def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
meta.bind = migrate_engine
table = meta.tables['USERS']
drop_column(COLUMN_N1, table)
table = meta.tables['BURST_CONFIGURATIONS']
drop_column(COLUMN_N2, table)
table = meta.tables['OPERATIONS']
alter_column(COLUMN_N3_OLD, table=table, name=COLUMN_N3_NEW.name)
try:
meta.bind = migrate_engine
session = SA_SESSIONMAKER()
session.execute(text("""UPDATE "DATA_TYPES" SET module='tvb.datatypes.region_mapping' WHERE "type" = 'RegionMapping' """))
session.execute(text("""UPDATE "DATA_TYPES" SET module='tvb.datatypes.local_connectivity' WHERE "type" = 'LocalConnectivity' """))
session.execute(text("""UPDATE "DATA_TYPES" SET module='tvb.datatypes.cortex' WHERE "type" = 'Cortex' """))
session.commit()
session.close()
except Exception:
LOGGER.exception("Cold not update datatypes")
raise
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table = meta.tables['DATA_TYPES_GROUPS']
drop_column(COL_RANGES_1, table)
drop_column(COL_RANGES_2, table)
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
meta.bind = migrate_engine
table = meta.tables['USERS']
drop_column(COLUMN_N1, table)
table = meta.tables['BURST_CONFIGURATIONS']
drop_column(COLUMN_N2, table)
table = meta.tables['OPERATIONS']
alter_column(COLUMN_N3_OLD, table=table, name=COLUMN_N3_NEW.name)
try:
meta.bind = migrate_engine
session = SA_SESSIONMAKER()
session.execute(text("""UPDATE "DATA_TYPES" SET module='tvb.datatypes.region_mapping' WHERE "type" = 'RegionMapping' """))
session.execute(text("""UPDATE "DATA_TYPES" SET module='tvb.datatypes.local_connectivity' WHERE "type" = 'LocalConnectivity' """))
session.execute(text("""UPDATE "DATA_TYPES" SET module='tvb.datatypes.cortex' WHERE "type" = 'Cortex' """))
session.commit()
session.close()
except Exception:
LOGGER.exception("Cold not update datatypes")
raise
def downgrade(migrate_engine):
"""
Operations to reverse the above upgrade go here.
"""
try:
meta.bind = migrate_engine
table = meta.tables['MAPPED_CONNECTIVITY_DATA']
drop_column(COL_NR_OF_CONNECTIONS, table)
except Exception:
LOGGER.warning("Cold not remove column as required by the downgrade")
raise
def downgrade(migrate_engine):
"""
Operations to reverse the above upgrade go here.
"""
try:
meta.bind = migrate_engine
table = meta.tables['MAPPED_CONNECTIVITY_DATA']
drop_column(COL_NR_OF_CONNECTIONS, table)
except Exception:
LOGGER.warning("Cold not remove column as required by the downgrade")
raise
def downgrade(migrate_engine):
"""
Operations to reverse the above upgrade go here.
"""
try:
meta.bind = migrate_engine
table = meta.tables['PROJECTS']
drop_column(COL_VERSION, table)
except Exception:
logger = get_logger(__name__)
logger.warning("Cold not remove column as required by the downgrade")
raise
def downgrade(migrate_engine):
"""
Operations to reverse the above upgrade go here.
"""
try:
meta.bind = migrate_engine
table = meta.tables['MAPPED_CORRELATION_COEFFICIENTS_DATA']
drop_column(COL_LABELS, table)
except Exception:
## This update is not critical. We can run even in case of error at update
logger = get_logger(__name__)
logger.warning("We do not update table MAPPED_CORRELATION_COEFFICIENTS_DATA, because it is not yet created")
def downgrade(migrate_engine):
"""
Operations to reverse the above upgrade go here.
"""
try:
meta.bind = migrate_engine
table = meta.tables['MAPPED_CORRELATION_COEFFICIENTS_DATA']
drop_column(COL_LABELS, table)
except Exception:
## This update is not critical. We can run even in case of error at update
logger = get_logger(__name__)
logger.warning("We do not update table MAPPED_CORRELATION_COEFFICIENTS_DATA, because it is not yet created")
def downgrade(migrate_engine):
"""
Operations to reverse the above upgrade go here.
