- galaxy-commits - lists.galaxyproject.org

[galaxyproject/ansible-galaxy] 558d46: Optional git clone/pull functionality.
by GitHub 27 Feb '15

27 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/ansible-galaxy Commit: 558d46ede9bc65567f921de3b6ecf2dc53361df2 https://github.com/galaxyproject/ansible-galaxy/commit/558d46ede9bc65567f92… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-27 (Fri, 27 Feb 2015) Changed paths: M README.md M defaults/main.yml M meta/main.yml M tasks/clone.yml Log Message: ----------- Optional git clone/pull functionality.

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[galaxyproject/usegalaxy-playbook] f3642c: Update datatypes_conf.xml for typo in text module ...
by GitHub 27 Feb '15

27 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: f3642c0b59048b1efab4878fbffc56c3c1c6c0c3 https://github.com/galaxyproject/usegalaxy-playbook/commit/f3642c0b59048b1e… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-27 (Fri, 27 Feb 2015) Changed paths: M templates/galaxy/test.galaxyproject.org/config/datatypes_conf.xml.j2 M templates/galaxy/usegalaxy.org/config/datatypes_conf.xml.j2 Log Message: ----------- Update datatypes_conf.xml for typo in text module name.

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[galaxyproject/usegalaxy-playbook] b970a8: Update Test
by GitHub 27 Feb '15

27 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: b970a8db17fbcce3b733ab2901d9665f199b534b https://github.com/galaxyproject/usegalaxy-playbook/commit/b970a8db17fbcce3… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-27 (Fri, 27 Feb 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test

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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 27 Feb '15

27 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f84ae130824f/ Changeset: f84ae130824f Branch: release_15.03 User: guerler Date: 2015-02-27 18:43:39+00:00 Summary: ToolForm: Make deep copy of current state in order to be on the safe side Affected #: 3 files diff -r 2a238115b21ccce4391355329e322132716daecc -r f84ae130824f6a1ef03214ac0ba43dbeaeedc5bc client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -108,7 +108,7 @@ var new_state = self.tree.finalize(); if (!_.isEqual(new_state, current_state)) { current_state = new_state; - self._updateModel($.extend({}, current_state)); + self._updateModel($.extend(true, {}, current_state)); } }); }); diff -r 2a238115b21ccce4391355329e322132716daecc -r f84ae130824f6a1ef03214ac0ba43dbeaeedc5bc static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -108,7 +108,7 @@ var new_state = self.tree.finalize(); if (!_.isEqual(new_state, current_state)) { current_state = new_state; - self._updateModel($.extend({}, current_state)); + self._updateModel($.extend(true, {}, current_state)); } }); }); diff -r 2a238115b21ccce4391355329e322132716daecc -r f84ae130824f6a1ef03214ac0ba43dbeaeedc5bc static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","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"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l._updateModel($.extend({},m))}})});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}})},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$("html, body").animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.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="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","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"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l._updateModel($.extend(true,{},m))}})});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}})},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$("html, body").animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.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="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/12a2f4524350/ Changeset: 12a2f4524350 Branch: release_15.03 User: natefoo Date: 2015-02-27 19:21:22+00:00 Summary: Fix a typo in datatypes_conf.xml.sample Affected #: 1 file diff -r f84ae130824f6a1ef03214ac0ba43dbeaeedc5bc -r 12a2f45243502295e324bf6656481a98c61101c0 config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -180,7 +180,7 @@ <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/><datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/><datatype extension="snpeffdb" type="galaxy.datatypes.text:SnpEffDb" display_in_upload="True"/> - <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.txt:SnpSiftDbNSFP" display_in_upload="True"/> + <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.text:SnpSiftDbNSFP" display_in_upload="True"/><datatype extension="dbnsfp.tabular" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"><converter file="tabular_to_dbnsfp.xml" target_datatype="snpsiftdbnsfp"/></datatype> 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 27 Feb '15

