[2] | 1 | from sqlalchemy import * |
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| 2 | from sqlalchemy.orm import * |
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| 3 | from sqlalchemy.exc import * |
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| 4 | from migrate import * |
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| 5 | from migrate.changeset import * |
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| 6 | import datetime |
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| 7 | now = datetime.datetime.utcnow |
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| 8 | import sys, logging |
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| 9 | # Need our custom types, but don't import anything else from model |
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| 10 | from galaxy.model.custom_types import * |
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| 11 | |
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| 12 | log = logging.getLogger( __name__ ) |
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| 13 | log.setLevel(logging.DEBUG) |
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| 14 | handler = logging.StreamHandler( sys.stdout ) |
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| 15 | format = "%(name)s %(levelname)s %(asctime)s %(message)s" |
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| 16 | formatter = logging.Formatter( format ) |
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| 17 | handler.setFormatter( formatter ) |
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| 18 | log.addHandler( handler ) |
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| 19 | |
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| 20 | metadata = MetaData( migrate_engine ) |
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| 21 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
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| 22 | |
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| 23 | def display_migration_details(): |
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| 24 | print "" |
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| 25 | print "========================================" |
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| 26 | print """This script creates a job_to_output_library_dataset table for allowing library |
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| 27 | uploads to run as regular jobs. To support this, a library_folder_id column is |
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| 28 | added to the job table, and library_folder/output_library_datasets relations |
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| 29 | are added to the Job object. An index is also added to the dataset.state |
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| 30 | column.""" |
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| 31 | print "========================================" |
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| 32 | |
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| 33 | JobToOutputLibraryDatasetAssociation_table = Table( "job_to_output_library_dataset", metadata, |
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| 34 | Column( "id", Integer, primary_key=True ), |
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| 35 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
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| 36 | Column( "ldda_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), index=True ), |
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| 37 | Column( "name", String(255) ) ) |
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| 38 | |
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| 39 | def upgrade(): |
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| 40 | display_migration_details() |
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| 41 | # Load existing tables |
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| 42 | metadata.reflect() |
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| 43 | # Create the job_to_output_library_dataset table |
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| 44 | try: |
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| 45 | JobToOutputLibraryDatasetAssociation_table.create() |
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| 46 | except Exception, e: |
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| 47 | print "Creating job_to_output_library_dataset table failed: %s" % str( e ) |
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| 48 | log.debug( "Creating job_to_output_library_dataset table failed: %s" % str( e ) ) |
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| 49 | # Create the library_folder_id column |
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| 50 | try: |
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| 51 | Job_table = Table( "job", metadata, autoload=True ) |
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| 52 | except NoSuchTableError: |
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| 53 | Job_table = None |
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| 54 | log.debug( "Failed loading table job" ) |
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| 55 | if Job_table: |
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| 56 | try: |
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| 57 | col = Column( "library_folder_id", Integer, index=True ) |
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| 58 | col.create( Job_table ) |
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| 59 | assert col is Job_table.c.library_folder_id |
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| 60 | except Exception, e: |
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| 61 | log.debug( "Adding column 'library_folder_id' to job table failed: %s" % ( str( e ) ) ) |
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| 62 | try: |
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| 63 | LibraryFolder_table = Table( "library_folder", metadata, autoload=True ) |
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| 64 | except NoSuchTableError: |
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| 65 | LibraryFolder_table = None |
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| 66 | log.debug( "Failed loading table library_folder" ) |
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| 67 | # Add 1 foreign key constraint to the job table |
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| 68 | if Job_table and LibraryFolder_table: |
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| 69 | try: |
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| 70 | cons = ForeignKeyConstraint( [Job_table.c.library_folder_id], |
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| 71 | [LibraryFolder_table.c.id], |
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| 72 | name='job_library_folder_id_fk' ) |
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| 73 | # Create the constraint |
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| 74 | cons.create() |
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| 75 | except Exception, e: |
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| 76 | log.debug( "Adding foreign key constraint 'job_library_folder_id_fk' to table 'library_folder' failed: %s" % ( str( e ) ) ) |
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| 77 | # Create the ix_dataset_state index |
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| 78 | try: |
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| 79 | Dataset_table = Table( "dataset", metadata, autoload=True ) |
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| 80 | except NoSuchTableError: |
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| 81 | Dataset_table = None |
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| 82 | log.debug( "Failed loading table dataset" ) |
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| 83 | i = Index( "ix_dataset_state", Dataset_table.c.state ) |
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| 84 | try: |
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| 85 | i.create() |
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| 86 | except Exception, e: |
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| 87 | print str(e) |
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| 88 | log.debug( "Adding index 'ix_dataset_state' to dataset table failed: %s" % str( e ) ) |
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| 89 | |
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| 90 | def downgrade(): |
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| 91 | metadata.reflect() |
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| 92 | # Drop the library_folder_id column |
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| 93 | try: |
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| 94 | Job_table = Table( "job", metadata, autoload=True ) |
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| 95 | except NoSuchTableError: |
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| 96 | Job_table = None |
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| 97 | log.debug( "Failed loading table job" ) |
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| 98 | if Job_table: |
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| 99 | try: |
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| 100 | col = Job_table.c.library_folder_id |
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| 101 | col.drop() |
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| 102 | except Exception, e: |
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| 103 | log.debug( "Dropping column 'library_folder_id' from job table failed: %s" % ( str( e ) ) ) |
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| 104 | # Drop the job_to_output_library_dataset table |
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| 105 | try: |
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| 106 | JobToOutputLibraryDatasetAssociation_table.drop() |
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| 107 | except Exception, e: |
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| 108 | print str(e) |
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| 109 | log.debug( "Dropping job_to_output_library_dataset table failed: %s" % str( e ) ) |
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| 110 | # Drop the ix_dataset_state index |
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| 111 | try: |
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| 112 | Dataset_table = Table( "dataset", metadata, autoload=True ) |
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| 113 | except NoSuchTableError: |
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| 114 | Dataset_table = None |
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| 115 | log.debug( "Failed loading table dataset" ) |
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| 116 | i = Index( "ix_dataset_state", Dataset_table.c.state ) |
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| 117 | try: |
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| 118 | i.drop() |
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| 119 | except Exception, e: |
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| 120 | print str(e) |
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| 121 | log.debug( "Dropping index 'ix_dataset_state' from dataset table failed: %s" % str( e ) ) |
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