1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/3947a9273550/
Changeset: 3947a9273550
User: dan
Date: 2015-02-11 20:39:38+00:00
Summary: Comment out igv local external display application link by default, since it is confusing users (most do not have a local igv running).
Affected #: 1 file
diff -r 11d7c10c1b5e2778f6a96bfa5e3e0e950a619634 -r 3947a92735506923a0f51abe36263bbc0aecfb79 tool-data/shared/igv/igv_build_sites.txt.sample
--- a/tool-data/shared/igv/igv_build_sites.txt.sample
+++ b/tool-data/shared/igv/igv_build_sites.txt.sample
@@ -1,4 +1,4 @@
#site_id site_name site_url dbkey ivg_build_name
web_link_main web current http://www.broadinstitute.org/igv/projects/current/igv.php hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
#web_jnlp_1.5 web 1.5 http://www.broadinstitute.org/igvdata/jws/prod hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
-local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
\ No newline at end of file
+#local_default local http://localhost:60151/load hg19,hg_g1k_v37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum hg19,b37,hg18,1kg_ref,hg17,hg16,mm9,mm8,mm7,panTro2,rheMac2,rn4,canFam2,bosTau6,bosTau4,bosTau3,susScrofa,galGal3,cavPor3,monDom5,xenTro2,taeGut1,zebrafish,danRer6,danRer7,gasAcu1,Aplysia,Plasmodium_3D7_v2.1,Plasmodium_3D7_v5.5,Plasmodium_6.1,PlasmoDB_7.0,pvivax,GSM552910,sacCer1,sacCer2,sk1,Y55,sacCer62,spombe_709,spombe_1.55,candida,mg8,spur_2.1,spur_2.5,spur_3.0,WS201,ce6,ce4,dm3,dm2,dmel_5.9,dmel_r5.22,dmel_r5.33,tcas_2.0,tcas_3.0,ncrassa_v3,nc10,Glamblia_2.0,me49,tb927,tbgambi,lmjr,anidulans_4.1,NC_009012,U00096.2,NC_000913.2,NC_002655.2,CSavignyi_v2.1,tair8,tair9,tair10,O_Sativa_r6,osativa_6.1,B73,ZmB73_5a,ppatens_1.2,D.discoideum
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/11d7c10c1b5e/
Changeset: 11d7c10c1b5e
User: martenson
Date: 2015-02-11 19:31:13+00:00
Summary: rename the link from toolform to the Tool Shed
Affected #: 3 files
diff -r c6915ffcd27c174d0d4c298855ce923d56bd2c62 -r 11d7c10c1b5e2778f6a96bfa5e3e0e950a619634 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
@@ -290,7 +290,7 @@
if (this.options.sharable_url) {
menu_button.addMenu({
icon : 'fa-external-link',
- title : 'Open in Toolshed',
+ title : 'See in Tool Shed',
tooltip : 'Access the repository',
onclick : function() {
window.open(self.options.sharable_url);
diff -r c6915ffcd27c174d0d4c298855ce923d56bd2c62 -r 11d7c10c1b5e2778f6a96bfa5e3e0e950a619634 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
@@ -290,7 +290,7 @@
if (this.options.sharable_url) {
menu_button.addMenu({
icon : 'fa-external-link',
- title : 'Open in Toolshed',
+ title : 'See in Tool Shed',
tooltip : 'Access the repository',
onclick : function() {
window.open(self.options.sharable_url);
diff -r c6915ffcd27c174d0d4c298855ce923d56bd2c62 -r 11d7c10c1b5e2778f6a96bfa5e3e0e950a619634 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(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l.deferred.reset();l.deferred.execute(function(){l._updateModel(m)})}});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}});this.trigger("refresh")},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){$(this.container).animate({scrollTop:o.$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.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"Open in Toolshed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$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.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l.deferred.reset();l.deferred.execute(function(){l._updateModel(m)})}});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).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
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1d9da5a9edfa/
Changeset: 1d9da5a9edfa
User: jmchilton
Date: 2015-02-11 18:15:21+00:00
Summary: Fix incorrect constant pointed out by Nicola.
https://bitbucket.org/galaxy/galaxy-central/pull-request/664/remove-test-da….
