def update_panels(context, mongodb, username, password, authdb, host, port, loglevel, config):
"""scout: manage interactions with a scout instance."""
coloredlogs.install(level=loglevel)
LOG.info("Running scout version %s", __version__)
LOG.debug("Debug logging enabled.")
mongo_config = {}
cli_config = {}
if config:
LOG.debug("Use config file %s", config)
with open(config, 'r') as in_handle:
cli_config = yaml.load(in_handle, Loader=yaml.FullLoader)
mongo_config['mongodb'] = (mongodb or cli_config.get('mongodb') or 'scout')
mongo_config['host'] = (host or cli_config.get('host') or 'localhost')
mongo_config['port'] = (port or cli_config.get('port') or 27017)
mongo_config['username'] = username or cli_config.get('username')
mongo_config['password'] = password or cli_config.get('password')
mongo_config['authdb'] = authdb or cli_config.get('authdb') or mongo_config['mongodb']
mongo_config['omim_api_key'] = cli_config.get('omim_api_key')
LOG.info("Setting database name to %s", mongo_config['mongodb'])
LOG.debug("Setting host to %s", mongo_config['host'])
LOG.debug("Setting port to %s", mongo_config['port'])
valid_connection = check_connection(
host=mongo_config['host'],
port=mongo_config['port'],
username=mongo_config['username'],
password=mongo_config['password'],
authdb=mongo_config['authdb'],
)
LOG.info("Test if mongod is running")
if not valid_connection:
LOG.warning("Connection could not be established")
context.abort()
try:
client = get_connection(**mongo_config)
except ConnectionFailure:
context.abort()
database = client[mongo_config['mongodb']]
LOG.info("Setting up a mongo adapter")
mongo_config['client'] = client
adapter = MongoAdapter(database)
requests = []
for case_obj in adapter.case_collection.find():
# pp(case_obj)
gene_to_panels = adapter.gene_to_panels(case_obj)
variants = adapter.variant_collection.find({
'case_id': case_obj['_id'],
'category': 'snv',
'variant_type': 'clinical',
})
for variant_obj in variants:
panel_names = set()
for hgnc_id in variant_obj['hgnc_ids']:
gene_panels = gene_to_panels.get(hgnc_id, set())
panel_names = panel_names.union(gene_panels)
if panel_names:
operation = pymongo.UpdateOne(
{'_id': variant_obj['_id']},
{
'$set': {
'panels': list(panel_names)
}
})
requests.append(operation)
if len(requests) > 5000:
adapter.variant_collection.bulk_write(requests, ordered=False)
requests = []
if requests:
adapter.variant_collection.bulk_write(requests, ordered=False)
requests = []
def update_panels(context, mongodb, username, password, authdb, host, port,
loglevel, config):
"""scout: manage interactions with a scout instance."""
coloredlogs.install(level=loglevel)
LOG.info("Running scout version %s", __version__)
LOG.debug("Debug logging enabled.")
