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Source code for galaxy.model.migrate.versions.0003_security_and_libraries

"""
"""

import datetime
import logging

from migrate import ForeignKeyConstraint
from sqlalchemy import (
    Boolean,
    Column,
    DateTime,
    ForeignKey,
    Index,
    Integer,
    MetaData,
    String,
    Table,
    TEXT
)

from galaxy.model.custom_types import (
    JSONType,
    MetadataType,
    TrimmedString
)
from galaxy.model.migrate.versions.util import (
    add_column,
    add_index,
    drop_column,
    drop_index,
    drop_table,
    engine_false,
    localtimestamp,
    nextval
)

log = logging.getLogger(__name__)
now = datetime.datetime.utcnow
metadata = MetaData()

# New tables as of changeset 2341:5498ac35eedd
Group_table = Table("galaxy_group", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", String(255), index=True, unique=True),
    Column("deleted", Boolean, index=True, default=False))

UserGroupAssociation_table = Table("user_group_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now))

UserRoleAssociation_table = Table("user_role_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now))

GroupRoleAssociation_table = Table("group_role_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("group_id", Integer, ForeignKey("galaxy_group.id"), index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now))

Role_table = Table("role", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", String(255), index=True, unique=True),
    Column("description", TEXT),
    Column("type", String(40), index=True),
    Column("deleted", Boolean, index=True, default=False))

DatasetPermissions_table = Table("dataset_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

LibraryPermissions_table = Table("library_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("library_id", Integer, ForeignKey("library.id"), nullable=True, index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

LibraryFolderPermissions_table = Table("library_folder_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("library_folder_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

LibraryDatasetPermissions_table = Table("library_dataset_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), nullable=True, index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

LibraryDatasetDatasetAssociationPermissions_table = Table("library_dataset_dataset_association_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))
Index("ix_lddap_library_dataset_dataset_association_id", LibraryDatasetDatasetAssociationPermissions_table.c.library_dataset_dataset_association_id)

LibraryItemInfoPermissions_table = Table("library_item_info_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("library_item_info_id", Integer, ForeignKey("library_item_info.id"), nullable=True, index=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

LibraryItemInfoTemplatePermissions_table = Table("library_item_info_template_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("action", TEXT),
    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id"), nullable=True),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))
Index("ix_liitp_library_item_info_template_id", LibraryItemInfoTemplatePermissions_table.c.library_item_info_template_id)

DefaultUserPermissions_table = Table("default_user_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("action", TEXT),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

DefaultHistoryPermissions_table = Table("default_history_permissions", metadata,
    Column("id", Integer, primary_key=True),
    Column("history_id", Integer, ForeignKey("history.id"), index=True),
    Column("action", TEXT),
    Column("role_id", Integer, ForeignKey("role.id"), index=True))

LibraryDataset_table = Table("library_dataset", metadata,
    Column("id", Integer, primary_key=True),
    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
    Column("folder_id", Integer, ForeignKey("library_folder.id"), index=True),
    Column("order_id", Integer),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", TrimmedString(255), key="_name"),  # when not None/null this will supercede display in library (but not when imported into user's history?)
    Column("info", TrimmedString(255), key="_info"),  # when not None/null this will supercede display in library (but not when imported into user's history?)
    Column("deleted", Boolean, index=True, default=False))

LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), index=True),
    Column("dataset_id", Integer, ForeignKey("dataset.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    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),
    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),
    Column("name", TrimmedString(255)),
    Column("info", TrimmedString(255)),
    Column("blurb", TrimmedString(255)),
    Column("peek", TEXT),
    Column("extension", TrimmedString(64)),
    Column("metadata", MetadataType(), key="_metadata"),
    Column("parent_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
    Column("designation", TrimmedString(255)),
    Column("deleted", Boolean, index=True, default=False),
    Column("visible", Boolean),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), index=True),
    Column("message", TrimmedString(255)))

Library_table = Table("library", metadata,
    Column("id", Integer, primary_key=True),
    Column("root_folder_id", Integer, ForeignKey("library_folder.id"), index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", String(255), index=True),
    Column("deleted", Boolean, index=True, default=False),
    Column("purged", Boolean, index=True, default=False),
    Column("description", TEXT))

LibraryFolder_table = Table("library_folder", metadata,
    Column("id", Integer, primary_key=True),
    Column("parent_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("name", TEXT),
    Column("description", TEXT),
    Column("order_id", Integer),
    Column("item_count", Integer),
    Column("deleted", Boolean, index=True, default=False),
    Column("purged", Boolean, index=True, default=False),
    Column("genome_build", TrimmedString(40)))

