[2] | 1 | """ |
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| 2 | This migration script removes the library_id & folder_id fields in the 'request' table and |
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| 3 | adds the same to the 'sample' table. This also adds a 'datatx' column to request_type table |
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| 4 | to store the sequencer login information. Finally, this adds a 'dataset_files' column to |
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| 5 | the sample table. |
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| 6 | """ |
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| 7 | from sqlalchemy import * |
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| 8 | from sqlalchemy.orm import * |
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| 9 | from migrate import * |
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| 10 | from migrate.changeset import * |
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| 11 | import sys, logging |
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| 12 | from galaxy.model.custom_types import * |
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| 13 | from sqlalchemy.exc import * |
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| 14 | import datetime |
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| 15 | now = datetime.datetime.utcnow |
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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 upgrade(): |
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| 29 | print __doc__ |
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| 30 | # Load existing tables |
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| 31 | metadata.reflect() |
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| 32 | # retuest_type table |
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| 33 | try: |
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| 34 | RequestType_table = Table( "request_type", metadata, autoload=True ) |
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| 35 | except NoSuchTableError: |
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| 36 | RequestType_table = None |
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| 37 | log.debug( "Failed loading table request_type" ) |
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| 38 | if RequestType_table: |
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| 39 | # Add the datatx_info column in 'request_type' table |
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| 40 | try: |
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| 41 | col = Column( "datatx_info", JSONType() ) |
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| 42 | col.create( RequestType_table ) |
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| 43 | assert col is RequestType_table.c.datatx_info |
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| 44 | except Exception, e: |
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| 45 | log.debug( "Adding column 'datatx_info' to request_type table failed: %s" % ( str( e ) ) ) |
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| 46 | # request table |
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| 47 | try: |
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| 48 | Request_table = Table( "request", metadata, autoload=True ) |
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| 49 | except NoSuchTableError: |
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| 50 | Request_table = None |
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| 51 | log.debug( "Failed loading table request" ) |
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| 52 | if Request_table: |
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| 53 | # Delete library_id & folder_id columns in the table 'request'. |
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| 54 | # if Galaxy is running on sqlite, the delete/recreate the table |
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| 55 | # otherwise remove the specific columns |
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| 56 | if migrate_engine.name == 'sqlite': |
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| 57 | # create a temporary table |
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| 58 | RequestTemp_table = Table( 'request_temp', metadata, |
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| 59 | Column( "id", Integer, primary_key=True), |
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| 60 | Column( "create_time", DateTime, default=now ), |
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| 61 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 62 | Column( "name", TrimmedString( 255 ), nullable=False ), |
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| 63 | Column( "desc", TEXT ), |
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| 64 | Column( "form_values_id", Integer, ForeignKey( "form_values.id" ), index=True ), |
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| 65 | Column( "request_type_id", Integer, ForeignKey( "request_type.id" ), index=True ), |
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| 66 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 67 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 68 | try: |
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| 69 | RequestTemp_table.create() |
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| 70 | except Exception, e: |
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| 71 | log.debug( "Creating request_temp table failed: %s" % str( e ) ) |
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| 72 | # insert all the rows from the request table to the request_temp table |
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| 73 | cmd = \ |
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| 74 | "INSERT INTO request_temp " + \ |
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| 75 | "SELECT id," + \ |
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| 76 | "create_time," + \ |
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| 77 | "update_time," + \ |
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| 78 | "name," + \ |
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| 79 | "desc," + \ |
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| 80 | "form_values_id," + \ |
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| 81 | "request_type_id," + \ |
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| 82 | "user_id," + \ |
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| 83 | "deleted " + \ |
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| 84 | "FROM request;" |
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| 85 | db_session.execute( cmd ) |
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| 86 | # delete the 'request' table |
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| 87 | try: |
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| 88 | Request_table.drop() |
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| 89 | except Exception, e: |
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| 90 | log.debug( "Dropping request table failed: %s" % str( e ) ) |
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| 91 | # rename table request_temp to request |
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| 92 | cmd = "ALTER TABLE request_temp RENAME TO request" |
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| 93 | db_session.execute( cmd ) |
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| 94 | else: |
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| 95 | # Delete the library_id column in 'request' table |
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| 96 | try: |
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| 97 | Request_table.c.library_id.drop() |
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| 98 | except Exception, e: |
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| 99 | log.debug( "Deleting column 'library_id' to request table failed: %s" % ( str( e ) ) ) |
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| 100 | # Delete the folder_id column in 'request' table |
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| 101 | try: |
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| 102 | Request_table.c.folder_id.drop() |
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| 103 | except Exception, e: |
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| 104 | log.debug( "Deleting column 'folder_id' to request table failed: %s" % ( str( e ) ) ) |
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| 105 | # sample table |
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| 106 | try: |
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| 107 | Sample_table = Table( "sample", metadata, autoload=True ) |
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| 108 | except NoSuchTableError: |
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| 109 | Sample_table = None |
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| 110 | log.debug( "Failed loading table sample" ) |
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| 111 | if Sample_table: |
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| 112 | # Add the dataset_files column in 'sample' table |
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| 113 | try: |
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| 114 | col = Column( "dataset_files", JSONType() ) |
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| 115 | col.create( Sample_table ) |
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| 116 | assert col is Sample_table.c.dataset_files |
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| 117 | except Exception, e: |
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| 118 | log.debug( "Adding column 'dataset_files' to sample table failed: %s" % ( str( e ) ) ) |
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| 119 | # library table |
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| 120 | try: |
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| 121 | Library_table = Table( "library", metadata, autoload=True ) |
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| 122 | except NoSuchTableError: |
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| 123 | Library_table = None |
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| 124 | log.debug( "Failed loading table library" ) |
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| 125 | if Library_table: |
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| 126 | # Add the library_id column in 'sample' table |
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| 127 | try: |
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| 128 | col = Column( "library_id", Integer, ForeignKey( "library.id" ), index=True ) |
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| 129 | col.create( Sample_table ) |
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| 130 | assert col is Sample_table.c.library_id |
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| 131 | except Exception, e: |
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| 132 | log.debug( "Adding column 'library_id' to sample table failed: %s" % ( str( e ) ) ) |
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| 133 | # library_folder table |
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| 134 | try: |
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| 135 | LibraryFolder_table = Table( "library_folder", metadata, autoload=True ) |
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| 136 | except NoSuchTableError: |
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| 137 | LibraryFolder_table = None |
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| 138 | log.debug( "Failed loading table library_folder" ) |
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| 139 | if LibraryFolder_table: |
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| 140 | # Add the library_id column in 'sample' table |
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| 141 | try: |
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| 142 | col = Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ) |
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| 143 | col.create( Sample_table ) |
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| 144 | assert col is Sample_table.c.folder_id |
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| 145 | except Exception, e: |
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| 146 | log.debug( "Adding column 'folder_id' to sample table failed: %s" % ( str( e ) ) ) |
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| 147 | |
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| 148 | def downgrade(): |
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| 149 | pass |
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