"""
try:
meta.bind = migrate_engine
table = meta.tables['PROJECTS']
drop_column(COL_VERSION, table)
except Exception:
logger = get_logger(__name__)
logger.warning("Cold not remove column as required by the downgrade")
raise
def downgrade(migrate_engine):
"""
Operations to reverse the above upgrade go here.
"""
meta.bind = migrate_engine
table1 = meta.tables['MAPPED_TIME_SERIES_DATA']
table2 = meta.tables['MAPPED_TIME_SERIES_REGION_DATA']
table3 = meta.tables['MAPPED_SENSORS_DATA']
drop_column(COL_REG1, table1)
drop_column(COL_REG2, table1)
drop_column(COL_REG3, table2)
drop_column(COL_REG4, table2)
drop_column(COL_SENSORS, table3)
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table1 = meta.tables['MAPPED_CONNECTIVITY_DATA']
create_column(COL_OLD, table1)
session = SA_SESSIONMAKER()
session.execute(text("UPDATE \"MAPPED_CONNECTIVITY_DATA\" set _unidirectional=_undirected"))
session.commit()
session.close()
drop_column(COL_NEW, table1)
create_column(COL_NOSE_CORRECTION, table1)
def downgrade(migrate_engine):
"""
Operations to reverse the above upgrade go here.
"""
meta.bind = migrate_engine
table1 = meta.tables['MAPPED_TIME_SERIES_DATA']
table2 = meta.tables['MAPPED_TIME_SERIES_REGION_DATA']
table3 = meta.tables['MAPPED_SENSORS_DATA']
drop_column(COL_REG1, table1)
drop_column(COL_REG2, table1)
drop_column(COL_REG3, table2)
drop_column(COL_REG4, table2)
drop_column(COL_SENSORS, table3)
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
meta.bind = migrate_engine
table1 = meta.tables['MAPPED_CONNECTIVITY_DATA']
create_column(COL_NEW, table1)
session = SA_SESSIONMAKER()
session.execute(text("UPDATE \"MAPPED_CONNECTIVITY_DATA\" set _undirected=_unidirectional"))
session.commit()
session.close()
drop_column(COL_OLD, table1)
drop_column(COL_NOSE_CORRECTION, table1)
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table = meta.tables['DATA_TYPES_GROUPS']
drop_column(COL_RANGES_1, table)
drop_column(COL_RANGES_2, table)
session = SA_SESSIONMAKER()
session.execute(text("""UPDATE "OPERATIONS"
SET status =
CASE
WHEN status = '4-FINISHED' THEN 'FINISHED'
WHEN status = '3-STARTED' THEN 'STARTED'
WHEN status = '2-CANCELED' THEN 'CANCELED'
ELSE 'ERROR'
END
WHERE status IN ('4-FINISHED', '2-CANCELED', '3-STARTED', '1-ERROR');"""))
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table1 = meta.tables['MAPPED_TIME_SERIES_DATA']
drop_column(COL_1, table1)
drop_column(COL_2, table1)
drop_column(COL_3, table1)
drop_column(COL_4, table1)
session = SA_SESSIONMAKER()
try:
session.execute(
text("ALTER TABLE \"MAPPED_TIME_SERIES_DATA\" "
"RENAME COLUMN _labels_ordering to _dim_labels"))
session.execute(
text("ALTER TABLE \"MAPPED_CROSS_CORRELATION_DATA\" "
"RENAME COLUMN _labels_ordering to _dim_labels"))
except sqlalchemy.exc.OperationalError:
session.execute(
text("ALTER TABLE \"MAPPED_TIME_SERIES_DATA\" "
"ADD COLUMN _dim_labels VARYING CHARACTER(255)"))
session.execute(
text("ALTER TABLE \"MAPPED_CROSS_CORRELATION_DATA\" "
"ADD COLUMN _dim_labels VARYING CHARACTER(255)"))
