- galaxy-commits - lists.galaxyproject.org

commit/galaxy-central: dannon: Merge stable changes.
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/934dc228aeee/ Changeset: 934dc228aeee User: dannon Date: 2014-10-10 13:13:32+00:00 Summary: Merge stable changes. Affected #: 1 file diff -r 060d5e65f5c50709aa6139fe2c6fb64b263af7f1 -r 934dc228aeeed80e4973af32a3686ffb8ab5d624 .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -bde1c35ef8e53d0436507c48ed9b08b1dc5b06a3 latest_2014.10.06 +a4f8476d787e254f11735896d0a3d2dced86e10b latest_2014.10.06 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: davebgx: More flexibility for tool data table configuration in the install and test framework.
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0f70d302b85e/ Changeset: 0f70d302b85e Branch: stable User: davebgx Date: 2014-10-09 18:17:33+00:00 Summary: More flexibility for tool data table configuration in the install and test framework. Affected #: 1 file diff -r 9bb2f032a455f0e63f407b396027102679d619ee -r 0f70d302b85e2a74d6c0c9ec7d4ccc6f11787eac test/install_and_test_tool_shed_repositories/base/util.py --- a/test/install_and_test_tool_shed_repositories/base/util.py +++ b/test/install_and_test_tool_shed_repositories/base/util.py @@ -115,13 +115,16 @@ additional_tool_data_tables = None additional_tool_data_path = None -# Set up default tool data tables. -if os.path.exists( 'tool_data_table_conf.xml' ): - tool_data_table_conf = 'tool_data_table_conf.xml' -elif os.path.exists( 'tool_data_table_conf.xml.sample' ): - tool_data_table_conf = 'tool_data_table_conf.xml.sample' -else: - tool_data_table_conf = None +tool_data_table_conf = None +# Set up default tool data tables. If a non-sample version is in config/, use that. Otherwise iterate through lower +# priority versions. +for conf in [ 'config/tool_data_table_conf.xml', + 'config/tool_data_table_conf.xml.sample', + 'tool_data_table_conf.xml', + 'tool_data_table_conf.xml.sample' ]: + if os.path.exists( conf ): + tool_data_table_conf = conf + break # The GALAXY_INSTALL_TEST_TOOL_SHED_URL and GALAXY_INSTALL_TEST_TOOL_SHED_API_KEY environment variables must be # set for this script to work correctly. If the value of GALAXY_INSTALL_TEST_TOOL_SHED_URL does not refer to one Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: natefoo: Update tag latest_2014.10.06 for changeset a4f8476d787e
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9bb2f032a455/ Changeset: 9bb2f032a455 Branch: stable User: natefoo Date: 2014-10-10 13:00:38+00:00 Summary: Update tag latest_2014.10.06 for changeset a4f8476d787e Affected #: 1 file diff -r a4f8476d787e254f11735896d0a3d2dced86e10b -r 9bb2f032a455f0e63f407b396027102679d619ee .hgtags --- a/.hgtags +++ b/.hgtags @@ -20,4 +20,4 @@ ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 -bde1c35ef8e53d0436507c48ed9b08b1dc5b06a3 latest_2014.10.06 +a4f8476d787e254f11735896d0a3d2dced86e10b latest_2014.10.06 Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: dannon: Merge from stable.
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/060d5e65f5c5/ Changeset: 060d5e65f5c5 User: dannon Date: 2014-10-10 11:24:02+00:00 Summary: Merge from stable. Affected #: 3 files diff -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 -r 060d5e65f5c50709aa6139fe2c6fb64b263af7f1 .hgtags --- a/.hgtags +++ b/.hgtags @@ -19,3 +19,5 @@ 2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11 548ab24667d6206780237bd807f7d857a484c461 latest_2014.08.11 +2092948937ac30ef82f71463a235c66d34987088 release_2014.10.06 +bde1c35ef8e53d0436507c48ed9b08b1dc5b06a3 latest_2014.10.06 diff -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 -r 060d5e65f5c50709aa6139fe2c6fb64b263af7f1 lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -39,7 +39,7 @@ .. seealso:: :attr:`galaxy.model.Library.dict_collection_visible_keys` """ - deleted = kwd.get( 'deleted', None ) + deleted = util.string_as_bool_or_none( kwd.get( 'deleted', None ) ) query = self.library_manager.list( trans, deleted ) libraries = [] for library in query: diff -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 -r 060d5e65f5c50709aa6139fe2c6fb64b263af7f1 lib/tool_shed/metadata/repository_metadata_manager.py --- a/lib/tool_shed/metadata/repository_metadata_manager.py +++ b/lib/tool_shed/metadata/repository_metadata_manager.py @@ -5,6 +5,7 @@ from galaxy import util from galaxy.util import inflector from galaxy.web.form_builder import SelectField +from galaxy.model.orm import or_ from tool_shed.metadata import metadata_generator from tool_shed.repository_types.metadata import TipOnly 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: martenson: fix a bug with parsing params in data libraries API introduced recently with refactoring into managers
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a4f8476d787e/ Changeset: a4f8476d787e Branch: stable User: martenson Date: 2014-10-10 00:36:54+00:00 Summary: fix a bug with parsing params in data libraries API introduced recently with refactoring into managers Affected #: 1 file diff -r ff30da7a2873416a332b7700eb15e26a1bf3c46e -r a4f8476d787e254f11735896d0a3d2dced86e10b lib/galaxy/webapps/galaxy/api/libraries.py --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -39,7 +39,7 @@ .. seealso:: :attr:`galaxy.model.Library.dict_collection_visible_keys` """ - deleted = kwd.get( 'deleted', None ) + deleted = util.string_as_bool_or_none( kwd.get( 'deleted', None ) ) query = self.library_manager.list( trans, deleted ) libraries = [] for library in query: Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: ToolForm: Fix link shown for tool sharing
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5321b19715b1/ Changeset: 5321b19715b1 User: guerler Date: 2014-10-10 04:11:21+00:00 Summary: ToolForm: Fix link shown for tool sharing Affected #: 3 files diff -r 10b4f2107e90f3821f94be4286f320628c518034 -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 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 @@ -158,7 +158,7 @@ title : 'Share', tooltip : 'Share this tool', onclick : function() { - prompt('Copy to clipboard: Ctrl+C, Enter', galaxy_config.root + 'root?tool_id=' + self.options.id); + prompt('Copy to clipboard: Ctrl+C, Enter', window.location.origin + galaxy_config.root + 'root?tool_id=' + self.options.id); } }); diff -r 10b4f2107e90f3821f94be4286f320628c518034 -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -158,7 +158,7 @@ title : 'Share', tooltip : 'Share this tool', onclick : function() { - prompt('Copy to clipboard: Ctrl+C, Enter', galaxy_config.root + 'root?tool_id=' + self.options.id); + prompt('Copy to clipboard: Ctrl+C, Enter', window.location.origin + galaxy_config.root + 'root?tool_id=' + self.options.id); } }); diff -r 10b4f2107e90f3821f94be4286f320628c518034 -r 5321b19715b144c7e93ae7567aa4a6681d3e59b7 static/scripts/packed/mvc/tools/tools-form.js --- a/static/scripts/packed/mvc/tools/tools-form.js +++ b/static/scripts/packed/mvc/tools/tools-form.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(j,i,m,k,a,f,d,g,l,c,h){var e=Backbone.Model.extend({initialize:function(n){this.url=galaxy_config.root+"api/tools/"+n.