.get_data( chrom, 0, chrom_len, **kwargs ) if chrom_data: chrom_data[ 'region' ] = "%s:%i-%i" % ( chrom, 0, chrom_len ) - chrom_data[ 'dataset_type' ] = self.dataset_type genome_data.append( chrom_data ) return { diff -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -602,6 +602,33 @@ return visualization + def _get_genome_data( self, trans, dataset, dbkey=None ): + """ + Returns genome-wide data for dataset if available; if not, message is returned. + """ + rval = None + + # Get data sources. + data_sources = dataset.get_datasources( trans ) + query_dbkey = dataset.dbkey + if query_dbkey == "?": + query_dbkey = dbkey + chroms_info = self.app.genomes.chroms( trans, dbkey=query_dbkey ) + + # If there are no messages (messages indicate data is not ready/available), preload data. + messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] + message = get_highest_priority_msg( messages_list ) + if message: + rval = message + else: + data_provider = trans.app.data_provider_registry.get_data_provider( trans, + original_dataset=dataset, + source='index' ) + # HACK: pass in additional params, which are only used for summary tree data, not BBI data. + rval = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) + + return rval + class UsesStoredWorkflowMixin( SharableItemSecurityMixin ): """ Mixin for controllers that use StoredWorkflow objects. """ def get_stored_workflow( self, trans, id, check_ownership=True, check_accessible=False ): diff -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -51,6 +51,8 @@ rval = self._raw_data( trans, dataset, **kwd ) elif data_type == 'track_config': rval = self.get_new_track_config( trans, dataset ) + elif data_type == 'genome_data': + rval = self._get_genome_data( self, trans, dataset, kwd.get('dbkey', None) ) else: # Default: return dataset as API value. rval = dataset.get_api_value() diff -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 -r 220b6683e8dad3028939ff6e5a7acd76d9e994b1 lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -772,18 +772,10 @@ # Add genome-wide summary tree data to each track in viz. tracks = viz_config.get( 'tracks', [] ) for track in tracks: - # Get dataset and data sources. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) - data_sources = dataset.get_datasources( trans ) - - # If there are no messages (messages indicate data is not ready/available), preload data. - messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] - if not get_highest_priority_msg( messages_list ): - data_provider = trans.app.data_provider_registry.get_data_provider( trans, - original_dataset=dataset, - source='index' ) - # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - track[ 'preloaded_data' ] = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) + genome_data = self._get_genome_data( trans, dataset, dbkey ) + if not isinstance( genome_data, str ): + track[ 'preloaded_data' ] = genome_data return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) 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: history.js: fix to HistoryView tagging functionality
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/3231b9ca8d82/ changeset: 3231b9ca8d82 user: carlfeberhard date: 2012-10-10 01:10:30 summary: history.js: fix to HistoryView tagging functionality affected #: 4 files diff -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 static/scripts/mvc/history.js --- a/static/scripts/mvc/history.js +++ b/static/scripts/mvc/history.js @@ -558,6 +558,14 @@ parent.append( this._render_displayApps() ); parent.append( this._render_peek() ); + + //TODO??: still needed? + //// If Mozilla, hide scrollbars in hidden items since they cause animation bugs + //if ( $.browser.mozilla ) { + // $( "div.historyItemBody" ).each( function() { + // if ( !$(this).is(":visible") ) { $(this).find( "pre.peek" ).css( "overflow", "hidden" ); } + // }); + //} }, _render_body : function(){ @@ -704,7 +712,13 @@ toggleBodyVisibility : function( visible ){ var $body = this.$el.find( '.historyItemBody' ); - $body.toggle(); + if( visible === undefined ){ + $body.toggle(); + } else if( visible ){ + $body.show(); + } else { + $body.hide(); + } this.trigger( 'toggleBodyVisibility', this.model.get( 'id' ), $body.is( ':visible' ) ); }, @@ -715,9 +729,7 @@ } }); - //------------------------------------------------------------------------------ -//HistoryItemView.templates = InDomTemplateLoader.getTemplates({ HistoryItemView.templates = { warningMsg : Handlebars.templates[ 'template-warningmessagesmall' ], @@ -875,7 +887,6 @@ //------------------------------------------------------------------------------ // view for the HistoryCollection (as per current right hand panel) -//var HistoryView = BaseView.extend( LoggableMixin ).extend( UsesStorageMixin ) .extend({ var HistoryView = BaseView.extend( LoggableMixin ).extend({ // uncomment this out see log messages @@ -894,16 +905,20 @@ ); // set up the individual history items/datasets this.initializeItems(); + }, initializeItems : function(){ this.itemViews = {}; var historyPanel = this; + + // set up a view for each item, init with model and listeners, cache to map ( model.id : view ) this.model.items.each( function( item ){ var itemId = item.get( 'id' ), + visible = historyPanel.storage.get( 'visibleItems' ).get( itemId ), itemView = new HistoryItemView({ - model: item, visible: - historyPanel.storage.get( 'visibleItems' ).get( itemId ) + model: item, + visible: visible }); historyPanel.setUpItemListeners( itemView ); historyPanel.itemViews[ itemId ] = itemView; @@ -912,6 +927,7 @@ setUpItemListeners : function( itemView ){ var HistoryPanel = this; + // use storage to maintain a list of items whose bodies are visible itemView.bind( 'toggleBodyVisibility', function( id, visible ){ if( visible ){ @@ -930,7 +946,34 @@ this.itemsDiv = this.$el.find( '#' + this.model.get( 'id' ) + '-datasets' ); //TODO: set up widgets, tooltips, etc. + async_save_text( + "history-name-container", + "history-name", + this.model.get( 'renameURL' ), + "new_name", + 18 + ); + this.$el.find( '.tooltip' ).tooltip(); + var historyAnnotationArea = this.$el.find( '#history-annotation-area' ); + $( '#history-annotate' ).click( function() { + if ( historyAnnotationArea.is( ":hidden" ) ) { + historyAnnotationArea.slideDown( "fast" ); + } else { + historyAnnotationArea.slideUp( "fast" ); + } + return false; + }); + async_save_text( + "history-annotation-container", + "history-annotation", + this.model.get( 'annotateURL' ), + "new_annotation", + 18, + true, + 4 + ); + if( this.model.items.length ){ // render to temp, move all at once, remove temp holder var tempDiv = this._render_items(); @@ -950,6 +993,53 @@ return div; }, + events : { + 'click #history-collapse-all' : 'hideAllItemBodies', + 'click #history-tag' : 'loadAndDisplayTags' + }, + + hideAllItemBodies : function(){ + _.each( this.itemViews, function( item ){ + item.toggleBodyVisibility( false ); + }); + }, + + loadAndDisplayTags : function( event ){ + //BUG: broken with latest + //TODO: this is a drop in from history.mako - should use MV as well + this.log( this + '.loadAndDisplayTags', event ); + var tagArea = this.$el.find( '#history-tag-area' ), + tagElt = tagArea.find( '.tag-elt' ); + this.log( '\t tagArea', tagArea, ' tagElt', tagElt ); + + // Show or hide tag area; if showing tag area and it's empty, fill it. + if( tagArea.is( ":hidden" ) ){ + if( !jQuery.trim( tagElt.html() ) ){ + var view = this; + // Need to fill tag element. + $.ajax({ + //TODO: the html from this breaks a couple of times + url: this.model.get( 'tagURL' ), + error: function() { alert( "Tagging failed" ); }, + success: function(tag_elt_html) { + view.log( view + ' tag elt html (ajax)', tag_elt_html ); + tagElt.html(tag_elt_html); + tagElt.find(".tooltip").tooltip(); + tagArea.slideDown("fast"); + } + }); + } else { + // Tag element is filled; show. + tagArea.slideDown("fast"); + } + + } else { + // Hide. + tagArea.slideUp("fast"); + } + return false; + }, + toString : function(){ var nameString = this.model.get( 'name' ) || ''; return 'HistoryView(' + nameString + ')'; diff -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 static/scripts/templates/compiled/template-history-historyPanel.js --- a/static/scripts/templates/compiled/template-history-historyPanel.js +++ b/static/scripts/templates/compiled/template-history-historyPanel.js @@ -23,21 +23,13 @@ else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(6, program6, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\""; - foundHelper = helpers.tagURL; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.tagURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"></a>\n <a id=\"history-annotate\" title=\""; + buffer += "\"\n class=\"icon-button tags tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n <a id=\"history-annotate\" title=\""; foundHelper = helpers.local; if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(8, program8, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\""; - foundHelper = helpers.annotateURL; - if (foundHelper) { stack1 = foundHelper.call(depth0, {hash:{}}); } - else { stack1 = depth0.annotateURL; stack1 = typeof stack1 === functionType ? stack1() : stack1; } - buffer += escapeExpression(stack1) + "\"></a>\n </div>\n "; + buffer += "\"\n class=\"icon-button annotate tooltip\" target=\"galaxy_main\" href=\"javascript:void(0)\"></a>\n </div>\n "; return buffer;} function program6(depth0,data) { @@ -143,9 +135,9 @@ var buffer = "", stack1; buffer += "\n"; - buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n <b>Tags:</b>\n "; + buffer += "\n<div style=\"margin: 0px 5px 10px 5px\">\n\n <div id=\"history-tag-area\" style=\"display: none\">\n "; buffer += "\n "; - buffer += "\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; + buffer += "\n <strong>Tags:</strong>\n <div class=\"tag-elt\"></div>\n </div>\n\n <div id=\"history-annotation-area\" style=\"display: none\">\n <strong>Annotation / Notes:</strong>\n <div id=\"history-annotation-container\">\n <div id=\"history-annotation\" class=\"tooltip editable-text\" title=\"Click to edit annotation\">\n "; stack1 = depth0.annotation; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.program(27, program27, data),fn:self.program(25, program25, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } @@ -228,7 +220,7 @@ else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1() : stack1; } if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(3, program3, data)}); } if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "' class='icon-button toggle tooltip' href='#' style=\"display: none\"></a>\n "; + buffer += "' id=\"history-collapse-all\"\n class='icon-button toggle tooltip' href='javascript:void(0);'></a>\n "; stack1 = depth0.userRoles; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(5, program5, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } @@ -252,7 +244,6 @@ if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n"; buffer += "\n"; - buffer += "\n"; stack1 = depth0.userRoles; stack1 = helpers['if'].call(depth0, stack1, {hash:{},inverse:self.noop,fn:self.program(24, program24, data)}); if(stack1 || stack1 === 0) { buffer += stack1; } diff -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -103,13 +103,14 @@ <script type="text/template" class="template-history" id="template-history-historyPanel"><div id="top-links" class="historyLinks"><a title="{{#local}}refresh{{/local}}" class="icon-button arrow-circle tooltip" href="{{baseURL}}"></a> - <a title='{{#local}}collapse all{{/local}}' class='icon-button toggle tooltip' href='#' style="display: none"></a> + <a title='{{#local}}collapse all{{/local}}' id="history-collapse-all" + class='icon-button toggle tooltip' href='javascript:void(0);'></a> {{#if userRoles}} <div style="width: 40px; float: right; white-space: nowrap;"><a id="history-tag" title="{{#local}}Edit history tags{{/local}}" - class="icon-button tags tooltip" target="galaxy_main" href="{{tagURL}}"></a> + class="icon-button tags tooltip" target="galaxy_main" href="javascript:void(0)"></a><a id="history-annotate" title="{{#local}}Edit history annotation{{/local}}" - class="icon-button annotate tooltip" target="galaxy_main" href="{{annotateURL}}"></a> + class="icon-button annotate tooltip" target="galaxy_main" href="javascript:void(0)"></a></div> {{/if}} </div> @@ -148,15 +149,15 @@ {{/if}} {{! tags and annotations }} -{{! TODO: wire these to js events }} {{#if userRoles}} {{! TODO: move inline styles out }} <div style="margin: 0px 5px 10px 5px"><div id="history-tag-area" style="display: none"> - <b>Tags:</b> {{! load via js render_individual_tagging_element }} {{! render_individual_tagging_element(user=trans.get_user(), tagged_item=history, elt_context="history.mako", use_toggle_link=False, input_size="20") }} + <strong>Tags:</strong> + <div class="tag-elt"></div></div><div id="history-annotation-area" style="display: none"> @@ -202,6 +203,3 @@ </div> {{/if}} </script> - - - diff -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d -r 3231b9ca8d82219cbef87cfeb4fc57013c11f3c5 templates/root/alternate_history.mako --- a/templates/root/alternate_history.mako +++ b/templates/root/alternate_history.mako @@ -291,9 +291,10 @@ ##TODO: move to API for_editing = True + encoded_history_id = trans.security.encode_id( history.id ) context_dict = { 'history' : { - 'id' : trans.security.encode_id( history.id ), + 'id' : encoded_history_id, 'name' : history.name, 'status' : status, @@ -324,11 +325,13 @@ 'annotation' : h.to_unicode( annotation ), ##TODO: broken - 'baseURL' : h.url_for( 'history', show_deleted=show_deleted ), - 'hideDeletedURL' : h.url_for( 'history', show_deleted=False ), - 'hideHiddenURL' : h.url_for( 'history', show_hidden=False ), - 'tagURL' : h.url_for( controller='history', action='tag' ), - 'annotateURL' : h.url_for( controller='history', action='annotate' ) + 'baseURL' : h.url_for( controller="/history", show_deleted=show_deleted ), + 'hideDeletedURL' : h.url_for( controller="/history", show_deleted=False ), + 'hideHiddenURL' : h.url_for( controller="/history", show_hidden=False ), + 'renameURL' : h.url_for( controller="/history", action="rename_async", id=encoded_history_id ), + 'tagURL' : h.url_for( controller='tag', action='get_tagging_elt_async', + item_class=history.__class__.__name__, item_id=encoded_history_id ), + 'annotateURL' : h.url_for( controller="/history", action="annotate_async", id=encoded_history_id ) }, 'hdas' : [ prep_hda( hda, for_editing ) for hda in datasets ], Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 3 new changesets
by Bitbucket 09 Oct '12

09 Oct '12

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/9635e2cc9a24/ changeset: 9635e2cc9a24 user: jgoecks date: 2012-10-09 18:33:02 summary: Trackster: accurately calculate track/tile heights by clearing previously set height before calculating new height. affected #: 1 file diff -r 79bb2432133f9b18450e142fc6b80ddab364b57e -r 9635e2cc9a249aea5d939c0f4ca955c5faa3dd58 static/scripts/viz/trackster/tracks.js --- a/static/scripts/viz/trackster/tracks.js +++ b/static/scripts/viz/trackster/tracks.js @@ -3020,13 +3020,10 @@ * an existing tile rather than reshowing it. */ show_tile: function(tile, parent_element, w_scale) { - var - track = this, + var track = this, tile_element = tile.html_elt; - // - // Show/move tile element. - // + // -- Show/move tile element. -- tile.predisplay_actions(); @@ -3046,14 +3043,12 @@ // Showing new tile. parent_element.append(tile_element); } + + // -- Update track, tile heights based on new tile. -- - track.after_show_tile(tile); - }, - - /** - * Actions to be taken after showing tile. - */ - after_show_tile: function(tile) { + // Clear any previous height settings for tile. + tile.html_elt.height('auto'); + // Update max height based on current tile. this.max_height_px = Math.max(this.max_height_px, tile.html_elt.height()); https://bitbucket.org/galaxy/galaxy-central/changeset/437b0d9ccb60/ changeset: 437b0d9ccb60 user: jgoecks date: 2012-10-09 20:16:16 summary: For Circster: only preload data if indexing is complete. affected #: 1 file diff -r 9635e2cc9a249aea5d939c0f4ca955c5faa3dd58 -r 437b0d9ccb60141d9378642893ce13bd50187cea lib/galaxy/webapps/galaxy/controllers/visualization.py --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -772,14 +772,18 @@ # Add genome-wide summary tree data to each track in viz. tracks = viz_config.get( 'tracks', [] ) for track in tracks: - # Get dataset and indexed datatype. + # Get dataset and data sources. dataset = self.get_hda_or_ldda( trans, track[ 'hda_ldda'], track[ 'dataset_id' ] ) data_sources = dataset.get_datasources( trans ) - data_provider = trans.app.data_provider_registry.get_data_provider( trans, - original_dataset=dataset, - source='index' ) - # HACK: pass in additional params, which are only used for summary tree data, not BBI data. - track[ 'preloaded_data' ] = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) + + # If there are no messages (messages indicate data is not ready/available), preload data. + messages_list = [ data_source_dict[ 'message' ] for data_source_dict in data_sources.values() ] + if not get_highest_priority_msg( messages_list ): + data_provider = trans.app.data_provider_registry.get_data_provider( trans, + original_dataset=dataset, + source='index' ) + # HACK: pass in additional params, which are only used for summary tree data, not BBI data. + track[ 'preloaded_data' ] = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0 ) return trans.fill_template( 'visualization/circster.mako', viz_config=viz_config, genome=genome ) https://bitbucket.org/galaxy/galaxy-central/changeset/dcb22217c175/ changeset: dcb22217c175 user: jgoecks date: 2012-10-09 20:16:27 summary: Merge affected #: 2 files diff -r 437b0d9ccb60141d9378642893ce13bd50187cea -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -345,13 +345,13 @@ def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): if values is None and context: - column_range = range( 1, context.columns+1, 1 ) + column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) values = zip( column_range, column_range ) return RangeParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) def get_html( self, value, context={}, other_values={}, values=None, **kwd ): if values is None and context: - column_range = range( 1, context.columns+1, 1 ) + column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) values = zip( column_range, column_range ) return RangeParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) diff -r 437b0d9ccb60141d9378642893ce13bd50187cea -r dcb22217c17527427c17f4ca3edeb5d6a98f6f4d lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -274,12 +274,18 @@ column_names = dataset.metadata.column_names elif hasattr(dataset.datatype, 'column_names'): column_names = dataset.datatype.column_names + column_types = dataset.metadata.column_types + if not column_types: + column_types = [] + column_number = dataset.metadata.columns + if column_number is None: + column_number = 'null' return trans.fill_template( "/dataset/tabular_chunked.mako", dataset = dataset, chunk = self.get_chunk(trans, dataset, 0), - column_number = dataset.metadata.columns, + column_number = column_number, column_names = column_names, - column_types = dataset.metadata.column_types) + column_types = column_types ) def set_peek( self, dataset, line_count=None, is_multi_byte=False): super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Fix for displaying metadata ColumnParameter type when columns is None.
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/6f017bc991a6/ changeset: 6f017bc991a6 user: dan date: 2012-10-09 19:57:19 summary: Fix for displaying metadata ColumnParameter type when columns is None. affected #: 1 file diff -r 8ce7bbba361a93a1a4a50029a3fd6a6266c1934d -r 6f017bc991a6e4617488768532adb56d49c1a688 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py +++ b/lib/galaxy/datatypes/metadata.py @@ -345,13 +345,13 @@ def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd ): if values is None and context: - column_range = range( 1, context.columns+1, 1 ) + column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) values = zip( column_range, column_range ) return RangeParameter.get_html_field( self, value=value, context=context, other_values=other_values, values=values, **kwd ) def get_html( self, value, context={}, other_values={}, values=None, **kwd ): if values is None and context: - column_range = range( 1, context.columns+1, 1 ) + column_range = range( 1, ( context.columns or 0 ) + 1, 1 ) values = zip( column_range, column_range ) return RangeParameter.get_html( self, value, context=context, other_values=other_values, values=values, **kwd ) 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 preview display of tabular items when column_number is None.
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/8ce7bbba361a/ changeset: 8ce7bbba361a user: dan date: 2012-10-09 19:50:47 summary: Fix for preview display of tabular items when column_number is None. affected #: 1 file diff -r 259a4e01f105b6f7396292db3ae0971d049b6ce7 -r 8ce7bbba361a93a1a4a50029a3fd6a6266c1934d lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -277,10 +277,13 @@ column_types = dataset.metadata.column_types if not column_types: column_types = [] + column_number = dataset.metadata.columns + if column_number is None: + column_number = 'null' return trans.fill_template( "/dataset/tabular_chunked.mako", dataset = dataset, chunk = self.get_chunk(trans, dataset, 0), - column_number = dataset.metadata.columns, + column_number = column_number, column_names = column_names, column_types = column_types ) 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 preview display of tabular items when column_types is None.
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/259a4e01f105/ changeset: 259a4e01f105 user: dan date: 2012-10-09 19:46:19 summary: Fix for preview display of tabular items when column_types is None. affected #: 1 file diff -r 79bb2432133f9b18450e142fc6b80ddab364b57e -r 259a4e01f105b6f7396292db3ae0971d049b6ce7 lib/galaxy/datatypes/tabular.py --- a/lib/galaxy/datatypes/tabular.py +++ b/lib/galaxy/datatypes/tabular.py @@ -274,12 +274,15 @@ column_names = dataset.metadata.column_names elif hasattr(dataset.datatype, 'column_names'): column_names = dataset.datatype.column_names + column_types = dataset.metadata.column_types + if not column_types: + column_types = [] return trans.fill_template( "/dataset/tabular_chunked.mako", dataset = dataset, chunk = self.get_chunk(trans, dataset, 0), column_number = dataset.metadata.columns, column_names = column_names, - column_types = dataset.metadata.column_types) + column_types = column_types ) def set_peek( self, dataset, line_count=None, is_multi_byte=False): super(Tabular, self).set_peek( dataset, line_count=line_count, is_multi_byte=is_multi_byte) 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: jgoecks: Fix typo in datasets API controller.
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/79bb2432133f/ changeset: 79bb2432133f user: jgoecks date: 2012-10-09 17:59:59 summary: Fix typo in datasets API controller. affected #: 1 file diff -r 04229b267b3e8dd112d3e66fd6826d2f66404424 -r 79bb2432133f9b18450e142fc6b80ddab364b57e lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -46,7 +46,7 @@ elif data_type == 'data': rval = self._data( trans, dataset, **kwd ) elif data_type == 'features': - rval = self._search_features( trans, dataset, kwd.get( 'query ' ) ) + rval = self._search_features( trans, dataset, kwd.get( 'query' ) ) elif data_type == 'raw_data': rval = self._raw_data( trans, dataset, **kwd ) elif data_type == 'track_config': 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: Some cleanup for shed_util.py
by Bitbucket 09 Oct '12

09 Oct '12

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04229b267b3e/ changeset: 04229b267b3e user: dan date: 2012-10-09 16:27:54 summary: Some cleanup for shed_util.py affected #: 1 file diff -r 429e895ee1b3bfb2fea1632d34a01d54faeac866 -r 04229b267b3e8dd112d3e66fd6826d2f66404424 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -387,8 +387,6 @@ else: tmp_url = repository_clone_url return tmp_url -def tool_shed_from_repository_clone_url( repository_clone_url ): - return clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' ) def clean_tool_shed_url( tool_shed_url ): if tool_shed_url.find( ':' ) > 0: # Eliminate the port, if any, since it will result in an invalid directory name. @@ -1772,42 +1770,6 @@ config_elems.remove( config_elem ) # Persist the altered in-memory version of the tool config. config_elems_to_xml_file( trans.app, config_elems, shed_tool_conf, tool_path ) -def update_in_shed_tool_config( app, repository ): - # A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list - # of config_elems instead of using the in-memory list. - shed_conf_dict = repository.get_shed_config_dict( app ) - shed_tool_conf = shed_conf_dict[ 'config_filename' ] - tool_path = shed_conf_dict[ 'tool_path' ] - - #hack for 'trans.app' used in lots of places. These places should just directly use app - trans = util.bunch.Bunch() - trans.app = app - - tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ) - repository_tools_tups = get_repository_tools_tups( app, repository.metadata ) - cleaned_repository_clone_url = clean_repository_clone_url( generate_clone_url( trans, repository ) ) - tool_shed = tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) - owner = repository.owner - if not owner: - owner = get_repository_owner( cleaned_repository_clone_url ) - guid_to_tool_elem_dict = {} - for tool_config_filename, guid, tool in repository_tools_tups: - guid_to_tool_elem_dict[ guid ] = generate_tool_elem( tool_shed, repository.name, repository.changeset_revision, repository.owner or '', tool_config_filename, tool, None ) - config_elems = [] - tree = util.parse_xml( shed_tool_conf ) - root = tree.getroot() - for elem in root: - if elem.tag == 'section': - for i, tool_elem in enumerate( elem ): - guid = tool_elem.attrib.get( 'guid' ) - if guid in guid_to_tool_elem_dict: - elem[i] = guid_to_tool_elem_dict[ guid ] - elif elem.tag == 'tool': - guid = elem.attrib.get( 'guid' ) - if guid in guid_to_tool_elem_dict: - elem = guid_to_tool_elem_dict[ guid ] - config_elems.append( elem ) - config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) def remove_from_tool_panel( trans, repository, shed_tool_conf, uninstall ): """A tool shed repository is being deactivated or uninstalled so handle tool panel alterations accordingly.""" # Determine where the tools are currently defined in the tool panel and store this information so the tools can be displayed @@ -2016,6 +1978,8 @@ elif c not in [ '\r' ]: translated.append( '' ) return ''.join( translated ) +def tool_shed_from_repository_clone_url( repository_clone_url ): + return clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' ) def translate_string( raw_text, to_html=True ): if raw_text: if to_html: @@ -2086,6 +2050,42 @@ sa_session.delete( tool_dependency ) sa_session.flush() return new_tool_dependency +def update_in_shed_tool_config( app, repository ): + # A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list + # of config_elems instead of using the in-memory list. + shed_conf_dict = repository.get_shed_config_dict( app ) + shed_tool_conf = shed_conf_dict[ 'config_filename' ] + tool_path = shed_conf_dict[ 'tool_path' ] + + #hack for 'trans.app' used in lots of places. These places should just directly use app + trans = util.bunch.Bunch() + trans.app = app + + tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ) + repository_tools_tups = get_repository_tools_tups( app, repository.metadata ) + cleaned_repository_clone_url = clean_repository_clone_url( generate_clone_url( trans, repository ) ) + tool_shed = tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) + owner = repository.owner + if not owner: + owner = get_repository_owner( cleaned_repository_clone_url ) + guid_to_tool_elem_dict = {} + for tool_config_filename, guid, tool in repository_tools_tups: + guid_to_tool_elem_dict[ guid ] = generate_tool_elem( tool_shed, repository.name, repository.changeset_revision, repository.owner or '', tool_config_filename, tool, None ) + config_elems = [] + tree = util.parse_xml( shed_tool_conf ) + root = tree.getroot() + for elem in root: + if elem.tag == 'section': + for i, tool_elem in enumerate( elem ): + guid = tool_elem.attrib.get( 'guid' ) + if guid in guid_to_tool_elem_dict: + elem[i] = guid_to_tool_elem_dict[ guid ] + elif elem.tag == 'tool': + guid = elem.attrib.get( 'guid' ) + if guid in guid_to_tool_elem_dict: + elem = guid_to_tool_elem_dict[ guid ] + config_elems.append( elem ) + config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) def update_repository( repo, ctx_rev=None ): """ Update the cloned repository to changeset_revision. It is critical that the installed repository is updated to the desired 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: 4 new changesets
