October 2014 - galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset 9bc08bc7f393
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5123ed7f1603/ Changeset: 5123ed7f1603 Branch: stable User: natefoo Date: 2014-10-23 14:00:16+00:00 Summary: Update tag latest_2014.10.06 for changeset 9bc08bc7f393 Affected #: 1 file diff -r 9bc08bc7f393362ee7e6cf1d04bb9d8cee68f2d8 -r 5123ed7f16037c67a66f90ce63ef5a15faab21c9 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -a7b2aabb27ffe5cc3216774ab01b18f13b4fc941 latest_2014.10.06 +9bc08bc7f393362ee7e6cf1d04bb9d8cee68f2d8 latest_2014.10.06 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: guerler: ToolForm: Pack scripts
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1f82617c0688/ Changeset: 1f82617c0688 User: guerler Date: 2014-10-23 13:54:05+00:00 Summary: ToolForm: Pack scripts Affected #: 2 files diff -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c -r 1f82617c06887e82e01175d24e45576da1e6ed92 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -283,6 +283,11 @@ console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').'); } + // deactivate dynamic fields + if (input_def.is_dynamic) { + this.app.incompatible = true; + } + // set field value if (input_def.value !== undefined) { field.value(input_def.value); diff -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c -r 1f82617c06887e82e01175d24e45576da1e6ed92 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){if(i.app.is_dynamic){i.app.rebuild()}var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.is_dynamic=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.is_dynamic){this.app.incompatible=true}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){if(i.app.is_dynamic){i.app.rebuild()}var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.is_dynamic=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: guerler: ToolForm: Add support for dynamic parameters, add tool version check
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/3b4784d5fc0d/ Changeset: 3b4784d5fc0d User: guerler Date: 2014-10-23 13:50:31+00:00 Summary: ToolForm: Add support for dynamic parameters, add tool version check Affected #: 14 files diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c client/galaxy/scripts/mvc/tools/tools-form.js --- a/client/galaxy/scripts/mvc/tools/tools-form.js +++ b/client/galaxy/scripts/mvc/tools/tools-form.js @@ -42,24 +42,11 @@ // creates the job handler this.job_handler = new ToolJobs(this); - // reset field list, which contains the input field elements - this.field_list = {}; - - // reset sequential input definition list, which contains the input definitions as provided from the api - this.input_list = {}; - - // reset input element list, which contains the dom elements of each input element (includes also the input field) - this.element_list = {}; - - // for now the initial tool model is parsed through the mako - this.model = this.options; - this.inputs = this.options.inputs; - // request history content and build form this.content = new ToolContent({ history_id : self.options.history_id, success : function() { - self._buildForm(); + self._buildForm(self.options); } }); }, @@ -137,7 +124,7 @@ }, // refresh form data - _refreshForm: function() { + rebuild: function() { // link this var self = this; @@ -161,6 +148,10 @@ url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', data : current_state, success : function(response) { + // rebuild form + self._rebuildForm(response); + + // log success console.debug('tools-form::_refreshForm() - Refreshed inputs/states.'); console.debug(response); }, @@ -171,11 +162,55 @@ }); }, + // rebuild the form elements + _rebuildForm: function(new_model) { + var self = this; + this.tree.matchModel(new_model, function(input_id, node) { + var input = self.input_list[input_id]; + if (input && input.options) { + if (JSON.stringify(input.options) != JSON.stringify(node.options)) { + // backup new options + input.options = node.options; + + // get/update field (currently only done for select fields) + var field = self.field_list[input_id]; + if (field.update && input.type == 'select') { + var new_options = []; + for (var i in node.options) { + var opt = node.options[i]; + if (opt.length > 2) { + new_options.push({ + 'label': opt[0], + 'value': opt[1] + }); + } + } + field.update(new_options); + console.debug('Updating options for ' + input_id); + } + } + } + }); + }, + // builds the tool form - _buildForm: function() { + _buildForm: function(options) { // link this var self = this; + // reset field list, which contains the input field elements + this.field_list = {}; + + // reset sequential input definition list, which contains the input definitions as provided from the api + this.input_list = {}; + + // reset input element list, which contains the dom elements of each input element (includes also the input field) + this.element_list = {}; + + // for now the initial tool model is parsed through the mako + this.model = options; + this.inputs = options.inputs; + // button menu var menu = new Ui.ButtonMenu({ icon : 'fa-gear', @@ -183,7 +218,7 @@ }); // configure button selection - if(this.options.biostar_url) { + if(options.biostar_url) { // add question option menu.addMenu({ icon : 'fa-question-circle', @@ -256,29 +291,30 @@ cls : 'btn btn-primary', floating : 'clear', onclick : function() { - //self._refreshForm(); + //self.rebuild(); self.job_handler.submit(); } }) } }); - // append form + // start form + this.$el.empty(); this.$el.append(this.portlet.$el); // append help - if (this.options.help != '') { - this.