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Correctly set history and handle output datasets for error cases in tool API. Allow specification of dataset name during uploads, exposing through API

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This commit is contained in:
Brad Chapman
2012-10-04 15:31:16 -04:00
parent f511605311
commit cf1407d471
3 changed files with 17 additions and 6 deletions
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lib/galaxy/tools/parameters/grouping.py
+2 -3
View File
@@ -209,7 +209,7 @@ class UploadDataset( Group ):
dataset_name = get_file_name( data_file['filename'] )
if not dataset_info:
dataset_info = 'uploaded file'
return Bunch( type='file', path=data_file['local_filename'], name=get_file_name( data_file['filename'] ) )
return Bunch( type='file', path=data_file['local_filename'], name=dataset_name )
#return 'file', data_file['local_filename'], get_file_name( data_file.filename ), dataset_name, dataset_info
except:
# The uploaded file should've been persisted by the upload tool action
@@ -227,14 +227,13 @@ class UploadDataset( Group ):
if line:
if not line.lower().startswith( 'http://' ) and not line.lower().startswith( 'ftp://' ) and not line.lower().startswith( 'https://' ):
continue # non-url line, ignore
precreated_name = line
dataset_name = override_name
if not dataset_name:
dataset_name = line
dataset_info = override_info
if not dataset_info:
dataset_info = 'uploaded url'
yield Bunch( type='url', path=line, name=precreated_name )
yield Bunch( type='url', path=line, name=dataset_name )
#yield ( 'url', line, precreated_name, dataset_name, dataset_info )
else:
dataset_name = dataset_info = precreated_name = 'Pasted Entry' #we need to differentiate between various url pastes here
lib/galaxy/webapps/galaxy/api/tools.py
+14 -3
View File
@@ -55,6 +55,17 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
tool = trans.app.toolbox.get_tool( tool_id )
if not tool:
return { "message": { "type": "error", "text" : messages.NO_TOOL } }
# Set running history from payload parameters.
# History not set correctly as part of this API call for
# dataset upload.
history_id = payload.get("history_id", None)
if history_id:
target_history = trans.sa_session.query(trans.app.model.History).get(
trans.security.decode_id(history_id))
trans.galaxy_session.current_history = target_history
else:
target_history = None
# Set up inputs.
inputs = payload[ 'inputs' ]
@@ -62,10 +73,10 @@ class ToolsController( BaseAPIController, UsesVisualizationMixin ):
inputs['runtool_btn'] = 'Execute'
# TODO: encode data ids and decode ids.
params = util.Params( inputs, sanitize = False )
template, vars = tool.handle_input( trans, params.__dict__ )
template, vars = tool.handle_input( trans, params.__dict__, history=target_history)
# TODO: check for errors and ensure that output dataset(s) are available.
output_datasets = vars[ 'out_data' ].values()
output_datasets = vars.get('out_data', {}).values()
rval = {
"outputs": []
}
tools/data_source/upload.xml
+1
View File
@@ -41,6 +41,7 @@
<param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand.">
<option value="Yes">Yes</option>
</param>
<param name="NAME" type="hidden" help="Name for dataset in upload"></param>
</upload_dataset>
<param name="dbkey" type="genomebuild" label="Genome" />
<conditional name="files_metadata" title="Specify metadata" value_from="self:app.datatypes_registry.get_upload_metadata_params" value_ref="file_type" value_ref_in_group="False" />