Python SA_SESSIONMAKER.execute方法代码示例

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
def _transfer_projection_matrices():
    """
    Previous ProjectionRegionM/EEG objects should be Removed,
    and ProjectionSurfaceM/EEG should be transported into the new DB tables.
    """
    session = SA_SESSIONMAKER()
    LOGGER.info("Transferring Projections Surface ...")

    try:
        # Ony after SqlAlchemy finished initialization the new table MAPPED_PROJECTION_DATA exists
        session.execute(text("""INSERT into "MAPPED_PROJECTION_DATA" (id, _sources, _sensors, _projection_type)
                            SELECT PS.id, PM._sources, PM._sensors, 'projEEG'
                            FROM "MAPPED_PROJECTION_SURFACE_EEG_DATA" PS, "MAPPED_PROJECTION_MATRIX_DATA" PM
                            WHERE PM.id=PS.id;"""))

        session.execute(text("""INSERT into "MAPPED_PROJECTION_DATA" (id, _sources, _sensors, _projection_type)
                            SELECT PS.id, PM._sources, PM._sensors, 'projMEG'
                            FROM "MAPPED_PROJECTION_SURFACE_MEG_DATA" PS, "MAPPED_PROJECTION_MATRIX_DATA" PM
                            WHERE PM.id=PS.id;"""))

        session.execute(text("""DROP TABLE "MAPPED_PROJECTION_SURFACE_EEG_DATA";"""))
        session.execute(text("""DROP TABLE "MAPPED_PROJECTION_SURFACE_MEG_DATA";"""))
        session.execute(text("""DROP TABLE "MAPPED_PROJECTION_MATRIX_DATA";"""))

        LOGGER.info("Removing Projections Region ...")

        session.execute(text("""DELETE from "DATA_TYPES"
                            WHERE type in ('ProjectionRegionEEG', 'ProjectionRegionMEG');"""))
        session.commit()

    except Exception:
        LOGGER.exception("Could not update Projection references")

    finally:
        session.close()

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
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

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
def reset_database():
    """
    Remove all tables in DB.
    """
    LOGGER.warning("Your Database tables will be deleted.")
    try:
        session = SA_SESSIONMAKER()
        LOGGER.debug("Delete connection initiated.")
        inspector = reflection.Inspector.from_engine(session.connection())
        for table in inspector.get_table_names():
            try:
                LOGGER.debug("Removing:" + table)
                session.execute(text("DROP TABLE \"%s\" CASCADE" % table))
            except Exception:
                try:
                    session.execute(text("DROP TABLE %s" % table))
                except Exception as excep1:
                    LOGGER.error("Could no drop table %s", table)
                    LOGGER.exception(excep1)
        session.commit()
        LOGGER.info("Database was cleanup!")
    except Exception as excep:
        LOGGER.warning(excep)
    finally:
        session.close()

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
def remove_visualizer_references():
    """
    As we removed an algorithm, remove left-overs.
    """

    LOGGER.info("Starting to remove references towards old viewer ....")

    session = SA_SESSIONMAKER()
    try:
        session.execute(text(
            """DELETE FROM "OPERATIONS" WHERE fk_from_algo IN
               (SELECT A.id FROM "ALGORITHMS" A, "ALGORITHM_GROUPS" AG
               WHERE  A.fk_algo_group = AG.id AND module = 'tvb.adapters.visualizers.cross_correlation'
                      AND classname = 'PearsonCorrelationCoefficientVisualizer');"""))

        session.execute(text(
            """DELETE FROM "WORKFLOW_VIEW_STEPS" WHERE fk_algorithm IN
               (SELECT A.id FROM "ALGORITHMS" A, "ALGORITHM_GROUPS" AG
               WHERE  A.fk_algo_group = AG.id AND module = 'tvb.adapters.visualizers.cross_correlation'
                      AND classname = 'PearsonCorrelationCoefficientVisualizer');"""))
        session.commit()
    except Exception as excep:
        LOGGER.exception(excep)
    finally:
        session.close()

    LOGGER.info("References removed.")

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
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)

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
def upgrade(_migrate_engine):
    """
    Upgrade operations go here.
    Don't create your own engine; bind migrate_engine to your metadata.
    """
    session = SA_SESSIONMAKER()
    session.execute(text("DROP TABLE \"MAPPED_STRUCTURAL_MRI_DATA\""))
    session.commit()
    session.close()

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
def change_algorithm(module, classname, new_module, new_class):
    """
    Change module and classname fields in ALGORITHM_GROUPS table.
    """
    session = SA_SESSIONMAKER()
    try:
        session.execute(text(
            """UPDATE "ALGORITHM_GROUPS"
               SET module = '""" + new_module + """', classname = '""" + new_class + """'
               WHERE module = '""" + module + """' AND classname = '""" + classname + """';"""))
        session.commit()
    except Exception, excep:
        LOGGER.exception(excep)

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
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()

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
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)

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
def downgrade(_migrate_engine):
    """Operations to reverse the above upgrade go here."""
    try:
        session = SA_SESSIONMAKER()
        session.execute(text("""UPDATE "BURST_CONFIGURATIONS" SET _simulator_configuration =
                                REPLACE(REPLACE(_simulator_configuration, "range_1", "first_range"),
                                                                          "range_2", "second_range");"""))
        session.execute(text("""UPDATE "OPERATIONS" SET parameters =
                                REPLACE(REPLACE(parameters, "range_1", "first_range"), "range_2", "second_range");"""))
        session.commit()
        session.close()
    except Exception as excep:
        ## This update is not critical. We can run even in case of error at update
        logger = get_logger(__name__)
        logger.exception(excep)

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
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()

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
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)

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
def upgrade(_migrate_engine):
    """
    Upgrade operations go here.
    Don't create your own engine; bind migrate_engine to your metadata.
    """
    try:
        session = SA_SESSIONMAKER()
        session.execute(text("""UPDATE "BURST_CONFIGURATIONS" SET _simulator_configuration =
                                REPLACE(REPLACE(_simulator_configuration, "first_range", "range_1"),
                                                                          "second_range", "range_2");"""))
        session.execute(text("""UPDATE "OPERATIONS" SET parameters =
                                REPLACE(REPLACE(parameters, "first_range", "range_1"), "second_range", "range_2");"""))
        session.commit()
        session.close()
    except Exception, excep:
        ## This update is not critical. We can run even in case of error at update
        logger = get_logger(__name__)
        logger.exception(excep)

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
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');"""))

# 需要导入模块: from tvb.core.entities.storage import SA_SESSIONMAKER [as 别名]
# 或者: from tvb.core.entities.storage.SA_SESSIONMAKER import execute [as 别名]
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()