$el.append(ToolTemplate.help(this.options.help)); + if (options.help != '') { + this.$el.append(ToolTemplate.help(options.help)); } // append citations - if (this.options.citations) { + if (options.citations) { // append html this.$el.append(ToolTemplate.citations()); // fetch citations var citations = new CitationModel.ToolCitationCollection(); - citations.tool_id = this.options.id; + citations.tool_id = options.id; var citation_list_view = new CitationView.CitationListView({ collection: citations } ); citation_list_view.render(); citations.fetch(); diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -50,7 +50,7 @@ var input_def = jQuery.extend(true, {}, input); // create unique id - input_def.id = Utils.uuid(); + input_def.id = input.id = Utils.uuid(); // add to sequential list of inputs this.app.input_list[input_def.id] = input_def; @@ -208,7 +208,7 @@ _addRow: function(field_type, input_def) { // get id var id = input_def.id; - + // field wrapper var field = null; @@ -283,6 +283,11 @@ console.debug('tools-form::_addRow() : Auto matched field type (' + field_type + ').'); } + // deactivate dynamic fields + if (input_def.is_dynamic) { + this.app.incompatible = true; + } + // set field value if (input_def.value !== undefined) { field.value(input_def.value); @@ -380,6 +385,11 @@ extensions : input_def.extensions, multiple : input_def.multiple, onchange : function(dict) { + // rebuild the form + if (self.app.is_dynamic) { + self.app.rebuild(); + } + // pick the first content only (todo: maybe collect multiple meta information) var content_def = dict.values[0]; var content_id = content_def.id; @@ -485,7 +495,7 @@ _fieldSelect : function (input_def) { // check compatibility if (input_def.is_dynamic) { - this.app.incompatible = true; + this.app.is_dynamic = true; } // configure options fields diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c client/galaxy/scripts/mvc/tools/tools-template.js --- a/client/galaxy/scripts/mvc/tools/tools-template.js +++ b/client/galaxy/scripts/mvc/tools/tools-template.js @@ -30,7 +30,7 @@ if (njobs == 1) { njobs_text = '1 job has'; } else { - njobs_text = njobs + ' jobs have been'; + njobs_text = njobs + ' jobs have'; } // create template string diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -146,7 +146,48 @@ return this.job_ids && this.job_ids[job_input_id]; }, - /** Matches identifier from api response to input element + /** Matches identifier from api model to input elements + */ + matchModel: function(model, callback) { + // final result dictionary + var result = {}; + + // link this + var self = this; + + // search throughout response + function search (id, head) { + for (var i in head) { + var node = head[i]; + var index = node.name; + if (id != '') { + index = id + '|' + index; + } + if (node.type == 'repeat') { + for (var j in node.cache) { + search (index + '_' + j, node.cache[j]); + } + } else { + if (node.type == 'conditional') { + search (index, node.inputs); + } else { + var input_id = self.app.tree.job_ids[index]; + if (input_id) { + callback(input_id, node); + } + } + } + } + } + + // match all ids and return messages + search('', model.inputs); + + // return matched results + return result; + }, + + /** Matches identifier from api response to input elements */ matchResponse: function(response) { // final result dictionary diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c 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 @@ -131,6 +131,7 @@ """ api_type = "file" encoded_id = trans.security.encode_id( hda.id ) + # TODO: handle failed_metadata here as well return { 'id' : encoded_id, diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -510,16 +510,18 @@ trans.response.status = 500 return { 'error': 'Failed to get job information.' } - # check if job was identified + # load job parameters into incoming + tool_message = '' if job: try: job_params = job.get_param_values( trans.app, ignore_errors = True ) job_messages = tool.check_and_update_param_values( job_params, trans, update_values=False ) + tool_message = self._compare_tool_version(trans, tool, job) params_to_incoming( kwd, tool.inputs, job_params, trans.app ) except Exception, exception: trans.response.status = 500 return { 'error': str( exception ) } - + # create parameter object params = galaxy.util.Params( kwd, sanitize = False ) @@ -644,8 +646,52 @@ tool_model.update({ 'help' : tool_help, 'citations' : tool_citations, - 'biostar_url' : trans.app.config.biostar_url + 'biostar_url' : trans.app.config.biostar_url, + 'message' : tool_message }) # return enriched tool model return tool_model + + def _get_tool_components( self, trans, tool_id, tool_version=None, get_loaded_tools_by_lineage=False, set_selected=False ): + return self.get_toolbox().get_tool_components( tool_id, tool_version, get_loaded_tools_by_lineage, set_selected ) + + def _compare_tool_version( self, trans, tool, job ): + """ + Compares a tool version with the tool version from a job (from ToolRunne. + """ + id = job.tool_id + version = job.tool_version + message = '' + try: + select_field, tools, tool = self._get_tool_components( trans, id, tool_version=version, get_loaded_tools_by_lineage=False, set_selected=True ) + if tool is None: + trans.response.status = 500 + return { 'error': 'This dataset was created by an obsolete tool (%s). Can\'t re-run.' % id } + if ( tool.id != id and tool.old_id != id ) or tool.version != version: + if tool.id == id: + if version == None: + # for some reason jobs don't always keep track of the tool version. + message = '' + else: + message = 