LibraryItemInfoTemplateElement_table = Table("library_item_info_template_element", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("optional", Boolean, index=True, default=True),
    Column("deleted", Boolean, index=True, default=False),
    Column("name", TEXT),
    Column("description", TEXT),
    Column("type", TEXT, default='string'),
    Column("order_id", Integer),
    Column("options", JSONType()),
    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")))
Index("ix_liite_library_item_info_template_id", LibraryItemInfoTemplateElement_table.c.library_item_info_template_id)

LibraryItemInfoTemplate_table = Table("library_item_info_template", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("optional", Boolean, index=True, default=True),
    Column("deleted", Boolean, index=True, default=False),
    Column("name", TEXT),
    Column("description", TEXT),
    Column("item_count", Integer, default=0))

LibraryInfoTemplateAssociation_table = Table("library_info_template_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("library_id", Integer, ForeignKey("library.id"), nullable=True, index=True),
    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")))
Index("ix_lita_library_item_info_template_id", LibraryInfoTemplateAssociation_table.c.library_item_info_template_id)

LibraryFolderInfoTemplateAssociation_table = Table("library_folder_info_template_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("library_folder_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")))
Index("ix_lfita_library_item_info_template_id", LibraryFolderInfoTemplateAssociation_table.c.library_item_info_template_id)

LibraryDatasetInfoTemplateAssociation_table = Table("library_dataset_info_template_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), nullable=True, index=True),
    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")))
Index("ix_ldita_library_item_info_template_id", LibraryDatasetInfoTemplateAssociation_table.c.library_item_info_template_id)

LibraryDatasetDatasetInfoTemplateAssociation_table = Table("library_dataset_dataset_info_template_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id")))
Index("ix_lddita_library_dataset_dataset_association_id", LibraryDatasetDatasetInfoTemplateAssociation_table.c.library_dataset_dataset_association_id)
Index("ix_lddita_library_item_info_template_id", LibraryDatasetDatasetInfoTemplateAssociation_table.c.library_item_info_template_id)

LibraryItemInfoElement_table = Table("library_item_info_element", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("contents", JSONType()),
    Column("library_item_info_id", Integer, ForeignKey("library_item_info.id"), index=True),
    Column("library_item_info_template_element_id", Integer, ForeignKey("library_item_info_template_element.id")))
Index("ix_liie_library_item_info_template_element_id", LibraryItemInfoElement_table.c.library_item_info_template_element_id)

LibraryItemInfo_table = Table("library_item_info", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("deleted", Boolean, index=True, default=False),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True),
    Column("library_item_info_template_id", Integer, ForeignKey("library_item_info_template.id"), nullable=True, index=True))

LibraryInfoAssociation_table = Table("library_info_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("library_id", Integer, ForeignKey("library.id"), nullable=True, index=True),
    Column("library_item_info_id", Integer, ForeignKey("library_item_info.id"), index=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True))

LibraryFolderInfoAssociation_table = Table("library_folder_info_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("library_folder_id", Integer, ForeignKey("library_folder.id"), nullable=True, index=True),
    Column("library_item_info_id", Integer, ForeignKey("library_item_info.id"), index=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True))

LibraryDatasetInfoAssociation_table = Table("library_dataset_info_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("library_dataset_id", Integer, ForeignKey("library_dataset.id"), nullable=True, index=True),
    Column("library_item_info_id", Integer, ForeignKey("library_item_info.id"), index=True),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True))

LibraryDatasetDatasetInfoAssociation_table = Table("library_dataset_dataset_info_association", metadata,
    Column("id", Integer, primary_key=True),
    Column("create_time", DateTime, default=now),
    Column("update_time", DateTime, default=now, onupdate=now),
    Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
    Column("library_item_info_id", Integer, ForeignKey("library_item_info.id")),
    Column("user_id", Integer, ForeignKey("galaxy_user.id"), nullable=True, index=True))
Index("ix_lddia_library_dataset_dataset_association_id", LibraryDatasetDatasetInfoAssociation_table.c.library_dataset_dataset_association_id)
Index("ix_lddia_library_item_info_id", LibraryDatasetDatasetInfoAssociation_table.c.library_item_info_id)

JobExternalOutputMetadata_table = Table("job_external_output_metadata", metadata,
    Column("id", Integer, primary_key=True),
    Column("job_id", Integer, ForeignKey("job.id"), index=True),
    Column("history_dataset_association_id", Integer, ForeignKey("history_dataset_association.id"), index=True, nullable=True),
    Column("library_dataset_dataset_association_id", Integer, ForeignKey("library_dataset_dataset_association.id"), nullable=True),
    Column("filename_in", String(255)),
    Column("filename_out", String(255)),
    Column("filename_results_code", String(255)),
    Column("filename_kwds", String(255)),
    Column("job_runner_external_pid", String(255)))
Index("ix_jeom_library_dataset_dataset_association_id", JobExternalOutputMetadata_table.c.library_dataset_dataset_association_id)


