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['DATA_TYPES_GROUPS']
create_column(COL_RANGES_1, table)
create_column(COL_RANGES_2, table)
try:
## Iterate DataTypeGroups from previous code-versions and try to update value for the new column.
previous_groups = dao.get_generic_entity(model.DataTypeGroup, "0", "no_of_ranges")
for group in previous_groups:
operation_group = dao.get_operationgroup_by_id(group.fk_operation_group)
#group.only_numeric_ranges = operation_group.has_only_numeric_ranges
if operation_group.range3 is not None:
group.no_of_ranges = 3
elif operation_group.range2 is not None:
group.no_of_ranges = 2
elif operation_group.range1 is not None:
group.no_of_ranges = 1
else:
group.no_of_ranges = 0
dao.store_entity(group)
except Exception, excep:
## we can live with a column only having default value. We will not stop the startup.
logger = get_logger(__name__)
logger.exception(excep)
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table = meta.tables['USERS']
create_column(COLUMN_N1, table)
table = meta.tables['BURST_CONFIGURATIONS']
create_column(COLUMN_N2, table)
table = meta.tables['OPERATIONS']
alter_column(COLUMN_N3_NEW, table=table, name=COLUMN_N3_OLD.name)
try:
meta.bind = migrate_engine
session = SA_SESSIONMAKER()
session.execute(
text(
"""UPDATE "DATA_TYPES" SET module='tvb.datatypes.surfaces' WHERE "type" = 'RegionMapping' """
))
session.execute(
text(
"""UPDATE "DATA_TYPES" SET module='tvb.datatypes.surfaces' WHERE "type" = 'LocalConnectivity' """
))
session.execute(
text(
"""UPDATE "DATA_TYPES" SET module='tvb.datatypes.surfaces' WHERE "type" = 'Cortex' """
))
session.commit()
session.close()
except Exception:
LOGGER.exception("Cold not update datatypes")
raise
def upgrade(migrate_engine):
meta.bind = migrate_engine
category_column = Column('category_id', Integer)
movie = Table('movie', meta, category_column)
create_column(category_column, movie)
Index('ix_movie_category_id', movie.c.category_id).create()
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['DATA_TYPES_GROUPS']
create_column(COL_RANGES_1, table)
create_column(COL_RANGES_2, table)
try:
## Iterate DataTypeGroups from previous code-versions and try to update value for the new column.
previous_groups = dao.get_generic_entity(model.DataTypeGroup, "0", "no_of_ranges")
for group in previous_groups:
operation_group = dao.get_operationgroup_by_id(group.fk_operation_group)
#group.only_numeric_ranges = operation_group.has_only_numeric_ranges
if operation_group.range3 is not None:
group.no_of_ranges = 3
elif operation_group.range2 is not None:
group.no_of_ranges = 2
elif operation_group.range1 is not None:
group.no_of_ranges = 1
else:
group.no_of_ranges = 0
dao.store_entity(group)
except Exception as excep:
## we can live with a column only having default value. We will not stop the startup.
logger = get_logger(__name__)
logger.exception(excep)
session = SA_SESSIONMAKER()
session.execute(text("""UPDATE "OPERATIONS"
SET status =
CASE
WHEN status = 'FINISHED' THEN '4-FINISHED'
WHEN status = 'STARTED' THEN '3-STARTED'
WHEN status = 'CANCELED' THEN '2-CANCELED'
ELSE '1-ERROR'
END
WHERE status IN ('FINISHED', 'CANCELED', 'STARTED', 'ERROR');"""))
session.commit()
session.close()
try:
session = SA_SESSIONMAKER()
for sim_state in session.query(SimulationState).filter(SimulationState.fk_datatype_group is not None).all():
session.delete(sim_state)
session.commit()
session.close()
except Exception as excep:
## It might happen that SimulationState table is not yet created, e.g. if user has version 1.0.2
logger = get_logger(__name__)
logger.exception(excep)
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
try:
meta.bind = migrate_engine
table = meta.tables['PROJECTS']
create_column(COL_VERSION, table)
except Exception:
logger = get_logger(__name__)
