[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 | |
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| 7 | import datetime |
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| 8 | now = datetime.datetime.utcnow |
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| 9 | |
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| 10 | import sys, logging |
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| 11 | log = logging.getLogger( __name__ ) |
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| 12 | log.setLevel(logging.DEBUG) |
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| 13 | handler = logging.StreamHandler( sys.stdout ) |
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| 14 | format = "%(name)s %(levelname)s %(asctime)s %(message)s" |
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| 15 | formatter = logging.Formatter( format ) |
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| 16 | handler.setFormatter( formatter ) |
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| 17 | log.addHandler( handler ) |
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| 18 | |
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| 19 | # Need our custom types, but don't import anything else from model |
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| 20 | from galaxy.model.custom_types import * |
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| 21 | |
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| 22 | metadata = MetaData( migrate_engine ) |
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| 23 | db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) |
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| 24 | |
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| 25 | if migrate_engine.name == 'postgres': |
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| 26 | # http://blog.pythonisito.com/2008/01/cascading-drop-table-with-sqlalchemy.html |
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| 27 | from sqlalchemy.databases import postgres |
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| 28 | class PGCascadeSchemaDropper(postgres.PGSchemaDropper): |
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| 29 | def visit_table(self, table): |
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| 30 | for column in table.columns: |
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| 31 | if column.default is not None: |
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| 32 | self.traverse_single(column.default) |
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| 33 | self.append("\nDROP TABLE " + |
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| 34 | self.preparer.format_table(table) + |
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| 35 | " CASCADE") |
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| 36 | self.execute() |
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| 37 | postgres.dialect.schemadropper = PGCascadeSchemaDropper |
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| 38 | |
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| 39 | def nextval( table, col='id' ): |
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| 40 | if migrate_engine.name == 'postgres': |
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| 41 | return "nextval('%s_%s_seq')" % ( table, col ) |
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| 42 | elif migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': |
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| 43 | return "null" |
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| 44 | else: |
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| 45 | raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) |
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| 46 | |
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| 47 | def localtimestamp(): |
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| 48 | if migrate_engine.name == 'postgres' or migrate_engine.name == 'mysql': |
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| 49 | return "LOCALTIMESTAMP" |
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| 50 | elif migrate_engine.name == 'sqlite': |
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| 51 | return "current_date || ' ' || current_time" |
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| 52 | else: |
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| 53 | raise Exception( 'Unable to convert data for unknown database type: %s' % db ) |
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| 54 | |
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| 55 | def boolean_false(): |
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| 56 | if migrate_engine.name == 'postgres' or migrate_engine.name == 'mysql': |
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| 57 | return False |
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| 58 | elif migrate_engine.name == 'sqlite': |
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| 59 | return 0 |
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| 60 | else: |
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| 61 | raise Exception( 'Unable to convert data for unknown database type: %s' % db ) |
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| 62 | |
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| 63 | # New tables as of changeset 2341:5498ac35eedd |
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| 64 | Group_table = Table( "galaxy_group", metadata, |
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| 65 | Column( "id", Integer, primary_key=True ), |
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| 66 | Column( "create_time", DateTime, default=now ), |
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| 67 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 68 | Column( "name", String( 255 ), index=True, unique=True ), |
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| 69 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 70 | |
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| 71 | UserGroupAssociation_table = Table( "user_group_association", metadata, |
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| 72 | Column( "id", Integer, primary_key=True ), |
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| 73 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 74 | Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), |
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| 75 | Column( "create_time", DateTime, default=now ), |
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| 76 | Column( "update_time", DateTime, default=now, onupdate=now ) ) |
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| 77 | |
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| 78 | UserRoleAssociation_table = Table( "user_role_association", metadata, |
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| 79 | Column( "id", Integer, primary_key=True ), |
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| 80 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 81 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ), |
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| 82 | Column( "create_time", DateTime, default=now ), |
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| 83 | Column( "update_time", DateTime, default=now, onupdate=now ) ) |