[docs]def upgrade(migrate_engine): print(__doc__) metadata.bind = migrate_engine metadata.reflect() # Add 2 new columns to the galaxy_user table User_table = Table("galaxy_user", metadata, autoload=True) col = Column('deleted', Boolean, index=True, default=False) add_column(col, User_table, metadata, index_name='ix_galaxy_user_deleted') col = Column('purged', Boolean, index=True, default=False) add_column(col, User_table, metadata, index_name='ix_galaxy_user_purged') # Add 1 new column to the history_dataset_association table HistoryDatasetAssociation_table = Table("history_dataset_association", metadata, autoload=True) col = Column('copied_from_library_dataset_dataset_association_id', Integer, nullable=True) add_column(col, HistoryDatasetAssociation_table, metadata) # Add 1 new column to the metadata_file table MetadataFile_table = Table("metadata_file", metadata, autoload=True) col = Column('lda_id', Integer, index=True, nullable=True) add_column(col, MetadataFile_table, metadata, index_name='ix_metadata_file_lda_id') # Add 1 new column to the stored_workflow table - changeset 2328 StoredWorkflow_table = Table("stored_workflow", metadata, Column("latest_workflow_id", Integer, ForeignKey("workflow.id", use_alter=True, name='stored_workflow_latest_workflow_id_fk'), index=True), autoload=True, extend_existing=True) col = Column('importable', Boolean, default=False) add_column(col, StoredWorkflow_table, metadata) # Create an index on the Job.state column - changeset 2192 add_index('ix_job_state', 'job', 'state', metadata) # Add all of the new tables above metadata.create_all() # Add 1 foreign key constraint to the history_dataset_association table LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_association", metadata, autoload=True) try: cons = ForeignKeyConstraint([HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id], [LibraryDatasetDatasetAssociation_table.c.id], name='history_dataset_association_copied_from_library_dataset_da_fkey') # Create the constraint cons.create() except Exception: log.exception("Adding foreign key constraint 'history_dataset_association_copied_from_library_dataset_da_fkey' to table 'history_dataset_association' failed.") # Add 1 foreign key constraint to the metadata_file table LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_association", metadata, autoload=True) if migrate_engine.name != 'sqlite': # Sqlite can't alter table add foreign key. try: cons = ForeignKeyConstraint([MetadataFile_table.c.lda_id], [LibraryDatasetDatasetAssociation_table.c.id], name='metadata_file_lda_id_fkey') # Create the constraint cons.create() except Exception: log.exception("Adding foreign key constraint 'metadata_file_lda_id_fkey' to table 'metadata_file' failed.") # Make sure we have at least 1 user cmd = "SELECT * FROM galaxy_user;" users = migrate_engine.execute(cmd).fetchall() if users: cmd = "SELECT * FROM role;" roles = migrate_engine.execute(cmd).fetchall() if not roles: # Create private roles for each user - pass 1 cmd = \ "INSERT INTO role " + \ "SELECT %s AS id," + \ "%s AS create_time," + \ "%s AS update_time," + \ "email AS name," + \ "email AS description," + \ "'private' As type," + \ "%s AS deleted " + \ "FROM galaxy_user " + \ "ORDER BY id;" cmd = cmd % (nextval(migrate_engine, 'role'), localtimestamp(migrate_engine), localtimestamp(migrate_engine), engine_false(migrate_engine)) migrate_engine.execute(cmd) # Create private roles for each user - pass 2 if migrate_engine.name in ['postgres', 'postgresql', 'sqlite']: cmd = "UPDATE role SET description = 'Private role for ' || description;" elif migrate_engine.name == 'mysql': cmd = "UPDATE role SET description = CONCAT( 'Private role for ', description );" migrate_engine.execute(cmd) # Create private roles for each user - pass 3 cmd = \ "INSERT INTO user_role_association " + \ "SELECT %s AS id," + \ "galaxy_user.id AS user_id," + \ "role.id AS role_id," + \ "%s AS create_time," + \ "%s AS update_time " + \ "FROM galaxy_user, role " + \ "WHERE galaxy_user.email = role.name " + \ "ORDER BY galaxy_user.id;" cmd = cmd % (nextval(migrate_engine, 'user_role_association'), localtimestamp(migrate_engine), localtimestamp(migrate_engine)) migrate_engine.execute(cmd) # Create default permissions for each user cmd = \ "INSERT INTO default_user_permissions " + \ "SELECT %s AS id," + \ "galaxy_user.id AS user_id," + \ "'manage permissions' AS action," + \ "user_role_association.role_id AS role_id " + \ "FROM galaxy_user " + \ "JOIN user_role_association ON user_role_association.user_id = galaxy_user.id " + \ "ORDER BY galaxy_user.id;" cmd = cmd % nextval(migrate_engine, 