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(o){var n=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new m.Modal.View()}this.options=o;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:o.id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){n._initializeToolForm()}})},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},refresh:function(){this.tree.refresh();for(var n in this.field_list){this.field_list[n].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;this.model.fetch({error:function(o){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");if(n.options.job_id){j.get({url:galaxy_config.root+"api/jobs/"+n.options.job_id,success:function(o){n._buildForm()}})}else{n._buildForm()}}})},_buildForm:function(){var p=this;var r=new m.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/p/new/post/")}});var s=new m.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/t/"+p.options.id+"/")}});var n=new m.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+p.options.id)}});var q={button_question:r,button_search:s,button_share:n};if(Galaxy.currUser.get("is_admin")){q.button_download=new m.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+p.options.id+"/download"}})}this.section=new l.View(p,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new i.View({icon:"fa-wrench",title:"<b>"+this.model.get("name")+"</b> "+this.model.get("description"),operations:q,buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){p.job_handler.submit()}})}});if(!this.options.biostar_url){r.$el.hide();s.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var o=new k.ToolCitationCollection();o.tool_id=this.options.id;var t=new a.CitationListView({collection:o});t.render();o.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(j,i,m,k,a,f,d,g,l,c,h){var e=Backbone.Model.extend({initialize:function(n){this.url=galaxy_config.root+"api/tools/"+n.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(o){var n=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new m.Modal.View()}this.options=o;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:o.id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){n._initializeToolForm()}})},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},refresh:function(){this.tree.refresh();for(var n in this.field_list){this.field_list[n].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;this.model.fetch({error:function(o){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");if(n.options.job_id){j.get({url:galaxy_config.root+"api/jobs/"+n.options.job_id,success:function(o){n._buildForm()}})}else{n._buildForm()}}})},_buildForm:function(){var p=this;var r=new m.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/p/new/post/")}});var s=new m.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/t/"+p.options.id+"/")}});var n=new m.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",window.location.origin+galaxy_config.root+"root?tool_id="+p.options.id)}});var q={button_question:r,button_search:s,button_share:n};if(Galaxy.currUser.get("is_admin")){q.button_download=new m.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+p.options.id+"/download"}})}this.section=new l.View(p,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new i.View({icon:"fa-wrench",title:"<b>"+this.model.get("name")+"</b> "+this.model.get("description"),operations:q,buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){p.job_handler.submit()}})}});if(!this.options.biostar_url){r.$el.hide();s.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var o=new k.ToolCitationCollection();o.tool_id=this.options.id;var t=new a.CitationListView({collection:o});t.render();o.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: ToolForm: Fix optional label, add file
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/10b4f2107e90/ Changeset: 10b4f2107e90 User: guerler Date: 2014-10-10 04:03:59+00:00 Summary: ToolForm: Fix optional label, add file Affected #: 3 files diff -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 -r 10b4f2107e90f3821f94be4286f320628c518034 client/galaxy/scripts/mvc/tools/tools-input.js --- /dev/null +++ b/client/galaxy/scripts/mvc/tools/tools-input.js @@ -0,0 +1,108 @@ +/** + This class creates a tool form input element wrapper +*/ +define([], function() { + + // input field element wrapper + return Backbone.View.extend({ + // initialize input wrapper + initialize: function(options) { + // link field + this.field = options.field; + + // set element + this.setElement(this._template(options)); + + // link elements + this.$field = this.$el.find('.ui-table-form-field'); + this.$title_optional = this.$el.find('.ui-table-form-title-optional'); + this.$error_text = this.$el.find('.ui-table-form-error-text'); + this.$error = this.$el.find('.ui-table-form-error'); + + // add field element + this.$field.prepend(this.field.$el); + + // hide optional field on initialization + if (options.optional) { + this.field.skip = true; + } else { + this.field.skip = false; + } + + // refresh view + this._refresh(); + + // add optional hide/show + var self = this; + this.$title_optional.on('click', function() { + // flip flag + self.field.skip = !self.field.skip; + + // refresh view + self._refresh(); + }); + }, + + /** Set error text + */ + error: function(text) { + this.$error_text.html(text); + this.$error.fadeIn(); + this.$el.addClass('ui-error'); + }, + + /** Reset this view + */ + reset: function() { + this.$error.hide(); + this.$el.removeClass('ui-error'); + }, + + /** Refresh element + */ + _refresh: function() { + // show/hide field element + if (!this.field.skip) { + this.$field.fadeIn('fast'); + this.$title_optional.html('Disable'); + } else { + this.$field.hide(); + this.$title_optional.html('Enable'); + } + }, + + /** Main Template + */ + _template: function(options) { + // create table element + var tmp = '<div class="ui-table-form-element">' + + '<div class="ui-table-form-error ui-error">' + + '<span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/>' + + '</div>' + + '<div class="ui-table-form-title-strong">'; + + // is optional + if (options.optional) { + tmp += 'Optional: ' + options.label + + '<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'; + } else { + tmp += options.label; + } + + // finalize title + tmp += '</div>' + + '<div class="ui-table-form-field">'; + // add help + if (options.help) { + tmp += '<div class="ui-table-form-info">' + options.help + '</div>'; + } + + // finalize + tmp += '</div>' + + '</div>'; + + // return input element + return tmp; + } + }); +}); diff -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 -r 10b4f2107e90f3821f94be4286f320628c518034 static/scripts/mvc/tools/tools-input.js --- a/static/scripts/mvc/tools/tools-input.js +++ b/static/scripts/mvc/tools/tools-input.js @@ -83,7 +83,7 @@ // is optional if (options.optional) { - tmp += '*Optional: ' + options.label + + tmp += 'Optional: ' + options.label + '<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'; } else { tmp += options.label; diff -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 -r 10b4f2107e90f3821f94be4286f320628c518034 static/scripts/packed/mvc/tools/tools-input.js --- a/static/scripts/packed/mvc/tools/tools-input.js +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.View.extend({initialize:function(b){this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="*Optional: "+a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file +define([],function(){return Backbone.View.extend({initialize:function(b){this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="Optional: "+a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