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| 84 | |
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| 85 | GroupRoleAssociation_table = Table( "group_role_association", metadata, |
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| 86 | Column( "id", Integer, primary_key=True ), |
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| 87 | Column( "group_id", Integer, ForeignKey( "galaxy_group.id" ), index=True ), |
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| 88 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ), |
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| 89 | Column( "create_time", DateTime, default=now ), |
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| 90 | Column( "update_time", DateTime, default=now, onupdate=now ) ) |
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| 91 | |
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| 92 | Role_table = Table( "role", metadata, |
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| 93 | Column( "id", Integer, primary_key=True ), |
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| 94 | Column( "create_time", DateTime, default=now ), |
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| 95 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 96 | Column( "name", String( 255 ), index=True, unique=True ), |
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| 97 | Column( "description", TEXT ), |
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| 98 | Column( "type", String( 40 ), index=True ), |
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| 99 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 100 | |
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| 101 | DatasetPermissions_table = Table( "dataset_permissions", metadata, |
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| 102 | Column( "id", Integer, primary_key=True ), |
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| 103 | Column( "create_time", DateTime, default=now ), |
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| 104 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 105 | Column( "action", TEXT ), |
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| 106 | Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), |
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| 107 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 108 | |
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| 109 | LibraryPermissions_table = Table( "library_permissions", metadata, |
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| 110 | Column( "id", Integer, primary_key=True ), |
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| 111 | Column( "create_time", DateTime, default=now ), |
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| 112 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 113 | Column( "action", TEXT ), |
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| 114 | Column( "library_id", Integer, ForeignKey( "library.id" ), nullable=True, index=True ), |
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| 115 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 116 | |
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| 117 | LibraryFolderPermissions_table = Table( "library_folder_permissions", metadata, |
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| 118 | Column( "id", Integer, primary_key=True ), |
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| 119 | Column( "create_time", DateTime, default=now ), |
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| 120 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 121 | Column( "action", TEXT ), |
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| 122 | Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), |
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| 123 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 124 | |
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| 125 | LibraryDatasetPermissions_table = Table( "library_dataset_permissions", metadata, |
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| 126 | Column( "id", Integer, primary_key=True ), |
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| 127 | Column( "create_time", DateTime, default=now ), |
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| 128 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 129 | Column( "action", TEXT ), |
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| 130 | Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), nullable=True, index=True ), |
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| 131 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 132 | |
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| 133 | LibraryDatasetDatasetAssociationPermissions_table = Table( "library_dataset_dataset_association_permissions", metadata, |
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| 134 | Column( "id", Integer, primary_key=True ), |
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| 135 | Column( "create_time", DateTime, default=now ), |
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| 136 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 137 | Column( "action", TEXT ), |
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| 138 | Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), |
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| 139 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 140 | Index( "ix_lddap_library_dataset_dataset_association_id", LibraryDatasetDatasetAssociationPermissions_table.c.library_dataset_dataset_association_id ) |
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| 141 | |
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| 142 | LibraryItemInfoPermissions_table = Table( "library_item_info_permissions", metadata, |
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| 143 | Column( "id", Integer, primary_key=True ), |
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| 144 | Column( "create_time", DateTime, default=now ), |
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| 145 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 146 | Column( "action", TEXT ), |
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| 147 | Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), nullable=True, index=True ), |
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| 148 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 149 | |
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| 150 | LibraryItemInfoTemplatePermissions_table = Table( "library_item_info_template_permissions", metadata, |
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| 151 | Column( "id", Integer, primary_key=True ), |
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| 152 | Column( "create_time", DateTime, default=now ), |
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| 153 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 154 | Column( "action", TEXT ), |
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| 155 | Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ), nullable=True ), |
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| 156 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 157 | Index( "ix_liitp_library_item_info_template_id", LibraryItemInfoTemplatePermissions_table.c.library_item_info_template_id ) |
