view galaxy-tools/biobank/updater/merge_individuals.py @ 0:ba6cf6ede027 draft default tip

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#======================================= 
# This tool moves all informations related to an individual (source) to
# another (target). Moved informations are:
# * children (Individual objects)
# * ActionOnInvidual
# * Enrollments
# * EHR records
#
# The tool expects as input a TSV file like this
#   source                               target
#   V0468D2D96999548BF9FC6AD24C055E038   V060BAA01C662240D181BB98A51885C498
#   V029CC0A614E2D42D0837602B15193EB58   V01B8122A7C75A452E9F80381CEA988557
#   V0B20C93E8A88D43EFB87A7E6911292A05   V0BED85E8E76A54AA7AB0AFB09F95798A8
#   ...
#
# NOTE WELL: 
# * Parents of the "source" indivudal WILL NOT BE ASSIGNED
#   to the "target" individual
# * For the Enrollmnent objects, if
#   "target" individual has already a code in the same study of "source"
#   individual, the script will try to move the Enrollment to the
#   "duplicated" study (this will be fixed when a proper ALIASES
#   manegement will be introduced)
# =======================================

import sys, argparse, csv, time, json, os

from bl.vl.kb import KnowledgeBase as KB
from bl.vl.kb import KBError
import bl.vl.utils.ome_utils as vlu
from bl.vl.utils import get_logger, LOG_LEVELS


def make_parser():
    parser = argparse.ArgumentParser(description='merge informations related to an individual ("source") to another one ("target")')
    parser.add_argument('--logfile', type=str, help='log file (default=stderr)')
    parser.add_argument('--loglevel', type=str, choices = LOG_LEVELS,
                        help='logging level (default=INFO)', default='INFO')
    parser.add_argument('-H', '--host', type=str, help='omero hostname')
    parser.add_argument('-U', '--user', type=str, help='omero user')
    parser.add_argument('-P', '--passwd', type=str, help='omero password')
    parser.add_argument('-O', '--operator', type=str, help='operator',
                        required=True)
    parser.add_argument('--in_file', type=str, required = True,
                        help='input TSV file')
    return parser


def update_object(obj, backup_values, operator, kb, logger):
    logger.debug('Building ActionOnAction for object %s::%s' %
                 (obj.get_ome_table(),
                  obj.id)
                 )
    act_setup = build_action_setup('merge-individuals-%f' % time.time(),
                                   backup_values, kb)
    aoa_conf = {
        'setup': act_setup,
        'actionCategory' : kb.ActionCategory.UPDATE,
        'operator': operator,
        'target': obj.lastUpdate if obj.lastUpdate else obj.action,
        'context': obj.action.context
        }
    logger.debug('Updating object with new ActionOnAction')
    obj.lastUpdate = kb.factory.create(kb.ActionOnAction, aoa_conf)


def build_action_setup(label, backup, kb, logger):
    logger.debug('Creating a new ActionSetup with label %s and backup %r' % (label, backup))
    conf = {
        'label': label,
        'conf': json.dumps({'backup' : backup})
        }
    asetup = kb.factory.create(kb.ActionSetup, conf)
    return asetup


def update_children(source_ind, target_ind, operator, kb, logger):
    if source_ind.gender.enum_label() == kb.Gender.MALE.enum_label():
        parent_type = 'father'
    elif source_ind.gender.enum_label() == kb.Gender.FEMALE.enum_label():
        parent_type = 'mother'
    else:
        raise ValueError('%s is not a valid gender value' % (source_ind.gender.enum_label()))
    query = '''
            SELECT ind FROM Individual ind
            JOIN ind.{0} AS {0}
            WHERE {0}.vid = :parent_vid
            '''.format(parent_type)
    children = kb.find_all_by_query(query, {'parent_vid' : source_ind.id})
    logger.info('Retrieved %d children for source individual' % len(children))
    for child in children:
        backup = {}
        logger.debug('Changing %s for individual %s' % (parent_type,
                                                        child.id))
        backup[parent_type] = getattr(child, parent_type).id
        setattr(child, parent_type, target_ind)
        update_object(child, backup, operator, kb)
    kb.save_array(children)