1 0

commit/galaxy-central: guerler: ToolForm: Fix optional parameters
by commits-noreply＠bitbucket.org 10 Oct '14

10 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/34e643839cda/ Changeset: 34e643839cda User: guerler Date: 2014-10-10 03:48:59+00:00 Summary: ToolForm: Fix optional parameters Affected #: 17 files diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 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 @@ -1,10 +1,10 @@ /** This is the main class of the tool form plugin. It is referenced as 'app' in all lower level modules. */ -define(['mvc/ui/ui-portlet', 'mvc/ui/ui-misc', +define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/citation/citation-model', 'mvc/citation/citation-view', 'mvc/tools', 'mvc/tools/tools-template', 'mvc/tools/tools-content', 'mvc/tools/tools-section', 'mvc/tools/tools-tree', 'mvc/tools/tools-jobs'], - function(Portlet, Ui, CitationModel, CitationView, + function(Utils, Portlet, Ui, CitationModel, CitationView, Tools, ToolTemplate, ToolContent, ToolSection, ToolTree, ToolJobs) { // create tool model @@ -42,8 +42,7 @@ // load tool model this.model = new Model({ - id : options.id, - job_id : options.job_id + id : options.id }); // creates a tree/json structure from the input form @@ -102,6 +101,37 @@ // link this var self = this; + // fetch model and render form + this.model.fetch({ + error: function(response) { + console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.'); + }, + success: function() { + // backup inputs + self.inputs = self.model.get('inputs'); + + // update inputs with job parameters + if (self.options.job_id) { + Utils.get({ + url: galaxy_config.root + 'api/jobs/' + self.options.job_id, + success: function(parameters) { + // TODO: Update input parameters + //self._updateInputs(self.inputs, parameters); + self._buildForm(); + } + }); + } else { + self._buildForm(); + } + } + }); + }, + + // builds the tool form + _buildForm: function() { + // link this + var self = this; + // create question button var button_question = new Ui.ButtonIcon({ icon : 'fa-question-circle', @@ -152,79 +182,70 @@ }); } - // fetch model and render form - this.model.fetch({ - error: function(response) { - console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.'); - }, - success: function() { - // create tool form section - self.section = new ToolSection.View(self, { - inputs : self.model.get('inputs'), - cls : 'ui-table-plain' - }); - - // TEMPORARY SWITCH - // switch to classic tool form mako if the form definition is incompatible - if (self.incompatible) { - self.$el.hide(); - $('#tool-form-classic').show(); - return; - } - - // create portlet - self.portlet = new Portlet.View({ - icon : 'fa-wrench', - title: '<b>' + self.model.get('name') + '</b> ' + self.model.get('description'), - operations: operations, - buttons: { - execute: new Ui.Button({ - icon : 'fa-check', - tooltip : 'Execute the tool', - title : 'Execute', - cls : 'btn btn-primary', - floating : 'clear', - onclick : function() { - self.job_handler.submit(); - } - }) + // create tool form section + this.section = new ToolSection.View(self, { + inputs : this.inputs, + cls : 'ui-table-plain' + }); + + // switch to classic tool form mako if the form definition is incompatible + if (this.incompatible) { + this.$el.hide(); + $('#tool-form-classic').show(); + return; + } + + // create portlet + this.portlet = new Portlet.View({ + icon : 'fa-wrench', + title: '<b>' + this.model.get('name') + '</b> ' + this.model.get('description'), + operations: operations, + buttons: { + execute: new Ui.Button({ + icon : 'fa-check', + tooltip : 'Execute the tool', + title : 'Execute', + cls : 'btn btn-primary', + floating : 'clear', + onclick : function() { + self.job_handler.submit(); } - }); - - // configure button selection - if(!self.options.biostar_url) { - button_question.$el.hide(); - button_search.$el.hide(); - } - - // append form - self.$el.append(self.portlet.$el); - - // append help - if (self.options.help != '') { - self.$el.append(ToolTemplate.help(self.options.help)); - } - - // append citations - if (self.options.citations) { - // append html - self.$el.append(ToolTemplate.citations()); - - // fetch citations - var citations = new CitationModel.ToolCitationCollection(); - citations.tool_id = self.options.id; - var citation_list_view = new CitationView.CitationListView({ collection: citations } ); - citation_list_view.render(); - citations.fetch(); - } - - // append tool section - self.portlet.append(self.section.$el); - - // trigger refresh - self.refresh(); + }) } }); + + // configure button selection + if(!this.options.biostar_url) { + button_question.$el.hide(); + button_search.$el.hide(); + } + + // append form + this.$el.append(this.portlet.$el); + + // append help + if (this.options.help != '') { + this.$el.append(ToolTemplate.help(this.options.help)); + } + + // append citations + if (this.options.citations) { + // append html + this.$el.append(ToolTemplate.citations()); + + // fetch citations + var citations = new CitationModel.ToolCitationCollection(); + citations.tool_id = this.options.id; + var citation_list_view = new CitationView.CitationListView({ collection: citations } ); + citation_list_view.render(); + citations.fetch(); + } + + // append tool section + this.portlet.append(this.section.$el); + + // trigger refresh + this.refresh(); } }); diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 client/galaxy/scripts/mvc/tools/tools-jobs.js --- a/client/galaxy/scripts/mvc/tools/tools-jobs.js +++ b/client/galaxy/scripts/mvc/tools/tools-jobs.js @@ -98,9 +98,9 @@ var input_id = this.app.tree.match(job_input_id); var input_field = this.app.field_list[input_id]; var input_def = this.app.input_list[input_id]; - + // check basic field validation - if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) { + if (input_def && input_field && input_field.validate && !input_field.validate()) { this._foundError(input_id); return false; } diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 client/galaxy/scripts/mvc/tools/tools-section.js --- a/client/galaxy/scripts/mvc/tools/tools-section.js +++ b/client/galaxy/scripts/mvc/tools/tools-section.js @@ -1,58 +1,8 @@ /** This class creates a tool form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections. New input elements can be plugged in by adding cases to the switch block defined in the _addRow() function. */ -define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content'], - function(Utils, Table, Ui, Repeat, SelectContent) { - - // input field element wrapper - var InputElement = Backbone.View.extend({ - // initialize input wrapper - initialize: function(options) { - this.setElement(this._template(options)); - }, - - /** Set error text - */ - error: function(text) { - // set text - this.$el.find('.ui-table-form-error-text').html(text); - this.$el.find('.ui-table-form-error').fadeIn(); - this.$el.addClass('ui-error'); - }, - - /** Reset this view - */ - reset: function() { - this.$el.find('.ui-table-form-error').hide(); - this.