Affected #: 1 file
diff -r 86ac99a2896b87915e35b81db1320fdfe73bf556 -r 1d9da5a9edfa536e8755ecafdb9f7a23694d6761 test/base/test_data.py
--- a/test/base/test_data.py
+++ b/test/base/test_data.py
@@ -75,7 +75,7 @@
def __init__(self, repository, environ):
self.repository = repository
self.updated = False
- repo_cache = environ.get("GALAXY_TEST_DATA_REPO_CACHE", "test-data-repos")
+ repo_cache = environ.get("GALAXY_TEST_DATA_REPO_CACHE", "test-data-cache")
m = hashlib.md5()
m.update(repository)
repo_path = os.path.join(repo_cache, m.hexdigest())
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/86ac99a2896b/
Changeset: 86ac99a2896b
User: guerler
Date: 2015-02-11 18:12:06+00:00
Summary: ToolForm: Reduce number of refresh events
Affected #: 9 files
diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 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
@@ -93,7 +93,7 @@
this._renderForm(options);
// rebuild the underlying data structure
- this.tree.finalize();
+ var current_state = this.tree.finalize();
// show errors on startup
if (options.initial_errors) {
@@ -102,9 +102,15 @@
// add refresh listener
this.on('refresh', function() {
- // by using/resetting the deferred ajax queue the number of redundant calls is reduced
- self.deferred.reset();
- self.deferred.execute(function(){self._updateModel()});
+ var new_state = self.tree.finalize();
+ if (!_.isEqual(new_state, current_state)) {
+ // backup current state
+ current_state = new_state;
+
+ // by using/resetting the deferred ajax queue the number of redundant calls is reduced
+ self.deferred.reset();
+ self.deferred.execute(function(){self._updateModel(current_state)});
+ }
});
// add reset listener
diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 client/galaxy/scripts/mvc/tools/tools-form-workflow.js
--- a/client/galaxy/scripts/mvc/tools/tools-form-workflow.js
+++ b/client/galaxy/scripts/mvc/tools/tools-form-workflow.js
@@ -274,15 +274,15 @@
/** Request a new model for an already created tool form and updates the form inputs
*/
- _updateModel: function() {
+ _updateModel: function(current_state) {
// link self
var self = this;
// create the request dictionary
- var current_state = {
+ current_state = {
tool_id : this.options.id,
tool_version : this.options.version,
- inputs : this.tree.finalize()
+ inputs : current_state
}
// log tool state
diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 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
@@ -115,7 +115,7 @@
});
// log tool state
- console.debug('tools-form::_refreshForm() - Refreshing states.');
+ console.debug('tools-form::_refreshForm() - Sending current state (see below).');
console.debug(current_state);
// activates/disables spinner for dynamic fields to indicate that they are currently being updated
@@ -188,7 +188,7 @@
self.deferred.done(process_id);
// log success
- console.debug('tools-form::_refreshForm() - States refreshed.');
+ console.debug('tools-form::_refreshForm() - Received new model (see below).');
console.debug(new_model);
},
error : function(response) {
diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 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
@@ -93,7 +93,7 @@
this._renderForm(options);
// rebuild the underlying data structure
- this.tree.finalize();
+ var current_state = this.tree.finalize();
// show errors on startup
if (options.initial_errors) {
@@ -102,9 +102,15 @@
// add refresh listener
this.on('refresh', function() {
- // by using/resetting the deferred ajax queue the number of redundant calls is reduced
- self.deferred.reset();
- self.deferred.execute(function(){self._updateModel()});
+ var new_state = self.tree.finalize();
+ if (!_.isEqual(new_state, current_state)) {
+ // backup current state
+ current_state = new_state;
+
+ // by using/resetting the deferred ajax queue the number of redundant calls is reduced
+ self.deferred.reset();
+ self.deferred.execute(function(){self._updateModel(current_state)});
+ }
});
// add reset listener
diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 static/scripts/mvc/tools/tools-form-workflow.js
