1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/4e51563b62b5/
Changeset: 4e51563b62b5
User: dan
Date: 2014-08-21 21:52:35
Summary: Fix for FASTQ datasets peek/display of sequence counts.
Affected #: 1 file
diff -r 41f9ca7a24c5748f80ed19315786ba51f4cc19b5 -r 4e51563b62b5bf497ad42c53868dc9d48d39146c lib/galaxy/datatypes/sequence.py
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -460,6 +460,7 @@
"""
Set the number of sequences and the number of data lines
in dataset.
+ FIXME: This does not properly handle line wrapping
"""
if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
dataset.metadata.data_lines = None
@@ -470,22 +471,17 @@
seq_counter = 0 # blocks should be 4 lines long
for line in file( dataset.file_name ):
line = line.strip()
- if line and line.startswith( '#' ) and not sequences:
+ if line and line.startswith( '#' ) and not data_lines:
# We don't count comment lines for sequence data types
continue
+ seq_counter += 1
+ data_lines += 1
if line and line.startswith( '@' ):
if seq_counter >= 4:
# count previous block
# blocks should be 4 lines long
sequences += 1
seq_counter = 1
- else:
- # in case quality line starts with @
- seq_counter += 1
- data_lines += 1
- else:
- data_lines += 1
- seq_counter += 1
if seq_counter >= 4:
# count final block
sequences += 1
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/41f9ca7a24c5/
Changeset: 41f9ca7a24c5
User: guerler
Date: 2014-08-22 20:32:07
Summary: ToolForm: Implements conditionals
Affected #: 2 files
diff -r 0c2fd93d22b796bb38687ca5489e7c57c3e14c21 -r 41f9ca7a24c5748f80ed19315786ba51f4cc19b5 static/scripts/mvc/tools/tools-form.js
--- a/static/scripts/mvc/tools/tools-form.js
+++ b/static/scripts/mvc/tools/tools-form.js
@@ -103,8 +103,11 @@
// reset table
this.table.delAll();
- // reset list
- this.list = [];
+ // reset field list
+ this.field_list = {};
+
+ // reset sequential input definition list
+ this.inputs_sequential = {};
// model
var data = new Backbone.Model();
@@ -115,65 +118,93 @@
}
// trigger change
- for (var id in this.list) {
- this.list[id].trigger('change');
+ for (var id in this.field_list) {
+ this.field_list[id].trigger('change');
}
},
// add table row
_add: function(inputs_def, data) {
- // link this
- var self = this;
-
+ // identify field type
+ var type = inputs_def.type;
+ switch(type) {
+ // conditional field
+ case 'conditional':
+ // add label to input definition root
+ inputs_def.label = inputs_def.test_param.label;
+
+ // add id to input definition root
+ inputs_def.name = inputs_def.test_param.name;
+
+ // build options field
+ this._addRow('conditional', inputs_def, data);
+
+ // add fields
+ for (var i in inputs_def.cases) {
+ var cases = inputs_def.cases[i];
+ for (var j in cases.inputs) {
+ // add element to form
+ this._add(cases.inputs[j], data);
+ }
+ }
+ break;
+
+ // default single element row
+ default:
+ this._addRow(type, inputs_def, data);
+ }
+ },
+
+ // add table row
+ _addRow: function(field_type, inputs_def, data) {
// get id
var id = inputs_def.name;
// field wrapper
var field = null;
- console.log(inputs_def);
- // create select field
- var type = inputs_def.type;
- switch(type) {
+
+ // identify field type
+ switch(field_type) {
// text input field
case 'text' :
- field = this.field_text(inputs_def, data);
+ field = this._field_text(inputs_def, data);
break;
// select field
case 'select' :
- field = this.field_select(inputs_def, data);
+ field = this._field_select(inputs_def, data);
break;
// radiobox field
case 'radiobutton' :
- field = this.field_radio(inputs_def, data);
+ field = this._field_radio(inputs_def, data);
break;
// dataset
case 'data':
- field = this.field_data(inputs_def, data);
+ field = this._field_data(inputs_def, data);
break;
// dataset column
case 'data_column':
- field = this.field_column(inputs_def, data);
+ field = this._field_column(inputs_def, data);
break;
// text area field
case 'textarea' :
- field = this.field_textarea(inputs_def, data);