logger.exception("Cold not create new column required by the update")
raise
def upgrade(migrate_engine):
meta.bind = migrate_engine
# Change release, add last_edit and index
last_edit_column = Column('last_edit', Integer)
release = Table('release', meta, last_edit_column)
create_column(last_edit_column, release)
Index('ix_release_last_edit', release.c.last_edit).create()
# Change movie last_edit
last_edit_column = Column('last_edit', Integer)
movie = Table('movie', meta, last_edit_column)
Index('ix_movie_last_edit', movie.c.last_edit).create()
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_TIME_SERIES_DATA']
table2 = meta.tables['MAPPED_TIME_SERIES_REGION_DATA']
table3 = meta.tables['MAPPED_SENSORS_DATA']
create_column(COL_REG1, table1)
create_column(COL_REG2, table1)
create_column(COL_REG3, table2)
create_column(COL_REG4, table2)
create_column(COL_SENSORS, table3)
session = SA_SESSIONMAKER()
session.execute(
text(
"""UPDATE "MAPPED_TIME_SERIES_REGION_DATA" tr SET _region_mapping =
(SELECT dt.gid
FROM "MAPPED_REGION_MAPPING_DATA" rm, "DATA_TYPES" dt
WHERE dt.id = rm.id AND tr._connectivity = rm._connectivity);"""
))
# session.execute(text("""UPDATE "MAPPED_TIME_SERIES_REGION_DATA" tr SET _region_mapping_volume =
# (SELECT dt.gid
# FROM "MAPPED_REGION_VOLUME_MAPPING_DATA" rm, "DATA_TYPES" dt
# WHERE dt.id = rm.id AND tr._connectivity = rm._connectivity);"""))
session.execute(
text(
"""UPDATE "MAPPED_TIME_SERIES_DATA" ts SET _has_surface_mapping = True
WHERE
EXISTS (SELECT * FROM "DATA_TYPES" dt
WHERE dt.id=ts.id AND dt.type in ('TimeSeriesSurface', 'TimeSeriesEEG',
'TimeSeriesSEEG', 'TimeSeriesMEG'))
OR EXISTS (SELECT * from "MAPPED_TIME_SERIES_REGION_DATA" tr
WHERE tr.id=ts.id AND tr._region_mapping is not NULL);"""
))
session.execute(
text(
"""UPDATE "MAPPED_TIME_SERIES_DATA" ts SET _has_volume_mapping = True
WHERE
EXISTS (SELECT * FROM "DATA_TYPES" dt
WHERE dt.id=ts.id AND dt.type in ('TimeSeriesVolume'))
OR EXISTS (SELECT * from "MAPPED_TIME_SERIES_REGION_DATA" tr
WHERE tr.id=ts.id AND tr._region_mapping_volume is not NULL);"""
))
session.commit()
session.close()
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 upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
try:
meta.bind = migrate_engine
table = meta.tables['PROJECTS']
create_column(COL_VERSION, table)
except Exception:
logger = get_logger(__name__)
logger.exception("Cold not create new column required by the update")
raise
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
try:
meta.bind = migrate_engine
table = meta.tables['MAPPED_CORRELATION_COEFFICIENTS_DATA']
create_column(COL_LABELS, table)
except Exception:
## This update might fail, in case people are having an older version of TVB
## (in which current datatypes does not even exists)
logger = get_logger(__name__)
logger.warning("We do not update table MAPPED_CORRELATION_COEFFICIENTS_DATA, because it is not yet created")
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
try:
meta.bind = migrate_engine
table = meta.tables['MAPPED_CORRELATION_COEFFICIENTS_DATA']
create_column(COL_LABELS, table)
except Exception:
## This update might fail, in case people are having an older version of TVB
## (in which current datatypes does not even exists)
logger = get_logger(__name__)
logger.warning("We do not update table MAPPED_CORRELATION_COEFFICIENTS_DATA, because it is not yet created")
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
try:
meta.bind = migrate_engine
table = meta.tables['MAPPED_CONNECTIVITY_DATA']
create_column(COL_NR_OF_CONNECTIONS, table)
remove_visualizer_references()
except Exception:
LOGGER.exception("Cold not create new column required by the update")
raise
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
try:
meta.bind = migrate_engine
table = meta.tables['MAPPED_CONNECTIVITY_DATA']
