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commit/galaxy-central: dan: Fix for server error caused by unicode substitution in url_for.
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1480f00e6bdc/ Changeset: 1480f00e6bdc Branch: stable User: dan Date: 2014-02-18 21:09:46 Summary: Fix for server error caused by unicode substitution in url_for. Affected #: 1 file diff -r 15e8a74a95215bf2cc775e9848ca4a5ecc7e945f -r 1480f00e6bdcebe043b695fa1daaa0220fc0c086 templates/webapps/galaxy/mobile/history/detail.mako --- a/templates/webapps/galaxy/mobile/history/detail.mako +++ b/templates/webapps/galaxy/mobile/history/detail.mako @@ -12,7 +12,7 @@ if data.state in ['no state','',None]: data_state = "queued" else: - data_state = data.state + data_state = str( data.state ) %><li id="historyItemContainer-${data.id}"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Add PyYAML 3.10 egg.
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c36dc4155beb/ Changeset: c36dc4155beb User: dannon Date: 2014-02-20 19:10:00 Summary: Add PyYAML 3.10 egg. Affected #: 1 file diff -r c7fa535a805f0cc654984fe9344ba70c90238a15 -r c36dc4155beb0ae5e117ca33e0ad231535186d6d eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -25,6 +25,7 @@ pysam = 0.4.2 pysqlite = 2.5.6 python_lzo = 1.08_2.03_static +PyYAML = 3.10 threadframe = 0.2 guppy = 0.1.10 SQLAlchemy = 0.7.9 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: Browser tests: update empty history message
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c7fa535a805f/ Changeset: c7fa535a805f User: carlfeberhard Date: 2014-02-20 17:56:45 Summary: Browser tests: update empty history message Affected #: 2 files diff -r baf2a8cc97ed720e10b6148254d7dd7478d8e839 -r c7fa535a805f0cc654984fe9344ba70c90238a15 test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -95,7 +95,7 @@ this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); this.test.assertVisible( emptyMsgSelector, 'Empty history message is visible' ); this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, - 'Message contains "' + emptyMsgStr + '"' ); + 'Message contains\n"' + emptyMsgStr + '":\n"' + this.fetchText( emptyMsgSelector ) + '"' ); }); // ------------------------------------------------------------------- name editing @@ -157,7 +157,7 @@ spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ this.test.comment( 'uploaded file should appear in history' ); - this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); + //this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); var hasHda = _uploadInfo.hdaElement, hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( wrapperOkClassName ) !== -1; diff -r baf2a8cc97ed720e10b6148254d7dd7478d8e839 -r c7fa535a805f0cc654984fe9344ba70c90238a15 test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -388,7 +388,7 @@ }, newName : 'Unnamed history', newSize : '0 bytes', - emptyMsg : "Your history is empty. Click 'Get Data' on the left pane to start" + emptyMsg : "This history is empty. Click 'Get Data' on the left pane to start" }, hda : { datasetFetchErrorMsg : 'There was an error getting the data for this dataset' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Fix for ToolEvaluator with optional Dataset Input selected with multiple inputs.
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/baf2a8cc97ed/ Changeset: baf2a8cc97ed User: dan Date: 2014-02-20 17:52:52 Summary: Fix for ToolEvaluator with optional Dataset Input selected with multiple inputs. Affected #: 1 file diff -r d01fc0370afece3ef77b63a116fd9a1c2105c2e4 -r baf2a8cc97ed720e10b6148254d7dd7478d8e839 lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -232,10 +232,11 @@ tool=self, name=name, ) - real_path = data.file_name - if real_path in input_dataset_paths: - dataset_path = input_dataset_paths[ real_path ] - wrapper_kwds[ 'dataset_path' ] = dataset_path + if data: + real_path = data.file_name + if real_path in input_dataset_paths: + dataset_path = input_dataset_paths[ real_path ] + wrapper_kwds[ 'dataset_path' ] = dataset_path param_dict[name] = DatasetFilenameWrapper( data, **wrapper_kwds ) if data: for child in data.children: 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: clayton_turner: Added ignore lines starting with specific characters to group tool
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ad5156120f53/ Changeset: ad5156120f53 User: clayton_turner Date: 2014-02-10 22:00:30 Summary: Added ignore lines starting with specific characters to group tool Affected #: 2 files diff -r c458a0fe1ba816098fed03370f425f346bb1df68 -r ad5156120f533aeecc1dc69d92ef19ec68a6223b tools/stats/grouping.py --- a/tools/stats/grouping.py +++ b/tools/stats/grouping.py @@ -37,7 +37,22 @@ round_val = [] data_ary = [] - for var in sys.argv[5:]: + if sys.argv[5] != "None": + oldfile = open(inputfile,'r') + oldfilelines = oldfile.readlines() + newinputfile = inputfile+'2' + newfile = open(newinputfile,'w') + asciitodelete = sys.argv[5].split(',') + for i in range(len(asciitodelete)): + asciitodelete[i] = chr(int(asciitodelete[i])) + for line in oldfilelines: + if line[0] not in asciitodelete: + newfile.write(line) + oldfile.close() + newfile.close() + inputfile = newinputfile + + for var in sys.argv[6:]: op, col, do_round = var.split() ops.append(op) cols.append(col) diff -r c458a0fe1ba816098fed03370f425f346bb1df68 -r ad5156120f533aeecc1dc69d92ef19ec68a6223b tools/stats/grouping.xml --- a/tools/stats/grouping.xml +++ b/tools/stats/grouping.xml @@ -6,6 +6,7 @@ $input1 $groupcol $ignorecase + $ignorelines #for $op in $operations '${op.optype} ${op.opcol} @@ -18,6 +19,24 @@ <param name="ignorecase" type="boolean" truevalue="1" falsevalue="0"><label>Ignore case while grouping?</label></param> + <param name="ignorelines" type="select" display="checkboxes" multiple="True" label="Ignore lines beginning with these characters" help="lines beginning with these are not grouped"> + <option value="62">></option> + <option value="64">@</option> + <option value="43">+</option> + <option value="60"><</option> + <option value="42">*</option> + <option value="45">-</option> + <option value="61">=</option> + <option value="124">|</option> + <option value="63">?</option> + <option value="36">$</option> + <option value="46">.</option> + <option value="58">:</option> + <option value="38">&</option> + <option value="37">%</option> + <option value="94">^</option> + <option value="35">#</option> + </param><repeat name="operations" title="Operation"><param name="optype" type="select" label="Type"><option value="mean">Mean</option> 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 published/shared/display as slug: use annotated-history-panel, search open by default, preserve whitespace in annotations, replace import button with 'switch to' if owned by user viewing; Annotated History Panel: panel view of history that shows datasets as a table with additional dataset info in a left cell
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/8e4196a87a2b/ Changeset: 8e4196a87a2b User: carlfeberhard Date: 2014-02-20 17:34:19 Summary: History published/shared/display as slug: use annotated-history-panel, search open by default, preserve whitespace in annotations, replace import button with 'switch to' if owned by user viewing; Annotated History Panel: panel view of history that shows datasets as a table with additional dataset info in a left cell Affected #: 10 files diff -r 32eadec01e3ebeb076b68938269e22f45fb202bb -r 8e4196a87a2b78521241adf104f524a5ea05caa1 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -760,7 +760,9 @@ return self.get_inaccessible_hda_dict( trans, hda ) hda_dict[ 'accessible' ] = True + #TODO: I'm unclear as to which access pattern is right hda_dict[ 'annotation' ] = hda.get_item_annotation_str( trans.sa_session, trans.user, hda ) + #annotation = getattr( hda, 'annotation', hda.get_item_annotation_str( trans.sa_session, trans.user, hda ) ) # ---- return here if deleted AND purged OR can't access purged = ( hda.purged or hda.dataset.purged ) diff -r 32eadec01e3ebeb076b68938269e22f45fb202bb -r 8e4196a87a2b78521241adf104f524a5ea05caa1 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -904,8 +904,9 @@ @web.expose def display_by_username_and_slug( self, trans, username, slug ): - """ Display history based on a username and slug. """ - + """ + Display history based on a username and slug. + """ # Get history. session = trans.sa_session user = session.query( model.User ).filter_by( username=username ).first() @@ -931,7 +932,19 @@ user_item_rating = 0 ave_item_rating, num_ratings = self.get_ave_item_rating_data( trans.sa_session, history ) + # create ownership flag for template, dictify models + # note: adding original annotation since this is published - get_dict returns user-based annos + user_is_owner = trans.user == history.user + hda_dicts = [] + for hda in datasets: + hda_dict = self.get_hda_dict( trans, hda ) + hda_dict[ 'annotation' ] = hda.annotation + hda_dicts.append( hda_dict ) + history_dict = self.get_history_dict( trans, history, hda_dictionaries=hda_dicts ) + history_dict[ 'annotation' ] = history.annotation + return trans.stream_template_mako( "history/display.mako", item=history, item_data=datasets, + user_is_owner=user_is_owner, history_dict=history_dict, hda_dicts=hda_dicts, user_item_rating = user_item_rating, ave_item_rating=ave_item_rating, num_ratings=num_ratings ) @web.expose diff -r 32eadec01e3ebeb076b68938269e22f45fb202bb -r 8e4196a87a2b78521241adf104f524a5ea05caa1 static/scripts/mvc/history/annotated-history-panel.js --- /dev/null +++ b/static/scripts/mvc/history/annotated-history-panel.js @@ -0,0 +1,118 @@ +define([ + "mvc/dataset/hda-model", + "mvc/dataset/hda-base", + "mvc/history/readonly-history-panel" +], function( hdaModel, hdaBase, readonlyPanel ){ +/* ============================================================================= +TODO: + +============================================================================= */ +/** @class View/Controller for a tabular view of the history model. + * @name AnnotatedHistoryPanel + * + * As ReadOnlyHistoryPanel, but with: + * history annotation always shown + * datasets displayed in a table: + * datasets in left cells, dataset annotations in the right + * + * @augments Backbone.View + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var AnnotatedHistoryPanel = readonlyPanel.ReadOnlyHistoryPanel.extend( +/** @lends HistoryPanel.prototype */{ + + ///** logger used to record this.log messages, commonly set to console */ + //// comment this out to suppress log output + //logger : console, + + className : 'annotated-history-panel', + + /** class to use for constructing the HDA views */ + HDAViewClass : hdaBase.HDABaseView, + + // ------------------------------------------------------------------------ panel rendering + renderModel : function( ){ + // huh? + this.$el.addClass( this.className ); + var $newRender = readonlyPanel.ReadOnlyHistoryPanel.prototype.renderModel.call( this ), + // move datasets from div to table + $datasetsList = $newRender.find( this.datasetsSelector ), + $datasetsTable = $( '<table/>' ).addClass( 'datasets-list datasets-table' ); + $datasetsTable.append( $datasetsList.children() ); + $newRender.find( this.datasetsSelector ).replaceWith( $datasetsTable ); + //TODO: it's possible to do this with css only, right? + + // add history annotation under subtitle + $newRender.find( '.history-subtitle' ).after( this.renderHistoryAnnotation() ); + + // hide search button, move search bar beneath controls (instead of above title), show, and set up + $newRender.find( '.history-search-btn' ).hide(); + $newRender.find( '.history-controls' ).after( $newRender.find( '.history-search-controls' ).show() ); + this.setUpSearchInput( $newRender.find( '.history-search-input' ) ); + + return $newRender; + }, + + renderHistoryAnnotation : function(){ + var annotation = this.model.get( 'annotation' ); + if( !annotation ){ return null; } + return $([ + '<div class="history-annotation">', annotation, '</div>' + ].join( '' )); + }, + + renderHdas : function( $whereTo ){ + $whereTo = $whereTo || this.$el; + var hdaViews = readonlyPanel.ReadOnlyHistoryPanel.prototype.renderHdas.call( this, $whereTo ); + $whereTo.find( this.datasetsSelector ).prepend( $( '<tr/>' ).addClass( 'headers' ).append([ + $( '<th/>' ).text( _l( 'Dataset' ) ), + $( '<th/>' ).text( _l( 'Annotation' ) ) + ])); + return hdaViews; + }, + + // ------------------------------------------------------------------------ hda sub-views + attachHdaView : function( hdaView, $whereTo ){ + $whereTo = $whereTo || this.$el; + // build a row around the dataset with the std hdaView in the first cell and the annotation in the next + var stateClass = _.find( hdaView.el.classList, function( c ){ return ( /^state\-/ ).test( c ); }), + annotation = hdaView.model.get( 'annotation' ) || '', + $tr = $( '<tr/>' ).addClass( 'dataset-row' ).append([ + $( '<td/>' ).addClass( 'dataset-container' ).append( hdaView.$el ) + // visually match the cell bg to the dataset at runtime (prevents the empty space) + // (getting bg via jq on hidden elem doesn't work on chrome/webkit - so use states) + //.css( 'background-color', hdaView.$el.css( 'background-color' ) ), + .addClass( stateClass? stateClass.replace( '-', '-color-' ): '' ), + $( '<td/>' ).addClass( 'additional-info' ).text( annotation ) + ]); + $whereTo.find( this.datasetsSelector ).append( $tr ); + }, + + // ------------------------------------------------------------------------ panel events + /** event map */ + events : _.extend( _.clone( readonlyPanel.ReadOnlyHistoryPanel.prototype.events ), { + 'click tr' : function( ev ){ + //if( !ev.target.hasAttribute( 'href' ) ){ + $( ev.currentTarget ).find( '.dataset-title-bar' ).click(); + //} + }, + // prevent propagation on icon btns so they won't bubble up to tr and toggleBodyVisibility + 'click .icon-btn' : function( ev ){ + ev.stopPropagation(); + } + }), + + // ........................................................................ misc + /** Return a string rep of the history */ + toString : function(){ + return 'AnnotatedHistoryPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; + } +}); + +//============================================================================== + return { + AnnotatedHistoryPanel : AnnotatedHistoryPanel + }; +}); diff -r 32eadec01e3ebeb076b68938269e22f45fb202bb -r 8e4196a87a2b78521241adf104f524a5ea05caa1 static/scripts/mvc/history/readonly-history-panel.js --- a/static/scripts/mvc/history/readonly-history-panel.js +++ b/static/scripts/mvc/history/readonly-history-panel.js @@ -526,7 +526,6 @@ $whereTo = $whereTo || this.$el; var historyView = this, newHdaViews = {}, - $datasetsList = $whereTo.find( this.datasetsSelector ), // only render the shown hdas //TODO: switch to more general filtered pattern visibleHdas = this.model.hdas.getVisible( @@ -536,7 +535,7 @@ ); //console.debug( 'renderHdas, visibleHdas:', visibleHdas, $whereTo ); //TODO: prepend to sep div, add as one - $datasetsList.empty(); + $whereTo.find( this.datasetsSelector ).empty(); if( visibleHdas.length ){ visibleHdas.each( function( hda ){ @@ -547,7 +546,7 @@ if( _.contains( historyView.selectedHdaIds, hdaId ) ){ hdaView.selected = true; } - $datasetsList.prepend( hdaView.render().$el ); + historyView.attachHdaView( hdaView.render(), $whereTo ); }); $whereTo.find( this.emptyMsgSelector ).hide(); @@ -561,6 +560,12 @@ return this.hdaViews; }, + attachHdaView : function( hdaView, $whereTo ){ + $whereTo = $whereTo || this.$el; + var $datasetsList = $whereTo.find( this.datasetsSelector ); + $datasetsList.prepend( hdaView.$el ); + }, + /** Add an hda view to the panel for the given hda * @param {HistoryDatasetAssociation} hda */ diff -r 32eadec01e3ebeb076b68938269e22f45fb202bb -r 8e4196a87a2b78521241adf104f524a5ea05caa1 static/scripts/packed/mvc/history/annotated-history-panel.js --- /dev/null +++ b/static/scripts/packed/mvc/history/annotated-history-panel.js @@ -0,0 +1,1 @@ +define(["mvc/dataset/hda-model","mvc/dataset/hda-base","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({className:"annotated-history-panel",HDAViewClass:a.HDABaseView,renderModel:function(){this.$el.addClass(this.className);var g=b.ReadOnlyHistoryPanel.prototype.renderModel.call(this),e=g.find(this.datasetsSelector),f=$("<table/>").addClass("datasets-list datasets-table");f.append(e.children());g.find(this.datasetsSelector).replaceWith(f);g.find(".history-subtitle").after(this.renderHistoryAnnotation());g.find(".history-search-btn").hide();g.find(".history-controls").after(g.find(".history-search-controls").show());this.setUpSearchInput(g.find(".history-search-input"));return g},renderHistoryAnnotation:function(){var e=this.model.get("annotation");if(!e){return null}return $(['<div class="history-annotation">',e,"</div>"].join(""))},renderHdas:function(f){f=f||this.$el;var e=b.ReadOnlyHistoryPanel.prototype.renderHdas.call(this,f);f.find(this.datasetsSelector).prepend($("<tr/>").addClass("headers").append([$("<th/>").text(_l("Dataset")),$("<th/>").text(_l("Annotation"))]));return e},attachHdaView:function(h,f){f=f||this.$el;var i=_.find(h.el.classList,function(j){return(/^state\-/).test(j)}),e=h.model.get("annotation")||"",g=$("<tr/>").addClass("dataset-row").append([$("<td/>").addClass("dataset-container").append(h.$el).addClass(i?i.replace("-","-color-"):""),$("<td/>").addClass("additional-info").text(e)]);f.find(this.datasetsSelector).append(g)},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click tr":function(e){$(e.currentTarget).find(".dataset-title-bar").click()},"click .icon-btn":function(e){e.stopPropagation()}}),toString:function(){return"AnnotatedHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{AnnotatedHistoryPanel:d}}); \ No newline at end of file diff -r 32eadec01e3ebeb076b68938269e22f45fb202bb -r 8e4196a87a2b78521241adf104f524a5ea05caa1 static/scripts/packed/mvc/history/readonly-history-panel.js --- a/static/scripts/packed/mvc/history/readonly-history-panel.js +++ b/static/scripts/packed/mvc/history/readonly-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/history/history-model","mvc/dataset/hda-base"],function(e,a){var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(f){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([f],[true])))},removeExpandedHda:function(f){this.save("expandedHdas",_.omit(this.get("expandedHdas"),f))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function c(f){if(!f){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+f)}return("history:"+f)};var b=Backbone.View.extend(LoggableMixin).extend({HDAViewClass:a.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",msgsSelector:".message-container",emptyMsgSelector:".empty-history-message",emptyMsg:_l("This history is empty"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.linkTarget=f.linkTarget||"_blank";this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];this.searchFor="";this._setUpListeners();if(this.model){this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers()}if(f.onready){f.onready.call(this)}},_setUpListeners:function(){this.on("error",function(g,j,f,i,h){this.errorHandler(g,j,f,i,h)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this.hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}},errorHandler:function(h,k,g,j,i){var f=this._parseErrorMessage(h,k,g,j,i);if(k&&k.status===0&&k.readyState===0){}else{if(k&&k.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",f.message,f.details)})}else{this.displayMessage("error",f.message,f.details)}}}},_parseErrorMessage:function(i,m,h,l,k){var g=Galaxy.currUser,f={message:this._bePolite(l),details:{user:(g instanceof User)?(g.toJSON()):(g+""),source:(i instanceof Backbone.Model)?(i.toJSON()):(i+""),xhr:m,options:(m)?(_.omit(h,"xhr")):(h)}};_.extend(f.details,k||{});if(m&&_.isFunction(m.getAllResponseHeaders)){var j=m.getAllResponseHeaders();j=_.compact(j.split("\n"));j=_.map(j,function(n){return n.split(": ")});f.details.xhr.responseHeaders=_.object(j)}return f},_bePolite:function(f){f=f||_l("An error occurred while getting updates from the server");return f+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadHistoryWithHDADetails:function(i,h,g,k){var f=this,j=function(l){return f.getExpandedHdaIds(l.id)};return this.loadHistory(i,h,g,k,j)},loadHistory:function(i,h,g,l,j){this.trigger("loading-history",this);h=h||{};var f=this;var k=e.History.getHistoryData(i,{historyFn:g,hdaFn:l,hdaDetailIds:h.initiallyExpanded||j});return this._loadHistoryFromXHR(k,h).fail(function(o,m,n){f.trigger("error",f,o,h,_l("An error was encountered while "+m),{historyId:i,history:n||{}})}).always(function(){f.trigger("loading-done",f)})},_loadHistoryFromXHR:function(h,g){var f=this;h.then(function(i,j){f.setModel(i,j,g)});h.fail(function(j,i){f.render()});return h},setModel:function(h,f,g){g=g||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){h.user=Galaxy.currUser.toJSON()}this.model=new e.History(h,f,g);this._setUpWebStorage(g.initiallyExpanded,g.show_deleted,g.show_hidden);this._setUpModelEventHandlers();this.selectedHdaIds=[];this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(g,f,h){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(g)){this.storage.set("exandedHdas",g)}if(_.isBoolean(f)){this.storage.set("show_deleted",f)}if(_.isBoolean(h)){this.storage.set("show_hidden",h)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var f in sessionStorage){if(f.indexOf("history:")===0){sessionStorage.removeItem(f)}}},getStoredOptions:function(g){if(!g||g==="current"){return(this.storage)?(this.storage.get()):({})}var f=sessionStorage.getItem(d.historyStorageKey(g));return(f===null)?({}):(JSON.parse(f))},getExpandedHdaIds:function(f){var g=this.getStoredOptions(f).expandedHdas;return((_.isEmpty(g))?([]):(_.keys(g)))},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addHdaView,this);this.model.on("error error:hdas",function(g,i,f,h){this.errorHandler(g,i,f,h)},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children())}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderWithoutModel:function(){var f=$("<div/>"),g=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return f.append(g)},renderModel:function(){var f=$("<div/>");f.append(b.templates.historyPanel(this.model.toJSON()));f.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(f);this.renderHdas(f);return f},_renderSearchButton:function(f){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(f){f=f||this.$el;f.find("[title]").tooltip({placement:"bottom"})},createHdaView:function(g){var f=g.get("id"),h=new this.HDAViewClass({model:g,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[f],hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(h);return h},_setUpHdaListeners:function(g){var f=this;g.on("body-expanded",function(h){f.storage.addExpandedHda(h)});g.on("body-collapsed",function(h){f.storage.removeExpandedHda(h)});g.on("error",function(i,k,h,j){f.errorHandler(i,k,h,j)})},renderHdas:function(h){h=h||this.$el;var g=this,j={},f=h.find(this.datasetsSelector),i=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);f.empty();if(i.length){i.each(function(l){var k=l.get("id"),m=g.createHdaView(l);j[k]=m;if(_.contains(g.selectedHdaIds,k)){m.selected=true}f.prepend(m.render().$el)});h.find(this.emptyMsgSelector).hide()}else{h.find(this.emptyMsgSelector).text((this.model.hdas.length&&this.searchFor)?(this.noneFoundMsg):(this.emptyMsg)).show()}this.hdaViews=j;return this.hdaViews},addHdaView:function(i){this.log("add."+this,i);var g=this;if(!i.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function h(k){var j=g.$el.find(g.emptyMsgSelector);if(j.is(":visible")){j.fadeOut(g.fxSpeed,k)}else{k()}},function f(k){g.scrollToTop();var j=g.$el.find(g.datasetsSelector),l=g.createHdaView(i);g.hdaViews[i.id]=l;l.render().$el.hide().prependTo(j).slideDown(g.fxSpeed)}])},refreshHdas:function(g,f){if(this.model){return this.model.refresh(g,f)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(f){f.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},setUpSearchInput:function(g){var h=this,k=".history-search-input";function j(l){h.searchFor=l;h.filters=[function(m){return m.matchesAll(h.searchFor)}];h.trigger("search:searching",l,h);h.renderHdas()}function f(l){if(h.model.hdas.haveDetails()){j(l);return}h.$el.find(k).searchInput("toggle-loading");h.model.hdas.fetchAllDetails({silent:true}).always(function(){h.$el.find(k).searchInput("toggle-loading")}).done(function(){j(l)})}function i(){h.searchFor="";h.filters=[];h.trigger("search:clear",h);h.renderHdas()}g.searchInput({initialVal:h.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:f,onsearch:j,onclear:i});return g},showSearchControls:function(g){g=(g===undefined)?(this.fxSpeed):(g);var f=this.$el.find(".history-search-controls"),h=f.find(".history-search-input");if(!h.children().size()){this.setUpSearchInput(h)}f.slideDown(g,function(){$(this).find("input").focus()})},hideSearchControls:function(f){f=(f===undefined)?(this.fxSpeed):(f);this.$el.find(".history-search-controls").slideUp(f)},toggleSearchControls:function(f){speed=(jQuery.type(f)==="number")?(f):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showLoadingIndicator:function(g,f,h){f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},hideLoadingIndicator:function(f,g){f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},displayMessage:function(k,l,j){var h=this;this.scrollToTop();var i=this.$el.find(this.msgsSelector),f=$("<div/>").addClass(k+"message").html(l);if(!_.isEmpty(j)){var g=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(h._messageToModalOptions(k,l,j));return false});f.append(" ",g)}return i.html(f)},_messageToModalOptions:function(j,l,i){var f=this,k=$("<div/>"),h={title:"Details"};function g(m){m=_.omit(m,_.functions(m));return["<table>",_.map(m,function(o,n){o=(_.isObject(o))?(g(o)):(o);return'<tr><td style="vertical-align: top; color: grey">'+n+'</td><td style="padding-left: 8px">'+o+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(i)){h.body=k.append(g(i))}else{h.body=k.html(i)}h.buttons={Ok:function(){Galaxy.modal.hide();f.clearMessages()}};return h},clearMessages:function(){var f=this.$el.find(this.msgsSelector);f.empty()},scrollPosition:function(){return this.$el.scrollTop()},scrollTo:function(f){this.$el.scrollTop(f);return this},scrollToTop:function(){this.$el.scrollTop(0);return this},scrollIntoView:function(k,g){if(g===undefined){this.scrollTo(k);return this}var f=window,j=this.$el.parent(),i=$(f).innerHeight(),h=(i/2)-(g/2);this.scrollTo(k-h);return this},scrollToId:function(g){if((!g)||(!this.hdaViews[g])){return this}var f=this.hdaViews[g].$el;this.scrollIntoView(f.offset().top,f.outerHeight());return this},scrollToHid:function(f){var g=this.model.hdas.getByHid(f);if(!g){return this}return this.scrollToId(g.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});b.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]};return{ReadOnlyHistoryPanel:b}}); \ No newline at end of file +define(["mvc/history/history-model","mvc/dataset/hda-base"],function(e,a){var d=SessionStorageModel.extend({defaults:{expandedHdas:{},show_deleted:false,show_hidden:false},addExpandedHda:function(f){this.save("expandedHdas",_.extend(this.get("expandedHdas"),_.object([f],[true])))},removeExpandedHda:function(f){this.save("expandedHdas",_.omit(this.get("expandedHdas"),f))},toString:function(){return"HistoryPrefs("+this.id+")"}});d.historyStorageKey=function c(f){if(!f){throw new Error("HistoryPrefs.historyStorageKey needs valid id: "+f)}return("history:"+f)};var b=Backbone.View.extend(LoggableMixin).extend({HDAViewClass:a.HDABaseView,tagName:"div",className:"history-panel",fxSpeed:"fast",datasetsSelector:".datasets-list",msgsSelector:".message-container",emptyMsgSelector:".empty-history-message",emptyMsg:_l("This history is empty"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};if(f.logger){this.logger=f.logger}this.log(this+".initialize:",f);this.linkTarget=f.linkTarget||"_blank";this.fxSpeed=_.has(f,"fxSpeed")?(f.fxSpeed):(this.fxSpeed);this.hdaViews={};this.indicator=new LoadingIndicator(this.$el);this.filters=[];this.searchFor="";this._setUpListeners();if(this.model){this._setUpWebStorage(f.initiallyExpanded,f.show_deleted,f.show_hidden);this._setUpModelEventHandlers()}if(f.onready){f.onready.call(this)}},_setUpListeners:function(){this.on("error",function(g,j,f,i,h){this.errorHandler(g,j,f,i,h)});this.on("loading-history",function(){this.showLoadingIndicator("loading history...",40)});this.on("loading-done",function(){this.hideLoadingIndicator(40);if(_.isEmpty(this.hdaViews)){this.trigger("empty-history",this)}});this.once("rendered",function(){this.trigger("rendered:initial",this);return false});if(this.logger){this.on("all",function(f){this.log(this+"",arguments)},this)}},errorHandler:function(h,k,g,j,i){var f=this._parseErrorMessage(h,k,g,j,i);if(k&&k.status===0&&k.readyState===0){}else{if(k&&k.status===502){}else{if(!this.$el.find(this.msgsSelector).is(":visible")){this.once("rendered",function(){this.displayMessage("error",f.message,f.details)})}else{this.displayMessage("error",f.message,f.details)}}}},_parseErrorMessage:function(i,m,h,l,k){var g=Galaxy.currUser,f={message:this._bePolite(l),details:{user:(g instanceof User)?(g.toJSON()):(g+""),source:(i instanceof Backbone.Model)?(i.toJSON()):(i+""),xhr:m,options:(m)?(_.omit(h,"xhr")):(h)}};_.extend(f.details,k||{});if(m&&_.isFunction(m.getAllResponseHeaders)){var j=m.getAllResponseHeaders();j=_.compact(j.split("\n"));j=_.map(j,function(n){return n.split(": ")});f.details.xhr.responseHeaders=_.object(j)}return f},_bePolite:function(f){f=f||_l("An error occurred while getting updates from the server");return f+". "+_l("Please contact a Galaxy administrator if the problem persists.")},loadHistoryWithHDADetails:function(i,h,g,k){var f=this,j=function(l){return f.getExpandedHdaIds(l.id)};return this.loadHistory(i,h,g,k,j)},loadHistory:function(i,h,g,l,j){this.trigger("loading-history",this);h=h||{};var f=this;var k=e.History.getHistoryData(i,{historyFn:g,hdaFn:l,hdaDetailIds:h.initiallyExpanded||j});return this._loadHistoryFromXHR(k,h).fail(function(o,m,n){f.trigger("error",f,o,h,_l("An error was encountered while "+m),{historyId:i,history:n||{}})}).always(function(){f.trigger("loading-done",f)})},_loadHistoryFromXHR:function(h,g){var f=this;h.then(function(i,j){f.setModel(i,j,g)});h.fail(function(j,i){f.render()});return h},setModel:function(h,f,g){g=g||{};if(this.model){this.model.clearUpdateTimeout();this.stopListening(this.model);this.stopListening(this.model.hdas)}this.hdaViews={};if(Galaxy&&Galaxy.currUser){h.user=Galaxy.currUser.toJSON()}this.model=new e.History(h,f,g);this._setUpWebStorage(g.initiallyExpanded,g.show_deleted,g.show_hidden);this._setUpModelEventHandlers();this.selectedHdaIds=[];this.trigger("new-model",this);this.render();return this},_setUpWebStorage:function(g,f,h){this.storage=new d({id:d.historyStorageKey(this.model.get("id"))});if(_.isObject(g)){this.storage.set("exandedHdas",g)}if(_.isBoolean(f)){this.storage.set("show_deleted",f)}if(_.isBoolean(h)){this.storage.set("show_hidden",h)}this.trigger("new-storage",this.storage,this);this.log(this+" (init'd) storage:",this.storage.get())},clearWebStorage:function(){for(var f in sessionStorage){if(f.indexOf("history:")===0){sessionStorage.removeItem(f)}}},getStoredOptions:function(g){if(!g||g==="current"){return(this.storage)?(this.storage.get()):({})}var f=sessionStorage.getItem(d.historyStorageKey(g));return(f===null)?({}):(JSON.parse(f))},getExpandedHdaIds:function(f){var g=this.getStoredOptions(f).expandedHdas;return((_.isEmpty(g))?([]):(_.keys(g)))},_setUpModelEventHandlers:function(){this.model.hdas.on("add",this.addHdaView,this);this.model.on("error error:hdas",function(g,i,f,h){this.errorHandler(g,i,f,h)},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children())}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderWithoutModel:function(){var f=$("<div/>"),g=$("<div/>").addClass("message-container").css({"margin-left":"4px","margin-right":"4px"});return f.append(g)},renderModel:function(){var f=$("<div/>");f.append(b.templates.historyPanel(this.model.toJSON()));f.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(f);this.renderHdas(f);return f},_renderSearchButton:function(f){return faIconButton({title:_l("Search datasets"),classes:"history-search-btn",faIcon:"fa-search"})},_setUpBehaviours:function(f){f=f||this.$el;f.find("[title]").tooltip({placement:"bottom"})},createHdaView:function(g){var f=g.get("id"),h=new this.HDAViewClass({model:g,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[f],hasUser:this.model.ownedByCurrUser(),logger:this.logger});this._setUpHdaListeners(h);return h},_setUpHdaListeners:function(g){var f=this;g.on("body-expanded",function(h){f.storage.addExpandedHda(h)});g.on("body-collapsed",function(h){f.storage.removeExpandedHda(h)});g.on("error",function(i,k,h,j){f.errorHandler(i,k,h,j)})},renderHdas:function(g){g=g||this.$el;var f=this,i={},h=this.model.hdas.getVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"),this.filters);g.find(this.datasetsSelector).empty();if(h.length){h.each(function(k){var j=k.get("id"),l=f.createHdaView(k);i[j]=l;if(_.contains(f.selectedHdaIds,j)){l.selected=true}f.attachHdaView(l.render(),g)});g.find(this.emptyMsgSelector).hide()}else{g.find(this.emptyMsgSelector).text((this.model.hdas.length&&this.searchFor)?(this.noneFoundMsg):(this.emptyMsg)).show()}this.hdaViews=i;return this.hdaViews},attachHdaView:function(h,g){g=g||this.$el;var f=g.find(this.datasetsSelector);f.prepend(h.$el)},addHdaView:function(i){this.log("add."+this,i);var g=this;if(!i.isVisible(this.storage.get("show_deleted"),this.storage.get("show_hidden"))){return}$({}).queue([function h(k){var j=g.$el.find(g.emptyMsgSelector);if(j.is(":visible")){j.fadeOut(g.fxSpeed,k)}else{k()}},function f(k){g.scrollToTop();var j=g.$el.find(g.datasetsSelector),l=g.createHdaView(i);g.hdaViews[i.id]=l;l.render().$el.hide().prependTo(j).slideDown(g.fxSpeed)}])},refreshHdas:function(g,f){if(this.model){return this.model.refresh(g,f)}return $.when()},events:{"click .message-container":"clearMessages","click .history-search-btn":"toggleSearchControls"},collapseAllHdaBodies:function(){_.each(this.hdaViews,function(f){f.toggleBodyVisibility(null,false)});this.storage.set("expandedHdas",{})},toggleShowDeleted:function(){this.storage.set("show_deleted",!this.storage.get("show_deleted"));this.renderHdas();return this.storage.get("show_deleted")},toggleShowHidden:function(){this.storage.set("show_hidden",!this.storage.get("show_hidden"));this.renderHdas();return this.storage.get("show_hidden")},setUpSearchInput:function(g){var h=this,k=".history-search-input";function j(l){h.searchFor=l;h.filters=[function(m){return m.matchesAll(h.searchFor)}];h.trigger("search:searching",l,h);h.renderHdas()}function f(l){if(h.model.hdas.haveDetails()){j(l);return}h.$el.find(k).searchInput("toggle-loading");h.model.hdas.fetchAllDetails({silent:true}).always(function(){h.$el.find(k).searchInput("toggle-loading")}).done(function(){j(l)})}function i(){h.searchFor="";h.filters=[];h.trigger("search:clear",h);h.renderHdas()}g.searchInput({initialVal:h.searchFor,name:"history-search",placeholder:"search datasets",classes:"history-search",onfirstsearch:f,onsearch:j,onclear:i});return g},showSearchControls:function(g){g=(g===undefined)?(this.fxSpeed):(g);var f=this.$el.find(".history-search-controls"),h=f.find(".history-search-input");if(!h.children().size()){this.setUpSearchInput(h)}f.slideDown(g,function(){$(this).find("input").focus()})},hideSearchControls:function(f){f=(f===undefined)?(this.fxSpeed):(f);this.$el.find(".history-search-controls").slideUp(f)},toggleSearchControls:function(f){speed=(jQuery.type(f)==="number")?(f):(this.fxSpeed);if(this.$el.find(".history-search-controls").is(":visible")){this.hideSearchControls(speed)}else{this.showSearchControls(speed)}},showLoadingIndicator:function(g,f,h){f=(f!==undefined)?(f):(this.fxSpeed);if(!this.indicator){this.indicator=new LoadingIndicator(this.$el,this.$el.parent())}if(!this.$el.is(":visible")){this.indicator.show(0,h)}else{this.$el.fadeOut(f);this.indicator.show(g,f,h)}},hideLoadingIndicator:function(f,g){f=(f!==undefined)?(f):(this.fxSpeed);if(this.indicator){this.indicator.hide(f,g)}},displayMessage:function(k,l,j){var h=this;this.scrollToTop();var i=this.$el.find(this.msgsSelector),f=$("<div/>").addClass(k+"message").html(l);if(!