'This job was initially run with tool version "%s", which is currently not available. ' % version + if len( tools ) > 1: + message += 'You can re-run the job with the selected tool or choose another derivation of the tool.' + else: + message += 'You can re-run the job with this tool version, which is a derivation of the original tool.' + else: + if len( tools ) > 1: + message = 'This job was initially run with tool version "%s", which is currently not available. ' % version + message += 'You can re-run the job with the selected tool or choose another derivation of the tool.' + else: + message = 'This job was initially run with tool id "%s", version "%s", which is ' % ( id, version ) + message += 'currently not available. You can re-run the job with this tool, which is a derivation of the original tool.' + except Exception, error: + trans.response.status = 500 + return { 'error': str (error) } + + # can't rerun upload, external data sources, et cetera. workflow compatible will proxy this for now + if not tool.is_workflow_compatible: + trans.response.status = 500 + return { 'error': 'The \'%s\' tool does currently not support re-running.' % tool.name } + return message diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -42,24 +42,11 @@ // creates the job handler this.job_handler = new ToolJobs(this); - // reset field list, which contains the input field elements - this.field_list = {}; - - // reset sequential input definition list, which contains the input definitions as provided from the api - this.input_list = {}; - - // reset input element list, which contains the dom elements of each input element (includes also the input field) - this.element_list = {}; - - // for now the initial tool model is parsed through the mako - this.model = this.options; - this.inputs = this.options.inputs; - // request history content and build form this.content = new ToolContent({ history_id : self.options.history_id, success : function() { - self._buildForm(); + self._buildForm(self.options); } }); }, @@ -137,7 +124,7 @@ }, // refresh form data - _refreshForm: function() { + rebuild: function() { // link this var self = this; @@ -161,6 +148,10 @@ url : galaxy_config.root + 'api/tools/' + this.options.id + '/build', data : current_state, success : function(response) { + // rebuild form + self._rebuildForm(response); + + // log success console.debug('tools-form::_refreshForm() - Refreshed inputs/states.'); console.debug(response); }, @@ -171,11 +162,55 @@ }); }, + // rebuild the form elements + _rebuildForm: function(new_model) { + var self = this; + this.tree.matchModel(new_model, function(input_id, node) { + var input = self.input_list[input_id]; + if (input && input.options) { + if (JSON.stringify(input.options) != JSON.stringify(node.options)) { + // backup new options + input.options = node.options; + + // get/update field (currently only done for select fields) + var field = self.field_list[input_id]; + if (field.update && input.type == 'select') { + var new_options = []; + for (var i in node.options) { + var opt = node.options[i]; + if (opt.length > 2) { + new_options.push({ + 'label': opt[0], + 'value': opt[1] + }); + } + } + field.update(new_options); + console.debug('Updating options for ' + input_id); + } + } + } + }); + }, + // builds the tool form - _buildForm: function() { + _buildForm: function(options) { // link this var self = this; + // reset field list, which contains the input field elements + this.field_list = {}; + + // reset sequential input definition list, which contains the input definitions as provided from the api + this.input_list = {}; + + // reset input element list, which contains the dom elements of each input element (includes also the input field) + this.element_list = {}; + + // for now the initial tool model is parsed through the mako + this.model = options; + this.inputs = options.inputs; + // button menu var menu = new Ui.ButtonMenu({ icon : 'fa-gear', @@ -183,7 +218,7 @@ }); // configure button selection - if(this.options.biostar_url) { + if(options.biostar_url) { // add question option menu.addMenu({ icon : 'fa-question-circle', @@ -256,29 +291,30 @@ cls : 'btn btn-primary', floating : 'clear', onclick : function() { - //self._refreshForm(); + //self.rebuild(); self.job_handler.submit(); } }) } }); - // append form + // start form + this.$el.empty(); this.$el.append(this.portlet.$el); // append help - if (this.options.help != '') { - this.$el.append(ToolTemplate.help(this.options.help)); + if (options.help != '') { + this.$el.append(ToolTemplate.help(options.help)); } // append citations - if (this.options.citations) { + if (options.citations) { // append html this.$el.append(ToolTemplate.citations()); // fetch citations var citations = new CitationModel.ToolCitationCollection(); - citations.tool_id = this.options.id; + citations.tool_id = options.id; var citation_list_view = new CitationView.CitationListView({ collection: citations } ); citation_list_view.render(); citations.fetch(); diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -50,7 +50,7 @@ var input_def = jQuery.extend(true, {}, input); // create unique id - input_def.id = Utils.uuid(); + input_def.id = input.id = Utils.uuid(); // add to sequential list of inputs this.app.input_list[input_def.id] = input_def; @@ -208,7 +208,7 @@ _addRow: function(field_type, input_def) { // get id var id = input_def.id; - + // field wrapper var field = null; @@ -380,6 +380,11 @@ extensions : input_def.extensions, multiple : input_def.multiple, onchange : function(dict) { + // rebuild the form + if (self.app.is_dynamic) { + self.app.rebuild(); + } + // pick the first content only (todo: maybe collect multiple meta information) var content_def = dict.values[0]; var content_id = content_def.id; @@ -485,7 +490,7 @@ _fieldSelect : function (input_def) { // check compatibility if (input_def.is_dynamic) { - this.app.incompatible = true; + this.app.is_dynamic = true; } // configure options fields diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/mvc/tools/tools-template.js --- a/static/scripts/mvc/tools/tools-template.js +++ b/static/scripts/mvc/tools/tools-template.js @@ -30,7 +30,7 @@ if (njobs == 1) { njobs_text = '1 job has'; } else { - njobs_text = njobs + ' jobs have been'; + njobs_text = njobs + ' jobs have'; } // create template string diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -146,7 +146,48 @@ return this.job_ids && this.job_ids[job_input_id]; }, - /** Matches identifier from api response to input element + /** Matches identifier from api model to input elements + */ + matchModel: function(model, callback) { + // final result dictionary + var result = {}; + + // link this + var self = this; + + // search throughout response + function search (id, head) { + for (var i in head) { + var node = head[i]; + var index = node.name; + if (id != '') { + index = id + '|' + index; + } + if (node.type == 'repeat') { + for (var j in node.cache) { + search (index + '_' + j, node.cache[j]); + } + } else { + if (node.type == 'conditional') { + search (index, node.inputs); + } else { + var input_id = self.app.tree.job_ids[index]; + if (input_id) { + callback(input_id, node); + } + } + } + } + } + + // match all ids and return messages + search('', model.inputs); + + // return matched results + return result; + }, + + /** Matches identifier from api response to input elements */ matchResponse: function(response) { // final result dictionary diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.field_list={};this.input_list={};this.element_list={};this.model=this.options;this.inputs=this.options.inputs;this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},_refreshForm:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_buildForm:function(){var n=this;var p=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(this.options.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:p},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=this.options.id;var o=new a.CitationListView({collection:m});o.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,h,l,j,a,e,d,f,k,c,g){var b=Backbone.View.extend({container:"body",initialize:function(n){console.debug(n);var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.tree=new c(this);this.job_handler=new g(this);this.content=new f({history_id:m.options.history_id,success:function(){m._buildForm(m.options)}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_buildModel:function(){var m=this;var n=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){n+="job_id="+this.options.job_id}else{if(this.options.dataset_id){n+="dataset_id="+this.options.dataset_id}else{var o=top.location.href;var p=o.indexOf("?");if(o.indexOf("tool_id=")!=-1&&p!==-1){n+=o.slice(p+1)}}}i.request({type:"GET",url:n,success:function(q){m.options=$.extend(m.options,q);m.model=q;m.inputs=q.inputs;console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(q);m._buildForm()},error:function(q){console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(q)}})},rebuild:function(){var m=this;var n=this.tree.finalize({data:function(o){if(o.values.length>0&&o.values[0]&&o.values[0].src==="hda"){return m.content.get({id:o.values[0].id}).dataset_id}return null}});console.debug("tools-form::_refreshForm() - Refreshing inputs/states.");console.debug(n);i.request({type:"GET",url:galaxy_config.root+"api/tools/"+this.options.id+"/build",data:n,success:function(o){m._rebuildForm(o);console.debug("tools-form::_refreshForm() - Refreshed inputs/states.");console.debug(o)},error:function(o){console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(o)}})},_rebuildForm:function(m){var n=this;this.tree.matchModel(m,function(p,t){var o=n.input_list[p];if(o&&o.options){if(JSON.stringify(o.options)!=JSON.stringify(t.options)){o.options=t.options;var u=n.field_list[p];if(u.update&&o.type=="select"){var s=[];for(var r in t.options){var q=t.options[r];if(q.length>2){s.push({label:q[0],value:q[1]})}}u.update(s);console.debug("Updating options for "+p)}}}})},_buildForm:function(o){var n=this;this.field_list={};this.input_list={};this.element_list={};this.model=o;this.inputs=o.inputs;var q=new l.ButtonMenu({icon:"fa-gear",tooltip:"Click to see a list of options."});if(o.biostar_url){q.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});q.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}})}q.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+n.options.id)}});if(Galaxy.currUser.get("is_admin")){q.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.section=new k.View(n,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new h.View({icon:"fa-wrench",title:"<b>"+this.model.name+"</b> "+this.model.description,operations:{menu:q},buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});this.$el.empty();this.$el.append(this.portlet.$el);if(o.help!=""){this.$el.append(d.help(o.help))}if(o.citations){this.$el.append(d.citations());var m=new j.ToolCitationCollection();m.tool_id=o.id;var p=new a.CitationListView({collection:m});p.render();m.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=j.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(o){var r=this;var p=0;function m(i,t){var s=o.id+"-section-"+(p++);var u=null;if(t){u=function(){k.del(s);k.retitle(o.title);r.app.refresh()}}var v=new f(r.app,{inputs:i,cls:"ui-table-plain"});k.add({id:s,title:o.title,$el:v.$el,ondel:u});k.retitle(o.title)}var k=new c.View({title_new:o.title,max:o.max,onnew:function(){m(o.inputs,true);r.app.refresh()}});var h=o.min;var q=_.size(o.cache);for(var l=0;l<Math.max(q,h);l++){var n=null;if(l<q){n=o.cache[l]}else{n=o.inputs}m(n,l>=h)}var j=new e({label:o.title,help:o.help,field:k});j.$el.addClass("ui-table-form-section");this.table.add(j.$el);this.table.append(o.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){if(i.app.is_dynamic){i.app.rebuild()}var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.is_dynamic=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){return new g.Slider.View({id:"field-"+h.id,precise:h.type=="float",min:h.min,max:h.max})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/packed/mvc/tools/tools-template.js --- a/static/scripts/packed/mvc/tools/tools-template.js +++ b/static/scripts/packed/mvc/tools/tools-template.js @@ -1,1 +1,1 @@ -define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have been"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file +define([],function(){return{help:function(a){return'<div class="toolHelp"><div class="toolHelpBody">'+a+"</div></div>"},citations:function(){return'<div id="citations"></div>'},success:function(c){if(!c.jobs||!c.jobs.length){console.debug("tools-template::success() - Failed jobs.");return}var a=c.jobs.length;var d="";if(a==1){d="1 job has"}else{d=a+" jobs have"}var b='<div class="donemessagelarge"><p>'+d+" been successfully added to the queue - resulting in the following datasets:</p>";for(var e in c.outputs){b+='<p style="padding: 10px 20px;"><b>'+(parseInt(e)+1)+": "+c.outputs[e].name+"</b></p>"}b+="<p>You can check the status of queued jobs and view the resulting data by refreshing the History pane. When the job has been run the status will change from 'running' to 'finished' if completed successfully or 'error' if problems were encountered.</p></div>";return b},error:function(a){return'<div><p>The server could not complete the request. Please contact the Galaxy Team if this error persists.</p><textarea class="ui-textarea" disabled style="color: black;" rows="6">'+JSON.stringify(a,undefined,4)+"</textarea></div>"},batchMode:function(){return'<div class="ui-table-form-info"><i class="fa fa-sitemap" style="font-size: 1.2em; padding: 2px 5px;"/>This is a batch mode input field. A separate job will be triggered for each dataset.';"</div>"}}}); \ No newline at end of file diff -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 -r 3b4784d5fc0d3687a51a64d10765edf54e6ed62c static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(k,n){for(var h in n){var f=n[h];if(f.input){var p=f.input;var j=k;if(k!=""){j+="|"}j+=p.name;switch(p.type){case"repeat":var e="section-";var s=[];var m=null;for(var r in f){var l=r.indexOf(e);if(l!=-1){l+=e.length;s.push(parseInt(r.substr(l)));if(!m){m=r.substr(0,l)}}}s.sort(function(t,i){return t-i});var h=0;for(var g in s){b(j+"_"+h++,f[m+s[g]])}break;case"conditional":var q=a.app.field_list[p.id].value();c(j+"|"+p.test_param.name,p.id,q);for(var g in p.cases){if(p.cases[g].value==q){b(j,n[p.id+"-section-"+g]);break}}break;default:var o=a.app.field_list[p.id];var q=o.value();if(d[p.type]){q=d[p.type](q)}if(!o.skip){c(j,p.id,q)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(d){d=d||{};var a=this;this.job_def={};this.job_ids={};function c(g,f,e){a.job_def[g]=e;a.job_ids[g]=f}function b(k,n){for(var h in n){var f=n[h];if(f.input){var p=f.input;var j=k;if(k!=""){j+="|"}j+=p.name;switch(p.type){case"repeat":var e="section-";var s=[];var m=null;for(var r in f){var l=r.indexOf(e);if(l!=-1){l+=e.length;s.push(parseInt(r.substr(l)));if(!m){m=r.substr(0,l)}}}s.sort(function(t,i){return t-i});var h=0;for(var g in s){b(j+"_"+h++,f[m+s[g]])}break;case"conditional":var q=a.app.field_list[p.id].value();c(j+"|"+p.test_param.name,p.id,q);for(var g in p.cases){if(p.cases[g].value==q){b(j,n[p.id+"-section-"+g]);break}}break;default:var o=a.app.field_list[p.id];var q=o.value();if(d[p.type]){q=d[p.type](q)}if(!o.skip){c(j,p.id,q)}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchModel:function(c,e){var a={};var b=this;function d(n,l){for(var k in l){var m=l[k];var h=m.name;if(n!=""){h=n+"|"+h}if(m.type=="repeat"){for(var g in m.cache){d(h+"_"+g,m.cache[g])}}else{if(m.type=="conditional"){d(h,m.inputs)}else{var f=b.app.tree.job_ids[h];if(f){e(f,m)}}}}}d("",c.inputs);return a},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,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: jmchilton: Fix bug in tool watching.
by commits-noreply＠bitbucket.org 23 Oct '14

23 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0d9ac8314a78/ Changeset: 0d9ac8314a78 User: jmchilton Date: 2014-10-23 13:08:03+00:00 Summary: Fix bug in tool watching. Affected #: 1 file diff -r 53e734a1532733df32dcf45ace3dea6aa3f3604d -r 0d9ac8314a78087f68f84c66e861dffb9a1ea203 lib/galaxy/tools/watcher.py --- a/lib/galaxy/tools/watcher.py +++ b/lib/galaxy/tools/watcher.py @@ -51,7 +51,7 @@ self.tool_dir_callbacks[tool_dir] = callback if tool_dir not in self.monitored_dirs: self.monitored_dirs[ tool_dir ] = tool_dir - self.restart( tool_dir ) + self.monitor( tool_dir ) class ToolFileEventHandler(FileSystemEventHandler): 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: natefoo: Implement the "memory_limit_reached" runner state for slurm and allow resubmission on that state.