+ field = this._field_textarea(inputs_def, data);
break;
-
- // default
- default:
- field = new Ui.Input({
- id : 'field-' + id,
- placeholder : inputs_def.placeholder,
- type : inputs_def.type,
- onchange : function() {
- data.set(id, field.value());
- }
- });
+
+ // conditional select field
+ case 'conditional':
+ field = this._field_conditional(inputs_def, data);
+ break;
+ }
+
+ // check if field type was detected
+ if (!field) {
+ console.debug('tools-form::_addRow() : Unmatched field type (' + field_type + ').');
+ return;
}
// set value
@@ -182,8 +213,11 @@
}
field.value(data.get(id));
- // add list
- this.list[id] = field;
+ // add to field list
+ this.field_list[id] = field;
+
+ // add to input definition into sequential list
+ this.inputs_sequential[id] = inputs_def;
// combine field and info
var $input = $('<div/>');
@@ -206,7 +240,7 @@
},
// text input field
- field_text : function(inputs_def, data) {
+ _field_text : function(inputs_def, data) {
var id = inputs_def.name;
return new Ui.Input({
id : 'field-' + id,
@@ -218,7 +252,7 @@
},
// text area
- field_textarea : function(inputs_def, data) {
+ _field_textarea : function(inputs_def, data) {
var id = inputs_def.name;
return new Ui.Textarea({
id : 'field-' + id,
@@ -228,8 +262,72 @@
});
},
+ // conditional input field
+ _field_conditional : function(inputs_def, data) {
+ // link this
+ var self = this;
+
+ // configure options fields
+ var options = [];
+ for (var i in inputs_def.test_param.options) {
+ var option = inputs_def.test_param.options[i];
+ options.push({
+ label: option[0],
+ value: option[1]
+ });
+ }
+
+ // select field
+ var id = inputs_def.name;
+ return new Ui.Select.View({
+ id : 'field-' + id,
+ data : options,
+ value : data.get(id),
+ onchange : function(value) {
+ // update value
+ data.set(id, value);
+
+ // recursively hide/show options
+ function _updateVisibility(root, show) {
+ // loop through all inputs
+ for (var i in root.inputs) {
+ // get input element
+ var element = root.inputs[i];
+
+ // identify element name
+ var element_id = element.name;
+
+ // identify row
+ var element_row = self.table.get(element_id);
+
+ // show/hide row
+ if (show) {
+ element_row.fadeIn();
+ } else {
+ element_row.hide();
+ }
+
+ // check if its a nested conditional
+ if (element.type == 'conditional') {
+ // identify all cases
+ for (var j in element.cases) {
+ _updateVisibility(element.cases[j], show);
+ }
+ }
+ }
+ }
+
+ // check value in order to hide/show options
+ for (var i in inputs_def.cases) {
+ var case_def = inputs_def.cases[i];
+ _updateVisibility(case_def, case_def.value == value);
+ }
+ }
+ });
+ },
+
// data input field
- field_data : function(inputs_def, data) {
+ _field_data : function(inputs_def, data) {
// link this
var self = this;
@@ -248,12 +346,6 @@
});
}
- // find referenced columns
- var column_list = _.where(this.inputs, {
- data_ref : id,
- type : 'data_column'
- });
-
// select field
return new Ui.Select.View({
id : 'field-' + id,
@@ -263,6 +355,12 @@
// update value
data.set(id, value);
+ // find referenced columns
+ var column_list = _.where(self.inputs_sequential, {
+ data_ref : id,
+ type : 'data_column'
+ });
+
// find selected dataset
var dataset = self.datasets.filter(value);
@@ -291,7 +389,7 @@
// update referenced columns
for (var i in column_list) {
- var column_field = self.list[column_list[i].name]
+ var column_field = self.field_list[column_list[i].name]
if (column_field) {
column_field.update(columns);
column_field.value(column_field.first());
@@ -306,7 +404,7 @@
},
// select field
- field_column : function (inputs_def, data) {
+ _field_column : function (inputs_def, data) {
// configure options fields
var options = [];
for (var i in inputs_def.options) {
@@ -330,7 +428,7 @@
},
// select field
- field_select : function (inputs_def, data) {
+ _field_select : function (inputs_def, data) {
// configure options fields
var options = [];
for (var i in inputs_def.options) {
@@ -360,7 +458,7 @@