_.isEmpty(j)){var g=$('<a href="javascript:void(0)">Details</a>').click(function(){Galaxy.modal.show(h._messageToModalOptions(k,l,j));return false});f.append(" ",g)}return i.html(f)},_messageToModalOptions:function(j,l,i){var f=this,k=$("<div/>"),h={title:"Details"};function g(m){m=_.omit(m,_.functions(m));return["<table>",_.map(m,function(o,n){o=(_.isObject(o))?(g(o)):(o);return'<tr><td style="vertical-align: top; color: grey">'+n+'</td><td style="padding-left: 8px">'+o+"</td></tr>"}).join(""),"</table>"].join("")}if(_.isObject(i)){h.body=k.append(g(i))}else{h.body=k.html(i)}h.buttons={Ok:function(){Galaxy.modal.hide();f.clearMessages()}};return h},clearMessages:function(){var f=this.$el.find(this.msgsSelector);f.empty()},scrollPosition:function(){return this.$el.scrollTop()},scrollTo:function(f){this.$el.scrollTop(f);return this},scrollToTop:function(){this.$el.scrollTop(0);return this},scrollIntoView:function(k,g){if(g===undefined){this.scrollTo(k);return this}var f=window,j=this.$el.parent(),i=$(f).innerHeight(),h=(i/2)-(g/2);this.scrollTo(k-h);return this},scrollToId:function(g){if((!g)||(!this.hdaViews[g])){return this}var f=this.hdaViews[g].$el;this.scrollIntoView(f.offset().top,f.outerHeight());return this},scrollToHid:function(f){var g=this.model.hdas.getByHid(f);if(!g){return this}return this.scrollToId(g.id)},toString:function(){return"ReadOnlyHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});b.templates={historyPanel:Handlebars.templates["template-history-historyPanel"]};return{ReadOnlyHistoryPanel:b}}); \ No newline at end of file diff -r 32eadec01e3ebeb076b68938269e22f45fb202bb -r 8e4196a87a2b78521241adf104f524a5ea05caa1 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1684,6 +1684,19 @@ .dataset.state-discarded{background:#eee}.dataset.state-discarded .state-icon:before{content:"\f014"} .dataset.state-noPermission{background:#eee;filter:alpha(opacity=60);-moz-opacity:.60;opacity:.60}.dataset.state-noPermission .state-icon{font-size:20px}.dataset.state-noPermission .state-icon:before{content:"\f023"} .dataset.state-new{background:#eee}.dataset.state-new .state-icon:before{content:"\f06a"} +.annotated-history-panel{padding-top:10px}.annotated-history-panel [class$=messagesmall]{margin:8px 0px 8px 0px} +.annotated-history-panel .history-controls{margin:0px 0px 16px 4px;padding:0px}.annotated-history-panel .history-controls .history-name{font-size:150%} +.annotated-history-panel .history-controls .history-subtitle{margin:0px;padding:0px 0px 0px 4px;padding-left:4px} +.annotated-history-panel .history-controls .history-annotation{border:1px solid lightgrey;border-width:1px 0px 0px 0px;padding:4px 0px 4px 0px;margin:4px;white-space:pre-wrap} +.annotated-history-panel .history-controls .history-annotation:empty{display:none} +.annotated-history-panel .history-controls .history-search-controls{padding:16px 0px 0px 0px} +.annotated-history-panel table.datasets-list{width:100%;table-layout:fixed}.annotated-history-panel table.datasets-list .headers{border-bottom:2px solid grey} +.annotated-history-panel table.datasets-list .headers th{padding:8px} +.annotated-history-panel table.datasets-list .dataset-row{cursor:pointer;border-bottom:1px solid grey} +.annotated-history-panel table.datasets-list .dataset-row>td{margin:0px;padding:0px;vertical-align:top} +.annotated-history-panel table.datasets-list .dataset-row>td:nth-child(1){width:50%} +.annotated-history-panel table.datasets-list .dataset-row>td:nth-child(2){padding:8px 16px 8px 16px;white-space:pre-wrap} +.annotated-history-panel table.datasets-list .dataset-row .dataset{border:0px} .hda .hda-hid:after{content:':'} body.historyPage{background:#dfe5f9;color:#000;margin:5px;border:0;padding:0} div.historyLinks{margin:5px 5px} diff -r 32eadec01e3ebeb076b68938269e22f45fb202bb -r 8e4196a87a2b78521241adf104f524a5ea05caa1 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -688,6 +688,78 @@ } +// ---------------------------------------------------------------------------- annotated-history-panel +.annotated-history-panel { + //TODO: most of these styles are specific to history/display.mako and not to this type of panel in general + //TODO: some of these styles are also overrides of history-panel - remove those from hpanel and revisit this + padding-top: 10px; + + [class$=messagesmall] { + margin: 8px 0px 8px 0px; + } + + .history-controls { + margin: 0px 0px 16px 4px; + padding: 0px; + + .history-name { + font-size: 150%; + } + .history-subtitle { + margin: 0px; + padding: 0px 0px 0px 4px; + padding-left: 4px; + } + + .history-annotation { + border: 1px solid lightgrey; + border-width: 1px 0px 0px 0px; + padding: 4px 0px 4px 0px; + margin: 4px; + white-space: pre-wrap; + } + .history-annotation:empty { + display: none; + } + + .history-search-controls { + padding: 16px 0px 0px 0px; + } + } + + table.datasets-list { + width: 100%; + table-layout: fixed; + + .headers { + border-bottom: 2px solid grey; + } + .headers th { + padding: 8px; + } + .dataset-row { + cursor: pointer; + border-bottom: 1px solid grey; + } + .dataset-row > td { + margin: 0px; + padding: 0px; + vertical-align: top; + } + .dataset-row > td:nth-child(1) { + width: 50%; + } + .dataset-row > td:nth-child(2) { + /* top and bottom should be <= title-bar padding */ + padding: 8px 16px 8px 16px; + white-space: pre-wrap; + } + .dataset-row .dataset { + border: 0px; + } + } +} + // ---------------------------------------------------------------------------- hdas .hda .hda-hid:after { content: ':'; diff -r 32eadec01e3ebeb076b68938269e22f45fb202bb -r 8e4196a87a2b78521241adf104f524a5ea05caa1 templates/display_base.mako --- a/templates/display_base.mako +++ b/templates/display_base.mako @@ -85,7 +85,7 @@ }); // Init history boxes. - init_history_items( $("div.historyItemWrapper"), false, "nochanges" ); + //init_history_items( $("div.historyItemWrapper"), false, "nochanges" ); // Init user item rating. $('.user_rating_star').rating({ @@ -115,7 +115,7 @@ <%def name="stylesheets()"> ${parent.stylesheets()} ${h.css( "autocomplete_tagging", "embed_item", "jquery.rating" )} - ${h.css( "history", "autocomplete_tagging", "trackster", "library", + ${h.css( "autocomplete_tagging", "trackster", "library", "jquery-ui/smoothness/jquery-ui" )} <style type="text/css"> diff -r 32eadec01e3ebeb076b68938269e22f45fb202bb -r 8e4196a87a2b78521241adf104f524a5ea05caa1 templates/webapps/galaxy/history/display.mako --- a/templates/webapps/galaxy/history/display.mako +++ b/templates/webapps/galaxy/history/display.mako @@ -1,84 +1,74 @@ <%inherit file="/display_base.mako"/> -<%namespace file="/root/history_common.mako" import="render_dataset" /> +<%namespace file="history_panel.mako" import="history_panel_javascripts" /> ## Set vars so that there's no need to change the code below. -<% +<% history = published_item datasets = published_item_data %><%def name="javascripts()"> ${parent.javascripts()} + ${history_panel_javascripts()} </%def><%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css( "history" )} <style type="text/css"> - .historyItemBody { - display: none; - } - .column { - float: left; - padding: 10px; - margin: 20px; - background: #666; - border: 5px solid #ccc; - width: 300px; - } </style> - - <noscript> - <style> - .historyItemBody { - display: block; - } - </style> - </noscript></%def><%def name="render_item_links( history )"> - <a - href="${h.url_for( controller='/history', action='imp', id=trans.security.encode_id(history.id) )}" - class="icon-button import" - ## Needed to overwide initial width so that link is floated left appropriately. - style="width: 100%" - title="Import history">Import history</a> +<% + encoded_history_id = history_dict[ 'id' ] + import_url = h.url_for( controller='history', action='imp', id=encoded_history_id ) + switch_url = h.url_for( controller='history', action='switch_to_history', hist_id=encoded_history_id ) +%> + ## Needed to overwide initial width so that link is floated left appropriately. + %if not user_is_owner: + <a href="${import_url}" style="width: 100%" title="${_('Make a copy of this history and switch to it')}"> + ${_('Import history')} + </a> + %else: + <a href="${switch_url}" style="width: 100%" title="${_('Make this history your current history')}"> + ${_('Switch to this history')} + </a> + %endif +</%def> + +<%def name="render_item_header( item )"></%def><%def name="render_item( history, datasets )"> - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} - </div> - <p></p> - %endif - %if not datasets: - <div class="infomessagesmall" id="emptyHistoryMessage"> - %else: - ## Render requested datasets, ordered from newest to oldest, including annotations. - <table class="annotated-item"> - <tr><th>Dataset</th><th class="annotation">Annotation</th></tr> - %for data in datasets: - <tr> - %if data.visible: - <td> - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} - </div> - </td> - <td class="annotation"> - %if hasattr( data, "annotation") and data.annotation is not None: - ${data.annotation} - %endif - </td> - %endif - </tr> - %endfor - </table> - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("This history is empty.")} - </div> +<div id="history-${ history_dict[ 'id' ] }" class="history-panel"> +</div> +<script type="text/javascript"> + var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, + historyJSON = ${h.to_json_string( history_dict )}, + hdaJSON = ${h.to_json_string( hda_dicts )}; + //window.historyJSON = historyJSON; + window.hdaJSON = hdaJSON; + + require.config({ + baseUrl : "${h.url_for( '/static/scripts' )}" + })([ 'mvc/history/annotated-history-panel' ], function( panelMod ){ + // history module is already in the dpn chain from the panel. We can re-scope it here. + var historyModel = require( 'mvc/history/history-model' ), + hdaBaseView = require( 'mvc/dataset/hda-base' ), + history = new historyModel.History( historyJSON, hdaJSON, { + logger: ( debugging )?( console ):( null ) + }); + + window.historyPanel = new panelMod.AnnotatedHistoryPanel({ + show_deleted : false, + show_hidden : false, + el : $( "#history-" + historyJSON.id ), + model : history, + onready : function(){ + this.render(); + } + }); + }); +</script></%def> 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: Rework logic for setting selection of DataToolParameter. Fixes issue seen with rerun where incorrect options were selected.
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/32eadec01e3e/ Changeset: 32eadec01e3e User: dan Date: 2014-02-20 17:31:07 Summary: Rework logic for setting selection of DataToolParameter. Fixes issue seen with rerun where incorrect options were selected. Affected #: 1 file diff -r 01a572fb8b4c463efa1b2091298fad3ec7ea2958 -r 32eadec01e3ebeb076b68938269e22f45fb202bb lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1621,7 +1621,7 @@ if type( value ) != list: value = [ value ] field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values=self.refresh_on_change_values ) - + # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field() def dataset_collector( hdas, parent_hid ): current_user_roles = trans.get_current_user_roles() @@ -1659,20 +1659,18 @@ # Also collect children via association object dataset_collector( hda.children, hid ) dataset_collector( history.active_datasets_children_and_roles, None ) - some_data = bool( field.options ) - if some_data: - if value is None or len( field.options ) == 1: - # Ensure that the last item is always selected - a, b, c = field.options[-1] - if self.optional: - field.options[-1] = a, b, False - else: - field.options[-1] = a, b, True + + set_selected = field.get_selected( return_label=True, return_value=True, multi=False ) is not None + # Ensure than an item is always selected if self.optional: - if not value: + if set_selected: + field.add_option( "Selection is Optional", 'None', False ) + else: field.add_option( "Selection is Optional", 'None', True ) - else: - field.add_option( "Selection is Optional", 'None', False ) + elif not set_selected and bool( field.options ): + # Select the last item + a, b, c = field.options[-1] + field.options[-1] = a, b, True return field def get_initial_value( self, trans, context, history=None ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/01a572fb8b4c/ Changeset: 01a572fb8b4c User: inithello Date: 2014-02-20 17:18:30 Summary: Enable specifying the install database connection when executing the install and test framework. Affected #: 2 files diff -r 952558f0dc0ba52355e87ef2d0ccef37f7f51bec -r 01a572fb8b4c463efa1b2091298fad3ec7ea2958 test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/repositories_with_tools/functional_tests.py @@ -412,6 +412,13 @@ database_connection = os.environ[ 'GALAXY_INSTALL_TEST_DBURI' ] else: database_connection = 'sqlite:///' + os.path.join( galaxy_db_path, 'install_and_test_repositories.sqlite' ) + if 'GALAXY_INSTALL_TEST_INSTALL_DBURI' in os.environ: + install_database_connection = os.environ[ 'GALAXY_INSTALL_TEST_INSTALL_DBURI' ] + elif asbool( os.environ.get( 'GALAXY_TEST_INSTALL_DB_MERGED', default_install_db_merged ) ): + install_database_connection = galaxy_database_connection + else: + install_db_path = os.path.join( galaxy_db_path, 'install.sqlite' ) + install_database_connection = 'sqlite:///%s' % install_galaxy_db_path kwargs = {} for dir in [ galaxy_test_tmp_dir ]: try: @@ -419,6 +426,7 @@ except OSError: pass print "Database connection: ", database_connection + print "Install database connection: ", install_database_connection # Generate the shed_tool_data_table_conf.xml file. file( shed_tool_data_table_conf_file, 'w' ).write( install_and_test_base_util.tool_data_table_conf_xml_template ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file @@ -446,6 +454,7 @@ datatype_converters_config_file = "datatype_converters_conf.xml.sample", file_path = galaxy_file_path, id_secret = install_and_test_base_util.galaxy_encode_secret, + install_database_connection = install_database_connection, job_config_file = galaxy_job_conf_file, job_queue_workers = 5, log_destination = "stdout", diff -r 952558f0dc0ba52355e87ef2d0ccef37f7f51bec -r 01a572fb8b4c463efa1b2091298fad3ec7ea2958 test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/tool_dependency_definitions/functional_tests.py @@ -264,6 +264,13 @@ database_connection = os.environ[ 'GALAXY_INSTALL_TEST_DBURI' ] else: database_connection = 'sqlite:///' + os.path.join( galaxy_db_path, 'install_and_test_repositories.sqlite' ) + if 'GALAXY_INSTALL_TEST_INSTALL_DBURI' in os.environ: + install_database_connection = os.environ[ 'GALAXY_INSTALL_TEST_INSTALL_DBURI' ] + elif asbool( os.environ.get( 'GALAXY_TEST_INSTALL_DB_MERGED', default_install_db_merged ) ): + install_database_connection = galaxy_database_connection + else: + install_db_path = os.path.join( galaxy_db_path, 'install.sqlite' ) + install_database_connection = 'sqlite:///%s' % install_galaxy_db_path kwargs = {} for dir in [ galaxy_test_tmp_dir ]: try: @@ -271,6 +278,7 @@ except OSError: pass print "Database connection: ", database_connection + print "Install database connection: ", install_database_connection # Generate the shed_tool_data_table_conf.xml file. file( shed_tool_data_table_conf_file, 'w' ).write( install_and_test_base_util.tool_data_table_conf_xml_template ) os.environ[ 'GALAXY_INSTALL_TEST_SHED_TOOL_DATA_TABLE_CONF' ] = shed_tool_data_table_conf_file @@ -298,6 +306,7 @@ datatype_converters_config_file = "datatype_converters_conf.xml.sample", file_path = galaxy_file_path, id_secret = install_and_test_base_util.galaxy_encode_secret, + install_database_connection = install_database_connection, job_config_file = galaxy_job_conf_file, job_queue_workers = 5, log_destination = "stdout", https://bitbucket.org/galaxy/galaxy-central/commits/6674cb6ced26/ Changeset: 6674cb6ced26 Branch: trevorw/specify-thirdparty-cookies-must-not-be-b-1392909850239 User: inithello Date: 2014-02-20 17:19:23 Summary: Close branch trevorw/specify-thirdparty-cookies-must-not-be-b-1392909850239. Affected #: 2 files diff -r c4145b92bc2a9e63778950aef4d53723bcd353ee -r 6674cb6ced267ba83d543f98fe1fe0b7e7de7324 lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/fabric_util.py @@ -4,9 +4,14 @@ import logging import os import shutil +import sys import tempfile -import shutil import td_common_util +import time +import shlex + +from subprocess import PIPE, Popen +from threading import Thread from contextlib import contextmanager from galaxy.util import unicodify from galaxy.util.template import fill_template @@ -16,12 +21,19 @@ eggs.require( 'paramiko' ) eggs.require( 'Fabric' ) +from fabric import state from fabric.api import env from fabric.api import hide from fabric.api import lcd from fabric.api import local from fabric.api import settings from fabric.api import prefix +from fabric.operations import _AttributeString + +try: + from Queue import Queue, Empty +except ImportError: + from queue import Queue, Empty log = logging.getLogger( __name__ ) @@ -120,6 +132,22 @@ if int( version.split( "." )[ 0 ] ) < 1: raise NotImplementedError( "Install Fabric version 1.0 or later." ) +def enqueue_output( stdout, stdout_queue, stderr, stderr_queue ): + stdout_logger = logging.getLogger( 'fabric_util.STDOUT' ) + stderr_logger = logging.getLogger( 'fabric_util.STDERR' ) + for line in iter( stdout.readline, b'' ): + output = line.rstrip() + stdout_logger.debug( output ) + stdout_queue.put( output ) + stdout.close() + stdout_queue.put(None) + for line in iter( stderr.readline, b'' ): + output = line.rstrip() + stderr_logger.debug( output ) + stderr_queue.put( output ) + stderr.close() + stderr_queue.put(None) + def file_append( text, file_path, skip_if_contained=True, make_executable=True ): ''' Append a line to a file unless skip_if_contained is True and the line already exists in the file. This method creates the file @@ -168,10 +196,9 @@ for shell_file_path in shell_file_paths: env_file_builder.append_line( action="source", value=shell_file_path ) -def handle_command( app, tool_dependency, install_dir, cmd, return_output=False ): +def handle_command( app, tool_dependency, install_dir, cmd, return_output=False, use_fabric=False ): context = app.install_model.context - with settings( warn_only=True ): - output = local( cmd, capture=True ) + output = run_local_command( cmd, capture_output=True, stream_output=True ) log_results( cmd, output, os.path.join( install_dir, INSTALLATION_LOG ) ) if output.return_code: tool_dependency.status = app.install_model.ToolDependency.installation_status.ERROR @@ -263,7 +290,7 @@ set_prior_environment_commands.append( 'echo "%s: $%s"' % ( inherited_env_var_name, inherited_env_var_name ) ) command = ' ; '.join( set_prior_environment_commands ) # Run the command and capture the output. - command_return = handle_command( app, tool_dependency, install_dir, command, return_output=True ) + command_return = handle_command( app, tool_dependency, install_dir, command, return_output=True, use_fabric=True ) # And extract anything labeled with the name of the environment variable we're populating here. if '%s: ' % inherited_env_var_name in command_return: environment_variable_value = command_return.split( '\n' ) @@ -370,7 +397,7 @@ filtered_actions = actions[ 1: ] return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] ) if return_code: - return tool_dependency + return tool_dependency dir = package_name elif action_type == 'download_file': # <action type="download_file">http://effectors.org/download/version/TTSS_GUI-1.0.1.jar</action> @@ -645,7 +672,7 @@ elif action_type == 'shell_command': with settings( warn_only=True ): cmd = install_environment.build_command( action_dict[ 'command' ] ) - return_code = handle_command( app, tool_dependency, install_dir, cmd ) + return_code = handle_command( app, tool_dependency, install_dir, cmd, use_fabric=False ) if return_code: return tool_dependency elif action_type == 'template_command': @@ -755,6 +782,31 @@ if os.path.exists( work_dir ): local( 'rm -rf %s' % work_dir ) +def run_local_command( command, capture_output=True, stream_output=True ): + wrapped_command = shlex.split( "/bin/sh -c '%s'" % command ) + log.debug( 'Executing command %s in path %s.' % ( command, state.env['lcwd'] ) ) + stdout_queue = Queue() + stderr_queue = Queue() + process_handle = Popen( wrapped_command, stdout=PIPE, stderr=PIPE, bufsize=1, close_fds=False, cwd=state.env['lcwd'] ) + stdio_thread = Thread( target=enqueue_output, args=( process_handle.stdout, stdout_queue, process_handle.stderr, stderr_queue ) ) + stdio_thread.daemon = True + stdio_thread.start() + stdout, stderr = wait_for_process( process_handle, stream_output, stdout_queue, stderr_queue ) + # Handle error condition (deal with stdout being None, too) + output = _AttributeString( stdout.strip() if stdout else "" ) + errors = _AttributeString( stderr.strip() if stderr else "" ) + output.failed = False + output.return_code = process_handle.returncode + output.stderr = errors + if process_handle.returncode not in env.ok_ret_codes: + output.failed = True + message = "local() encountered an error (return code %s) while executing '%s'" % ( process_handle.returncode, command ) + log.error( message ) + output.succeeded = not output.failed + # If we were capturing, this will be a string; otherwise it will be None. + if capture_output: + return output + def set_galaxy_environment( galaxy_user, tool_dependency_dir, host='localhost', shell='/bin/bash -l -c' ): """General Galaxy environment configuration. This method is not currently used.""" env.user = galaxy_user @@ -764,3 +816,21 @@ env.use_sudo = False env.safe_cmd = local return env + +def wait_for_process( process_handle, stream_output, stdout_queue, stderr_queue ): + standard_out = [] + standard_err = [] + process_handle.wait() + while True: + line = stdout_queue.get() + if line is None: + break + standard_out.append(line) + while True: + line = stderr_queue.get() + if line is None: + break + standard_err.append(line) + stdout = '\n'.join( standard_out ) + stderr = '\n'.join( standard_err ) + return stdout, stderr diff -r c4145b92bc2a9e63778950aef4d53723bcd353ee -r 6674cb6ced267ba83d543f98fe1fe0b7e7de7324 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1719,7 +1719,7 @@ """ if text: if app.name == 'galaxy': - route_to_images = 'admin_toolshed/static/images/%s' % encoded_repository_id + route_to_images = '/admin_toolshed/static/images/%s' % encoded_repository_id else: # We're in the tool shed. route_to_images = '/repository/static/images/%s' % encoded_repository_id Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c4145b92bc2a/ Changeset: c4145b92bc2a Branch: trevorw/specify-thirdparty-cookies-must-not-be-b-1392909850239 User: trevorw Date: 2014-02-20 16:27:57 Summary: specify third-party cookies must not be blocked - repository.py third-party cookies are normally (and hopefully) disabled for privacy Affected #: 1 file diff -r eae95d5fa975e1eef4de219564cb976720f18440 -r c4145b92bc2a9e63778950aef4d53723bcd353ee lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -870,7 +870,7 @@ 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) else: - message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url + message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable third-party cookies in your browser. ' % galaxy_url return trans.show_error_message( message ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. @@ -2047,7 +2047,7 @@ return trans.response.send_redirect( url ) else: message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url - message += 'You may need to enable cookies in your browser. ' + message += 'You may need to enable third-party cookies in your browser. ' status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', action='browse_valid_categories', https://bitbucket.org/galaxy/galaxy-central/commits/952558f0dc0b/ Changeset: 952558f0dc0b User: greg Date: 2014-02-20 17:14:38 Summary: Merged in trevorw/galaxy-central-2/trevorw/specify-thirdparty-cookies-must-not-be-b-1392909850239 (pull request #326) specify third-party cookies must not be blocked - repository.py Affected #: 1 file diff -r 3158b15d961f6bef5db25b26d4bc0593f1b58d57 -r 952558f0dc0ba52355e87ef2d0ccef37f7f51bec lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -870,7 +870,7 @@ 'admin_toolshed/update_to_changeset_revision?tool_shed_url=%s&name=%s&owner=%s&changeset_revision=%s&latest_changeset_revision=' % \ ( web.url_for( '/', qualified=True ), repository.name, repository.user.username, changeset_revision ) ) else: - message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable cookies in your browser. ' % galaxy_url + message = 'Unable to check for updates due to an invalid Galaxy URL: <b>%s</b>. You may need to enable third-party cookies in your browser. ' % galaxy_url return trans.show_error_message( message ) if changeset_revision == repository.tip( trans.app ): # If changeset_revision is the repository tip, there are no additional updates. @@ -2047,7 +2047,7 @@ return trans.response.send_redirect( url ) else: message = 'Repository installation is not possible due to an invalid Galaxy URL: <b>%s</b>. ' % galaxy_url - message += 'You may need to enable cookies in your browser. ' + message += 'You may need to enable third-party cookies in your browser. ' status = 'error' return trans.response.send_redirect( web.url_for( controller='repository', action='browse_valid_categories', 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 ToolEvaluator with optional Dataset Input selected.
by commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3158b15d961f/ Changeset: 3158b15d961f User: dan Date: 2014-02-20 17:07:16 Summary: Fix for ToolEvaluator with optional Dataset Input selected. Affected #: 1 file diff -r 3789ce7ddf1ac171a10956989818b4425486c44d -r 3158b15d961f6bef5db25b26d4bc0593f1b58d57 lib/galaxy/tools/evaluation.py --- a/lib/galaxy/tools/evaluation.py +++ b/lib/galaxy/tools/evaluation.py @@ -181,9 +181,11 @@ tool=self, name=input.name ) - real_path = dataset.file_name - if real_path in input_dataset_paths: - wrapper_kwds[ "dataset_path" ] = input_dataset_paths[ real_path ] + if dataset: + #A None dataset does not have a filename + real_path = dataset.file_name + if real_path in input_dataset_paths: + wrapper_kwds[ "dataset_path" ] = input_dataset_paths[ real_path ] input_values[ input.name ] = \ DatasetFilenameWrapper( dataset, **wrapper_kwds ) elif isinstance( input, SelectToolParameter ): 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 commits-noreply＠bitbucket.org 20 Feb '14

20 Feb '14

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c82a791e23a6/ Changeset: c82a791e23a6 User: natefoo Date: 2014-02-20 16:51:42 Summary: Remove obsolete DRMAA_python egg from eggs.ini. Affected #: 1 file diff -r 9c673e0ea8919fea6941f24fdf6936686840bb71 -r c82a791e23a62b0821ad0b0f1bccc49541eb3583 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -9,12 +9,11 @@ [general] repository = http://eggs.galaxyproject.org ; these eggs must be scrambled for your local environment -no_auto = pbs_python DRMAA_python +no_auto = pbs_python [eggs:platform] bx_python = 0.7.1 Cheetah = 2.2.2 -DRMAA_python = 0.2 MarkupSafe = 0.12 mercurial = 2.2.3 MySQL_python = 1.2.3c1 https://bitbucket.org/galaxy/galaxy-central/commits/59e325832026/ Changeset: 59e325832026 User: natefoo Date: 2014-02-20 16:52:19 Summary: Minor updates to comments/documentation in universe_wsgi.ini.sample Affected #: 1 file diff -r c82a791e23a62b0821ad0b0f1bccc49541eb3583 -r 59e325832026a2f3cbdb031eef02c8ef690c3f03 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -3,7 +3,7 @@ # environment. To tune the application for a multi-user production # environment, see the documentation at: # -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Production%20Server +# http://usegalaxy.org/production # # Throughout this sample configuration file, except where stated otherwise, @@ -11,7 +11,7 @@ # values are set to the default value. # Examples of many of these options are explained in more detail in the wiki: # -# http://wiki.g2.bx.psu.edu/Admin/Config +# https://wiki.galaxyproject.org/Admin/Config # # Config hackers are encouraged to check there before asking for help. @@ -140,9 +140,12 @@ # Other tool config files must include the tool_path as an attribute in the <toolbox> tag. #tool_path = tools -# Path to the directory in which managed tool dependencies are placed. To use -# the dependency system, see the documentation at: -# http://wiki.g2.bx.psu.edu/Admin/Config/Tool%20Dependencies +# Path to the directory in which tool dependencies are placed. This is used by +# the tool shed to install dependencies and can also be used by administrators +# to manually install or link to dependencies. For details, see: +# https://wiki.galaxyproject.org/Admin/Config/ToolDependencies +# If this option is not set to a valid path, installing tools with dependencies +# from the Tool Shed will fail. #tool_dependency_dir = None # Enable automatic polling of relative tool sheds to see if any updates @@ -169,7 +172,7 @@ # Directory where data used by tools is located, see the samples in that # directory and the wiki for help: -# http://wiki.g2.bx.psu.edu/Admin/Data%20Integration +# https://wiki.galaxyproject.org/Admin/DataIntegration #tool_data_path = tool-data # Directory where chrom len files are kept, currently mainly used by trackster @@ -196,6 +199,10 @@ # directory. #cluster_files_directory = database/pbs +# Mako templates are compiled as needed and cached for reuse, this directory is +# used for the cache +#template_cache_path = database/compiled_templates + # External service types config file, defines what types of external_services configurations # are available in Galaxy. #external_service_type_config_file = external_service_types_conf.xml @@ -532,7 +539,7 @@ # -- Data Libraries # These library upload options are described in much more detail in the wiki: -# http://wiki.g2.bx.psu.edu/Admin/Data%20Libraries/Uploading%20Library%20Files +# https://wiki.galaxyproject.org/Admin/DataLibraries/UploadingLibraryFiles # Add an option to the library upload form which allows administrators to # upload a directory of files. @@ -590,7 +597,7 @@ # User authentication can be delegated to an upstream proxy server (usually # Apache). The upstream proxy should set a REMOTE_USER header in the request. # Enabling remote user disables regular logins. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Config/Apache%20Proxy +# https://wiki.galaxyproject.org/Admin/Config/ApacheProxy #use_remote_user = False # If use_remote_user is enabled and your external authentication @@ -618,7 +625,7 @@ # users (email addresses). These users will have access to the Admin section # of the server, and will have access to create users, groups, roles, # libraries, and more. For more information, see: -# http://wiki.g2.bx.psu.edu/Admin/Interface +# https://wiki.galaxyproject.org/Admin/Interface #admin_users = None # Force everyone to log in (disable anonymous access). @@ -723,8 +730,8 @@ # separate Galaxy into multiple processes. There are more than one way to do # this, and they are explained in detail in the documentation: # -# http://wiki.g2.bx.psu.edu/Admin/Config/Performance/Web%20Application%20Scal… -# +# https://wiki.galaxyproject.org/Admin/Config/Performance/Scaling + # By default, Galaxy manages and executes jobs from within a single process and # notifies itself of new jobs via in-memory queues. Jobs are run locally on # the system on which Galaxy is started. Advanced job running capabilities can https://bitbucket.org/galaxy/galaxy-central/commits/3789ce7ddf1a/ Changeset: 3789ce7ddf1a User: natefoo Date: 2014-02-20 16:52:31 Summary: Remove empty/renamed sections in tool_conf.xml.main Affected #: 1 file diff -r 59e325832026a2f3cbdb031eef02c8ef690c3f03 -r 3789ce7ddf1ac171a10956989818b4425486c44d tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -154,9 +154,6 @@ <tool file="multivariate_stats/kpca.xml" /><tool file="multivariate_stats/kcca.xml" /></section> - <section id="clustal" name="Multiple Alignments"> - <tool file="rgenetics/rgClustalw.xml" /> - </section><section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /> @@ -227,8 +224,4 @@ <tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section></toolbox> https://bitbucket.org/galaxy/galaxy-central/commits/15e8a74a9521/ Changeset: 15e8a74a9521 Branch: stable User: natefoo Date: 2014-02-20 16:52:31 Summary: Remove empty/renamed sections in tool_conf.xml.main Affected #: 1 file diff -r a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21 -r 15e8a74a95215bf2cc775e9848ca4a5ecc7e945f tool_conf.xml.main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -154,9 +154,6 @@ <tool file="multivariate_stats/kpca.xml" /><tool file="multivariate_stats/kcca.xml" /></section> - <section id="clustal" name="Multiple Alignments"> - <tool file="rgenetics/rgClustalw.xml" /> - </section><section id="hgv" name="Phenotype Association"><tool file="evolution/codingSnps.xml" /><tool file="evolution/add_scores.xml" /> @@ -227,8 +224,4 @@ <tool file="gatk/variant_eval.xml" /><tool file="gatk/variant_combine.xml" /></section> - <section id="ngs-rna-tools" name="NGS: RNA Analysis"> - <label id="rna_seq" text="RNA-seq" /> - <label id="filtering" text="Filtering" /> - </section></toolbox> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Update boto to 2.25.0 in anticipation of supporting VPC
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/eae95d5fa975/ Changeset: eae95d5fa975 User: dannon Date: 2014-02-20 01:33:27 Summary: Update boto to 2.25.0 in anticipation of supporting VPC Affected #: 1 file diff -r 85c38536c31583ef06db42c1f54d6248b79f96a5 -r eae95d5fa975e1eef4de219564cb976720f18440 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -35,7 +35,7 @@ amqp = 1.4.3 anyjson = 0.3.3 Beaker = 1.4 -boto = 2.5.2 +boto = 2.25.0 decorator = 3.1.2 docutils = 0.7 drmaa = 0.6 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 19 Feb '14

19 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a89bbdfd4a71/ Changeset: a89bbdfd4a71 Branch: stable User: inithello Date: 2014-02-19 22:34:01 Summary: Ensure that symlinks are moved before regular files, since this can in some cases causes a 'No such file or directory' error when the symlink target is moved before the symlink itself. Affected #: 1 file diff -r 0770af01a257818ee82f11a191d4305880ea0b91 -r a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -303,9 +303,19 @@ destination_directory = os.path.join( destination_dir ) if not os.path.isdir( destination_directory ): os.makedirs( destination_directory ) + symlinks = [] + regular_files = [] for file_name in os.listdir( source_directory ): source_file = os.path.join( source_directory, file_name ) destination_file = os.path.join( destination_directory, file_name ) + files_tuple = ( source_file, destination_file ) + if os.path.islink( source_file ): + symlinks.append( files_tuple ) + else: + regular_files.append( files_tuple ) + for source_file, destination_file in symlinks: + shutil.move( source_file, destination_file ) + for source_file, destination_file in regular_files: shutil.move( source_file, destination_file ) def move_file( current_dir, source, destination, rename_to=None ): https://bitbucket.org/galaxy/galaxy-central/commits/85c38536c315/ Changeset: 85c38536c315 User: inithello Date: 2014-02-19 22:34:22 Summary: Merge with a89bbdfd4a71671d575d9a0a3a9f8abeba3f7b21 Affected #: 1 file diff -r ee315625cf4e394bca8a05f25c82e78c978ed50c -r 85c38536c31583ef06db42c1f54d6248b79f96a5 lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py --- a/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/td_common_util.py @@ -303,9 +303,19 @@ destination_directory = os.path.join( destination_dir ) if not os.path.isdir( destination_directory ): os.makedirs( destination_directory ) + symlinks = [] + regular_files = [] for file_name in os.listdir( source_directory ): source_file = os.path.join( source_directory, file_name ) destination_file = os.path.join( destination_directory, file_name ) + files_tuple = ( source_file, destination_file ) + if os.path.islink( source_file ): + symlinks.append( files_tuple ) + else: + regular_files.append( files_tuple ) + for source_file, destination_file in symlinks: + shutil.move( source_file, destination_file ) + for source_file, destination_file in regular_files: shutil.move( source_file, destination_file ) def move_file( current_dir, source, destination, rename_to=None ): 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 DatasetListWrapper with optional inputs.