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| 158 | |
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| 159 | DefaultUserPermissions_table = Table( "default_user_permissions", metadata, |
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| 160 | Column( "id", Integer, primary_key=True ), |
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| 161 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 162 | Column( "action", TEXT ), |
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| 163 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 164 | |
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| 165 | DefaultHistoryPermissions_table = Table( "default_history_permissions", metadata, |
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| 166 | Column( "id", Integer, primary_key=True ), |
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| 167 | Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), |
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| 168 | Column( "action", TEXT ), |
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| 169 | Column( "role_id", Integer, ForeignKey( "role.id" ), index=True ) ) |
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| 170 | |
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| 171 | LibraryDataset_table = Table( "library_dataset", metadata, |
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| 172 | Column( "id", Integer, primary_key=True ), |
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| 173 | Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name="library_dataset_dataset_association_id_fk" ), nullable=True, index=True ),#current version of dataset, if null, there is not a current version selected |
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| 174 | Column( "folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), |
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| 175 | Column( "order_id", Integer ), |
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| 176 | Column( "create_time", DateTime, default=now ), |
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| 177 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 178 | Column( "name", TrimmedString( 255 ), key="_name" ), #when not None/null this will supercede display in library (but not when imported into user's history?) |
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| 179 | Column( "info", TrimmedString( 255 ), key="_info" ), #when not None/null this will supercede display in library (but not when imported into user's history?) |
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| 180 | Column( "deleted", Boolean, index=True, default=False ) ) |
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| 181 | |
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| 182 | LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, |
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| 183 | Column( "id", Integer, primary_key=True ), |
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| 184 | Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), index=True ), |
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| 185 | Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), |
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| 186 | Column( "create_time", DateTime, default=now ), |
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| 187 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 188 | Column( "copied_from_history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id", use_alter=True, name='history_dataset_association_dataset_id_fkey' ), nullable=True ), |
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| 189 | Column( "copied_from_library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id", use_alter=True, name='library_dataset_dataset_association_id_fkey' ), nullable=True ), |
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| 190 | Column( "name", TrimmedString( 255 ) ), |
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| 191 | Column( "info", TrimmedString( 255 ) ), |
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| 192 | Column( "blurb", TrimmedString( 255 ) ), |
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| 193 | Column( "peek" , TEXT ), |
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| 194 | Column( "extension", TrimmedString( 64 ) ), |
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| 195 | Column( "metadata", MetadataType(), key="_metadata" ), |
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| 196 | Column( "parent_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), |
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| 197 | Column( "designation", TrimmedString( 255 ) ), |
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| 198 | Column( "deleted", Boolean, index=True, default=False ), |
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| 199 | Column( "visible", Boolean ), |
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| 200 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), index=True ), |
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| 201 | Column( "message", TrimmedString( 255 ) ) ) |
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| 202 | |
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| 203 | Library_table = Table( "library", metadata, |
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| 204 | Column( "id", Integer, primary_key=True ), |
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| 205 | Column( "root_folder_id", Integer, ForeignKey( "library_folder.id" ), index=True ), |
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| 206 | Column( "create_time", DateTime, default=now ), |
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| 207 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 208 | Column( "name", String( 255 ), index=True ), |
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| 209 | Column( "deleted", Boolean, index=True, default=False ), |
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| 210 | Column( "purged", Boolean, index=True, default=False ), |
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| 211 | Column( "description", TEXT ) ) |
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| 212 | |
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| 213 | LibraryFolder_table = Table( "library_folder", metadata, |
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| 214 | Column( "id", Integer, primary_key=True ), |
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| 215 | Column( "parent_id", Integer, ForeignKey( "library_folder.id" ), nullable = True, index=True ), |
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| 216 | Column( "create_time", DateTime, default=now ), |
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| 217 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 218 | Column( "name", TEXT ), |
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| 219 | Column( "description", TEXT ), |
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| 220 | Column( "order_id", Integer ), |
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| 221 | Column( "item_count", Integer ), |
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| 222 | Column( "deleted", Boolean, index=True, default=False ), |