$el.removeClass('ui-error'); - }, - - /** Main Template - */ - _template: function(options) { - // create table element - var $input = $('<div class="ui-table-element"/>'); - - // add error - $input.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>'); - - // add label - if (options.label) { - $input.append('<div class="ui-table-form-title-strong">' + options.label + '</div>'); - } - - // add input element - $input.append(options.$el); - - // add help - if (options.help) { - $input.append('<div class="ui-table-form-info">' + options.help + '</div>'); - } - - // return input element - return $input; - } - }); +define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content', 'mvc/tools/tools-input'], + function(Utils, Table, Ui, Repeat, SelectContent, InputElement) { // create form view var View = Backbone.View.extend({ @@ -234,7 +184,7 @@ var input_element = new InputElement({ label : input_def.title, help : input_def.help, - $el : repeat.$el + field : repeat }); // displays as grouped subsection @@ -337,9 +287,10 @@ // create input field wrapper var input_element = new InputElement({ - label : input_def.label, - help : input_def.help, - $el : field.$el + label : input_def.label, + optional : input_def.optional, + help : input_def.help, + field : field }); // add to element list diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 client/galaxy/scripts/mvc/tools/tools-tree.js --- a/client/galaxy/scripts/mvc/tools/tools-tree.js +++ b/client/galaxy/scripts/mvc/tools/tools-tree.js @@ -110,8 +110,13 @@ } break; default: + // get conditional value + var field = self.app.field_list[input.id]; + // handle default value - add (job_input_id, input.id, self.app.field_list[input.id].value()); + if (!field.skip) { + add (job_input_id, input.id, field.value()); + } } } } diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -200,6 +200,7 @@ pass #HACK for assert trans.history, 'requires a history' tool_dict[ 'model_class' ] = self.__class__.__name__ + tool_dict[ 'optional' ] = self.optional if hasattr( self, 'value' ): tool_dict[ 'value' ] = self.value return tool_dict diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/mvc/tools/tools-form.js --- a/static/scripts/mvc/tools/tools-form.js +++ b/static/scripts/mvc/tools/tools-form.js @@ -1,10 +1,10 @@ /** This is the main class of the tool form plugin. It is referenced as 'app' in all lower level modules. */ -define(['mvc/ui/ui-portlet', 'mvc/ui/ui-misc', +define(['utils/utils', 'mvc/ui/ui-portlet', 'mvc/ui/ui-misc', 'mvc/citation/citation-model', 'mvc/citation/citation-view', 'mvc/tools', 'mvc/tools/tools-template', 'mvc/tools/tools-content', 'mvc/tools/tools-section', 'mvc/tools/tools-tree', 'mvc/tools/tools-jobs'], - function(Portlet, Ui, CitationModel, CitationView, + function(Utils, Portlet, Ui, CitationModel, CitationView, Tools, ToolTemplate, ToolContent, ToolSection, ToolTree, ToolJobs) { // create tool model @@ -42,8 +42,7 @@ // load tool model this.model = new Model({ - id : options.id, - job_id : options.job_id + id : options.id }); // creates a tree/json structure from the input form @@ -102,6 +101,37 @@ // link this var self = this; + // fetch model and render form + this.model.fetch({ + error: function(response) { + console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.'); + }, + success: function() { + // backup inputs + self.inputs = self.model.get('inputs'); + + // update inputs with job parameters + if (self.options.job_id) { + Utils.get({ + url: galaxy_config.root + 'api/jobs/' + self.options.job_id, + success: function(parameters) { + // TODO: Update input parameters + //self._updateInputs(self.inputs, parameters); + self._buildForm(); + } + }); + } else { + self._buildForm(); + } + } + }); + }, + + // builds the tool form + _buildForm: function() { + // link this + var self = this; + // create question button var button_question = new Ui.ButtonIcon({ icon : 'fa-question-circle', @@ -152,79 +182,70 @@ }); } - // fetch model and render form - this.model.fetch({ - error: function(response) { - console.debug('tools-form::_initializeToolForm() : Attempt to fetch tool model failed.'); - }, - success: function() { - // create tool form section - self.section = new ToolSection.View(self, { - inputs : self.model.get('inputs'), - cls : 'ui-table-plain' - }); - - // TEMPORARY SWITCH - // switch to classic tool form mako if the form definition is incompatible - if (self.incompatible) { - self.$el.hide(); - $('#tool-form-classic').show(); - return; - } - - // create portlet - self.portlet = new Portlet.View({ - icon : 'fa-wrench', - title: '<b>' + self.model.get('name') + '</b> ' + self.model.get('description'), - operations: operations, - buttons: { - execute: new Ui.Button({ - icon : 'fa-check', - tooltip : 'Execute the tool', - title : 'Execute', - cls : 'btn btn-primary', - floating : 'clear', - onclick : function() { - self.job_handler.submit(); - } - }) + // create tool form section + this.section = new ToolSection.View(self, { + inputs : this.inputs, + cls : 'ui-table-plain' + }); + + // switch to classic tool form mako if the form definition is incompatible + if (this.incompatible) { + this.$el.hide(); + $('#tool-form-classic').show(); + return; + } + + // create portlet + this.portlet = new Portlet.View({ + icon : 'fa-wrench', + title: '<b>' + this.model.get('name') + '</b> ' + this.model.get('description'), + operations: operations, + buttons: { + execute: new Ui.Button({ + icon : 'fa-check', + tooltip : 'Execute the tool', + title : 'Execute', + cls : 'btn btn-primary', + floating : 'clear', + onclick : function() { + self.job_handler.submit(); } - }); - - // configure button selection - if(!self.options.biostar_url) { - button_question.$el.hide(); - button_search.$el.hide(); - } - - // append form - self.$el.append(self.portlet.$el); - - // append help - if (self.options.help != '') { - self.$el.append(ToolTemplate.help(self.options.help)); - } - - // append citations - if (self.options.citations) { - // append html - self.$el.append(ToolTemplate.citations()); - - // fetch citations - var citations = new CitationModel.ToolCitationCollection(); - citations.tool_id = self.options.id; - var citation_list_view = new CitationView.CitationListView({ collection: citations } ); - citation_list_view.render(); - citations.fetch(); - } - - // append tool section - self.portlet.append(self.section.$el); - - // trigger refresh - self.refresh(); + }) } }); + + // configure button selection + if(!this.options.biostar_url) { + button_question.$el.hide(); + button_search.$el.hide(); + } + + // append form + this.$el.append(this.portlet.$el); + + // append help + if (this.options.help != '') { + this.$el.append(ToolTemplate.help(this.options.help)); + } + + // append citations + if (this.options.citations) { + // append html + this.$el.append(ToolTemplate.citations()); + + // fetch citations + var citations = new CitationModel.ToolCitationCollection(); + citations.tool_id = this.options.id; + var citation_list_view = new CitationView.CitationListView({ collection: citations } ); + citation_list_view.render(); + citations.fetch(); + } + + // append tool section + this.portlet.append(this.section.