27 Feb '15

4 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2d3cbc0bf197/ Changeset: 2d3cbc0bf197 User: natefoo Date: 2015-02-27 16:35:13+00:00 Summary: Add some pointers for developers and deployers in README.rst regarding the Github move. Affected #: 1 file diff -r 8b70692766ec172eb4ac141a5d7266b88526f852 -r 2d3cbc0bf1971ab40a3d0b079aea7f6c48e50f12 README.rst --- a/README.rst +++ b/README.rst @@ -38,7 +38,7 @@ https://wiki.galaxyproject.org/Admin/Tools/ToolDependencies Issues ------- +====== Issues can be submitted to trello via the `galaxyproject website <http://galaxyproject.org/trello/>`__ and viewed on the `Galaxy @@ -51,6 +51,19 @@ Galaxy welcomes new development! There is extensive documentation on developing with Galaxy on the `wiki <https://wiki.galaxyproject.org/Develop>`__. +Source Repository +----------------- + +Galaxy development has moved to `Github +<https://github.com/galaxyproject/galaxy>`__. + +**Developers** should develop against the ``dev`` branch in the Github +repository. + +**Deployers** can continue to pull Galaxy changes from Bitbucket without +interruption. Alternatively, deployers can track the ``master`` branch in +Github. + Syncing a Fork -------------- https://bitbucket.org/galaxy/galaxy-central/commits/097f826b47ee/ Changeset: 097f826b47ee User: martenson Date: 2015-02-27 18:29:05+00:00 Summary: use proper placeholder instead of input value to prevent various search glitches Affected #: 2 files diff -r 2d3cbc0bf1971ab40a3d0b079aea7f6c48e50f12 -r 097f826b47ee3d758e51dbebede467c15f496846 client/galaxy/scripts/templates/tool_search.handlebars --- a/client/galaxy/scripts/templates/tool_search.handlebars +++ b/client/galaxy/scripts/templates/tool_search.handlebars @@ -1,3 +1,3 @@ -<input type="text" name="query" value="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> +<input type="text" name="query" placeholder="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /><a id="search-clear-btn" title="clear search (esc)"></a> -<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> \ No newline at end of file +<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> diff -r 2d3cbc0bf1971ab40a3d0b079aea7f6c48e50f12 -r 097f826b47ee3d758e51dbebede467c15f496846 static/scripts/templates/tool_search.handlebars --- a/static/scripts/templates/tool_search.handlebars +++ b/static/scripts/templates/tool_search.handlebars @@ -1,3 +1,3 @@ -<input type="text" name="query" value="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /> +<input type="text" name="query" placeholder="{{search_hint_string}}" id="tool-search-query" autocomplete="off" class="search-query parent-width" /><a id="search-clear-btn" title="clear search (esc)"></a> -<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> \ No newline at end of file +<img src="{{spinner_url}}" id="search-spinner" class="search-spinner"/> https://bitbucket.org/galaxy/galaxy-central/commits/99d18d1fa46b/ Changeset: 99d18d1fa46b User: guerler Date: 2015-02-27 18:43:39+00:00 Summary: ToolForm: Make deep copy of current state in order to be on the safe side Affected #: 3 files diff -r 097f826b47ee3d758e51dbebede467c15f496846 -r 99d18d1fa46b506225dad08b0688212c9493edba client/galaxy/scripts/mvc/tools/tools-form-base.js --- a/client/galaxy/scripts/mvc/tools/tools-form-base.js +++ b/client/galaxy/scripts/mvc/tools/tools-form-base.js @@ -108,7 +108,7 @@ var new_state = self.tree.finalize(); if (!_.isEqual(new_state, current_state)) { current_state = new_state; - self._updateModel($.extend({}, current_state)); + self._updateModel($.extend(true, {}, current_state)); } }); }); diff -r 097f826b47ee3d758e51dbebede467c15f496846 -r 99d18d1fa46b506225dad08b0688212c9493edba static/scripts/mvc/tools/tools-form-base.js --- a/static/scripts/mvc/tools/tools-form-base.js +++ b/static/scripts/mvc/tools/tools-form-base.js @@ -108,7 +108,7 @@ var new_state = self.tree.finalize(); if (!_.isEqual(new_state, current_state)) { current_state = new_state; - self._updateModel($.extend({}, current_state)); + self._updateModel($.extend(true, {}, current_state)); } }); }); diff -r 097f826b47ee3d758e51dbebede467c15f496846 -r 99d18d1fa46b506225dad08b0688212c9493edba static/scripts/packed/mvc/tools/tools-form-base.js --- a/static/scripts/packed/mvc/tools/tools-form-base.js +++ b/static/scripts/packed/mvc/tools/tools-form-base.js @@ -1,1 +1,1 @@ -define(["utils/utils","utils/deferred","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"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l._updateModel($.extend({},m))}})});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}})},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$("html, body").animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.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="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ No newline at end of file +define(["utils/utils","utils/deferred","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"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l._updateModel($.extend(true,{},m))}})});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}})},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$("html, body").animate({scrollTop:o.$el.offset().top-20},500)}}},_errors:function(n){this.trigger("reset");if(n&&n.errors){var o=this.tree.matchResponse(n.errors);for(var m in this.element_list){var l=this.element_list[m];if(o[m]){this.highlight(m,o[m],true)}}}},_renderForm:function(t){var s=this;this.message=new k.Message();var m=new k.ButtonMenu({icon:"fa-cubes",title:(!t.narrow&&"Versions")||null,tooltip:"Select another tool version"});if(t.versions&&t.versions.length>1){for(var o in t.versions){var q=t.versions[o];if(q!=t.version){m.addMenu({title:"Switch to "+q,version:q,icon:"fa-cube",onclick:function(){s.options.id=s.options.id.replace(s.options.version,this.version);s.options.version=this.version;s.deferred.reset();s.deferred.execute(function(){s._buildModel()})}})}}}else{m.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.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="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"See in Tool Shed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new f.View({icon:"fa-wrench",title:"<b>"+t.name+"</b> "+t.description+" (Galaxy Tool Version "+t.version+")",cls:this.options.cls_portlet,operations:{menu:p,versions:m},buttons:this.buttons});this.portlet.append(this.message.$el.addClass("ui-margin-top"));this.portlet.append(this.section.$el);this.$el.empty();this.$el.append(this.portlet.$el);if(t.help!=""){this.$el.append(c.help(t.help))}if(t.citations){var r=$("<div/>");var l=new i.ToolCitationCollection();l.tool_id=t.id;var n=new a.CitationListView({el:r,collection:l});n.render();l.fetch();this.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}console.debug("tools-form-base::initialize() - Completed.")}})}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/179c7c3fbb0d/ Changeset: 179c7c3fbb0d User: natefoo Date: 2015-02-27 19:21:22+00:00 Summary: Fix a typo in datatypes_conf.xml.sample Affected #: 1 file diff -r 99d18d1fa46b506225dad08b0688212c9493edba -r 179c7c3fbb0db10765a97eb632bfc34c570ef0ff config/datatypes_conf.xml.sample --- a/config/datatypes_conf.xml.sample +++ b/config/datatypes_conf.xml.sample @@ -180,7 +180,7 @@ <datatype extension="scf" type="galaxy.datatypes.binary:Scf" mimetype="application/octet-stream" display_in_upload="true" description="A binary sequence file in 'scf' format with a '.scf' file extension. You must manually select this 'File Format' when uploading the file." description_url="https://wiki.galaxyproject.org/Learn/Datatypes#Scf"/><datatype extension="Sequences" type="galaxy.datatypes.assembly:Sequences" display_in_upload="false"/><datatype extension="snpeffdb" type="galaxy.datatypes.text:SnpEffDb" display_in_upload="True"/> - <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.txt:SnpSiftDbNSFP" display_in_upload="True"/> + <datatype extension="snpsiftdbnsfp" type="galaxy.datatypes.text:SnpSiftDbNSFP" display_in_upload="True"/><datatype extension="dbnsfp.tabular" type="galaxy.datatypes.tabular:Tabular" subclass="True" display_in_upload="True"><converter file="tabular_to_dbnsfp.xml" target_datatype="snpsiftdbnsfp"/></datatype> 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 27 Feb '15

