Commit ffe46d58 authored by Jay's avatar Jay
Browse files

Streamlines connections to the DB

parent 6ef538d5

autocnet/graph/cluster_submit.py

+1 −1
Original line number Original line Diff line number Diff line
@@ -215,7 +215,7 @@ def main(): # pragma: no cover 
    logging.basicConfig(level=os.environ.get("AUTOCNET_LOGLEVEL", "INFO"))

    logging.basicConfig(level=os.environ.get("AUTOCNET_LOGLEVEL", "INFO"))

    # Get the message

    # Get the message

    queue = StrictRedis(host=args['host'], port=args['port'], db=0,

    queue = StrictRedis(host=args['host'], port=args['port'], db=0,

                        socket_timeout=30, socket_connect_timeout=300)

                        socket_timeout=30, socket_connect_timeout=30)

    manage_messages(args, queue)

    manage_messages(args, queue)





if __name__ == '__main__':

if __name__ == '__main__':

autocnet/graph/network.py

+1 −1
Original line number Original line Diff line number Diff line
@@ -2418,7 +2418,7 @@ class NetworkCandidateGraph(CandidateGraph): 
        >>> ncg.add_from_remote_database(source_db_config, outpath, query_string=query)

        >>> ncg.add_from_remote_database(source_db_config, outpath, query_string=query)

        """

        """





        sourceSession, _ = new_connection(source_db_config)

        sourceSession, _ = new_connection(source_db_config, with_session=True)

        sourcesession = sourceSession()

        sourcesession = sourceSession()





        sourceimages = sourcesession.execute(query_string).fetchall()

        sourceimages = sourcesession.execute(query_string).fetchall()

autocnet/io/db/connection.py

+9 −6
Original line number Original line Diff line number Diff line
@@ -29,8 +29,8 @@ def retry(max_retries=5, wait_time=300): 
        return wrapper

        return wrapper

    return decorator

    return decorator





@retry

@retry()

def new_connection(dbconfig):

def new_connection(dbconfig, with_session=False):

    """

    """

    Using the user supplied config create a NullPool database connection.

    Using the user supplied config create a NullPool database connection.
@@ -40,6 +40,8 @@ def new_connection(dbconfig): 
               Dictionary defining necessary parameters for the database

               Dictionary defining necessary parameters for the database

               connection

               connection





    with_session : boolean

                   If true return a SQL Alchemy session factory. Default False.

    Returns

    Returns

    -------

    -------

    Session : object

    Session : object
@@ -57,8 +59,9 @@ def new_connection(dbconfig): 
    engine = create_engine(db_uri,

    engine = create_engine(db_uri,

                poolclass=pool.NullPool,

                poolclass=pool.NullPool,

                connect_args={"application_name":f"AutoCNet_{hostname}"},

                connect_args={"application_name":f"AutoCNet_{hostname}"},

                isolation_level="AUTOCOMMIT",

                pool_pre_ping=True)

                pool_pre_ping=True)

    if with_session:

        Session = orm.sessionmaker(bind=engine, autocommit=False)

        Session = orm.sessionmaker(bind=engine, autocommit=False)

        log.debug(Session, engine)

        log.debug(Session, engine)

        return Session, engine

        return Session, engine

    return engine

autocnet/matcher/subpixel.py

+3 −1
Original line number Original line Diff line number Diff line
@@ -1156,7 +1156,9 @@ def validate_candidate_measure(point, 
    sample = measure_to_register['sample']

    sample = measure_to_register['sample']

    line = measure_to_register['line']

    line = measure_to_register['line']





    log.info(f'Validating measure: {measure_to_register['id']} on image: {source_imageid}')

    mid = measure_to_register['id']

    sid = measure_to_register['imageid']

    log.info(f'Validating measure: {mid} on image: {sid}')





    reference_roi = roi.Roi(source_node.geodata, 

    reference_roi = roi.Roi(source_node.geodata, 

                            sample, 

                            sample,

autocnet/spatial/overlap.py

+2 −2
Original line number Original line Diff line number Diff line
@@ -228,7 +228,7 @@ def place_points_in_overlap(overlap, 
    log.info(f'Have {len(candidate_points)} potential points to place in overlap {overlap.id}.')

    log.info(f'Have {len(candidate_points)} potential points to place in overlap {overlap.id}.')

    

    

    nodes = get_nodes_for_overlap(ncg, session, overlap)

    nodes = get_nodes_for_overlap(ncg, session, overlap)



    logging.debug(f'Nodes: {nodes}')

    points_to_commit = []

    points_to_commit = []

    for valid in candidate_points:

    for valid in candidate_points:

        log.debug(f'Valid point: {valid}')

        log.debug(f'Valid point: {valid}')