mongo_config = {}
cli_config = {}
if config:
LOG.debug("Use config file %s", config)
with open(config, "r") as in_handle:
cli_config = yaml.load(in_handle, Loader=yaml.FullLoader)
mongo_config["mongodb"] = mongodb or cli_config.get("mongodb") or "scout"
mongo_config["host"] = host or cli_config.get("host") or "localhost"
mongo_config["port"] = port or cli_config.get("port") or 27017
mongo_config["username"] = username or cli_config.get("username")
mongo_config["password"] = password or cli_config.get("password")
mongo_config["authdb"] = (authdb or cli_config.get("authdb")
or mongo_config["mongodb"])
mongo_config["omim_api_key"] = cli_config.get("omim_api_key")
LOG.info("Setting database name to %s", mongo_config["mongodb"])
LOG.debug("Setting host to %s", mongo_config["host"])
LOG.debug("Setting port to %s", mongo_config["port"])
valid_connection = check_connection(
host=mongo_config["host"],
port=mongo_config["port"],
username=mongo_config["username"],
password=mongo_config["password"],
authdb=mongo_config["authdb"],
)
LOG.info("Test if mongod is running")
if not valid_connection:
LOG.warning("Connection could not be established")
context.abort()
try:
client = get_connection(**mongo_config)
except ConnectionFailure:
context.abort()
database = client[mongo_config["mongodb"]]
LOG.info("Setting up a mongo adapter")
mongo_config["client"] = client
adapter = MongoAdapter(database)
requests = []
for case_obj in adapter.case_collection.find():
# pp(case_obj)
gene_to_panels = adapter.gene_to_panels(case_obj)
variants = adapter.variant_collection.find({
"case_id": case_obj["_id"],
"category": "snv",
"variant_type": "clinical"
})
for variant_obj in variants:
panel_names = set()
for hgnc_id in variant_obj["hgnc_ids"]:
gene_panels = gene_to_panels.get(hgnc_id, set())
panel_names = panel_names.union(gene_panels)
if panel_names:
operation = pymongo.UpdateOne(
{"_id": variant_obj["_id"]},
{"$set": {
"panels": list(panel_names)
}})
requests.append(operation)
if len(requests) > 5000:
adapter.variant_collection.bulk_write(requests, ordered=False)
requests = []
if requests:
adapter.variant_collection.bulk_write(requests, ordered=False)
requests = []
def update_panels(context, mongodb, username, password, authdb, host, port,
loglevel, config):
"""scout: manage interactions with a scout instance."""
coloredlogs.install(level=loglevel)
LOG.info("Running scout version %s", __version__)
LOG.debug("Debug logging enabled.")
mongo_config = {}
cli_config = {}
if config:
LOG.debug("Use config file %s", config)
with open(config, 'r') as in_handle:
cli_config = yaml.load(in_handle)
mongo_config['mongodb'] = (mongodb or cli_config.get('mongodb') or 'scout')
mongo_config['host'] = (host or cli_config.get('host') or 'localhost')
mongo_config['port'] = (port or cli_config.get('port') or 27017)
mongo_config['username'] = username or cli_config.get('username')
mongo_config['password'] = password or cli_config.get('password')
mongo_config['authdb'] = authdb or cli_config.get(
'authdb') or mongo_config['mongodb']
mongo_config['omim_api_key'] = cli_config.get('omim_api_key')
LOG.info("Setting database name to %s", mongo_config['mongodb'])
LOG.debug("Setting host to %s", mongo_config['host'])
LOG.debug("Setting port to %s", mongo_config['port'])
valid_connection = check_connection(
host=mongo_config['host'],
port=mongo_config['port'],
username=mongo_config['username'],
password=mongo_config['password'],
authdb=mongo_config['authdb'],
)
LOG.info("Test if mongod is running")
if not valid_connection:
LOG.warning("Connection could not be established")
context.abort()
try:
client = get_connection(**mongo_config)
except ConnectionFailure:
context.abort()
database = client[mongo_config['mongodb']]
LOG.info("Setting up a mongo adapter")
mongo_config['client'] = client
adapter = MongoAdapter(database)
requests = []
for case_obj in adapter.case_collection.find():
# pp(case_obj)
gene_to_panels = adapter.gene_to_panels(case_obj)
variants = adapter.variant_collection.find({
'case_id': case_obj['_id'],
'category': 'snv',
'variant_type': 'clinical',
})
for variant_obj in variants:
panel_names = set()
for hgnc_id in variant_obj['hgnc_ids']:
gene_panels = gene_to_panels.get(hgnc_id, set())
panel_names = panel_names.union(gene_panels)
if panel_names:
operation = pymongo.UpdateOne(
{'_id': variant_obj['_id']},
{'$set': {
'panels': list(panel_names)
}})
requests.append(operation)
if len(requests) > 5000:
adapter.variant_collection.bulk_write(requests, ordered=False)
requests = []
if requests:
adapter.variant_collection.bulk_write(requests, ordered=False)
requests = []