$el); + + // trigger refresh + this.refresh(); } }); diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/mvc/tools/tools-input.js --- /dev/null +++ b/static/scripts/mvc/tools/tools-input.js @@ -0,0 +1,108 @@ +/** + This class creates a tool form input element wrapper +*/ +define([], function() { + + // input field element wrapper + return Backbone.View.extend({ + // initialize input wrapper + initialize: function(options) { + // link field + this.field = options.field; + + // set element + this.setElement(this._template(options)); + + // link elements + this.$field = this.$el.find('.ui-table-form-field'); + this.$title_optional = this.$el.find('.ui-table-form-title-optional'); + this.$error_text = this.$el.find('.ui-table-form-error-text'); + this.$error = this.$el.find('.ui-table-form-error'); + + // add field element + this.$field.prepend(this.field.$el); + + // hide optional field on initialization + if (options.optional) { + this.field.skip = true; + } else { + this.field.skip = false; + } + + // refresh view + this._refresh(); + + // add optional hide/show + var self = this; + this.$title_optional.on('click', function() { + // flip flag + self.field.skip = !self.field.skip; + + // refresh view + self._refresh(); + }); + }, + + /** Set error text + */ + error: function(text) { + this.$error_text.html(text); + this.$error.fadeIn(); + this.$el.addClass('ui-error'); + }, + + /** Reset this view + */ + reset: function() { + this.$error.hide(); + this.$el.removeClass('ui-error'); + }, + + /** Refresh element + */ + _refresh: function() { + // show/hide field element + if (!this.field.skip) { + this.$field.fadeIn('fast'); + this.$title_optional.html('Disable'); + } else { + this.$field.hide(); + this.$title_optional.html('Enable'); + } + }, + + /** Main Template + */ + _template: function(options) { + // create table element + var tmp = '<div class="ui-table-form-element">' + + '<div class="ui-table-form-error ui-error">' + + '<span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/>' + + '</div>' + + '<div class="ui-table-form-title-strong">'; + + // is optional + if (options.optional) { + tmp += '*Optional: ' + options.label + + '<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'; + } else { + tmp += options.label; + } + + // finalize title + tmp += '</div>' + + '<div class="ui-table-form-field">'; + // add help + if (options.help) { + tmp += '<div class="ui-table-form-info">' + options.help + '</div>'; + } + + // finalize + tmp += '</div>' + + '</div>'; + + // return input element + return tmp; + } + }); +}); diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/mvc/tools/tools-jobs.js --- a/static/scripts/mvc/tools/tools-jobs.js +++ b/static/scripts/mvc/tools/tools-jobs.js @@ -98,9 +98,9 @@ var input_id = this.app.tree.match(job_input_id); var input_field = this.app.field_list[input_id]; var input_def = this.app.input_list[input_id]; - + // check basic field validation - if (input_def && !input_def.optional && input_field && input_field.validate && !input_field.validate()) { + if (input_def && input_field && input_field.validate && !input_field.validate()) { this._foundError(input_id); return false; } diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/mvc/tools/tools-section.js --- a/static/scripts/mvc/tools/tools-section.js +++ b/static/scripts/mvc/tools/tools-section.js @@ -1,58 +1,8 @@ /** This class creates a tool form section and populates it with input elements. It also handles repeat blocks and conditionals by recursively creating new sub sections. New input elements can be plugged in by adding cases to the switch block defined in the _addRow() function. */ -define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content'], - function(Utils, Table, Ui, Repeat, SelectContent) { - - // input field element wrapper - var InputElement = Backbone.View.extend({ - // initialize input wrapper - initialize: function(options) { - this.setElement(this._template(options)); - }, - - /** Set error text - */ - error: function(text) { - // set text - this.$el.find('.ui-table-form-error-text').html(text); - this.$el.find('.ui-table-form-error').fadeIn(); - this.$el.addClass('ui-error'); - }, - - /** Reset this view - */ - reset: function() { - this.$el.find('.ui-table-form-error').hide(); - this.$el.removeClass('ui-error'); - }, - - /** Main Template - */ - _template: function(options) { - // create table element - var $input = $('<div class="ui-table-element"/>'); - - // add error - $input.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>'); - - // add label - if (options.label) { - $input.append('<div class="ui-table-form-title-strong">' + options.label + '</div>'); - } - - // add input element - $input.append(options.$el); - - // add help - if (options.help) { - $input.append('<div class="ui-table-form-info">' + options.help + '</div>'); - } - - // return input element - return $input; - } - }); +define(['utils/utils', 'mvc/ui/ui-table', 'mvc/ui/ui-misc', 'mvc/tools/tools-repeat', 'mvc/tools/tools-select-content', 'mvc/tools/tools-input'], + function(Utils, Table, Ui, Repeat, SelectContent, InputElement) { // create form view var View = Backbone.View.extend({ @@ -234,7 +184,7 @@ var input_element = new InputElement({ label : input_def.title, help : input_def.help, - $el : repeat.$el + field : repeat }); // displays as grouped subsection @@ -337,9 +287,10 @@ // create input field wrapper var input_element = new InputElement({ - label : input_def.label, - help : input_def.help, - $el : field.$el + label : input_def.label, + optional : input_def.optional, + help : input_def.help, + field : field }); // add to element list diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/mvc/tools/tools-tree.js --- a/static/scripts/mvc/tools/tools-tree.js +++ b/static/scripts/mvc/tools/tools-tree.js @@ -110,8 +110,13 @@ } break; default: + // get conditional value + var field = self.app.field_list[input.id]; + // handle default value - add (job_input_id, input.id, self.app.field_list[input.id].value()); + if (!field.skip) { + add (job_input_id, input.id, field.value()); + } } } } diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 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(["mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(i,l,j,a,f,d,g,k,c,h){var e=Backbone.Model.extend({initialize:function(m){this.url=galaxy_config.root+"api/tools/"+m.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(n){var m=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new l.Modal.View()}this.options=n;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:n.id,job_id:n.job_id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){m._initializeToolForm()}})},message:function(m){$(this.container).empty();$(this.container).append(m)},reset:function(){for(var m in this.element_list){this.element_list[m].reset()}},refresh:function(){this.tree.refresh();for(var m in this.field_list){this.field_list[m].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;var p=new l.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/p/new/post/")}});var q=new l.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(n.options.biostar_url+"/t/"+n.options.id+"/")}});var m=new l.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+n.options.id)}});var o={button_question:p,button_search:q,button_share:m};if(Galaxy.currUser.get("is_admin")){o.button_download=new l.