27 Feb '15

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/becbbe264e9d/ Changeset: becbbe264e9d User: roalva1 Date: 2015-02-25 22:25:32+00:00 Summary: Restore function necessary for splitting. Affected #: 1 file diff -r df564c852b3c1b462d095d2a0249ce5b84e1cd9f -r becbbe264e9d2780949dd5b2df27809db02c7fb7 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -203,7 +203,26 @@ return None raise NotImplementedError("Can't split generic sequence files") + def get_split_commands_sequential(is_compressed, input_name, output_name, start_sequence, sequence_count): + """ + Does a brain-dead sequential scan & extract of certain sequences + >>> Sequence.get_split_commands_sequential(True, './input.gz', './output.gz', start_sequence=0, sequence_count=10) + ['zcat "./input.gz" | ( tail -n +1 2> /dev/null) | head -40 | gzip -c > "./output.gz"'] + >>> Sequence.get_split_commands_sequential(False, './input.fastq', './output.fastq', start_sequence=10, sequence_count=10) + ['tail -n +41 "./input.fastq" 2> /dev/null | head -40 > "./output.fastq"'] + """ + start_line = start_sequence * 4 + line_count = sequence_count * 4 + # TODO: verify that tail can handle 64-bit numbers + if is_compressed: + cmd = 'zcat "%s" | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c' % (input_name, start_line+1, line_count) + else: + cmd = 'tail -n +%s "%s" 2> /dev/null | head -%s' % (start_line+1, input_name, line_count) + cmd += ' > "%s"' % output_name + return [cmd] + get_split_commands_sequential = staticmethod(get_split_commands_sequential) + class Alignment( data.Text ): """Class describing an alignment""" https://bitbucket.org/galaxy/galaxy-central/commits/8b70692766ec/ Changeset: 8b70692766ec User: roalva1 Date: 2015-02-26 15:00:12+00:00 Summary: added get_split_commands_with_toc method Affected #: 1 file diff -r becbbe264e9d2780949dd5b2df27809db02c7fb7 -r 8b70692766ec172eb4ac141a5d7266b88526f852 lib/galaxy/datatypes/sequence.py --- a/lib/galaxy/datatypes/sequence.py +++ b/lib/galaxy/datatypes/sequence.py @@ -203,6 +203,75 @@ return None raise NotImplementedError("Can't split generic sequence files") + def get_split_commands_with_toc(input_name, output_name, toc_file, start_sequence, sequence_count): + """ + Uses a Table of Contents dict, parsed from an FQTOC file, to come up with a set of + shell commands that will extract the parts necessary + >>> three_sections=[dict(start=0, end=74, sequences=10), dict(start=74, end=148, sequences=10), dict(start=148, end=148+76, sequences=10)] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=10) + ['dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=1, sequence_count=5) + ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +5 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=0, sequence_count=20) + ['dd bs=1 skip=0 count=148 if=./input.gz 2> /dev/null >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=10) + ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', '(dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=10, sequence_count=10) + ['dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz'] + >>> Sequence.get_split_commands_with_toc('./input.gz', './output.gz', dict(sections=three_sections), start_sequence=5, sequence_count=20) + ['(dd bs=1 skip=0 count=74 if=./input.gz 2> /dev/null )| zcat | ( tail -n +21 2> /dev/null) | head -20 | gzip -c >> ./output.gz', 'dd bs=1 skip=74 count=74 if=./input.gz 2> /dev/null >> ./output.gz', '(dd bs=1 skip=148 count=76 if=./input.gz 2> /dev/null )| zcat | ( tail -n +1 2> /dev/null) | head -20 | gzip -c >> ./output.gz'] + """ + sections = toc_file['sections'] + result = [] + + current_sequence = long(0) + i=0 + # skip to the section that contains my starting sequence + while i < len(sections) and start_sequence >= current_sequence + long(sections[i]['sequences']): + current_sequence += long(sections[i]['sequences']) + i += 1 + if i == len(sections): # bad input data! + raise Exception('No FQTOC section contains starting sequence %s' % start_sequence) + + # These two variables act as an accumulator for consecutive entire blocks that + # can be copied verbatim (without decompressing) + start_chunk = long(-1) + end_chunk = long(-1) + copy_chunk_cmd = 'dd bs=1 skip=%s count=%s if=%s 2> /dev/null >> %s' + + while sequence_count > 0 and i < len(sections): + # we need to extract partial data. So, find the byte offsets of the chunks that contain the data we need + # use a combination of dd (to pull just the right sections out) tail (to skip lines) and head (to get the + # right number of lines + sequences = long(sections[i]['sequences']) + skip_sequences = start_sequence-current_sequence + sequences_to_extract = min(sequence_count, sequences-skip_sequences) + start_copy = long(sections[i]['start']) + end_copy = long(sections[i]['end']) + if sequences_to_extract < sequences: + if start_chunk > -1: + result.append(copy_chunk_cmd % (start_chunk, end_chunk-start_chunk, input_name, output_name)) + start_chunk = -1 + # extract, unzip, trim, recompress + result.append('(dd bs=1 skip=%s count=%s if=%s 2> /dev/null )| zcat | ( tail -n +%s 2> /dev/null) | head -%s | gzip -c >> %s' % + (start_copy, end_copy-start_copy, input_name, skip_sequences*4+1, sequences_to_extract*4, output_name)) + else: # whole section - add it to the start_chunk/end_chunk accumulator + if start_chunk == -1: + start_chunk = start_copy + end_chunk = end_copy + sequence_count -= sequences_to_extract + start_sequence += sequences_to_extract + current_sequence += sequences + i += 1 + if start_chunk > -1: + result.append(copy_chunk_cmd % (start_chunk, end_chunk-start_chunk, input_name, output_name)) + + if sequence_count > 0: + raise Exception('%s sequences not found in file' % sequence_count) + + return result + get_split_commands_with_toc = staticmethod(get_split_commands_with_toc) + def get_split_commands_sequential(is_compressed, input_name, output_name, start_sequence, sequence_count): """ Does a brain-dead sequential scan & extract of certain sequences @@ -222,7 +291,7 @@ return [cmd] get_split_commands_sequential = staticmethod(get_split_commands_sequential) - + class Alignment( data.Text ): """Class describing an alignment""" 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