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ee315625cf4e/ Changeset: ee315625cf4e User: dan Date: 2014-02-19 22:15:48 Summary: Fix for DatasetListWrapper with optional inputs. Affected #: 1 file diff -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b -r ee315625cf4e394bca8a05f25c82e78c978ed50c lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -206,10 +206,12 @@ datasets = [datasets] def to_wrapper( dataset ): - real_path = dataset.file_name wrapper_kwds = kwargs.copy() - if real_path in dataset_paths: - wrapper_kwds[ "dataset_path" ] = dataset_paths[ real_path ] + if dataset: + #A None dataset does not have a filename + real_path = dataset.file_name + if real_path in dataset_paths: + wrapper_kwds[ "dataset_path" ] = dataset_paths[ real_path ] return DatasetFilenameWrapper( dataset, **wrapper_kwds ) list.__init__( self, map( to_wrapper, datasets ) ) 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 19 Feb '14

19 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a94e57976adf/ Changeset: a94e57976adf User: inithello Date: 2014-02-19 21:21:12 Summary: Fix for situation where duplicate database records would be created if a repository was uninstalled and reinstalled after getting updates from the tool shed. Affected #: 2 files diff -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 -r a94e57976adf8cee859bbe14e8275b73b16206bc 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 @@ -1381,7 +1381,7 @@ repository_dependencies = repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans, tool_shed_repository ) repo_info_dict = repository_util.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.changeset_revision, + changeset_revision=tool_shed_repository.installed_changeset_revision, ctx_rev=tool_shed_repository.ctx_rev, repository_owner=tool_shed_repository.owner, repository_name=tool_shed_repository.name, diff -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 -r a94e57976adf8cee859bbe14e8275b73b16206bc lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -1617,6 +1617,13 @@ except: pass +def __repository_query( app ): + if app.name == "galaxy": + query = app.install_model.context.query( app.install_model.ToolShedRepository ) + else: + query = app.model.context.query( app.model.Repository ) + return query + def repository_was_previously_installed( trans, tool_shed_url, repository_name, repo_info_tuple ): """ Find out if a repository is already installed into Galaxy - there are several scenarios where this @@ -1866,10 +1873,3 @@ for arg in args: parts.append( arg.strip( '/' ) ) return '/'.join( parts ) - -def __repository_query( app ): - if app.name == "galaxy": - query = app.install_model.context.query( app.install_model.ToolShedRepository ) - else: - query = app.model.context.query( app.model.Repository ) - return query https://bitbucket.org/galaxy/galaxy-central/commits/c38c0a6893e4/ Changeset: c38c0a6893e4 User: inithello Date: 2014-02-19 21:23:45 Summary: Situations where a migration warning would be incorrectly displayed, and tools with matching filenames would be removed from the tool_conf.xml after running a migration script. Affected #: 9 files diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b lib/tool_shed/galaxy_install/install_manager.py --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -186,8 +186,7 @@ # Tools outside of sections. file_path = elem.get( 'file', None ) if file_path: - file_name = suc.strip_path( file_path ) - if file_name in tool_configs_to_filter: + if file_path in tool_configs_to_filter: root.remove( elem ) persist_required = True elif elem.tag == 'section': @@ -196,8 +195,7 @@ if section_elem.tag == 'tool': file_path = section_elem.get( 'file', None ) if file_path: - file_name = suc.strip_path( file_path ) - if file_name in tool_configs_to_filter or file_path in tool_configs_to_filter: + if file_path in tool_configs_to_filter: elem.remove( section_elem ) persist_required = True if persist_required: @@ -221,8 +219,7 @@ if proprietary_tool_panel_elem.tag == 'tool': # The proprietary_tool_panel_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = proprietary_tool_panel_elem.get( 'file' ) - proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name or tool_config == proprietary_tool_config: + if tool_config == proprietary_tool_config: # The tool is loaded outside of any sections. tool_sections.append( None ) if not is_displayed: @@ -233,8 +230,7 @@ if section_elem.tag == 'tool': # The section_elem looks something like <tool file="emboss_5/emboss_antigenic.xml" />. proprietary_tool_config = section_elem.get( 'file' ) - proprietary_name = suc.strip_path( proprietary_tool_config ) - if tool_config == proprietary_name or tool_config == proprietary_tool_config: + if tool_config == proprietary_tool_config: # The tool is loaded inside of the section_elem. tool_sections.append( ToolSection( proprietary_tool_panel_elem ) ) if not is_displayed: @@ -312,8 +308,7 @@ # Tools outside of sections. file_path = elem.get( 'file', None ) if file_path: - name = suc.strip_path( file_path ) - if name in migrated_tool_configs or file_path in migrated_tool_configs: + if file_path in migrated_tool_configs: if elem not in tool_panel_elems: tool_panel_elems.append( elem ) elif elem.tag == 'section': @@ -322,8 +317,7 @@ if section_elem.tag == 'tool': file_path = section_elem.get( 'file', None ) if file_path: - name = suc.strip_path( file_path ) - if name in migrated_tool_configs or file_path in migrated_tool_configs: + if file_path in migrated_tool_configs: # Append the section, not the tool. if elem not in tool_panel_elems: tool_panel_elems.append( elem ) @@ -361,10 +355,8 @@ for tool_panel_dict in v: # Keep track of tool config file names associated with entries that have been made to the # migrated_tools_conf.xml file so they can be eliminated from all non-shed-related tool panel configs. - tool_config_file = tool_panel_dict.get( 'tool_config', None ) - if tool_config_file: - if tool_config_file not in tool_configs_to_filter: - tool_configs_to_filter.append( tool_config_file ) + if tool_config not in tool_configs_to_filter: + tool_configs_to_filter.append( tool_config ) else: print 'The tool "%s" (%s) has not been enabled because it is not defined in a proprietary tool config (%s).' \ % ( guid, tool_config, ", ".join( self.proprietary_tool_confs or [] ) ) diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0002_tools.xml --- a/scripts/migrate_tools/0002_tools.xml +++ b/scripts/migrate_tools/0002_tools.xml @@ -2,112 +2,112 @@ <toolshed name="toolshed.g2.bx.psu.edu"><repository name="emboss_datatypes" description="Datatypes for Emboss tools" changeset_revision="a89163f31369" /><repository name="emboss_5" description="Galaxy wrappers for EMBOSS version 5.0.0 tools" changeset_revision="7334f6d0ac17"> - <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_antigenic.xml" /> - <tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_backtranseq.xml" /> - <tool id="EMBOSS: banana3" version="5.0.0" file="emboss_banana.xml" /> - <tool id="EMBOSS: biosed4" version="5.0.0" file="emboss_biosed.xml" /> - <tool id="EMBOSS: btwisted5" version="5.0.0" file="emboss_btwisted.xml" /> - <tool id="EMBOSS: cai_custom6" version="5.0.0" file="emboss_cai_custom.xml" /> - <tool id="EMBOSS: cai6" version="5.0.0" file="emboss_cai.xml" /> - <tool id="EMBOSS: chaos7" version="5.0.0" file="emboss_chaos.xml" /> - <tool id="EMBOSS: charge8" version="5.0.0" file="emboss_charge.xml" /> - <tool id="EMBOSS: checktrans9" version="5.0.0" file="emboss_checktrans.xml" /> - <tool id="EMBOSS: chips10" version="5.0.0" file="emboss_chips.xml" /> - <tool id="EMBOSS: cirdna11" version="5.0.0" file="emboss_cirdna.xml" /> - <tool id="EMBOSS: codcmp12" version="5.0.0" file="emboss_codcmp.xml" /> - <tool id="EMBOSS: coderet13" version="5.0.0" file="emboss_coderet.xml" /> - <tool id="EMBOSS: compseq14" version="5.0.0" file="emboss_compseq.xml" /> - <tool id="EMBOSS: cpgplot15" version="5.0.0" file="emboss_cpgplot.xml" /> - <tool id="EMBOSS: cpgreport16" version="5.0.0" file="emboss_cpgreport.xml" /> - <tool id="EMBOSS: cusp17" version="5.0.0" file="emboss_cusp.xml" /> - <tool id="EMBOSS: cutseq18" version="5.0.0" file="emboss_cutseq.xml" /> - <tool id="EMBOSS: dan19" version="5.0.0" file="emboss_dan.xml" /> - <tool id="EMBOSS: degapseq20" version="5.0.0" file="emboss_degapseq.xml" /> - <tool id="EMBOSS: descseq21" version="5.0.0" file="emboss_descseq.xml" /> - <tool id="EMBOSS: diffseq22" version="5.0.0" file="emboss_diffseq.xml" /> - <tool id="EMBOSS: digest23" version="5.0.0" file="emboss_digest.xml" /> - <tool id="EMBOSS: dotmatcher24" version="5.0.0" file="emboss_dotmatcher.xml" /> - <tool id="EMBOSS: dotpath25" version="5.0.0" file="emboss_dotpath.xml" /> - <tool id="EMBOSS: dottup26" version="5.0.0" file="emboss_dottup.xml" /> - <tool id="EMBOSS: dreg27" version="5.0.0" file="emboss_dreg.xml" /> - <tool id="EMBOSS: einverted28" version="5.0.0" file="emboss_einverted.xml" /> - <tool id="EMBOSS: epestfind29" version="5.0.0" file="emboss_epestfind.xml" /> - <tool id="EMBOSS: equicktandem31" version="5.0.0" file="emboss_equicktandem.xml" /> - <tool id="EMBOSS: est2genome32" version="5.0.0" file="emboss_est2genome.xml" /> - <tool id="EMBOSS: etandem33" version="5.0.0" file="emboss_etandem.xml" /> - <tool id="EMBOSS: extractfeat34" version="5.0.0" file="emboss_extractfeat.xml" /> - <tool id="EMBOSS: extractseq35" version="5.0.0" file="emboss_extractseq.xml" /> - <tool id="EMBOSS: freak36" version="5.0.0" file="emboss_freak.xml" /> - <tool id="EMBOSS: fuzznuc37" version="5.0.0" file="emboss_fuzznuc.xml" /> - <tool id="EMBOSS: fuzzpro38" version="5.0.0" file="emboss_fuzzpro.xml" /> - <tool id="EMBOSS: fuzztran39" version="5.0.0" file="emboss_fuzztran.xml" /> - <tool id="EMBOSS: garnier40" version="5.0.0" file="emboss_garnier.xml" /> - <tool id="EMBOSS: geecee41" version="5.0.0" file="emboss_geecee.xml" /> - <tool id="EMBOSS: getorf42" version="5.0.0" file="emboss_getorf.xml" /> - <tool id="EMBOSS: helixturnhelix43" version="5.0.0" file="emboss_helixturnhelix.xml" /> - <tool id="EMBOSS: hmoment44" version="5.0.0" file="emboss_hmoment.xml" /> - <tool id="EMBOSS: iep45" version="5.0.0" file="emboss_iep.xml" /> - <tool id="EMBOSS: infoseq46" version="5.0.0" file="emboss_infoseq.xml" /> - <tool id="EMBOSS: isochore47" version="5.0.0" file="emboss_isochore.xml" /> - <tool id="EMBOSS: lindna48" version="5.0.0" file="emboss_lindna.xml" /> - <tool id="EMBOSS: marscan49" version="5.0.0" file="emboss_marscan.xml" /> - <tool id="EMBOSS: maskfeat50" version="5.0.0" file="emboss_maskfeat.xml" /> - <tool id="EMBOSS: maskseq51" version="5.0.0" file="emboss_maskseq.xml" /> - <tool id="EMBOSS: matcher52" version="5.0.0" file="emboss_matcher.xml" /> - <tool id="EMBOSS: megamerger53" version="5.0.0" file="emboss_megamerger.xml" /> - <tool id="EMBOSS: merger54" version="5.0.0" file="emboss_merger.xml" /> - <tool id="EMBOSS: msbar55" version="5.0.0" file="emboss_msbar.xml" /> - <tool id="EMBOSS: needle56" version="5.0.0" file="emboss_needle.xml" /> - <tool id="EMBOSS: newcpgreport57" version="5.0.0" file="emboss_newcpgreport.xml" /> - <tool id="EMBOSS: newcpgseek58" version="5.0.0" file="emboss_newcpgseek.xml" /> - <tool id="EMBOSS: newseq59" version="5.0.0" file="emboss_newseq.xml" /> - <tool id="EMBOSS: noreturn60" version="5.0.0" file="emboss_noreturn.xml" /> - <tool id="EMBOSS: notseq61" version="5.0.0" file="emboss_notseq.xml" /> - <tool id="EMBOSS: nthseq62" version="5.0.0" file="emboss_nthseq.xml" /> - <tool id="EMBOSS: octanol63" version="5.0.0" file="emboss_octanol.xml" /> - <tool id="EMBOSS: oddcomp64" version="5.0.0" file="emboss_oddcomp.xml" /> - <tool id="EMBOSS: palindrome65" version="5.0.0" file="emboss_palindrome.xml" /> - <tool id="EMBOSS: pasteseq66" version="5.0.0" file="emboss_pasteseq.xml" /> - <tool id="EMBOSS: patmatdb67" version="5.0.0" file="emboss_patmatdb.xml" /> - <tool id="EMBOSS: pepcoil68" version="5.0.0" file="emboss_pepcoil.xml" /> - <tool id="EMBOSS: pepinfo69" version="5.0.0" file="emboss_pepinfo.xml" /> - <tool id="EMBOSS: pepnet70" version="5.0.0" file="emboss_pepnet.xml" /> - <tool id="EMBOSS: pepstats71" version="5.0.0" file="emboss_pepstats.xml" /> - <tool id="EMBOSS: pepwheel72" version="5.0.0" file="emboss_pepwheel.xml" /> - <tool id="EMBOSS: pepwindow73" version="5.0.0" file="emboss_pepwindow.xml" /> - <tool id="EMBOSS: pepwindowall74" version="5.0.0" file="emboss_pepwindowall.xml" /> - <tool id="EMBOSS: plotcon75" version="5.0.0" file="emboss_plotcon.xml" /> - <tool id="EMBOSS: plotorf76" version="5.0.0" file="emboss_plotorf.xml" /> - <tool id="EMBOSS: polydot77" version="5.0.0" file="emboss_polydot.xml" /> - <tool id="EMBOSS: preg78" version="5.0.0" file="emboss_preg.xml" /> - <tool id="EMBOSS: prettyplot79" version="5.0.0" file="emboss_prettyplot.xml" /> - <tool id="EMBOSS: prettyseq80" version="5.0.0" file="emboss_prettyseq.xml" /> - <tool id="EMBOSS: primersearch81" version="5.0.0" file="emboss_primersearch.xml" /> - <tool id="EMBOSS: revseq82" version="5.0.0" file="emboss_revseq.xml" /> - <tool id="EMBOSS: seqmatchall83" version="5.0.0" file="emboss_seqmatchall.xml" /> - <tool id="EMBOSS: seqret84" version="5.0.0" file="emboss_seqret.xml" /> - <tool id="EMBOSS: showfeat85" version="5.0.0" file="emboss_showfeat.xml" /> - <tool id="EMBOSS: shuffleseq87" version="5.0.0" file="emboss_shuffleseq.xml" /> - <tool id="EMBOSS: sigcleave88" version="5.0.0" file="emboss_sigcleave.xml" /> - <tool id="EMBOSS: sirna89" version="5.0.0" file="emboss_sirna.xml" /> - <tool id="EMBOSS: sixpack90" version="5.0.0" file="emboss_sixpack.xml" /> - <tool id="EMBOSS: skipseq91" version="5.0.0" file="emboss_skipseq.xml" /> - <tool id="EMBOSS: splitter92" version="5.0.0" file="emboss_splitter.xml" /> - <tool id="EMBOSS: supermatcher95" version="5.0.0" file="emboss_supermatcher.xml" /> - <tool id="EMBOSS: syco96" version="5.0.0" file="emboss_syco.xml" /> - <tool id="EMBOSS: tcode97" version="5.0.0" file="emboss_tcode.xml" /> - <tool id="EMBOSS: textsearch98" version="5.0.0" file="emboss_textsearch.xml" /> - <tool id="EMBOSS: tmap99" version="5.0.0" file="emboss_tmap.xml" /> - <tool id="EMBOSS: tranalign100" version="5.0.0" file="emboss_tranalign.xml" /> - <tool id="EMBOSS: transeq101" version="5.0.0" file="emboss_transeq.xml" /> - <tool id="EMBOSS: trimest102" version="5.0.0" file="emboss_trimest.xml" /> - <tool id="EMBOSS: trimseq103" version="5.0.0" file="emboss_trimseq.xml" /> - <tool id="EMBOSS: twofeat104" version="5.0.0" file="emboss_twofeat.xml" /> - <tool id="EMBOSS: union105" version="5.0.0" file="emboss_union.xml" /> - <tool id="EMBOSS: vectorstrip106" version="5.0.0" file="emboss_vectorstrip.xml" /> - <tool id="EMBOSS: water107" version="5.0.0" file="emboss_water.xml" /> - <tool id="EMBOSS: wobble108" version="5.0.0" file="emboss_wobble.xml" /> - <tool id="EMBOSS: wordcount109" version="5.0.0" file="emboss_wordcount.xml" /> - <tool id="EMBOSS: wordmatch110" version="5.0.0" file="emboss_wordmatch.xml" /> + <tool id="EMBOSS: antigenic1" version="5.0.0" file="emboss_5/emboss_antigenic.xml" /> + <tool id="EMBOSS: backtranseq2" version="5.0.0" file="emboss_5/emboss_backtranseq.xml" /> + <tool id="EMBOSS: banana3" version="5.0.0" file="emboss_5/emboss_banana.xml" /> + <tool id="EMBOSS: biosed4" version="5.0.0" file="emboss_5/emboss_biosed.xml" /> + <tool id="EMBOSS: btwisted5" version="5.0.0" file="emboss_5/emboss_btwisted.xml" /> + <tool id="EMBOSS: cai_custom6" version="5.0.0" file="emboss_5/emboss_cai_custom.xml" /> + <tool id="EMBOSS: cai6" version="5.0.0" file="emboss_5/emboss_cai.xml" /> + <tool id="EMBOSS: chaos7" version="5.0.0" file="emboss_5/emboss_chaos.xml" /> + <tool id="EMBOSS: charge8" version="5.0.0" file="emboss_5/emboss_charge.xml" /> + <tool id="EMBOSS: checktrans9" version="5.0.0" file="emboss_5/emboss_checktrans.xml" /> + <tool id="EMBOSS: chips10" version="5.0.0" file="emboss_5/emboss_chips.xml" /> + <tool id="EMBOSS: cirdna11" version="5.0.0" file="emboss_5/emboss_cirdna.xml" /> + <tool id="EMBOSS: codcmp12" version="5.0.0" file="emboss_5/emboss_codcmp.xml" /> + <tool id="EMBOSS: coderet13" version="5.0.0" file="emboss_5/emboss_coderet.xml" /> + <tool id="EMBOSS: compseq14" version="5.0.0" file="emboss_5/emboss_compseq.xml" /> + <tool id="EMBOSS: cpgplot15" version="5.0.0" file="emboss_5/emboss_cpgplot.xml" /> + <tool id="EMBOSS: cpgreport16" version="5.0.0" file="emboss_5/emboss_cpgreport.xml" /> + <tool id="EMBOSS: cusp17" version="5.0.0" file="emboss_5/emboss_cusp.xml" /> + <tool id="EMBOSS: cutseq18" version="5.0.0" file="emboss_5/emboss_cutseq.xml" /> + <tool id="EMBOSS: dan19" version="5.0.0" file="emboss_5/emboss_dan.xml" /> + <tool id="EMBOSS: degapseq20" version="5.0.0" file="emboss_5/emboss_degapseq.xml" /> + <tool id="EMBOSS: descseq21" version="5.0.0" file="emboss_5/emboss_descseq.xml" /> + <tool id="EMBOSS: diffseq22" version="5.0.0" file="emboss_5/emboss_diffseq.xml" /> + <tool id="EMBOSS: digest23" version="5.0.0" file="emboss_5/emboss_digest.xml" /> + <tool id="EMBOSS: dotmatcher24" version="5.0.0" file="emboss_5/emboss_dotmatcher.xml" /> + <tool id="EMBOSS: dotpath25" version="5.0.0" file="emboss_5/emboss_dotpath.xml" /> + <tool id="EMBOSS: dottup26" version="5.0.0" file="emboss_5/emboss_dottup.xml" /> + <tool id="EMBOSS: dreg27" version="5.0.0" file="emboss_5/emboss_dreg.xml" /> + <tool id="EMBOSS: einverted28" version="5.0.0" file="emboss_5/emboss_einverted.xml" /> + <tool id="EMBOSS: epestfind29" version="5.0.0" file="emboss_5/emboss_epestfind.xml" /> + <tool id="EMBOSS: equicktandem31" version="5.0.0" file="emboss_5/emboss_equicktandem.xml" /> + <tool id="EMBOSS: est2genome32" version="5.0.0" file="emboss_5/emboss_est2genome.xml" /> + <tool id="EMBOSS: etandem33" version="5.0.0" file="emboss_5/emboss_etandem.xml" /> + <tool id="EMBOSS: extractfeat34" version="5.0.0" file="emboss_5/emboss_extractfeat.xml" /> + <tool id="EMBOSS: extractseq35" version="5.0.0" file="emboss_5/emboss_extractseq.xml" /> + <tool id="EMBOSS: freak36" version="5.0.0" file="emboss_5/emboss_freak.xml" /> + <tool id="EMBOSS: fuzznuc37" version="5.0.0" file="emboss_5/emboss_fuzznuc.xml" /> + <tool id="EMBOSS: fuzzpro38" version="5.0.0" file="emboss_5/emboss_fuzzpro.xml" /> + <tool id="EMBOSS: fuzztran39" version="5.0.0" file="emboss_5/emboss_fuzztran.xml" /> + <tool id="EMBOSS: garnier40" version="5.0.0" file="emboss_5/emboss_garnier.xml" /> + <tool id="EMBOSS: geecee41" version="5.0.0" file="emboss_5/emboss_geecee.xml" /> + <tool id="EMBOSS: getorf42" version="5.0.0" file="emboss_5/emboss_getorf.xml" /> + <tool id="EMBOSS: helixturnhelix43" version="5.0.0" file="emboss_5/emboss_helixturnhelix.xml" /> + <tool id="EMBOSS: hmoment44" version="5.0.0" file="emboss_5/emboss_hmoment.xml" /> + <tool id="EMBOSS: iep45" version="5.0.0" file="emboss_5/emboss_iep.xml" /> + <tool id="EMBOSS: infoseq46" version="5.0.0" file="emboss_5/emboss_infoseq.xml" /> + <tool id="EMBOSS: isochore47" version="5.0.0" file="emboss_5/emboss_isochore.xml" /> + <tool id="EMBOSS: lindna48" version="5.0.0" file="emboss_5/emboss_lindna.xml" /> + <tool id="EMBOSS: marscan49" version="5.0.0" file="emboss_5/emboss_marscan.xml" /> + <tool id="EMBOSS: maskfeat50" version="5.0.0" file="emboss_5/emboss_maskfeat.xml" /> + <tool id="EMBOSS: maskseq51" version="5.0.0" file="emboss_5/emboss_maskseq.xml" /> + <tool id="EMBOSS: matcher52" version="5.0.0" file="emboss_5/emboss_matcher.xml" /> + <tool id="EMBOSS: megamerger53" version="5.0.0" file="emboss_5/emboss_megamerger.xml" /> + <tool id="EMBOSS: merger54" version="5.0.0" file="emboss_5/emboss_merger.xml" /> + <tool id="EMBOSS: msbar55" version="5.0.0" file="emboss_5/emboss_msbar.xml" /> + <tool id="EMBOSS: needle56" version="5.0.0" file="emboss_5/emboss_needle.xml" /> + <tool id="EMBOSS: newcpgreport57" version="5.0.0" file="emboss_5/emboss_newcpgreport.xml" /> + <tool id="EMBOSS: newcpgseek58" version="5.0.0" file="emboss_5/emboss_newcpgseek.xml" /> + <tool id="EMBOSS: newseq59" version="5.0.0" file="emboss_5/emboss_newseq.xml" /> + <tool id="EMBOSS: noreturn60" version="5.0.0" file="emboss_5/emboss_noreturn.xml" /> + <tool id="EMBOSS: notseq61" version="5.0.0" file="emboss_5/emboss_notseq.xml" /> + <tool id="EMBOSS: nthseq62" version="5.0.0" file="emboss_5/emboss_nthseq.xml" /> + <tool id="EMBOSS: octanol63" version="5.0.0" file="emboss_5/emboss_octanol.xml" /> + <tool id="EMBOSS: oddcomp64" version="5.0.0" file="emboss_5/emboss_oddcomp.xml" /> + <tool id="EMBOSS: palindrome65" version="5.0.0" file="emboss_5/emboss_palindrome.xml" /> + <tool id="EMBOSS: pasteseq66" version="5.0.0" file="emboss_5/emboss_pasteseq.xml" /> + <tool id="EMBOSS: patmatdb67" version="5.0.0" file="emboss_5/emboss_patmatdb.xml" /> + <tool id="EMBOSS: pepcoil68" version="5.0.0" file="emboss_5/emboss_pepcoil.xml" /> + <tool id="EMBOSS: pepinfo69" version="5.0.0" file="emboss_5/emboss_pepinfo.xml" /> + <tool id="EMBOSS: pepnet70" version="5.0.0" file="emboss_5/emboss_pepnet.xml" /> + <tool id="EMBOSS: pepstats71" version="5.0.0" file="emboss_5/emboss_pepstats.xml" /> + <tool id="EMBOSS: pepwheel72" version="5.0.0" file="emboss_5/emboss_pepwheel.xml" /> + <tool id="EMBOSS: pepwindow73" version="5.0.0" file="emboss_5/emboss_pepwindow.xml" /> + <tool id="EMBOSS: pepwindowall74" version="5.0.0" file="emboss_5/emboss_pepwindowall.xml" /> + <tool id="EMBOSS: plotcon75" version="5.0.0" file="emboss_5/emboss_plotcon.xml" /> + <tool id="EMBOSS: plotorf76" version="5.0.0" file="emboss_5/emboss_plotorf.xml" /> + <tool id="EMBOSS: polydot77" version="5.0.0" file="emboss_5/emboss_polydot.xml" /> + <tool id="EMBOSS: preg78" version="5.0.0" file="emboss_5/emboss_preg.xml" /> + <tool id="EMBOSS: prettyplot79" version="5.0.0" file="emboss_5/emboss_prettyplot.xml" /> + <tool id="EMBOSS: prettyseq80" version="5.0.0" file="emboss_5/emboss_prettyseq.xml" /> + <tool id="EMBOSS: primersearch81" version="5.0.0" file="emboss_5/emboss_primersearch.xml" /> + <tool id="EMBOSS: revseq82" version="5.0.0" file="emboss_5/emboss_revseq.xml" /> + <tool id="EMBOSS: seqmatchall83" version="5.0.0" file="emboss_5/emboss_seqmatchall.xml" /> + <tool id="EMBOSS: seqret84" version="5.0.0" file="emboss_5/emboss_seqret.xml" /> + <tool id="EMBOSS: showfeat85" version="5.0.0" file="emboss_5/emboss_showfeat.xml" /> + <tool id="EMBOSS: shuffleseq87" version="5.0.0" file="emboss_5/emboss_shuffleseq.xml" /> + <tool id="EMBOSS: sigcleave88" version="5.0.0" file="emboss_5/emboss_sigcleave.xml" /> + <tool id="EMBOSS: sirna89" version="5.0.0" file="emboss_5/emboss_sirna.xml" /> + <tool id="EMBOSS: sixpack90" version="5.0.0" file="emboss_5/emboss_sixpack.xml" /> + <tool id="EMBOSS: skipseq91" version="5.0.0" file="emboss_5/emboss_skipseq.xml" /> + <tool id="EMBOSS: splitter92" version="5.0.0" file="emboss_5/emboss_splitter.xml" /> + <tool id="EMBOSS: supermatcher95" version="5.0.0" file="emboss_5/emboss_supermatcher.xml" /> + <tool id="EMBOSS: syco96" version="5.0.0" file="emboss_5/emboss_syco.xml" /> + <tool id="EMBOSS: tcode97" version="5.0.0" file="emboss_5/emboss_tcode.xml" /> + <tool id="EMBOSS: textsearch98" version="5.0.0" file="emboss_5/emboss_textsearch.xml" /> + <tool id="EMBOSS: tmap99" version="5.0.0" file="emboss_5/emboss_tmap.xml" /> + <tool id="EMBOSS: tranalign100" version="5.0.0" file="emboss_5/emboss_tranalign.xml" /> + <tool id="EMBOSS: transeq101" version="5.0.0" file="emboss_5/emboss_transeq.xml" /> + <tool id="EMBOSS: trimest102" version="5.0.0" file="emboss_5/emboss_trimest.xml" /> + <tool id="EMBOSS: trimseq103" version="5.0.0" file="emboss_5/emboss_trimseq.xml" /> + <tool id="EMBOSS: twofeat104" version="5.0.0" file="emboss_5/emboss_twofeat.xml" /> + <tool id="EMBOSS: union105" version="5.0.0" file="emboss_5/emboss_union.xml" /> + <tool id="EMBOSS: vectorstrip106" version="5.0.0" file="emboss_5/emboss_vectorstrip.xml" /> + <tool id="EMBOSS: water107" version="5.0.0" file="emboss_5/emboss_water.xml" /> + <tool id="EMBOSS: wobble108" version="5.0.0" file="emboss_5/emboss_wobble.xml" /> + <tool id="EMBOSS: wordcount109" version="5.0.0" file="emboss_5/emboss_wordcount.xml" /> + <tool id="EMBOSS: wordmatch110" version="5.0.0" file="emboss_5/emboss_wordmatch.xml" /></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0003_tools.xml --- a/scripts/migrate_tools/0003_tools.xml +++ b/scripts/migrate_tools/0003_tools.xml @@ -1,6 +1,6 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="freebayes" description="Galaxy Freebayes Bayesian genetic variant detector tool" changeset_revision="213a3d6b579a"> - <tool id="freebayes" version="0.0.2 " file="freebayes.xml" /> + <tool id="freebayes" version="0.0.2 " file="variant_detection/freebayes.xml" /></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0004_tools.xml --- a/scripts/migrate_tools/0004_tools.xml +++ b/scripts/migrate_tools/0004_tools.xml @@ -2,11 +2,11 @@ <toolshed name="toolshed.g2.bx.psu.edu"><repository name="blast_datatypes" description="Datatypes for BLAST" changeset_revision="e1c29f302301" /><repository name="ncbi_blast_plus" description="Galaxy wrappers for NCBI BLAST+" changeset_revision="d375502056f1"> - <tool id="blastxml_to_tabular" version="0.0.8" file="blastxml_to_tabular.xml"/> - <tool id="ncbi_blastn_wrapper" version="0.0.11" file="ncbi_blastn_wrapper.xml"/> - <tool id="ncbi_blastp_wrapper" version="0.0.11" file="ncbi_blastp_wrapper.xml"/> - <tool id="ncbi_blastx_wrapper" version="0.0.11" file="ncbi_blastx_wrapper.xml"/> - <tool id="ncbi_tblastn_wrapper" version="0.0.11" file="ncbi_tblastn_wrapper.xml"/> - <tool id="ncbi_tblastx_wrapper" version="0.0.11" file="ncbi_tblastx_wrapper.xml"/> + <tool id="blastxml_to_tabular" version="0.0.8" file="ncbi_blast_plus/blastxml_to_tabular.xml"/> + <tool id="ncbi_blastn_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastn_wrapper.xml"/> + <tool id="ncbi_blastp_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastp_wrapper.xml"/> + <tool id="ncbi_blastx_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_blastx_wrapper.xml"/> + <tool id="ncbi_tblastn_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_tblastn_wrapper.xml"/> + <tool id="ncbi_tblastx_wrapper" version="0.0.11" file="ncbi_blast_plus/ncbi_tblastx_wrapper.xml"/></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0005_tools.xml --- a/scripts/migrate_tools/0005_tools.xml +++ b/scripts/migrate_tools/0005_tools.xml @@ -1,7 +1,7 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="bwa_wrappers" description="Galaxy wrappers for the BWA short read aligner." changeset_revision="ffa8aaa14f7c"> - <tool id="bwa_wrapper" version="1.2.3" file="bwa_wrapper.xml"/> - <tool id="bwa_color_wrapper" version="1.0.2" file="bwa_color_wrapper.xml"/> + <tool id="bwa_wrapper" version="1.2.3" file="sr_mapping/bwa_wrapper.xml"/> + <tool id="bwa_color_wrapper" version="1.0.2" file="sr_mapping/bwa_color_wrapper.xml"/></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0006_tools.xml --- a/scripts/migrate_tools/0006_tools.xml +++ b/scripts/migrate_tools/0006_tools.xml @@ -1,18 +1,18 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="picard" description="Galaxy wrappers for the Picard SAM/BAM manipulation tools." changeset_revision="e0232cbac965"> - <tool id="picard_FastqToSam" version="1.56.0" file="picard_FastqToSam.xml" /> - <tool id="picard_SamToFastq" version="1.56.1" file="picard_SamToFastq.xml" /> - <tool id="picard_BamIndexStats" version="1.56.0" file="picard_BamIndexStats.xml" /> - <tool id="PicardASMetrics" version="1.56.0" file="rgPicardASMetrics.xml" /> - <tool id="PicardGCBiasMetrics" version="1.56.0" file="rgPicardGCBiasMetrics.xml" /> - <tool id="rgEstLibComp" version="1.56.0" file="rgPicardLibComplexity.xml" /> - <tool id="PicardInsertSize" version="1.56.0" file="rgPicardInsertSize.xml" /> - <tool id="PicardHsMetrics" version="1.56.0" file="rgPicardHsMetrics.xml" /> - <tool id="picard_ARRG" version="1.56.0" file="picard_AddOrReplaceReadGroups.xml" /> - <tool id="picard_ReorderSam" version="1.56.0" file="picard_ReorderSam.xml" /> - <tool id="picard_ReplaceSamHeader" version="1.56.0" file="picard_ReplaceSamHeader.xml" /> - <tool id="rgPicFixMate" version="1.56.0" file="rgPicardFixMate.xml" /> - <tool id="rgPicardMarkDups" version="1.56.0" file="rgPicardMarkDups.xml" /> + <tool id="picard_FastqToSam" version="1.56.0" file="picard/picard_FastqToSam.xml" /> + <tool id="picard_SamToFastq" version="1.56.1" file="picard/picard_SamToFastq.xml" /> + <tool id="picard_BamIndexStats" version="1.56.0" file="picard/picard_BamIndexStats.xml" /> + <tool id="PicardASMetrics" version="1.56.0" file="picard/rgPicardASMetrics.xml" /> + <tool id="PicardGCBiasMetrics" version="1.56.0" file="picard/rgPicardGCBiasMetrics.xml" /> + <tool id="rgEstLibComp" version="1.56.0" file="picard/rgPicardLibComplexity.xml" /> + <tool id="PicardInsertSize" version="1.56.0" file="picard/rgPicardInsertSize.xml" /> + <tool id="PicardHsMetrics" version="1.56.0" file="picard/rgPicardHsMetrics.xml" /> + <tool id="picard_ARRG" version="1.56.0" file="picard/picard_AddOrReplaceReadGroups.xml" /> + <tool id="picard_ReorderSam" version="1.56.0" file="picard/picard_ReorderSam.xml" /> + <tool id="picard_ReplaceSamHeader" version="1.56.0" file="picard/picard_ReplaceSamHeader.xml" /> + <tool id="rgPicFixMate" version="1.56.0" file="picard/rgPicardFixMate.xml" /> + <tool id="rgPicardMarkDups" version="1.56.0" file="picard/rgPicardMarkDups.xml" /></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0007_tools.xml --- a/scripts/migrate_tools/0007_tools.xml +++ b/scripts/migrate_tools/0007_tools.xml @@ -1,15 +1,15 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository name="bowtie_wrappers" description="Galaxy wrappers for the Bowtie short read mapping tools." changeset_revision="0c7e4eadfb3c"> - <tool id="bowtie_wrapper" version="1.1.2" file="bowtie_wrapper.xml" /> + <tool id="bowtie_wrapper" version="1.1.2" file="sr_mapping/bowtie_wrapper.xml" /></repository><repository name="bowtie_color_wrappers" description="Galaxy wrappers for the Bowtie short read mapping tools on color space reads" changeset_revision="fd0914e451c5"> - <tool id="bowtie_color_wrapper" version="1.1.2" file="bowtie_color_wrapper.xml" /> + <tool id="bowtie_color_wrapper" version="1.1.2" file="sr_mapping/bowtie_color_wrapper.xml" /></repository><repository name="lastz" description="Galaxy wrappers for the Lastz alignment tool" changeset_revision="0801f8207d30"> - <tool id="lastz_wrapper_2" version="1.1.2" file="lastz_wrapper.xml" /> + <tool id="lastz_wrapper_2" version="1.1.2" file="sr_mapping/lastz_wrapper.xml" /></repository><repository name="lastz_paired_reads" description="Galaxy wrapper for the Lastz alignment tool on paired reads" changeset_revision="96825cee5c25"> - <tool id="lastz_paired_reads_wrapper" version="1.1.1" file="lastz_paired_reads_wrapper.xml" /> + <tool id="lastz_paired_reads_wrapper" version="1.1.1" file="sr_mapping/lastz_paired_reads_wrapper.xml" /></repository></toolshed> diff -r a94e57976adf8cee859bbe14e8275b73b16206bc -r c38c0a6893e4831b536ce5b4e7004690aa8bb77b scripts/migrate_tools/0008_tools.xml --- a/scripts/migrate_tools/0008_tools.xml +++ b/scripts/migrate_tools/0008_tools.xml @@ -1,147 +1,147 @@ <?xml version="1.0"?><toolshed name="toolshed.g2.bx.psu.edu"><repository owner="devteam" changeset_revision="dc20f447c0e2" name="bam_to_sam" description="Galaxy wrappers for the tool BAM-to-SAM: converts BAM format to SAM format"> - <tool id="bam_to_sam" version="1.0.3" file="bam_to_sam.xml" /> + <tool id="bam_to_sam" version="1.0.3" file="samtools/bam_to_sam.xml" /></repository><repository owner="devteam" changeset_revision="586c1f0e1515" name="categorize_elements_satisfying_criteria" description="Galaxy wrappers for the tool Categorize Elements: satisfying criteria"> - <tool id="categorize_elements_satisfying_criteria" version="1.0.0" file="categorize_elements_satisfying_criteria.xml" /> + <tool id="categorize_elements_satisfying_criteria" version="1.0.0" file="regVariation/categorize_elements_satisfying_criteria.xml" /></repository><repository owner="devteam" changeset_revision="acc3dc5d26e3" name="compute_motif_frequencies_for_all_motifs" description="Galaxy wrappers for the tool Compute Motif Frequencies For All Motifs: motif by motif"> - <tool id="compute_motif_frequencies_for_all_motifs" version="1.0.0" file="compute_motif_frequencies_for_all_motifs.xml" /> + <tool id="compute_motif_frequencies_for_all_motifs" version="1.0.0" file="regVariation/compute_motif_frequencies_for_all_motifs.xml" /></repository><repository owner="devteam" changeset_revision="46325357b948" name="compute_motifs_frequency" description="Galaxy wrappers for the tool Compute Motif Frequencies: in indel flanking regions"> - <tool id="compute_motifs_frequency" version="1.0.0" file="compute_motifs_frequency.xml" /> + <tool id="compute_motifs_frequency" version="1.0.0" file="regVariation/compute_motifs_frequency.xml" /></repository><repository owner="devteam" changeset_revision="4a32700dcaa2" name="ctd_batch" description="Galaxy wrappers for the tool CTD: analysis of chemicals, diseases, or genes"> - <tool id="ctdBatch_1" version="1.0.0" file="ctd.xml" /> + <tool id="ctdBatch_1" version="1.0.0" file="phenotype_association/ctd.xml" /></repository><repository owner="devteam" changeset_revision="9a3f7a890da6" name="cuffcompare" description="Galaxy wrappers for the Cuffcompare tool."> - <tool id="cuffcompare" version="0.0.5" file="cuffcompare_wrapper.xml" /> + <tool id="cuffcompare" version="0.0.5" file="ngs_rna/cuffcompare_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="0dabb2ed6eb1" name="cuffdiff" description="Galaxy wrappers for the Cuffdiff tool."