create_column(COL_NR_OF_CONNECTIONS, table)
remove_visualizer_references()
except Exception:
LOGGER.exception("Cold not create new column required by the update")
raise
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 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_TIME_SERIES_DATA']
table2 = meta.tables['MAPPED_TIME_SERIES_REGION_DATA']
table3 = meta.tables['MAPPED_SENSORS_DATA']
create_column(COL_REG1, table1)
create_column(COL_REG2, table1)
create_column(COL_REG3, table2)
create_column(COL_REG4, table2)
create_column(COL_SENSORS, table3)
logger = get_logger(__name__)
sqlite = _exec_update("1", logger)
if not sqlite:
_exec_update("True", logger)
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()
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_TIME_SERIES_DATA']
table2 = meta.tables['MAPPED_TIME_SERIES_REGION_DATA']
table3 = meta.tables['MAPPED_SENSORS_DATA']
create_column(COL_REG1, table1)
create_column(COL_REG2, table1)
create_column(COL_REG3, table2)
create_column(COL_REG4, table2)
create_column(COL_SENSORS, table3)
logger = get_logger(__name__)
sqlite = _exec_update("1", logger)
if not sqlite:
_exec_update("True", logger)
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_TIME_SERIES_DATA']
table2 = meta.tables['MAPPED_TIME_SERIES_REGION_DATA']
table3 = meta.tables['MAPPED_SENSORS_DATA']
create_column(COL_REG1, table1)
create_column(COL_REG2, table1)
create_column(COL_REG3, table2)
create_column(COL_REG4, table2)
create_column(COL_SENSORS, table3)
session = SA_SESSIONMAKER()
session.execute(text("""UPDATE "MAPPED_TIME_SERIES_REGION_DATA" tr SET _region_mapping =
(SELECT dt.gid
FROM "MAPPED_REGION_MAPPING_DATA" rm, "DATA_TYPES" dt
WHERE dt.id = rm.id AND tr._connectivity = rm._connectivity);"""))
# session.execute(text("""UPDATE "MAPPED_TIME_SERIES_REGION_DATA" tr SET _region_mapping_volume =
# (SELECT dt.gid
# FROM "MAPPED_REGION_VOLUME_MAPPING_DATA" rm, "DATA_TYPES" dt
# WHERE dt.id = rm.id AND tr._connectivity = rm._connectivity);"""))
session.execute(text("""UPDATE "MAPPED_TIME_SERIES_DATA" ts SET _has_surface_mapping = True
WHERE
EXISTS (SELECT * FROM "DATA_TYPES" dt
WHERE dt.id=ts.id AND dt.type in ('TimeSeriesSurface', 'TimeSeriesEEG',
'TimeSeriesSEEG', 'TimeSeriesMEG'))
OR EXISTS (SELECT * from "MAPPED_TIME_SERIES_REGION_DATA" tr
WHERE tr.id=ts.id AND tr._region_mapping is not NULL);"""))
session.execute(text("""UPDATE "MAPPED_TIME_SERIES_DATA" ts SET _has_volume_mapping = True
WHERE
EXISTS (SELECT * FROM "DATA_TYPES" dt
WHERE dt.id=ts.id AND dt.type in ('TimeSeriesVolume'))
OR EXISTS (SELECT * from "MAPPED_TIME_SERIES_REGION_DATA" tr
WHERE tr.id=ts.id AND tr._region_mapping_volume is not NULL);"""))
session.commit()
session.close()
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
try:
meta.bind = migrate_engine
table1 = meta.tables['MAPPED_SURFACE_DATA']
create_column(COL_1, table1)
create_column(COL_2, table1)
create_column(COL_3, table1)
try:
session = SA_SESSIONMAKER()
session.execute(text("UPDATE \"DATA_TYPES\" SET invalid=1 WHERE exists "
"(SELECT * FROM \"MAPPED_SURFACE_DATA\" WHERE _number_of_split_slices > 1 "
"and \"DATA_TYPES\".id = \"MAPPED_SURFACE_DATA\".id)"))
session.commit()
session.close()
except ProgrammingError:
# PostgreSQL
session = SA_SESSIONMAKER()
session.execute(text("UPDATE \"DATA_TYPES\" SET invalid=TRUE WHERE exists "
"(SELECT * FROM \"MAPPED_SURFACE_DATA\" WHERE _number_of_split_slices > 1 "
"and \"DATA_TYPES\".id = \"MAPPED_SURFACE_DATA\".id)"))
session.commit()
session.close()
except Exception:
logger = get_logger(__name__)
logger.exception("Cold not create new column required by the update")
raise
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()
def downgrade(migrate_engine):
"""Operations to reverse the above upgrade go here."""
