1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d00255be341d/
Changeset: d00255be341d
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 da99d403f3375c31e8d784a91d430fe7068de1ab -r d00255be341d2b08af3fceeb2c8f46d3d6ce610b lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -386,6 +386,7 @@
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"
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/da99d403f337/
Changeset: da99d403f337
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 70caaa5b7ff7dd4a11ddead7d946cb145e58686a -r da99d403f3375c31e8d784a91d430fe7068de1ab lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -353,11 +353,13 @@
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
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/70caaa5b7ff7/
Changeset: 70caaa5b7ff7
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 75d1aa0e7663ec42f004a785ece731fd992f979d -r 70caaa5b7ff7dd4a11ddead7d946cb145e58686a lib/galaxy/tools/data/__init__.py
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -513,7 +513,7 @@
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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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/75d1aa0e7663/
Changeset: 75d1aa0e7663
User: guerler
Date: 2015-02-11 17:27:18+00:00
Summary: ToolForm: Move debug output
Affected #: 6 files
diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d client/galaxy/scripts/mvc/tools/tools-content.js
--- a/client/galaxy/scripts/mvc/tools/tools-content.js
+++ b/client/galaxy/scripts/mvc/tools/tools-content.js
@@ -15,9 +15,6 @@
this.summary[c.id + '_' + c.src] = c;
}
}
-
- // log
- console.debug('tools-content::initialize() - Completed.');
},
/** Returns matched content from summary.
diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d 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
@@ -350,6 +350,9 @@
message : options.message
});
}
+
+ // log
+ console.debug('tools-form-base::initialize() - Completed.');
}
});
});
diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d static/scripts/mvc/tools/tools-content.js
--- a/static/scripts/mvc/tools/tools-content.js
+++ b/static/scripts/mvc/tools/tools-content.js
@@ -15,9 +15,6 @@
this.summary[c.id + '_' + c.src] = c;
}
}
-
- // log
- console.debug('tools-content::initialize() - Completed.');
},
/** Returns matched content from summary.
diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d 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
@@ -350,6 +350,9 @@
message : options.message
});
}
+
+ // log
+ console.debug('tools-form-base::initialize() - Completed.');
}
});
});
diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d static/scripts/packed/mvc/tools/tools-content.js
--- a/static/scripts/packed/mvc/tools/tools-content.js
+++ b/static/scripts/packed/mvc/tools/tools-content.js
@@ -1,1 +1,1 @@
-define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.summary={}},add:function(e){for(var d in e){for(var b in e[d]){var f=e[d][b];this.summary[f.id+"_"+f.src]=f}}console.debug("tools-content::initialize() - Completed.")},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})}})});
\ No newline at end of file
+define(["utils/utils"],function(a){return Backbone.Model.extend({initialize:function(b){this.summary={}},add:function(e){for(var d in e){for(var b in e[d]){var f=e[d][b];this.summary[f.id+"_"+f.src]=f}}},get:function(b){return _.findWhere(this.summary,b)||{}},getDetails:function(b){if(!b.id||b.id==="null"){b.success&&b.success();return}var c=this.base_url+"/datasets/"+b.id;if(b.src=="hdca"){c=this.base_url+"/dataset_collections/"+b.id}a.get({url:c,success:function(d){b.success&&b.success(d)},error:function(d){b.success&&b.success();console.debug("tools-content::getDetails() - Ajax request for content failed.");console.debug(d)}})}})});
\ No newline at end of file
diff -r bbd5375d27aaeac049a37c29a3c7fa98e96f7e5e -r 75d1aa0e7663ec42f004a785ece731fd992f979d 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.$el.append(r)}if(t.message){this.message.update({persistent:true,status:"warning",message:t.message})}}})});
\ No newline at end of file
+define(["utils/utils","utils/deferred","mvc/ui/ui-portlet","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-content","mvc/tools/tools-section","mvc/tools/tools-tree"],function(g,h,f,k,i,a,d,c,e,j,b){return Backbone.View.extend({initialize:function(l){this.optionsDefault={is_dynamic:true,narrow:false,initial_errors:false,cls_portlet:"ui-portlet-limited"};this.options=g.merge(l,this.optionsDefault);console.debug(this.options);var m=parent.Galaxy;if(m&&m.modal){this.modal=m.modal}else{this.modal=new k.Modal.View()}if(m&&m.currUser){this.is_admin=m.currUser.get("is_admin")}else{this.is_admin=false}this.container=this.options.container||"body";this.deferred=new h();this.setElement("<div/>");$(this.container).append(this.$el);this.build(this.options)},build:function(m){var l=this;this.off("refresh");this.off("reset");this.field_list={};this.input_list={};this.element_list={};this.tree=new b(this);this.content=new e(this);l.options.inputs=m&&m.inputs;this._renderForm(m);this.tree.finalize();if(m.initial_errors){this._errors(m)}this.on("refresh",function(){l.deferred.reset();l.deferred.execute(function(){l._updateModel()})});this.on("reset",function(){for(var n in this.element_list){this.element_list[n].reset()}});this.trigger("refresh")},reciept:function(l){$(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
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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