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+n.options.id+"/download"}})}this.model.fetch({error:function(r){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.section=new k.View(n,{inputs:n.model.get("inputs"),cls:"ui-table-plain"});if(n.incompatible){n.$el.hide();$("#tool-form-classic").show();return}n.portlet=new i.View({icon:"fa-wrench",title:"<b>"+n.model.get("name")+"</b> "+n.model.get("description"),operations:o,buttons:{execute:new l.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){n.job_handler.submit()}})}});if(!n.options.biostar_url){p.$el.hide();q.$el.hide()}n.$el.append(n.portlet.$el);if(n.options.help!=""){n.$el.append(d.help(n.options.help))}if(n.options.citations){n.$el.append(d.citations());var r=new j.ToolCitationCollection();r.tool_id=n.options.id;var s=new a.CitationListView({collection:r});s.render();r.fetch()}n.portlet.append(n.section.$el);n.refresh()}})}});return{View:b}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree","mvc/tools/tools-jobs"],function(j,i,m,k,a,f,d,g,l,c,h){var e=Backbone.Model.extend({initialize:function(n){this.url=galaxy_config.root+"api/tools/"+n.id+"?io_details=true"}});var b=Backbone.View.extend({container:"body",initialize:function(o){var n=this;if(parent.Galaxy&&parent.Galaxy.modal){this.modal=parent.Galaxy.modal}else{this.modal=new m.Modal.View()}this.options=o;this.setElement("<div/>");$(this.container).append(this.$el);this.model=new e({id:o.id});this.tree=new c(this);this.job_handler=new h(this);this.field_list={};this.input_list={};this.element_list={};this.content=new g({history_id:this.options.history_id,success:function(){n._initializeToolForm()}})},message:function(n){$(this.container).empty();$(this.container).append(n)},reset:function(){for(var n in this.element_list){this.element_list[n].reset()}},refresh:function(){this.tree.refresh();for(var n in this.field_list){this.field_list[n].trigger("change")}console.debug("tools-form::refresh() - Recreated data structure. Refresh.")},_initializeToolForm:function(){var n=this;this.model.fetch({error:function(o){console.debug("tools-form::_initializeToolForm() : Attempt to fetch tool model failed.")},success:function(){n.inputs=n.model.get("inputs");if(n.options.job_id){j.get({url:galaxy_config.root+"api/jobs/"+n.options.job_id,success:function(o){n._buildForm()}})}else{n._buildForm()}}})},_buildForm:function(){var p=this;var r=new m.ButtonIcon({icon:"fa-question-circle",title:"Question?",tooltip:"Ask a question about this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/p/new/post/")}});var s=new m.ButtonIcon({icon:"fa-search",title:"Search",tooltip:"Search help for this tool (Biostar)",onclick:function(){window.open(p.options.biostar_url+"/t/"+p.options.id+"/")}});var n=new m.ButtonIcon({icon:"fa-share",title:"Share",tooltip:"Share this tool",onclick:function(){prompt("Copy to clipboard: Ctrl+C, Enter",galaxy_config.root+"root?tool_id="+p.options.id)}});var q={button_question:r,button_search:s,button_share:n};if(Galaxy.currUser.get("is_admin")){q.button_download=new m.ButtonIcon({icon:"fa-download",title:"Download",tooltip:"Download this tool",onclick:function(){window.location.href=galaxy_config.root+"api/tools/"+p.options.id+"/download"}})}this.section=new l.View(p,{inputs:this.inputs,cls:"ui-table-plain"});if(this.incompatible){this.$el.hide();$("#tool-form-classic").show();return}this.portlet=new i.View({icon:"fa-wrench",title:"<b>"+this.model.get("name")+"</b> "+this.model.get("description"),operations:q,buttons:{execute:new m.Button({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",cls:"btn btn-primary",floating:"clear",onclick:function(){p.job_handler.submit()}})}});if(!this.options.biostar_url){r.$el.hide();s.$el.hide()}this.$el.append(this.portlet.$el);if(this.options.help!=""){this.$el.append(d.help(this.options.help))}if(this.options.citations){this.$el.append(d.citations());var o=new k.ToolCitationCollection();o.tool_id=this.options.id;var t=new a.CitationListView({collection:o});t.render();o.fetch()}this.portlet.append(this.section.$el);this.refresh()}});return{View:b}}); \ No newline at end of file diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/packed/mvc/tools/tools-input.js --- /dev/null +++ b/static/scripts/packed/mvc/tools/tools-input.js @@ -0,0 +1,1 @@ +define([],function(){return Backbone.View.extend({initialize:function(b){this.field=b.field;this.setElement(this._template(b));this.$field=this.$el.find(".ui-table-form-field");this.$title_optional=this.$el.find(".ui-table-form-title-optional");this.$error_text=this.$el.find(".ui-table-form-error-text");this.$error=this.$el.find(".ui-table-form-error");this.$field.prepend(this.field.$el);if(b.optional){this.field.skip=true}else{this.field.skip=false}this._refresh();var a=this;this.$title_optional.on("click",function(){a.field.skip=!a.field.skip;a._refresh()})},error:function(a){this.$error_text.html(a);this.$error.fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$error.hide();this.$el.removeClass("ui-error")},_refresh:function(){if(!this.field.skip){this.$field.fadeIn("fast");this.$title_optional.html("Disable")}else{this.$field.hide();this.$title_optional.html("Enable")}},_template:function(a){var b='<div class="ui-table-form-element"><div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"/></div><div class="ui-table-form-title-strong">';if(a.optional){b+="*Optional: "+a.label+'<span>&nbsp[<span class="ui-table-form-title-optional"/>]</span>'}else{b+=a.label}b+='</div><div class="ui-table-form-field">';if(a.help){b+='<div class="ui-table-form-info">'+a.help+"</div>"}b+="</div></div>";return b}})}); \ No newline at end of file diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/packed/mvc/tools/tools-jobs.js --- a/static/scripts/packed/mvc/tools/tools-jobs.js +++ b/static/scripts/packed/mvc/tools/tools-jobs.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(d);console.debug(e)}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&!h.optional&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file +define(["utils/utils","mvc/tools/tools-template"],function(b,a){return Backbone.Model.extend({initialize:function(d,c){this.app=d;this.options=b.merge(c,this.optionsDefault)},submit:function(){var c=this;var d={tool_id:this.app.options.id,inputs:this.app.tree.finalize()};this.app.reset();if(!this._validation(d)){console.debug("tools-jobs::submit - Submission canceled. Validation failed.");return}console.debug(d);this.app.modal.show({title:"Please wait...",body:"progress",buttons:{Close:function(){c.app.modal.hide()}}});b.request({type:"POST",url:galaxy_config.root+"api/tools",data:d,success:function(e){c.app.modal.hide();c.app.message(a.success(e));c._refreshHdas()},error:function(e,g){c.app.modal.hide();if(e&&e.message&&e.message.data){var h=c.app.tree.matchResponse(e.message.data);for(var f in h){c._foundError(f,h[f])}}else{console.debug(d);console.debug(e)}}})},_foundError:function(c,d){var e=this.app.element_list[c];e.error(d||"Please verify this parameter.");$(this.app.container).animate({scrollTop:e.$el.offset().top-20},500)},_validation:function(g){var c=g.inputs;var k=-1;for(var i in c){var e=c[i];var j=this.app.tree.match(i);var d=this.app.field_list[j];var h=this.app.input_list[j];if(h&&d&&d.validate&&!d.validate()){this._foundError(j);return false}if(e.batch){var f=e.values.length;if(k===-1){k=f}else{if(k!