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| 223 | Column( "purged", Boolean, index=True, default=False ), |
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| 224 | Column( "genome_build", TrimmedString( 40 ) ) ) |
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| 225 | |
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| 226 | LibraryItemInfoTemplateElement_table = Table( "library_item_info_template_element", metadata, |
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| 227 | Column( "id", Integer, primary_key=True ), |
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| 228 | Column( "create_time", DateTime, default=now ), |
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| 229 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 230 | Column( "optional", Boolean, index=True, default=True ), |
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| 231 | Column( "deleted", Boolean, index=True, default=False ), |
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| 232 | Column( "name", TEXT ), |
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| 233 | Column( "description", TEXT ), |
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| 234 | Column( "type", TEXT, default='string' ), |
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| 235 | Column( "order_id", Integer ), |
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| 236 | Column( "options", JSONType() ), |
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| 237 | Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ) ) ) |
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| 238 | Index( "ix_liite_library_item_info_template_id", LibraryItemInfoTemplateElement_table.c.library_item_info_template_id ) |
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| 239 | |
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| 240 | LibraryItemInfoTemplate_table = Table( "library_item_info_template", metadata, |
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| 241 | Column( "id", Integer, primary_key=True ), |
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| 242 | Column( "create_time", DateTime, default=now ), |
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| 243 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 244 | Column( "optional", Boolean, index=True, default=True ), |
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| 245 | Column( "deleted", Boolean, index=True, default=False ), |
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| 246 | Column( "name", TEXT ), |
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| 247 | Column( "description", TEXT ), |
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| 248 | Column( "item_count", Integer, default=0 ) ) |
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| 249 | |
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| 250 | LibraryInfoTemplateAssociation_table = Table( "library_info_template_association", metadata, |
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| 251 | Column( "id", Integer, primary_key=True ), |
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| 252 | Column( "create_time", DateTime, default=now ), |
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| 253 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 254 | Column( "library_id", Integer, ForeignKey( "library.id" ), nullable=True, index=True ), |
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| 255 | Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ) ) ) |
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| 256 | Index( "ix_lita_library_item_info_template_id", LibraryInfoTemplateAssociation_table.c.library_item_info_template_id ) |
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| 257 | |
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| 258 | LibraryFolderInfoTemplateAssociation_table = Table( "library_folder_info_template_association", metadata, |
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| 259 | Column( "id", Integer, primary_key=True ), |
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| 260 | Column( "create_time", DateTime, default=now ), |
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| 261 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 262 | Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), |
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| 263 | Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ) ) ) |
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| 264 | Index( "ix_lfita_library_item_info_template_id", LibraryFolderInfoTemplateAssociation_table.c.library_item_info_template_id ) |
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| 265 | |
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| 266 | LibraryDatasetInfoTemplateAssociation_table = Table( "library_dataset_info_template_association", metadata, |
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| 267 | Column( "id", Integer, primary_key=True ), |
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| 268 | Column( "create_time", DateTime, default=now ), |
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| 269 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 270 | Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), nullable=True, index=True ), |
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| 271 | Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ) ) ) |
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| 272 | Index( "ix_ldita_library_item_info_template_id", LibraryDatasetInfoTemplateAssociation_table.c.library_item_info_template_id ) |
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| 273 | |
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| 274 | LibraryDatasetDatasetInfoTemplateAssociation_table = Table( "library_dataset_dataset_info_template_association", metadata, |
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| 275 | Column( "id", Integer, primary_key=True ), |
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| 276 | Column( "create_time", DateTime, default=now ), |
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| 277 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 278 | Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), |
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| 279 | Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ) ) ) |
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| 280 | Index( "ix_lddita_library_dataset_dataset_association_id", LibraryDatasetDatasetInfoTemplateAssociation_table.c.library_dataset_dataset_association_id ) |
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| 281 | Index( "ix_lddita_library_item_info_template_id", LibraryDatasetDatasetInfoTemplateAssociation_table.c.library_item_info_template_id ) |
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| 282 | |
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| 283 | LibraryItemInfoElement_table = Table( "library_item_info_element", metadata, |
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| 284 | Column( "id", Integer, primary_key=True ), |
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| 285 | Column( "create_time", DateTime, default=now ), |
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| 286 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 287 | Column( "contents", JSONType() ), |
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| 288 | Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), index=True ), |