},
// radio field
- field_radio : function(inputs_def, data) {
+ _field_radio : function(inputs_def, data) {
var id = inputs_def.name;
return new Ui.RadioButton({
id : 'field-' + id,
diff -r 0c2fd93d22b796bb38687ca5489e7c57c3e14c21 -r 41f9ca7a24c5748f80ed19315786ba51f4cc19b5 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-table","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets"],function(f,i,j,h,a,e,c,g){var d=Backbone.Model.extend({initialize:function(k){this.url=galaxy_config.root+"api/tools/"+k.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(l){var k=this;this.options=l;this.model=new d({id:l.id});this.datasets=new g({success:function(){k._initializeToolForm()}})},_initializeToolForm:function(){var k=this;this.model.fetch({success:function(){k.inputs=k.model.get("inputs");k.portlet=new f.View({icon:"fa-wrench",title:"<b>"+k.model.get("name")+"</b> "+k.model.get("description"),buttons:{execute:new j.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});k.table=new i.View();k.message=new j.Message();k.portlet.append(k.message.$el);$(k.main_el).append(k.portlet.$el);if(k.options.help!=""){$(k.main_el).append(c.help(k.options.help))}if(k.options.citations){$(k.main_el).append(c.citations());var l=new h.ToolCitationCollection();l.tool_id=k.options.id;var m=new a.CitationListView({collection:l});m.render();l.fetch()}k.setElement(k.portlet.content());k.portlet.append(k.table.$el);k.render()}})},render:function(){this.table.delAll();this.list=[];var k=new Backbone.Model();for(var l in this.inputs){this._add(this.inputs[l],k)}for(var l in this.list){this.list[l].trigger("change")}},_add:function(l,n){var k=this;var q=l.name;var o=null;console.log(l);var m=l.type;switch(m){case"text":o=this.field_text(l,n);break;case"select":o=this.field_select(l,n);break;case"radiobutton":o=this.field_radio(l,n);break;case"data":o=this.field_data(l,n);break;case"data_column":o=this.field_column(l,n);break;case"textarea":o=this.field_textarea(l,n);break;default:o=new j.Input({id:"field-"+q,placeholder:l.placeholder,type:l.type,onchange:function(){n.set(q,o.value())}})}if(!n.get(q)){n.set(q,l.value)}o.value(n.get(q));this.list[q]=o;var p=$("<div/>");p.append(o.$el);if(l.info){p.append('<div class="ui-table-form-info">'+l.info+"</div>")}this.table.add('<span class="ui-table-form-title">'+l.label+"</span>","25%");this.table.add(p);this.table.append(q);if(l.hide){this.table.get(q).hide()}},field_text:function(k,l){var m=k.name;return new j.Input({id:"field-"+m,value:l.get(m),onchange:function(n){l.set(m,n)}})},field_textarea:function(k,l){var m=k.name;return new j.Textarea({id:"field-"+m,onchange:function(){l.set(m,field.value())}})},field_data:function(n,q){var l=this;var r=n.name;var p=this.datasets.filterType();var m=[];for(var o in p){m.push({label:p[o].get("name"),value:p[o].get("id")})}var k=_.where(this.inputs,{data_ref:r,type:"data_column"});return new j.Select.View({id:"field-"+r,data:m,value:m[0].value,onchange:function(w){q.set(r,w);var y=l.datasets.filter(w);if(y&&k.length>0){console.debug("tool-form::field_data() - Selected dataset "+w+".");var x=y.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+w+".")}var v=[];for(var u in x){v.push({label:"Column: "+(parseInt(u)+1)+" ["+x[u]+"]",value:u})}for(var t in k){var s=l.list[k[t].name];if(s){s.update(v);s.value(s.first())}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+w+".")}}})},field_column:function(l,o){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var p=l.name;return new j.Select.View({id:"field-"+p,data:k,value:o.get(p),onchange:function(q){o.set(p,q)}})},field_select:function(l,p){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var o=j.Select;if(l.display=="checkboxes"){o=j.Checkbox}var q=l.name;return new o.View({id:"field-"+q,data:k,value:p.get(q),onchange:function(r){p.set(q,r)}})},field_radio:function(k,l){var m=k.name;return new j.RadioButton({id:"field-"+m,data:k.data,value:l.get(m),onchange:function(n){l.set(m,n)}})}});return{View:b}});
