root/galaxy-central/lib/galaxy/model/migrate/versions/0020_library_upload_job.py

リビジョン 2, 4.9 KB (コミッタ: hatakeyama, 14 年 前)

import galaxy-central

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