==f){this._foundError(j,"Please make sure that you select the same number of inputs for all batch mode fields. This field contains <b>"+f+"</b> selection(s) while a previous field contains <b>"+k+"</b>.");return false}}}}return true},_refreshHdas:function(){if(parent.Galaxy&&parent.Galaxy.currHistoryPanel){parent.Galaxy.currHistoryPanel.refreshContents()}}})}); \ No newline at end of file diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/packed/mvc/tools/tools-section.js --- a/static/scripts/packed/mvc/tools/tools-section.js +++ b/static/scripts/packed/mvc/tools/tools-section.js @@ -1,1 +1,1 @@ -define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content"],function(d,b,g,c,a){var e=Backbone.View.extend({initialize:function(h){this.setElement(this._template(h))},error:function(h){this.$el.find(".ui-table-form-error-text").html(h);this.$el.find(".ui-table-form-error").fadeIn();this.$el.addClass("ui-error")},reset:function(){this.$el.find(".ui-table-form-error").hide();this.$el.removeClass("ui-error")},_template:function(h){var i=$('<div class="ui-table-element"/>');i.append('<div class="ui-table-form-error ui-error"><span class="fa fa-arrow-down"/><span class="ui-table-form-error-text"></div>');if(h.label){i.append('<div class="ui-table-form-title-strong">'+h.label+"</div>")}i.append(h.$el);if(h.help){i.append('<div class="ui-table-form-info">'+h.help+"</div>")}return i}});var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,$el:m.$el});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,help:h.help,$el:i.$el});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file +define(["utils/utils","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/tools/tools-repeat","mvc/tools/tools-select-content","mvc/tools/tools-input"],function(d,b,g,c,a,e){var f=Backbone.View.extend({initialize:function(i,h){this.app=i;this.inputs=h.inputs;h.cls_tr="section-row";this.table=new b.View(h);this.setElement(this.table.$el);this.render()},render:function(){this.table.delAll();for(var h in this.inputs){this._add(this.inputs[h])}},_add:function(j){var i=this;var h=jQuery.extend(true,{},j);h.id=d.uuid();this.app.input_list[h.id]=h;var k=h.type;switch(k){case"conditional":this._addConditional(h);break;case"repeat":this._addRepeat(h);break;default:this._addRow(k,h)}},_addConditional:function(h){h.label=h.test_param.label;h.value=h.test_param.value;var j=this._addRow("conditional",h);for(var l in h.cases){var k=h.id+"-section-"+l;var m=new f(this.app,{inputs:h.cases[l].inputs,cls:"ui-table-plain"});m.$el.addClass("ui-table-form-section");this.table.add(m.$el);this.table.append(k)}},_addRepeat:function(h){var j=this;var n=0;var m=new c.View({title_new:h.title,max:h.max,onnew:function(){var i=h.id+"-section-"+(n++);var q=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:i,title:h.title,$el:q.$el,ondel:function(){m.del(i);m.retitle(h.title);j.app.refresh()}});m.retitle(h.title);j.app.refresh()}});for(var l=0;l<h.min;l++){var k=h.id+"-section-"+(n++);var p=new f(j.app,{inputs:h.inputs,cls:"ui-table-plain"});m.add({id:k,title:h.title,$el:p.$el})}m.retitle(h.title);var o=new e({label:h.title,help:h.help,field:m});o.$el.addClass("ui-table-form-section");this.table.add(o.$el);this.table.append(h.id)},_addRow:function(j,h){var l=h.id;var i=null;switch(j){case"text":i=this._fieldText(h);break;case"select":i=this._fieldSelect(h);break;case"data":i=this._fieldData(h);break;case"data_column":h.is_dynamic=false;i=this._fieldSelect(h);break;case"conditional":i=this._fieldConditional(h);break;case"hidden":i=this._fieldHidden(h);break;case"integer":i=this._fieldSlider(h);break;case"float":i=this._fieldSlider(h);break;case"boolean":i=this._fieldBoolean(h);break;case"genomebuild":i=this._fieldSelect(h);break;default:this.app.incompatible=true;if(h.options){i=this._fieldSelect(h)}else{i=this._fieldText(h)}console.debug("tools-form::_addRow() : Auto matched field type ("+j+").")}if(h.value!==undefined){i.value(h.value)}this.app.field_list[l]=i;var k=new e({label:h.label,optional:h.optional,help:h.help,field:i});this.app.element_list[l]=k;this.table.add(k.$el);this.table.append(l);return this.table.get(l)},_fieldConditional:function(h){var j=this;var k=[];for(var l in h.test_param.options){var m=h.test_param.options[l];k.push({label:m[0],value:m[1]})}return new g.Select.View({id:"field-"+h.id,data:k,onchange:function(u){for(var s in h.cases){var o=h.cases[s];var r=h.id+"-section-"+s;var n=j.table.get(r);var q=false;for(var p in o.inputs){var t=o.inputs[p].type;if(t&&t!=="hidden"){q=true;break}}if(o.value==u&&q){n.fadeIn("fast")}else{n.hide()}}}})},_fieldData:function(h){var i=this;var j=h.id;return new a.View(this.app,{id:"field-"+j,extensions:h.extensions,multiple:h.multiple,onchange:function(q){var o=q.values[0];var m=o.id;var p=o.src;var l=i.app.tree.references(j,"data_column");if(l.length<=0){console.debug("tool-form::field_data() - Data column parameters unavailable.");return}for(var n in l){var k=i.app.field_list[l[n]];k.wait&&k.wait()}i.app.content.getDetails({id:m,src:p,success:function(y){var B=null;if(y){console.debug("tool-form::field_data() - Selected content "+m+".");if(p=="hdca"&&y.elements&&y.elements.length>0){y=y.elements[0].object}B=y.metadata_column_types;if(!B){console.debug("tool-form::field_data() - FAILED: Could not find metadata for content "+m+".")}}else{console.debug("tool-form::field_data() - FAILED: Could not find content "+m+".")}for(var u in l){var w=i.app.input_list[l[u]];var x=i.app.field_list[l[u]];if(!w||!x){console.debug("tool-form::field_data() - FAILED: Column not found.")}var t=w.numerical;var s=[];for(var A in B){var z=B[A];var r=(parseInt(A)+1);var v="Text";if(z=="int"||z=="float"){v="Number"}if(z=="int"||z=="float"||!t){s.push({label:"Column: "+r+" ["+v+"]",value:r})}}if(x){x.update(s);if(!x.exists(x.value())){x.value(x.first())}x.show()}}}})}})},_fieldSelect:function(h){if(h.is_dynamic){this.app.incompatible=true}var j=[];for(var k in h.options){var l=h.options[k];j.push({label:l[0],value:l[1]})}var m=g.Select;switch(h.display){case"checkboxes":m=g.Checkbox;break;case"radio":m=g.Radio;break}return new m.View({id:"field-"+h.id,data:j,multiple:h.multiple})},_fieldText:function(h){return new g.Input({id:"field-"+h.id,area:h.area})},_fieldSlider:function(h){h.min=h.min||0;h.max=h.max||100000;var i=1;if(h.type=="float"){i=(h.max-h.min)/10000}return new g.Slider.View({id:"field-"+h.id,min:h.min,max:h.max,step:i})},_fieldHidden:function(h){return new g.Hidden({id:"field-"+h.id})},_fieldBoolean:function(h){return new g.RadioButton.View({id:"field-"+h.id,data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]})}});return{View:f}}); \ No newline at end of file diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/scripts/packed/mvc/tools/tools-tree.js --- a/static/scripts/packed/mvc/tools/tools-tree.js +++ b/static/scripts/packed/mvc/tools/tools-tree.js @@ -1,1 +1,1 @@ -define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(j,m){for(var g in m){var e=m[g];if(e.input){var n=e.input;var h=j;if(j!=""){h+="|"}h+=n.name;switch(n.type){case"repeat":var d="section-";var q=[];var l=null;for(var p in e){var k=p.indexOf(d);if(k!=-1){k+=d.length;q.push(parseInt(p.substr(k)));if(!l){l=p.substr(0,k)}}}q.sort(function(r,i){return r-i});var g=0;for(var f in q){b(h+"_"+g++,e[l+q[f]])}break;case"conditional":var o=a.app.field_list[n.id].value();c(h+"|"+n.test_param.name,n.id,o);for(var f in n.cases){if(n.cases[f].value==o){b(h,m[n.id+"-section-"+f]);break}}break;default:c(h,n.id,a.app.field_list[n.id].value())}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file +define([],function(){return Backbone.Model.extend({initialize:function(a){this.app=a},refresh:function(){this.dict={};this.xml=$("<div/>");if(!this.app.section){return{}}this._iterate(this.app.section.$el,this.dict,this.xml)},finalize:function(){var a=this;this.job_def={};this.job_ids={};function c(f,e,d){a.job_def[f]=d;a.job_ids[f]=e}function b(j,m){for(var g in m){var e=m[g];if(e.input){var o=e.input;var h=j;if(j!=""){h+="|"}h+=o.name;switch(o.type){case"repeat":var d="section-";var r=[];var l=null;for(var q in e){var k=q.indexOf(d);if(k!=-1){k+=d.length;r.push(parseInt(q.substr(k)));if(!l){l=q.substr(0,k)}}}r.sort(function(s,i){return s-i});var g=0;for(var f in r){b(h+"_"+g++,e[l+r[f]])}break;case"conditional":var p=a.app.field_list[o.id].value();c(h+"|"+o.test_param.name,o.id,p);for(var f in o.cases){if(o.cases[f].value==p){b(h,m[o.id+"-section-"+f]);break}}break;default:var n=a.app.field_list[o.id];if(!n.skip){c(h,o.id,n.value())}}}}}b("",this.dict);return this.job_def},match:function(a){return this.job_ids&&this.job_ids[a]},matchResponse:function(c){var a={};var b=this;function d(j,h){if(typeof h==="string"){var f=b.app.tree.job_ids[j];if(f){a[f]=h}}else{for(var g in h){var e=g;if(j!==""){e=j+"|"+e}d(e,h[g])}}}d("",c);return a},references:function(c,e){var g=[];var b=this;function d(h,j){var i=$(j).children();var l=[];var k=false;i.each(function(){var o=this;var n=$(o).attr("id");if(n!==c){var m=b.app.input_list[n];if(m){if(m.name==h){k=true;return false}if(m.data_ref==h&&m.type==e){l.push(n)}}}});if(!k){g=g.concat(l);i.each(function(){d(h,this)})}}var f=this.xml.find("#"+c);if(f.length>0){var a=this.app.input_list[c];if(a){d(a.name,f.parent())}}return g},_iterate:function(d,e,b){var a=this;var c=$(d).children();c.each(function(){var i=this;var h=$(i).attr("id");if($(i).hasClass("section-row")){e[h]={};var f=a.app.input_list[h];if(f){e[h]={input:f}}var g=$('<div id="'+h+'"/>');b.append(g);a._iterate(i,e[h],g)}else{a._iterate(i,e,b)}})}})}); \ No newline at end of file diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1284,8 +1284,10 @@ .ui-table tbody{cursor:pointer} .ui-table-plain tbody td{padding:5px 0px 5px 0px !important;border:none !important} .ui-table-plain tbody{cursor:auto !important} +.ui-table-form-element .ui-table-form-title-optional{font-weight:bold;text-decoration:underline;cursor:pointer} +.ui-table-form-element .ui-table-form-field{margin-top:5px} .ui-table-form-section{border-left:solid 3px #ebd9b2;border-radius:5px !important;padding-left:10px} -.ui-table-form-title-strong{font-weight:bold;padding-bottom:5px} +.ui-table-form-title-strong{font-weight:bold} .ui-table-form-info{clear:both !important} .ui-table-form-separator{font-weight:bold;font-size:0.9em} .ui-label{font-weight:bold} diff -r 46523237518bb9ec8ed9fa4cf30453c800580c24 -r 34e643839cdace531f6ebf1a7d08e5d735be51a6 static/style/src/less/ui.less --- a/static/style/src/less/ui.less +++ b/static/style/src/less/ui.less @@ -44,6 +44,17 @@ } } +.ui-table-form-element { + .ui-table-form-title-optional { + font-weight: bold; + text-decoration: underline; + cursor: pointer; + } + .ui-table-form-field { + margin-top: 5px; + } +} + .ui-table-form-section { border-left: solid 3px @form-heading-bg; border-radius: 5px !important; @@ -52,7 +63,6 @@ .ui-table-form-title-strong { font-weight: bold; - padding-bottom: 5px; } .ui-table-form-info { 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] 6f878b: Overhaul job running on Test.
by GitHub 09 Oct '14

09 Oct '14

Branch: refs/heads/master Home: https://github.com/galaxyproject/usegalaxy-playbook Commit: 6f878bbac19e180d9417e8445695269edbebdc1c https://github.com/galaxyproject/usegalaxy-playbook/commit/6f878bbac19e180d… Author: Nate Coraor <nate(a)bx.psu.edu> Date: 2014-10-09 (Thu, 09 Oct 2014) Changed paths: M files/galaxy/test.galaxyproject.org/config/job_resource_params_conf.xml A files/galaxy/test.galaxyproject.org/dynamic_rules/multi_dynamic_walltime.py M files/galaxy/test.galaxyproject.org/dynamic_rules/reserved.py R files/galaxy/test.galaxyproject.org/dynamic_rules/roundup_multi_walltime.py A files/galaxy/test.galaxyproject.org/dynamic_rules/stampede_select.py M stage/group_vars/galaxyservers.yml M templates/galaxy/test.galaxyproject.org/config/job_conf.xml.j2 Log Message: ----------- Overhaul job running on Test.

1 0

commit/galaxy-central: jmchilton: More informative exceptions for startup failure due to job config XML errors.
by commits-noreply＠bitbucket.org 09 Oct '14

09 Oct '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/46523237518b/ Changeset: 46523237518b User: jmchilton Date: 2014-10-09 19:04:38+00:00 Summary: More informative exceptions for startup failure due to job config XML errors. Describe that this is an XML formatting issue that is causing the problem and include the full path of the file when to the user starting Galaxy. Inspired by problems described here: https://biostar.usegalaxy.org/p/9245/. Affected #: 1 file diff -r dd0d4fa44feb1d620a288093cb72e1b83811ce0f -r 46523237518bb9ec8ed9fa4cf30453c800580c24 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -91,6 +91,15 @@ return self.get( "resources", None ) +def config_exception(e, file): + abs_path = os.path.abspath(file) + message = 'Problem parsing the XML in file %s, ' % abs_path + message += 'please correct the indicated portion of the file and restart Galaxy.' + message += str(e) + log.exception(message) + return Exception(message) + + class JobConfiguration( object ): """A parser and interface to advanced job management features. @@ -118,12 +127,15 @@ self.__parse_resource_parameters() # Initialize the config + job_config_file = self.app.config.job_config_file try: - tree = util.parse_xml(self.app.config.job_config_file) + tree = util.parse_xml(job_config_file) self.__parse_job_conf_xml(tree) except IOError: log.warning( 'Job configuration "%s" does not exist, using legacy job configuration from Galaxy config file "%s" instead' % ( self.app.config.job_config_file, self.app.config.config_file ) ) self.__parse_job_conf_legacy() + except Exception as e: + raise config_exception(e, job_config_file) def __parse_job_conf_xml(self, tree): """Loads the new-style job configuration from options in the job config file (by default, job_conf.xml). @@ -358,7 +370,12 @@ if not os.path.exists( self.app.config.job_resource_params_file ): return - resource_definitions = util.parse_xml( self.app.config.job_resource_params_file ) + resource_param_file = self.app.config.job_resource_params_file + try: + resource_definitions = util.parse_xml( resource_param_file ) + except Exception as e: + raise config_exception(e, resource_param_file) + resource_definitions_root = resource_definitions.getroot() # TODO: Also handling conditionals would be awesome! for parameter_elem in resource_definitions_root.findall( "param" ): 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