> - <tool id="cuffdiff" version="0.0.6" file="cuffdiff_wrapper.xml" /> + <tool id="cuffdiff" version="0.0.6" file="ngs_rna/cuffdiff_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="b01956f26c36" name="cufflinks" description="Galaxy wrappers for the Cufflinks tool."> - <tool id="cufflinks" version="0.0.6" file="cufflinks_wrapper.xml" /> + <tool id="cufflinks" version="0.0.6" file="ngs_rna/cufflinks_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="fdc55fd74f78" name="cuffmerge" description="Galaxy wrappers for the Cuffmerge tool."> - <tool id="cuffmerge" version="0.0.5" file="cuffmerge_wrapper.xml" /> + <tool id="cuffmerge" version="0.0.5" file="ngs_rna/cuffmerge_wrapper.xml" /></repository><repository owner="devteam" changeset_revision="f16000dc644b" name="delete_overlapping_indels" description="Galaxy wrappers for the tool Delete Overlapping Indels: from a chromosome indels file"> - <tool id="delete_overlapping_indels" version="1.0.0" file="delete_overlapping_indels.xml" /> + <tool id="delete_overlapping_indels" version="1.0.0" file="regVariation/delete_overlapping_indels.xml" /></repository><repository owner="devteam" changeset_revision="de839553d2a2" name="divide_pg_snp" description="Galaxy wrappers for the tool Separate pgSnp alleles: into columns"> - <tool id="dividePgSnp" version="1.0.0" file="dividePgSnpAlleles.xml" /> + <tool id="dividePgSnp" version="1.0.0" file="phenotype_association/dividePgSnpAlleles.xml" /></repository><repository owner="devteam" changeset_revision="063ecbe59faf" name="draw_stacked_barplots" description="Galaxy wrappers for the tool Draw Stacked Bar Plots: for different categories and different criteria"> - <tool id="draw_stacked_barplots" version="1.0.0" file="draw_stacked_barplots.xml" /> + <tool id="draw_stacked_barplots" version="1.0.0" file="regVariation/draw_stacked_barplots.xml" /></repository><repository owner="devteam" changeset_revision="f2ab5b44870d" name="fasta_clipping_histogram" description="Galaxy wrappers for the tool Length Distribution chart"> - <tool id="cshl_fasta_clipping_histogram" version="1.0.0" file="fasta_clipping_histogram.xml" /> + <tool id="cshl_fasta_clipping_histogram" version="1.0.0" file="fastx_toolkit/fasta_clipping_histogram.xml" /></repository><repository owner="devteam" changeset_revision="8f0ae92440b8" name="fasta_formatter" description="Galaxy wrappers for the tool FASTA Width: formatter"> - <tool id="cshl_fasta_formatter" version="1.0.0" file="fasta_formatter.xml" /> + <tool id="cshl_fasta_formatter" version="1.0.0" file="fastx_toolkit/fasta_formatter.xml" /></repository><repository owner="devteam" changeset_revision="4b41e3076a50" name="fasta_nucleotide_changer" description="Galaxy wrappers for the tool RNA/DNA: converter"> - <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" file="fasta_nucleotide_changer.xml" /> + <tool id="cshl_fasta_nucleotides_changer" version="1.0.0" file="fastx_toolkit/fasta_nucleotide_changer.xml" /></repository><repository owner="devteam" changeset_revision="e359ce20fbd9" name="fastq_quality_boxplot" description="Galaxy wrappers for the tool Draw quality score boxplot"> - <tool id="cshl_fastq_quality_boxplot" version="1.0.0" file="fastq_quality_boxplot.xml" /> + <tool id="cshl_fastq_quality_boxplot" version="1.0.0" file="fastx_toolkit/fastq_quality_boxplot.xml" /></repository><repository owner="devteam" changeset_revision="b87c74b61d81" name="fastq_quality_converter" description="Galaxy wrappers for the tool Quality format converter: (ASCII-Numeric)"> - <tool id="cshl_fastq_quality_converter" version="1.0.0" file="fastq_quality_converter.xml" /> + <tool id="cshl_fastq_quality_converter" version="1.0.0" file="fastx_toolkit/fastq_quality_converter.xml" /></repository><repository owner="devteam" changeset_revision="b145b9b26648" name="fastq_quality_filter" description="Galaxy wrappers for the Filter by quality tool."> - <tool id="cshl_fastq_quality_filter" version="1.0.0" file="fastq_quality_filter.xml" /> + <tool id="cshl_fastq_quality_filter" version="1.0.0" file="fastx_toolkit/fastq_quality_filter.xml" /></repository><repository owner="devteam" changeset_revision="04614cf6ed39" name="fastq_to_fasta" description="Galaxy wrappers for the tool FASTQ to FASTA: converter"> - <tool id="cshl_fastq_to_fasta" version="1.0.0" file="fastq_to_fasta.xml" /> + <tool id="cshl_fastq_to_fasta" version="1.0.0" file="fastx_toolkit/fastq_to_fasta.xml" /></repository><repository owner="devteam" changeset_revision="7f9660a246c0" name="fastx_artifacts_filter" description="Galaxy wrappers for the Remove sequencing artifacts tool."> - <tool id="cshl_fastx_artifacts_filter" version="1.0.0" file="fastx_artifacts_filter.xml" /> + <tool id="cshl_fastx_artifacts_filter" version="1.0.0" file="fastx_toolkit/fastx_artifacts_filter.xml" /></repository><repository owner="devteam" changeset_revision="a12850d0559b" name="fastx_barcode_splitter" description="Galaxy wrappers for the Barcode Splitter tool."> - <tool id="cshl_fastx_barcode_splitter" version="1.0.0" file="fastx_barcode_splitter.xml" /> + <tool id="cshl_fastx_barcode_splitter" version="1.0.0" file="fastx_toolkit/fastx_barcode_splitter.xml" /></repository><repository owner="devteam" changeset_revision="2fe2d2b9e8e4" name="fastx_clipper" description="Galaxy wrappers for the tool Clip: adapter sequences"> - <tool id="cshl_fastx_clipper" version="1.0.1" file="fastx_clipper.xml" /> + <tool id="cshl_fastx_clipper" version="1.0.1" file="fastx_toolkit/fastx_clipper.xml" /></repository><repository owner="devteam" changeset_revision="e942fd3a76a5" name="fastx_collapser" description="Galaxy wrappers for the tool Collapse: sequences"> - <tool id="cshl_fastx_collapser" version="1.0.0" file="fastx_collapser.xml" /> + <tool id="cshl_fastx_collapser" version="1.0.0" file="fastx_toolkit/fastx_collapser.xml" /></repository><repository owner="devteam" changeset_revision="bcc5424a4a3c" name="fastx_nucleotides_distribution" description="Galaxy wrappers for the Draw nucleotides distribution chart tool."> - <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" file="fastx_nucleotides_distribution.xml" /> + <tool id="cshl_fastx_nucleotides_distribution" version="1.0.0" file="fastx_toolkit/fastx_nucleotides_distribution.xml" /></repository><repository owner="devteam" changeset_revision="45f077341b24" name="fastx_quality_statistics" description="Galaxy wrappers for the Compute quality statistics tool."> - <tool id="cshl_fastx_quality_statistics" version="1.0.0" file="fastx_quality_statistics.xml" /> + <tool id="cshl_fastx_quality_statistics" version="1.0.0" file="fastx_toolkit/fastx_quality_statistics.xml" /></repository><repository owner="devteam" changeset_revision="d7bce63e6e09" name="fastx_renamer" description="Galaxy wrappers for the Rename sequences tool."> - <tool id="cshl_fastx_renamer" version="0.0.11" file="fastx_renamer.xml" /> + <tool id="cshl_fastx_renamer" version="0.0.11" file="fastx_toolkit/fastx_renamer.xml" /></repository><repository owner="devteam" changeset_revision="c58871138668" name="fastx_reverse_complement" description="Galaxy wrappers for the Reverse-Complement tool."> - <tool id="cshl_fastx_reverse_complement" version="1.0.0" file="fastx_reverse_complement.xml" /> + <tool id="cshl_fastx_reverse_complement" version="1.0.0" file="fastx_toolkit/fastx_reverse_complement.xml" /></repository><repository owner="devteam" changeset_revision="9cb372481a71" name="fastx_trimmer" description="Galaxy wrappers for the Trim sequences tool."> - <tool id="cshl_fastx_trimmer" version="1.0.0" file="fastx_trimmer.xml" /> + <tool id="cshl_fastx_trimmer" version="1.0.0" file="fastx_toolkit/fastx_trimmer.xml" /></repository><repository owner="devteam" changeset_revision="64133669255f" name="hgv_fundo" description="Galaxy wrappers for the tool FunDO: human genes associated with disease terms"> - <tool id="hgv_funDo" version="1.0.0" file="funDo.xml" /> + <tool id="hgv_funDo" version="1.0.0" file="phenotype_association/funDo.xml" /></repository><repository owner="devteam" changeset_revision="0e80ffa5b7f7" name="hgv_hilbertvis" description="Galaxy wrappers for the tool HVIS: visualization of genomic data with the Hilbert curve"> - <tool id="hgv_hilbertvis" version="1.0.0" file="hilbertvis.xml" /> + <tool id="hgv_hilbertvis" version="1.0.0" file="phenotype_association/hilbertvis.xml" /></repository><repository owner="devteam" changeset_revision="5ad24b81dd10" name="indels_3way" description="Galaxy wrappers for the tool Fetch Indels: from 3-way alignments"> - <tool id="indels_3way" version="1.0.3" file="getIndels_3way.xml" /> + <tool id="indels_3way" version="1.0.3" file="regVariation/getIndels_3way.xml" /></repository><repository owner="devteam" changeset_revision="4e31fad3f08e" name="microsatellite_birthdeath" description="Galaxy wrappers for the tool Identify microsatellite births and deaths: and causal mutational mechanisms from previously identified orthologous microsatellite sets"> - <tool id="microsatellite_birthdeath" version="1.0.0" file="microsatellite_birthdeath.xml" /> + <tool id="microsatellite_birthdeath" version="1.0.0" file="regVariation/microsatellite_birthdeath.xml" /></repository><repository 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file="rgWebLogo3.xml" /> + <tool id="rgweblogo3" version="0.4" file="rgenetics/rgWebLogo3.xml" /></repository></toolshed> \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Swap amqplib for amqp. This was mostly a drop-in replacement, since it's a currently-maintained fork of amqplib, with slight updates to work with amqp 0-9-1.
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/890e70b0fd27/ Changeset: 890e70b0fd27 User: dannon Date: 2014-02-19 20:27:10 Summary: Swap amqplib for amqp. This was mostly a drop-in replacement, since it's a currently-maintained fork of amqplib, with slight updates to work with amqp 0-9-1. Affected #: 6 files diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 eggs.ini --- a/eggs.ini +++ b/eggs.ini @@ -33,7 +33,6 @@ [eggs:noplatform] amqp = 1.4.3 -amqplib = 0.6.1 anyjson = 0.3.3 Beaker = 1.4 boto = 2.5.2 diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -45,7 +45,7 @@ from sqlalchemy.orm.exc import NoResultFound eggs.require( "pexpect" ) -eggs.require( "amqplib" ) +eggs.require( "amqp" ) import logging log = logging.getLogger( __name__ ) diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 lib/galaxy/webapps/demo_sequencer/framework/__init__.py --- a/lib/galaxy/webapps/demo_sequencer/framework/__init__.py +++ b/lib/galaxy/webapps/demo_sequencer/framework/__init__.py @@ -31,7 +31,7 @@ import mako.runtime pkg_resources.require( "pexpect" ) -pkg_resources.require( "amqplib" ) +pkg_resources.require( "amqp" ) import logging log = logging.getLogger( __name__ ) diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 lib/galaxy/webapps/galaxy/controllers/requests_admin.py --- a/lib/galaxy/webapps/galaxy/controllers/requests_admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/requests_admin.py @@ -6,7 +6,9 @@ from galaxy import model, util from galaxy.web.form_builder import * from .requests_common import RequestsGrid, invalid_id_redirect -from amqplib import client_0_8 as amqp +from galaxy import eggs +eggs.require("amqp") +import amqp import logging, os, pexpect, ConfigParser log = logging.getLogger( __name__ ) @@ -696,8 +698,7 @@ conn = amqp.Connection( host=trans.app.config.amqp[ 'host' ] + ":" + trans.app.config.amqp[ 'port' ], userid=trans.app.config.amqp[ 'userid' ], password=trans.app.config.amqp[ 'password' ], - virtual_host=trans.app.config.amqp[ 'virtual_host' ], - insist=False ) + virtual_host=trans.app.config.amqp[ 'virtual_host' ]) chan = conn.channel() msg = amqp.Message( rmq_msg, content_type='text/plain', diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 scripts/galaxy_messaging/client/amqp_publisher.py --- a/scripts/galaxy_messaging/client/amqp_publisher.py +++ b/scripts/galaxy_messaging/client/amqp_publisher.py @@ -1,18 +1,23 @@ ''' -This script gets barcode data from a barcode scanner using serial communication +This script gets barcode data from a barcode scanner using serial communication and sends the state representated by the barcode scanner & the barcode string -to the Galaxy LIMS RabbitMQ server. The message is sent in XML which has 2 tags, +to the Galaxy LIMS RabbitMQ server. The message is sent in XML which has 2 tags, barcode & state. The state of the scanner should be set in the galaxy_amq.ini -file as a configuration variable. +file as a configuration variable. ''' -from amqplib import client_0_8 as amqp +import array import ConfigParser -import sys, os +import optparse +import os import serial -import array +import sys import time -import optparse + +from galaxy import eggs +eggs.require("amqp") + +import amqp xml = \ @@ -31,14 +36,14 @@ print values data = xml % values print data - conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], - userid=amqp_config['userid'], - password=amqp_config['password'], - virtual_host=amqp_config['virtual_host'], - insist=False) + conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], + userid=amqp_config['userid'], + password=amqp_config['password'], + virtual_host=amqp_config['virtual_host'],) + chan = conn.channel() - msg = amqp.Message(data, - content_type='text/plain', + msg = amqp.Message(data, + content_type='text/plain', application_headers={'msg_type': 'sample_state_update'}) msg.properties["delivery_mode"] = 2 chan.basic_publish(msg, @@ -55,13 +60,13 @@ msg = s.read(bytes) print msg handle_scan(states, amqp_config, msg.strip()) - - + + def main(): parser = optparse.OptionParser() - parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters', + parser.add_option('-c', '--config-file', help='config file with all the AMQP config parameters', dest='config_file', action='store') - parser.add_option('-p', '--port', help='Name of the port where the scanner is connected', + parser.add_option('-p', '--port', help='Name of the port where the scanner is connected', dest='port', action='store') (opts, args) = parser.parse_args() config = ConfigParser.ConfigParser() @@ -81,7 +86,7 @@ states[config.get(section, 'prefix')] = config.get(section, 'state') count = count + 1 else: - break + break print amqp_config print states s = serial.Serial(int(opts.port)) @@ -90,6 +95,6 @@ s.close() print 'Port %s is open: %s' %( opts.port, s.isOpen()) - + if __name__ == '__main__': main() diff -r dcca6c291a6972ecd9024781667eb670de191c40 -r 890e70b0fd27d78d5982930f0176c26c4bebbfc0 scripts/galaxy_messaging/server/amqp_consumer.py --- a/scripts/galaxy_messaging/server/amqp_consumer.py +++ b/scripts/galaxy_messaging/server/amqp_consumer.py @@ -1,8 +1,8 @@ ''' Galaxy Messaging with AMQP (RabbitMQ) -Galaxy uses AMQ protocol to receive messages from external sources like +Galaxy uses AMQ protocol to receive messages from external sources like bar code scanners. Galaxy has been tested against RabbitMQ AMQP implementation. -For Galaxy to receive messages from a message queue the RabbitMQ server has +For Galaxy to receive messages from a message queue the RabbitMQ server has to be set up with a user account and other parameters listed in the [galaxy_amqp] section in the universe_wsgi.ini config file Once the RabbitMQ server has been setup and started with the given parameters, @@ -32,8 +32,8 @@ from galaxy import eggs from galaxy.web.api.requests import RequestsAPIController import pkg_resources -pkg_resources.require( "amqplib" ) -from amqplib import client_0_8 as amqp +pkg_resources.require( "amqp" ) +import amqp import logging log = logging.getLogger("GalaxyAMQP") @@ -45,7 +45,7 @@ log.addHandler(fh) # data transfer script -data_transfer_script = os.path.join( os.getcwd(), +data_transfer_script = os.path.join( os.getcwd(), "scripts/galaxy_messaging/server/data_transfer.py" ) global config global config_file_name @@ -54,13 +54,13 @@ def start_data_transfer( message ): # fork a new process to transfer datasets - cmd = '%s "%s" "%s" "%s"' % ( "python", - data_transfer_script, + cmd = '%s "%s" "%s" "%s"' % ( "python", + data_transfer_script, message.body, config_file_name ) # Galaxy config file name pid = subprocess.Popen(cmd, shell=True).pid log.debug('Started process (%i): %s' % (pid, str(cmd))) - + def update_sample_state( message ): dom = xml.dom.minidom.parseString(message.body) barcode = get_value(dom, 'barcode') @@ -69,7 +69,7 @@ log.debug('Barcode: ' + barcode) log.debug('State: ' + state) log.debug('API Key: ' + api_key) - # validate + # validate if not barcode or not state or not api_key: log.debug( 'Incomplete sample_state_update message received. Sample barcode, desired state and user API key is required.' ) return @@ -78,13 +78,13 @@ galaxydb = GalaxyDbInterface( dbconnstr ) sample_id = galaxydb.get_sample_id( field_name='bar_code', value=barcode ) if sample_id == -1: - log.debug( 'Invalid barcode.' ) + log.debug( 'Invalid barcode.' ) return galaxydb.change_state(sample_id, state) # after updating the sample state, update request status request_id = galaxydb.get_request_id(sample_id) update_request( api_key, request_id ) - + def update_request( api_key, request_id ): encoded_request_id = api.encode_id( config.get( "app:main", "id_secret" ), request_id ) data = dict( update_type=RequestsAPIController.update_types.REQUEST ) @@ -111,9 +111,9 @@ def main(): parser = optparse.OptionParser() - parser.add_option('-c', '--config-file', help='Galaxy configuration file', + parser.add_option('-c', '--config-file', help='Galaxy configuration file', dest='config_file', action='store') - parser.add_option('-s', '--http-server-section', help='Name of the HTTP server section in the Galaxy configuration file', + parser.add_option('-s', '--http-server-section', help='Name of the HTTP server section in the Galaxy configuration file', dest='http_server_section', action='store') (opts, args) = parser.parse_args() log.debug( "GALAXY LISTENER PID: " + str(os.getpid()) + " - " + str( opts ) ) @@ -129,33 +129,32 @@ for option in config.options("galaxy_amqp"): amqp_config[option] = config.get("galaxy_amqp", option) log.debug( str( amqp_config ) ) - # connect - conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], - userid=amqp_config['userid'], - password=amqp_config['password'], - virtual_host=amqp_config['virtual_host'], - insist=False) + # connect + conn = amqp.Connection(host=amqp_config['host']+":"+amqp_config['port'], + userid=amqp_config['userid'], + password=amqp_config['password'], + virtual_host=amqp_config['virtual_host']) chan = conn.channel() - chan.queue_declare( queue=amqp_config['queue'], - durable=True, - exclusive=True, + chan.queue_declare( queue=amqp_config['queue'], + durable=True, + exclusive=True, auto_delete=False) - chan.exchange_declare( exchange=amqp_config['exchange'], - type="direct", - durable=True, - auto_delete=False,) - chan.queue_bind( queue=amqp_config['queue'], - exchange=amqp_config['exchange'], + chan.exchange_declare( exchange=amqp_config['exchange'], + type="direct", + durable=True, + auto_delete=False,) + chan.queue_bind( queue=amqp_config['queue'], + exchange=amqp_config['exchange'], routing_key=amqp_config['routing_key']) - chan.basic_consume( queue=amqp_config['queue'], - no_ack=True, - callback=recv_callback, + chan.basic_consume( queue=amqp_config['queue'], + no_ack=True, + callback=recv_callback, consumer_tag="testtag") log.debug('Connected to rabbitmq server - '+amqp_config['host']+":"+amqp_config['port']) while True: chan.wait() - chan.basic_cancel("testtag") + chan.basic_cancel("testtag") chan.close() conn.close() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: History panel: remove anonymous template
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dcca6c291a69/ Changeset: dcca6c291a69 User: carlfeberhard Date: 2014-02-19 19:54:55 Summary: History panel: remove anonymous template Affected #: 11 files diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/mvc/history/current-history-panel.js --- a/static/scripts/mvc/history/current-history-panel.js +++ b/static/scripts/mvc/history/current-history-panel.js @@ -272,12 +272,6 @@ } }); -//------------------------------------------------------------------------------ TEMPLATES -CurrentHistoryPanel.templates = { - historyPanel : Handlebars.templates[ 'template-history-historyPanel' ], - anonHistoryPanel : Handlebars.templates[ 'template-history-historyPanel-anon' ] -}; - //============================================================================== return { CurrentHistoryPanel : CurrentHistoryPanel diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/mvc/history/history-panel.js --- a/static/scripts/mvc/history/history-panel.js +++ b/static/scripts/mvc/history/history-panel.js @@ -401,12 +401,6 @@ } }); -//------------------------------------------------------------------------------ TEMPLATES -HistoryPanel.templates = { - historyPanel : Handlebars.templates[ 'template-history-historyPanel' ], - anonHistoryPanel : Handlebars.templates[ 'template-history-historyPanel-anon' ] -}; - //============================================================================== return { HistoryPanel : HistoryPanel diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/packed/mvc/history/current-history-panel.js --- a/static/scripts/packed/mvc/history/current-history-panel.js +++ b/static/scripts/packed/mvc/history/current-history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-edit","mvc/history/history-panel"],function(b,e){var c=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});c.storageKey=function d(){return("history-panel")};var a=e.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left pane to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};this.preferences=new c(_.extend({id:c.storageKey()},_.pick(f,_.keys(c.prototype.defaults))));e.HistoryPanel.prototype.initialize.call(this,f);if(this.model){console.debug(this.model);this.model.checkForUpdates()}},loadCurrentHistory:function(g){var f=this;return this.loadHistoryWithHDADetails("current",g).then(function(i,h){f.trigger("current-history",f)})},switchToHistory:function(i,h){var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories/"+i+"/set_as_current")};return this.loadHistoryWithHDADetails(i,h,g).then(function(k,j){f.trigger("switched-history",f)})},createNewHistory:function(h){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,h,g).then(function(j,i){f.trigger("new-history",f)})},setModel:function(h,f,g){g=g||{};e.HistoryPanel.prototype.setModel.call(this,h,f,g);this.model.checkForUpdates();return this},_setUpModelEventHandlers:function(){e.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(g,h,f){if((!g.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[g.id])}},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children());f.renderBasedOnPrefs()}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},connectToQuotaMeter:function(f){if(!f){return this}this.listenTo(f,"quota:over",this.showQuotaMessage);this.listenTo(f,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(f&&f.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var f=this.$el.find(".quota-message");if(f.is(":hidden")){f.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var f=this.$el.find(".quota-message");if(!f.is(":hidden")){f.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(f){if(!f){return this}this.on("new-storage",function(h,g){if(f&&h){f.findItemByHtml(_l("Include Deleted Datasets")).checked=h.get("show_deleted");f.findItemByHtml(_l("Include Hidden Datasets")).checked=h.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});a.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{CurrentHistoryPanel:a}}); \ No newline at end of file +define(["mvc/dataset/hda-edit","mvc/history/history-panel"],function(b,e){var c=SessionStorageModel.extend({defaults:{searching:false,tagsEditorShown:false,annotationEditorShown:false},toString:function(){return"HistoryPanelPrefs("+JSON.stringify(this.toJSON())+")"}});c.storageKey=function d(){return("history-panel")};var a=e.HistoryPanel.extend({HDAViewClass:b.HDAEditView,emptyMsg:_l("This history is empty. Click 'Get Data' on the left pane to start"),noneFoundMsg:_l("No matching datasets found"),initialize:function(f){f=f||{};this.preferences=new c(_.extend({id:c.storageKey()},_.pick(f,_.keys(c.prototype.defaults))));e.HistoryPanel.prototype.initialize.call(this,f);if(this.model){console.debug(this.model);this.model.checkForUpdates()}},loadCurrentHistory:function(g){var f=this;return this.loadHistoryWithHDADetails("current",g).then(function(i,h){f.trigger("current-history",f)})},switchToHistory:function(i,h){var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories/"+i+"/set_as_current")};return this.loadHistoryWithHDADetails(i,h,g).then(function(k,j){f.trigger("switched-history",f)})},createNewHistory:function(h){if(!Galaxy||!Galaxy.currUser||Galaxy.currUser.isAnonymous()){this.displayMessage("error",_l("You must be logged in to create histories"));return $.when()}var f=this,g=function(){return jQuery.post(galaxy_config.root+"api/histories",{current:true})};return this.loadHistory(undefined,h,g).then(function(j,i){f.trigger("new-history",f)})},setModel:function(h,f,g){g=g||{};e.HistoryPanel.prototype.setModel.call(this,h,f,g);this.model.checkForUpdates();return this},_setUpModelEventHandlers:function(){e.HistoryPanel.prototype._setUpModelEventHandlers.call(this);if(Galaxy&&Galaxy.quotaMeter){this.listenTo(this.model,"change:nice_size",function(){Galaxy.quotaMeter.update()})}this.model.hdas.on("state:ready",function(g,h,f){if((!g.get("visible"))&&(!this.storage.get("show_hidden"))){this.removeHdaView(this.hdaViews[g.id])}},this)},render:function(h,i){h=(h===undefined)?(this.fxSpeed):(h);var f=this,g;if(this.model){g=this.renderModel()}else{g=this.renderWithoutModel()}$(f).queue("fx",[function(j){if(h&&f.$el.is(":visible")){f.$el.fadeOut(h,j)}else{j()}},function(j){f.$el.empty();if(g){f.$el.append(g.children());f.renderBasedOnPrefs()}j()},function(j){if(h&&!f.$el.is(":visible")){f.$el.fadeIn(h,j)}else{j()}},function(j){if(i){i.call(this)}f.trigger("rendered",this);j()}]);return this},renderBasedOnPrefs:function(){if(this.preferences.get("searching")){this.showSearchControls(0)}},connectToQuotaMeter:function(f){if(!f){return this}this.listenTo(f,"quota:over",this.showQuotaMessage);this.listenTo(f,"quota:under",this.hideQuotaMessage);this.on("rendered rendered:initial",function(){if(f&&f.isOverQuota()){this.showQuotaMessage()}});return this},showQuotaMessage:function(){var f=this.$el.find(".quota-message");if(f.is(":hidden")){f.slideDown(this.fxSpeed)}},hideQuotaMessage:function(){var f=this.$el.find(".quota-message");if(!f.is(":hidden")){f.slideUp(this.fxSpeed)}},connectToOptionsMenu:function(f){if(!f){return this}this.on("new-storage",function(h,g){if(f&&h){f.findItemByHtml(_l("Include Deleted Datasets")).checked=h.get("show_deleted");f.findItemByHtml(_l("Include Hidden Datasets")).checked=h.get("show_hidden")}});return this},toString:function(){return"CurrentHistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{CurrentHistoryPanel:a}}); \ No newline at end of file diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/packed/mvc/history/history-panel.js --- a/static/scripts/packed/mvc/history/history-panel.js +++ b/static/scripts/packed/mvc/history/history-panel.js @@ -1,1 +1,1 @@ -define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.isHidden()),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.isHidden())});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});d.templates={historyPanel:Handlebars.templates["template-history-historyPanel"],anonHistoryPanel:Handlebars.templates["template-history-historyPanel-anon"]};return{HistoryPanel:d}}); \ No newline at end of file +define(["mvc/dataset/hda-model","mvc/dataset/hda-edit","mvc/history/readonly-history-panel"],function(c,a,b){var d=b.ReadOnlyHistoryPanel.extend({HDAViewClass:a.HDAEditView,initialize:function(e){e=e||{};this.selectedHdaIds=[];this.tagsEditor=null;this.annotationEditor=null;this.selecting=e.selecting||false;this.annotationEditorShown=e.annotationEditorShown||false;this.tagsEditorShown=e.tagsEditorShown||false;b.ReadOnlyHistoryPanel.prototype.initialize.call(this,e)},_setUpModelEventHandlers:function(){b.ReadOnlyHistoryPanel.prototype._setUpModelEventHandlers.call(this);this.model.on("change:nice_size",this.updateHistoryDiskSize,this);this.model.hdas.on("change:deleted",this.handleHdaDeletionChange,this);this.model.hdas.on("change:visible",this.handleHdaVisibleChange,this);this.model.hdas.on("change:purged",function(e){this.model.fetch()},this)},renderModel:function(){var e=$("<div/>");e.append(d.templates.historyPanel(this.model.toJSON()));if(Galaxy.currUser.id&&Galaxy.currUser.id===this.model.get("user_id")){this._renderTags(e);this._renderAnnotation(e)}e.find(".history-secondary-actions").prepend(this._renderSelectButton());e.find(".history-dataset-actions").toggle(this.selecting);e.find(".history-secondary-actions").prepend(this._renderSearchButton());this._setUpBehaviours(e);this.renderHdas(e);return e},_renderTags:function(e){var f=this;this.tagsEditor=new TagsEditor({model:this.model,el:e.find(".history-controls .tags-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDATagEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDATagEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history tags"),classes:"history-tag-btn",faIcon:"fa-tags"}).appendTo(e.find(".history-secondary-actions"))})},_renderAnnotation:function(e){var f=this;this.annotationEditor=new AnnotationEditor({model:this.model,el:e.find(".history-controls .annotation-display"),onshowFirstTime:function(){this.render()},onshow:function(){f.toggleHDAAnnotationEditors(true,f.fxSpeed)},onhide:function(){f.toggleHDAAnnotationEditors(false,f.fxSpeed)},$activator:faIconButton({title:_l("Edit history Annotation"),classes:"history-annotate-btn",faIcon:"fa-comment"}).appendTo(e.find(".history-secondary-actions"))})},_renderSelectButton:function(e){return faIconButton({title:_l("Operations on multiple datasets"),classes:"history-select-btn",faIcon:"fa-check-square-o"})},_setUpBehaviours:function(e){e=e||this.$el;e.find("[title]").tooltip({placement:"bottom"});if(!this.model){return}this._setUpDatasetActionsPopup(e);if((!Galaxy.currUser||Galaxy.currUser.isAnonymous())||(Galaxy.currUser.id!==this.model.get("user_id"))){return}var f=this;e.find(".history-name").attr("title",_l("Click to rename history")).tooltip({placement:"bottom"}).make_text_editable({on_finish:function(g){var h=f.model.get("name");if(g&&g!==h){f.$el.find(".history-name").text(g);f.model.save({name:g}).fail(function(){f.$el.find(".history-name").text(f.model.previous("name"))})}else{f.$el.find(".history-name").text(h)}}})},_setUpDatasetActionsPopup:function(e){var f=this;(new PopupMenu(e.find(".history-dataset-action-popup-btn"),[{html:_l("Hide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.hide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Unhide datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.unhide;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Delete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype["delete"];f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Undelete datasets"),func:function(){var g=c.HistoryDatasetAssociation.prototype.undelete;f.getSelectedHdaCollection().ajaxQueue(g)}},{html:_l("Permanently delete datasets"),func:function(){if(confirm(_l("This will permanently remove the data in your datasets. Are you sure?"))){var g=c.HistoryDatasetAssociation.prototype.purge;f.getSelectedHdaCollection().ajaxQueue(g)}}}]))},handleHdaDeletionChange:function(e){if(e.get("deleted")&&!this.storage.get("show_deleted")){this.removeHdaView(this.hdaViews[e.id])}},handleHdaVisibleChange:function(e){if(e.hidden()&&!this.storage.get("show_hidden")){this.removeHdaView(this.hdaViews[e.id])}},createHdaView:function(f){var e=f.get("id"),g=new this.HDAViewClass({model:f,linkTarget:this.linkTarget,expanded:this.storage.get("expandedHdas")[e],selectable:this.selecting,hasUser:this.model.ownedByCurrUser(),logger:this.logger,tagsEditorShown:(this.tagsEditor&&!this.tagsEditor.isHidden()),annotationEditorShown:(this.annotationEditor&&!this.annotationEditor.isHidden())});this._setUpHdaListeners(g);return g},_setUpHdaListeners:function(f){var e=this;b.ReadOnlyHistoryPanel.prototype._setUpHdaListeners.call(this,f);f.on("selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.union(e.selectedHdaIds,[h])});f.on("de-selected",function(g){var h=g.model.get("id");e.selectedHdaIds=_.without(e.selectedHdaIds,h)})},toggleHDATagEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.tagsEditor){g.tagsEditor.toggle.apply(g.tagsEditor,f)}})},toggleHDAAnnotationEditors:function(e){var f=arguments;_.each(this.hdaViews,function(g){if(g.annotationEditor){g.annotationEditor.toggle.apply(g.annotationEditor,f)}})},removeHdaView:function(f){if(!f){return}var e=this;f.$el.fadeOut(e.fxSpeed,function(){f.off();f.remove();delete e.hdaViews[f.model.id];if(_.isEmpty(e.hdaViews)){e.$el.find(e.emptyMsgSelector).fadeIn(e.fxSpeed,function(){e.trigger("empty-history",e)})}})},events:_.extend(_.clone(b.ReadOnlyHistoryPanel.prototype.events),{"click .history-select-btn":function(f){this.toggleSelectors(this.fxSpeed)},"click .history-select-all-datasets-btn":"selectAllDatasets","click .history-deselect-all-datasets-btn":"deselectAllDatasets"}),updateHistoryDiskSize:function(){this.$el.find(".history-size").text(this.model.get("nice_size"))},showSelectors:function(e){this.selecting=true;this.$el.find(".history-dataset-actions").slideDown(e);_.each(this.hdaViews,function(f){f.showSelector(e)});this.selectedHdaIds=[]},hideSelectors:function(e){this.selecting=false;this.