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