[galaxyproject/usegalaxy-playbook] a634b7: Update Test again
by GitHub 27 Feb '15

27 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a634b792e9e5b8fcfb99da5fc5a3fec697a7556c https://github.com/galaxyproject/usegalaxy-playbook/commit/a634b792e9e5b8fc… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-27 (Fri, 27 Feb 2015) Changed paths: M stage/group_vars/all.yml Log Message: ----------- Update Test again

1 0

commit/galaxy-central: guerler: ToolForm: Fix dataset order for multi select run
by commits-noreply＠bitbucket.org 27 Feb '15

27 Feb '15

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/df564c852b3c/ Changeset: df564c852b3c User: guerler Date: 2015-02-27 15:12:13+00:00 Summary: ToolForm: Fix dataset order for multi select run Affected #: 3 files diff -r 6bd6c350296c94817de06d3c239b9bf8d2b9978c -r df564c852b3c1b462d095d2a0249ce5b84e1cd9f client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -277,6 +277,11 @@ } } + // sort by history ids + result.values.sort(function(a, b){ + return a.hid - b.hid; + }); + // return return result; }, diff -r 6bd6c350296c94817de06d3c239b9bf8d2b9978c -r df564c852b3c1b462d095d2a0249ce5b84e1cd9f static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -277,6 +277,11 @@ } } + // sort by history ids + result.values.sort(function(a, b){ + return a.hid - b.hid; + }); + // return return result; }, diff -r 6bd6c350296c94817de06d3c239b9bf8d2b9978c -r df564c852b3c1b462d095d2a0249ce5b84e1cd9f static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ 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

[galaxyproject/usegalaxy-playbook] a8df06: Update Main
by GitHub 27 Feb '15

27 Feb '15

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: a8df0635efc627a83ba685dfaabfc99e835ae6fa https://github.com/galaxyproject/usegalaxy-playbook/commit/a8df0635efc627a8… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2015-02-27 (Fri, 27 Feb 2015) Changed paths: M production/group_vars/all.yml Log Message: ----------- Update Main

1 0

commit/galaxy-central: 10 new changesets
by commits-noreply＠bitbucket.org 27 Feb '15

