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fix old jobparam hack for importing files to library

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This commit is contained in:
Martin Cech
2016-01-13 12:16:53 -05:00
parent 790953e6e7
commit 74afe4127a
3 changed files with 13 additions and 10 deletions
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lib/galaxy/tools/actions/upload_common.py
+5 -2
View File
@@ -350,7 +350,7 @@ def create_paramfile( trans, uploaded_datasets ):
return json_file_path
def create_job( trans, params, tool, json_file_path, data_list, folder=None, history=None ):
def create_job( trans, params, tool, json_file_path, data_list, folder=None, history=None, job_params=None ):
"""
Create the upload job.
"""
@@ -395,7 +395,10 @@ def create_job( trans, params, tool, json_file_path, data_list, folder=None, his
# open( dataset.file_name, "w" ).close()
job.object_store_id = object_store_id
job.set_state( job.states.NEW )
job.set_handler(tool.get_job_handler(None))
job.set_handler( tool.get_job_handler( None ) )
if job_params:
for name, value in job_params.iteritems():
job.add_parameter( name, value )
trans.sa_session.add( job )
trans.sa_session.flush()
lib/galaxy/webapps/galaxy/api/lda_datasets.py
+4 -4
View File
@@ -517,10 +517,10 @@ class LibraryDatasetsController( BaseAPIController, UsesVisualizationMixin ):
abspath_datasets.append( ud )
json_file_path = upload_common.create_paramfile( trans, abspath_datasets )
data_list = [ ud.data for ud in abspath_datasets ]
job, output = upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=folder )
# HACK: Prevent outputs_to_working_directory from overwriting inputs when "linking"
job.add_parameter( 'link_data_only', dumps( kwd.get( 'link_data_only', 'copy_files' ) ) )
job.add_parameter( 'uuid', dumps( kwd.get( 'uuid', None ) ) )
job_params = {}
job_params['link_data_only'] = dumps( kwd.get( 'link_data_only', 'copy_files' ) )
job_params['uuid'] = dumps( kwd.get( 'uuid', None ) )
job, output = upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=folder, job_params=job_params )
trans.sa_session.add( job )
trans.sa_session.flush()
job_dict = job.to_dict()
lib/galaxy/webapps/galaxy/controllers/library_common.py
+4 -4
View File
@@ -1115,10 +1115,10 @@ class LibraryCommon( BaseUIController, UsesFormDefinitionsMixin, UsesExtendedMet
status='error' ) )
json_file_path = upload_common.create_paramfile( trans, uploaded_datasets )
data_list = [ ud.data for ud in uploaded_datasets ]
job, output = upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder )
# HACK: Prevent outputs_to_working_directory from overwriting inputs when "linking"
job.add_parameter( 'link_data_only', dumps( kwd.get( 'link_data_only', 'copy_files' ) ) )
job.add_parameter( 'uuid', dumps( kwd.get( 'uuid', None ) ) )
job_params = {}
job_params['link_data_only'] = dumps( kwd.get( 'link_data_only', 'copy_files' ) )
job_params['uuid'] = dumps( kwd.get( 'uuid', None ) )
job, output = upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder, job_params=job_params )
trans.sa_session.add( job )
trans.sa_session.flush()
return output