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| 289 | Column( "library_item_info_template_element_id", Integer, ForeignKey( "library_item_info_template_element.id" ) ) ) |
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| 290 | Index( "ix_liie_library_item_info_template_element_id", LibraryItemInfoElement_table.c.library_item_info_template_element_id ) |
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| 291 | |
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| 292 | LibraryItemInfo_table = Table( "library_item_info", metadata, |
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| 293 | Column( "id", Integer, primary_key=True ), |
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| 294 | Column( "create_time", DateTime, default=now ), |
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| 295 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 296 | Column( "deleted", Boolean, index=True, default=False ), |
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| 297 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True, index=True ), |
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| 298 | Column( "library_item_info_template_id", Integer, ForeignKey( "library_item_info_template.id" ), nullable=True, index=True ) ) |
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| 299 | |
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| 300 | LibraryInfoAssociation_table = Table( "library_info_association", metadata, |
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| 301 | Column( "id", Integer, primary_key=True ), |
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| 302 | Column( "create_time", DateTime, default=now ), |
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| 303 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 304 | Column( "library_id", Integer, ForeignKey( "library.id" ), nullable=True, index=True ), |
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| 305 | Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), index=True ), |
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| 306 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True, index=True ) ) |
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| 307 | |
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| 308 | LibraryFolderInfoAssociation_table = Table( "library_folder_info_association", metadata, |
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| 309 | Column( "id", Integer, primary_key=True ), |
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| 310 | Column( "create_time", DateTime, default=now ), |
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| 311 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 312 | Column( "library_folder_id", Integer, ForeignKey( "library_folder.id" ), nullable=True, index=True ), |
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| 313 | Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), index=True ), |
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| 314 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True, index=True ) ) |
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| 315 | |
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| 316 | LibraryDatasetInfoAssociation_table = Table( "library_dataset_info_association", metadata, |
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| 317 | Column( "id", Integer, primary_key=True ), |
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| 318 | Column( "create_time", DateTime, default=now ), |
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| 319 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 320 | Column( "library_dataset_id", Integer, ForeignKey( "library_dataset.id" ), nullable=True, index=True ), |
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| 321 | Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ), index=True ), |
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| 322 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True, index=True ) ) |
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| 323 | |
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| 324 | LibraryDatasetDatasetInfoAssociation_table = Table( "library_dataset_dataset_info_association", metadata, |
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| 325 | Column( "id", Integer, primary_key=True ), |
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| 326 | Column( "create_time", DateTime, default=now ), |
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| 327 | Column( "update_time", DateTime, default=now, onupdate=now ), |
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| 328 | Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), |
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| 329 | Column( "library_item_info_id", Integer, ForeignKey( "library_item_info.id" ) ), |
---|
| 330 | Column( "user_id", Integer, ForeignKey( "galaxy_user.id" ), nullable=True, index=True ) ) |
---|
| 331 | Index( "ix_lddia_library_dataset_dataset_association_id", LibraryDatasetDatasetInfoAssociation_table.c.library_dataset_dataset_association_id ) |
---|
| 332 | Index( "ix_lddia_library_item_info_id", LibraryDatasetDatasetInfoAssociation_table.c.library_item_info_id ) |
---|
| 333 | |
---|
| 334 | JobExternalOutputMetadata_table = Table( "job_external_output_metadata", metadata, |
---|
| 335 | Column( "id", Integer, primary_key=True ), |
---|
| 336 | Column( "job_id", Integer, ForeignKey( "job.id" ), index=True ), |
---|
| 337 | Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True, nullable=True ), |
---|
| 338 | Column( "library_dataset_dataset_association_id", Integer, ForeignKey( "library_dataset_dataset_association.id" ), nullable=True ), |
---|
| 339 | Column( "filename_in", String( 255 ) ), |
---|
| 340 | Column( "filename_out", String( 255 ) ), |
---|
| 341 | Column( "filename_results_code", String( 255 ) ), |
---|
| 342 | Column( "filename_kwds", String( 255 ) ), |
---|
| 343 | Column( "job_runner_external_pid", String( 255 ) ) ) |
---|
| 344 | Index( "ix_jeom_library_dataset_dataset_association_id", JobExternalOutputMetadata_table.c.library_dataset_dataset_association_id ) |
---|
| 345 | |
---|
| 346 | def upgrade(): |
---|
| 347 | # Load existing tables |
---|
| 348 | metadata.reflect() |
---|
| 349 | # Add 2 new columns to the galaxy_user table |
---|
| 350 | try: |
---|
| 351 | User_table = Table( "galaxy_user", metadata, autoload=True ) |
---|
| 352 | except NoSuchTableError: |
---|
| 353 | User_table = None |
---|
| 354 | log.debug( "Failed loading table galaxy_user" ) |
---|
| 355 | if User_table: |
---|
| 356 | try: |
---|
| 357 | col = Column( 'deleted', Boolean, index=True, default=False ) |
---|
| 358 | col.create( User_table ) |
---|
| 359 | assert col is User_table.c.deleted |
---|
| 360 | except Exception, e: |
---|
| 361 | log.debug( "Adding column 'deleted' to galaxy_user table failed: %s" % ( str( e ) ) ) |
---|
| 362 | try: |
---|
| 363 | col = Column( 'purged', Boolean, index=True, default=False ) |
---|
| 364 | col.create( User_table ) |
---|
| 365 | assert col is User_table.c.purged |
---|
| 366 | except Exception, e: |
---|
| 367 | log.debug( "Adding column 'purged' to galaxy_user table failed: %s" % ( str( e ) ) ) |
---|
| 368 | # Add 1 new column to the history_dataset_association table |
---|
| 369 | try: |
