def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() # TODO: Dropping a column used in a foreign key fails in MySQL, need to remove the FK first. for ix, table, col in indexes: drop_index(ix, table, col, metadata)
def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() drop_index('ix_hda_ta_history_dataset_association_id', 'history_dataset_association_tag_association', 'history_dataset_association_id', metadata)
def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() if migrate_engine.name == 'mysql': drop_index('ix_hdadaa_history_dataset_association_id', 'history_dataset_association_display_at_authorization', 'history_dataset_association_id', metadata)
def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() # Drop the ix_dataset_state index drop_index('ix_dataset_state', 'dataset', 'state', metadata) # Drop the library_folder_id column drop_column('library_folder_id', 'job', metadata) # Drop the job_to_output_library_dataset table drop_table(JobToOutputLibraryDataset_table)
def upgrade(migrate_engine): print(__doc__) metadata.bind = migrate_engine metadata.reflect() Page_table = Table("page", metadata, autoload=True) try: # Sqlite doesn't support .alter, so we need to drop an recreate drop_index("ix_page_slug", Page_table, 'slug') add_index("ix_page_slug", Page_table, 'slug', unique=False) except Exception: # Mysql doesn't have a named index, but alter should work Page_table.c.slug.alter(unique=False)
def upgrade(migrate_engine): print(__doc__) metadata.bind = migrate_engine metadata.reflect() OldWorkflowStepConnection_table = Table("workflow_step_connection", metadata, autoload=True) for fkc in OldWorkflowStepConnection_table.foreign_key_constraints: mfkc = MigrateForeignKeyConstraint([_.parent for _ in fkc.elements], [_.column for _ in fkc.elements], name=fkc.name) try: mfkc.drop() except Exception: log.exception("Dropping foreign key constraint '%s' from table '%s' failed", mfkc.name, OldWorkflowStepConnection_table) for index in OldWorkflowStepConnection_table.indexes: drop_index(index, OldWorkflowStepConnection_table) OldWorkflowStepConnection_table.rename("workflow_step_connection_preupgrade145") # Try to deregister that table to work around some caching problems it seems. OldWorkflowStepConnection_table.deregister() metadata._remove_table("workflow_step_connection", metadata.schema) metadata.reflect() NewWorkflowStepConnection_table = Table( "workflow_step_connection", metadata, Column("id", Integer, primary_key=True), Column("output_step_id", Integer, ForeignKey("workflow_step.id"), index=True), Column("input_step_input_id", Integer, ForeignKey("workflow_step_input.id"), index=True), Column("output_name", TEXT), Column("input_subworkflow_step_id", Integer, ForeignKey("workflow_step.id"), index=True), ) for table in (WorkflowStepInput_table, NewWorkflowStepConnection_table): create_table(table) insert_step_inputs_cmd = \ "INSERT INTO workflow_step_input (workflow_step_id, name) " + \ "SELECT DISTINCT input_step_id, input_name FROM workflow_step_connection_preupgrade145" migrate_engine.execute(insert_step_inputs_cmd) insert_step_connections_cmd = \ "INSERT INTO workflow_step_connection (output_step_id, input_step_input_id, output_name, input_subworkflow_step_id) " + \ "SELECT wsc.output_step_id, wsi.id, wsc.output_name, wsc.input_subworkflow_step_id " + \ "FROM workflow_step_connection_preupgrade145 AS wsc JOIN workflow_step_input AS wsi ON wsc.input_step_id = wsi.workflow_step_id AND wsc.input_name = wsi.name ORDER BY wsc.id" migrate_engine.execute(insert_step_connections_cmd) drop_table(OldWorkflowStepConnection_table)
def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() drop_index('ix_library_dataset_name', 'library_dataset', 'name', metadata) drop_index('ix_library_dataset_dataset_association_name', 'library_dataset_dataset_association', 'name', metadata) drop_index('ix_library_folder_name', 'library_folder', 'name', metadata)
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 try: MetadataFile_table = Table("metadata_file", metadata, autoload=True) except NoSuchTableError: MetadataFile_table = None log.debug("Failed loading table metadata_file") try: LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True) except NoSuchTableError: LibraryDatasetDatasetAssociation_table = None log.debug("Failed loading table library_dataset_dataset_association") if MetadataFile_table is not None and LibraryDatasetDatasetAssociation_table is not None: 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 try: HistoryDatasetAssociation_table = Table("history_dataset_association", metadata, autoload=True) except NoSuchTableError: HistoryDatasetAssociation_table = None log.debug("Failed loading table history_dataset_association") try: LibraryDatasetDatasetAssociation_table = Table( "library_dataset_dataset_association", metadata, autoload=True) except NoSuchTableError: LibraryDatasetDatasetAssociation_table = None log.debug("Failed loading table library_dataset_dataset_association") if HistoryDatasetAssociation_table is not None and LibraryDatasetDatasetAssociation_table is not None: 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 try: UserGroupAssociation_table.drop() except Exception: log.exception("Dropping user_group_association table failed.") try: UserRoleAssociation_table.drop() except Exception: log.exception("Dropping user_role_association table failed.") try: GroupRoleAssociation_table.drop() except Exception: log.exception("Dropping group_role_association table failed.") try: Group_table.drop() except Exception: log.exception("Dropping galaxy_group table failed.") try: DatasetPermissions_table.drop() except Exception: log.exception("Dropping dataset_permissions table