27 Feb '15

10 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/563defcf9c83/ Changeset: 563defcf9c83 Branch: release_15.03 User: dan Date: 2015-02-26 22:16:55+00:00 Summary: Allow TabularToolDataTable to be loaded from a url instead of a path. Affected #: 1 file diff -r b046e38c21d140d9fdbba80fc1861cd6cf4e8352 -r 563defcf9c838cf11ac179890b2ca28b27c7fd1f lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -14,6 +14,8 @@ import hashlib from glob import glob +from tempfile import NamedTemporaryFile +from urllib2 import urlopen from galaxy import util from galaxy.util.odict import odict @@ -279,7 +281,22 @@ repo_info = None # Read every file for file_element in config_element.findall( 'file' ): - filename = file_path = expand_here_template( file_element.get( 'path', None ), here=self.here ) + tmp_file = None + filename = file_element.get( 'path', None ) + if filename is None: + # Handle URLs as files + filename = file_element.get( 'url', None ) + if filename: + tmp_file = NamedTemporaryFile( prefix='TTDT_URL_%s-' % self.name ) + try: + tmp_file.write( urlopen( filename ).read() ) + except Exception, e: + log.error( 'Error loading Data Table URL "%s": %s', filename, e ) + continue + log.debug( 'Loading Data Table URL "%s" as filename "%s".', filename, tmp_file.name ) + filename = tmp_file.name + tmp_file.flush() + filename = file_path = expand_here_template( filename, here=self.here ) found = False if file_path is None: log.debug( "Encountered a file element (%s) that does not contain a path value when loading tool data table '%s'.", util.xml_to_string( file_element ), self.name ) @@ -325,6 +342,9 @@ config_element=config_element, tool_shed_repository=repo_info, errors=errors ) else: log.debug( "Filename '%s' already exists in filenames (%s), not adding", filename, self.filenames.keys() ) + # Remove URL tmp file + if tmp_file is not None: + tmp_file.close() def merge_tool_data_table( self, other_table, allow_duplicates=True, persist=False, persist_on_error=False, entry_source=None, **kwd ): assert self.columns == other_table.columns, "Merging tabular data tables with non matching columns is not allowed: %s:%s != %s:%s" % ( self.name, self.columns, other_table.name, other_table.columns ) https://bitbucket.org/galaxy/galaxy-central/commits/c35498a73b41/ Changeset: c35498a73b41 Branch: release_15.03 User: guerler Date: 2015-02-27 06:30:48+00:00 Summary: ToolForm: Show initial validation errors on re-run Affected #: 3 files diff -r 563defcf9c838cf11ac179890b2ca28b27c7fd1f -r c35498a73b41c76446223123721f8a9c08bec03c 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 @@ -22,6 +22,7 @@ } }) } + options.initial_errors = options.job_id; ToolFormBase.prototype.initialize.call(this, options); }, diff -r 563defcf9c838cf11ac179890b2ca28b27c7fd1f -r c35498a73b41c76446223123721f8a9c08bec03c static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -22,6 +22,7 @@ } }) } + options.initial_errors = options.job_id; ToolFormBase.prototype.initialize.call(this, options); }, diff -r 563defcf9c838cf11ac179890b2ca28b27c7fd1f -r c35498a73b41c76446223123721f8a9c08bec03c 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-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{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);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{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);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/441d5188382c/ Changeset: 441d5188382c Branch: release_15.03 User: guerler Date: 2015-02-27 06:35:38+00:00 Summary: ToolForm/Collections: Re-introduce parameter expansion Affected #: 4 files diff -r c35498a73b41c76446223123721f8a9c08bec03c -r 441d5188382c775009e6612c57e9317d8cb9a944 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 @@ -110,17 +110,6 @@ inputs : current_state } - // patch data tool parameters - // TODO: This needs to be removed and handled in the api - for (var i in current_state.inputs) { - var dict = current_state.inputs[i]; - try { - if (dict && dict.values[0].src === 'hda') { - current_state.inputs[i] = self.content.get({id: dict.values[0].id, src: 'hda'}).id_uncoded; - } - } catch (err) {} - } - // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { diff -r c35498a73b41c76446223123721f8a9c08bec03c -r 441d5188382c775009e6612c57e9317d8cb9a944 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2366,7 +2366,7 @@ else: value, error = check_param(trans, input, default_value, context) except Exception, err: - log.error('Checking parameter failed. %s', str(err)) + log.error('Checking parameter %s failed. %s', input.name, str(err)) pass return [value, error] @@ -2482,6 +2482,11 @@ else: state[k] = jsonify(state[k]) + # expand incoming parameters (parameters might trigger multiple tool executions, + # here we select the first execution only in order to resolve dynamic parameters) + expanded_incomings, _ = expand_meta_parameters( trans, self, params.__dict__ ) + params.__dict__ = expanded_incomings[ 0 ] + # do param translation here, used by datasource tools if self.input_translator: self.input_translator.translate( params ) diff -r c35498a73b41c76446223123721f8a9c08bec03c -r 441d5188382c775009e6612c57e9317d8cb9a944 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -110,17 +110,6 @@ inputs : current_state } - // patch data tool parameters - // TODO: This needs to be removed and handled in the api - for (var i in current_state.inputs) { - var dict = current_state.inputs[i]; - try { - if (dict && dict.values[0].src === 'hda') { - current_state.inputs[i] = self.content.get({id: dict.values[0].id, src: 'hda'}).id_uncoded; - } - } catch (err) {} - } - // activates/disables spinner for dynamic fields to indicate that they are currently being updated function wait(active) { for (var i in self.input_list) { diff -r c35498a73b41c76446223123721f8a9c08bec03c -r 441d5188382c775009e6612c57e9317d8cb9a944 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-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};for(var h in g.inputs){var n=g.inputs[h];try{if(n&&n.values[0].src==="hda"){g.inputs[h]=f.content.get({id:n.values[0].id,src:"hda"}).id_uncoded}}catch(k){}}function m(r){for(var p in f.input_list){var q=f.field_list[p];var o=f.input_list[p];if(o.is_dynamic&&q.wait&&q.unwait){if(r){q.wait()}else{q.unwait()}}}}m(true);var l=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var j=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:j,data:g,success:function(i){f.tree.matchModel(i,function(p,t){var o=f.input_list[p];if(o&&o.options){if(!