Merge pull request #1488 from martenson/fix-jobparam-hack

fix old jobparam hack for importing files to library
galaxyproject · Jan 14, 2016 · f41550f · f41550f
2 parents 84fd89d + 74afe41
commit f41550f
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Showing 3 changed files with 13 additions and 10 deletions.
diff --git a/lib/galaxy/tools/actions/upload_common.py b/lib/galaxy/tools/actions/upload_common.py
@@ -350,7 +350,7 @@ def _chown( path ):
     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()
 

diff --git a/lib/galaxy/webapps/galaxy/api/lda_datasets.py b/lib/galaxy/webapps/galaxy/api/lda_datasets.py
@@ -517,10 +517,10 @@ def load( self, trans, **kwd ):
                 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()

diff --git a/lib/galaxy/webapps/galaxy/controllers/library_common.py b/lib/galaxy/webapps/galaxy/controllers/library_common.py
@@ -1115,10 +1115,10 @@ def upload_dataset( self, trans, cntrller, library_id, folder_id, replace_datase
                                                        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