\ No newline at end of file
+define(["mvc/ui/ui-portlet","mvc/ui/ui-table","mvc/ui/ui-misc","mvc/citation/citation-model","mvc/citation/citation-view","mvc/tools","mvc/tools/tools-template","mvc/tools/tools-datasets"],function(f,i,j,h,a,e,c,g){var d=Backbone.Model.extend({initialize:function(k){this.url=galaxy_config.root+"api/tools/"+k.id+"?io_details=true"}});var b=Backbone.View.extend({main_el:"body",initialize:function(l){var k=this;this.options=l;this.model=new d({id:l.id});this.datasets=new g({success:function(){k._initializeToolForm()}})},_initializeToolForm:function(){var k=this;this.model.fetch({success:function(){k.inputs=k.model.get("inputs");k.portlet=new f.View({icon:"fa-wrench",title:"<b>"+k.model.get("name")+"</b> "+k.model.get("description"),buttons:{execute:new j.ButtonIcon({icon:"fa-check",tooltip:"Execute the tool",title:"Execute",floating:"clear",onclick:function(){}})}});k.table=new i.View();k.message=new j.Message();k.portlet.append(k.message.$el);$(k.main_el).append(k.portlet.$el);if(k.options.help!=""){$(k.main_el).append(c.help(k.options.help))}if(k.options.citations){$(k.main_el).append(c.citations());var l=new h.ToolCitationCollection();l.tool_id=k.options.id;var m=new a.CitationListView({collection:l});m.render();l.fetch()}k.setElement(k.portlet.content());k.portlet.append(k.table.$el);k.render()}})},render:function(){this.table.delAll();this.field_list={};this.inputs_sequential={};var k=new Backbone.Model();for(var l in this.inputs){this._add(this.inputs[l],k)}for(var l in this.field_list){this.field_list[l].trigger("change")}},_add:function(l,p){var n=l.type;switch(n){case"conditional":l.label=l.test_param.label;l.name=l.test_param.name;this._addRow("conditional",l,p);for(var m in l.cases){var o=l.cases[m];for(var k in o.inputs){this._add(o.inputs[k],p)}}break;default:this._addRow(n,l,p)}},_addRow:function(n,k,l){var p=k.name;var m=null;switch(n){case"text":m=this._field_text(k,l);break;case"select":m=this._field_select(k,l);break;case"radiobutton":m=this._field_radio(k,l);break;case"data":m=this._field_data(k,l);break;case"data_column":m=this._field_column(k,l);break;case"textarea":m=this._field_textarea(k,l);break;case"conditional":m=this._field_conditional(k,l);break}if(!m){console.debug("tools-form::_addRow() : Unmatched field type ("+n+").");return}if(!l.get(p)){l.set(p,k.value)}m.value(l.get(p));this.field_list[p]=m;this.inputs_sequential[p]=k;var o=$("<div/>");o.append(m.$el);if(k.info){o.append('<div class="ui-table-form-info">'+k.info+"</div>")}this.table.add('<span class="ui-table-form-title">'+k.label+"</span>","25%");this.table.add(o);this.table.append(p);if(k.hide){this.table.get(p).hide()}},_field_text:function(k,l){var m=k.name;return new j.Input({id:"field-"+m,value:l.get(m),onchange:function(n){l.set(m,n)}})},_field_textarea:function(k,l){var m=k.name;return new j.Textarea({id:"field-"+m,onchange:function(){l.set(m,field.value())}})},_field_conditional:function(m,p){var k=this;var l=[];for(var n in m.test_param.options){var o=m.test_param.options[n];l.push({label:o[0],value:o[1]})}var q=m.name;return new j.Select.View({id:"field-"+q,data:l,value:p.get(q),onchange:function(u){p.set(q,u);function t(x,w){for(var A in x.inputs){var z=x.inputs[A];var v=z.name;var B=k.table.get(v);if(w){B.fadeIn()}else{B.hide()}if(z.type=="conditional"){for(var y in z.cases){t(z.cases[y],w)}}}}for(var s in m.cases){var r=m.cases[s];t(r,r.value==u)}}})},_field_data:function(m,p){var k=this;var q=m.name;var o=this.datasets.filterType();var l=[];for(var n in o){l.push({label:o[n].get("name"),value:o[n].get("id")})}return new j.Select.View({id:"field-"+q,data:l,value:l[0].value,onchange:function(w){p.set(q,w);var s=_.where(k.inputs_sequential,{data_ref:q,type:"data_column"});var y=k.datasets.filter(w);if(y&&s.length>0){console.debug("tool-form::field_data() - Selected dataset "+w+".");var x=y.get("metadata_column_types");if(!x){console.debug("tool-form::field_data() - FAILED: Could not find metadata for dataset "+w+".")