_.isEqual(o.options,t.options)){o.options=t.options;var u=f.field_list[p];if(u.update){var s=[];if((["data","data_collection","drill_down"]).indexOf(o.type)!=-1){s=o.options}else{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);u.trigger("change");console.debug("Updating options for "+p)}}}});m(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(i);f.deferred.done(l)},error:function(i){f.deferred.done(l);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(i)}})}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/tools/tools-form-base","mvc/tools/tools-jobs"],function(c,e,b,a){var d=b.extend({initialize:function(g){var f=this;this.job_handler=new a(this);this.buttons={execute:new e.Button({icon:"fa-check",tooltip:"Execute: "+g.name,title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){f.job_handler.submit()}})};g.initial_errors=g.job_id;b.prototype.initialize.call(this,g)},_buildModel:function(){var f=this;var g=galaxy_config.root+"api/tools/"+this.options.id+"/build?";if(this.options.job_id){g+="job_id="+this.options.job_id}else{if(this.options.dataset_id){g+="dataset_id="+this.options.dataset_id}else{g+="tool_version="+this.options.version+"&";var i=top.location.href;var j=i.indexOf("?");if(i.indexOf("tool_id=")!=-1&&j!==-1){g+=i.slice(j+1)}}}var h=this.deferred.register();c.request({type:"GET",url:g,success:function(k){f.build(k);f.message.update({status:"success",message:"Now you are using '"+f.options.name+"' version "+f.options.version+".",persistent:false});f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model ready.");console.debug(k)},error:function(k){f.deferred.done(h);console.debug("tools-form::initialize() - Initial tool model request failed.");console.debug(k);var l=k.error||"Uncaught error.";f.modal.show({title:"Tool cannot be executed",body:l,buttons:{Close:function(){f.modal.hide()}}})}})},_updateModel:function(g){var f=this;var g={tool_id:this.options.id,tool_version:this.options.version,inputs:g};function j(n){for(var l in f.input_list){var m=f.field_list[l];var k=f.input_list[l];if(k.is_dynamic&&m.wait&&m.unwait){if(n){m.wait()}else{m.unwait()}}}}j(true);var i=this.deferred.register();console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(g);var h=galaxy_config.root+"api/tools/"+this.options.id+"/build";c.request({type:"POST",url:h,data:g,success:function(k){f.tree.matchModel(k,function(m,q){var l=f.input_list[m];if(l&&l.options){if(!_.isEqual(l.options,q.options)){l.options=q.options;var r=f.field_list[m];if(r.update){var p=[];if((["data","data_collection","drill_down"]).indexOf(l.type)!=-1){p=l.options}else{for(var o in q.options){var n=q.options[o];if(n.length>2){p.push({label:n[0],value:n[1]})}}}r.update(p);r.trigger("change");console.debug("Updating options for "+m)}}}});j(false);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(k);f.deferred.done(i)},error:function(k){f.deferred.done(i);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(k)}})}});return{View:d}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/9e16f3d9fafe/ Changeset: 9e16f3d9fafe Branch: release_15.03 User: guerler Date: 2015-02-27 06:49:53+00:00 Summary: Parameters: Prevent uncaught exception on unavailable datasets in column validation Affected #: 1 file diff -r 441d5188382c775009e6612c57e9317d8cb9a944 -r 9e16f3d9fafebfe078fd1d36f59ec1380d6eeab5 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1335,6 +1335,10 @@ datasets = util.listify( context[ self.data_ref ] ) for dataset in datasets: if dataset: + # Check if metadata is available + if not hasattr(dataset, 'metadata'): + return True + # Check if the dataset does not have the expected metadata for columns if not dataset.metadata.columns: # Only allow late validation if the dataset is not yet ready https://bitbucket.org/galaxy/galaxy-central/commits/84e665326798/ Changeset: 84e665326798 Branch: release_15.03 User: guerler Date: 2015-02-27 06:57:39+00:00 Summary: ToolForm/Ui: Limit selection to available options Affected #: 3 files diff -r 9e16f3d9fafebfe078fd1d36f59ec1380d6eeab5 -r 84e665326798aba03ff4e9acca501a7a96d16741 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -78,9 +78,11 @@ if (new_value === null) { new_value = '__null__'; } - this.$select.val(new_value); - if (this.$select.select2) { - this.$select.select2('val', new_value); + if (this.exists(new_value)) { + this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } } diff -r 9e16f3d9fafebfe078fd1d36f59ec1380d6eeab5 -r 84e665326798aba03ff4e9acca501a7a96d16741 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -78,9 +78,11 @@ if (new_value === null) { new_value = '__null__'; } - this.$select.val(new_value); - if (this.$select.select2) { - this.$select.select2('val', new_value); + if (this.exists(new_value)) { + this.$select.val(new_value); + if (this.$select.select2) { + this.$select.select2('val', new_value); + } } } diff -r 9e16f3d9fafebfe078fd1d36f59ec1380d6eeab5 -r 84e665326798aba03ff4e9acca501a7a96d16741 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/ba82b4086c84/ Changeset: ba82b4086c84 Branch: release_15.03 User: guerler Date: 2015-02-27 06:59:43+00:00 Summary: Parameters: Fix deleted datasets validation message Affected #: 1 file diff -r 84e665326798aba03ff4e9acca501a7a96d16741 -r ba82b4086c84446e0f2e5f75873fc94f52306be7 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2016,7 +2016,7 @@ for v in values: if v: if v.deleted: - raise ValueError( "The previously selected dataset has been previously deleted" ) + raise ValueError( "The previously selected dataset has been deleted." ) if hasattr( v, "dataset" ) and v.dataset.state in [ galaxy.model.Dataset.states.ERROR, galaxy.model.Dataset.states.DISCARDED ]: raise ValueError( "The previously selected dataset has entered an unusable state" ) if not self.multiple: https://bitbucket.org/galaxy/galaxy-central/commits/a3bc4324eb02/ Changeset: a3bc4324eb02 Branch: release_15.03 User: guerler Date: 2015-02-27 09:26:15+00:00 Summary: Parameters: Set hidden attribute for hidden dataset parameter Affected #: 1 file diff -r ba82b4086c84446e0f2e5f75873fc94f52306be7 -r a3bc4324eb0280cd73c49ed0ca6327b5be96b6ff lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2420,6 +2420,7 @@ DataToolParameter.