--- a/static/scripts/mvc/tools/tools-form-workflow.js
+++ b/static/scripts/mvc/tools/tools-form-workflow.js
@@ -274,15 +274,15 @@
/** Request a new model for an already created tool form and updates the form inputs
*/
- _updateModel: function() {
+ _updateModel: function(current_state) {
// link self
var self = this;
// create the request dictionary
- var current_state = {
+ current_state = {
tool_id : this.options.id,
tool_version : this.options.version,
- inputs : this.tree.finalize()
+ inputs : current_state
}
// log tool state
diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -115,7 +115,7 @@
});
// log tool state
- console.debug('tools-form::_refreshForm() - Refreshing states.');
+ console.debug('tools-form::_refreshForm() - Sending current state (see below).');
console.debug(current_state);
// activates/disables spinner for dynamic fields to indicate that they are currently being updated
@@ -188,7 +188,7 @@
self.deferred.done(process_id);
// log success
- console.debug('tools-form::_refreshForm() - States refreshed.');
+ console.debug('tools-form::_refreshForm() - Received new model (see below).');
console.debug(new_model);
},
error : function(response) {
diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 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(m){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=m&&m.inputs;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},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){$(this.container).animate({scrollTop:o.$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.$el.hide()}var p=new k.ButtonMenu({icon:"fa-caret-down",title:(!t.narrow&&"Options")||null,tooltip:"View available options"});if(t.biostar_url){p.addMenu({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/p/new/post/")}});p.addMenu({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(t.biostar_url+"/t/"+t.id+"/")}})}p.addMenu({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+t.id)}});if(this.is_admin){p.addMenu({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+t.id+"/download"}})}if(t.requirements&&t.requirements.length>0){p.addMenu({icon:"fa-info-circle",title:"Requirements",tooltip:"Display tool requirements",onclick:function(){if(!this.visible){this.visible=true;s.message.update({persistent:true,message:c.requirements(t),status:"info"})}else{this.visible=false;s.message.update({message:""})}}})}if(this.options.sharable_url){p.addMenu({icon:"fa-external-link",title:"Open in Toolshed",tooltip:"Access the repository",onclick:function(){window.open(s.options.sharable_url)}})}this.section=new j.View(s,{inputs:t.inputs});if(this.incompatible){this.$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.$el);this.build(this.options)},build:function(n){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=n&&n.inputs;this._renderForm(n);var m=this.tree.finalize();if(n.initial_errors){this._errors(n)}this.on("refresh",function(){var o=l.tree.finalize();if(!_.isEqual(o,m)){m=o;l.deferred.reset();l.deferred.execute(function(){l._updateModel(m)})}});this.on("reset",function(){for(var o in this.element_list){this.element_list[o].reset()}});this.trigger("refresh")},reciept:function(l){$(this.container).empty();$(this.container).append(l)},highlight:function(m,n,l){var o=this.element_list[m];if(o){o.error(n||"Please verify this parameter.");if(!l){$(this.container).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:"Open in Toolshed",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
diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 static/scripts/packed/mvc/tools/tools-form-workflow.js
--- a/static/scripts/packed/mvc/tools/tools-form-workflow.js
+++ b/static/scripts/packed/mvc/tools/tools-form-workflow.js
@@ -1,1 +1,1 @@
-define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(){var d=this;var e={tool_id:this.options.id,tool_version:this.options.version,inputs:this.tree.finalize()};console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"api/workflows/build_module";b.request({type:"POST",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}});
\ No newline at end of file
