[2] | 1 | """ |
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| 2 | Add a user_id column to the job table. |
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| 3 | """ |
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| 4 | |
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| 5 | from sqlalchemy import * |
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| 6 | from sqlalchemy.orm import * |
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| 7 | from sqlalchemy.exc import * |
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| 8 | from migrate import * |
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| 9 | from migrate.changeset import * |
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| 10 | from galaxy.model.custom_types import * |
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| 11 | |
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| 12 | import datetime |
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| 13 | now = datetime.datetime.utcnow |
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| 14 | |
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| 15 | import sys, logging |
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| 16 | log = logging.getLogger( __name__ ) |
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| 17 | log.setLevel(logging.DEBUG) |
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| 18 | handler = logging.StreamHandler( sys.stdout ) |
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| 19 | format = "%(name)s %(levelname)s %(asctime)s %(message)s" |
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| 20 | formatter = logging.Formatter( format ) |
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| 21 | handler.setFormatter( formatter ) |
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| 22 | log.addHandler( handler ) |
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| 23 | |
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| 24 | metadata = MetaData( migrate_engine ) |
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| 25 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
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| 26 | |
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| 27 | def upgrade(): |
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| 28 | print __doc__ |
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| 29 | metadata.reflect() |
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| 30 | try: |
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| 31 | Job_table = Table( "job", metadata, autoload=True ) |
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| 32 | except NoSuchTableError: |
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| 33 | Job_table = None |
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| 34 | log.debug( "Failed loading table job" ) |
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| 35 | if Job_table: |
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| 36 | try: |
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| 37 | col = Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True, nullable=True ) |
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| 38 | col.create( Job_table ) |
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| 39 | assert col is Job_table.c.user_id |
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| 40 | except Exception, e: |
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| 41 | log.debug( "Adding column 'user_id' to job table failed: %s" % ( str( e ) ) ) |
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| 42 | try: |
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| 43 | i = Index( "ix_job_user_id", Job_table.c.user_id ) |
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| 44 | i.create() |
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| 45 | except Exception, e: |
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| 46 | log.debug( "Adding index 'ix_job_user_id' failed: %s" % str( e ) ) |
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| 47 | try: |
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| 48 | cmd = "SELECT job.id AS galaxy_job_id, " \ |
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| 49 | + "galaxy_session.user_id AS galaxy_user_id " \ |
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| 50 | + "FROM job " \ |
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| 51 | + "JOIN galaxy_session ON job.session_id = galaxy_session.id;" |
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| 52 | job_users = db_session.execute( cmd ).fetchall() |
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| 53 | print "Updating user_id column in job table for ", len( job_users ), " rows..." |
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| 54 | print "" |
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| 55 | update_count = 0 |
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| 56 | for row in job_users: |
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| 57 | if row.galaxy_user_id: |
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| 58 | cmd = "UPDATE job SET user_id = %d WHERE id = %d" % ( int( row.galaxy_user_id ), int( row.galaxy_job_id ) ) |
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| 59 | update_count += 1 |
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| 60 | db_session.execute( cmd ) |
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| 61 | print "Updated the user_id column for ", update_count, " rows in the job table. " |
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| 62 | print len( job_users ) - update_count, " rows have no user_id since the value was NULL in the galaxy_session table." |
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| 63 | print "" |
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| 64 | except Exception, e: |
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| 65 | log.debug( "Updating job.user_id column failed: %s" % str( e ) ) |
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| 66 | def downgrade(): |
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| 67 | metadata.reflect() |
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| 68 | try: |
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| 69 | Job_table = Table( "job", metadata, autoload=True ) |
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| 70 | except NoSuchTableError: |
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| 71 | Job_table = None |
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| 72 | log.debug( "Failed loading table job" ) |
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| 73 | if Job_table: |
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| 74 | try: |
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| 75 | col = Job_table.c.user_id |
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| 76 | col.drop() |
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| 77 | except Exception, e: |
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| 78 | log.debug( "Dropping column 'user_id' from job table failed: %s" % ( str( e ) ) ) |
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