by commits-noreply＠bitbucket.org 22 Oct '14

22 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/53e734a15327/ Changeset: 53e734a15327 User: natefoo Date: 2014-10-23 03:05:07+00:00 Summary: Implement the "memory_limit_reached" runner state for slurm and allow resubmission on that state. Affected #: 4 files diff -r 74499e753e0f28b4353a27e241c1fce0f0895964 -r 53e734a1532733df32dcf45ace3dea6aa3f3604d config/job_conf.xml.sample_advanced --- a/config/job_conf.xml.sample_advanced +++ b/config/job_conf.xml.sample_advanced @@ -399,8 +399,11 @@ the terminal condition of a job will be used. The 'condition' attribute is optional, if not present, the - resubmit destination will be used for all conditions. Currently, - only the "walltime_reached" condition is implemented. + resubmit destination will be used for all conditions. The + conditions currently implemented are: + + - "walltime_reached" + - "memory_limit_reached" The 'handler' tag is optional, if not present, the job's original handler will be reused for the resubmitted job. @@ -413,6 +416,10 @@ <param id="nativeSpecification">-l h_rt=96:00:00</param></destination> + <destination id="smallmem" runner="slurm"> + <param id="nativeSpecification">--mem-per-cpu=512</param> + <resubmit condition="memory_limit_reached" destination="bigmem" /> + </destination></destinations><resources default="default"> diff -r 74499e753e0f28b4353a27e241c1fce0f0895964 -r 53e734a1532733df32dcf45ace3dea6aa3f3604d lib/galaxy/jobs/runners/__init__.py --- a/lib/galaxy/jobs/runners/__init__.py +++ b/lib/galaxy/jobs/runners/__init__.py @@ -337,6 +337,7 @@ """ runner_states = Bunch( WALLTIME_REACHED = 'walltime_reached', + MEMORY_LIMIT_REACHED = 'memory_limit_reached', GLOBAL_WALLTIME_REACHED = 'global_walltime_reached', OUTPUT_SIZE_LIMIT = 'output_size_limit' ) diff -r 74499e753e0f28b4353a27e241c1fce0f0895964 -r 53e734a1532733df32dcf45ace3dea6aa3f3604d lib/galaxy/jobs/runners/slurm.py --- a/lib/galaxy/jobs/runners/slurm.py +++ b/lib/galaxy/jobs/runners/slurm.py @@ -13,6 +13,8 @@ __all__ = [ 'SlurmJobRunner' ] +SLURM_MEMORY_LIMIT_EXCEEDED_MSG = 'slurmstepd: error: Exceeded job memory limit' + class SlurmJobRunner( DRMAAJobRunner ): runner_name = "SlurmRunner" @@ -62,8 +64,14 @@ except: ajs.fail_message = "This job failed due to a cluster node failure, and an attempt to resubmit the job failed." elif job_info['JobState'] == 'CANCELLED': - log.info( '(%s/%s) Job was cancelled via slurm (e.g. with scancel(1))', ajs.job_wrapper.get_id_tag(), ajs.job_id ) - ajs.fail_message = "This job failed because it was cancelled by an administrator." + # Check to see if the job was killed for exceeding memory consumption + if self.__check_memory_limit( ajs.error_file ): + log.info( '(%s/%s) Job hit memory limit', ajs.job_wrapper.get_id_tag(), ajs.job_id ) + ajs.fail_message = "This job was terminated because it used more memory than it was allocated." + ajs.runner_state = ajs.runner_states.MEMORY_LIMIT_REACHED + else: + log.info( '(%s/%s) Job was cancelled via slurm (e.g. with scancel(1))', ajs.job_wrapper.get_id_tag(), ajs.job_id ) + ajs.fail_message = "This job failed because it was cancelled by an administrator." else: log.warning( '(%s/%s) Job failed due to unknown reasons, JobState was: %s', ajs.job_wrapper.get_id_tag(), ajs.job_id, job_info['JobState'] ) ajs.fail_message = "This job failed for reasons that could not be determined." @@ -77,3 +85,31 @@ super( SlurmJobRunner, self )._complete_terminal_job( ajs, drmaa_state = drmaa_state ) # by default, finish as if the job was successful. super( SlurmJobRunner, self )._complete_terminal_job( ajs, drmaa_state = drmaa_state ) + + def __check_memory_limit( self, efile_path ): + """ + A very poor implementation of tail, but it doesn't need to be fancy + since we are only searching the last 2K + """ + try: + log.debug( 'Checking %s for exceeded memory message from slurm', efile_path ) + with open( efile_path ) as f: + pos = 2 + bof = False + while pos < 2048: + try: + f.seek(-pos, 2) + pos += 1 + except: + f.seek(-pos + 1, 2) + bof = True + + if (bof or f.read(1) == '\n') and f.readline().strip() == SLURM_MEMORY_LIMIT_EXCEEDED_MSG: + return True + + if bof: + break + except: + log.exception('Error reading end of %s:', path) + + return False diff -r 74499e753e0f28b4353a27e241c1fce0f0895964 -r 53e734a1532733df32dcf45ace3dea6aa3f3604d lib/galaxy/jobs/runners/state_handlers/resubmit.py --- a/lib/galaxy/jobs/runners/state_handlers/resubmit.py +++ b/lib/galaxy/jobs/runners/state_handlers/resubmit.py @@ -6,14 +6,24 @@ log = logging.getLogger(__name__) +MESSAGES = dict( + walltime_reached = 'it reached the walltime', + memory_limit_reached = 'it exceeded the amount of allocated memory' +) + def