failed.") try: LibraryPermissions_table.drop() except Exception: log.exception("Dropping library_permissions table failed.") try: LibraryFolderPermissions_table.drop() except Exception: log.exception("Dropping library_folder_permissions table failed.") try: LibraryDatasetPermissions_table.drop() except Exception: log.exception("Dropping library_dataset_permissions table failed.") try: LibraryDatasetDatasetAssociationPermissions_table.drop() except Exception: log.exception( "Dropping library_dataset_dataset_association_permissions table failed." ) try: LibraryItemInfoPermissions_table.drop() except Exception: log.exception("Dropping library_item_info_permissions table failed.") try: LibraryItemInfoTemplatePermissions_table.drop() except Exception: log.exception( "Dropping library_item_info_template_permissions table failed.") try: DefaultUserPermissions_table.drop() except Exception: log.exception("Dropping default_user_permissions table failed.") try: DefaultHistoryPermissions_table.drop() except Exception: log.exception("Dropping default_history_permissions table failed.") try: Role_table.drop() except Exception: log.exception("Dropping role table failed.") try: LibraryDatasetDatasetInfoAssociation_table.drop() except Exception: log.exception( "Dropping library_dataset_dataset_info_association table failed.") try: LibraryDataset_table.drop() except Exception: log.exception("Dropping library_dataset table failed.") try: LibraryDatasetDatasetAssociation_table.drop() except Exception: log.exception( "Dropping library_dataset_dataset_association table failed.") try: LibraryDatasetDatasetInfoTemplateAssociation_table.drop() except Exception: log.exception( "Dropping library_dataset_dataset_info_template_association table failed." ) try: JobExternalOutputMetadata_table.drop() except Exception: log.exception("Dropping job_external_output_metadata table failed.") try: Library_table.drop() except Exception: log.exception("Dropping library table failed.") try: LibraryFolder_table.drop() except Exception: log.exception("Dropping library_folder table failed.") try: LibraryItemInfoTemplateElement_table.drop() except Exception: log.exception( "Dropping library_item_info_template_element table failed.") try: LibraryInfoTemplateAssociation_table.drop() except Exception: log.exception( "Dropping library_info_template_association table failed.") try: LibraryFolderInfoTemplateAssociation_table.drop() except Exception: log.exception( "Dropping library_folder_info_template_association table failed.") try: LibraryDatasetInfoTemplateAssociation_table.drop() except Exception: log.exception( "Dropping library_dataset_info_template_association table failed.") try: LibraryInfoAssociation_table.drop() except Exception: log.exception("Dropping library_info_association table failed.") try: LibraryFolderInfoAssociation_table.drop() except Exception: log.exception("Dropping library_folder_info_association table failed.") try: LibraryDatasetInfoAssociation_table.drop() except Exception: log.exception( "Dropping library_dataset_info_association table failed.") try: LibraryItemInfoElement_table.drop() except Exception: log.exception("Dropping library_item_info_element table failed.") try: LibraryItemInfo_table.drop() except Exception: log.exception("Dropping library_item_info table failed.") try: LibraryItemInfoTemplate_table.drop() except Exception: log.exception("Dropping library_item_info_template table failed.") # 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 try: StoredWorkflow_table = Table("stored_workflow", metadata, autoload=True) except NoSuchTableError: StoredWorkflow_table = None log.debug("Failed loading table stored_workflow") if StoredWorkflow_table is not None: try: col = StoredWorkflow_table.c.importable col.drop() except Exception: log.exception( "Dropping column 'importable' from stored_workflow table failed." ) # Drop 1 column from the metadata_file table try: MetadataFile_table = Table("metadata_file", metadata, autoload=True) except NoSuchTableError: MetadataFile_table = None log.debug("Failed loading table metadata_file") if MetadataFile_table is not None: try: col = MetadataFile_table.c.lda_id col.drop() except Exception: log.exception( "Dropping column 'lda_id' from metadata_file table failed.") # Drop 1 column from the history_dataset_association table try: HistoryDatasetAssociation_table = Table("history_dataset_association", metadata, autoload=True) except NoSuchTableError: HistoryDatasetAssociation_table = None log.debug("Failed loading table history_dataset_association") if HistoryDatasetAssociation_table is not None: try: col = HistoryDatasetAssociation_table.c.copied_from_library_dataset_dataset_association_id col.drop() except Exception: log.exception( "Dropping column 'copied_from_library_dataset_dataset_association_id' from history_dataset_association table failed." ) # Drop 2 columns from the galaxy_user table try: User_table = Table("galaxy_user", metadata, autoload=True) except NoSuchTableError: User_table = None log.debug("Failed loading table galaxy_user") if User_table is not None: try: col = User_table.c.deleted col.drop() except Exception: log.exception( "Dropping column 'deleted' from galaxy_user table failed.") try: col = User_table.c.purged col.drop() except Exception: log.exception( "Dropping column 'purged' from galaxy_user table failed.")
def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() for ix, table, col in indexes: drop_index(ix, table, col, metadata)
def downgrade(migrate_engine): metadata.bind = migrate_engine metadata.reflect() drop_index('ix_job_job_runner_external_id', 'job', 'job_runner_external_id', metadata)
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)