}var v=[];for(var u in x){v.push({label:"Column: "+(parseInt(u)+1)+" ["+x[u]+"]",value:u})}for(var t in s){var r=k.field_list[s[t].name];if(r){r.update(v);r.value(r.first())}}}else{console.debug("tool-form::field_data() - FAILED: Could not find dataset "+w+".")}}})},_field_column:function(l,o){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var p=l.name;return new j.Select.View({id:"field-"+p,data:k,value:o.get(p),onchange:function(q){o.set(p,q)}})},_field_select:function(l,p){var k=[];for(var m in l.options){var n=l.options[m];k.push({label:n[0],value:n[1]})}var o=j.Select;if(l.display=="checkboxes"){o=j.Checkbox}var q=l.name;return new o.View({id:"field-"+q,data:k,value:p.get(q),onchange:function(r){p.set(q,r)}})},_field_radio:function(k,l){var m=k.name;return new j.RadioButton({id:"field-"+m,data:k.data,value:l.get(m),onchange:function(n){l.set(m,n)}})}});return{View:b}});
\ No newline at end of file
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d86834553f0e/
Changeset: d86834553f0e
Branch: stable
User: natefoo
Date: 2014-08-22 15:00:42
Summary: Update tag latest_2014.08.11 for changeset 7e22f3579852
Affected #: 1 file
diff -r 7e22f35798522100ff03e1fdd4eced962b292360 -r d86834553f0e2d3636b3f545f61ae3250ead31e9 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -18,4 +18,4 @@
81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
-6445c0fe761258410a17b95ad2f221a9e60fc5c7 latest_2014.08.11
+7e22f35798522100ff03e1fdd4eced962b292360 latest_2014.08.11
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/7e22f3579852/
Changeset: 7e22f3579852
Branch: stable
User: dan
Date: 2014-08-21 21:52:35
Summary: Fix for FASTQ datasets peek/display of sequence counts.
Affected #: 1 file
diff -r b6c8afd2c2a1a214ef96c4ccf05aab8c8bc826f2 -r 7e22f35798522100ff03e1fdd4eced962b292360 lib/galaxy/datatypes/sequence.py
--- a/lib/galaxy/datatypes/sequence.py
+++ b/lib/galaxy/datatypes/sequence.py
@@ -460,6 +460,7 @@
"""
Set the number of sequences and the number of data lines
in dataset.
+ FIXME: This does not properly handle line wrapping
"""
if self.max_optional_metadata_filesize >= 0 and dataset.get_size() > self.max_optional_metadata_filesize:
dataset.metadata.data_lines = None
@@ -470,22 +471,17 @@
seq_counter = 0 # blocks should be 4 lines long
for line in file( dataset.file_name ):
line = line.strip()
- if line and line.startswith( '#' ) and not sequences:
+ if line and line.startswith( '#' ) and not data_lines:
# We don't count comment lines for sequence data types
continue
+ seq_counter += 1
+ data_lines += 1
if line and line.startswith( '@' ):
if seq_counter >= 4:
# count previous block
# blocks should be 4 lines long
sequences += 1
seq_counter = 1
- else:
- # in case quality line starts with @
- seq_counter += 1
- data_lines += 1
- else:
- data_lines += 1
- seq_counter += 1
if seq_counter >= 4:
# count final block
sequences += 1
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/b6c8afd2c2a1/
Changeset: b6c8afd2c2a1
Branch: stable
User: natefoo
Date: 2014-08-21 15:00:21
Summary: Update tag latest_2014.08.11 for changeset 6445c0fe7612
Affected #: 1 file
diff -r 6445c0fe761258410a17b95ad2f221a9e60fc5c7 -r b6c8afd2c2a1a214ef96c4ccf05aab8c8bc826f2 .hgtags
--- a/.hgtags
+++ b/.hgtags
@@ -18,4 +18,4 @@
81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04
2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10
ca45b78adb4152fc6e7395514d46eba6b7d0b838 release_2014.08.11
-7748a83f33617f450b23557420c753754e54ee4d latest_2014.08.11
+6445c0fe761258410a17b95ad2f221a9e60fc5c7 latest_2014.08.11
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/059dd17a77e0/
Changeset: 059dd17a77e0
User: natefoo
Date: 2014-08-20 23:51:33
Summary: Style fixes for sample universe_wsgi.ini
Affected #: 1 file
diff -r 871a781a05070d5a227469c55c4249dbe6945e2d -r 059dd17a77e02c515e42b63bf50d2a9e37058b6c universe_wsgi.ini.sample
