Fixes for db migration script 47: add sql to update the new user_id column in the job table with valid data.

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

@@ -3,6 +3,8 @@ Add a user_id column to the job table.
 """
 
 from sqlalchemy import *
+from sqlalchemy.orm import *
+from sqlalchemy.exc import *
 from migrate import *
 from migrate.changeset import *
 from galaxy.model.custom_types import *
@@ -10,10 +12,17 @@ from galaxy.model.custom_types import *
 import datetime
 now = datetime.datetime.utcnow
 
-import logging
+import sys, logging
 log = logging.getLogger( __name__ )
+log.setLevel(logging.DEBUG)
+handler = logging.StreamHandler( sys.stdout )
+format = "%(name)s %(levelname)s %(asctime)s %(message)s"
+formatter = logging.Formatter( format )
+handler.setFormatter( formatter )
+log.addHandler( handler )
 
 metadata = MetaData( migrate_engine )
+db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) )
 
 def upgrade():
     print __doc__
@@ -22,30 +31,48 @@ def upgrade():
         Job_table = Table( "job", metadata, autoload=True )
     except NoSuchTableError:
         Job_table = None
-        log.error( "Failed loading table job" )
+        log.debug( "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 ) ) )
+            log.debug( "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 ) )
-
+            log.debug( "Adding index 'ix_job_user_id' failed: %s" % str( e ) )
+        try:
+            cmd = "SELECT job.id AS galaxy_job_id, " \
+                + "galaxy_session.user_id AS galaxy_user_id " \
+                + "FROM job " \
+                + "JOIN galaxy_session ON job.session_id = galaxy_session.id;"
+            job_users = db_session.execute( cmd ).fetchall()
+            print "Updating user_id column in job table for ", len( job_users ), " rows..."
+            print ""
+            update_count = 0
+            for row in job_users:
+                if row.galaxy_user_id:
+                    cmd = "UPDATE job SET user_id = %d WHERE id = %d" % ( int( row.galaxy_user_id ), int( row.galaxy_job_id ) )
+                    update_count += 1
+                db_session.execute( cmd )
+            print "Updated the user_id column for ", update_count, " rows in the job table.  "
+            print len( job_users ) - update_count, " rows have no user_id since the value was NULL in the galaxy_session table."
+            print ""
+        except Exception, e:
+            log.debug( "Updating job.user_id column 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" )
+        log.debug( "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 ) ) )
+            log.debug( "Dropping column 'user_id' from job table failed: %s" % ( str( e ) ) )