$el.find(".history-dataset-actions").slideUp(e);_.each(this.hdaViews,function(f){f.hideSelector(e)});this.selectedHdaIds=[]},toggleSelectors:function(e){if(!this.selecting){this.showSelectors(e)}else{this.hideSelectors(e)}},selectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.select(e)})},deselectAllDatasets:function(e){_.each(this.hdaViews,function(f){f.deselect(e)})},getSelectedHdaViews:function(){return _.filter(this.hdaViews,function(e){return e.selected})},getSelectedHdaCollection:function(){return new c.HDACollection(_.map(this.getSelectedHdaViews(),function(e){return e.model}),{historyId:this.model.id})},toString:function(){return"HistoryPanel("+((this.model)?(this.model.get("name")):(""))+")"}});return{HistoryPanel:d}}); \ No newline at end of file diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/packed/templates/compiled/history-templates.js --- a/static/scripts/packed/templates/compiled/history-templates.js +++ b/static/scripts/packed/templates/compiled/history-templates.js @@ -1,1 +1,1 @@ -(function(){var b=Handlebars.template,a=Handlebars.templates=Handlebars.templates||{};a["template-hda-body"]=b(function(g,r,p,k,z){this.compilerInfo=[4,">= 1.0.0"];p=this.merge(p,g.helpers);z=z||{};var q="",h,e="function",d=this.escapeExpression,o=this,c=p.blockHelperMissing;function n(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';if(B=p.body){B=B.call(D,{hash:{},data:C})}else{B=D.body;B=typeof B===e?B.apply(D):B}if(B||B===0){A+=B}A+='\n </div>\n <div class="dataset-actions clear">\n <div class="left"></div>\n <div class="right"></div>\n </div>\n\n ';return A}function m(D,C){var A="",B;A+='\n <div class="dataset-summary">\n ';B=p["if"].call(D,D.misc_blurb,{hash:{},inverse:o.noop,fn:o.program(4,l,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.data_type,{hash:{},inverse:o.noop,fn:o.program(6,j,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.metadata_dbkey,{hash:{},inverse:o.noop,fn:o.program(9,f,C),data:C});if(B||B===0){A+=B}A+="\n\n ";B=p["if"].call(D,D.misc_info,{hash:{},inverse:o.noop,fn:o.program(12,x,C),data:C});if(B||B===0){A+=B}A+='\n </div>\n\n <div class="dataset-actions clear">\n <div class="left"></div>\n <div class="right"></div>\n </div>\n\n ';B=p.unless.call(D,D.deleted,{hash:{},inverse:o.noop,fn:o.program(14,w,C),data:C});if(B||B===0){A+=B}A+="\n\n ";return A}function l(D,C){var A="",B;A+='\n <div class="dataset-blurb">\n <span class="value">';if(B=p.misc_blurb){B=B.call(D,{hash:{},data:C})}else{B=D.misc_blurb;B=typeof B===e?B.apply(D):B}A+=d(B)+"</span>\n </div>\n ";return A}function j(E,D){var A="",C,B;A+='\n <div class="dataset-datatype">\n <label class="prompt">';B={hash:{},inverse:o.noop,fn:o.program(7,i,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+='</label>\n <span class="value">';if(C=p.data_type){C=C.call(E,{hash:{},data:D})}else{C=E.data_type;C=typeof C===e?C.apply(E):C}A+=d(C)+"</span>\n </div>\n ";return A}function i(B,A){return"format"}function f(E,D){var A="",C,B;A+='\n <div class="dataset-dbkey">\n <label class="prompt">';B={hash:{},inverse:o.noop,fn:o.program(10,y,D),data:D};if(C=p.local){C=C.call(E,B)}else{C=E.local;C=typeof C===e?C.apply(E):C}if(!p.local){C=c.call(E,C,B)}if(C||C===0){A+=C}A+='</label>\n <span class="value">\n ';if(C=p.metadata_dbkey){C=C.call(E,{hash:{},data:D})}else{C=E.metadata_dbkey;C=typeof C===e?C.apply(E):C}A+=d(C)+"\n </span>\n </div>\n ";return A}function 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Click 'Get Data' on the left pane to start"}r+='<div class="history-controls">\n <div class="history-search-controls">\n <div class="history-search-input"></div>\n </div>\n\n <div class="history-title">\n ';i=q["if"].call(s,s.name,{hash:{},inverse:p.noop,fn:p.program(1,o,y),data:y});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="history-subtitle clear">\n ';i=q["if"].call(s,s.nice_size,{hash:{},inverse:p.noop,fn:p.program(3,n,y),data:y});if(i||i===0){r+=i}r+='\n\n <div class="history-secondary-actions"></div>\n </div>\n\n ';i=q["if"].call(s,s.deleted,{hash:{},inverse:p.noop,fn:p.program(5,l,y),data:y});if(i||i===0){r+=i}r+='\n\n <div class="message-container">\n ';i=q["if"].call(s,s.message,{hash:{},inverse:p.noop,fn:p.program(8,h,y),data:y});if(i||i===0){r+=i}r+='\n </div>\n\n <div class="quota-message errormessage">\n ';f={hash:{},inverse:p.noop,fn:p.program(10,x,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+=".\n ";f={hash:{},inverse:p.noop,fn:p.program(12,w,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='.\n </div>\n \n <div class="tags-display"></div>\n <div class="annotation-display"></div>\n\n <div class="history-dataset-actions">\n <div class="btn-group">\n <button class="history-select-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:p.noop,fn:p.program(14,v,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='</button>\n <button class="history-deselect-all-datasets-btn btn btn-default"\n data-mode="select">';f={hash:{},inverse:p.noop,fn:p.program(16,u,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='</button>\n </div>\n <button class="history-dataset-action-popup-btn btn btn-default"\n >';f={hash:{},inverse:p.noop,fn:p.program(18,t,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+='...</button>\n </div>\n\n </div>\n\n \n <div class="datasets-list"></div>\n\n <div class="empty-history-message infomessagesmall">\n ';f={hash:{},inverse:p.noop,fn:p.program(20,j,y),data:y};if(i=q.local){i=i.call(s,f)}else{i=s.local;i=typeof i===e?i.apply(s):i}if(!q.local){i=c.call(s,i,f)}if(i||i===0){r+=i}r+="\n </div>";return r})})(); \ No newline at end of file diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/templates/compiled/history-templates.js --- a/static/scripts/templates/compiled/history-templates.js +++ b/static/scripts/templates/compiled/history-templates.js @@ -302,261 +302,6 @@ }); })();(function() { var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-hda-skeleton'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"errormessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(2, program2, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ":\n "; - options = {hash:{},inverse:self.noop,fn:self.program(4, program4, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n "; - return buffer; - } -function program2(depth0,data) { - - - return "There was an error getting the data for this dataset"; - } - -function program4(depth0,data) { - - var stack1; - if (stack1 = helpers.error) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.error; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - return escapeExpression(stack1); - } - -function program6(depth0,data) { - - var buffer = "", stack1; - buffer += "\n "; - stack1 = helpers['if'].call(depth0, depth0.purged, {hash:{},inverse:self.program(10, program10, data),fn:self.program(7, program7, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n "; - return buffer; - } -function program7(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-purged-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(8, program8, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n\n "; - return buffer; - } -function program8(depth0,data) { - - - return "This dataset has been deleted and removed from disk."; - } - -function program10(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-deleted-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program11(depth0,data) { - - - return "This dataset has been deleted."; - } - -function program13(depth0,data) { - - var buffer = "", stack1, options; - buffer += "\n <div class=\"dataset-hidden-msg warningmessagesmall\"><strong>\n "; - options = {hash:{},inverse:self.noop,fn:self.program(14, program14, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </strong></div>\n "; - return buffer; - } -function program14(depth0,data) { - - - return "This dataset has been hidden."; - } - - buffer += "<div class=\"dataset hda\">\n <div class=\"dataset-warnings\">\n "; - stack1 = helpers['if'].call(depth0, depth0.error, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(6, program6, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n "; - stack1 = helpers.unless.call(depth0, depth0.visible, {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"dataset-selector\"><span class=\"fa fa-2x fa-square-o\"></span></div>\n <div class=\"dataset-primary-actions\"></div>\n " - + "\n <div class=\"dataset-title-bar clear\" tabindex=\"0\">\n <span class=\"dataset-state-icon state-icon\"></span>\n <div class=\"dataset-title\">\n <span class=\"hda-hid\">"; - if (stack1 = helpers.hid) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.hid; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n <span class=\"dataset-name\">"; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</span>\n </div>\n </div>\n\n <div class=\"dataset-body\"></div>\n</div>"; - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-historyPanel-anon'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-name\">\n "; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </div>\n "; - return buffer; - } - -function program3(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-size\">"; - if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program5(depth0,data) { - - var buffer = "", stack1; - buffer += "\n " - + "\n <div class=\""; - if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "message\">"; - if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program7(depth0,data) { - - - return "You are over your disk quota"; - } - -function program9(depth0,data) { - - - return "Tool execution is on hold until your disk usage drops below your allocated quota"; - } - -function program11(depth0,data) { - - - return "All"; - } - -function program13(depth0,data) { - - - return "None"; - } - -function program15(depth0,data) { - - - return "For all selected"; - } - -function program17(depth0,data) { - - - return "Your history is empty. Click 'Get Data' on the left pane to start"; - } - - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n " - + "\n "; - stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; - stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n <div class=\"message-container\">\n "; - stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n "; - options = {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n\n <div class=\"history-dataset-actions\">\n <div class=\"btn-group\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n <button class=\"history-deselect-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n </div>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; - options = {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "...</button>\n </div>\n\n </div>" - + "\n\n " - + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>"; - return buffer; - }); -})();(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; templates['template-history-historyPanel'] = template(function (Handlebars,depth0,helpers,partials,data) { this.compilerInfo = [4,'>= 1.0.0']; helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; @@ -660,7 +405,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n "; + buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n <div class=\"message-container\">\n "; diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/templates/compiled/template-history-historyPanel-anon.js --- a/static/scripts/templates/compiled/template-history-historyPanel-anon.js +++ /dev/null @@ -1,133 +0,0 @@ -(function() { - var template = Handlebars.template, templates = Handlebars.templates = Handlebars.templates || {}; -templates['template-history-historyPanel-anon'] = template(function (Handlebars,depth0,helpers,partials,data) { - this.compilerInfo = [4,'>= 1.0.0']; -helpers = this.merge(helpers, Handlebars.helpers); data = data || {}; - var buffer = "", stack1, options, functionType="function", escapeExpression=this.escapeExpression, self=this, blockHelperMissing=helpers.blockHelperMissing; - -function program1(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-name\">\n "; - if (stack1 = helpers.name) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.name; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "\n </div>\n "; - return buffer; - } - -function program3(depth0,data) { - - var buffer = "", stack1; - buffer += "\n <div class=\"history-size\">"; - if (stack1 = helpers.nice_size) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.nice_size; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program5(depth0,data) { - - var buffer = "", stack1; - buffer += "\n " - + "\n <div class=\""; - if (stack1 = helpers.status) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.status; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "message\">"; - if (stack1 = helpers.message) { stack1 = stack1.call(depth0, {hash:{},data:data}); } - else { stack1 = depth0.message; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - buffer += escapeExpression(stack1) - + "</div>\n "; - return buffer; - } - -function program7(depth0,data) { - - - return "You are over your disk quota"; - } - -function program9(depth0,data) { - - - return "Tool execution is on hold until your disk usage drops below your allocated quota"; - } - -function program11(depth0,data) { - - - return "All"; - } - -function program13(depth0,data) { - - - return "None"; - } - -function program15(depth0,data) { - - - return "For all selected"; - } - -function program17(depth0,data) { - - - return "Your history is empty. Click 'Get Data' on the left pane to start"; - } - - buffer += "<div class=\"history-controls\">\n <div class=\"history-search-controls\">\n <div class=\"history-search-input\"></div>\n </div>\n\n <div class=\"history-title\">\n " - + "\n "; - stack1 = helpers['if'].call(depth0, depth0.name, {hash:{},inverse:self.noop,fn:self.program(1, program1, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; - stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n <div class=\"message-container\">\n "; - stack1 = helpers['if'].call(depth0, depth0.message, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>\n\n <div class=\"quota-message errormessage\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(7, program7, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n "; - options = {hash:{},inverse:self.noop,fn:self.program(9, program9, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += ".\n </div>\n\n <div class=\"history-dataset-actions\">\n <div class=\"btn-group\">\n <button class=\"history-select-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(11, program11, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n <button class=\"history-deselect-all-datasets-btn btn btn-default\"\n data-mode=\"select\">"; - options = {hash:{},inverse:self.noop,fn:self.program(13, program13, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "</button>\n </div>\n <button class=\"history-dataset-action-popup-btn btn btn-default\"\n >"; - options = {hash:{},inverse:self.noop,fn:self.program(15, program15, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "...</button>\n </div>\n\n </div>" - + "\n\n " - + "\n <div class=\"datasets-list\"></div>\n\n <div class=\"empty-history-message infomessagesmall\">\n "; - options = {hash:{},inverse:self.noop,fn:self.program(17, program17, data),data:data}; - if (stack1 = helpers.local) { stack1 = stack1.call(depth0, options); } - else { stack1 = depth0.local; stack1 = typeof stack1 === functionType ? stack1.apply(depth0) : stack1; } - if (!helpers.local) { stack1 = blockHelperMissing.call(depth0, stack1, options); } - if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n </div>"; - return buffer; - }); -})(); \ No newline at end of file diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 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 @@ -103,7 +103,7 @@ buffer += "\n </div>\n\n <div class=\"history-subtitle clear\">\n "; stack1 = helpers['if'].call(depth0, depth0.nice_size, {hash:{},inverse:self.noop,fn:self.program(3, program3, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } - buffer += "\n\n <div class=\"history-secondary-actions btn-group\"></div>\n </div>\n\n "; + buffer += "\n\n <div class=\"history-secondary-actions\"></div>\n </div>\n\n "; stack1 = helpers['if'].call(depth0, depth0.deleted, {hash:{},inverse:self.noop,fn:self.program(5, program5, data),data:data}); if(stack1 || stack1 === 0) { buffer += stack1; } buffer += "\n\n <div class=\"message-container\">\n "; diff -r 538382c91a75b12f6004ea87c2f7c459f7977f91 -r dcca6c291a6972ecd9024781667eb670de191c40 static/scripts/templates/history-templates.html --- a/static/scripts/templates/history-templates.html +++ b/static/scripts/templates/history-templates.html @@ -63,62 +63,3 @@ {{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} </div></script> - - - -<script type="text/template" class="template-history" id="template-history-historyPanel-anon"> - - <div class="history-controls"> - <div class="history-search-controls"> - <div class="history-search-input"></div> - </div> - - <div class="history-title"> - {{! wouldn't this always be 'unnamed history'? }} - {{#if name }} - <div class="history-name"> - {{name}} - </div> - {{/if}} - </div> - - <div class="history-subtitle clear"> - {{#if nice_size }} - <div class="history-size">{{nice_size}}</div> - {{/if}} - - <div class="history-secondary-actions"></div> - </div> - - <div class="message-container"> - {{#if message}} - {{! should already be localized }} - <div class="{{status}}message">{{message}}</div> - {{/if}} - </div> - - <div class="quota-message errormessage"> - {{#local}}You are over your disk quota{{/local}}. - {{#local}}Tool execution is on hold until your disk usage drops below your allocated quota{{/local}}. - </div> - - <div class="history-dataset-actions"> - <div class="btn-group"> - <button class="history-select-all-datasets-btn btn btn-default" - data-mode="select">{{#local}}All{{/local}}</button> - <button class="history-deselect-all-datasets-btn btn btn-default" - data-mode="select">{{#local}}None{{/local}}</button> - </div> - <button class="history-dataset-action-popup-btn btn btn-default" - >{{#local}}For all selected{{/local}}...</button> - </div> - - </div>{{! end history-controls }} - - {{! where the datasets/hdas are added }} - <div class="datasets-list"></div> - - <div class="empty-history-message infomessagesmall"> - {{#local}}Your history is empty. Click 'Get Data' on the left pane to start{{/local}} - </div> -</script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Grids: Fix negative page numbers
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b31e0927331b/ Changeset: b31e0927331b User: guerler Date: 2014-02-19 19:20:42 Summary: Grids: Fix negative page numbers Affected #: 2 files diff -r 057069969de059c08a6b6e8343b10bb7cfeea926 -r b31e0927331b7890590585bc9e2d7621b05bce88 static/scripts/mvc/grid/grid-template.js --- a/static/scripts/mvc/grid/grid-template.js +++ b/static/scripts/mvc/grid/grid-template.js @@ -246,7 +246,7 @@ var page_link_range = num_page_links / 2; var min_page = cur_page_num - page_link_range var min_offset = 0; - if (min_page == 0) { + if (min_page <= 0) { // Min page is too low. min_page = 1; min_offset = page_link_range - ( cur_page_num - min_page ); diff -r 057069969de059c08a6b6e8343b10bb7cfeea926 -r b31e0927331b7890590585bc9e2d7621b05bce88 static/scripts/packed/mvc/grid/grid-template.js --- a/static/scripts/packed/mvc/grid/grid-template.js +++ b/static/scripts/packed/mvc/grid/grid-template.js @@ -1,1 +1,1 @@ -define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g==0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}); \ No newline at end of file +define([],function(){return{grid:function(b){var a="";if(b.embedded){a=this.grid_header(b)+this.grid_table(b)}else{a='<div class="loading-elt-overlay"></div><table><tr><td width="75%">'+this.grid_header(b)+'</td><td></td><td></td></tr><tr><td width="100%" id="grid-message" valign="top"></td><td></td><td></td></tr></table>'+this.grid_table(b)}if(b.info_text){a+='<br><div class="toolParamHelp" style="clear: both;">'+b.info_text+"</div>"}return a},grid_table:function(a){return'<form method="post" onsubmit="return false;"><table id="grid-table" class="grid"><thead id="grid-table-header"></thead><tbody id="grid-table-body"></tbody><tfoot id="grid-table-footer"></tfoot></table></form>'},grid_header:function(c){var b='<div class="grid-header">';if(!c.embedded){b+="<h2>"+c.title+"</h2>"}if(c.global_actions){b+='<ul class="manage-table-actions">';var d=(c.global_actions.length>=3);if(d){b+='<li><a class="action-button" id="popup-global-actions" class="menubutton">Actions</a></li><div popupmenu="popup-global-actions">'}for(i in c.global_actions){var e=c.global_actions[i];var a="";if(e.inbound){a="use-inbound"}else{a="use-outbound"}b+='<li><a class="action-button '+a+'" href="'+e.url_args+'" onclick="return false;">'+e.label+"</a></li>"}if(d){b+="</div>"}b+="</ul>"}if(c.insert){b+=c.insert}b+=this.grid_filters(c);b+="</div>";return b},header:function(b){var a="<tr>";if(b.show_item_checkboxes){a+="<th>";if(b.items.length>0){a+='<input type="checkbox" id="check_all" name=select_all_checkbox value="true"><input type="hidden" name=select_all_checkbox value="true">'}a+="</th>"}for(var c in b.columns){var d=b.columns[c];if(d.visible){a+='<th id="'+d.key+'-header">';if(d.href){a+='<a href="'+d.href+'" class="sort-link" sort_key="'+d.key+'">'+d.label+"</a>"}else{a+=d.label}a+='<span class="sort-arrow">'+d.extra+"</span></th>"}}a+="</tr>";return a},body:function(r){var k="";var s=0;var e=r.items.length;if(e==0){k+='<tr><td colspan="100"><em>No Items</em></td></tr>';s=1}for(var f in r.items){var p=r.items[f];var a=p.encode_id;var g="grid-"+f+"-popup";k+="<tr ";if(r.current_item_id==p.id){k+='class="current"'}k+=">";if(r.show_item_checkboxes){k+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+a+'" id="'+a+'" class="grid-row-select-checkbox" /></td>'}for(j in r.columns){var d=r.columns[j];if(d.visible){var c="";if(d.nowrap){c='style="white-space:nowrap;"'}var q=p.column_config[d.label];var h=q.link;var l=q.value;var o=q.inbound;if(jQuery.type(l)==="string"){l=l.replace(/\/\//g,"/")}var b="";var n="";if(d.attach_popup){b="grid-"+f+"-popup";n="menubutton";if(h!=""){n+=" split"}n+=" popup"}k+="<td "+c+">";if(h){if(r.operations.length!=0){k+='<div id="'+b+'" class="'+n+'" style="float: left;">'}var m="";if(o){m="use-inbound"}else{m="use-outbound"}k+='<a class="label '+m+'" href="'+h+'" onclick="return false;">'+l+"</a>";if(r.operations.length!=0){k+="</div>"}}else{k+='<div id="'+b+'" class="'+n+'"><label id="'+d.label_id_prefix+a+'" for="'+a+'">'+l+"</label></div>"}k+="</td>"}}k+="</tr>";s++}return k},footer:function(o){var k="";if(o.use_paging&&o.num_pages>1){var m=o.num_page_links;var a=o.cur_page_num;var n=o.num_pages;var h=m/2;var g=a-h;var e=0;if(g<=0){g=1;e=h-(a-g)}var d=h+e;var c=a+d;if(c<=n){max_offset=0}else{c=n;max_offset=d-(c+1-a)}if(max_offset!=0){g-=max_offset;if(g<1){g=1}}k+='<tr id="page-links-row">';if(o.show_item_checkboxes){k+="<td></td>"}k+='<td colspan="100"><span id="page-link-container">Page:';if(g>1){k+='<span class="page-link" id="page-link-1"><a href="javascript:void(0);" page_num="1" onclick="return false;">1</a></span> ...'}for(var l=g;l<c+1;l++){if(l==o.cur_page_num){k+='<span class="page-link inactive-link" id="page-link-'+l+'">'+l+"</span>"}else{k+='<span class="page-link" id="page-link-'+l+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+l+'">'+l+"</a></span>"}}if(c<n){k+='...<span class="page-link" id="page-link-'+n+'"><a href="javascript:void(0);" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}k+="</span>";k+='<span class="page-link" id="show-all-link-span"> | <a href="javascript:void(0);" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(o.show_item_checkboxes){k+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+o.get_class_plural+": ";for(i in o.operations){var b=o.operations[i];if(b.allow_multiple){k+='<input type="button" value="'+b.label+'" class="operation-button action-button"> '}}k+="</td></tr>"}var f=false;for(i in o.operations){if(o.operations[i].global_operation){f=true;break}}if(f){k+='<tr><td colspan="100">';for(i in o.operations){var b=o.operations[i];if(b.global_operation){k+='<a class="action-button" href="'+b.global_operation+'">'+b.label+"</a>"}}k+="</td></tr>"}if(o.legend){k+='<tr><td colspan="100">'+o.legend+"</td></tr>"}return k},message:function(a){return'<p><div class="'+a.status+'message transient-message">'+a.message+'</div><div style="clear: both"></div></p>'},grid_filters:function(n){var a=n.default_filter_dict;var b=n.filters;var e="none";if(n.advanced_search){e="block"}var m=false;for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){var l=d.key;var c=b[l];var f=a[l];if(c&&f&&c!=f){e="block"}m=true}}var k="block";if(e=="block"){k="none"}var h='<div id="standard-search" style="display: '+k+';"><table><tr><td style="padding: 0;"><table>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="standard"){h+=this.grid_column_filter(n,d)}}h+="</table></td></tr><tr><td>";if(m){h+='<a href="" class="advanced-search-toggle">Advanced Search</a>'}h+="</td></tr></table></div>";h+='<div id="advanced-search" style="display: '+e+'; margin-top: 5px; border: 1px solid #ccc;"><table><tr><td style="text-align: left" colspan="100"><a href="" class="advanced-search-toggle">Close Advanced Search</a></td></tr>';for(var g in n.columns){var d=n.columns[g];if(d.filterable=="advanced"){h+=this.grid_column_filter(n,d)}}h+="</table></div>";return h},grid_column_filter:function(e,c){var t=e.default_filter_dict;var l=e.filters;var a=c.label;var b=c.key;if(c.filterable=="advanced"){a=a.toLowerCase()}var k="<tr>";if(c.filterable=="advanced"){k+='<td align="left" style="padding-left: 10px">'+a+":</td>"}k+='<td style="padding-bottom: 1px;">';if(c.is_text){k+='<form class="text-filter-form" column_key="'+b+'" action="'+e.url+'" method="get" >';for(u in e.columns){var g=e.columns[u];var p=l[g.key];if(p){if(p!="All"){if(g.is_text){p=JSON.stringify(p)}k+='<input type="hidden" id="'+g.key+'" name="f-'+g.key+'" value="'+p+'"/>'}}}k+='<span id="'+b+'-filtering-criteria">';var h=l[b];if(h){var f=jQuery.type(h);if(f=="string"){if(h!="All"){k+=this.filter_element(b,h)}}if(f=="array"){for(var u in h){var n=h[u];var v=h;v=v.slice(u);k+=this.filter_element(b,n)}}}k+="</span>";var r="";if(c.filterable=="standard"){r=c.label.toLowerCase();var q=r.length;if(q<20){q=20}q=q+4}k+='<span class="search-box"><input class="search-box-input" id="input-'+b+'-filter" name="f-'+b+'" type="text" placeholder="'+r+'" size="'+q+'"/><button type="submit" style="background: transparent; border: none; padding: 4px; margin: 0px;"><i class="fa fa-search"></i></button></span></form>'}else{k+='<span id="'+b+'-filtering-criteria">';var s=false;for(cf_label in e.categorical_filters[b]){var o=e.categorical_filters[b][cf_label];var d="";var m="";for(key in o){d=key;m=o[key]}if(s){k+=" | "}s=true;var n=l[b];if(n&&o[b]&&n==m){k+='<span class="categorical-filter '+b+'-filter current-filter">'+cf_label+"</span>"}else{k+='<span class="categorical-filter '+b+'-filter"><a href="javascript:void(0);" filter_key="'+d+'" filter_val="'+m+'">'+cf_label+"</a></span>"}}k+="</span>"}k+="</td></tr>";return k},filter_element:function(b,a){return'<span class="text-filter-val">'+a+'<a href="javascript:void(0);" filter_key="'+b+'" filter_val="'+a+'"><i class="fa fa-times" style="padding-left: 5px; padding-bottom: 6px;"/></a></span>'}}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Merge
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/057069969de0/ Changeset: 057069969de0 User: guerler Date: 2014-02-19 19:18:37 Summary: Merge Affected #: 0 files Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Grids: Fix negative page numbers
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0770af01a257/ Changeset: 0770af01a257 Branch: stable User: guerler Date: 2014-02-19 19:16:36 Summary: Grids: Fix negative page numbers Affected #: 2 files diff -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc -r 0770af01a257818ee82f11a191d4305880ea0b91 static/scripts/galaxy.grids.js --- a/static/scripts/galaxy.grids.js +++ b/static/scripts/galaxy.grids.js @@ -847,7 +847,7 @@ var page_link_range = num_page_links / 2; var min_page = cur_page_num - page_link_range var min_offset = 0; - if (min_page == 0) { + if (min_page <= 0) { // Min page is too low. min_page = 1; min_offset = page_link_range - ( cur_page_num - min_page ); diff -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc -r 0770af01a257818ee82f11a191d4305880ea0b91 static/scripts/packed/galaxy.grids.js --- a/static/scripts/packed/galaxy.grids.js +++ b/static/scripts/packed/galaxy.grids.js @@ -1,1 +1,1 @@ -jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var c={async:this.attributes.async,sort:this.attributes.sort_key,page:this.attributes.cur_page,show_item_checkboxes:this.attributes.show_item_checkboxes,advanced_search:this.attributes.advanced_search};if(this.attributes.operation){c.operation=this.attributes.operation}if(this.attributes.item_ids){c.id=this.attributes.item_ids}var d=this;_.each(_.pairs(d.attributes.filters),function(e){c["f-"+e[0]]=e[1]});return c},get_url:function(c){return this.get("url_base")+"?"+$.param(this.get_url_data())+"&"+$.param(c)}});var b=Backbone.View.extend({grid:null,initialize:function(c){this.init_grid(c);this.init_grid_controls();$("input[type=text]").each(function(){$(this).click(function(){$(this).select()}).keyup(function(){$(this).css("font-style","normal")})})},handle_refresh:function(c){if(c){if($.inArray("history",c)>-1){if(top.Galaxy&&top.Galaxy.currHistoryPanel){top.Galaxy.currHistoryPanel.loadCurrentHistory()}}}},init_grid:function(e){this.grid=new a(e);var d=this.grid.attributes;this.handle_refresh(d.refresh_frames);var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));if(d.use_hide_message){setTimeout(function(){$("#grid-message").html("")},5000)}}this.init_grid_elements();init_refresh_on_change()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return false})});$(".text-filter-form").each(function(){$(this).submit(function(){var g=$(this).attr("column_key");var f=$("#input-"+g+"-filter");var h=f.val();f.val("");c.add_filter_condition(g,h);return false})});var d=$("#input-tags-filter");if(d.length){d.autocomplete(this.grid.history_tag_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}var e=$("#input-name-filter");if(e.length){e.autocomplete(this.grid.history_name_autocomplete_url,{selectFirst:false,autoFill:false,highlight:false,mustMatch:false})}$(".advanced-search-toggle").each(function(){$(this).click(function(){$("#standard-search").slideToggle("fast");$("#advanced-search").slideToggle("fast");return false})})},init_grid_elements:function(){$(".grid").each(function(){var s=$(this).find("input.grid-row-select-checkbox");var r=$(this).find("span.grid-selected-count");var t=function(){r.text($(s).filter(":checked").length)};$(s).each(function(){$(this).change(t)});t()});if($(".community_rating_star").length!==0){$(".community_rating_star").rating({})}var q=this.grid.attributes;var p=this;$(".page-link > a").each(function(){$(this).click(function(){p.set_page($(this).attr("page_num"));return false})});$(".use-inbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href"),inbound:true});return false})});$(".use-outbound").each(function(){$(this).click(function(r){p.execute({href:$(this).attr("href")});return false})});var f=q.items.length;if(f==0){return}for(var k in q.items){var o=q.items[k];var l=$("#grid-"+k+"-popup");l.off();var d=new PopupMenu(l);for(var h in q.operations){var e=q.operations[h];var m=e.label;var c=o.operation_config[m];var g=o.encode_id;if(c.allowed&&e.allow_popup){var n={html:e.label,href:c.url_args,target:c.target,confirmation_text:e.confirm,inbound:e.inbound};n.func=function(t){t.preventDefault();var s=$(t.target).html();var r=this.findItemByHtml(s);p.execute(r)};d.addItem(n)}}}},add_filter_condition:function(e,g){if(g===""){return false}this.grid.add_filter(e,g,true);var f=$("<span>"+g+"<a href='javascript:void(0);'><span class='delete-search-icon' /></span></a>");f.addClass("text-filter-val");var d=this;f.click(function(){d.grid.remove_filter(e,g);$(this).remove();d.go_page_one();d.execute()});var c=$("#"+e+"-filtering-criteria");c.append(f);this.go_page_one();this.execute()},set_sort_condition:function(h){var g=this.grid.get("sort_key");var f=h;if(g.indexOf(h)!==-1){if(g.substring(0,1)!=="-"){f="-"+h}else{}}$(".sort-arrow").remove();var e=(f.substring(0,1)=="-")?"↑":"↓";var c=$("<span>"+e+"</span>").addClass("sort-arrow");var d=$("#"+h+"-header");d.append(c);this.grid.set("sort_key",f);this.go_page_one();this.execute()},set_categorical_filter:function(e,g){var d=this.grid.get("categorical_filters")[e],f=this.grid.get("filters")[e];var c=this;$("."+e+"-filter").each(function(){var m=$.trim($(this).text());var k=d[m];var l=k[e];if(l==g){$(this).empty();$(this).addClass("current-filter");$(this).append(m)}else{if(l==f){$(this).empty();var h=$("<a href='#'>"+m+"</a>");h.click(function(){c.set_categorical_filter(e,l)});$(this).removeClass("current-filter");$(this).append(h)}}});this.grid.add_filter(e,g);this.go_page_one();this.execute()},set_page:function(c){var d=this;$(".page-link").each(function(){var k=$(this).attr("id"),g=parseInt(k.split("-")[2],10),e=d.grid.get("cur_page"),h;if(g===c){h=$(this).children().text();$(this).empty();$(this).addClass("inactive-link");$(this).text(h)}else{if(g===e){h=$(this).text();$(this).empty();$(this).removeClass("inactive-link");var f=$("<a href='#'>"+h+"</a>");f.click(function(){d.set_page(g)});$(this).append(f)}}});if(c==="all"){this.grid.set("cur_page",c)}else{this.grid.set("cur_page",parseInt(c,10))}this.execute()},submit_operation:function(f,g){var e=$('input[name="id"]:checked').length;if(!e>0){return false}var d=$(f).val();var c=[];$("input[name=id]:checked").each(function(){c.push($(this).val())});this.execute({operation:d,id:c,confirmation_text:g});return true},execute:function(n){var f=null;var e=null;var g=null;var c=null;var m=null;if(n){e=n.href;g=n.operation;f=n.id;c=n.confirmation_text;m=n.inbound;if(e!==undefined&&e.indexOf("operation=")!=-1){var l=e.split("?");if(l.length>1){var k=l[1];var d=k.split("&");for(var h=0;h<d.length;h++){if(d[h].indexOf("operation")!=-1){g=d[h].split("=")[1];g=g.replace(/\+/g," ")}else{if(d[h].indexOf("id")!=-1){f=d[h].split("=")[1]}}}}}}if(g&&f){if(c&&c!=""&&c!="None"&&c!="null"){if(!confirm(c)){return false}}g=g.toLowerCase();this.grid.set({operation:g,item_ids:f});if(this.grid.can_async_op(g)){this.update_grid()}else{this.go_to(m,"")}return false}if(e){this.go_to(m,e);return false}if(this.grid.get("async")){this.update_grid()}else{this.go_to(m,"")}return false},go_to:function(f,d){var e=this.grid.get("async");this.grid.set("async",false);advanced_search=$("#advanced-search").is(":visible");this.grid.set("advanced_search",advanced_search);if(!d){d=this.grid.get("url_base")+"?"+$.param(this.grid.get_url_data())}this.grid.set({operation:undefined,item_ids:undefined,async:e});if(f){var c=$(".grid-header").closest(".inbound");if(c.length!==0){c.load(d);return}}window.location=d},update_grid:function(){var d=(this.grid.get("operation")?"POST":"GET");$(".loading-elt-overlay").show();var c=this;$.ajax({type:d,url:c.grid.get("url_base"),data:c.grid.get_url_data(),error:function(e){alert("Grid refresh failed")},success:function(e){c.init_grid($.parseJSON(e));$(".loading-elt-overlay").hide()},complete:function(){c.grid.set({operation:undefined,item_ids:undefined})}})},check_all_items:function(){var c=document.getElementById("check_all"),d=document.getElementsByTagName("input"),f=0,e;if(c.checked===true){for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=true;f++}}}else{for(e=0;e<d.length;e++){if(d[e].name.indexOf("id")!==-1){d[e].checked=false}}}this.init_grid_elements()},go_page_one:function(){var c=this.grid.get("cur_page");if(c!==null&&c!==undefined&&c!=="all"){this.grid.set("cur_page",1)}},template_body:function(t){var m="";var u=0;var g=t.items.length;if(g==0){m+='<tr><td colspan="100"><em>No Items</em></td></tr>';u=1}for(var h in t.items){var r=t.items[h];var c=r.encode_id;var k="grid-"+h+"-popup";m+="<tr ";if(t.current_item_id==r.id){m+='class="current"'}m+=">";if(t.show_item_checkboxes){m+='<td style="width: 1.5em;"><input type="checkbox" name="id" value="'+c+'" id="'+c+'" class="grid-row-select-checkbox" /></td>'}for(j in t.columns){var f=t.columns[j];if(f.visible){var e="";if(f.nowrap){e='style="white-space:nowrap;"'}var s=r.column_config[f.label];var l=s.link;var n=s.value;var q=s.inbound;if(jQuery.type(n)==="string"){n=n.replace(/\/\//g,"/")}var d="";var p="";if(f.attach_popup){d="grid-"+h+"-popup";p="menubutton";if(l!=""){p+=" split"}p+=" popup"}m+="<td "+e+">";if(l){if(t.operations.length!=0){m+='<div id="'+d+'" class="'+p+'" style="float: left;">'}var o="";if(q){o="use-inbound"}else{o="use-outbound"}m+='<a class="label '+o+'" href="'+l+'" onclick="return false;">'+n+"</a>";if(t.operations.length!=0){m+="</div>"}}else{m+='<div id="'+d+'" class="'+p+'"><label id="'+f.label_id_prefix+c+'" for="'+c+'">'+n+"</label></div>"}m+="</td>"}}m+="</tr>";u++}return m},template_footer:function(q){var m="";if(q.use_paging&&q.num_pages>1){var o=q.num_page_links;var c=q.cur_page_num;var p=q.num_pages;var l=o/2;var k=c-l;var g=0;if(k==0){k=1;g=l-(c-k)}var f=l+g;var e=c+f;if(e<=p){max_offset=0}else{e=p;max_offset=f-(e+1-c)}if(max_offset!=0){k-=max_offset;if(k<1){k=1}}m+='<tr id="page-links-row">';if(q.show_item_checkboxes){m+="<td></td>"}m+='<td colspan="100"><span id="page-link-container">Page:';if(k>1){m+='<span class="page-link" id="page-link-1"><a href="'+this.grid.get_url({page:n})+'" page_num="1" onclick="return false;">1</a></span> ...'}for(var n=k;n<e+1;n++){if(n==q.cur_page_num){m+='<span class="page-link inactive-link" id="page-link-'+n+'">'+n+"</span>"}else{m+='<span class="page-link" id="page-link-'+n+'"><a href="'+this.grid.get_url({page:n})+'" onclick="return false;" page_num="'+n+'">'+n+"</a></span>"}}if(e<p){m+='...<span class="page-link" id="page-link-'+p+'"><a href="'+this.grid.get_url({page:p})+'" onclick="return false;" page_num="'+p+'">'+p+"</a></span>"}m+="</span>";m+='<span class="page-link" id="show-all-link-span"> | <a href="'+this.grid.get_url({page:"all"})+'" onclick="return false;" page_num="all">Show All</a></span></td></tr>'}if(q.show_item_checkboxes){m+='<tr><input type="hidden" id="operation" name="operation" value=""><td></td><td colspan="100">For <span class="grid-selected-count"></span> selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file +jQuery.ajaxSettings.traditional=true;define(["mvc/ui"],function(){var a=Backbone.Model.extend({defaults:{url_base:"",async:false,async_ops:[],categorical_filters:[],filters:{},sort_key:null,show_item_checkboxes:false,advanced_search:false,cur_page:1,num_pages:1,operation:undefined,item_ids:undefined},can_async_op:function(c){return _.indexOf(this.attributes.async_ops,c)!==-1},add_filter:function(g,h,d){if(d){var e=this.attributes.filters[g],c;if(e===null||e===undefined){c=h}else{if(typeof(e)=="string"){if(e=="All"){c=h}else{var f=[];f[0]=e;f[1]=h;c=f}}else{c=e;c.push(h)}}this.attributes.filters[g]=c}else{this.attributes.filters[g]=h}},remove_filter:function(d,g){var c=this.attributes.filters[d];if(c===null||c===undefined){return false}var f=true;if(typeof(c)==="string"){if(c=="All"){f=false}else{delete this.attributes.filters[d]}}else{var e=_.indexOf(c,g);if(e!==-1){c.splice(e,1)}else{f=false}}return f},get_url_data:function(){var 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d=this.grid.attributes;this.handle_refresh(d.refresh_frames);var c=this.grid.get("url_base");c=c.replace(/^.*\/\/[^\/]+/,"");this.grid.set("url_base",c);$("#grid-table-body").html(this.template_body(d));$("#grid-table-footer").html(this.template_footer(d));if(d.message){$("#grid-message").html(this.template_message(d));if(d.use_hide_message){setTimeout(function(){$("#grid-message").html("")},5000)}}this.init_grid_elements();init_refresh_on_change()},init_grid_controls:function(){$(".submit-image").each(function(){$(this).mousedown(function(){$(this).addClass("gray-background")});$(this).mouseup(function(){$(this).removeClass("gray-background")})});var c=this;$(".sort-link").each(function(){$(this).click(function(){c.set_sort_condition($(this).attr("sort_key"));return false})});$(".categorical-filter > a").each(function(){$(this).click(function(){c.set_categorical_filter($(this).attr("filter_key"),$(this).attr("filter_val"));return 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selected '+q.get_class_plural+": ";for(i in q.operations){var d=q.operations[i];if(d.allow_multiple){m+='<input type="button" value="'+d.label+'" class="action-button" onclick="gridView.submit_operation(this, \''+d.confirm+"')\"> "}}m+="</td></tr>"}var h=false;for(i in q.operations){if(q.operations[i].global_operation){h=true;break}}if(h){m+='<tr><td colspan="100">';for(i in q.operations){var d=q.operations[i];if(d.global_operation){m+='<a class="action-button" href="'+d.global_operation+'">'+d.label+"</a>"}}m+="</td></tr>"}if(q.legend){m+='<tr><td colspan="100">'+q.legend+"</td></tr>"}return m},template_message:function(c){return'<p><div class="'+c.status+'message transient-message">'+c.message+'</div><div style="clear: both"></div></p>'}});return{Grid:a,GridView:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d270d3cf7627/ Changeset: d270d3cf7627 Branch: stable User: greg Date: 2014-02-19 19:05:25 Summary: Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances. Affected #: 6 files diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -95,6 +95,7 @@ self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) + self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', True ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) try: diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc 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 @@ -271,9 +271,10 @@ if remove_from_disk_checked: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED tool_shed_repository.error_message = None - # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the - # installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) + if trans.app.config.manage_dependency_relationships: + # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the + # installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) else: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED trans.install_model.context.add( tool_shed_repository ) diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -62,8 +62,9 @@ # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key # at runtime. The value defines the entire tool dependency tree. self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} - # Load defined dependency relationships for installed tool shed repositories and their contents. - self.load_dependency_relationships() + if app.config.manage_dependency_relationships: + # Load defined dependency relationships for installed tool shed repositories and their contents. + self.load_dependency_relationships() def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ): """ diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -602,8 +602,9 @@ suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.install_model.ToolShedRepository.installation_status.INSTALLED ) - # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) + if trans.app.config.manage_dependency_relationships: + # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) else: # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. set_repository_attributes( trans, diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -507,8 +507,9 @@ if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, app.install_model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + if app.config.manage_dependency_relationships: + # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. + app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) elif elem.tag == 'set_environment': # <set_environment version="1.0"> # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> diff -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 -r d270d3cf7627a42b6fac2aa69701deadb89c8ffc universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -152,6 +152,11 @@ #enable_tool_shed_check = False #hours_between_check = 12 +# Enable use of an in-memory registry with bi-directional relationships +# between repositories (i.e., in addition to lists of dependencies for a +# repository, keep an in-memory registry of dependent items for each repository. +#manage_dependency_relationships = True + # XML config file that contains data table entries for the ToolDataTableManager. This file is manually # maintained by the Galaxy administrator. #tool_data_table_config_path = tool_data_table_conf.xml https://bitbucket.org/galaxy/galaxy-central/commits/ef0654f99261/ Changeset: ef0654f99261 User: inithello Date: 2014-02-19 19:09:03 Summary: Merge bugfix from stable. Affected #: 1 file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: greg: Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances.
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4df1be355e4f/ Changeset: 4df1be355e4f User: greg Date: 2014-02-19 19:05:25 Summary: Make managing an in-memory registry of bi-directional installed repository dependency relationships a configurable option for Galaxy instances. Affected #: 6 files diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -95,6 +95,7 @@ self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.shed_tool_data_table_config = resolve_path( kwargs.get( 'shed_tool_data_table_config', 'shed_tool_data_table_conf.xml' ), self.root ) self.enable_tool_shed_check = string_as_bool( kwargs.get( 'enable_tool_shed_check', False ) ) + self.manage_dependency_relationships = string_as_bool( kwargs.get( 'manage_dependency_relationships', True ) ) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) self.hours_between_check = kwargs.get( 'hours_between_check', 12 ) try: diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f 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 @@ -271,9 +271,10 @@ if remove_from_disk_checked: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED tool_shed_repository.error_message = None - # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the - # installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) + if trans.app.config.manage_dependency_relationships: + # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the + # installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) else: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED trans.install_model.context.add( tool_shed_repository ) diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/galaxy_install/installed_repository_manager.py --- a/lib/tool_shed/galaxy_install/installed_repository_manager.py +++ b/lib/tool_shed/galaxy_install/installed_repository_manager.py @@ -62,8 +62,9 @@ # whose values are a list of tuples defining tool_dependency objects (whose status is 'Installed') that require the key # at runtime. The value defines the entire tool dependency tree. self.installed_runtime_dependent_tool_dependencies_of_installed_tool_dependencies = {} - # Load defined dependency relationships for installed tool shed repositories and their contents. - self.load_dependency_relationships() + if app.config.manage_dependency_relationships: + # Load defined dependency relationships for installed tool shed repositories and their contents. + self.load_dependency_relationships() def add_entry_to_installed_repository_dependencies_of_installed_repositories( self, repository ): """ diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -602,8 +602,9 @@ suc.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.install_model.ToolShedRepository.installation_status.INSTALLED ) - # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) + if trans.app.config.manage_dependency_relationships: + # Add the installed repository and any tool dependencies to the in-memory dictionaries in the installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_install( tool_shed_repository ) else: # An error occurred while cloning the repository, so reset everything necessary to enable another attempt. set_repository_attributes( trans, diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f lib/tool_shed/util/common_install_util.py --- a/lib/tool_shed/util/common_install_util.py +++ b/lib/tool_shed/util/common_install_util.py @@ -507,8 +507,9 @@ if tool_dependency and tool_dependency.status in [ app.install_model.ToolDependency.installation_status.INSTALLED, app.install_model.ToolDependency.installation_status.ERROR ]: installed_tool_dependencies.append( tool_dependency ) - # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. - app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) + if app.config.manage_dependency_relationships: + # Add the tool_dependency to the in-memory dictionaries in the installed_repository_manager. + app.installed_repository_manager.handle_tool_dependency_install( tool_shed_repository, tool_dependency ) elif elem.tag == 'set_environment': # <set_environment version="1.0"> # <environment_variable name="R_SCRIPT_PATH"action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable> diff -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 -r 4df1be355e4f7cdbbc927027ce60b81cf222956f universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -152,6 +152,11 @@ #enable_tool_shed_check = False #hours_between_check = 12 +# Enable use of an in-memory registry with bi-directional relationships +# between repositories (i.e., in addition to lists of dependencies for a +# repository, keep an in-memory registry of dependent items for each repository. +#manage_dependency_relationships = True + # XML config file that contains data table entries for the ToolDataTableManager. This file is manually # maintained by the Galaxy administrator. #tool_data_table_config_path = tool_data_table_conf.xml Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1298d3f6aca5/ Changeset: 1298d3f6aca5 Branch: stable User: natefoo Date: 2014-02-19 19:00:33 Summary: Stop jobs when all output datasets are deleted via the API. Affected #: 3 files diff -r 44968207ddd283d0023c72e3d25fd39b1c71eb99 -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -849,6 +849,18 @@ break return job + def stop_hda_creating_job( self, hda ): + """ + Stops an HDA's creating job if all the job's other outputs are deleted. + """ + if hda.parent_id is None and len( hda.creating_job_associations ) > 0: + # Mark associated job for deletion + job = hda.creating_job_associations[0].job + if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]: + # Are *all* of the job's other output datasets deleted? + if job.check_if_output_datasets_deleted(): + job.mark_deleted( self.app.config.track_jobs_in_database ) + self.app.job_manager.job_stop_queue.put( job.id ) class UsesLibraryMixin: diff -r 44968207ddd283d0023c72e3d25fd39b1c71eb99 -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -278,6 +278,8 @@ # get_dataset can return a string during an error if hda and isinstance( hda, trans.model.HistoryDatasetAssociation ): changed = self.set_hda_from_dict( trans, hda, payload ) + if payload.get( 'deleted', False ): + self.stop_hda_creating_job( hda ) except Exception, exception: log.error( 'Update of history (%s), HDA (%s) failed: %s', history_id, id, str( exception ), exc_info=True ) @@ -347,6 +349,8 @@ trans.sa_session.flush() rval[ 'purged' ] = True + self.stop_hda_creating_job( hda ) + trans.sa_session.flush() rval[ 'deleted' ] = True diff -r 44968207ddd283d0023c72e3d25fd39b1c71eb99 -r 1298d3f6aca59825d0eb3d32afd5686c4b1b9294 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -839,14 +839,7 @@ hda.mark_deleted() hda.clear_associated_files() trans.log_event( "Dataset id %s marked as deleted" % str(id) ) - if hda.parent_id is None and len( hda.creating_job_associations ) > 0: - # Mark associated job for deletion - job = hda.creating_job_associations[0].job - if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]: - # Are *all* of the job's other output datasets deleted? - if job.check_if_output_datasets_deleted(): - job.mark_deleted( self.app.config.track_jobs_in_database ) - self.app.job_manager.job_stop_queue.put( job.id ) + self.stop_hda_creating_job( hda ) trans.sa_session.flush() except Exception, e: msg = 'HDA deletion failed (encoded: %s, decoded: %s)' % ( dataset_id, id ) https://bitbucket.org/galaxy/galaxy-central/commits/0db8172d6d36/ Changeset: 0db8172d6d36 User: natefoo Date: 2014-02-19 19:01:03 Summary: merge. Affected #: 3 files diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -892,6 +892,18 @@ break return job + def stop_hda_creating_job( self, hda ): + """ + Stops an HDA's creating job if all the job's other outputs are deleted. + """ + if hda.parent_id is None and len( hda.creating_job_associations ) > 0: + # Mark associated job for deletion + job = hda.creating_job_associations[0].job + if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]: + # Are *all* of the job's other output datasets deleted? + if job.check_if_output_datasets_deleted(): + job.mark_deleted( self.app.config.track_jobs_in_database ) + self.app.job_manager.job_stop_queue.put( job.id ) class UsesLibraryMixin: diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -280,6 +280,8 @@ # get_dataset can return a string during an error if hda and isinstance( hda, trans.model.HistoryDatasetAssociation ): changed = self.set_hda_from_dict( trans, hda, payload ) + if payload.get( 'deleted', False ): + self.stop_hda_creating_job( hda ) except Exception, exception: log.error( 'Update of history (%s), HDA (%s) failed: %s', history_id, id, str( exception ), exc_info=True ) @@ -349,6 +351,8 @@ trans.sa_session.flush() rval[ 'purged' ] = True + self.stop_hda_creating_job( hda ) + trans.sa_session.flush() rval[ 'deleted' ] = True diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 lib/galaxy/webapps/galaxy/controllers/dataset.py --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -839,14 +839,7 @@ hda.mark_deleted() hda.clear_associated_files() trans.log_event( "Dataset id %s marked as deleted" % str(id) ) - if hda.parent_id is None and len( hda.creating_job_associations ) > 0: - # Mark associated job for deletion - job = hda.creating_job_associations[0].job - if job.state in [ self.app.model.Job.states.QUEUED, self.app.model.Job.states.RUNNING, self.app.model.Job.states.NEW ]: - # Are *all* of the job's other output datasets deleted? - if job.check_if_output_datasets_deleted(): - job.mark_deleted( self.app.config.track_jobs_in_database ) - self.app.job_manager.job_stop_queue.put( job.id ) + self.stop_hda_creating_job( hda ) trans.sa_session.flush() except Exception, e: msg = 'HDA deletion failed (encoded: %s, decoded: %s)' % ( dataset_id, id ) https://bitbucket.org/galaxy/galaxy-central/commits/e51429649b44/ Changeset: e51429649b44 User: natefoo Date: 2014-02-19 19:02:12 Summary: merge. Affected #: 6 files diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -843,35 +843,6 @@ history. <br>You can <a href="%s">continue and import this history</a> or %s. """ % ( web.url_for(controller='history', action='imp', id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True ) - # Replaced with view (below) but kept (available via manual URL editing) for now - @web.expose - def original_view( self, trans, id=None, show_deleted=False, use_panels=True ): - """View a history. If a history is importable, then it is viewable by any user.""" - # Get history to view. - if not id: - return trans.show_error_message( "You must specify a history you want to view." ) - history_to_view = self.get_history( trans, id, False) - # Integrity checks. - if not history_to_view: - return trans.show_error_message( "The specified history does not exist." ) - # Admin users can view any history - if( ( history_to_view.user != trans.user ) - and ( not trans.user_is_admin() ) - and ( not history_to_view.importable ) ): - error( "Either you are not allowed to view this history or the owner of this history has not made it accessible." ) - # View history. - show_deleted = galaxy.util.string_as_bool( show_deleted ) - datasets = self.get_history_datasets( trans, history_to_view, show_deleted=show_deleted ) - try: - use_panels = galaxy.util.string_as_bool( use_panels ) - except: - pass # already a bool - return trans.stream_template_mako( "history/original_view.mako", - history = history_to_view, - datasets = datasets, - show_deleted = show_deleted, - use_panels = use_panels ) - @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): """ diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -783,77 +783,110 @@ * }); * $( '.myElement' ).modeButton( 'callModeFn', 'bler' ); */ + /** constructor */ function ModeButton( element, options ){ this.currModeIndex = 0; - return this.init( element, options ); + return this._init( element, options ); } + /** html5 data key to store this object inside an element */ ModeButton.prototype.DATA_KEY = 'mode-button'; + /** default options */ ModeButton.prototype.defaults = { - modes : [ - { mode: 'default' } - ] + switchModesOnClick : true }; - ModeButton.prototype.init = function _init( element, options ){ + // ---- private interface + /** set up options, intial mode, and the click handler */ + ModeButton.prototype._init = function _init( element, options ){ + //console.debug( 'ModeButton._init:', element, options ); options = options || {}; this.$element = $( element ); this.options = jQuery.extend( true, {}, this.defaults, options ); + if( !options.modes ){ + throw new Error( 'ModeButton requires a "modes" array' ); + } var modeButton = this; this.$element.click( function _ModeButtonClick( event ){ - // call the curr mode fn modeButton.callModeFn(); // inc the curr mode index - modeButton._incModeIndex(); + if( modeButton.options.switchModesOnClick ){ modeButton._incModeIndex(); } // set the element html $( this ).html( modeButton.options.modes[ modeButton.currModeIndex ].html ); }); - - this.currModeIndex = 0; - if( this.options.initialMode ){ - this.currModeIndex = this._getModeIndex( this.options.initialMode ); - } - return this; + return this.reset(); }; - - - ModeButton.prototype._getModeIndex = function __getModeIndex( modeKey ){ - for( var i=0; i<this.options.modes.length; i+=1 ){ - if( this.options.modes[ i ].mode === modeKey ){ return i; } - } - throw new Error( 'mode not found: ' + modeKey ); - }; - ModeButton.prototype.getCurrMode = function _getCurrMode(){ - return this.options.modes[ this.currModeIndex ]; - }; - ModeButton.prototype.getMode = function _getMode( modeKey ){ - if( !modeKey ){ return this.getCurrMode(); } - return this.options.modes[( this._getModeIndex( modeKey ) )]; - }; - ModeButton.prototype.hasMode = function _hasMode( modeKey ){ - return !!this.getMode( modeKey ); - }; - ModeButton.prototype.currentMode = function _currentMode(){ - return this.options.modes[ this.currModeIndex ]; - }; - ModeButton.prototype.setMode = function _setMode( newModeKey ){ - var newMode = this.getMode( newModeKey ); - this.$element.html( newMode.html || null ); - return this; - }; - ModeButton.prototype._incModeIndex = function __incModeIndex(){ + /** increment the mode index to the next in the array, looping back to zero if at the last */ + ModeButton.prototype._incModeIndex = function _incModeIndex(){ this.currModeIndex += 1; if( this.currModeIndex >= this.options.modes.length ){ this.currModeIndex = 0; } return this; }; - ModeButton.prototype.callModeFn = function _callModeFn( modeKey ){ + /** get the mode index in the modes array for the given key (mode name) */ + ModeButton.prototype._getModeIndex = function _getModeIndex( modeKey ){ + for( var i=0; i<this.options.modes.length; i+=1 ){ + if( this.options.modes[ i ].mode === modeKey ){ return i; } + } + throw new Error( 'mode not found: ' + modeKey ); + }; + /** set the current mode to the one with the given index and set button html */ + ModeButton.prototype._setModeByIndex = function _setModeByIndex( index ){ + var newMode = this.options.modes[ index ]; + if( !newMode ){ + throw new Error( 'mode index not found: ' + index ); + } + this.currModeIndex = index; + if( newMode.html ){ + this.$element.html( newMode.html ); + } + return this; + }; + + // ---- public interface + /** get the current mode object (not just the mode name) */ + ModeButton.prototype.currentMode = function currentMode(){ + return this.options.modes[ this.currModeIndex ]; + }; + /** return the mode key of the current mode */ + ModeButton.prototype.current = function current(){ + // sugar for returning mode name + return this.currentMode().mode; + }; + /** get the mode with the given modeKey or the current mode if modeKey is undefined */ + ModeButton.prototype.getMode = function getMode( modeKey ){ + if( !modeKey ){ return this.currentMode(); } + return this.options.modes[( this._getModeIndex( modeKey ) )]; + }; + /** T/F if the button has the given mode */ + ModeButton.prototype.hasMode = function hasMode( modeKey ){ + try { + return !!this.getMode( modeKey ); + } catch( err ){} + return false; + }; + /** set the current mode to the mode with the given name */ + ModeButton.prototype.setMode = function setMode( modeKey ){ + return this._setModeByIndex( this._getModeIndex( modeKey ) ); + }; + /** reset to the initial mode */ + ModeButton.prototype.reset = function reset(){ + this.currModeIndex = 0; + if( this.options.initialMode ){ + this.currModeIndex = this._getModeIndex( this.options.initialMode ); + } + return this._setModeByIndex( this.currModeIndex ); + }; + /** manually call the click handler of the given mode */ + ModeButton.prototype.callModeFn = function callModeFn( modeKey ){ var modeFn = this.getMode( modeKey ).onclick; if( modeFn && jQuery.type( modeFn === 'function' ) ){ - return modeFn.call( this ); + // call with the element as context (std jquery pattern) + modeFn.call( this.$element.get(0) ); + return this; } return undefined; }; @@ -861,26 +894,32 @@ // as jq plugin jQuery.fn.extend({ modeButton : function $modeButton( options ){ - var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 ); + if( !this.size() ){ return this; } + //TODO: does map still work with jq multi selection (i.e. $( '.class-for-many-btns' ).modeButton)? - return this.map( function(){ - var $this = $( this ), - data = $this.data( 'mode-button' ); + if( jQuery.type( options ) === 'object' ){ + return this.map( function(){ + var $this = $( this ); + $this.data( 'mode-button', new ModeButton( $this, options ) ); + return this; + }); + } - if( jQuery.type( options ) === 'object' ){ - data = new ModeButton( $this, options ); - $this.data( 'mode-button', data ); + var $first = $( this[0] ), + button = $first.data( 'mode-button' ); + console.debug( 'first, button', $first, button ); - } else if( data && jQuery.type( options ) === 'string' ){ - var fn = data[ options ]; - if( jQuery.type( fn ) === 'function' ){ - return fn.apply( data, nonOptionsArgs ); - } - } else if ( data ){ - return data; + if( !button ){ + throw new Error( 'modeButton needs an options object or string name of a function' ); + } + + if( button && jQuery.type( options ) === 'string' ){ + var fnName = options; + if( button && jQuery.type( button[ fnName ] ) === 'function' ){ + return button[ fnName ].apply( button, jQuery.makeArray( arguments ).slice( 1 ) ); } - return this; - }); + } + return button; } }); }()); diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b;if(!this.$button.size()){this.$button=$("<div/>")}this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var c=this;function a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.create=function _create(b,a){return new PopupMenu(b,a)};PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((!a.disabled&&a.target)?(' target="'+a.target+'"'):("")),' href="',((!a.disabled&&a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};function LoadingIndicator(a,c){var 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b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}(function(){function a(j,p){var d=27,m=13,c=$(j),e=true,g={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(q){},minSearchLen:0,escWillClear:true,oninit:function(){}};function i(q){var r=$(this).parent().children("input");r.val("");r.trigger("clear:searchInput");p.onclear()}function o(r,q){$(this).trigger("search:searchInput",q);if(typeof p.onfirstsearch==="function"&&e){e=false;p.onfirstsearch(q)}else{p.onsearch(q)}}function f(){return['<input type="text" name="',p.name,'" placeholder="',p.placeholder,'" ','class="search-query ',p.classes,'" ',"/>"].join("")}function l(){return 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a(this,c)})}})}());(function(){function b(m,l){this.currModeIndex=0;return this.init(m,l)}b.prototype.DATA_KEY="mode-button";b.prototype.defaults={modes:[{mode:"default"}]};b.prototype.init=function f(m,l){l=l||{};this.$element=$(m);this.options=jQuery.extend(true,{},this.defaults,l);var o=this;this.$element.click(function n(p){o.callModeFn();o._incModeIndex();$(this).html(o.options.modes[o.currModeIndex].html)});this.currModeIndex=0;if(this.options.initialMode){this.currModeIndex=this._getModeIndex(this.options.initialMode)}return this};b.prototype._getModeIndex=function j(l){for(var m=0;m<this.options.modes.length;m+=1){if(this.options.modes[m].mode===l){return m}}throw new Error("mode not found: "+l)};b.prototype.getCurrMode=function a(){return this.options.modes[this.currModeIndex]};b.prototype.getMode=function g(l){if(!l){return this.getCurrMode()}return this.options.modes[(this._getModeIndex(l))]};b.prototype.hasMode=function k(l){return 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d(){this.$element.empty().append([this._renderKeySelect(),this._renderOpSelect(),this._renderValueInput()]);return this};e.prototype._renderKeySelect=function a(){var j=this;var k=this.options.filters.map(function(l){return l.key});this.$keySelect=dropDownSelect(k,this.currFilter.key).addClass("filter-control-key").on("change.dropdown-select",function(m,l){j.currFilter=_.findWhere(j.options.filters,{key:l});j.render()._triggerChange()});return this.$keySelect};e.prototype._renderOpSelect=function i(){var j=this,k=this.currFilter.ops;this.$opSelect=dropDownSelect(k,k[0]).addClass("filter-control-op").on("change.dropdown-select",function(m,l){j._triggerChange()});return this.$opSelect};e.prototype._renderValueInput=function c(){var j=this;if(this.currFilter.values){this.$valueSelect=dropDownSelect(this.currFilter.values,this.currFilter.values[0]).on("change.dropdown-select",function(l,k){j._triggerChange()})}else{this.$valueSelect=$("<input/>").addClass("form-control").on("change",function(k,l){j._triggerChange()})}this.$valueSelect.addClass("filter-control-value");return this.$valueSelect};e.prototype.val=function b(){var k=this.$element.find(".filter-control-key .dropdown-select-selected").text(),m=this.$element.find(".filter-control-op .dropdown-select-selected").text(),j=this.$element.find(".filter-control-value"),l=(j.hasClass("dropdown-select"))?(j.find(".dropdown-select-selected").text()):(j.val());return{key:k,op:m,value:l}};e.prototype._triggerChange=function h(){this.$element.trigger("change.filter-control",this.val())};jQuery.fn.extend({filterControl:function f(k){var j=jQuery.makeArray(arguments).slice(1);return this.map(function(){var n=$(this),m=n.data(e.prototype.DATA_KEY);if(jQuery.type(k)==="object"){m=new e(n,k);n.data(e.prototype.DATA_KEY,m)}if(m&&jQuery.type(k)==="string"){var l=m[k];if(jQuery.type(l)==="function"){return l.apply(m,j)}}return this})}})}());(function(){function i(o,n){this.numPages=null;this.currPage=0;return this.init(o,n)}i.prototype.DATA_KEY="pagination";i.prototype.defaults={startingPage:0,perPage:20,totalDataSize:null,currDataSize:null};i.prototype.init=function g(n,o){o=o||{};this.