session.commit()
session.close()
table2 = meta.tables['MAPPED_CONNECTIVITY_DATA']
drop_column(COL_7, table2)
for mapping in TABLE_RENAMES:
session = SA_SESSIONMAKER()
session.execute(
text("ALTER TABLE \"%s\" RENAME TO \"%s\"" %
(mapping[1], mapping[0])))
session.commit()
session.close()
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table1 = meta.tables['BURST_CONFIGURATIONS']
drop_column(COLUMN_BURST, table1)
table2 = meta.tables['ALGORITHM_CATEGORIES']
drop_column(COLUMN_CATEGORY, table2)
table3 = meta.tables['ALGORITHM_GROUPS']
drop_column(COLUMN_GROUP, table3)
table4 = meta.tables['MAPPED_SURFACE_DATA']
drop_column(COLUMN_VALID_SURFACE, table4)
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table1 = meta.tables['BURST_CONFIGURATIONS']
drop_column(COLUMN_BURST, table1)
table2 = meta.tables['ALGORITHM_CATEGORIES']
drop_column(COLUMN_CATEGORY, table2)
table3 = meta.tables['ALGORITHM_GROUPS']
drop_column(COLUMN_GROUP, table3)
table4 = meta.tables['MAPPED_SURFACE_DATA']
drop_column(COLUMN_VALID_SURFACE, table4)
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table1 = meta.tables['MAPPED_TIME_SERIES_DATA']
drop_column(COL_1, table1)
drop_column(COL_2, table1)
drop_column(COL_3, table1)
drop_column(COL_4, table1)
session = SA_SESSIONMAKER()
try:
session.execute(text("ALTER TABLE \"MAPPED_TIME_SERIES_DATA\" "
"RENAME COLUMN _labels_ordering to _dim_labels"))
session.execute(text("ALTER TABLE \"MAPPED_CROSS_CORRELATION_DATA\" "
"RENAME COLUMN _labels_ordering to _dim_labels"))
except sqlalchemy.exc.OperationalError:
session.execute(text("ALTER TABLE \"MAPPED_TIME_SERIES_DATA\" "
"ADD COLUMN _dim_labels VARYING CHARACTER(255)"))
session.execute(text("ALTER TABLE \"MAPPED_CROSS_CORRELATION_DATA\" "
"ADD COLUMN _dim_labels VARYING CHARACTER(255)"))
session.commit()
session.close()
table2 = meta.tables['MAPPED_CONNECTIVITY_DATA']
drop_column(COL_7, table2)
for mapping in TABLE_RENAMES:
session = SA_SESSIONMAKER()
session.execute(text("ALTER TABLE \"%s\" RENAME TO \"%s\"" % (mapping[1], mapping[0])))
session.commit()
session.close()
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table = meta.tables['MAPPED_SURFACE_DATA']
drop_column(COLUMN_N1, table)
drop_column(COLUMN_N2, table)
drop_column(COLUMN_N3, table)
session = SA_SESSIONMAKER()
session.execute(text("""UPDATE "OPERATIONS" SET status='4-FINISHED' WHERE status = '5-FINISHED' """))
session.execute(text("""UPDATE "OPERATIONS" SET status='3-STARTED' WHERE status = '4-PENDING' """))
session.commit()
session.close()
def downgrade(migrate_engine):
"""
Operations to reverse the above upgrade go here.
"""
try:
meta.bind = migrate_engine
table1 = meta.tables['MAPPED_SURFACE_DATA']
drop_column(COL_1, table1)
drop_column(COL_2, table1)
drop_column(COL_3, table1)
except Exception:
logger = get_logger(__name__)
logger.warning("Cold not remove column as required by the downgrade")
raise
def downgrade(migrate_engine):
"""
Operations to reverse the above upgrade go here.