---|
| 370 | HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) |
---|
| 371 | except NoSuchTableError: |
---|
| 372 | HistoryDatasetAssociation_table = None |
---|
| 373 | log.debug( "Failed loading table history_dataset_association" ) |
---|
| 374 | if HistoryDatasetAssociation_table: |
---|
| 375 | try: |
---|
| 376 | col = Column( 'copied_from_library_dataset_dataset_association_id', Integer, index=True, nullable=True ) |
---|
| 377 | col.create( HistoryDatasetAssociation_table ) |
---|
| 378 | assert col is HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id |
---|
| 379 | except Exception, e: |
---|
| 380 | log.debug( "Adding column 'copied_from_library_dataset_dataset_association_id' to history_dataset_association table failed: %s" % ( str( e ) ) ) |
---|
| 381 | # Add 1 new column to the metadata_file table |
---|
| 382 | try: |
---|
| 383 | MetadataFile_table = Table( "metadata_file", metadata, autoload=True ) |
---|
| 384 | except NoSuchTableError: |
---|
| 385 | MetadataFile_table = None |
---|
| 386 | log.debug( "Failed loading table metadata_file" ) |
---|
| 387 | if MetadataFile_table: |
---|
| 388 | try: |
---|
| 389 | col = Column( 'lda_id', Integer, index=True, nullable=True ) |
---|
| 390 | col.create( MetadataFile_table ) |
---|
| 391 | assert col is MetadataFile_table.c.lda_id |
---|
| 392 | except Exception, e: |
---|
| 393 | log.debug( "Adding column 'lda_id' to metadata_file table failed: %s" % ( str( e ) ) ) |
---|
| 394 | # Add 1 new column to the stored_workflow table - changeset 2328 |
---|
| 395 | try: |
---|
| 396 | StoredWorkflow_table = Table( "stored_workflow", metadata, |
---|
| 397 | Column( "latest_workflow_id", Integer, |
---|
| 398 | ForeignKey( "workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk' ), index=True ), |
---|
| 399 | autoload=True, useexisting=True ) |
---|
| 400 | except NoSuchTableError: |
---|
| 401 | StoredWorkflow_table = None |
---|
| 402 | log.debug( "Failed loading table stored_workflow" ) |
---|
| 403 | if StoredWorkflow_table: |
---|
| 404 | try: |
---|
| 405 | col = Column( 'importable', Boolean, default=False ) |
---|
| 406 | col.create( StoredWorkflow_table ) |
---|
| 407 | assert col is StoredWorkflow_table.c.importable |
---|
| 408 | except Exception, e: |
---|
| 409 | log.debug( "Adding column 'importable' to stored_workflow table failed: %s" % ( str( e ) ) ) |
---|
| 410 | # Create an index on the Job.state column - changeset 2192 |
---|
| 411 | try: |
---|
| 412 | Job_table = Table( "job", metadata, autoload=True ) |
---|
| 413 | except NoSuchTableError: |
---|
| 414 | Job_table = None |
---|
| 415 | log.debug( "Failed loading table job" ) |
---|
| 416 | if Job_table: |
---|
| 417 | try: |
---|
| 418 | i = Index( 'ix_job_state', Job_table.c.state ) |
---|
| 419 | i.create() |
---|
| 420 | except Exception, e: |
---|
| 421 | log.debug( "Adding index to job.state column failed: %s" % ( str( e ) ) ) |
---|
| 422 | # Add all of the new tables above |
---|
| 423 | metadata.create_all() |
---|
| 424 | # Add 1 foreign key constraint to the history_dataset_association table |
---|
| 425 | try: |
---|
| 426 | HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) |
---|
| 427 | except NoSuchTableError: |
---|
| 428 | HistoryDatasetAssociation_table = None |
---|
| 429 | log.debug( "Failed loading table history_dataset_association" ) |
---|
| 430 | try: |
---|
| 431 | LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) |
---|
| 432 | except NoSuchTableError: |
---|
| 433 | LibraryDatasetDatasetAssociation_table = None |
---|
| 434 | log.debug( "Failed loading table library_dataset_dataset_association" ) |
---|
| 435 | if HistoryDatasetAssociation_table and LibraryDatasetDatasetAssociation_table: |
---|
| 436 | try: |
---|
| 437 | cons = ForeignKeyConstraint( [HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id], |
---|
| 438 | [LibraryDatasetDatasetAssociation_table.c.id], |
---|
| 439 | name='history_dataset_association_copied_from_library_dataset_da_fkey' ) |
---|
| 440 | # Create the constraint |
---|
| 441 | cons.create() |
---|
| 442 | except Exception, e: |
---|
| 443 | log.debug( "Adding foreign key constraint 'history_dataset_association_copied_from_library_dataset_da_fkey' to table 'history_dataset_association' failed: %s" % ( str( e ) ) ) |
---|
| 444 | # Add 1 foreign key constraint to the metadata_file table |
---|
| 445 | try: |
---|
| 446 | MetadataFile_table = Table( "metadata_file", metadata, autoload=True ) |
---|
| 447 | except NoSuchTableError: |
---|
| 448 | MetadataFile_table = None |
---|
| 449 | log.debug( "Failed loading table metadata_file" ) |
---|
| 450 | try: |
---|
| 451 | LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) |
---|
| 452 | except NoSuchTableError: |
---|
| 453 | LibraryDatasetDatasetAssociation_table = None |
---|
| 454 | log.debug( "Failed loading table library_dataset_dataset_association" ) |
---|
| 455 | if MetadataFile_table and LibraryDatasetDatasetAssociation_table: |
---|
| 456 | try: |
---|
| 457 | cons = ForeignKeyConstraint( [MetadataFile_table.c.lda_id], |
---|
| 458 | [LibraryDatasetDatasetAssociation_table.c.id], |
---|
| 459 | name='metadata_file_lda_id_fkey' ) |
---|
| 460 | # Create the constraint |
---|
| 461 | cons.create() |
---|
| 462 | except Exception, e: |
---|
| 463 | log.debug( "Adding foreign key constraint 'metadata_file_lda_id_fkey' to table 'metadata_file' failed: %s" % ( str( e ) ) ) |
---|
| 464 | # Make sure we have at least 1 user |
---|
| 465 | cmd = "SELECT * FROM galaxy_user;" |
---|
| 466 | users = db_session.execute( cmd ).fetchall() |
---|
| 467 | if users: |
---|
| 468 | cmd = "SELECT * FROM role;" |
---|
| 469 | roles = db_session.execute( cmd ).fetchall() |
---|
| 470 | if not roles: |
---|
| 471 | # Create private roles for each user - pass 1 |
---|
| 472 | cmd = \ |
---|
| 473 | "INSERT INTO role " + \ |
---|
| 474 | "SELECT %s AS id," + \ |
---|
| 475 | "%s AS create_time," + \ |
---|
| 476 | "%s AS update_time," + \ |
---|
| 477 | "email AS name," + \ |
---|
| 478 | "email AS description," + \ |
---|
| 479 | "'private' As type," + \ |
---|
| 480 | "%s AS deleted " + \ |
---|
| 481 | "FROM galaxy_user " + \ |
---|
| 482 | "ORDER BY id;" |
---|
| 483 | cmd = cmd % ( nextval('role'), localtimestamp(), localtimestamp(), boolean_false() ) |
---|
| 484 | db_session.execute( cmd ) |
---|
| 485 | # Create private roles for each user - pass 2 |
---|
| 486 | if migrate_engine.name == 'postgres' or migrate_engine.name == 'sqlite': |
---|
| 487 | cmd = "UPDATE role SET description = 'Private role for ' || description;" |
---|
| 488 | elif migrate_engine.name == 'mysql': |
---|
| 489 | cmd = "UPDATE role SET description = CONCAT( 'Private role for ', description );" |
---|
| 490 | db_session.execute( cmd ) |
---|
| 491 | # Create private roles for each user - pass 3 |
---|
| 492 | cmd = \ |
---|
| 493 | "INSERT INTO user_role_association " + \ |
---|
| 494 | "SELECT %s AS id," + \ |
---|
| 495 | "galaxy_user.id AS user_id," + \ |
---|
| 496 | "role.id AS role_id," + \ |
---|
| 497 | "%s AS create_time," + \ |
---|
| 498 | "%s AS update_time " + \ |
---|
| 499 | "FROM galaxy_user, role " + \ |
---|
| 500 | "WHERE galaxy_user.email = role.name " + \ |
---|
| 501 | "ORDER BY galaxy_user.id;" |
---|
| 502 | cmd = cmd % ( nextval('user_role_association'), localtimestamp(), localtimestamp() ) |