meta.bind = migrate_engine
table = meta.tables['USERS']
create_column(COLUMN_N1, table)
table = meta.tables['BURST_CONFIGURATIONS']
create_column(COLUMN_N2, table)
table = meta.tables['OPERATIONS']
alter_column(COLUMN_N3_NEW, table=table, name=COLUMN_N3_OLD.name)
try:
meta.bind = migrate_engine
session = SA_SESSIONMAKER()
session.execute(text("""UPDATE "DATA_TYPES" SET module='tvb.datatypes.surfaces' WHERE "type" = 'RegionMapping' """))
session.execute(text("""UPDATE "DATA_TYPES" SET module='tvb.datatypes.surfaces' WHERE "type" = 'LocalConnectivity' """))
session.execute(text("""UPDATE "DATA_TYPES" SET module='tvb.datatypes.surfaces' WHERE "type" = 'Cortex' """))
session.commit()
session.close()
except Exception:
LOGGER.exception("Cold not update datatypes")
raise
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['BURST_CONFIGURATIONS']
create_column(COLUMN_BURST, table1)
table2 = meta.tables['ALGORITHM_CATEGORIES']
create_column(COLUMN_CATEGORY, table2)
table3 = meta.tables['ALGORITHM_GROUPS']
create_column(COLUMN_GROUP, table3)
table4 = meta.tables['MAPPED_SURFACE_DATA']
create_column(COLUMN_VALID_SURFACE, table4)
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['BURST_CONFIGURATIONS']
create_column(COLUMN_BURST, table1)
table2 = meta.tables['ALGORITHM_CATEGORIES']
create_column(COLUMN_CATEGORY, table2)
table3 = meta.tables['ALGORITHM_GROUPS']
create_column(COLUMN_GROUP, table3)
table4 = meta.tables['MAPPED_SURFACE_DATA']
create_column(COLUMN_VALID_SURFACE, table4)
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['MAPPED_SURFACE_DATA']
create_column(COLUMN_N1, table)
create_column(COLUMN_N2, table)
create_column(COLUMN_N3, table)
session = SA_SESSIONMAKER()
session.execute(text("""UPDATE "OPERATIONS" SET status='5-FINISHED' WHERE status = '4-FINISHED' """))
session.commit()
session.close()
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['MAPPED_SURFACE_DATA']
create_column(COLUMN_N1, table)
create_column(COLUMN_N2, table)
create_column(COLUMN_N3, table)
session = SA_SESSIONMAKER()
session.execute(
text(
"""UPDATE "OPERATIONS" SET status='5-FINISHED' WHERE status = '4-FINISHED' """
))
session.commit()
session.close()
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
try:
meta.bind = migrate_engine
table1 = meta.tables['MAPPED_SURFACE_DATA']
create_column(COL_1, table1)
create_column(COL_2, table1)
create_column(COL_3, table1)
try:
session = SA_SESSIONMAKER()
session.execute(
text(
"UPDATE \"DATA_TYPES\" SET invalid=1 WHERE exists "
"(SELECT * FROM \"MAPPED_SURFACE_DATA\" WHERE _number_of_split_slices > 1 "
"and \"DATA_TYPES\".id = \"MAPPED_SURFACE_DATA\".id)"))
session.commit()
session.close()
except ProgrammingError:
# PostgreSQL
session = SA_SESSIONMAKER()
session.execute(
text(
"UPDATE \"DATA_TYPES\" SET invalid=TRUE WHERE exists "
"(SELECT * FROM \"MAPPED_SURFACE_DATA\" WHERE _number_of_split_slices > 1 "
"and \"DATA_TYPES\".id = \"MAPPED_SURFACE_DATA\".id)"))
session.commit()
session.close()
except Exception:
logger = get_logger(__name__)
logger.exception("Cold not create new column required by the update")
raise
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['DATA_TYPES_GROUPS']
create_column(COL_RANGES_1, table)
create_column(COL_RANGES_2, table)
try:
## Iterate DataTypeGroups from previous code-versions and try to update value for the new column.
previous_groups = dao.get_generic_entity(model.DataTypeGroup, "0",
"no_of_ranges")
for group in previous_groups:
operation_group = dao.get_operationgroup_by_id(
group.fk_operation_group)
#group.only_numeric_ranges = operation_group.has_only_numeric_ranges
if operation_group.range3 is not None:
group.no_of_ranges = 3
elif operation_group.range2 is not None:
group.no_of_ranges = 2
elif operation_group.range1 is not None:
group.no_of_ranges = 1
else:
group.no_of_ranges = 0
dao.store_entity(group)
except Exception as excep:
## we can live with a column only having default value. We will not stop the startup.
logger = get_logger(__name__)
logger.exception(excep)
session = SA_SESSIONMAKER()
session.execute(
text("""UPDATE "OPERATIONS"
SET status =
CASE
WHEN status = 'FINISHED' THEN '4-FINISHED'
WHEN status = 'STARTED' THEN '3-STARTED'
WHEN status = 'CANCELED' THEN '2-CANCELED'
ELSE '1-ERROR'
END
WHERE status IN ('FINISHED', 'CANCELED', 'STARTED', 'ERROR');"""
))
session.commit()
session.close()
try:
session = SA_SESSIONMAKER()
# TODO: fix me
# for sim_state in session.query(SimulationState).filter(SimulationState.fk_datatype_group is not None).all():
# session.delete(sim_state)
session.commit()
session.close()
except Exception as excep:
## It might happen that SimulationState table is not yet created, e.g. if user has version 1.0.2
logger = get_logger(__name__)
logger.exception(excep)
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
meta = MetaData(bind=migrate_engine)
table = _prepare_table(meta, 'USER_PREFERENCES')
table.c.user_id.alter(name='fk_user')
table = _prepare_table(meta, 'BURST_CONFIGURATIONS')
table.c.project_id.alter(name='fk_project')
table = _prepare_table(
meta,
'WORKFLOWS',
)
table.c.project_id.alter(name='fk_project')
table.c.burst_id.alter(name='fk_burst')
table = _prepare_table(meta, 'WORKFLOW_STEPS')
table.c.workflow_id.alter(name='fk_workflow')
table.c.algorithm_id.alter(name='fk_algorithm')
table.c.resulted_op_id.alter(name='fk_operation')
table = _prepare_table(meta, 'MAPPED_DATATYPE_MEASURE')
table.c.analyzed_datatype.alter(name='_analyzed_datatype')
## Fix Lookup Table mapping.
table = _prepare_table(meta, 'MAPPED_LOOK_UP_TABLE_DATA')
create_column(COL_1, table)
create_column(COL_2, table)
create_column(COL_3, table)
create_column(COL_4, table)
create_column(COL_5, table)
create_column(COL_6, table)
create_column(COL_7, table)
session = SA_SESSIONMAKER()
session.execute(text('DELETE FROM "MAPPED_LOOK_UP_TABLE_DATA";'))
session.execute(
text(
'insert into "MAPPED_LOOK_UP_TABLE_DATA"(id, _equation, _number_of_values, _invdx, _xmax, _xmin, _df, _dx, _data) '
'select id, \'\', _number_of_values, _invdx, _xmax, _xmin, _df, _dx, _data from "MAPPED_NERF_TABLE_DATA";'
))
session.execute(
text(
'insert into "MAPPED_LOOK_UP_TABLE_DATA"(id, _equation, _number_of_values, _invdx, _xmax, _xmin, _df, _dx, _data) '
'select id, \'\', _number_of_values, _invdx, _xmax, _xmin, _df, _dx, _data from "MAPPED_PSI_TABLE_DATA";'
))
session.commit()
session.close()
table = _prepare_table(meta, 'MAPPED_NERF_TABLE_DATA')
table.drop()
table = _prepare_table(meta, 'MAPPED_PSI_TABLE_DATA')
table.drop()
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_TIME_SERIES_DATA']
create_column(COL_1, table1)
create_column(COL_2, table1)
create_column(COL_3, table1)
create_column(COL_4, table1)
create_column(COL_5, table1)
session = SA_SESSIONMAKER()
try:
# We have a database that supports renaming columns. This way we save data from old timeseries.
session.execute(
text("ALTER TABLE \"MAPPED_TIME_SERIES_DATA\" "
"RENAME COLUMN _dim_labels to _labels_ordering"))
session.execute(
text("ALTER TABLE \"MAPPED_CROSS_CORRELATION_DATA\" "
"RENAME COLUMN _dim_labels to _labels_ordering"))
except sqlalchemy.exc.OperationalError:
# We have a database like sqlite. Just create a new column, we're gonna miss old data in this case.
session.execute(
text("ALTER TABLE \"MAPPED_TIME_SERIES_DATA\" "
"ADD COLUMN _labels_ordering VARYING CHARACTER(255)"))
session.execute(
text("ALTER TABLE \"MAPPED_CROSS_CORRELATION_DATA\" "
"ADD COLUMN _labels_ordering VARYING CHARACTER(255)"))
session.execute(text("DROP TABLE \"MAPPED_PSI_TABLE_DATA\""))
session.execute(text("DROP TABLE \"MAPPED_NERF_TABLE_DATA\""))
session.execute(text("DROP TABLE \"MAPPED_LOOK_UP_TABLES_DATA\""))
session.commit()
session.close()
table2 = meta.tables['MAPPED_CONNECTIVITY_DATA']
create_column(COL_7, table2)
for mapping in TABLE_RENAMES:
session = SA_SESSIONMAKER()
session.execute(
text("ALTER TABLE \"%s\" RENAME TO \"%s\"" %
(mapping[0], mapping[1])))
session.commit()
session.close()
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_TIME_SERIES_DATA']
create_column(COL_1, table1)
create_column(COL_2, table1)
create_column(COL_3, table1)
create_column(COL_4, table1)
create_column(COL_5, table1)
session = SA_SESSIONMAKER()
try:
# We have a database that supports renaming columns. This way we save data from old timeseries.
session.execute(text("ALTER TABLE \"MAPPED_TIME_SERIES_DATA\" "
"RENAME COLUMN _dim_labels to _labels_ordering"))
session.execute(text("ALTER TABLE \"MAPPED_CROSS_CORRELATION_DATA\" "
"RENAME COLUMN _dim_labels to _labels_ordering"))
except sqlalchemy.exc.OperationalError:
# We have a database like sqlite. Just create a new column, we're gonna miss old data in this case.
session.execute(text("ALTER TABLE \"MAPPED_TIME_SERIES_DATA\" "
"ADD COLUMN _labels_ordering VARYING CHARACTER(255)"))
session.execute(text("ALTER TABLE \"MAPPED_CROSS_CORRELATION_DATA\" "
"ADD COLUMN _labels_ordering VARYING CHARACTER(255)"))
session.execute(text("DROP TABLE \"MAPPED_PSI_TABLE_DATA\""))
session.execute(text("DROP TABLE \"MAPPED_NERF_TABLE_DATA\""))
session.execute(text("DROP TABLE \"MAPPED_LOOK_UP_TABLES_DATA\""))
session.commit()
session.close()
table2 = meta.tables['MAPPED_CONNECTIVITY_DATA']
create_column(COL_7, table2)
for mapping in TABLE_RENAMES:
session = SA_SESSIONMAKER()
session.execute(text("ALTER TABLE \"%s\" RENAME TO \"%s\"" % (mapping[0], mapping[1])))
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()
def upgrade(migrate_engine):
"""
Upgrade operations go here.
Don't create your own engine; bind migrate_engine to your metadata.
"""
meta = MetaData(bind=migrate_engine)
table = _prepare_table(meta, 'USER_PREFERENCES')
table.c.user_id.alter(name='fk_user')
table = _prepare_table(meta, 'BURST_CONFIGURATIONS')
table.c.project_id.alter(name='fk_project')
table = _prepare_table(meta, 'WORKFLOWS',)
table.c.project_id.alter(name='fk_project')
table.c.burst_id.alter(name='fk_burst')
table = _prepare_table(meta, 'WORKFLOW_STEPS')
table.c.workflow_id.alter(name='fk_workflow')
table.c.algorithm_id.alter(name='fk_algorithm')
table.c.resulted_op_id.alter(name='fk_operation')
table = _prepare_table(meta, 'MAPPED_DATATYPE_MEASURE')
table.c.analyzed_datatype.alter(name='_analyzed_datatype')
## Fix Lookup Table mapping.
table = _prepare_table(meta, 'MAPPED_LOOK_UP_TABLE_DATA')
create_column(COL_1, table)
create_column(COL_2, table)
create_column(COL_3, table)
create_column(COL_4, table)
create_column(COL_5, table)
create_column(COL_6, table)
create_column(COL_7, table)
session = SA_SESSIONMAKER()
session.execute(text('DELETE FROM "MAPPED_LOOK_UP_TABLE_DATA";'))
session.execute(text('insert into "MAPPED_LOOK_UP_TABLE_DATA"(id, _equation, _number_of_values, _invdx, _xmax, _xmin, _df, _dx, _data) '
'select id, \'\', _number_of_values, _invdx, _xmax, _xmin, _df, _dx, _data from "MAPPED_NERF_TABLE_DATA";'))
session.execute(text('insert into "MAPPED_LOOK_UP_TABLE_DATA"(id, _equation, _number_of_values, _invdx, _xmax, _xmin, _df, _dx, _data) '
'select id, \'\', _number_of_values, _invdx, _xmax, _xmin, _df, _dx, _data from "MAPPED_PSI_TABLE_DATA";'))
session.commit()
session.close()
table = _prepare_table(meta, 'MAPPED_NERF_TABLE_DATA')
table.drop()
table = _prepare_table(meta, 'MAPPED_PSI_TABLE_DATA')
table.drop()
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()