--- a/universe_wsgi.ini.sample
+++ b/universe_wsgi.ini.sample
@@ -229,9 +229,9 @@
# Citation related caching. Tool citations information maybe fetched from
# external sources such as http://dx.doi.org/ by Galaxy - the following parameters
# can be used to control the caching used to store this information.
-#citation_cache_type=file
-#citation_cache_data_dir=database/citations/data
-#citation_cache_lock_dir=database/citations/lock
+#citation_cache_type = file
+#citation_cache_data_dir = database/citations/data
+#citation_cache_lock_dir = database/citations/lock
# External service types config file, defines what types of external_services configurations
# are available in Galaxy.
@@ -309,7 +309,7 @@
#smtp_password = None
# If your SMTP server requires SSL from the beginning of the connection
-# smtp_ssl= False
+# smtp_ssl = False
# On the user registration form, users may choose to join the mailing list.
# This is the address of the list they'll be subscribed to.
@@ -450,7 +450,7 @@
# The URL linked by the "Galaxy Q&A" link in the "Help" menu
# The Galaxy Q&A site is under development; when the site is done, this URL
# will be set and uncommented.
-# qa_url =
+#qa_url =
# Serve static content, which must be enabled if you're not serving it via a
# proxy server. These options should be self explanatory and so are not
@@ -620,7 +620,7 @@
#enable_lucene_library_search = False
# maxiumum file size to index for searching, in MB
#fulltext_max_size = 500
-#fulltext_noindex_filetypes=bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger
+#fulltext_noindex_filetypes = bam,sam,wig,bigwig,fasta,fastq,fastqsolexa,fastqillumina,fastqsanger
# base URL of server providing search functionality using lucene
#fulltext_url = http://localhost:8081
@@ -709,7 +709,7 @@
# Master key that allows many API admin actions to be used without actually
# having a defined admin user in the database/config. Only set this if you need
# to bootstrap Galaxy, you probably do not want to set this on public servers.
-#master_api_key=changethis
+#master_api_key = changethis
# Enable tool tags (associating tools with tags). This has its own option
# since its implementation has a few performance implications on startup for
https://bitbucket.org/galaxy/galaxy-central/commits/0c2fd93d22b7/
Changeset: 0c2fd93d22b7
User: natefoo
Date: 2014-08-20 23:51:49
Summary: Set defaults for static so they do not need to be explicitly defined in the Galaxy config.
Affected #: 1 file
diff -r 059dd17a77e02c515e42b63bf50d2a9e37058b6c -r 0c2fd93d22b796bb38687ca5489e7c57c3e14c21 lib/galaxy/webapps/galaxy/buildapp.py
--- a/lib/galaxy/webapps/galaxy/buildapp.py
+++ b/lib/galaxy/webapps/galaxy/buildapp.py
@@ -561,12 +561,12 @@
# Send to dynamic app by default
urlmap["/"] = app
# Define static mappings from config
- urlmap["/static"] = Static( conf.get( "static_dir" ), cache_time )
- urlmap["/images"] = Static( conf.get( "static_images_dir" ), cache_time )
- urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir" ), cache_time )
- urlmap["/static/style"] = Static( conf.get( "static_style_dir" ), cache_time )
- urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir" ), cache_time )
- urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", 'static/robots.txt'), cache_time )
+ urlmap["/static"] = Static( conf.get( "static_dir", "./static/" ), cache_time )
+ urlmap["/images"] = Static( conf.get( "static_images_dir", "./static/images" ), cache_time )
+ urlmap["/static/scripts"] = Static( conf.get( "static_scripts_dir", "./static/scripts/" ), cache_time )
+ urlmap["/static/style"] = Static( conf.get( "static_style_dir", "./static/style/blue" ), cache_time )
+ urlmap["/favicon.ico"] = Static( conf.get( "static_favicon_dir", "./static/favicon.ico" ), cache_time )
+ urlmap["/robots.txt"] = Static( conf.get( "static_robots_txt", "./static/robots.txt" ), cache_time )
# wrap any static dirs for plugins
plugin_frameworks = plugin_frameworks or []
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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