+define(["utils/utils","mvc/tools/tools-form-base"],function(b,a){var c=a.extend({initialize:function(e){this.node=workflow.active_node;if(!this.node){console.debug("FAILED - tools-form-workflow:initialize() - Node not found in workflow.");return}this.post_job_actions=this.node.post_job_actions||{};this.options=e;this.options.text_enable="In Advance";this.options.text_disable="At Runtime";this.options.is_dynamic=false;this.options.narrow=true;this.options.initial_errors=true;this.options.cls_portlet="ui-portlet-narrow";b.deepeach(e.inputs,function(f){if(f.type){f.optional=(["data","data_hidden","hidden","drill_down","repeat","conditional"]).indexOf(f.type)==-1}});b.deepeach(e.inputs,function(f){if(f.type){if(f.type=="conditional"){f.test_param.optional=false}}});var d=this;b.get({url:galaxy_config.root+"api/datatypes",cache:true,success:function(f){d.datatypes=f;d._makeSections(e.inputs);a.prototype.initialize.call(d,e)}})},_makeSections:function(d){d[b.uuid()]={label:"Annotation / Notes",name:"annotation",type:"text",area:true,help:"Add an annotation or note for this step. It will be shown with the workflow.",value:this.node.annotation};var f=this.node.output_terminals&&Object.keys(this.node.output_terminals)[0];if(f){d[b.uuid()]={name:"pja__"+f+"__EmailAction",label:"Email notification",type:"boolean",value:String(Boolean(this.post_job_actions["EmailAction"+f])),ignore:"false",help:"An email notification will be send when the job has completed.",payload:{host:window.location.host}};d[b.uuid()]={name:"pja__"+f+"__DeleteIntermediatesAction",label:"Output cleanup",type:"boolean",value:String(Boolean(this.post_job_actions["DeleteIntermediatesAction"+f])),ignore:"false",help:"Delete intermediate outputs if they are not used as input for another job."};for(var e in this.node.output_terminals){d[b.uuid()]=this._makeSection(e)}}},_makeSection:function(h){var g=[];for(key in this.datatypes){g.push({0:this.datatypes[key],1:this.datatypes[key]})}g.sort(function(j,i){return j.label>i.label?1:j.label<i.label?-1:0});g.unshift({0:"Sequences",1:"Sequences"});g.unshift({0:"Roadmaps",1:"Roadmaps"});g.unshift({0:"Leave unchanged",1:""});var f={label:"Add Actions: '"+h+"'",type:"section",inputs:[{action:"RenameDatasetAction",argument:"newname",label:"Rename dataset",type:"text",value:"",ignore:"",help:'This action will rename the result dataset. Click <a href="https://wiki.galaxyproject.org/Learn/AdvancedWorkflow/Variables">here</a> for more information.'},{action:"ChangeDatatypeAction",argument:"newtype",label:"Change datatype",type:"select",ignore:"",options:g,help:"This action will change the datatype of the output to the indicated value."},{action:"TagDatasetAction",argument:"tags",label:"Tags",type:"text",value:"",ignore:"",help:"This action will set tags for the dataset."},{label:"Assign columns",type:"section",inputs:[{action:"ColumnSetAction",argument:"chromCol",label:"Chrom column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"startCol",label:"Start column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"endCol",label:"End column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"strandCol",label:"Strand column",type:"integer",value:"",ignore:""},{action:"ColumnSetAction",argument:"nameCol",label:"Name column",type:"integer",value:"",ignore:""}],help:"This action will set column assignments in the output dataset. Blank fields are ignored."}]};var d=this;function e(n,o){o=o||[];o.push(n);for(var m in n.inputs){var k=n.inputs[m];if(k.action){k.name="pja__"+h+"__"+k.action;if(k.argument){k.name+="__"+k.argument}if(k.payload){for(var s in k.payload){var q=k.payload[s];k.payload[k.name+"__"+s]=q;delete q}}var r=d.post_job_actions[k.action+h];if(r){for(var l in o){o[l].expand=true}if(k.argument){k.value=r.action_arguments&&r.action_arguments[k.argument]||k.value}else{k.value="true"}}}if(k.inputs){e(k,o.slice(0))}}}e(f);return f},_buildModel:function(){Galaxy.modal.show({title:"Coming soon...",body:"This feature has not been implemented yet.",buttons:{Close:function(){Galaxy.modal.hide()}}})},_updateModel:function(e){var d=this;e={tool_id:this.options.id,tool_version:this.options.version,inputs:e};console.debug("tools-form-workflow::_refreshForm() - Refreshing states.");console.debug(e);var g=this.deferred.register();var f=galaxy_config.root+"api/workflows/build_module";b.request({type:"POST",url:f,data:e,success:function(h){d.node.update_field_data(h);d._errors(h&&h.tool_model);d.deferred.done(g);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(h)},error:function(h){d.deferred.done(g);console.debug("tools-form::_refreshForm() - Refresh request failed.");console.debug(h)}})}});return{View:c}});