---|
| 503 | db_session.execute( cmd ) |
---|
| 504 | # Create default permissions for each user |
---|
| 505 | cmd = \ |
---|
| 506 | "INSERT INTO default_user_permissions " + \ |
---|
| 507 | "SELECT %s AS id," + \ |
---|
| 508 | "galaxy_user.id AS user_id," + \ |
---|
| 509 | "'manage permissions' AS action," + \ |
---|
| 510 | "user_role_association.role_id AS role_id " + \ |
---|
| 511 | "FROM galaxy_user " + \ |
---|
| 512 | "JOIN user_role_association ON user_role_association.user_id = galaxy_user.id " + \ |
---|
| 513 | "ORDER BY galaxy_user.id;" |
---|
| 514 | cmd = cmd % nextval('default_user_permissions') |
---|
| 515 | db_session.execute( cmd ) |
---|
| 516 | # Create default history permissions for each active history associated with a user |
---|
| 517 | |
---|
| 518 | cmd = \ |
---|
| 519 | "INSERT INTO default_history_permissions " + \ |
---|
| 520 | "SELECT %s AS id," + \ |
---|
| 521 | "history.id AS history_id," + \ |
---|
| 522 | "'manage permissions' AS action," + \ |
---|
| 523 | "user_role_association.role_id AS role_id " + \ |
---|
| 524 | "FROM history " + \ |
---|
| 525 | "JOIN user_role_association ON user_role_association.user_id = history.user_id " + \ |
---|
| 526 | "WHERE history.purged = %s AND history.user_id IS NOT NULL;" |
---|
| 527 | cmd = cmd % ( nextval('default_history_permissions'), boolean_false() ) |
---|
| 528 | db_session.execute( cmd ) |
---|
| 529 | # Create "manage permissions" dataset_permissions for all activate-able datasets |
---|
| 530 | cmd = \ |
---|
| 531 | "INSERT INTO dataset_permissions " + \ |
---|
| 532 | "SELECT %s AS id," + \ |
---|
| 533 | "%s AS create_time," + \ |
---|
| 534 | "%s AS update_time," + \ |
---|
| 535 | "'manage permissions' AS action," + \ |
---|
| 536 | "history_dataset_association.dataset_id AS dataset_id," + \ |
---|
| 537 | "user_role_association.role_id AS role_id " + \ |
---|
| 538 | "FROM history " + \ |
---|
| 539 | "JOIN history_dataset_association ON history_dataset_association.history_id = history.id " + \ |
---|
| 540 | "JOIN dataset ON history_dataset_association.dataset_id = dataset.id " + \ |
---|
| 541 | "JOIN user_role_association ON user_role_association.user_id = history.user_id " + \ |
---|
| 542 | "WHERE dataset.purged = %s AND history.user_id IS NOT NULL;" |
---|
| 543 | cmd = cmd % ( nextval('dataset_permissions'), localtimestamp(), localtimestamp(), boolean_false() ) |
---|
| 544 | db_session.execute( cmd ) |
---|
| 545 | |
---|
| 546 | def downgrade(): |
---|
| 547 | # Load existing tables |
---|
| 548 | metadata.reflect() |
---|
| 549 | # NOTE: all new data added in the upgrade method is eliminated here via table drops |
---|
| 550 | # Drop 1 foreign key constraint from the metadata_file table |
---|
| 551 | try: |
---|
| 552 | MetadataFile_table = Table( "metadata_file", metadata, autoload=True ) |
---|
| 553 | except NoSuchTableError: |
---|
| 554 | MetadataFile_table = None |
---|
| 555 | log.debug( "Failed loading table metadata_file" ) |
---|
| 556 | try: |
---|
| 557 | LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) |
---|
| 558 | except NoSuchTableError: |
---|
| 559 | LibraryDatasetDatasetAssociation_table = None |
---|
| 560 | log.debug( "Failed loading table library_dataset_dataset_association" ) |
---|
| 561 | if MetadataFile_table and LibraryDatasetDatasetAssociation_table: |
---|
| 562 | try: |
---|
| 563 | cons = ForeignKeyConstraint( [MetadataFile_table.c.lda_id], |
---|
| 564 | [LibraryDatasetDatasetAssociation_table.c.id], |
---|
| 565 | name='metadata_file_lda_id_fkey' ) |
---|
| 566 | # Drop the constraint |
---|
| 567 | cons.drop() |
---|
| 568 | except Exception, e: |
---|
| 569 | log.debug( "Dropping foreign key constraint 'metadata_file_lda_id_fkey' from table 'metadata_file' failed: %s" % ( str( e ) ) ) |
---|
| 570 | # Drop 1 foreign key constraint from the history_dataset_association table |
---|
| 571 | try: |
---|
| 572 | HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) |
---|
| 573 | except NoSuchTableError: |
---|
| 574 | HistoryDatasetAssociation_table = None |
---|
| 575 | log.debug( "Failed loading table history_dataset_association" ) |
---|
| 576 | try: |
---|
| 577 | LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True ) |
---|
| 578 | except NoSuchTableError: |
---|
| 579 | LibraryDatasetDatasetAssociation_table = None |
---|
| 580 | log.debug( "Failed loading table library_dataset_dataset_association" ) |
---|
| 581 | if HistoryDatasetAssociation_table and LibraryDatasetDatasetAssociation_table: |
---|
| 582 | try: |
---|
| 583 | cons = ForeignKeyConstraint( [HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id], |
---|
| 584 | [LibraryDatasetDatasetAssociation_table.c.id], |
---|
| 585 | name='history_dataset_association_copied_from_library_dataset_da_fkey' ) |
---|
| 586 | # Drop the constraint |
---|
| 587 | cons.drop() |
---|
| 588 | except Exception, e: |
---|
| 589 | log.debug( "Dropping foreign key constraint 'history_dataset_association_copied_from_library_dataset_da_fkey' from table 'history_dataset_association' failed: %s" % ( str( e ) ) ) |
---|
| 590 | # Drop all of the new tables above |
---|
| 591 | try: |
---|
| 592 | UserGroupAssociation_table.drop() |
---|
| 593 | except Exception, e: |
---|
| 594 | log.debug( "Dropping user_group_association table failed: %s" % str( e ) ) |
---|
| 595 | try: |
---|
| 596 | UserRoleAssociation_table.drop() |
---|
| 597 | except Exception, e: |
---|
| 598 | log.debug( "Dropping user_role_association table failed: %s" % str( e ) ) |
---|
| 599 | try: |
---|
| 600 | GroupRoleAssociation_table.drop() |
---|
| 601 | except Exception, e: |
---|
| 602 | log.debug( "Dropping group_role_association table failed: %s" % str( e ) ) |
---|
| 603 | try: |
---|
| 604 | Group_table.drop() |
---|
| 605 | except Exception, e: |
---|
| 606 | log.debug( "Dropping galaxy_group table failed: %s" % str( e ) ) |
---|
| 607 | try: |
---|
| 608 | DatasetPermissions_table.drop() |
---|
| 609 | except Exception, e: |
---|
| 610 | log.debug( "Dropping dataset_permissions table failed: %s" % str( e ) ) |
---|
| 611 | try: |
---|
| 612 | LibraryPermissions_table.drop() |
---|
| 613 | except Exception, e: |
---|
| 614 | log.debug( "Dropping library_permissions table failed: %s" % str( e ) ) |
---|
| 615 | try: |
---|
| 616 | LibraryFolderPermissions_table.drop() |
---|
| 617 | except Exception, e: |
---|
| 618 | log.debug( "Dropping library_folder_permissions table failed: %s" % str( e ) ) |
---|
| 619 | try: |
---|
| 620 | LibraryDatasetPermissions_table.drop() |
---|
| 621 | except Exception, e: |
---|
| 622 | log.debug( "Dropping library_dataset_permissions table failed: %s" % str( e ) ) |
---|
| 623 | try: |
---|
| 624 | LibraryDatasetDatasetAssociationPermissions_table.drop() |
---|
| 625 | except Exception, e: |
---|
| 626 | log.debug( "Dropping library_dataset_dataset_association_permissions table failed: %s" % str( e ) ) |
---|
| 627 | try: |
---|
| 628 | LibraryItemInfoPermissions_table.drop() |
---|
| 629 | except Exception, e: |
---|
| 630 | log.debug( "Dropping library_item_info_permissions table failed: %s" % str( e ) ) |
---|
| 631 | try: |
---|
| 632 | LibraryItemInfoTemplatePermissions_table.drop() |
---|
| 633 | except Exception, e: |
---|
| 634 | log.debug( "Dropping library_item_info_template_permissions table failed: %s" % str( e ) ) |
---|