"""
try:
meta.bind = migrate_engine
table1 = meta.tables['MAPPED_SURFACE_DATA']
drop_column(COL_1, table1)
drop_column(COL_2, table1)
drop_column(COL_3, table1)
except Exception:
logger = get_logger(__name__)
logger.warning("Cold not remove column as required by the downgrade")
raise
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table = meta.tables['MAPPED_SURFACE_DATA']
drop_column(COLUMN_N1, table)
drop_column(COLUMN_N2, table)
drop_column(COLUMN_N3, table)
session = SA_SESSIONMAKER()
session.execute(
text(
"""UPDATE "OPERATIONS" SET status='4-FINISHED' WHERE status = '5-FINISHED' """
))
session.execute(
text(
"""UPDATE "OPERATIONS" SET status='3-STARTED' WHERE status = '4-PENDING' """
))
session.commit()
session.close()
def upgrade(migrate_engine):
"""
Alter existing table ALGORITHMS, by moving columns from the old ALGORITHM_GROUPS table.
"""
meta.bind = migrate_engine
table_algo = meta.tables["ALGORITHMS"]
for col in ADD_COLUMNS:
create_column(col, table_algo)
session = SA_SESSIONMAKER()
try:
session.execute(text("ALTER TABLE \"MAPPED_SIMULATION_STATE\" "
"ADD COLUMN _current_state VARYING CHARACTER(255)"))
session.commit()
except Exception:
session.close()
session = SA_SESSIONMAKER()
session.execute(text("ALTER TABLE \"MAPPED_SIMULATION_STATE\" "
"ADD COLUMN _current_state character varying;"))
session.commit()
finally:
session.close()
session = SA_SESSIONMAKER()
try:
session.execute(text(
"""UPDATE "ALGORITHMS" SET
module = (select G.module FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
classname = (select G.classname FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
displayname = (select G.displayname FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
fk_category = (select G.fk_category FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id);"""))
session.commit()
# Delete old columns, no longer needed
for col in DEL_COLUMNS:
drop_column(col, table_algo)
# Create constraint only after rows are being populated
table_algo = meta.tables["ALGORITHMS"]
fk_constraint = ForeignKeyConstraint(["fk_category"], ["ALGORITHM_CATEGORIES.id"],
ondelete="CASCADE", table=table_algo)
fk_constraint.create()
# Drop old table
session = SA_SESSIONMAKER()
session.execute(text("""DROP TABLE "ALGORITHM_GROUPS";"""))
session.commit()
except Exception as excep:
LOGGER.exception(excep)
finally:
session.close()
session = SA_SESSIONMAKER()
try:
session.execute(text("""ALTER TABLE "MAPPED_CONNECTIVITY_ANNOTATIONS"
RENAME TO "MAPPED_CONNECTIVITY_ANNOTATIONS_DATA"; """))
session.execute(text("""ALTER TABLE "MAPPED_DATATYPE_MEASURE" RENAME TO "MAPPED_DATATYPE_MEASURE_DATA"; """))
session.execute(text("""ALTER TABLE "MAPPED_SIMULATION_STATE" RENAME TO "MAPPED_SIMULATION_STATE_DATA"; """))
session.execute(text("""ALTER TABLE "MAPPED_VALUE_WRAPPER" RENAME TO "MAPPED_VALUE_WRAPPER_DATA"; """))
session.execute(text("""ALTER TABLE "MAPPED_PROJECTION_DATA" RENAME TO "MAPPED_PROJECTION_MATRIX_DATA"; """))
session.commit()
except Exception as excep:
LOGGER.exception(excep)
finally:
session.close()
finally:
session.close()
session = SA_SESSIONMAKER()
try:
session.execute(text(
"""UPDATE "ALGORITHMS" SET
module = (select G.module FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
classname = (select G.classname FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
displayname = (select G.displayname FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
fk_category = (select G.fk_category FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id);"""))
session.commit()
# Delete old columns, no longer needed
for col in DEL_COLUMNS:
drop_column(col, table_algo)
# Create constraint only after rows are being populated
table_algo = meta.tables["ALGORITHMS"]
fk_constraint = ForeignKeyConstraint(["fk_category"], ["ALGORITHM_CATEGORIES.id"],
ondelete="CASCADE", table=table_algo)
fk_constraint.create()
# Drop old table
session = SA_SESSIONMAKER()
session.execute(text("""DROP TABLE "ALGORITHM_GROUPS";"""))
session.commit()
except Exception, excep:
LOGGER.exception(excep)
finally:
def upgrade(migrate_engine):
"""
Alter existing table ALGORITHMS, by moving columns from the old ALGORITHM_GROUPS table.