\ No newline at end of file
diff -r 12b6e7c9d5667d280de5c1cfcbe7946bed324510 -r 86ac99a2896b87915e35b81db1320fdfe73bf556 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(){var f=this;var g=this.tree.finalize({data:function(l){try{if(l&&l.values[0].src==="hda"){return f.content.get({id:l.values[0].id,src:"hda"}).id_uncoded}}catch(k){console.debug("tools-form::_updateModel - Invalid or empty data input value.")}return null}});console.debug("tools-form::_refreshForm() - Refreshing states.");console.debug(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();var h=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;c.request({type:"GET",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);f.deferred.done(i);console.debug("tools-form::_refreshForm() - States refreshed.");console.debug(k)},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
+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(){var f=this;var g=this.tree.finalize({data:function(l){try{if(l&&l.values[0].src==="hda"){return f.content.get({id:l.values[0].id,src:"hda"}).id_uncoded}}catch(k){console.debug("tools-form::_updateModel - Invalid or empty data input value.")}return null}});console.debug("tools-form::_refreshForm() - Sending current state (see below).");console.debug(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();var h=galaxy_config.root+"api/tools/"+this.options.id+"/build?tool_version="+this.options.version;c.request({type:"GET",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);f.deferred.done(i);console.debug("tools-form::_refreshForm() - Received new model (see below).");console.debug(k)},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
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/577b270034b4/
Changeset: 577b270034b4
Branch: stable
User: jmchilton
Date: 2015-02-11 17:54:36+00:00
Summary: Merged in dan/galaxy-central-prs/stable (pull request #666)
[STABLE] Several Fixes for Tool Data Tables
Affected #: 1 file
diff -r 32e4527bab2d79f0797c28500a379b6b6c7a3900 -r 577b270034b48d90e58ffbea296e700d229545c9 lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -335,11 +335,13 @@
def get_named_fields_list( self ):
rval = []
- named_colums = self.get_column_name_list()
+ named_columns = self.get_column_name_list()
for fields in self.get_fields():
field_dict = {}
for i, field in enumerate( fields ):
- field_name = named_colums[i]
+ if i == len( named_columns ):
+ break
+ field_name = named_columns[i]
if field_name is None:
field_name = i #check that this is supposed to be 0 based.
field_dict[ field_name ] = field
@@ -366,6 +368,7 @@
self.columns[ name ] = index
self.largest_index = index
else:
+ self.largest_index = 0
for column_elem in config_element.findall( 'column' ):
name = column_elem.get( 'name', None )
assert name is not None, "Required 'name' attribute missing from column def"
@@ -495,7 +498,7 @@
try:
data_table_fh = open( filename, 'r+b' )
except IOError, e:
- log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', self.filename, e )
+ log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', filename, e )
data_table_fh = open( filename, 'wb' )
if os.stat( filename )[6] != 0:
# ensure last existing line ends with new line
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
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this email.
4 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/0d61e421e06c/
Changeset: 0d61e421e06c
Branch: stable
User: dan
Date: 2015-02-11 17:33:49+00:00
Summary: Fix for Data Tables persisting when .loc file doesn't exist.
