Add a user_id column to the job table. This is necessary to decouple jobs from sessions, which is required for the forthcoming API.

lib/galaxy/jobs/__init__.py

@@ -277,6 +277,7 @@ class JobWrapper( object ):
     def __init__(self, job, tool, queue ):
         self.job_id = job.id
         self.session_id = job.session_id
+        self.user_id = job.user_id
         self.tool = tool
         self.queue = queue
         self.app = queue.app

lib/galaxy/model/__init__.py

@@ -101,6 +101,7 @@ class Job( object ):
                     DELETED = 'deleted' )
     def __init__( self ):
         self.session_id = None
+        self.user_id = None
         self.tool_id = None
         self.tool_version = None
         self.command_line = None

lib/galaxy/model/mapping.py

@@ -330,6 +330,7 @@ Job.table = Table( "job", metadata,
     Column( "stderr", TEXT ),
     Column( "traceback", TEXT ),
     Column( "session_id", Integer, ForeignKey( "galaxy_session.id" ), index=True, nullable=True ),
+    Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ),
     Column( "job_runner_name", String( 255 ) ),
     Column( "job_runner_external_id", String( 255 ) ) )
     

lib/galaxy/model/migrate/versions/0047_job_table_user_id_column.py

@@ -0,0 +1,51 @@
+"""
+Add a user_id column to the job table.
+"""
+
+from sqlalchemy import *
+from migrate import *
+from migrate.changeset import *
+from galaxy.model.custom_types import *
+
+import datetime
+now = datetime.datetime.utcnow
+
+import logging
+log = logging.getLogger( __name__ )
+
+metadata = MetaData( migrate_engine )
+
+def upgrade():
+    print __doc__
+    metadata.reflect()
+    try:
+        Job_table = Table( "job", metadata, autoload=True )
+    except NoSuchTableError:
+        Job_table = None
+        log.error( "Failed loading table job" )
+    if Job_table:
+        try:
+            col = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True )
+            col.create( Job_table )
+            assert col is Job_table.c.user_id
+        except Exception, e:
+            log.error( "Adding column 'user_id' to job table failed: %s" % ( str( e ) ) )
+        try:
+            i = Index( "ix_job_user_id", Job_table.c.user_id )
+            i.create()
+        except Exception, e:
+            log.error( "Adding index 'ix_job_user_id' failed: %s" % str( e ) )
+
+def downgrade():
+    metadata.reflect()
+    try:
+        Job_table = Table( "job", metadata, autoload=True )
+    except NoSuchTableError:
+        Job_table = None
+        log.error( "Failed loading table job" )
+    if Job_table:
+        try:
+            col = Job_table.c.user_id
+            col.drop()
+        except Exception, e:
+            log.error( "Dropping column 'user_id' from job table failed: %s" % ( str( e ) ) )

lib/galaxy/tools/actions/__init__.py

@@ -308,7 +308,12 @@ class DefaultToolAction( object ):
         trans.sa_session.flush()
         # Create the job object
         job = trans.app.model.Job()
-        job.session_id = trans.get_galaxy_session().id
+        galaxy_session = trans.get_galaxy_session().id
+        # If we're submitting from the API, there won't be a session.
+        if type( galaxy_session ) == trans.model.GalaxySession:
+            job.session_id = galaxy_session.id
+        if trans.user is not None:
+            job.user_id = trans.user.id
         job.history_id = trans.history.id
         job.tool_id = tool.id
         try:

lib/galaxy/tools/actions/upload_common.py

@@ -297,7 +297,11 @@ def create_job( trans, params, tool, json_file_path, data_list, folder=None, ret
     Create the upload job.
     """
     job = trans.app.model.Job()
-    job.session_id = trans.get_galaxy_session().id
+    galaxy_session = trans.get_galaxy_session()
+    if type( galaxy_session ) == trans.model.GalaxySession:
+        job.session_id = galaxy_session.id
+    if trans.user is not None:
+        job.user_id = trans.user.id
     if folder:
         job.library_folder_id = folder.id
     else: