Merge branch 'release_15.03' into dev

Conflicts:
	lib/galaxy/tools/actions/metadata.py

lib/galaxy/datatypes/metadata.py

@@ -705,6 +705,11 @@ class JobExternalOutputMetadataWrapper( object ):
         kwds = kwds or {}
         if tmp_dir is None:
             tmp_dir = MetadataTempFile.tmp_dir
+        else:
+            MetadataTempFile.tmp_dir = tmp_dir
+
+        if not os.path.exists(tmp_dir):
+            os.makedirs(tmp_dir)
 
         # path is calculated for Galaxy, may be different on compute - rewrite
         # for the compute server.

lib/galaxy/jobs/handler.py

@@ -680,7 +680,7 @@ class JobHandlerStopQueue( object ):
         except Empty:
             pass
         for job, error_msg in jobs_to_check:
-            if job.finished:
+            if job.state != job.states.DELETED_NEW and job.finished:
                 log.debug('Job %s already finished, not deleting or stopping', job.id)
                 continue
             final_state = job.states.DELETED

lib/galaxy/tools/actions/metadata.py

@@ -1,12 +1,15 @@
+import logging
+
 from __init__ import ToolAction
 from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper
 from galaxy.util.odict import odict
 from galaxy.util.json import dumps
 from galaxy.jobs.datasets import DatasetPath
 
-import logging
+
 log = logging.getLogger( __name__ )
 
+
 class SetMetadataToolAction( ToolAction ):
     """Tool action used for setting external metadata on an existing dataset"""
 
@@ -67,11 +70,12 @@ class SetMetadataToolAction( ToolAction ):
         # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)?
         incoming[ '__ORIGINAL_DATASET_STATE__' ] = dataset.state
         input_paths = [DatasetPath( dataset.id, real_path=dataset.file_name, mutable=False )]
+        job_working_dir = app.object_store.get_filename(job, base_dir='job_work', dir_only=True, extra_dir=str(job.id))
         external_metadata_wrapper = JobExternalOutputMetadataWrapper( job )
         cmd_line = external_metadata_wrapper.setup_external_metadata( dataset,
                                                                       sa_session,
                                                                       exec_dir = None,
-                                                                      tmp_dir = app.config.new_file_path,
+                                                                      tmp_dir = job_working_dir,
                                                                       dataset_files_path = app.model.Dataset.file_path,
                                                                       output_fnames = input_paths,
                                                                       config_root = app.config.root,