[2] | 1 | """ |
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| 2 | This script adds the filename_override_metadata column to the JobExternalOutputMetadata table, |
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| 3 | allowing existing metadata files to be written when using external metadata and a cluster |
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| 4 | set up with read-only access to database/files |
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| 5 | """ |
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| 6 | from sqlalchemy import * |
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| 7 | from sqlalchemy.orm import * |
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| 8 | from sqlalchemy.exceptions import * |
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| 9 | from migrate import * |
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| 10 | from migrate.changeset import * |
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| 11 | import datetime |
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| 12 | now = datetime.datetime.utcnow |
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| 13 | import sys, logging |
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| 14 | # Need our custom types, but don't import anything else from model |
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| 15 | from galaxy.model.custom_types import * |
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| 16 | |
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| 17 | log = logging.getLogger( __name__ ) |
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| 18 | log.setLevel(logging.DEBUG) |
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| 19 | handler = logging.StreamHandler( sys.stdout ) |
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| 20 | format = "%(name)s %(levelname)s %(asctime)s %(message)s" |
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| 21 | formatter = logging.Formatter( format ) |
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| 22 | handler.setFormatter( formatter ) |
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| 23 | log.addHandler( handler ) |
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| 24 | |
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| 25 | metadata = MetaData( migrate_engine ) |
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| 26 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
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| 27 | |
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| 28 | def display_migration_details(): |
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| 29 | print "========================================" |
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| 30 | print "This script adds the filename_override_metadata column to the JobExternalOutputMetadata table," |
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| 31 | print" allowing existing metadata files to be written when using external metadata and a cluster" |
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| 32 | print "set up with read-only access to database/files" |
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| 33 | print "========================================" |
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| 34 | def upgrade(): |
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| 35 | display_migration_details() |
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| 36 | # Load existing tables |
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| 37 | metadata.reflect() |
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| 38 | try: |
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| 39 | job_external_output_metadata = Table( "job_external_output_metadata", metadata, autoload=True ) |
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| 40 | col = Column( "filename_override_metadata", String( 255 ) ) |
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| 41 | col.create( job_external_output_metadata ) |
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| 42 | assert col is job_external_output_metadata.c.filename_override_metadata |
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| 43 | except Exception, e: |
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| 44 | log.debug( "Adding column 'filename_override_metadata' to job_external_output_metadata table failed: %s" % ( str( e ) ) ) |
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| 45 | |
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| 46 | def downgrade(): |
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| 47 | pass |
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