by Bitbucket 09 Oct '12

09 Oct '12

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/921a612db28a/ changeset: 921a612db28a user: dan date: 2012-10-09 16:24:58 summary: Enhance Galaxy's model.ToolShedRepository to handle shed_conf_dict easier. affected #: 1 file diff -r 413cf15e4065a9f8d559ca110e6e86b84f8a6620 -r 921a612db28a69a33dc1ea8bef5ed20ffa63bba2 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -2987,6 +2987,78 @@ return relative_path return None @property + def tool_shed_path_name( self ): + tool_shed_url = self.tool_shed + if tool_shed_url.find( ':' ) > 0: + # Eliminate the port, if any, since it will result in an invalid directory name. + tool_shed_url = tool_shed_url.split( ':' )[ 0 ] + return tool_shed_url.rstrip( '/' ) + def get_tool_relative_path( self, app ): + shed_conf_dict = self.get_shed_config_dict( app ) + tool_path = None + relative_path = None + if shed_conf_dict: + tool_path = shed_conf_dict[ 'tool_path' ] + relative_path = os.path.join( self.tool_shed_path_name, 'repos', self.owner, self.name, self.installed_changeset_revision ) + return tool_path, relative_path + def get_shed_config_filename( self ): + shed_config_filename = None + if self.metadata: + shed_config_filename = self.metadata.get( 'shed_config_filename', shed_config_filename ) + return shed_config_filename + def set_shed_config_filename( self, value ): + self.metadata[ 'shed_config_filename' ] = value + shed_config_filename = property( get_shed_config_filename, set_shed_config_filename ) + def guess_shed_config( self, app, default=None ): + tool_ids = [] + metadata = self.metadata or {} + for tool in metadata.get( 'tools', [] ): + tool_ids.append( tool.get( 'guid' ) ) + for shed_tool_conf_dict in app.toolbox.shed_tool_confs: + name = shed_tool_conf_dict[ 'config_filename' ] + for elem in shed_tool_conf_dict[ 'config_elems' ]: + if elem.tag == 'tool': + for sub_elem in elem.findall( 'id' ): + tool_id = sub_elem.text.strip() + if tool_id in tool_ids: + self.shed_config_filename = name + return shed_tool_conf_dict + elif elem.tag == "section": + for tool_elem in elem.findall( 'tool' ): + for sub_elem in tool_elem.findall( 'id' ): + tool_id = sub_elem.text.strip() + if tool_id in tool_ids: + self.shed_config_filename = name + return shed_tool_conf_dict + if self.includes_datatypes: + #we need to search by filepaths here, which is less desirable + tool_shed_url = self.tool_shed + if tool_shed_url.find( ':' ) > 0: + # Eliminate the port, if any, since it will result in an invalid directory name. + tool_shed_url = tool_shed_url.split( ':' )[ 0 ] + tool_shed = tool_shed_url.rstrip( '/' ) + for shed_tool_conf_dict in app.toolbox.shed_tool_confs: + tool_path = shed_tool_conf_dict[ 'tool_path' ] + relative_path = os.path.join( tool_path, tool_shed, 'repos', self.owner, self.name, self.installed_changeset_revision ) + if os.path.exists( relative_path ): + self.shed_config_filename = shed_tool_conf_dict[ 'config_filename' ] + return shed_tool_conf_dict + #if self.dist_to_shed: + # #return ./migrated_tools.xml + return default + def get_shed_config_dict( self, app, default=None ): + """ + Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry + in the shed_tool_conf_dict. + """ + if not self.shed_config_filename: + self.guess_shed_config( app, default=default ) + if self.shed_config_filename: + for shed_tool_conf_dict in app.toolbox.shed_tool_confs: + if self.shed_config_filename == shed_tool_conf_dict[ 'config_filename' ]: + return shed_tool_conf_dict + return default + @property def can_install( self ): return self.status == self.installation_status.NEW @property https://bitbucket.org/galaxy/galaxy-central/changeset/0263d37b08e6/ changeset: 0263d37b08e6 user: dan date: 2012-10-09 16:24:58 summary: Add a helper method to the toolbox to provide a shed_config_dict based upon the provided filename. affected #: 1 file diff -r 921a612db28a69a33dc1ea8bef5ed20ffa63bba2 -r 0263d37b08e610e572b5f08940c19a6f19f0931d lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -150,6 +150,11 @@ tool_path=tool_path, config_elems=config_elems ) self.shed_tool_confs.append( shed_tool_conf_dict ) + def get_shed_config_dict_by_filename( self, filename, default=None ): + for shed_config_dict in self.shed_tool_confs: + if shed_config_dict[ 'config_filename' ] == filename: + return shed_config_dict + return default def __add_tool_to_tool_panel( self, tool_id, panel_component, section=False ): # See if a version of this tool is already loaded into the tool panel. The value of panel_component # will be a ToolSection (if the value of section=True) or self.tool_panel (if section=False). https://bitbucket.org/galaxy/galaxy-central/changeset/97eb5bde48da/ changeset: 97eb5bde48da user: dan date: 2012-10-09 16:24:59 summary: Enhance Galaxy's handling of Tool Shed Repositories to work with hierarchical relative paths. affected #: 3 files diff -r 0263d37b08e610e572b5f08940c19a6f19f0931d -r 97eb5bde48da4575e8de4fed64fe910a4df45dce lib/galaxy/tool_shed/install_manager.py --- a/lib/galaxy/tool_shed/install_manager.py +++ b/lib/galaxy/tool_shed/install_manager.py @@ -33,9 +33,12 @@ root = tree.getroot() self.tool_shed = clean_tool_shed_url( root.get( 'name' ) ) self.repository_owner = REPOSITORY_OWNER + index, self.shed_config_dict = get_shed_tool_conf_dict( app, self.migrated_tools_config ) for repository_elem in root: self.install_repository( repository_elem, install_dependencies ) def get_guid( self, repository_clone_url, relative_install_dir, tool_config ): + if self.shed_config_dict.get( 'tool_path' ): + relative_install_dir = os.path.join( self.shed_config_dict['tool_path'], relative_install_dir ) found = False for root, dirs, files in os.walk( relative_install_dir ): if root.find( '.hg' ) < 0 and root.find( 'hgrc' ) < 0: @@ -122,6 +125,10 @@ def handle_repository_contents( self, tool_shed_repository, repository_clone_url, relative_install_dir, repository_elem, install_dependencies ): """Generate the metadata for the installed tool shed repository, among other things.""" tool_panel_dict_for_display = odict() + if self.tool_path: + repo_install_dir = os.path.join( self.tool_path, relative_install_dir ) + else: + repo_install_dir = relative_install_dir for tool_elem in repository_elem: # The tool_elem looks something like this: <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> tool_config = tool_elem.get( 'file' ) @@ -135,6 +142,7 @@ metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=self.app, repository=tool_shed_repository, repository_clone_url=repository_clone_url, + shed_config_dict = self.shed_config_dict, relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, @@ -150,7 +158,7 @@ if 'tools' in metadata_dict: sample_files = metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = get_tool_index_sample_files( sample_files ) - copy_sample_files( self.app, tool_index_sample_files ) + copy_sample_files( self.app, tool_index_sample_files, tool_path=self.tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] repository_tools_tups = get_repository_tools_tups( self.app, metadata_dict ) if repository_tools_tups: @@ -163,14 +171,14 @@ repository_tools_tups, sample_files_copied ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. - copy_sample_files( self.app, sample_files, sample_files_copied=sample_files_copied ) + copy_sample_files( self.app, sample_files, tool_path=self.tool_path, sample_files_copied=sample_files_copied ) if install_dependencies and tool_dependencies and 'tool_dependencies' in metadata_dict: # Install tool dependencies. update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from disk. - tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', repo_install_dir ) installed_tool_dependencies = handle_tool_dependencies( app=self.