__init__( self, tool, elem ) self.value = "None" self.type = "hidden_data" + self.hidden = True def get_initial_value( self, trans, context, history=None ): return None https://bitbucket.org/galaxy/galaxy-central/commits/1a1cc1be950f/ Changeset: 1a1cc1be950f Branch: release_15.03 User: guerler Date: 2015-02-27 09:36:20+00:00 Summary: ToolForm/Ui: Restrict available option requirement to single select fields Affected #: 3 files diff -r a3bc4324eb0280cd73c49ed0ca6327b5be96b6ff -r 1a1cc1be950f0d7170e6a758b395681aefff3d45 client/galaxy/scripts/mvc/ui/ui-select-default.js --- a/client/galaxy/scripts/mvc/ui/ui-select-default.js +++ b/client/galaxy/scripts/mvc/ui/ui-select-default.js @@ -78,7 +78,7 @@ if (new_value === null) { new_value = '__null__'; } - if (this.exists(new_value)) { + if (this.exists(new_value) || this.options.multiple) { this.$select.val(new_value); if (this.$select.select2) { this.$select.select2('val', new_value); diff -r a3bc4324eb0280cd73c49ed0ca6327b5be96b6ff -r 1a1cc1be950f0d7170e6a758b395681aefff3d45 static/scripts/mvc/ui/ui-select-default.js --- a/static/scripts/mvc/ui/ui-select-default.js +++ b/static/scripts/mvc/ui/ui-select-default.js @@ -78,7 +78,7 @@ if (new_value === null) { new_value = '__null__'; } - if (this.exists(new_value)) { + if (this.exists(new_value) || this.options.multiple) { this.$select.val(new_value); if (this.$select.select2) { this.$select.select2('val', new_value); diff -r a3bc4324eb0280cd73c49ed0ca6327b5be96b6ff -r 1a1cc1be950f0d7170e6a758b395681aefff3d45 static/scripts/packed/mvc/ui/ui-select-default.js --- a/static/scripts/packed/mvc/ui/ui-select-default.js +++ b/static/scripts/packed/mvc/ui/ui-select-default.js @@ -1,1 +1,1 @@ -define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file +define(["utils/utils"],function(a){var b=Backbone.View.extend({optionsDefault:{id:"",cls:"ui-select",error_text:"No data available",empty_text:"No selection",visible:true,wait:false,multiple:false,searchable:true,optional:false},initialize:function(d){this.options=a.merge(d,this.optionsDefault);this.setElement(this._template(this.options));this.$select=this.$el.find(".select");this.$icon=this.$el.find(".icon");this.$button=this.$el.find(".button");if(this.options.multiple){this.$el.addClass("ui-select-multiple");this.$select.prop("multiple",true);this.$button.remove()}this.update(this.options.data);if(this.options.value!==undefined){this.value(this.options.value)}if(!this.options.visible){this.hide()}if(this.options.wait){this.wait()}else{this.show()}var c=this;this.$select.on("change",function(){c._change()});this.on("change",function(){c._change()})},value:function(c){if(c!==undefined){if(c===null){c="__null__"}if(this.exists(c)||this.options.multiple){this.$select.val(c);if(this.$select.select2){this.$select.select2("val",c)}}}return this._getValue()},first:function(){var c=this.$select.find("option").first();if(c.length>0){return c.val()}else{return null}},text:function(){return this.$select.find("option:selected").text()},show:function(){this.unwait();this.$select.show();this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-spinner fa-spin")},unwait:function(){this.$icon.removeClass();this.$icon.addClass("fa fa-caret-down")},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",false)},disable:function(){this.$select.prop("disabled",true)},add:function(c){this.$select.append(this._templateOption(c));this._refresh()},del:function(c){this.$select.find("option[value="+c+"]").remove();this.$select.trigger("change");this._refresh()},update:function(c){var e=this._getValue();this.$select.find("option").remove();if(!this.options.multiple&&this.options.optional){this.$select.append(this._templateOption({value:"__null__",label:this.options.empty_text}))}for(var d in c){this.$select.append(this._templateOption(c[d]))}this._refresh();if(this.options.searchable){this.$select.select2("destroy");this.$select.select2()}this.value(e);if(this._getValue()===null){this.value(this.first())}},setOnChange:function(c){this.options.onchange=c},exists:function(c){return this.$select.find('option[value="'+c+'"]').length>0},_change:function(){if(this.options.onchange){this.options.onchange(this._getValue())}},_getValue:function(){var c=this.$select.val();if(!a.validate(c)){return null}return c},_refresh:function(){var c=this.$select.find("option").length;if(c==0){this.disable();this.$select.empty();this.$select.append(this._templateOption({value:"__null__",label:this.options.error_text}))}else{this.enable()}},_templateOption:function(c){return'<option value="'+c.value+'">'+c.label+"</option>"},_template:function(c){return'<div id="'+c.id+'" class="'+c.cls+'"><select id="'+c.id+'_select" class="select"/><div class="button"><i class="icon"/></div></div>'}});return{View:b}}); \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/04d4f727c2ff/ Changeset: 04d4f727c2ff Branch: release_15.03 User: carlfeberhard Date: 2015-02-27 15:03:47+00:00 Summary: Fix display_structure by using serializer; fix structure by removing extra decode_id Affected #: 2 files diff -r 1a1cc1be950f0d7170e6a758b395681aefff3d45 -r 04d4f727c2ffc85475cc2423faf051d45f8f2aaa lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -543,8 +543,10 @@ def structure( self, trans, id=None, **kwargs ): """ """ - id = self.decode_id( id ) if id else trans.history.id - history_to_view = self.history_manager.get_accessible( trans, id, trans.user ) + unencoded_history_id = trans.history.id + if id: + unencoded_history_id = self.decode_id( id ) + history_to_view = self.history_manager.get_accessible( trans, unencoded_history_id, trans.user ) history_data = self.history_manager._get_history_data( trans, history_to_view ) history_dictionary = history_data[ 'history' ] @@ -552,7 +554,7 @@ jobs = ( trans.sa_session.query( trans.app.model.Job ) .filter( trans.app.model.Job.user == trans.user ) - .filter( trans.app.model.Job.history_id == self.decode_id( id ) ) ).all() + .filter( trans.app.model.Job.history_id == unencoded_history_id ) ).all() jobs = map( lambda j: self.encode_all_ids( trans, j.to_dict( 'element' ), True ), jobs ) tools = {} diff -r 1a1cc1be950f0d7170e6a758b395681aefff3d45 -r 04d4f727c2ffc85475cc2423faf051d45f8f2aaa templates/webapps/galaxy/history/display_structured.mako --- a/templates/webapps/galaxy/history/display_structured.mako +++ b/templates/webapps/galaxy/history/display_structured.mako @@ -128,13 +128,15 @@ ## ---------------------------------------------------------------------------- <%def name="javascripts()"><% + from galaxy.managers import hdas + hda_serializer = hdas.HDASerializer( trans.app ) self.js_app = 'display-structured' controller = trans.webapp.controllers[ 'history' ] hda_dicts = [] id_hda_dict_map = {} for hda in history.active_datasets: - hda_dict = controller.get_hda_dict( trans, hda ) + hda_dict = hda_serializer.serialize_to_view( trans, hda, 'detailed' ) id_hda_dict_map[ hda_dict[ 'id' ] ] = hda_dict hda_dicts.append( hda_dict ) %> https://bitbucket.org/galaxy/galaxy-central/commits/2a238115b21c/ Changeset: 2a238115b21c Branch: release_15.03 User: guerler Date: 2015-02-27 15:12:13+00:00 Summary: ToolForm: Fix dataset order for multi select run Affected #: 3 files diff -r 04d4f727c2ffc85475cc2423faf051d45f8f2aaa -r 2a238115b21ccce4391355329e322132716daecc client/galaxy/scripts/mvc/tools/tools-select-content.js --- a/client/galaxy/scripts/mvc/tools/tools-select-content.js +++ b/client/galaxy/scripts/mvc/tools/tools-select-content.js @@ -277,6 +277,11 @@ } } + // sort by history ids + result.values.sort(function(a, b){ + return a.hid - b.hid; + }); + // return return result; }, diff -r 04d4f727c2ffc85475cc2423faf051d45f8f2aaa -r 2a238115b21ccce4391355329e322132716daecc static/scripts/mvc/tools/tools-select-content.js --- a/static/scripts/mvc/tools/tools-select-content.js +++ b/static/scripts/mvc/tools/tools-select-content.js @@ -277,6 +277,11 @@ } } + // sort by history ids + result.values.sort(function(a, b){ + return a.hid - b.hid; + }); + // return return result; }, diff -r 04d4f727c2ffc85475cc2423faf051d45f8f2aaa -r 2a238115b21ccce4391355329e322132716daecc static/scripts/packed/mvc/tools/tools-select-content.js --- a/static/scripts/packed/mvc/tools/tools-select-content.js +++ b/static/scripts/packed/mvc/tools/tools-select-content.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-misc","mvc/ui/ui-tabs","mvc/tools/tools-template"],function(c,e,b,a){var d=Backbone.View.extend({initialize:function(g,p){this.app=g;this.options=p;var o=this;this.setElement('<div class="ui-select-content"/>');this.list={};var m=[];if(p.type=="data_collection"){this.mode="collection"}else{if(p.multiple){this.mode="multiple"}else{this.mode="single"}}this.current=this.mode;this.list={};var k=c.textify(p.extensions);var j="No dataset available.";if(k){j="No "+k+" dataset available."}var l="No dataset list available.";if(k){l="No "+k+" dataset collection available."}if(this.mode=="single"){m.push({icon:"fa-file-o",value:"single",tooltip:"Single dataset"});this.select_single=new e.Select.View({optional:p.optional,error_text:j,onchange:function(){o.trigger("change")}});this.list.single={field:this.select_single,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"){m.push({icon:"fa-files-o",value:"multiple",tooltip:"Multiple datasets"});this.select_multiple=new e.Select.View({multiple:true,searchable:false,error_text:j,onchange:function(){o.trigger("change")}});this.list.multiple={field:this.select_multiple,type:"hda"}}if(this.mode=="single"||this.mode=="multiple"||this.mode=="collection"){m.push({icon:"fa-folder-o",value:"collection",tooltip:"Dataset collection"});this.select_collection=new e.Select.View({error_text:l,optional:p.optional,onchange:function(){o.trigger("change")}});this.list.collection={field:this.select_collection,type:"hdca"}}this.button_type=new e.RadioButton.View({value:this.current,data:m,onchange:function(i){o.current=i;o.refresh();o.trigger("change")}});this.$batch=$(a.batchMode());var f=_.size(this.list);var n=0;if(f>1){this.$el.append(this.button_type.$el);n=Math.max(0,_.size(this.list)*35)+"px"}for(var h in this.list){this.$el.append(this.list[h].field.$el.css({"margin-left":n}))}this.$el.append(this.$batch.css({"margin-left":n}));this.update(p.data);if(this.options.value!==undefined){this.value(this.options.value)}this.refresh();this.on("change",function(){if(p.onchange){p.onchange(o.value())}})},wait:function(){for(var f in this.list){this.list[f].field.wait()}},unwait:function(){for(var f in this.list){this.list[f].field.unwait()}},update:function(g){function f(l,h){if(l){var m=[];for(var j in h){var k=h[j];m.push({label:k.hid+": "+k.name,value:k.id})}l.update(m)}}f(this.select_single,g.hda);f(this.select_multiple,g.hda);f(this.select_collection,g.hdca);this.app.content.add(g)},value:function(j){if(j!==undefined){if(j&&j.values){try{var m=[];for(var h in j.values){m.push(j.values[h].id)}if(j&&j.values.length>0&&j.values[0].src=="hcda"){this.current="collection";this.select_collection.value(m[0])}else{if(this.mode=="multiple"){this.current="multiple";this.select_multiple.value(m)}else{this.current="single";this.select_single.value(m[0])}}}catch(l){console.debug("tools-select-content::value() - Skipped.")}}else{for(var h in this.list){this.list[h].field.value(null)}}}this.refresh();var k=this._select().value();if(k===null){return null}if(!(k instanceof Array)){k=[k]}if(k.length===0){return null}var f={batch:this._batch(),values:[]};for(var h in k){var g=this.app.content.get({id:k[h],src:this.list[this.current].type});if(g){f.values.push(g)}else{return null}}f.values.sort(function(n,i){return n.hid-i.hid});return f},refresh:function(){this.button_type.value(this.current);for(var g in this.list){var f=this.list[g].field.$el;if(this.current==g){f.show()}else{f.hide()}}if(this._batch()){this.$batch.show()}else{this.$batch.hide()}},_select:function(){return this.list[this.current].field},_batch:function(){if(this.current=="collection"){var f=this.app.content.get({id:this._select().value(),src:"hdca"});if(f&&f.map_over_type){return true}}if(this.current!="single"){if(this.mode=="single"){return true}}return false}});return{View:d}}); 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