failure(app, job_runner, job_state): - if getattr( job_state, 'runner_state', None ) and job_state.runner_state == job_state.runner_states.WALLTIME_REACHED: + if getattr( job_state, 'runner_state', None ) and job_state.runner_state in ( job_state.runner_states.WALLTIME_REACHED, job_state.runner_states.MEMORY_LIMIT_REACHED ): # Intercept jobs that hit the walltime and have a walltime or nonspecific resubmit destination configured for resubmit in job_state.job_destination.get('resubmit'): - if resubmit.get('condition', None) and resubmit['condition'] != 'walltime_reached': + if resubmit.get('condition', None) and resubmit['condition'] != job_state.runner_state: continue # There is a resubmit defined for the destination but its condition is not for walltime_reached - log.info("(%s/%s) Job will be resubmitted to '%s' because it reached the walltime at the '%s' destination", job_state.job_wrapper.job_id, job_state.job_id, resubmit['destination'], job_state.job_wrapper.job_destination.id ) + log.info("(%s/%s) Job will be resubmitted to '%s' because %s at the '%s' destination", + job_state.job_wrapper.job_id, + job_state.job_id, + resubmit['destination'], + MESSAGES[job_state.runner_state], + job_state.job_wrapper.job_destination.id ) # fetch JobDestination for the id or tag new_destination = app.job_config.get_destination(resubmit['destination']) # Resolve dynamic if necessary Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Merge stable.
by commits-noreply＠bitbucket.org 22 Oct '14

22 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/74499e753e0f/ Changeset: 74499e753e0f User: dannon Date: 2014-10-23 02:52:11+00:00 Summary: Merge stable. Affected #: 1 file diff -r 7844d02f9c4731dcdbf78b99ba810805506a6c05 -r 74499e753e0f28b4353a27e241c1fce0f0895964 cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample +++ b/cron/updateucsc.sh.sample @@ -4,8 +4,8 @@ # the update fails, not replace current data/tables with error # messages. -# Edit this line to refer to galaxy's path: -GALAXY=/galaxy/path +## Uncomment and edit this line to refer to galaxy's path: +#GALAXY=/galaxy/path PYTHONPATH=${GALAXY}/lib export PYTHONPATH 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: Merged in BjoernGruening/galaxy-central/stable (pull request #537)
by commits-noreply＠bitbucket.org 22 Oct '14

22 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9bc08bc7f393/ Changeset: 9bc08bc7f393 Branch: stable User: dannon Date: 2014-10-23 02:50:21+00:00 Summary: Merged in BjoernGruening/galaxy-central/stable (pull request #537) [STABLE] Hide the GALAXY env variable. Affected #: 1 file diff -r ba1447685bc2470cb545612450b6364057b6d8c5 -r 9bc08bc7f393362ee7e6cf1d04bb9d8cee68f2d8 cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample +++ b/cron/updateucsc.sh.sample @@ -4,8 +4,8 @@ # the update fails, not replace current data/tables with error # messages. -# Edit this line to refer to galaxy's path: -GALAXY=/galaxy/path +## Uncomment and edit this line to refer to galaxy's path: +#GALAXY=/galaxy/path PYTHONPATH=${GALAXY}/lib export PYTHONPATH 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 22 Oct '14

22 Oct '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/96eb54eec55b/ Changeset: 96eb54eec55b Branch: stable User: BjoernGruening Date: 2014-10-22 13:10:32+00:00 Summary: Hide the GALAXY env variable. This enables us to set it externally and just call the script. Very useful in docker containers. Affected #: 1 file diff -r 78c9a97be4b6bfe55136b055477fd1b9f22fd848 -r 96eb54eec55b362399fd9b6c856612218172983e cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample +++ b/cron/updateucsc.sh.sample @@ -4,8 +4,8 @@ # the update fails, not replace current data/tables with error # messages. -# Edit this line to refer to galaxy's path: -GALAXY=/galaxy/path +## Uncomment and edit this line to refer to galaxy's path: +#GALAXY=/galaxy/path PYTHONPATH=${GALAXY}/lib export PYTHONPATH https://bitbucket.org/galaxy/galaxy-central/commits/9bc08bc7f393/ Changeset: 9bc08bc7f393 Branch: stable User: dannon Date: 2014-10-23 02:50:21+00:00 Summary: Merged in BjoernGruening/galaxy-central/stable (pull request #537) [STABLE] Hide the GALAXY env variable. Affected #: 1 file diff -r ba1447685bc2470cb545612450b6364057b6d8c5 -r 9bc08bc7f393362ee7e6cf1d04bb9d8cee68f2d8 cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample +++ b/cron/updateucsc.sh.sample @@ -4,8 +4,8 @@ # the update fails, not replace current data/tables with error # messages. -# Edit this line to refer to galaxy's path: -GALAXY=/galaxy/path +## Uncomment and edit this line to refer to galaxy's path: +#GALAXY=/galaxy/path PYTHONPATH=${GALAXY}/lib export PYTHONPATH 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: natefoo: Merge stable.