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, @@ -195,10 +203,10 @@ self.app.sa_session.add( tool_shed_repository ) self.app.sa_session.flush() work_dir = tempfile.mkdtemp() - datatypes_config = get_config_from_disk( 'datatypes_conf.xml', relative_install_dir ) + datatypes_config = get_config_from_disk( 'datatypes_conf.xml', repo_install_dir ) # Load proprietary data types required by tools. The value of override is not important here since the Galaxy server will be started # after this installation completes. - converter_path, display_path = alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, relative_install_dir, override=False ) + converter_path, display_path = alter_config_and_load_prorietary_datatypes( self.app, datatypes_config, repo_install_dir, override=False ) #repo_install_dir was relative_install_dir if converter_path or display_path: # Create a dictionary of tool shed repository related information. repository_dict = create_repository_dict_for_proprietary_datatypes( tool_shed=self.tool_shed, @@ -224,13 +232,15 @@ description = repository_elem.get( 'description' ) installed_changeset_revision = repository_elem.get( 'changeset_revision' ) # Install path is of the form: <tool path>/<tool shed>/repos/<repository owner>/<repository name>/<installed changeset revision> - clone_dir = os.path.join( self.tool_path, self.tool_shed, 'repos', self.repository_owner, name, installed_changeset_revision ) + relative_clone_dir = os.path.join( self.tool_shed, 'repos', self.repository_owner, name, installed_changeset_revision ) + clone_dir = os.path.join( self.tool_path, relative_clone_dir ) if self.__isinstalled( clone_dir ): print "Skipping automatic install of repository '", name, "' because it has already been installed in location ", clone_dir else: tool_shed_url = self.__get_url_from_tool_shed( self.tool_shed ) repository_clone_url = os.path.join( tool_shed_url, 'repos', self.repository_owner, name ) - relative_install_dir = os.path.join( clone_dir, name ) + relative_install_dir = os.path.join( relative_clone_dir, name ) + install_dir = os.path.join( clone_dir, name ) ctx_rev = get_ctx_rev( tool_shed_url, name, self.repository_owner, installed_changeset_revision ) print "Adding new row (or updating an existing row) for repository '%s' in the tool_shed_repository table." % name tool_shed_repository = create_or_update_tool_shed_repository( app=self.app, @@ -245,7 +255,7 @@ owner=self.repository_owner, dist_to_shed=True ) update_tool_shed_repository_status( self.app, tool_shed_repository, self.app.model.ToolShedRepository.installation_status.CLONING ) - cloned_ok, error_message = clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + cloned_ok, error_message = clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) if cloned_ok: self.handle_repository_contents( tool_shed_repository=tool_shed_repository, repository_clone_url=repository_clone_url, diff -r 0263d37b08e610e572b5f08940c19a6f19f0931d -r 97eb5bde48da4575e8de4fed64fe910a4df45dce lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -387,6 +387,8 @@ else: tmp_url = repository_clone_url return tmp_url +def tool_shed_from_repository_clone_url( repository_clone_url ): + return clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' ) def clean_tool_shed_url( tool_shed_url ): if tool_shed_url.find( ':' ) > 0: # Eliminate the port, if any, since it will result in an invalid directory name. @@ -421,7 +423,7 @@ # Only create the .loc file if it does not yet exist. We don't overwrite it in case it contains stuff proprietary to the local instance. if not os.path.exists( os.path.join( dest_path, copied_file ) ): shutil.copy( full_source_path, os.path.join( dest_path, copied_file ) ) -def copy_sample_files( app, sample_files, sample_files_copied=None, dest_path=None ): +def copy_sample_files( app, sample_files, tool_path=None, sample_files_copied=None, dest_path=None ): """ Copy all files to dest_path in the local Galaxy environment that have not already been copied. Those that have been copied are contained in sample_files_copied. The default value for dest_path is ~/tool-data. @@ -429,6 +431,8 @@ sample_files_copied = util.listify( sample_files_copied ) for filename in sample_files: if filename not in sample_files_copied: + if tool_path: + filename=os.path.join( tool_path, filename ) copy_sample_file( app, filename, dest_path=dest_path ) def create_repo_info_dict( repository, owner, repository_clone_url, changeset_revision, ctx_rev, metadata ): repo_info_dict = {} @@ -504,6 +508,9 @@ def create_tool_dependency_objects( app, tool_shed_repository, relative_install_dir, set_status=True ): # Create or update a ToolDependency for each entry in tool_dependencies_config. This method is called when installing a new tool_shed_repository. tool_dependency_objects = [] + shed_config_dict = tool_shed_repository.get_shed_config_dict( app ) + if shed_config_dict.get( 'tool_path' ): + relative_install_dir = os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) try: @@ -601,7 +608,7 @@ else: tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return tool_dependencies_dict -def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, relative_install_dir=None, repository_files_dir=None, +def generate_metadata_for_changeset_revision( app, repository, repository_clone_url, shed_config_dict={}, relative_install_dir=None, repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False ): """ Generate metadata for a repository using it's files on disk. To generate metadata for changeset revisions older than the repository tip, @@ -616,7 +623,7 @@ else: original_repository_metadata = None readme_file_names = get_readme_file_names( repository.name ) - metadata_dict = {} + metadata_dict = { 'shed_config_filename': shed_config_dict.get( 'config_filename' ) } invalid_file_tups = [] invalid_tool_configs = [] tool_dependencies_config = None @@ -637,6 +644,8 @@ work_dir = tempfile.mkdtemp() # All other files are on disk in the repository's repo_path, which is the value of relative_install_dir. files_dir = relative_install_dir + if shed_config_dict.get( 'tool_path' ): + files_dir = os.path.join( shed_config_dict['tool_path'], files_dir ) app.config.tool_data_path = work_dir app.config.tool_data_table_config_path = work_dir # Handle proprietary datatypes, if any. @@ -645,6 +654,7 @@ metadata_dict = generate_datatypes_metadata( datatypes_config, metadata_dict ) # Get the relative path to all sample files included in the repository for storage in the repository's metadata. sample_file_metadata_paths, sample_file_copy_paths = get_sample_files_from_disk( repository_files_dir=files_dir, + tool_path=shed_config_dict.get( 'tool_path' ), relative_install_dir=relative_install_dir, resetting_all_metadata_on_repository=resetting_all_metadata_on_repository ) if sample_file_metadata_paths: @@ -674,6 +684,8 @@ relative_path_to_readme = os.path.join( relative_install_dir, stripped_path_to_readme ) else: relative_path_to_readme = os.path.join( root, name ) + if relative_install_dir and shed_config_dict.get( 'tool_path' ) and relative_path_to_readme.startswith( os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) ): + relative_path_to_readme = relative_path_to_readme[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] metadata_dict[ 'readme' ] = relative_path_to_readme # See if we have a tool config. elif name not in NOT_TOOL_CONFIGS and name.endswith( '.xml' ): @@ -711,6 +723,8 @@ relative_path_to_tool_config = os.path.join( relative_install_dir, stripped_path_to_tool_config ) else: relative_path_to_tool_config = os.path.join( root, name ) + if relative_install_dir and shed_config_dict.get( 'tool_path' ) and relative_path_to_tool_config.startswith( os.path.join( shed_config_dict.get( 'tool_path' ), relative_install_dir ) ): + relative_path_to_tool_config = relative_path_to_tool_config[ len( shed_config_dict.get( 'tool_path' ) ) + 1: ] metadata_dict = generate_tool_metadata( relative_path_to_tool_config, tool, repository_clone_url, metadata_dict ) else: for tup in invalid_files_and_errors_tups: @@ -844,13 +858,35 @@ else: metadata_dict[ 'tools' ] = [ tool_dict ] return metadata_dict +def generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ): + if tool_section is not None: + tool_elem = SubElement( tool_section, 'tool' ) + else: + tool_elem = Element( 'tool' ) + tool_elem.attrib[ 'file' ] = tool_file_path + tool_elem.attrib[ 'guid' ] = tool.guid + tool_shed_elem = SubElement( tool_elem, 'tool_shed' ) + tool_shed_elem.text = tool_shed + repository_name_elem = SubElement( tool_elem, 'repository_name' ) + repository_name_elem.text = repository_name + repository_owner_elem = SubElement( tool_elem, 'repository_owner' ) + repository_owner_elem.text = owner + changeset_revision_elem = SubElement( tool_elem, 'installed_changeset_revision' ) + changeset_revision_elem.text = changeset_revision + id_elem = SubElement( tool_elem, 'id' ) + id_elem.text = tool.id + version_elem = SubElement( tool_elem, 'version' ) + version_elem.text = tool.version + return tool_elem + def generate_tool_panel_elem_list( repository_name, repository_clone_url, changeset_revision, tool_panel_dict, repository_tools_tups, owner='' ): """Generate a list of ElementTree Element objects for each section or tool.""" elem_list = [] tool_elem = None - tmp_url = clean_repository_clone_url( repository_clone_url ) + cleaned_repository_clone_url = clean_repository_clone_url( repository_clone_url ) if not owner: - owner = get_repository_owner( tmp_url ) + owner = get_repository_owner( cleaned_repository_clone_url ) + tool_shed = cleaned_repository_clone_url.split( 'repos' )[ 0 ].rstrip( '/' ) for guid, tool_section_dicts in tool_panel_dict.items(): for tool_section_dict in tool_section_dicts: tool_section = None @@ -874,23 +910,9 @@ if tup_guid == guid: break if inside_section: - tool_elem = SubElement( tool_section, 'tool' ) + tool_elem = generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, tool_section ) else: - tool_elem = Element( 'tool' ) - tool_elem.attrib[ 'file' ] = tool_file_path - tool_elem.attrib[ 'guid' ] = guid - tool_shed_elem = SubElement( tool_elem, 'tool_shed' ) - tool_shed_elem.text = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' ) - repository_name_elem = SubElement( tool_elem, 'repository_name' ) - repository_name_elem.text = repository_name - repository_owner_elem = SubElement( tool_elem, 'repository_owner' ) - repository_owner_elem.text = owner - changeset_revision_elem = SubElement( tool_elem, 'installed_changeset_revision' ) - changeset_revision_elem.text = changeset_revision - id_elem = SubElement( tool_elem, 'id' ) - id_elem.text = tool.id - version_elem = SubElement( tool_elem, 'version' ) - version_elem.text = tool.version + tool_elem = generate_tool_elem( tool_shed, repository_name, changeset_revision, owner, tool_file_path, tool, None ) if inside_section: if section_in_elem_list: elem_list[ index ] = tool_section @@ -1253,18 +1275,21 @@ return get_repository_owner( tmp_url ) def get_repository_tools_tups( app, metadata_dict ): repository_tools_tups = [] + index, shed_conf_dict = get_shed_tool_conf_dict( app, metadata_dict.get( 'shed_config_filename' ) ) if 'tools' in metadata_dict: for tool_dict in metadata_dict[ 'tools' ]: - relative_path = tool_dict.get( 'tool_config', None ) + load_relative_path = relative_path = tool_dict.get( 'tool_config', None ) + if shed_conf_dict.get( 'tool_path' ): + load_relative_path = os.path.join( shed_conf_dict.get( 'tool_path' ), relative_path ) guid = tool_dict.get( 'guid', None ) if relative_path and guid: - tool = app.toolbox.load_tool( os.path.abspath( relative_path ), guid=guid ) + tool = app.toolbox.load_tool( os.path.abspath( load_relative_path ), guid=guid ) else: tool = None if tool: repository_tools_tups.append( ( relative_path, guid, tool ) ) return repository_tools_tups -def get_sample_files_from_disk( repository_files_dir, relative_install_dir=None, resetting_all_metadata_on_repository=False ): +def get_sample_files_from_disk( repository_files_dir, tool_path = None, relative_install_dir=None, resetting_all_metadata_on_repository=False ): if resetting_all_metadata_on_repository: # Keep track of the location where the repository is temporarily cloned so that we can strip it when setting metadata. work_dir = repository_files_dir @@ -1287,6 +1312,9 @@ else: relative_path_to_sample_file = os.path.join( root, name ) sample_file_copy_paths.append( relative_path_to_sample_file ) + if tool_path and relative_install_dir: + if relative_path_to_sample_file.startswith( os.path.join( tool_path, relative_install_dir ) ): + relative_path_to_sample_file = relative_path_to_sample_file[ len( tool_path ) + 1 :] sample_file_metadata_paths.append( relative_path_to_sample_file ) return sample_file_metadata_paths, sample_file_copy_paths def get_shed_tool_conf_dict( app, shed_tool_conf ): @@ -1327,46 +1355,16 @@ partial_install_dir = '%s/repos/%s/%s/%s' % ( tool_shed, repository.owner, repository.name, repository.installed_changeset_revision ) # Get the relative tool installation paths from each of the shed tool configs. relative_install_dir = None - for shed_tool_conf_dict in app.toolbox.shed_tool_confs: - shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ] - if repository.dist_to_shed: - # The repository is owned by devteam and contains tools migrated from the Galaxy distribution to the tool shed, so - # the reserved tool panel config is migrated_tools_conf.xml, to which app.config.migrated_tools_config refers. - if shed_tool_conf == app.config.migrated_tools_config: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - relative_install_dir = os.path.join( tool_path, partial_install_dir ) - if tool_path and relative_install_dir: - return shed_tool_conf, tool_path, relative_install_dir - elif repository.uninstalled: - # Since the repository is uninstalled we don't know what tool panel config was originally used to - # define the tools in the repository, so we'll just make sure not to use the reserved migrated_tools_conf.xml. - if shed_tool_conf != app.config.migrated_tools_config: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - relative_install_dir = os.path.join( tool_path, partial_install_dir ) - if tool_path and relative_install_dir: - return shed_tool_conf, tool_path, relative_install_dir - else: - if repository.includes_tools: - metadata = repository.metadata - for tool_dict in metadata[ 'tools' ]: - # Parse the tool panel config to get the entire set of config_elems. # We'll check config_elems until we - # find an element that matches one of the tools in the repository's metadata. - tool_panel_config = shed_tool_conf_dict[ 'config_filename' ] - tree = util.parse_xml( tool_panel_config ) - root = tree.getroot() - tool_path, relative_install_dir = get_tool_path_install_dir( partial_install_dir, - shed_tool_conf_dict, - tool_dict, - root ) - if tool_path and relative_install_dir: - return shed_tool_conf, tool_path, relative_install_dir - else: - # Nothing will be loaded into the tool panel, so look for the installed repository on disk. - tool_path = shed_tool_conf_dict[ 'tool_path' ] - relative_install_dir = os.path.join( tool_path, partial_install_dir ) - if tool_path and relative_install_dir and os.path.isdir( relative_install_dir ): - return shed_tool_conf, tool_path, relative_install_dir - return None, None, None + shed_config_dict = repository.get_shed_config_dict( app ) + if not shed_config_dict: + #just pick a semi-random shed config + for shed_config_dict in app.toolbox.shed_tool_confs: + if ( repository.dist_to_shed and shed_config_dict['config_filename'] == app.config.migrated_tools_config ) or ( not repository.dist_to_shed and shed_config_dict['config_filename'] != app.config.migrated_tools_config ): + break + shed_tool_conf = shed_config_dict[ 'config_filename' ] + tool_path = shed_config_dict[ 'tool_path' ] + relative_install_dir = partial_install_dir + return shed_tool_conf, tool_path, relative_install_dir def get_tool_path_install_dir( partial_install_dir, shed_tool_conf_dict, tool_dict, config_elems ): for elem in config_elems: if elem.tag == 'tool': @@ -1774,6 +1772,42 @@ config_elems.remove( config_elem ) # Persist the altered in-memory version of the tool config. config_elems_to_xml_file( trans.app, config_elems, shed_tool_conf, tool_path ) +def update_in_shed_tool_config( app, repository ): + # A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list + # of config_elems instead of using the in-memory list. + shed_conf_dict = repository.get_shed_config_dict( app ) + shed_tool_conf = shed_conf_dict[ 'config_filename' ] + tool_path = shed_conf_dict[ 'tool_path' ] + + #hack for 'trans.app' used in lots of places. These places should just directly use app + trans = util.bunch.Bunch() + trans.app = app + + tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ) + repository_tools_tups = get_repository_tools_tups( app, repository.metadata ) + cleaned_repository_clone_url = clean_repository_clone_url( generate_clone_url( trans, repository ) ) + tool_shed = tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) + owner = repository.owner + if not owner: + owner = get_repository_owner( cleaned_repository_clone_url ) + guid_to_tool_elem_dict = {} + for tool_config_filename, guid, tool in repository_tools_tups: + guid_to_tool_elem_dict[ guid ] = generate_tool_elem( tool_shed, repository.name, repository.changeset_revision, repository.owner or '', tool_config_filename, tool, None ) + config_elems = [] + tree = util.parse_xml( shed_tool_conf ) + root = tree.getroot() + for elem in root: + if elem.tag == 'section': + for i, tool_elem in enumerate( elem ): + guid = tool_elem.attrib.get( 'guid' ) + if guid in guid_to_tool_elem_dict: + elem[i] = guid_to_tool_elem_dict[ guid ] + elif elem.tag == 'tool': + guid = elem.attrib.get( 'guid' ) + if guid in guid_to_tool_elem_dict: + elem = guid_to_tool_elem_dict[ guid ] + config_elems.append( elem ) + config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) def remove_from_tool_panel( trans, repository, shed_tool_conf, uninstall ): """A tool shed repository is being deactivated or uninstalled so handle tool panel alterations accordingly.""" # Determine where the tools are currently defined in the tool panel and store this information so the tools can be displayed diff -r 0263d37b08e610e572b5f08940c19a6f19f0931d -r 97eb5bde48da4575e8de4fed64fe910a4df45dce lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -655,15 +655,17 @@ update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING ) repo_info_tuple = repo_info_dict[ tool_shed_repository.name ] description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, tool_dependencies = repo_info_tuple - clone_dir = os.path.join( tool_path, self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) ) - relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) - cloned_ok, error_message = clone_repository( repository_clone_url, os.path.abspath( relative_install_dir ), ctx_rev ) + relative_clone_dir = self.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) + clone_dir = os.path.join( tool_path, relative_clone_dir ) + relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name ) + install_dir = os.path.join( tool_path, relative_install_dir ) + cloned_ok, error_message = clone_repository( repository_clone_url, os.path.abspath( install_dir ), ctx_rev ) if cloned_ok: if reinstalling: # Since we're reinstalling the repository we need to find the latest changeset revision to which is can be updated. current_changeset_revision, current_ctx_rev = get_update_to_changeset_revision_and_ctx_rev( trans, tool_shed_repository ) if current_ctx_rev != ctx_rev: - repo = hg.repository( get_configured_ui(), path=os.path.abspath( relative_install_dir ) ) + repo = hg.repository( get_configured_ui(), path=os.path.abspath( install_dir ) ) pull_repository( repo, repository_clone_url, current_changeset_revision ) update_repository( repo, ctx_rev=current_ctx_rev ) self.handle_repository_contents( trans, @@ -704,7 +706,7 @@ tool_shed_repository, trans.model.ToolShedRepository.installation_status.INSTALLING_TOOL_DEPENDENCIES ) # Get the tool_dependencies.xml file from the repository. - tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', relative_install_dir ) + tool_dependencies_config = get_config_from_disk( 'tool_dependencies.xml', install_dir )#relative_install_dir ) installed_tool_dependencies = handle_tool_dependencies( app=trans.app, tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, @@ -736,6 +738,7 @@ metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=tool_shed_repository, repository_clone_url=repository_clone_url, + shed_config_dict = trans.app.toolbox.get_shed_config_dict_by_filename( shed_tool_conf ), relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, @@ -749,7 +752,7 @@ tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata_dict[ 'tools' ], tool_section ) sample_files = metadata_dict.get( 'sample_files', [] ) tool_index_sample_files = get_tool_index_sample_files( sample_files ) - copy_sample_files( self.app, tool_index_sample_files ) + copy_sample_files( self.app, tool_index_sample_files, tool_path=tool_path ) sample_files_copied = [ s for s in tool_index_sample_files ] repository_tools_tups = get_repository_tools_tups( trans.app, metadata_dict ) if repository_tools_tups: @@ -762,7 +765,7 @@ repository_tools_tups, sample_files_copied ) # Copy remaining sample files included in the repository to the ~/tool-data directory of the local Galaxy instance. - copy_sample_files( trans.app, sample_files, sample_files_copied=sample_files_copied ) + copy_sample_files( trans.app, sample_files, tool_path=tool_path, sample_files_copied=sample_files_copied ) add_to_tool_panel( app=trans.app, repository_name=tool_shed_repository.name, repository_clone_url=repository_clone_url, @@ -805,6 +808,8 @@ repository_id = kwd[ 'id' ] operation = kwd.get( 'operation', None ) repository = get_repository( trans, repository_id ) + if not repository: + return trans.show_error_message( 'Invalid repository specified.' ) if repository.status in [ trans.model.ToolShedRepository.installation_status.CLONING ]: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', @@ -822,7 +827,7 @@ description = util.restore_text( params.get( 'description', repository.description ) ) shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if relative_install_dir: - repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) + repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, repository.name ) ) else: repo_files_dir = None if repository.in_error_state: @@ -1447,20 +1452,27 @@ repository = get_repository( trans, id ) tool_shed_url = get_url_from_repository_tool_shed( trans.app, repository ) repository_clone_url = self.__generate_clone_url( trans, repository ) - relative_install_dir = repository.repo_path( trans.app ) + tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: + original_metadata_dict = repository.metadata metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False ) repository.metadata = metadata_dict - trans.sa_session.add( repository ) - trans.sa_session.flush() - message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name - status = 'done' + if metadata_dict != original_metadata_dict: + update_in_shed_tool_config( trans.app, repository )#def update_in_shed_tool_config( trans, shed_tool_conf_dict, elem_list ): + trans.sa_session.add( repository ) + trans.sa_session.flush() + message = 'Metadata has been reset on repository <b>%s</b>.' % repository.name + status = 'done' + else: + message = 'Metadata did not need to be reset on repository <b>%s</b>.' % repository.name + status = 'done' else: message = 'Error locating installation directory for repository <b>%s</b>.' % repository.name status = 'error' @@ -1618,7 +1630,10 @@ else: shed_tool_conf, tool_path, relative_install_dir = get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if relative_install_dir: - repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, name ) ) + if tool_path: + repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, name ) ) + else: + repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, name ) ) repo = hg.repository( get_configured_ui(), path=repo_files_dir ) repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) pull_repository( repo, repository_clone_url, latest_ctx_rev ) @@ -1628,6 +1643,7 @@ metadata_dict, invalid_file_tups = generate_metadata_for_changeset_revision( app=trans.app, repository=repository, repository_clone_url=repository_clone_url, + shed_config_dict = repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, @@ -1667,8 +1683,13 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, id ) metadata = repository.metadata + shed_config_dict = repository.get_shed_config_dict( trans.app ) + tool_path = shed_config_dict.get( 'tool_path', None ) if metadata and 'readme' in metadata: - f = open( metadata[ 'readme' ], 'r' ) + readme_filename = metadata[ 'readme' ] + if tool_path: + readme_filename = os.path.join( tool_path, readme_filename ) + f = open( readme_filename, 'r' ) raw_text = f.read() f.close() readme_text = translate_string( raw_text, to_html=True ) @@ -1691,6 +1712,7 @@ status = params.get( 'status', 'done' ) repository = get_repository( trans, repository_id ) repository_metadata = repository.metadata + shed_config_dict = repository.get_shed_config_dict( trans.app ) tool_metadata = {} tool_lineage = [] tool = None @@ -1698,7 +1720,10 @@ for tool_metadata_dict in repository_metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: tool_metadata = tool_metadata_dict - tool = trans.app.toolbox.load_tool( os.path.abspath( tool_metadata[ 'tool_config' ] ), guid=tool_metadata[ 'guid' ] ) + tool_config = tool_metadata[ 'tool_config' ] + if shed_config_dict and shed_config_dict.get( 'tool_path' ): + tool_config = os.path.join( shed_config_dict.get( 'tool_path' ), tool_config ) + tool = trans.app.toolbox.load_tool( os.path.abspath( tool_config ), guid=tool_metadata[ 'guid' ] ) if tool: tool_lineage = self.get_versions_of_tool( trans.app, tool.id ) break https://bitbucket.org/galaxy/galaxy-central/changeset/429e895ee1b3/ changeset: 429e895ee1b3 user: dan date: 2012-10-09 16:24:59 summary: Enhance manage_repository.mako to handle null repository metadata. affected #: 1 file diff -r 97eb5bde48da4575e8de4fed64fe910a4df45dce -r 429e895ee1b3bfb2fea1632d34a01d54faeac866 templates/admin/tool_shed_repository/manage_repository.mako --- a/templates/admin/tool_shed_repository/manage_repository.mako +++ b/templates/admin/tool_shed_repository/manage_repository.mako @@ -95,7 +95,7 @@ <div class="toolFormTitle">${repository.name}</div><div class="toolFormBody"><% - metadata = repository.metadata + metadata = repository.metadata or {} missing_tool_dependencies = repository.missing_tool_dependencies installed_tool_dependencies = repository.installed_tool_dependencies %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by Bitbucket 09 Oct '12

09 Oct '12

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/40b252052087/ changeset: 40b252052087 user: chapmanb date: 2012-10-04 21:31:16 summary: Correctly set history and handle output datasets for error cases in tool API. Allow specification of dataset name during uploads, exposing through API affected #: 3 files diff -r f3b183e756f9b209ef0904718ed547e04c74ab7a -r 40b252052087bc06fd1adc47f9633a496a7dd07c lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -209,7 +209,7 @@ dataset_name = get_file_name( data_file['filename'] ) if not dataset_info: dataset_info = 'uploaded file' - return Bunch( type='file', path=data_file['local_filename'], name=get_file_name( data_file['filename'] ) ) + return Bunch( type='file', path=data_file['local_filename'], name=dataset_name ) #return 'file', data_file['local_filename'], get_file_name( data_file.filename ), dataset_name, dataset_info except: # The uploaded file should've been persisted by the upload tool action @@ -227,14 +227,13 @@ if line: if not line.lower().startswith( 'http://' ) and not line.lower().startswith( 'ftp://' ) and not line.lower().startswith( 'https://' ): continue # non-url line, ignore - precreated_name = line dataset_name = override_name if not dataset_name: dataset_name = line dataset_info = override_info if not dataset_info: dataset_info = 'uploaded url' - yield Bunch( type='url', path=line, name=precreated_name ) + yield Bunch( type='url', path=line, name=dataset_name ) #yield ( 'url', line, precreated_name, dataset_name, dataset_info ) else: dataset_name = dataset_info = precreated_name = 'Pasted Entry' #we need to differentiate between various url pastes here diff -r f3b183e756f9b209ef0904718ed547e04c74ab7a -r 40b252052087bc06fd1adc47f9633a496a7dd07c lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -55,6 +55,17 @@ tool = trans.app.toolbox.get_tool( tool_id ) if not tool: return { "message": { "type": "error", "text" : messages.NO_TOOL } } + + # Set running history from payload parameters. + # History not set correctly as part of this API call for + # dataset upload. + history_id = payload.get("history_id", None) + if history_id: + target_history = trans.sa_session.query(trans.app.model.History).get( + trans.security.decode_id(history_id)) + trans.galaxy_session.current_history = target_history + else: + target_history = None # Set up inputs. inputs = payload[ 'inputs' ] @@ -62,10 +73,10 @@ inputs['runtool_btn'] = 'Execute' # TODO: encode data ids and decode ids. params = util.Params( inputs, sanitize = False ) - template, vars = tool.handle_input( trans, params.__dict__ ) - + template, vars = tool.handle_input( trans, params.__dict__, history=target_history) + # TODO: check for errors and ensure that output dataset(s) are available. - output_datasets = vars[ 'out_data' ].values() + output_datasets = vars.get('out_data', {}).values() rval = { "outputs": [] } diff -r f3b183e756f9b209ef0904718ed547e04c74ab7a -r 40b252052087bc06fd1adc47f9633a496a7dd07c tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -41,6 +41,7 @@ <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand."><option value="Yes">Yes</option></param> + <param name="NAME" type="hidden" help="Name for dataset in upload"></param></upload_dataset><param name="dbkey" type="genomebuild" label="Genome" /><conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" /> https://bitbucket.org/galaxy/galaxy-central/changeset/413cf15e4065/ changeset: 413cf15e4065 user: jgoecks date: 2012-10-09 05:44:02 summary: Merged in chapmanb/galaxy-central-apiupload (pull request #74) affected #: 3 files diff -r 8269f76312af60e356707bc660b6e9903e402106 -r 413cf15e4065a9f8d559ca110e6e86b84f8a6620 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py +++ b/lib/galaxy/tools/parameters/grouping.py @@ -209,7 +209,7 @@ dataset_name = get_file_name( data_file['filename'] ) if not dataset_info: dataset_info = 'uploaded file' - return Bunch( type='file', path=data_file['local_filename'], name=get_file_name( data_file['filename'] ) ) + return Bunch( type='file', path=data_file['local_filename'], name=dataset_name ) #return 'file', data_file['local_filename'], get_file_name( data_file.filename ), dataset_name, dataset_info except: # The uploaded file should've been persisted by the upload tool action @@ -227,14 +227,13 @@ if line: if not line.lower().startswith( 'http://' ) and not line.lower().startswith( 'ftp://' ) and not line.lower().startswith( 'https://' ): continue # non-url line, ignore - precreated_name = line dataset_name = override_name if not dataset_name: dataset_name = line dataset_info = override_info if not dataset_info: dataset_info = 'uploaded url' - yield Bunch( type='url', path=line, name=precreated_name ) + yield Bunch( type='url', path=line, name=dataset_name ) #yield ( 'url', line, precreated_name, dataset_name, dataset_info ) else: dataset_name = dataset_info = precreated_name = 'Pasted Entry' #we need to differentiate between various url pastes here diff -r 8269f76312af60e356707bc660b6e9903e402106 -r 413cf15e4065a9f8d559ca110e6e86b84f8a6620 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -55,6 +55,17 @@ tool = trans.app.toolbox.get_tool( tool_id ) if not tool: return { "message": { "type": "error", "text" : messages.NO_TOOL } } + + # Set running history from payload parameters. + # History not set correctly as part of this API call for + # dataset upload. + history_id = payload.get("history_id", None) + if history_id: + target_history = trans.sa_session.query(trans.app.model.History).get( + trans.security.decode_id(history_id)) + trans.galaxy_session.current_history = target_history + else: + target_history = None # Set up inputs. inputs = payload[ 'inputs' ] @@ -62,10 +73,10 @@ inputs['runtool_btn'] = 'Execute' # TODO: encode data ids and decode ids. params = util.Params( inputs, sanitize = False ) - template, vars = tool.handle_input( trans, params.__dict__ ) - + template, vars = tool.handle_input( trans, params.__dict__, history=target_history) + # TODO: check for errors and ensure that output dataset(s) are available. - output_datasets = vars[ 'out_data' ].values() + output_datasets = vars.get('out_data', {}).values() rval = { "outputs": [] } diff -r 8269f76312af60e356707bc660b6e9903e402106 -r 413cf15e4065a9f8d559ca110e6e86b84f8a6620 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -41,6 +41,7 @@ <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand."><option value="Yes">Yes</option></param> + <param name="NAME" type="hidden" help="Name for dataset in upload"></param></upload_dataset><param name="dbkey" type="genomebuild" label="Genome" /><conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" /> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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