Affected #: 1 file
diff -r 0b9127ab708d7d8497e80169a3b8636aea1e37c6 -r 0d61e421e06c25f7658b8405574a2aafa63d04f0 lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -495,7 +495,7 @@
try:
data_table_fh = open( filename, 'r+b' )
except IOError, e:
- log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', self.filename, e )
+ log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', filename, e )
data_table_fh = open( filename, 'wb' )
if os.stat( filename )[6] != 0:
# ensure last existing line ends with new line
https://bitbucket.org/galaxy/galaxy-central/commits/7df1519a9fbe/
Changeset: 7df1519a9fbe
Branch: stable
User: dan
Date: 2015-02-11 17:37:59+00:00
Summary: Fix for TabularToolDataTable.get_named_fields_list() when a data line has extra columns.
Affected #: 1 file
diff -r 0d61e421e06c25f7658b8405574a2aafa63d04f0 -r 7df1519a9fbecfc8c07e0dde3bf9845714c9a2ac lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -335,11 +335,13 @@
def get_named_fields_list( self ):
rval = []
- named_colums = self.get_column_name_list()
+ named_columns = self.get_column_name_list()
for fields in self.get_fields():
field_dict = {}
for i, field in enumerate( fields ):
- field_name = named_colums[i]
+ if i == len( named_columns ):
+ break
+ field_name = named_columns[i]
if field_name is None:
field_name = i #check that this is supposed to be 0 based.
field_dict[ field_name ] = field
https://bitbucket.org/galaxy/galaxy-central/commits/ca653e8d044d/
Changeset: ca653e8d044d
Branch: stable
User: dan
Date: 2015-02-11 17:40:33+00:00
Summary: Fix for parsing Tool Data Table columns that are defined as individual xml elements.
Affected #: 1 file
diff -r 7df1519a9fbecfc8c07e0dde3bf9845714c9a2ac -r ca653e8d044d29e15d4ff3266e333aa75c09e5d7 lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -368,6 +368,7 @@
self.columns[ name ] = index
self.largest_index = index
else:
+ self.largest_index = 0
for column_elem in config_element.findall( 'column' ):
name = column_elem.get( 'name', None )
assert name is not None, "Required 'name' attribute missing from column def"
https://bitbucket.org/galaxy/galaxy-central/commits/577b270034b4/
Changeset: 577b270034b4
Branch: stable
User: jmchilton
Date: 2015-02-11 17:54:36+00:00
Summary: Merged in dan/galaxy-central-prs/stable (pull request #666)
[STABLE] Several Fixes for Tool Data Tables
Affected #: 1 file
diff -r 32e4527bab2d79f0797c28500a379b6b6c7a3900 -r 577b270034b48d90e58ffbea296e700d229545c9 lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -335,11 +335,13 @@
def get_named_fields_list( self ):
rval = []
- named_colums = self.get_column_name_list()
+ named_columns = self.get_column_name_list()
for fields in self.get_fields():
field_dict = {}
for i, field in enumerate( fields ):
- field_name = named_colums[i]
+ if i == len( named_columns ):
+ break
+ field_name = named_columns[i]
if field_name is None:
field_name = i #check that this is supposed to be 0 based.
field_dict[ field_name ] = field
@@ -366,6 +368,7 @@
self.columns[ name ] = index
self.largest_index = index
else:
+ self.largest_index = 0
for column_elem in config_element.findall( 'column' ):
name = column_elem.get( 'name', None )
assert name is not None, "Required 'name' attribute missing from column def"
@@ -495,7 +498,7 @@
try:
data_table_fh = open( filename, 'r+b' )
except IOError, e:
- log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', self.filename, e )
+ log.warning( 'Error opening data table file (%s) with r+b, assuming file does not exist and will open as wb: %s', filename, e )
data_table_fh = open( filename, 'wb' )
if os.stat( filename )[6] != 0:
# ensure last existing line ends with new line
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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