'default_user_permissions') migrate_engine.execute(cmd) # Create default history permissions for each active history associated with a user cmd = \ "INSERT INTO default_history_permissions " + \ "SELECT %s AS id," + \ "history.id AS history_id," + \ "'manage permissions' AS action," + \ "user_role_association.role_id AS role_id " + \ "FROM history " + \ "JOIN user_role_association ON user_role_association.user_id = history.user_id " + \ "WHERE history.purged = %s AND history.user_id IS NOT NULL;" cmd = cmd % (nextval(migrate_engine, 'default_history_permissions'), engine_false(migrate_engine)) migrate_engine.execute(cmd) # Create "manage permissions" dataset_permissions for all activate-able datasets cmd = \ "INSERT INTO dataset_permissions " + \ "SELECT %s AS id," + \ "%s AS create_time," + \ "%s AS update_time," + \ "'manage permissions' AS action," + \ "history_dataset_association.dataset_id AS dataset_id," + \ "user_role_association.role_id AS role_id " + \ "FROM history " + \ "JOIN history_dataset_association ON history_dataset_association.history_id = history.id " + \ "JOIN dataset ON history_dataset_association.dataset_id = dataset.id " + \ "JOIN user_role_association ON user_role_association.user_id = history.user_id " + \ "WHERE dataset.purged = %s AND history.user_id IS NOT NULL;" cmd = cmd % (nextval(migrate_engine, 'dataset_permissions'), localtimestamp(migrate_engine), localtimestamp(migrate_engine), engine_false(migrate_engine)) migrate_engine.execute(cmd)
[docs]def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() # NOTE: all new data added in the upgrade method is eliminated here via table drops # Drop 1 foreign key constraint from the metadata_file table MetadataFile_table = Table("metadata_file", metadata, autoload=True) LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_association", metadata, autoload=True) try: cons = ForeignKeyConstraint([MetadataFile_table.c.lda_id], [LibraryDatasetDatasetAssociation_table.c.id], name='metadata_file_lda_id_fkey') # Drop the constraint cons.drop() except Exception: log.exception("Dropping foreign key constraint 'metadata_file_lda_id_fkey' from table 'metadata_file' failed.") # Drop 1 foreign key constraint from the history_dataset_association table HistoryDatasetAssociation_table = Table("history_dataset_association", metadata, autoload=True) LibraryDatasetDatasetAssociation_table = Table("library_dataset_dataset_association", metadata, autoload=True) try: cons = ForeignKeyConstraint([HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id], [LibraryDatasetDatasetAssociation_table.c.id], name='history_dataset_association_copied_from_library_dataset_da_fkey') # Drop the constraint cons.drop() except Exception: log.exception("Dropping foreign key constraint 'history_dataset_association_copied_from_library_dataset_da_fkey' from table 'history_dataset_association' failed.") # Drop all of the new tables above TABLES = [ UserGroupAssociation_table, UserRoleAssociation_table, GroupRoleAssociation_table, Group_table, DatasetPermissions_table, LibraryPermissions_table, LibraryFolderPermissions_table, LibraryDatasetPermissions_table, LibraryDatasetDatasetAssociationPermissions_table, LibraryItemInfoPermissions_table, LibraryItemInfoTemplatePermissions_table, DefaultUserPermissions_table, DefaultHistoryPermissions_table, Role_table, LibraryDatasetDatasetInfoAssociation_table, LibraryDataset_table, LibraryDatasetDatasetAssociation_table, LibraryDatasetDatasetInfoTemplateAssociation_table, JobExternalOutputMetadata_table, Library_table, LibraryFolder_table, LibraryItemInfoTemplateElement_table, LibraryInfoTemplateAssociation_table, LibraryFolderInfoTemplateAssociation_table, LibraryDatasetInfoTemplateAssociation_table, LibraryInfoAssociation_table, LibraryFolderInfoAssociation_table, LibraryDatasetInfoAssociation_table, LibraryItemInfoElement_table, LibraryItemInfo_table, LibraryItemInfoTemplate_table, ] for table in TABLES: drop_table(table) # Drop the index on the Job.state column - changeset 2192 drop_index('ix_job_state', 'job', 'state', metadata) # Drop 1 column from the stored_workflow table - changeset 2328 drop_column('importable', 'stored_workflow', metadata) # Drop 1 column from the metadata_file table drop_column('lda_id', 'metadata_file', metadata) # Drop 1 column from the history_dataset_association table drop_column('copied_from_library_dataset_dataset_association_id', HistoryDatasetAssociation_table) # Drop 2 columns from the galaxy_user table User_table = Table("galaxy_user", metadata, autoload=True) drop_column('deleted', User_table) drop_column('purged', User_table)