$element=n;this.options=jQuery.extend(true,{},this.defaults,o);this.currPage=this.options.startingPage;if(this.options.totalDataSize!==null){this.numPages=Math.ceil(this.options.totalDataSize/this.options.perPage);if(this.currPage>=this.numPages){this.currPage=this.numPages-1}}this.$element.data(i.prototype.DATA_KEY,this);this._render();return this};function m(n){return $(['<li><a href="javascript:void(0);">',n,"</a></li>"].join(""))}i.prototype._render=function e(){if(this.options.totalDataSize===0){return this}if(this.numPages===1){return this}if(this.numPages>0){this._renderPages();this._scrollToActivePage()}else{this._renderPrevNext()}return this};i.prototype._renderPrevNext=function b(){var o=this,p=m("Prev"),n=m("Next"),q=$("<ul/>").addClass("pagination pagination-prev-next");if(this.currPage===0){p.addClass("disabled")}else{p.click(function(){o.prevPage()})}if((this.numPages&&this.currPage===(this.numPages-1))||(this.options.currDataSize&&this.options.currDataSize<this.options.perPage)){n.addClass("disabled")}else{n.click(function(){o.nextPage()})}this.$element.html(q.append([p,n]));return this.$element};i.prototype._renderPages=function a(){var n=this,q=$("<div>").addClass("pagination-scroll-container"),s=$("<ul/>").addClass("pagination pagination-page-list"),r=function(t){n.goToPage($(this).data("page"))};for(var o=0;o<this.numPages;o+=1){var p=m(o+1).attr("data-page",o).click(r);if(o===this.currPage){p.addClass("active")}s.append(p)}return this.$element.html(q.html(s))};i.prototype._scrollToActivePage=function l(){var p=this.$element.find(".pagination-scroll-container");if(!p.size()){return this}var o=this.$element.find("li.active"),n=p.width()/2;p.scrollLeft(p.scrollLeft()+o.position().left-n);return this};i.prototype.goToPage=function j(n){if(n<=0){n=0}if(this.numPages&&n>=this.numPages){n=this.numPages-1}if(n===this.currPage){return this}this.currPage=n;this.$element.trigger("pagination.page-change",this.currPage);this._render();return this};i.prototype.prevPage=function c(){return this.goToPage(this.currPage-1)};i.prototype.nextPage=function h(){return this.goToPage(this.currPage+1)};i.prototype.page=function f(){return this.currPage};i.create=function k(n,o){return new i(n,o)};jQuery.fn.extend({pagination:function d(o){var n=jQuery.makeArray(arguments).slice(1);if(jQuery.type(o)==="object"){return this.map(function(){i.create($(this),o);return this})}var q=$(this[0]),r=q.data(i.prototype.DATA_KEY);if(r){if(jQuery.type(o)==="string"){var p=r[o];if(jQuery.type(p)==="function"){return p.apply(r,n)}}else{return r}}return undefined}})}());(function(){var g={renameColumns:false,columnNames:[],commentChar:"#",hideCommentRows:false,includePrompts:true,topLeftContent:"Columns:"},s="peek-control.change",t="peek-control.rename",l="peek-control",v="control",f="control-prompt",c="selected",n="disabled",u="button",q="renamable-header",p="column-index",a="column-name";function i(w){if(w.disabled&&jQuery.type(w.disabled)!=="array"){throw new Error('"disabled" must be defined as an array of indeces: '+JSON.stringify(w))}if(w.multiselect&&w.selected&&jQuery.type(w.selected)!=="array"){throw new Error('Mulitselect rows need an array for "selected": '+JSON.stringify(w))}if(!w.label||!w.id){throw new Error("Peek controls need a label and id for each control row: "+JSON.stringify(w))}if(w.disabled&&w.disabled.indexOf(w.selected)!==-1){throw new Error("Selected column is in the list of disabled columns: "+JSON.stringify(w))}return w}function o(x,w){return $("<div/>").addClass(u).text(x.label)}function k(x,w){var y=$("<td/>").html(o(x,w)).attr("data-"+p,w);if(x.disabled&&x.disabled.indexOf(w)!==-1){y.addClass(n)}return y}function e(y,z,w){var x=y.children("."+u);if(y.hasClass(c)){x.html((z.selectedText!==undefined)?(z.selectedText):(z.label))}else{x.html((z.unselectedText!==undefined)?(z.unselectedText):(z.label))}}function h(z,x){var y=k(z,x);if(z.selected===x){y.addClass(c)}e(y,z,x);if(!y.hasClass(n)){y.click(function w(D){var E=$(this);if(!E.hasClass(c)){var A=E.parent().children("."+c).removeClass(c);A.each(function(){e($(this),z,x)});E.addClass(c);e(E,z,x);var C={},B=E.parent().attr("id"),F=E.data(p);C[B]=F;E.parents(".peek").trigger(s,C)}})}return y}function m(z,x){var y=k(z,x);if(z.selected&&z.selected.indexOf(x)!==-1){y.addClass(c)}e(y,z,x);if(!y.hasClass(n)){y.click(function w(D){var E=$(this);E.toggleClass(c);e(E,z,x);var C=E.parent().find("."+c).map(function(G,H){return $(H).data(p)});var B={},A=E.parent().attr("id"),F=jQuery.makeArray(C);B[A]=F;E.parents(".peek").trigger(s,B)})}return y}function j(y,z){var w=[];for(var x=0;x<y;x+=1){w.push(z.multiselect?m(z,x):h(z,x))}return w}function r(y,z,x){var A=$("<tr/>").attr("id",z.id).addClass(v);if(x){var w=$("<td/>").addClass(f).text(z.label+":");A.append(w)}A.append(j(y,z));return A}function b(E){E=jQuery.extend(true,{},g,E);var D=$(this).addClass(l),A=D.find("table"),z=A.find("th").size(),C=A.find("tr").size(),w=A.find("td[colspan]").map(function(H,F){var G=$(this);if(G.text()&&G.text().match(new RegExp("^"+E.commentChar))){return $(this).css("color","grey").parent().get(0)}return null});if(E.hideCommentRows){w.hide();C-=w.size()}if(E.includePrompts){var y=$("<th/>").addClass("top-left").text(E.topLeftContent).attr("rowspan",C);A.find("tr").first().prepend(y)}var B=A.find("th:not(.top-left)").each(function(G,I){var H=$(this),J=H.text().replace(/^\d+\.*/,""),F=E.columnNames[G]||J;H.attr("data-"+a,F).text((G+1)+((F)?("."+F):("")))});if(E.renameColumns){B.addClass(q).click(function x(){var G=$(this),F=G.index()+(E.includePrompts?0:1),I=G.data(a),H=prompt("New column name:",I);if(H!==null&&H!==I){G.text(F+(H?("."+H):"")).data(a,H).attr("data-",a,H);var J=jQuery.makeArray(G.parent().children("th:not(.top-left)").map(function(){return $(this).data(a)}));G.parents(".peek").trigger(t,J)}})}E.controls.forEach(function(G,F){i(G);var H=r(z,G,E.includePrompts);A.find("tbody").append(H)});return this}jQuery.fn.extend({peekControl:function d(w){return this.map(function(){return b.call(this,w)})}})}()); \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b;if(!this.$button.size()){this.$button=$("<div/>")}this.options=a||[];var 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H=$(this),J=H.text().replace(/^\d+\.*/,""),F=E.columnNames[G]||J;H.attr("data-"+a,F).text((G+1)+((F)?("."+F):("")))});if(E.renameColumns){B.addClass(q).click(function x(){var G=$(this),F=G.index()+(E.includePrompts?0:1),I=G.data(a),H=prompt("New column name:",I);if(H!==null&&H!==I){G.text(F+(H?("."+H):"")).data(a,H).attr("data-",a,H);var J=jQuery.makeArray(G.parent().children("th:not(.top-left)").map(function(){return $(this).data(a)}));G.parents(".peek").trigger(t,J)}})}E.controls.forEach(function(G,F){i(G);var H=r(z,G,E.includePrompts);A.find("tbody").append(H)});return this}jQuery.fn.extend({peekControl:function d(w){return this.map(function(){return b.call(this,w)})}})}()); \ No newline at end of file diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 templates/webapps/galaxy/history/original_view.mako --- a/templates/webapps/galaxy/history/original_view.mako +++ /dev/null @@ -1,173 +0,0 @@ -<%namespace file="/display_common.mako" import="get_history_link, get_controller_name" /> -<%namespace file="/root/history_common.mako" import="render_dataset" /> -<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/galaxy/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jstorage" )} - <script type="text/javascript"> - $(function() { - init_history_items( $("div.historyItemWrapper"), false, "nochanges" ); - $( '#switch-to-link' ).click( function( event ){ - var galaxy = window.Galaxy || window.parent.Galaxy; - if( galaxy ){ - galaxy.currHistoryPanel.switchToHistory( '${ trans.security.encode_id( history.id ) }' ); - } - }); - $( '#refresh' ).click( function( event ){ window.location.reload( true ); }) - }); - </script> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history", "autocomplete_tagging" )} - - <style type="text/css"> - - /* these don't appear to be used? */ - .page-body - { - padding: 10px; - float: left; - width: 65%; - } - .page-meta - { - float: right; - width: 27%; - padding: 0.5em; - margin: 0.25em; - vertical-align: text-top; - border: 2px solid #DDDDDD; - border-top: 4px solid #DDDDDD; - } - - - body { - padding: 0px; - margin: 0px; - } - - div.unified-panel-body { - position: absolute; - top: 0px; - width: 100%; - } - - #history-name-area { - margin: 12px 0px 0px 16px; - font-size: 120%; - } - #top-links { - margin: 4px 0px 8px 16px; - } - - .historyItemContainer { - /*padding-right: 3px;*/ - } - .historyItemBody { - display: none; - } - div.historyItemWrapper { - margin: 0px 4px 0px 4px ; - border-left: 1px solid #999999; - border-right: 1px solid #999999; - } - /* TODO: unify with other history css and into .less */ - </style> - - <noscript> - <style> - .historyItemBody { - display: block; - } - </style> - </noscript> -</%def> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.message_box_visible=False -%> -</%def> - -<%def name="body()"> - ${center_panel()} -</%def> - -<%def name="center_panel()"> - ## Get URL to other histories owned by user that owns this history. - <% - ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. - href_to_published_histories = h.url_for( controller='/history', action='list_published') - if history.user is not None: - href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username') - else: - href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? - %> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - ## Render view of history. - <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - <div id="history-name">${history.get_display_name()}</div> - </div> - - <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> - %if not history.purged and history.user != trans.user: - ##TODO: need to remove _top - <a href="${h.url_for(controller='history', action='imp', id=trans.security.encode_id(history.id) )}" - >import and start using history</a> | - <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | - %endif - %if not history.purged and history.user == trans.user: - <a id="switch-to-link" href="javascript:void(0)">${_('switch to this history')}</a> | - <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | - %endif - %if show_deleted: - <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> | - %else: - <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> | - %endif - <a href="#" class="toggle">collapse all</a> - </div> - - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} - </div> - <p></p> - %endif - - %if not datasets: - <div class="infomessagesmall" id="emptyHistoryMessage"> - - %else: - ## Render requested datasets, ordered from newest to oldest - %for data in datasets: - %if data.visible: - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} - </div> - %endif - %endfor - - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} - </div> - </div> - </div> -</%def> diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -77,6 +77,7 @@ %endif <script type="text/javascript"> + ##TODO: remove when Galaxy is either ensured or removed from the history panel var using_panels = ${ 'false' if not use_panels else 'true' }; %if not use_panels: window.Galaxy = {}; @@ -87,113 +88,107 @@ ## ---------------------------------------------------------------------------- <%def name="center_panel()"> +<% + show_deleted = context.get( 'show_deleted', None ) + show_hidden = context.get( 'show_hidden', None ) + + user_is_owner_json = 'true' if user_is_owner else 'false' + show_deleted_json = h.to_json_string( show_deleted ) + show_hidden_json = h.to_json_string( show_hidden ) + + imp_with_deleted_url = h.url_for( controller='history', action='imp', id=history['id'], all_datasets=True ) + imp_without_deleted_url = h.url_for( controller='history', action='imp', id=history['id'] ) +%> + <div id="header" class="clear"><div id="history-view-controls" class="pull-right"> - <% - show_deleted = context.get( 'show_deleted', None ) - show_hidden = context.get( 'show_hidden', None ) - - show_deleted_js = 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) - show_hidden_js = 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) - print 'user_is_owner:', user_is_owner - %> %if not user_is_owner and not history[ 'purged' ]: - <a id="import" class="btn btn-default" style="display: none;" - href="${h.url_for( controller='history', action='imp', id=history['id'], all_datasets=show_deleted )}"> - ${_('Import and start using history')} - </a> + <button id="import" class="btn btn-default"></button> %endif - <button id="toggle-deleted" class="btn btn-default"> - ${_('Exclude deleted') if show_deleted else _('Include deleted')} - </button> - <button id="toggle-hidden" class="btn btn-default"> - ${_('Exclude hidden') if show_hidden else _('Include hidden')} - </button> + <button id="toggle-deleted" class="btn btn-default"></button> + <button id="toggle-hidden" class="btn btn-default"></button></div></div><div id="history-${ history[ 'id' ] }" class="history-panel unified-panel-body" style="overflow: auto;"></div><script type="text/javascript"> + $(function(){ + $( '#toggle-deleted' ).modeButton({ + initialMode : "${ 'showing_deleted' if show_deleted else 'not_showing_deleted' }", + modes: [ + { mode: 'showing_deleted', html: _l( 'Exclude deleted' ) }, + { mode: 'not_showing_deleted', html: _l( 'Include deleted' ) } + ] + }).click( function(){ + // allow the 'include/exclude deleted' button to control whether the 'import' button includes deleted + // datasets when importing or not; when deleted datasets are shown, they'll be imported + $( '#import' ).modeButton( 'setMode', + $( this ).modeButton( 'current' ) === 'showing_deleted'? 'with_deleted': 'without_deleted' ) + }); + + $( '#toggle-hidden' ).modeButton({ + initialMode : "${ 'showing_hidden' if show_hidden else 'not_showing_hidden' }", + modes: [ + { mode: 'showing_hidden', html: _l( 'Exclude hidden' ) }, + { mode: 'not_showing_hidden', html: _l( 'Include hidden' ) } + ] + }); + + $( '#import' ).modeButton({ + switchModesOnClick : false, + initialMode : "${ 'with_deleted' if show_deleted else 'without_deleted' }", + modes: [ + { mode: 'with_deleted', html: _l( 'Import with deleted datasets and start using history' ), + onclick: function importWithDeleted(){ + window.location = '${imp_with_deleted_url}'; + } + }, + { mode: 'without_deleted', html: _l( 'Import and start using history' ), + onclick: function importWithoutDeleted(){ + window.location = '${imp_without_deleted_url}'; + } + }, + ] + }); + }); + var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, userIsOwner = ${'true' if user_is_owner else 'false'}, historyJSON = ${h.to_json_string( history )}, hdaJSON = ${h.to_json_string( hdas )}; - window.hdaJSON = hdaJSON; - - $( '#toggle-deleted' ).modeButton({ - initialMode : (${ show_deleted_js })?( 'exclude' ):( 'include' ), - modes: [ - { mode: 'exclude', html: _l( 'Exclude deleted' ) }, - { mode: 'include', html: _l( 'Include deleted' ) } - ] - }).click( function(){ - // allow the 'include/exclude deleted' button to control whether the 'import' button includes deleted datasets - // when importing or not; when deleted datasets are shown, they'll be imported - var $importBtn = $( '#import' ); - if( $importBtn.size() ){ - // a bit hacky - var href = $importBtn.attr( 'href' ), - includeDeleted = $( this ).modeButton()[0].getMode().mode === 'exclude'; - href = href.replace( /all_datasets=True|False/, ( includeDeleted )?( 'True' ):( 'False' ) ); - $importBtn.attr( 'href', href ); - $importBtn.text( includeDeleted ? _l( 'Import with deleted datasets and start using history' ) - : _l( 'Import and start using history' ) ); - } - }); - - $( '#toggle-hidden' ).modeButton({ - initialMode : (${ show_hidden_js })?( 'exclude' ):( 'include' ), - modes: [ - { mode: 'exclude', html: _l( 'Exclude hidden' ) }, - { mode: 'include', html: _l( 'Include hidden' ) } - ] - }); - - ##TODO: move to mako - if( Galaxy.currUser.id !== historyJSON.user_id ){ - $( '#import' ).show(); - } + panelToUse = ( userIsOwner )? + ({ location: 'mvc/history/history-panel', className: 'HistoryPanel' }): + ({ location: 'mvc/history/readonly-history-panel', className: 'ReadOnlyHistoryPanel' }); require.config({ baseUrl : "${h.url_for( '/static/scripts' )}" - })([ - %if user_is_owner: - 'mvc/history/history-panel' - %else: - 'mvc/history/readonly-history-panel' - %endif - ${ } - ], function( panelMod ){ - //require([ "mvc/history/history-panel" ], function( historyPanel ){ - // history module is already in the dpn chain from the panel. We can re-scope it here. - var historyModel = require( 'mvc/history/history-model' ), - hdaBaseView = require( 'mvc/dataset/hda-base' ), - history = new historyModel.History( historyJSON, hdaJSON, { - logger: ( debugging )?( console ):( null ) + })([ panelToUse.location ], function( panelMod ){ + $(function(){ + var panelClass = panelMod[ panelToUse.className ], + // history module is already in the dpn chain from the panel. We can re-scope it here. + historyModel = require( 'mvc/history/history-model' ), + hdaBaseView = require( 'mvc/dataset/hda-base' ), + history = new historyModel.History( historyJSON, hdaJSON, { + logger: ( debugging )?( console ):( null ) + }); + + window.historyPanel = new panelClass({ + show_deleted : ${show_deleted_json}, + show_hidden : ${show_hidden_json}, + el : $( "#history-" + historyJSON.id ), + model : history, + onready : function(){ + var panel = this; + $( '#toggle-deleted' ).on( 'click', function(){ + panel.toggleShowDeleted(); + }); + $( '#toggle-hidden' ).on( 'click', function(){ + panel.toggleShowHidden(); + }); + this.render(); + } }); - - window.panelMod = panelMod; - %if user_is_owner: - window.panelClass = panelMod.HistoryPanel; - %else: - window.panelClass = panelMod.ReadOnlyHistoryPanel; - %endif - window.historyPanel = new panelClass({ - show_deleted : ${show_deleted_js}, - show_hidden : ${show_hidden_js}, - el : $( "#history-" + historyJSON.id ), - model : history, - onready : function(){ - var panel = this; - $( '#toggle-deleted' ).on( 'click', function(){ - panel.toggleShowDeleted(); - }); - $( '#toggle-hidden' ).on( 'click', function(){ - panel.toggleShowHidden(); - }); - this.render(); - } }); }); </script> diff -r 0db8172d6d363ba1010df08a79f6db435f4f0ee7 -r e51429649b44d5b434a6b6f4e10daa1dbf390c20 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -1,7 +1,6 @@ <?xml version="1.0"?><tool name="Upload File" id="upload1" version="1.1.4" workflow_compatible="false"> - <hidden>True</hidden><description> from your computer </description> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: Add get data back to to tool panel (will be replaced by a placeholder soon)
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/742b4ffd3b99/ Changeset: 742b4ffd3b99 User: guerler Date: 2014-02-19 18:51:52 Summary: Add get data back to to tool panel (will be replaced by a placeholder soon) Affected #: 1 file diff -r 7ebec9da47844efbf37942faab3809cb0169e5c2 -r 742b4ffd3b99160cae864049f09defe710dd7ee4 tools/data_source/upload.xml --- a/tools/data_source/upload.xml +++ b/tools/data_source/upload.xml @@ -1,7 +1,6 @@ <?xml version="1.0"?><tool name="Upload File" id="upload1" version="1.1.4" workflow_compatible="false"> - <hidden>True</hidden><description> from your computer </description> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: carlfeberhard: history/view: clean up, replace import link with window.location; UI mode button: several fixes, clean up, docs; Remove original_view from controllers/history (and templates)
by commits-noreply＠bitbucket.org 19 Feb '14

19 Feb '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7ebec9da4784/ Changeset: 7ebec9da4784 User: carlfeberhard Date: 2014-02-19 18:32:06 Summary: history/view: clean up, replace import link with window.location; UI mode button: several fixes, clean up, docs; Remove original_view from controllers/history (and templates) Affected #: 5 files diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 7ebec9da47844efbf37942faab3809cb0169e5c2 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -843,35 +843,6 @@ history. <br>You can <a href="%s">continue and import this history</a> or %s. """ % ( web.url_for(controller='history', action='imp', id=id, confirm=True, referer=trans.request.referer ), referer_message ), use_panels=True ) - # Replaced with view (below) but kept (available via manual URL editing) for now - @web.expose - def original_view( self, trans, id=None, show_deleted=False, use_panels=True ): - """View a history. If a history is importable, then it is viewable by any user.""" - # Get history to view. - if not id: - return trans.show_error_message( "You must specify a history you want to view." ) - history_to_view = self.get_history( trans, id, False) - # Integrity checks. - if not history_to_view: - return trans.show_error_message( "The specified history does not exist." ) - # Admin users can view any history - if( ( history_to_view.user != trans.user ) - and ( not trans.user_is_admin() ) - and ( not history_to_view.importable ) ): - error( "Either you are not allowed to view this history or the owner of this history has not made it accessible." ) - # View history. - show_deleted = galaxy.util.string_as_bool( show_deleted ) - datasets = self.get_history_datasets( trans, history_to_view, show_deleted=show_deleted ) - try: - use_panels = galaxy.util.string_as_bool( use_panels ) - except: - pass # already a bool - return trans.stream_template_mako( "history/original_view.mako", - history = history_to_view, - datasets = datasets, - show_deleted = show_deleted, - use_panels = use_panels ) - @web.expose def view( self, trans, id=None, show_deleted=False, show_hidden=False, use_panels=True ): """ diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 7ebec9da47844efbf37942faab3809cb0169e5c2 static/scripts/mvc/ui.js --- a/static/scripts/mvc/ui.js +++ b/static/scripts/mvc/ui.js @@ -783,77 +783,110 @@ * }); * $( '.myElement' ).modeButton( 'callModeFn', 'bler' ); */ + /** constructor */ function ModeButton( element, options ){ this.currModeIndex = 0; - return this.init( element, options ); + return this._init( element, options ); } + /** html5 data key to store this object inside an element */ ModeButton.prototype.DATA_KEY = 'mode-button'; + /** default options */ ModeButton.prototype.defaults = { - modes : [ - { mode: 'default' } - ] + switchModesOnClick : true }; - ModeButton.prototype.init = function _init( element, options ){ + // ---- private interface + /** set up options, intial mode, and the click handler */ + ModeButton.prototype._init = function _init( element, options ){ + //console.debug( 'ModeButton._init:', element, options ); options = options || {}; this.$element = $( element ); this.options = jQuery.extend( true, {}, this.defaults, options ); + if( !options.modes ){ + throw new Error( 'ModeButton requires a "modes" array' ); + } var modeButton = this; this.$element.click( function _ModeButtonClick( event ){ - // call the curr mode fn modeButton.callModeFn(); // inc the curr mode index - modeButton._incModeIndex(); + if( modeButton.options.switchModesOnClick ){ modeButton._incModeIndex(); } // set the element html $( this ).html( modeButton.options.modes[ modeButton.currModeIndex ].html ); }); - - this.currModeIndex = 0; - if( this.options.initialMode ){ - this.currModeIndex = this._getModeIndex( this.options.initialMode ); - } - return this; + return this.reset(); }; - - - ModeButton.prototype._getModeIndex = function __getModeIndex( modeKey ){ - for( var i=0; i<this.options.modes.length; i+=1 ){ - if( this.options.modes[ i ].mode === modeKey ){ return i; } - } - throw new Error( 'mode not found: ' + modeKey ); - }; - ModeButton.prototype.getCurrMode = function _getCurrMode(){ - return this.options.modes[ this.currModeIndex ]; - }; - ModeButton.prototype.getMode = function _getMode( modeKey ){ - if( !modeKey ){ return this.getCurrMode(); } - return this.options.modes[( this._getModeIndex( modeKey ) )]; - }; - ModeButton.prototype.hasMode = function _hasMode( modeKey ){ - return !!this.getMode( modeKey ); - }; - ModeButton.prototype.currentMode = function _currentMode(){ - return this.options.modes[ this.currModeIndex ]; - }; - ModeButton.prototype.setMode = function _setMode( newModeKey ){ - var newMode = this.getMode( newModeKey ); - this.$element.html( newMode.html || null ); - return this; - }; - ModeButton.prototype._incModeIndex = function __incModeIndex(){ + /** increment the mode index to the next in the array, looping back to zero if at the last */ + ModeButton.prototype._incModeIndex = function _incModeIndex(){ this.currModeIndex += 1; if( this.currModeIndex >= this.options.modes.length ){ this.currModeIndex = 0; } return this; }; - ModeButton.prototype.callModeFn = function _callModeFn( modeKey ){ + /** get the mode index in the modes array for the given key (mode name) */ + ModeButton.prototype._getModeIndex = function _getModeIndex( modeKey ){ + for( var i=0; i<this.options.modes.length; i+=1 ){ + if( this.options.modes[ i ].mode === modeKey ){ return i; } + } + throw new Error( 'mode not found: ' + modeKey ); + }; + /** set the current mode to the one with the given index and set button html */ + ModeButton.prototype._setModeByIndex = function _setModeByIndex( index ){ + var newMode = this.options.modes[ index ]; + if( !newMode ){ + throw new Error( 'mode index not found: ' + index ); + } + this.currModeIndex = index; + if( newMode.html ){ + this.$element.html( newMode.html ); + } + return this; + }; + + // ---- public interface + /** get the current mode object (not just the mode name) */ + ModeButton.prototype.currentMode = function currentMode(){ + return this.options.modes[ this.currModeIndex ]; + }; + /** return the mode key of the current mode */ + ModeButton.prototype.current = function current(){ + // sugar for returning mode name + return this.currentMode().mode; + }; + /** get the mode with the given modeKey or the current mode if modeKey is undefined */ + ModeButton.prototype.getMode = function getMode( modeKey ){ + if( !modeKey ){ return this.currentMode(); } + return this.options.modes[( this._getModeIndex( modeKey ) )]; + }; + /** T/F if the button has the given mode */ + ModeButton.prototype.hasMode = function hasMode( modeKey ){ + try { + return !!this.getMode( modeKey ); + } catch( err ){} + return false; + }; + /** set the current mode to the mode with the given name */ + ModeButton.prototype.setMode = function setMode( modeKey ){ + return this._setModeByIndex( this._getModeIndex( modeKey ) ); + }; + /** reset to the initial mode */ + ModeButton.prototype.reset = function reset(){ + this.currModeIndex = 0; + if( this.options.initialMode ){ + this.currModeIndex = this._getModeIndex( this.options.initialMode ); + } + return this._setModeByIndex( this.currModeIndex ); + }; + /** manually call the click handler of the given mode */ + ModeButton.prototype.callModeFn = function callModeFn( modeKey ){ var modeFn = this.getMode( modeKey ).onclick; if( modeFn && jQuery.type( modeFn === 'function' ) ){ - return modeFn.call( this ); + // call with the element as context (std jquery pattern) + modeFn.call( this.$element.get(0) ); + return this; } return undefined; }; @@ -861,26 +894,32 @@ // as jq plugin jQuery.fn.extend({ modeButton : function $modeButton( options ){ - var nonOptionsArgs = jQuery.makeArray( arguments ).slice( 1 ); + if( !this.size() ){ return this; } + //TODO: does map still work with jq multi selection (i.e. $( '.class-for-many-btns' ).modeButton)? - return this.map( function(){ - var $this = $( this ), - data = $this.data( 'mode-button' ); + if( jQuery.type( options ) === 'object' ){ + return this.map( function(){ + var $this = $( this ); + $this.data( 'mode-button', new ModeButton( $this, options ) ); + return this; + }); + } - if( jQuery.type( options ) === 'object' ){ - data = new ModeButton( $this, options ); - $this.data( 'mode-button', data ); + var $first = $( this[0] ), + button = $first.data( 'mode-button' ); + console.debug( 'first, button', $first, button ); - } else if( data && jQuery.type( options ) === 'string' ){ - var fn = data[ options ]; - if( jQuery.type( fn ) === 'function' ){ - return fn.apply( data, nonOptionsArgs ); - } - } else if ( data ){ - return data; + if( !button ){ + throw new Error( 'modeButton needs an options object or string name of a function' ); + } + + if( button && jQuery.type( options ) === 'string' ){ + var fnName = options; + if( button && jQuery.type( button[ fnName ] ) === 'function' ){ + return button[ fnName ].apply( button, jQuery.makeArray( arguments ).slice( 1 ) ); } - return this; - }); + } + return button; } }); }()); diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 7ebec9da47844efbf37942faab3809cb0169e5c2 static/scripts/packed/mvc/ui.js --- a/static/scripts/packed/mvc/ui.js +++ b/static/scripts/packed/mvc/ui.js @@ -1,1 +1,1 @@ -var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b;if(!this.$button.size()){this.$button=$("<div/>")}this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var c=this;function a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.create=function _create(b,a){return new PopupMenu(b,a)};PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((!a.disabled&&a.target)?(' target="'+a.target+'"'):("")),' href="',((!a.disabled&&a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};function LoadingIndicator(a,c){var 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b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}(function(){function a(j,p){var d=27,m=13,c=$(j),e=true,g={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(q){},minSearchLen:0,escWillClear:true,oninit:function(){}};function i(q){var r=$(this).parent().children("input");r.val("");r.trigger("clear:searchInput");p.onclear()}function o(r,q){$(this).trigger("search:searchInput",q);if(typeof p.onfirstsearch==="function"&&e){e=false;p.onfirstsearch(q)}else{p.onsearch(q)}}function f(){return['<input type="text" name="',p.name,'" placeholder="',p.placeholder,'" ','class="search-query ',p.classes,'" ',"/>"].join("")}function l(){return 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a(this,c)})}})}());(function(){function b(m,l){this.currModeIndex=0;return this.init(m,l)}b.prototype.DATA_KEY="mode-button";b.prototype.defaults={modes:[{mode:"default"}]};b.prototype.init=function f(m,l){l=l||{};this.$element=$(m);this.options=jQuery.extend(true,{},this.defaults,l);var o=this;this.$element.click(function n(p){o.callModeFn();o._incModeIndex();$(this).html(o.options.modes[o.currModeIndex].html)});this.currModeIndex=0;if(this.options.initialMode){this.currModeIndex=this._getModeIndex(this.options.initialMode)}return this};b.prototype._getModeIndex=function j(l){for(var m=0;m<this.options.modes.length;m+=1){if(this.options.modes[m].mode===l){return m}}throw new Error("mode not found: "+l)};b.prototype.getCurrMode=function a(){return this.options.modes[this.currModeIndex]};b.prototype.getMode=function g(l){if(!l){return this.getCurrMode()}return this.options.modes[(this._getModeIndex(l))]};b.prototype.hasMode=function k(l){return !!this.getMode(l)};b.prototype.currentMode=function e(){return this.options.modes[this.currModeIndex]};b.prototype.setMode=function c(m){var l=this.getMode(m);this.$element.html(l.html||null);return this};b.prototype._incModeIndex=function d(){this.currModeIndex+=1;if(this.currModeIndex>=this.options.modes.length){this.currModeIndex=0}return this};b.prototype.callModeFn=function h(l){var m=this.getMode(l).onclick;if(m&&jQuery.type(m==="function")){return m.call(this)}return undefined};jQuery.fn.extend({modeButton:function i(m){var l=jQuery.makeArray(arguments).slice(1);return this.map(function(){var p=$(this),o=p.data("mode-button");if(jQuery.type(m)==="object"){o=new b(p,m);p.data("mode-button",o)}else{if(o&&jQuery.type(m)==="string"){var n=o[m];if(jQuery.type(n)==="function"){return n.apply(o,l)}}else{if(o){return o}}}return this})}})}());function dropDownSelect(b,c){c=c||((!_.isEmpty(b))?(b[0]):(""));var a=$(['<div class="dropdown-select btn-group">','<button type="button" class="btn btn-default">','<span class="dropdown-select-selected">'+c+"</span>","</button>","</div>"].join("\n"));if(b&&b.length>1){a.find("button").addClass("dropdown-toggle").attr("data-toggle","dropdown").append(' <span class="caret"></span>');a.append(['<ul class="dropdown-menu" role="menu">',_.map(b,function(e){return['<li><a href="javascript:void(0)">',e,"</a></li>"].join("")}).join("\n"),"</ul>"].join("\n"))}function d(g){var h=$(this),f=h.parents(".dropdown-select"),e=h.text();f.find(".dropdown-select-selected").text(e);f.trigger("change.dropdown-select",e)}a.find("a").click(d);return a}(function(){function e(k,j){return this.init(k,j)}e.prototype.DATA_KEY="filter-control";e.prototype.init=function g(k,j){j=j||{filters:[]};this.$element=$(k).addClass("filter-control btn-group");this.options=jQuery.extend(true,{},this.defaults,j);this.currFilter=this.options.filters[0];return this.render()};e.prototype.render=function d(){this.$element.empty().append([this._renderKeySelect(),this._renderOpSelect(),this._renderValueInput()]);return this};e.prototype._renderKeySelect=function a(){var j=this;var k=this.options.filters.map(function(l){return l.key});this.