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)