def update_action_on_ind(source_ind, target_ind, operator, kb, logger):
    query = '''SELECT act FROM ActionOnIndividual act
               JOIN act.target AS ind
               WHERE ind.vid = :ind_vid
            '''
    src_acts = kb.find_all_by_query(query, {'ind_vid' : source_ind.id})
    logger.info('Retrieved %d actions for source individual' % len(src_acts))
    connected = kb.dt.get_connected(source_ind, direction=kb.dt.DIRECTION_OUTGOING, 
                                    query_depth=1)
    if source_ind in connected:
        connected.remove(source_ind)
    for sa in src_acts:
        logger.debug('Changing target for action %s' % sa.id)
        sa.target = target_ind
        logger.debug('Action %s target updated' % sa.id)
    kb.save_array(src_acts)
    for conn in connected:
        kb.dt.destroy_edge(source_ind, conn)
        kb.dt.create_edge(conn.action, target_ind, conn)


def update_enrollments(source_ind, target_ind, operator, kb, logger):
    query = '''SELECT en FROM Enrollment en
               JOIN en.individual AS ind
               WHERE ind.vid = :ind_vid
            '''
    enrolls = kb.find_all_by_query(query, {'ind_vid' : source_ind.id})
    logger.info('Retrieved %d enrollments for source individual' % len(enrolls))
    for sren in enrolls:
        try:
            sren.individual = target_ind
            logger.debug('Changing individual for enrollment %s in study %s' % (sren.studyCode,
                                                                                sren.study.label))
            kb.save(sren)
            logger.info('Changed individual for enrollment %s (study code %s -- study %s)' % (sren.id,
                                                                                              sren.studyCode,
                                                                                              sren.study.label))
        except KBError, kbe:
            logger.warning('Unable to update enrollment %s (study code %s -- study %s)' % (sren.id,
                                                                                           sren.studyCode,
                                                                                           sren.study.label))
            move_to_duplicated(sren, operator, kb, logger)


def update_ehr_records(source_ind, target_ind, kb):
    kb.update_table_rows(kb.eadpt.EAV_EHR_TABLE, '(i_vid == "%s")' % source_ind.id,
                         {'i_vid' : target_ind.id})
                                    

# This method should be considered as a temporary hack that will be
# used untill a proper ALIAS management will be introduced into the
# system
def move_to_duplicated(enrollment, operator, kb, logger):
    old_st = enrollment.study
    dupl_st = kb.get_study('%s_DUPLICATI' % old_st.label)
    if not dupl_st:
        logger.warning('No "duplicated" study ({0}_DUPLICATI) found for study {0}'.format(old_st.label))
        return
    enrollment.study = dupl_st
    try:
        kb.save(enrollment)
        logger.info('Enrollmnet %s moved from study %s to study %s' % (enrollment.studyCode,
                                                                       old_st.label, dupl_st.label))
    except:
        logger.error('An error occurred while moving enrollment %s from study %s to %s' % (enrollment.studyCode,
                                                                                           old_st.label,
                                                                                           dupl_st.label))


def main(argv):
    parser = make_parser()
    args = parser.parse_args(argv)

    logger = get_logger('merge_individuals', level=args.loglevel,
                         filename=args.logfile)

    try:
        host = args.host or vlu.ome_host()
        user = args.user or vlu.ome_user()
        passwd = args.passwd or vlu.ome_passwd()
    except ValueError, ve:
        logger.critical(ve)
        sys.exit(ve)

    kb = KB(driver='omero')(host, user, passwd)

    logger.debug('Retrieving Individuals')
    individuals = kb.get_objects(kb.Individual)
    logger.debug('Retrieved %d Individuals' % len(individuals))
    ind_lookup = {}
    for i in individuals:
        ind_lookup[i.id] = i

    with open(args.in_file) as in_file:
        reader = csv.DictReader(in_file, delimiter='\t')
        for row in reader:            
            try:
                source = ind_lookup[row['source']]
                logger.info('Selected as source individual with ID %s' % source.id)
                target = ind_lookup[row['target']]
                logger.info('Selected as destination individual with ID %s' % target.id)
            except KeyError, ke:
                logger.warning('Unable to retrieve individual with ID %s, skipping row' % ke)
                continue

            logger.info('Updating children connected to source individual')
            update_children(source, target, args.operator, kb, logger)
            logger.info('Children update complete')

            logger.info('Updating ActionOnIndividual related to source individual')
            update_action_on_ind(source, target, args.operator, kb, logger)
            logger.info('ActionOnIndividual update completed')

            logger.info('Updating enrollments related to source individual')
            update_enrollments(source, target, args.operator, kb, logger)
            logger.info('Enrollments update completed')
            
            logger.info('Updating EHR records related to source individual')
            update_ehr_records(source, target, kb)
            logger.info('EHR records update completed')
    
if __name__ == '__main__':
    main(sys.argv[1:])