$keySelect=dropDownSelect(k,this.currFilter.key).addClass("filter-control-key").on("change.dropdown-select",function(m,l){j.currFilter=_.findWhere(j.options.filters,{key:l});j.render()._triggerChange()});return this.$keySelect};e.prototype._renderOpSelect=function i(){var j=this,k=this.currFilter.ops;this.$opSelect=dropDownSelect(k,k[0]).addClass("filter-control-op").on("change.dropdown-select",function(m,l){j._triggerChange()});return this.$opSelect};e.prototype._renderValueInput=function c(){var j=this;if(this.currFilter.values){this.$valueSelect=dropDownSelect(this.currFilter.values,this.currFilter.values[0]).on("change.dropdown-select",function(l,k){j._triggerChange()})}else{this.$valueSelect=$("<input/>").addClass("form-control").on("change",function(k,l){j._triggerChange()})}this.$valueSelect.addClass("filter-control-value");return this.$valueSelect};e.prototype.val=function b(){var k=this.$element.find(".filter-control-key .dropdown-select-selected").text(),m=this.$element.find(".filter-control-op .dropdown-select-selected").text(),j=this.$element.find(".filter-control-value"),l=(j.hasClass("dropdown-select"))?(j.find(".dropdown-select-selected").text()):(j.val());return{key:k,op:m,value:l}};e.prototype._triggerChange=function h(){this.$element.trigger("change.filter-control",this.val())};jQuery.fn.extend({filterControl:function f(k){var j=jQuery.makeArray(arguments).slice(1);return this.map(function(){var n=$(this),m=n.data(e.prototype.DATA_KEY);if(jQuery.type(k)==="object"){m=new e(n,k);n.data(e.prototype.DATA_KEY,m)}if(m&&jQuery.type(k)==="string"){var l=m[k];if(jQuery.type(l)==="function"){return l.apply(m,j)}}return this})}})}());(function(){function i(o,n){this.numPages=null;this.currPage=0;return this.init(o,n)}i.prototype.DATA_KEY="pagination";i.prototype.defaults={startingPage:0,perPage:20,totalDataSize:null,currDataSize:null};i.prototype.init=function g(n,o){o=o||{};this.$element=n;this.options=jQuery.extend(true,{},this.defaults,o);this.currPage=this.options.startingPage;if(this.options.totalDataSize!==null){this.numPages=Math.ceil(this.options.totalDataSize/this.options.perPage);if(this.currPage>=this.numPages){this.currPage=this.numPages-1}}this.$element.data(i.prototype.DATA_KEY,this);this._render();return this};function m(n){return $(['<li><a href="javascript:void(0);">',n,"</a></li>"].join(""))}i.prototype._render=function e(){if(this.options.totalDataSize===0){return this}if(this.numPages===1){return this}if(this.numPages>0){this._renderPages();this._scrollToActivePage()}else{this._renderPrevNext()}return this};i.prototype._renderPrevNext=function b(){var o=this,p=m("Prev"),n=m("Next"),q=$("<ul/>").addClass("pagination pagination-prev-next");if(this.currPage===0){p.addClass("disabled")}else{p.click(function(){o.prevPage()})}if((this.numPages&&this.currPage===(this.numPages-1))||(this.options.currDataSize&&this.options.currDataSize<this.options.perPage)){n.addClass("disabled")}else{n.click(function(){o.nextPage()})}this.$element.html(q.append([p,n]));return this.$element};i.prototype._renderPages=function a(){var n=this,q=$("<div>").addClass("pagination-scroll-container"),s=$("<ul/>").addClass("pagination pagination-page-list"),r=function(t){n.goToPage($(this).data("page"))};for(var o=0;o<this.numPages;o+=1){var p=m(o+1).attr("data-page",o).click(r);if(o===this.currPage){p.addClass("active")}s.append(p)}return this.$element.html(q.html(s))};i.prototype._scrollToActivePage=function l(){var p=this.$element.find(".pagination-scroll-container");if(!p.size()){return this}var o=this.$element.find("li.active"),n=p.width()/2;p.scrollLeft(p.scrollLeft()+o.position().left-n);return this};i.prototype.goToPage=function j(n){if(n<=0){n=0}if(this.numPages&&n>=this.numPages){n=this.numPages-1}if(n===this.currPage){return this}this.currPage=n;this.$element.trigger("pagination.page-change",this.currPage);this._render();return this};i.prototype.prevPage=function c(){return this.goToPage(this.currPage-1)};i.prototype.nextPage=function h(){return this.goToPage(this.currPage+1)};i.prototype.page=function f(){return this.currPage};i.create=function k(n,o){return new i(n,o)};jQuery.fn.extend({pagination:function d(o){var n=jQuery.makeArray(arguments).slice(1);if(jQuery.type(o)==="object"){return this.map(function(){i.create($(this),o);return this})}var q=$(this[0]),r=q.data(i.prototype.DATA_KEY);if(r){if(jQuery.type(o)==="string"){var p=r[o];if(jQuery.type(p)==="function"){return p.apply(r,n)}}else{return r}}return undefined}})}());(function(){var g={renameColumns:false,columnNames:[],commentChar:"#",hideCommentRows:false,includePrompts:true,topLeftContent:"Columns:"},s="peek-control.change",t="peek-control.rename",l="peek-control",v="control",f="control-prompt",c="selected",n="disabled",u="button",q="renamable-header",p="column-index",a="column-name";function i(w){if(w.disabled&&jQuery.type(w.disabled)!=="array"){throw new Error('"disabled" must be defined as an array of indeces: '+JSON.stringify(w))}if(w.multiselect&&w.selected&&jQuery.type(w.selected)!=="array"){throw new Error('Mulitselect rows need an array for "selected": '+JSON.stringify(w))}if(!w.label||!w.id){throw new Error("Peek controls need a label and id for each control row: "+JSON.stringify(w))}if(w.disabled&&w.disabled.indexOf(w.selected)!==-1){throw new Error("Selected column is in the list of disabled columns: "+JSON.stringify(w))}return w}function o(x,w){return $("<div/>").addClass(u).text(x.label)}function k(x,w){var y=$("<td/>").html(o(x,w)).attr("data-"+p,w);if(x.disabled&&x.disabled.indexOf(w)!==-1){y.addClass(n)}return y}function e(y,z,w){var x=y.children("."+u);if(y.hasClass(c)){x.html((z.selectedText!==undefined)?(z.selectedText):(z.label))}else{x.html((z.unselectedText!==undefined)?(z.unselectedText):(z.label))}}function h(z,x){var y=k(z,x);if(z.selected===x){y.addClass(c)}e(y,z,x);if(!y.hasClass(n)){y.click(function w(D){var E=$(this);if(!E.hasClass(c)){var A=E.parent().children("."+c).removeClass(c);A.each(function(){e($(this),z,x)});E.addClass(c);e(E,z,x);var C={},B=E.parent().attr("id"),F=E.data(p);C[B]=F;E.parents(".peek").trigger(s,C)}})}return y}function m(z,x){var y=k(z,x);if(z.selected&&z.selected.indexOf(x)!==-1){y.addClass(c)}e(y,z,x);if(!y.hasClass(n)){y.click(function w(D){var E=$(this);E.toggleClass(c);e(E,z,x);var C=E.parent().find("."+c).map(function(G,H){return $(H).data(p)});var B={},A=E.parent().attr("id"),F=jQuery.makeArray(C);B[A]=F;E.parents(".peek").trigger(s,B)})}return y}function j(y,z){var w=[];for(var x=0;x<y;x+=1){w.push(z.multiselect?m(z,x):h(z,x))}return w}function r(y,z,x){var A=$("<tr/>").attr("id",z.id).addClass(v);if(x){var w=$("<td/>").addClass(f).text(z.label+":");A.append(w)}A.append(j(y,z));return A}function b(E){E=jQuery.extend(true,{},g,E);var D=$(this).addClass(l),A=D.find("table"),z=A.find("th").size(),C=A.find("tr").size(),w=A.find("td[colspan]").map(function(H,F){var G=$(this);if(G.text()&&G.text().match(new RegExp("^"+E.commentChar))){return $(this).css("color","grey").parent().get(0)}return null});if(E.hideCommentRows){w.hide();C-=w.size()}if(E.includePrompts){var y=$("<th/>").addClass("top-left").text(E.topLeftContent).attr("rowspan",C);A.find("tr").first().prepend(y)}var B=A.find("th:not(.top-left)").each(function(G,I){var H=$(this),J=H.text().replace(/^\d+\.*/,""),F=E.columnNames[G]||J;H.attr("data-"+a,F).text((G+1)+((F)?("."+F):("")))});if(E.renameColumns){B.addClass(q).click(function x(){var G=$(this),F=G.index()+(E.includePrompts?0:1),I=G.data(a),H=prompt("New column name:",I);if(H!==null&&H!==I){G.text(F+(H?("."+H):"")).data(a,H).attr("data-",a,H);var J=jQuery.makeArray(G.parent().children("th:not(.top-left)").map(function(){return $(this).data(a)}));G.parents(".peek").trigger(t,J)}})}E.controls.forEach(function(G,F){i(G);var H=r(z,G,E.includePrompts);A.find("tbody").append(H)});return this}jQuery.fn.extend({peekControl:function d(w){return this.map(function(){return b.call(this,w)})}})}()); \ No newline at end of file +var IconButton=Backbone.Model.extend({defaults:{title:"",icon_class:"",on_click:null,menu_options:null,is_menu_button:true,id:null,href:null,target:null,enabled:true,visible:true,tooltip_config:{}}});var IconButtonView=Backbone.View.extend({initialize:function(){this.model.attributes.tooltip_config={placement:"bottom"};this.model.bind("change",this.render,this)},render:function(){this.$el.tooltip("hide");var a=this.template(this.model.toJSON());a.tooltip(this.model.get("tooltip_config"));this.$el.replaceWith(a);this.setElement(a);return this},events:{click:"click"},click:function(a){if(_.isFunction(this.model.get("on_click"))){this.model.get("on_click")(a);return false}return true},template:function(b){var a='title="'+b.title+'" class="icon-button';if(b.is_menu_button){a+=" menu-button"}a+=" "+b.icon_class;if(!b.enabled){a+="_disabled"}a+='"';if(b.id){a+=' id="'+b.id+'"'}a+=' href="'+b.href+'"';if(b.target){a+=' target="'+b.target+'"'}if(!b.visible){a+=' style="display: none;"'}if(b.enabled){a="<a "+a+"/>"}else{a="<span "+a+"/>"}return $(a)}});var IconButtonCollection=Backbone.Collection.extend({model:IconButton});var IconButtonMenuView=Backbone.View.extend({tagName:"div",initialize:function(){this.render()},render:function(){var a=this;this.collection.each(function(d){var b=$("<a/>").attr("href","javascript:void(0)").attr("title",d.attributes.title).addClass("icon-button menu-button").addClass(d.attributes.icon_class).appendTo(a.$el).click(d.attributes.on_click);if(d.attributes.tooltip_config){b.tooltip(d.attributes.tooltip_config)}var c=d.get("options");if(c){make_popupmenu(b,c)}});return this}});var create_icon_buttons_menu=function(b,a){if(!a){a={}}var c=new IconButtonCollection(_.map(b,function(d){return new IconButton(_.extend(d,a))}));return new IconButtonMenuView({collection:c})};var Grid=Backbone.Collection.extend({});var GridView=Backbone.View.extend({});var PopupMenu=Backbone.View.extend({initialize:function(b,a){this.$button=b;if(!this.$button.size()){this.$button=$("<div/>")}this.options=a||[];var c=this;this.$button.click(function(d){$(".popmenu-wrapper").remove();c._renderAndShow(d);return false})},_renderAndShow:function(a){this.render();this.$el.appendTo("body").css(this._getShownPosition(a)).show();this._setUpCloseBehavior()},render:function(){this.$el.addClass("popmenu-wrapper").hide().css({position:"absolute"}).html(this.template(this.$button.attr("id"),this.options));if(this.options.length){var a=this;this.$el.find("li").each(function(c,b){var d=a.options[c];if(d.func){$(this).children("a.popupmenu-option").click(function(e){d.func.call(a,e,d)})}})}return this},template:function(b,a){return['<ul id="',b,'-menu" class="dropdown-menu">',this._templateOptions(a),"</ul>"].join("")},_templateOptions:function(a){if(!a.length){return"<li>(no options)</li>"}return _.map(a,function(d){if(d.divider){return'<li class="divider"></li>'}else{if(d.header){return['<li class="head"><a href="javascript:void(0);">',d.html,"</a></li>"].join("")}}var c=d.href||"javascript:void(0);",e=(d.target)?(' target="'+d.target+'"'):(""),b=(d.checked)?('<span class="fa fa-check"></span>'):("");return['<li><a class="popupmenu-option" href="',c,'"',e,">",b,d.html,"</a></li>"].join("")}).join("")},_getShownPosition:function(b){var c=this.$el.width();var a=b.pageX-c/2;a=Math.min(a,$(document).scrollLeft()+$(window).width()-c-5);a=Math.max(a,$(document).scrollLeft()+5);return{top:b.pageY,left:a}},_setUpCloseBehavior:function(){var c=this;function a(e){$(document).off("click.close_popup");if(window.parent!==window){try{$(window.parent.document).off("click.close_popup")}catch(d){}}else{try{$("iframe#galaxy_main").contents().off("click.close_popup")}catch(d){}}c.remove()}$("html").one("click.close_popup",a);if(window.parent!==window){try{$(window.parent.document).find("html").one("click.close_popup",a)}catch(b){}}else{try{$("iframe#galaxy_main").contents().one("click.close_popup",a)}catch(b){}}},addItem:function(b,a){a=(a>=0)?a:this.options.length;this.options.splice(a,0,b);return this},removeItem:function(a){if(a>=0){this.options.splice(a,1)}return this},findIndexByHtml:function(b){for(var a=0;a<this.options.length;a++){if(_.has(this.options[a],"html")&&(this.options[a].html===b)){return a}}return null},findItemByHtml:function(a){return this.options[(this.findIndexByHtml(a))]},toString:function(){return"PopupMenu"}});PopupMenu.create=function _create(b,a){return new PopupMenu(b,a)};PopupMenu.make_popupmenu=function(b,c){var a=[];_.each(c,function(f,d){var e={html:d};if(f===null){e.header=true}else{if(jQuery.type(f)==="function"){e.func=f}}a.push(e)});return new PopupMenu($(b),a)};PopupMenu.convertLinksToOptions=function(c,a){c=$(c);a=a||"a";var b=[];c.find(a).each(function(g,e){var f={},d=$(g);f.html=d.text();if(d.attr("href")){var j=d.attr("href"),k=d.attr("target"),h=d.attr("confirm");f.func=function(){if((h)&&(!confirm(h))){return}switch(k){case"_parent":window.parent.location=j;break;case"_top":window.top.location=j;break;default:window.location=j}}}b.push(f)});return b};PopupMenu.fromExistingDom=function(d,c,a){d=$(d);c=$(c);var b=PopupMenu.convertLinksToOptions(c,a);c.remove();return new PopupMenu(d,b)};PopupMenu.make_popup_menus=function(c,b,d){c=c||document;b=b||"div[popupmenu]";d=d||function(e,f){return"#"+e.attr("popupmenu")};var a=[];$(c).find(b).each(function(){var e=$(this),f=$(c).find(d(e,c));a.push(PopupMenu.fromDom(f,e));f.addClass("popup")});return a};var faIconButton=function(a){a=a||{};a.tooltipConfig=a.tooltipConfig||{placement:"bottom"};a.classes=["icon-btn"].concat(a.classes||[]);if(a.disabled){a.classes.push("disabled")}var b=['<a class="',a.classes.join(" "),'"',((a.title)?(' title="'+a.title+'"'):("")),((!a.disabled&&a.target)?(' target="'+a.target+'"'):("")),' href="',((!a.disabled&&a.href)?(a.href):("javascript:void(0);")),'">','<span class="fa ',a.faIcon,'"></span>',"</a>"].join("");var c=$(b).tooltip(a.tooltipConfig);if(_.isFunction(a.onclick)){c.click(a.onclick)}return c};function LoadingIndicator(a,c){var b=this;c=jQuery.extend({cover:false},c||{});function d(){var e=['<div class="loading-indicator">','<div class="loading-indicator-text">','<span class="fa fa-spinner fa-spin fa-lg"></span>','<span class="loading-indicator-message">loading...</span>',"</div>","</div>"].join("\n");var g=$(e).hide().css(c.css||{position:"fixed"}),f=g.children(".loading-indicator-text");if(c.cover){g.css({"z-index":2,top:a.css("top"),bottom:a.css("bottom"),left:a.css("left"),right:a.css("right"),opacity:0.5,"background-color":"white","text-align":"center"});f=g.children(".loading-indicator-text").css({"margin-top":"20px"})}else{f=g.children(".loading-indicator-text").css({margin:"12px 0px 0px 10px",opacity:"0.85",color:"grey"});f.children(".loading-indicator-message").css({margin:"0px 8px 0px 0px","font-style":"italic"})}return g}b.show=function(f,e,g){f=f||"loading...";e=e||"fast";b.$indicator=d().insertBefore(a);b.message(f);b.$indicator.fadeIn(e,g);return b};b.message=function(e){b.$indicator.find("i").text(e)};b.hide=function(e,f){e=e||"fast";if(b.$indicator&&b.$indicator.size()){b.$indicator.fadeOut(e,function(){b.$indicator.remove();if(f){f()}})}else{if(f){f()}}return b};return b}(function(){function a(j,p){var d=27,m=13,c=$(j),e=true,g={initialVal:"",name:"search",placeholder:"search",classes:"",onclear:function(){},onfirstsearch:null,onsearch:function(q){},minSearchLen:0,escWillClear:true,oninit:function(){}};function i(q){var r=$(this).parent().children("input");r.val("");r.trigger("clear:searchInput");p.onclear()}function o(r,q){$(this).trigger("search:searchInput",q);if(typeof p.onfirstsearch==="function"&&e){e=false;p.onfirstsearch(q)}else{p.onsearch(q)}}function f(){return['<input type="text" name="',p.name,'" placeholder="',p.placeholder,'" ','class="search-query ',p.classes,'" ',"/>"].join("")}function l(){return $(f()).focus(function(q){$(this).select()}).keyup(function(r){if(r.which===d&&p.escWillClear){i.call(this,r)}else{var q=$(this).val();if((r.which===m)||(p.minSearchLen&&q.length>=p.minSearchLen)){o.call(this,r,q)}else{if(!q.length){i.call(this,r)}}}}).val(p.initialVal)}function k(){return $(['<span class="search-clear fa fa-times-circle" ','title="',_l("clear search 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o}})}());function dropDownSelect(b,c){c=c||((!_.isEmpty(b))?(b[0]):(""));var a=$(['<div class="dropdown-select btn-group">','<button type="button" class="btn btn-default">','<span class="dropdown-select-selected">'+c+"</span>","</button>","</div>"].join("\n"));if(b&&b.length>1){a.find("button").addClass("dropdown-toggle").attr("data-toggle","dropdown").append(' <span class="caret"></span>');a.append(['<ul class="dropdown-menu" role="menu">',_.map(b,function(e){return['<li><a href="javascript:void(0)">',e,"</a></li>"].join("")}).join("\n"),"</ul>"].join("\n"))}function d(g){var h=$(this),f=h.parents(".dropdown-select"),e=h.text();f.find(".dropdown-select-selected").text(e);f.trigger("change.dropdown-select",e)}a.find("a").click(d);return a}(function(){function e(k,j){return this.init(k,j)}e.prototype.DATA_KEY="filter-control";e.prototype.init=function g(k,j){j=j||{filters:[]};this.$element=$(k).addClass("filter-control 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j=this;if(this.currFilter.values){this.$valueSelect=dropDownSelect(this.currFilter.values,this.currFilter.values[0]).on("change.dropdown-select",function(l,k){j._triggerChange()})}else{this.$valueSelect=$("<input/>").addClass("form-control").on("change",function(k,l){j._triggerChange()})}this.$valueSelect.addClass("filter-control-value");return this.$valueSelect};e.prototype.val=function b(){var k=this.$element.find(".filter-control-key .dropdown-select-selected").text(),m=this.$element.find(".filter-control-op .dropdown-select-selected").text(),j=this.$element.find(".filter-control-value"),l=(j.hasClass("dropdown-select"))?(j.find(".dropdown-select-selected").text()):(j.val());return{key:k,op:m,value:l}};e.prototype._triggerChange=function h(){this.$element.trigger("change.filter-control",this.val())};jQuery.fn.extend({filterControl:function f(k){var j=jQuery.makeArray(arguments).slice(1);return this.map(function(){var n=$(this),m=n.data(e.prototype.DATA_KEY);if(jQuery.type(k)==="object"){m=new e(n,k);n.data(e.prototype.DATA_KEY,m)}if(m&&jQuery.type(k)==="string"){var l=m[k];if(jQuery.type(l)==="function"){return l.apply(m,j)}}return this})}})}());(function(){function i(o,n){this.numPages=null;this.currPage=0;return this.init(o,n)}i.prototype.DATA_KEY="pagination";i.prototype.defaults={startingPage:0,perPage:20,totalDataSize:null,currDataSize:null};i.prototype.init=function g(n,o){o=o||{};this.$element=n;this.options=jQuery.extend(true,{},this.defaults,o);this.currPage=this.options.startingPage;if(this.options.totalDataSize!==null){this.numPages=Math.ceil(this.options.totalDataSize/this.options.perPage);if(this.currPage>=this.numPages){this.currPage=this.numPages-1}}this.$element.data(i.prototype.DATA_KEY,this);this._render();return this};function m(n){return $(['<li><a href="javascript:void(0);">',n,"</a></li>"].join(""))}i.prototype._render=function e(){if(this.options.totalDataSize===0){return 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E=$(this);E.toggleClass(c);e(E,z,x);var C=E.parent().find("."+c).map(function(G,H){return $(H).data(p)});var B={},A=E.parent().attr("id"),F=jQuery.makeArray(C);B[A]=F;E.parents(".peek").trigger(s,B)})}return y}function j(y,z){var w=[];for(var x=0;x<y;x+=1){w.push(z.multiselect?m(z,x):h(z,x))}return w}function r(y,z,x){var A=$("<tr/>").attr("id",z.id).addClass(v);if(x){var w=$("<td/>").addClass(f).text(z.label+":");A.append(w)}A.append(j(y,z));return A}function b(E){E=jQuery.extend(true,{},g,E);var D=$(this).addClass(l),A=D.find("table"),z=A.find("th").size(),C=A.find("tr").size(),w=A.find("td[colspan]").map(function(H,F){var G=$(this);if(G.text()&&G.text().match(new RegExp("^"+E.commentChar))){return $(this).css("color","grey").parent().get(0)}return null});if(E.hideCommentRows){w.hide();C-=w.size()}if(E.includePrompts){var y=$("<th/>").addClass("top-left").text(E.topLeftContent).attr("rowspan",C);A.find("tr").first().prepend(y)}var B=A.find("th:not(.top-left)").each(function(G,I){var H=$(this),J=H.text().replace(/^\d+\.*/,""),F=E.columnNames[G]||J;H.attr("data-"+a,F).text((G+1)+((F)?("."+F):("")))});if(E.renameColumns){B.addClass(q).click(function x(){var G=$(this),F=G.index()+(E.includePrompts?0:1),I=G.data(a),H=prompt("New column name:",I);if(H!==null&&H!==I){G.text(F+(H?("."+H):"")).data(a,H).attr("data-",a,H);var J=jQuery.makeArray(G.parent().children("th:not(.top-left)").map(function(){return $(this).data(a)}));G.parents(".peek").trigger(t,J)}})}E.controls.forEach(function(G,F){i(G);var H=r(z,G,E.includePrompts);A.find("tbody").append(H)});return this}jQuery.fn.extend({peekControl:function d(w){return this.map(function(){return b.call(this,w)})}})}()); \ No newline at end of file diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 7ebec9da47844efbf37942faab3809cb0169e5c2 templates/webapps/galaxy/history/original_view.mako --- a/templates/webapps/galaxy/history/original_view.mako +++ /dev/null @@ -1,173 +0,0 @@ -<%namespace file="/display_common.mako" import="get_history_link, get_controller_name" /> -<%namespace file="/root/history_common.mako" import="render_dataset" /> -<%namespace file="/tagging_common.mako" import="render_individual_tagging_element, render_community_tagging_element" /> - -<%! - def inherit(context): - if context.get('use_panels'): - return '/webapps/galaxy/base_panels.mako' - else: - return '/base.mako' -%> -<%inherit file="${inherit(context)}"/> - -<%def name="javascripts()"> - ${parent.javascripts()} - ${h.js( "libs/jquery/jstorage" )} - <script type="text/javascript"> - $(function() { - init_history_items( $("div.historyItemWrapper"), false, "nochanges" ); - $( '#switch-to-link' ).click( function( event ){ - var galaxy = window.Galaxy || window.parent.Galaxy; - if( galaxy ){ - galaxy.currHistoryPanel.switchToHistory( '${ trans.security.encode_id( history.id ) }' ); - } - }); - $( '#refresh' ).click( function( event ){ window.location.reload( true ); }) - }); - </script> -</%def> - -<%def name="stylesheets()"> - ${parent.stylesheets()} - ${h.css( "history", "autocomplete_tagging" )} - - <style type="text/css"> - - /* these don't appear to be used? */ - .page-body - { - padding: 10px; - float: left; - width: 65%; - } - .page-meta - { - float: right; - width: 27%; - padding: 0.5em; - margin: 0.25em; - vertical-align: text-top; - border: 2px solid #DDDDDD; - border-top: 4px solid #DDDDDD; - } - - - body { - padding: 0px; - margin: 0px; - } - - div.unified-panel-body { - position: absolute; - top: 0px; - width: 100%; - } - - #history-name-area { - margin: 12px 0px 0px 16px; - font-size: 120%; - } - #top-links { - margin: 4px 0px 8px 16px; - } - - .historyItemContainer { - /*padding-right: 3px;*/ - } - .historyItemBody { - display: none; - } - div.historyItemWrapper { - margin: 0px 4px 0px 4px ; - border-left: 1px solid #999999; - border-right: 1px solid #999999; - } - /* TODO: unify with other history css and into .less */ - </style> - - <noscript> - <style> - .historyItemBody { - display: block; - } - </style> - </noscript> -</%def> - -<%def name="init()"> -<% - self.has_left_panel=False - self.has_right_panel=False - self.message_box_visible=False -%> -</%def> - -<%def name="body()"> - ${center_panel()} -</%def> - -<%def name="center_panel()"> - ## Get URL to other histories owned by user that owns this history. - <% - ##TODO: is there a better way to create this URL? Can't use 'f-username' as a key b/c it's not a valid identifier. - href_to_published_histories = h.url_for( controller='/history', action='list_published') - if history.user is not None: - href_to_user_histories = h.url_for( controller='/history', action='list_published', xxx=history.user.username).replace( 'xxx', 'f-username') - else: - href_to_user_histories = h.url_for( controller='/history', action='list_published' )##should this instead be be None or empty string? - %> - - <div class="unified-panel-body"> - <div style="overflow: auto; height: 100%;"> - ## Render view of history. - <div id="history-name-area" class="historyLinks" style="color: gray; font-weight: bold; padding: 0px 0px 5px 0px"> - <div id="history-name">${history.get_display_name()}</div> - </div> - - <div id="top-links" class="historyLinks" style="padding: 0px 0px 5px 0px"> - %if not history.purged and history.user != trans.user: - ##TODO: need to remove _top - <a href="${h.url_for(controller='history', action='imp', id=trans.security.encode_id(history.id) )}" - >import and start using history</a> | - <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | - %endif - %if not history.purged and history.user == trans.user: - <a id="switch-to-link" href="javascript:void(0)">${_('switch to this history')}</a> | - <a id="refresh" href="javascript:void(0)" >${_('refresh')}</a> | - %endif - %if show_deleted: - <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=False, use_panels=use_panels )}">${_('hide deleted')}</a> | - %else: - <a href="${h.url_for(controller='history', action='view', id=trans.security.encode_id(history.id), show_deleted=True, use_panels=use_panels )}">${_('show deleted')}</a> | - %endif - <a href="#" class="toggle">collapse all</a> - </div> - - %if history.deleted: - <div class="warningmessagesmall"> - ${_('You are currently viewing a deleted history!')} - </div> - <p></p> - %endif - - %if not datasets: - <div class="infomessagesmall" id="emptyHistoryMessage"> - - %else: - ## Render requested datasets, ordered from newest to oldest - %for data in datasets: - %if data.visible: - <div class="historyItemContainer visible-right-border" id="historyItemContainer-${data.id}"> - ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing=False )} - </div> - %endif - %endfor - - <div class="infomessagesmall" id="emptyHistoryMessage" style="display:none;"> - %endif - ${_("Your history is empty. Click 'Get Data' on the left pane to start")} - </div> - </div> - </div> -</%def> diff -r c85f8fb5d63e667b63e10cdce518254f56002f55 -r 7ebec9da47844efbf37942faab3809cb0169e5c2 templates/webapps/galaxy/history/view.mako --- a/templates/webapps/galaxy/history/view.mako +++ b/templates/webapps/galaxy/history/view.mako @@ -77,6 +77,7 @@ %endif <script type="text/javascript"> + ##TODO: remove when Galaxy is either ensured or removed from the history panel var using_panels = ${ 'false' if not use_panels else 'true' }; %if not use_panels: window.Galaxy = {}; @@ -87,113 +88,107 @@ ## ---------------------------------------------------------------------------- <%def name="center_panel()"> +<% + show_deleted = context.get( 'show_deleted', None ) + show_hidden = context.get( 'show_hidden', None ) + + user_is_owner_json = 'true' if user_is_owner else 'false' + show_deleted_json = h.to_json_string( show_deleted ) + show_hidden_json = h.to_json_string( show_hidden ) + + imp_with_deleted_url = h.url_for( controller='history', action='imp', id=history['id'], all_datasets=True ) + imp_without_deleted_url = h.url_for( controller='history', action='imp', id=history['id'] ) +%> + <div id="header" class="clear"><div id="history-view-controls" class="pull-right"> - <% - show_deleted = context.get( 'show_deleted', None ) - show_hidden = context.get( 'show_hidden', None ) - - show_deleted_js = 'true' if show_deleted == True else ( 'null' if show_deleted == None else 'false' ) - show_hidden_js = 'true' if show_hidden == True else ( 'null' if show_hidden == None else 'false' ) - print 'user_is_owner:', user_is_owner - %> %if not user_is_owner and not history[ 'purged' ]: - <a id="import" class="btn btn-default" style="display: none;" - href="${h.url_for( controller='history', action='imp', id=history['id'], all_datasets=show_deleted )}"> - ${_('Import and start using history')} - </a> + <button id="import" class="btn btn-default"></button> %endif - <button id="toggle-deleted" class="btn btn-default"> - ${_('Exclude deleted') if show_deleted else _('Include deleted')} - </button> - <button id="toggle-hidden" class="btn btn-default"> - ${_('Exclude hidden') if show_hidden else _('Include hidden')} - </button> + <button id="toggle-deleted" class="btn btn-default"></button> + <button id="toggle-hidden" class="btn btn-default"></button></div></div><div id="history-${ history[ 'id' ] }" class="history-panel unified-panel-body" style="overflow: auto;"></div><script type="text/javascript"> + $(function(){ + $( '#toggle-deleted' ).modeButton({ + initialMode : "${ 'showing_deleted' if show_deleted else 'not_showing_deleted' }", + modes: [ + { mode: 'showing_deleted', html: _l( 'Exclude deleted' ) }, + { mode: 'not_showing_deleted', html: _l( 'Include deleted' ) } + ] + }).click( function(){ + // allow the 'include/exclude deleted' button to control whether the 'import' button includes deleted + // datasets when importing or not; when deleted datasets are shown, they'll be imported + $( '#import' ).modeButton( 'setMode', + $( this ).modeButton( 'current' ) === 'showing_deleted'? 'with_deleted': 'without_deleted' ) + }); + + $( '#toggle-hidden' ).modeButton({ + initialMode : "${ 'showing_hidden' if show_hidden else 'not_showing_hidden' }", + modes: [ + { mode: 'showing_hidden', html: _l( 'Exclude hidden' ) }, + { mode: 'not_showing_hidden', html: _l( 'Include hidden' ) } + ] + }); + + $( '#import' ).modeButton({ + switchModesOnClick : false, + initialMode : "${ 'with_deleted' if show_deleted else 'without_deleted' }", + modes: [ + { mode: 'with_deleted', html: _l( 'Import with deleted datasets and start using history' ), + onclick: function importWithDeleted(){ + window.location = '${imp_with_deleted_url}'; + } + }, + { mode: 'without_deleted', html: _l( 'Import and start using history' ), + onclick: function importWithoutDeleted(){ + window.location = '${imp_without_deleted_url}'; + } + }, + ] + }); + }); + var debugging = JSON.parse( sessionStorage.getItem( 'debugging' ) ) || false, userIsOwner = ${'true' if user_is_owner else 'false'}, historyJSON = ${h.to_json_string( history )}, hdaJSON = ${h.to_json_string( hdas )}; - window.hdaJSON = hdaJSON; - - $( '#toggle-deleted' ).modeButton({ - initialMode : (${ show_deleted_js })?( 'exclude' ):( 'include' ), - modes: [ - { mode: 'exclude', html: _l( 'Exclude deleted' ) }, - { mode: 'include', html: _l( 'Include deleted' ) } - ] - }).click( function(){ - // allow the 'include/exclude deleted' button to control whether the 'import' button includes deleted datasets - // when importing or not; when deleted datasets are shown, they'll be imported - var $importBtn = $( '#import' ); - if( $importBtn.size() ){ - // a bit hacky - var href = $importBtn.attr( 'href' ), - includeDeleted = $( this ).modeButton()[0].getMode().mode === 'exclude'; - href = href.replace( /all_datasets=True|False/, ( includeDeleted )?( 'True' ):( 'False' ) ); - $importBtn.attr( 'href', href ); - $importBtn.text( includeDeleted ? _l( 'Import with deleted datasets and start using history' ) - : _l( 'Import and start using history' ) ); - } - }); - - $( '#toggle-hidden' ).modeButton({ - initialMode : (${ show_hidden_js })?( 'exclude' ):( 'include' ), - modes: [ - { mode: 'exclude', html: _l( 'Exclude hidden' ) }, - { mode: 'include', html: _l( 'Include hidden' ) } - ] - }); - - ##TODO: move to mako - if( Galaxy.currUser.id !== historyJSON.user_id ){ - $( '#import' ).show(); - } + panelToUse = ( userIsOwner )? + ({ location: 'mvc/history/history-panel', className: 'HistoryPanel' }): + ({ location: 'mvc/history/readonly-history-panel', className: 'ReadOnlyHistoryPanel' }); require.config({ baseUrl : "${h.url_for( '/static/scripts' )}" - })([ - %if user_is_owner: - 'mvc/history/history-panel' - %else: - 'mvc/history/readonly-history-panel' - %endif - ${ } - ], function( panelMod ){ - //require([ "mvc/history/history-panel" ], function( historyPanel ){ - // history module is already in the dpn chain from the panel. We can re-scope it here. - var historyModel = require( 'mvc/history/history-model' ), - hdaBaseView = require( 'mvc/dataset/hda-base' ), - history = new historyModel.History( historyJSON, hdaJSON, { - logger: ( debugging )?( console ):( null ) + })([ panelToUse.location ], function( panelMod ){ + $(function(){ + var panelClass = panelMod[ panelToUse.className ], + // history module is already in the dpn chain from the panel. We can re-scope it here. + historyModel = require( 'mvc/history/history-model' ), + hdaBaseView = require( 'mvc/dataset/hda-base' ), + history = new historyModel.History( historyJSON, hdaJSON, { + logger: ( debugging )?( console ):( null ) + }); + + window.historyPanel = new panelClass({ + show_deleted : ${show_deleted_json}, + show_hidden : ${show_hidden_json}, + el : $( "#history-" + historyJSON.id ), + model : history, + onready : function(){ + var panel = this; + $( '#toggle-deleted' ).on( 'click', function(){ + panel.toggleShowDeleted(); + }); + $( '#toggle-hidden' ).on( 'click', function(){ + panel.toggleShowHidden(); + }); + this.render(); + } }); - - window.panelMod = panelMod; - %if user_is_owner: - window.panelClass = panelMod.HistoryPanel; - %else: - window.panelClass = panelMod.ReadOnlyHistoryPanel; - %endif - window.historyPanel = new panelClass({ - show_deleted : ${show_deleted_js}, - show_hidden : ${show_hidden_js}, - el : $( "#history-" + historyJSON.id ), - model : history, - onready : function(){ - var panel = this; - $( '#toggle-deleted' ).on( 'click', function(){ - panel.toggleShowDeleted(); - }); - $( '#toggle-hidden' ).on( 'click', function(){ - panel.toggleShowHidden(); - }); - this.render(); - } }); }); </script> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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