| 635 | try: |
---|
| 636 | DefaultUserPermissions_table.drop() |
---|
| 637 | except Exception, e: |
---|
| 638 | log.debug( "Dropping default_user_permissions table failed: %s" % str( e ) ) |
---|
| 639 | try: |
---|
| 640 | DefaultHistoryPermissions_table.drop() |
---|
| 641 | except Exception, e: |
---|
| 642 | log.debug( "Dropping default_history_permissions table failed: %s" % str( e ) ) |
---|
| 643 | try: |
---|
| 644 | Role_table.drop() |
---|
| 645 | except Exception, e: |
---|
| 646 | log.debug( "Dropping role table failed: %s" % str( e ) ) |
---|
| 647 | try: |
---|
| 648 | LibraryDatasetDatasetInfoAssociation_table.drop() |
---|
| 649 | except Exception, e: |
---|
| 650 | log.debug( "Dropping library_dataset_dataset_info_association table failed: %s" % str( e ) ) |
---|
| 651 | try: |
---|
| 652 | LibraryDataset_table.drop() |
---|
| 653 | except Exception, e: |
---|
| 654 | log.debug( "Dropping library_dataset table failed: %s" % str( e ) ) |
---|
| 655 | try: |
---|
| 656 | LibraryDatasetDatasetAssociation_table.drop() |
---|
| 657 | except Exception, e: |
---|
| 658 | log.debug( "Dropping library_dataset_dataset_association table failed: %s" % str( e ) ) |
---|
| 659 | try: |
---|
| 660 | LibraryDatasetDatasetInfoTemplateAssociation_table.drop() |
---|
| 661 | except Exception, e: |
---|
| 662 | log.debug( "Dropping library_dataset_dataset_info_template_association table failed: %s" % str( e ) ) |
---|
| 663 | try: |
---|
| 664 | JobExternalOutputMetadata_table.drop() |
---|
| 665 | except Exception, e: |
---|
| 666 | log.debug( "Dropping job_external_output_metadata table failed: %s" % str( e ) ) |
---|
| 667 | try: |
---|
| 668 | Library_table.drop() |
---|
| 669 | except Exception, e: |
---|
| 670 | log.debug( "Dropping library table failed: %s" % str( e ) ) |
---|
| 671 | try: |
---|
| 672 | LibraryFolder_table.drop() |
---|
| 673 | except Exception, e: |
---|
| 674 | log.debug( "Dropping library_folder table failed: %s" % str( e ) ) |
---|
| 675 | try: |
---|
| 676 | LibraryItemInfoTemplateElement_table.drop() |
---|
| 677 | except Exception, e: |
---|
| 678 | log.debug( "Dropping library_item_info_template_element table failed: %s" % str( e ) ) |
---|
| 679 | try: |
---|
| 680 | LibraryInfoTemplateAssociation_table.drop() |
---|
| 681 | except Exception, e: |
---|
| 682 | log.debug( "Dropping library_info_template_association table failed: %s" % str( e ) ) |
---|
| 683 | try: |
---|
| 684 | LibraryFolderInfoTemplateAssociation_table.drop() |
---|
| 685 | except Exception, e: |
---|
| 686 | log.debug( "Dropping library_folder_info_template_association table failed: %s" % str( e ) ) |
---|
| 687 | try: |
---|
| 688 | LibraryDatasetInfoTemplateAssociation_table.drop() |
---|
| 689 | except Exception, e: |
---|
| 690 | log.debug( "Dropping library_dataset_info_template_association table failed: %s" % str( e ) ) |
---|
| 691 | try: |
---|
| 692 | LibraryInfoAssociation_table.drop() |
---|
| 693 | except Exception, e: |
---|
| 694 | log.debug( "Dropping library_info_association table failed: %s" % str( e ) ) |
---|
| 695 | try: |
---|
| 696 | LibraryFolderInfoAssociation_table.drop() |
---|
| 697 | except Exception, e: |
---|
| 698 | log.debug( "Dropping library_folder_info_association table failed: %s" % str( e ) ) |
---|
| 699 | try: |
---|
| 700 | LibraryDatasetInfoAssociation_table.drop() |
---|
| 701 | except Exception, e: |
---|
| 702 | log.debug( "Dropping library_dataset_info_association table failed: %s" % str( e ) ) |
---|
| 703 | try: |
---|
| 704 | LibraryItemInfoElement_table.drop() |
---|
| 705 | except Exception, e: |
---|
| 706 | log.debug( "Dropping library_item_info_element table failed: %s" % str( e ) ) |
---|
| 707 | try: |
---|
| 708 | LibraryItemInfo_table.drop() |
---|
| 709 | except Exception, e: |
---|
| 710 | log.debug( "Dropping library_item_info table failed: %s" % str( e ) ) |
---|
| 711 | try: |
---|
| 712 | LibraryItemInfoTemplate_table.drop() |
---|
| 713 | except Exception, e: |
---|
| 714 | log.debug( "Dropping library_item_info_template table failed: %s" % str( e ) ) |
---|
| 715 | # Drop the index on the Job.state column - changeset 2192 |
---|
| 716 | try: |
---|
| 717 | Job_table = Table( "job", metadata, autoload=True ) |
---|
| 718 | except NoSuchTableError: |
---|
| 719 | Job_table = None |
---|
| 720 | log.debug( "Failed loading table job" ) |
---|
| 721 | if Job_table: |
---|
| 722 | try: |
---|
| 723 | i = Index( 'ix_job_state', Job_table.c.state ) |
---|
| 724 | i.drop() |
---|
| 725 | except Exception, e: |
---|
| 726 | log.debug( "Dropping index from job.state column failed: %s" % ( str( e ) ) ) |
---|
| 727 | # Drop 1 column from the stored_workflow table - changeset 2328 |
---|
| 728 | try: |
---|
| 729 | StoredWorkflow_table = Table( "stored_workflow", metadata, autoload=True ) |
---|
| 730 | except NoSuchTableError: |
---|
| 731 | StoredWorkflow_table = None |
---|
| 732 | log.debug( "Failed loading table stored_workflow" ) |
---|
| 733 | if StoredWorkflow_table: |
---|
| 734 | try: |
---|
| 735 | col = StoredWorkflow_table.c.importable |
---|
| 736 | col.drop() |
---|
| 737 | except Exception, e: |
---|
| 738 | log.debug( "Dropping column 'importable' from stored_workflow table failed: %s" % ( str( e ) ) ) |
---|
| 739 | # Drop 1 column from the metadata_file table |
---|
| 740 | try: |
---|
| 741 | MetadataFile_table = Table( "metadata_file", metadata, autoload=True ) |
---|
| 742 | except NoSuchTableError: |
---|
| 743 | MetadataFile_table = None |
---|
| 744 | log.debug( "Failed loading table metadata_file" ) |
---|
| 745 | if MetadataFile_table: |
---|
| 746 | try: |
---|
| 747 | col = MetadataFile_table.c.lda_id |
---|
| 748 | col.drop() |
---|
| 749 | except Exception, e: |
---|
| 750 | log.debug( "Dropping column 'lda_id' from metadata_file table failed: %s" % ( str( e ) ) ) |
---|
| 751 | # Drop 1 column from the history_dataset_association table |
---|
| 752 | try: |
---|
| 753 | HistoryDatasetAssociation_table = Table( "history_dataset_association", metadata, autoload=True ) |
---|
| 754 | except NoSuchTableError: |
---|
| 755 | HistoryDatasetAssociation_table = None |
---|
| 756 | log.debug( "Failed loading table history_dataset_association" ) |
---|
| 757 | if HistoryDatasetAssociation_table: |
---|
| 758 | try: |
---|
| 759 | col = HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id |
---|
| 760 | col.drop() |
---|
| 761 | except Exception, e: |
---|
| 762 | log.debug( "Dropping column 'copied_from_library_dataset_dataset_association_id' from history_dataset_association table failed: %s" % ( str( e ) ) ) |
---|
| 763 | # Drop 2 columns from the galaxy_user table |
---|
| 764 | try: |
---|
| 765 | User_table = Table( "galaxy_user", metadata, autoload=True ) |
---|
| 766 | except NoSuchTableError: |
---|
| 767 | User_table = None |
---|
| 768 | log.debug( "Failed loading table galaxy_user" ) |
---|
| 769 | if User_table: |
---|
| 770 | try: |
---|
| 771 | col = User_table.c.deleted |
---|
| 772 | col.drop() |
---|
| 773 | except Exception, e: |
---|
| 774 | log.debug( "Dropping column 'deleted' from galaxy_user table failed: %s" % ( str( e ) ) ) |
---|
| 775 | try: |
---|
| 776 | col = User_table.c.purged |
---|
| 777 | col.drop() |
---|
| 778 | except Exception, e: |
---|
| 779 | log.debug( "Dropping column 'purged' from galaxy_user table failed: %s" % ( str( e ) ) ) |
---|