def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
for table_name in DATASET_INSTANCE_TABLE_NAMES:
drop_column('state', table_name, metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('filename_override_metadata', 'job_external_output_metadata',
metadata)
def drop_timestamps(metadata, table_name):
target_table = Table(table_name, metadata, autoload=True)
drop_column("create_time", target_table)
drop_column("update_time", target_table)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('imported', 'job', metadata)
def downgrade(migrate_engine):
metadata = MetaData()
metadata.bind = migrate_engine
metadata.reflect()
drop_column('pid', 'worker_process', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column("last_action", "galaxy_session", metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('installed_changeset_revision', 'tool_shed_repository', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column("label", "workflow_step", metadata)
drop_column("uuid", "workflow_step", metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
drop_column("from_path", "stored_workflow", metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('content_format', 'page_revision', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('notify', 'request', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('job_id', 'dataset', 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)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('dbkey', 'visualization', metadata)
drop_column('dbkey', 'visualization_revision', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('form_values_id', 'galaxy_user', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
for table in TABLES:
drop_table(table)
drop_column("state", "workflow_invocation", metadata)
drop_column("scheduler", "workflow_invocation", metadata)
drop_column("uuid", "workflow_invocation", metadata)
drop_column("history_id", "workflow_invocation", metadata)
drop_column("handler", "workflow_invocation", metadata)
drop_column("action", "workflow_invocation_step", metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('importable', 'history', metadata)
drop_table(HistoryUserShareAssociation_table)
def downgrade(migrate_engine):
metadata = MetaData()
metadata.bind = migrate_engine
metadata.reflect()
drop_column('uuid', 'metadata_file', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('slug', 'history', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('requires_domain', 'interactivetool_entry_point', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
# SQLAlchemy Migrate has a bug when dropping a boolean column in SQLite
if migrate_engine.name != 'sqlite':
drop_column("is_valid", "job_external_output_metadata", metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
cloudauthz_table = Table("cloudauthz", metadata, autoload=True)
drop_column('create_time', cloudauthz_table)
def upgrade(migrate_engine):
print(__doc__)
metadata.bind = migrate_engine
metadata.reflect()
drop_column('installed_changeset_revision', 'tool_dependency', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('created_from_basename', 'dataset', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('handler', 'job', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('slug', 'stored_workflow', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('ctx_rev', 'tool_shed_repository', metadata)
def downgrade(migrate_engine):
metadata.bind = migrate_engine
metadata.reflect()
drop_column('ldda_parent_id', 'implicitly_converted_dataset_association',
metadata)
def upgrade(migrate_engine):
print(__doc__)
metadata.bind = migrate_engine
metadata.reflect()
# rename 'sequencer' table to 'external_service'
Sequencer_table = Table("sequencer", metadata, autoload=True)
Sequencer_table.rename('external_service')
# if running PostgreSQL, rename the primary key sequence too
if migrate_engine.name in ['postgres', 'postgresql']:
cmd = "ALTER SEQUENCE sequencer_id_seq RENAME TO external_service_id_seq"
migrate_engine.execute(cmd)
# Add 'external_services_id' column to 'sample_dataset' table
SampleDataset_table = Table("sample_dataset", metadata, autoload=True)
# SQLAlchemy Migrate has a bug when adding a column with both a ForeignKey and a index in SQLite
if migrate_engine.name != 'sqlite':
col = Column("external_service_id",
Integer,
ForeignKey("external_service.id",
name='sample_dataset_external_services_id_fk'),
index=True)
else:
col = Column("external_service_id", Integer, index=True)
add_column(col,
SampleDataset_table,
index_name="ix_sample_dataset_external_service_id")
# populate the column
cmd = "SELECT sample_dataset.id, request_type.sequencer_id " \
+ " FROM sample_dataset, sample, request, request_type " \
+ " WHERE sample.id=sample_dataset.sample_id and request.id=sample.request_id and request.request_type_id=request_type.id " \
+ " ORDER BY sample_dataset.id"
try:
result = migrate_engine.execute(cmd)
for r in result:
sample_dataset_id = int(r[0])
sequencer_id = int(r[1])
cmd = "UPDATE sample_dataset SET external_service_id='%i' where id=%i" % (
sequencer_id, sample_dataset_id)
migrate_engine.execute(cmd)
except Exception:
log.exception("Exception executing SQL command: %s", cmd)
# rename 'sequencer_type_id' column to 'external_service_type_id' in the table 'external_service'
# create the column as 'external_service_type_id'
ExternalServices_table = Table("external_service", metadata, autoload=True)
col = Column("external_service_type_id", TrimmedString(255))
add_column(col, ExternalServices_table)
# populate this new column
cmd = "UPDATE external_service SET external_service_type_id=sequencer_type_id"
migrate_engine.execute(cmd)
# remove the 'sequencer_type_id' column
drop_column('sequencer_type_id', ExternalServices_table)
# create 'request_type_external_service_association' table
RequestTypeExternalServiceAssociation_table = Table(
"request_type_external_service_association", metadata,
Column("id", Integer, primary_key=True),
Column("request_type_id",
Integer,
ForeignKey("request_type.id"),
index=True),
Column("external_service_id",
Integer,
ForeignKey("external_service.id"),
index=True))
create_table(RequestTypeExternalServiceAssociation_table)
# populate 'request_type_external_service_association' table
cmd = "SELECT id, sequencer_id FROM request_type ORDER BY id ASC"
result = migrate_engine.execute(cmd)
results_list = result.fetchall()
# Proceed only if request_types exists
for row in results_list:
request_type_id = row[0]
sequencer_id = row[1]
if not sequencer_id:
sequencer_id = 'null'
cmd = "INSERT INTO request_type_external_service_association VALUES ( %s, %s, %s )" % (
nextval(migrate_engine,
'request_type_external_service_association'),
request_type_id, sequencer_id)
migrate_engine.execute(cmd)
# drop the 'sequencer_id' column in the 'request_type' table
drop_column('sequencer_id', 'request_type', metadata)
