1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/e001809f8d6e/
Changeset: e001809f8d6e
User: guerler
Date: 2015-02-16 21:14:05+00:00
Summary: Workflow: Remove tool model from module data
Affected #: 1 file
diff -r 669f3cf60128e9a891e0e8ea7e16db4efef37b40 -r e001809f8d6e28607162e558ece72f5590fad6ab lib/galaxy/webapps/galaxy/controllers/workflow.py
--- a/lib/galaxy/webapps/galaxy/controllers/workflow.py
+++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py
@@ -652,9 +652,6 @@
trans.workflow_building_mode = True
module = module_factory.new( trans, type, **kwargs )
tool_model = None
- if type == 'tool':
- tool_model = module.tool.to_json(trans, is_dynamic=False)
- module.state.inputs = copy.deepcopy(tool_model['state_inputs'])
return {
'type': module.type,
'name': module.get_name(),
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/669f3cf60128/
Changeset: 669f3cf60128
User: carlfeberhard
Date: 2015-02-16 20:19:35+00:00
Summary: Dataproviders, column: correct max split in filter parsing
Affected #: 1 file
diff -r d61dbf796cb5ca7500782e511490740c25010486 -r 669f3cf60128e9a891e0e8ea7e16db4efef37b40 lib/galaxy/datatypes/dataproviders/column.py
--- a/lib/galaxy/datatypes/dataproviders/column.py
+++ b/lib/galaxy/datatypes/dataproviders/column.py
@@ -116,8 +116,8 @@
self.column_filters.append( parsed )
def parse_filter( self, filter_param_str ):
- split = filter_param_str.split( '-', 3 )
- if not len( split ) == 3:
+ split = filter_param_str.split( '-', 2 )
+ if not len( split ) >= 3:
return None
column, op, val = split
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/d61dbf796cb5/
Changeset: d61dbf796cb5
User: carlfeberhard
Date: 2015-02-16 19:25:03+00:00
Summary: History, API: allow purging with url parameter passing e.g. '...?purge=True', add test
Affected #: 3 files
diff -r a7d53e97af6fcdc4da90d20c897541771cecd963 -r d61dbf796cb5ca7500782e511490740c25010486 lib/galaxy/webapps/galaxy/api/histories.py
--- a/lib/galaxy/webapps/galaxy/api/histories.py
+++ b/lib/galaxy/webapps/galaxy/api/histories.py
@@ -259,23 +259,23 @@
:type id: str
:param id: the encoded id of the history to delete
:type kwd: dict
- :param kwd: (optional) dictionary structure containing:
+ :param kwd: (optional) dictionary structure containing extra parameters
- * payload: a dictionary itself containing:
- * purge: if True, purge the history and all of its HDAs
+ You can purge a history, removing all it's datasets from disk (if unshared),
+ by passing in ``purge=True`` in the url.
:param keys: same as the use of `keys` in the `index` function above
:param view: same as the use of `view` in the `index` function above
:rtype: dict
- :returns: an error object if an error occurred or a dictionary containing:
- * id: the encoded id of the history,
- * deleted: if the history was marked as deleted,
- * purged: if the history was purged
+ :returns: the deleted or purged history
"""
history_id = id
# a request body is optional here
purge = False
+ if 'purge' in kwd:
+ purge = string_as_bool( kwd.get( 'purge' ) )
+ # for backwards compat, keep the payload sub-dictionary
if kwd.get( 'payload', None ):
purge = string_as_bool( kwd['payload'].get( 'purge', False ) )
diff -r a7d53e97af6fcdc4da90d20c897541771cecd963 -r d61dbf796cb5ca7500782e511490740c25010486 test/casperjs/api-history-tests.js
--- a/test/casperjs/api-history-tests.js
+++ b/test/casperjs/api-history-tests.js
@@ -118,7 +118,7 @@
"Id of last history (from index) DOES appear after undeletion: " + newFirstHistory.id );
//TODO: show, deleted flag
- //TODO: delete, purge flag
+
// ------------------------------------------------------------------------------------------- UPDATE
// ........................................................................................... name
@@ -294,6 +294,28 @@
//this.test.comment( 'calling show with /deleted should raise a bad request' );
/*
*/
+
+ // ------------------------------------------------------------------------------------------- PURGE
+ var newHistoryId = null;
+ spaceghost.then( function(){
+ this.test.comment( 'calling purge should mark a history, its datasets, and remove the files' );
+ // create new history
+ var newHistory = this.api.histories.create({ name: 'To Purge' });
+ newHistoryId = newHistory.id;
+ });
+ spaceghost.openHomePage().api.tools.thenUploadToCurrent({
+ filepath: '../../test-data/1.sam'
+ });
+ spaceghost.then( function(){
+ var recent = this.api.histories.show( newHistoryId );
+ this.debug( 'size:\n' + recent.size );
+
+ this.api.assertRaises( function(){
+ this.api.histories.delete_( recent.id, true );
+ }, 403, 'This instance does not allow user dataset purging', 'Config does not allow thrown' );
+ });
+ //TODO: a way to set the config to allow user purging and then being able to test this would be good.
+
//this.debug( this.jsonStr( historyShow ) );
});
diff -r a7d53e97af6fcdc4da90d20c897541771cecd963 -r d61dbf796cb5ca7500782e511490740c25010486 test/casperjs/modules/api.js
--- a/test/casperjs/modules/api.js
+++ b/test/casperjs/modules/api.js
@@ -267,10 +267,12 @@
this.api.spaceghost.info( 'histories.delete: ' + [ id, (( purge )?( '(purge!)' ):( '' )) ] );
// py.payload <-> ajax.data
- var payload = ( purge )?({ purge: true }):({});
- return this.api._ajax( utils.format( this.urlTpls.delete_, this.api.ensureId( id ) ), {
- type : 'DELETE',
- data : payload
+ var url = utils.format( this.urlTpls.delete_, this.api.ensureId( id ) );
+ if( purge ){
+ url += '?purge=True';
+ }
+ return this.api._ajax( url, {
+ type : 'DELETE'
});
};
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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