by commits-noreply＠bitbucket.org 22 Oct '14

22 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7844d02f9c47/ Changeset: 7844d02f9c47 User: natefoo Date: 2014-10-23 02:47:52+00:00 Summary: Merge stable. Affected #: 2 files diff -r f25e90163bbd16626ce9adf7854ff493c79b469d -r 7844d02f9c4731dcdbf78b99ba810805506a6c05 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -e1404e285ccb9e52bd09c5827934cd0da1974acc latest_2014.10.06 +a7b2aabb27ffe5cc3216774ab01b18f13b4fc941 latest_2014.10.06 diff -r f25e90163bbd16626ce9adf7854ff493c79b469d -r 7844d02f9c4731dcdbf78b99ba810805506a6c05 lib/galaxy/jobs/runners/slurm.py --- a/lib/galaxy/jobs/runners/slurm.py +++ b/lib/galaxy/jobs/runners/slurm.py @@ -19,13 +19,20 @@ def _complete_terminal_job( self, ajs, drmaa_state, **kwargs ): def __get_jobinfo(): - p = subprocess.Popen( ( 'scontrol', '-o', 'show', 'job', ajs.job_id ), stdout=subprocess.PIPE, stderr=subprocess.PIPE ) + job_id = ajs.job_id + cmd = [ 'scontrol', '-o' ] + if '.' in ajs.job_id: + # custom slurm-drmaa-with-cluster-support job id syntax + job_id, cluster = ajs.job_id.split('.', 1) + cmd.extend( [ '-M', cluster ] ) + cmd.extend( [ 'show', 'job', job_id ] ) + p = subprocess.Popen( cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE ) stdout, stderr = p.communicate() if p.returncode != 0: # Will need to be more clever here if this message is not consistent if stderr == 'slurm_load_jobs error: Invalid job id specified\n': return dict( JobState='NOT_FOUND' ) - raise Exception( '`scontrol -o show job %s` returned %s, stderr: %s' % ( ajs.job_id, p.returncode, stderr ) ) + raise Exception( '`%s` returned %s, stderr: %s' % ( ' '.join( cmd ), p.returncode, stderr ) ) return dict( [ out_param.split( '=', 1 ) for out_param in stdout.split() ] ) if drmaa_state == self.drmaa_job_states.FAILED: try: 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: natefoo: Fix slurm job post-mortem for `clusters` functionality added to slurm-drmaa (and currently in use on usegalaxy.org).
by commits-noreply＠bitbucket.org 22 Oct '14

22 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/ba1447685bc2/ Changeset: ba1447685bc2 Branch: stable User: natefoo Date: 2014-10-22 22:00:15+00:00 Summary: Fix slurm job post-mortem for `clusters` functionality added to slurm-drmaa (and currently in use on usegalaxy.org) Affected #: 1 file diff -r d1e1beeb532239250396dd8fbdc0156508c6744e -r ba1447685bc2470cb545612450b6364057b6d8c5 lib/galaxy/jobs/runners/slurm.py --- a/lib/galaxy/jobs/runners/slurm.py +++ b/lib/galaxy/jobs/runners/slurm.py @@ -19,13 +19,20 @@ def _complete_terminal_job( self, ajs, drmaa_state, **kwargs ): def __get_jobinfo(): - p = subprocess.Popen( ( 'scontrol', '-o', 'show', 'job', ajs.job_id ), stdout=subprocess.PIPE, stderr=subprocess.PIPE ) + job_id = ajs.job_id + cmd = [ 'scontrol', '-o' ] + if '.' in ajs.job_id: + # custom slurm-drmaa-with-cluster-support job id syntax + job_id, cluster = ajs.job_id.split('.', 1) + cmd.extend( [ '-M', cluster ] ) + cmd.extend( [ 'show', 'job', job_id ] ) + p = subprocess.Popen( cmd, stdout=subprocess.PIPE, stderr=subprocess.PIPE ) stdout, stderr = p.communicate() if p.returncode != 0: # Will need to be more clever here if this message is not consistent if stderr == 'slurm_load_jobs error: Invalid job id specified\n': return dict( JobState='NOT_FOUND' ) - raise Exception( '`scontrol -o show job %s` returned %s, stderr: %s' % ( ajs.job_id, p.returncode, stderr ) ) + raise Exception( '`%s` returned %s, stderr: %s' % ( ' '.join( cmd ), p.returncode, stderr ) ) return dict( [ out_param.split( '=', 1 ) for out_param in stdout.split() ] ) if drmaa_state == self.drmaa_job_states.FAILED: try: 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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