"""
meta.bind = migrate_engine
table_algo = meta.tables["ALGORITHMS"]
for col in ADD_COLUMNS:
create_column(col, table_algo)
session = SA_SESSIONMAKER()
try:
session.execute(
text("ALTER TABLE \"MAPPED_SIMULATION_STATE\" "
"ADD COLUMN _current_state VARYING CHARACTER(255)"))
session.commit()
except Exception:
session.close()
session = SA_SESSIONMAKER()
session.execute(
text("ALTER TABLE \"MAPPED_SIMULATION_STATE\" "
"ADD COLUMN _current_state character varying;"))
session.commit()
finally:
session.close()
session = SA_SESSIONMAKER()
try:
session.execute(
text("""UPDATE "ALGORITHMS" SET
module = (select G.module FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
classname = (select G.classname FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
displayname = (select G.displayname FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
fk_category = (select G.fk_category FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id);"""
))
session.commit()
# Delete old columns, no longer needed
for col in DEL_COLUMNS:
drop_column(col, table_algo)
# Create constraint only after rows are being populated
table_algo = meta.tables["ALGORITHMS"]
fk_constraint = ForeignKeyConstraint(["fk_category"],
["ALGORITHM_CATEGORIES.id"],
ondelete="CASCADE",
table=table_algo)
fk_constraint.create()
# Drop old table
session = SA_SESSIONMAKER()
session.execute(text("""DROP TABLE "ALGORITHM_GROUPS";"""))
session.commit()
except Exception as excep:
LOGGER.exception(excep)
finally:
session.close()
session = SA_SESSIONMAKER()
try:
session.execute(
text("""ALTER TABLE "MAPPED_CONNECTIVITY_ANNOTATIONS"
RENAME TO "MAPPED_CONNECTIVITY_ANNOTATIONS_DATA"; """
))
session.execute(
text(
"""ALTER TABLE "MAPPED_DATATYPE_MEASURE" RENAME TO "MAPPED_DATATYPE_MEASURE_DATA"; """
))
session.execute(
text(
"""ALTER TABLE "MAPPED_SIMULATION_STATE" RENAME TO "MAPPED_SIMULATION_STATE_DATA"; """
))
session.execute(
text(
"""ALTER TABLE "MAPPED_VALUE_WRAPPER" RENAME TO "MAPPED_VALUE_WRAPPER_DATA"; """
))
session.execute(
text(
"""ALTER TABLE "MAPPED_PROJECTION_DATA" RENAME TO "MAPPED_PROJECTION_MATRIX_DATA"; """
))
session.commit()
except Exception as excep:
LOGGER.exception(excep)
finally:
session.close()
session.close()
session = SA_SESSIONMAKER()
try:
session.execute(
text("""UPDATE "ALGORITHMS" SET
module = (select G.module FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
classname = (select G.classname FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
displayname = (select G.displayname FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id),
fk_category = (select G.fk_category FROM "ALGORITHM_GROUPS" G WHERE "ALGORITHMS".fk_algo_group=G.id);"""
))
session.commit()
# Delete old columns, no longer needed
for col in DEL_COLUMNS:
drop_column(col, table_algo)
# Create constraint only after rows are being populated
table_algo = meta.tables["ALGORITHMS"]
fk_constraint = ForeignKeyConstraint(["fk_category"],
["ALGORITHM_CATEGORIES.id"],
ondelete="CASCADE",
table=table_algo)
fk_constraint.create()
# Drop old table
session = SA_SESSIONMAKER()
session.execute(text("""DROP TABLE "ALGORITHM_GROUPS";"""))
session.commit()
except Exception, excep:
