def migrate(uri: str, archive_uri: str, case_id: str, dry: bool, force: bool):
"""Update all information that was manually annotated from a old instance."""
scout_client = MongoClient(uri)
scout_database = scout_client[uri.rsplit('/', 1)[-1]]
scout_adapter = MongoAdapter(database=scout_database)
scout_case = scout_adapter.case(case_id)
if not force and scout_case.get('is_migrated'):
print("case already migrated")
return
archive_client = MongoClient(archive_uri)
archive_database = archive_client[archive_uri.rsplit('/', 1)[-1]]
archive_case = archive_database.case.find_one({
'owner':
scout_case['owner'],
'display_name':
scout_case['display_name']
})
archive_data = archive_info(archive_database, archive_case)
if dry:
print(ruamel.yaml.safe_dump(archive_data))
else:
#migrate_case(scout_adapter, scout_case, archive_data)
pass
def load_delivery_report(adapter: MongoAdapter,
report_path: str,
case_id: str,
update: bool = False):
"""Load a delivery report into a case in the database
If the report already exists the function will exit.
If the user want to load a report that is already in the database
'update' has to be 'True'
Args:
adapter (MongoAdapter): Connection to the database
report_path (string): Path to delivery report
case_id (string): Optional case identifier
update (bool): If an existing report should be replaced
Returns:
updated_case(dict)
"""
case_obj = adapter.case(case_id=case_id)
if case_obj is None:
raise DataNotFoundError("no case found")
if update or case_obj.get("delivery_report") is None:
_update_report_path(case_obj, report_path, "delivery_report")
else:
raise IntegrityError("Existing report found, use update = True to "
"overwrite")
LOG.info("Saving report for case {} in database".format(case_obj["_id"]))
return adapter.replace_case(case_obj)
def real_database(request, database_name, institute_obj, user_obj, genes,
parsed_panel):
"""Setup a real database with populated data"""
mongo_client = pymongo.MongoClient()
mongo_client.drop_database(database_name)
database = mongo_client[database_name]
adapter = MongoAdapter(database)
# Populate the database
adapter.add_institute(institute_obj)
adapter.add_user(user_obj)
load_hgnc_genes(adapter, genes)
adapter.hgnc_collection.create_index([('build', pymongo.ASCENDING),
('hgnc_symbol', pymongo.ASCENDING)])
adapter.load_panel(parsed_panel=parsed_panel)
# load_hpo(adapter=gene_database, hpo_lines=hpo_terms_handle, disease_lines=genemap_handle)
# adapter.add_case(case_obj)
# for variant in variant_objs:
# adapter.load_variant(variant)
def teardown():
mongo_client.drop_database(database_name)
request.addfinalizer(teardown)
return adapter
def setup(context, institute, user_mail, user_name):
"""
Setup scout instances: a demo database or a production database, according to the
according to the subcommand specified by user.
"""
setup_config = {
"institute_name": institute,
"user_name": user_name,
"user_mail": user_mail,
}
mongodb_name = current_app.config["MONGO_DBNAME"]
client = current_app.config["MONGO_CLIENT"]
if context.invoked_subcommand == "demo":
# Modify the name of the database that will be created
LOG.debug("Change database name to scout-demo")
mongodb_name = "scout-demo"
mongo_database = client[mongodb_name]
LOG.info("Test if mongod is running")
try:
mongo_database.test.find_one()
except ServerSelectionTimeoutError as err:
LOG.warning("Connection could not be established")
LOG.warning("Please check if mongod is running")
LOG.warning(err)
raise click.Abort()
setup_config["mongodb"] = mongodb_name
setup_config["adapter"] = MongoAdapter(mongo_database)
context.obj = setup_config
def upload_research_variants(
adapter: MongoAdapter,
case_obj: dict,
variant_type: str,
category: str,
rank_treshold: int,
):
"""Delete existing variants and upload new variants"""
adapter.delete_variants(case_id=case_obj["_id"], variant_type=variant_type, category=category)
LOG.info("Load %s %s for: %s", variant_type, category.upper(), case_obj["_id"])
adapter.load_variants(
case_obj=case_obj,
variant_type=variant_type,
category=category,
rank_threshold=rank_treshold,
)
def load_delivery_report(adapter: MongoAdapter,
report_path: str,
case_id: str,
update: bool = False):
""" Load a delivery report into a case in the database
If the report already exists the function will exit.
If the user want to load a report that is already in the database
'update' has to be 'True'
Args:
adapter (MongoAdapter): Connection to the database
report_path (string): Path to delivery report
case_id (string): Optional case identifier
update (bool): If an existing report should be replaced
Returns:
updated_case(dict)
"""
case_obj = adapter.case(
case_id=case_id,
)
if case_obj is None:
raise DataNotFoundError("no case found")
if not case_obj.get('delivery_report'):
_put_report_in_case_root(case_obj, report_path)
else:
if update:
_put_report_in_case_root(case_obj, report_path)
else:
raise IntegrityError('Existing delivery report found, use update = True to '
'overwrite')
logger.info('Saving report for case {} in database'.format(case_obj['_id']))
return adapter.replace_case(case_obj)
def migrate_case(adapter: MongoAdapter, scout_case: dict, archive_data: dict):
"""Migrate case information from archive."""
# update collaborators
collaborators = list(
set(scout_case['collaborators'] + archive_data['collaborators']))
if collaborators != scout_case['collaborators']:
LOG.info(f"set collaborators: {', '.join(collaborators)}")
scout_case['collaborators'] = collaborators
# update assignees
if len(scout_case.get('assignees', [])) == 0:
scout_user = adapter.user(archive_data['assignee'])
if scout_user:
scout_case['assignees'] = [archive_data['assignee']]
else:
LOG.warning(
f"{archive_data['assignee']}: unable to find assigned user")
# add/update suspected/causative variants
for key in ['suspects', 'causatives']:
scout_case[key] = scout_case.get(key, [])
for archive_variant in archive_data[key]:
variant_id = get_variantid(archive_variant, scout_case['_id'])
scout_variant = adapter.variant(variant_id)
if scout_variant:
if scout_variant['_id'] in scout_case[key]:
LOG.info(
f"{scout_variant['_id']}: variant already in {key}")
else:
LOG.info(f"{scout_variant['_id']}: add to {key}")
scout_variant[key].append(scout_variant['_id'])
else:
LOG.warning(
f"{scout_variant['_id']}: unable to find variant ({key})")
scout_variant[key].append(variant_id)
if not scout_case.get('synopsis'):
# update synopsis
scout_case['synopsis'] = archive_data['synopsis']
scout_case['is_migrated'] = True
adapter.case_collection.find_one_and_replace(
{'_id': scout_case['_id']},
scout_case,
)
# add/update phenotype groups/terms
scout_institute = adapter.institute(scout_case['owner'])
scout_user = adapter.user('*****@*****.**')
for key in ['phenotype_terms', 'phenotype_groups']:
for archive_term in archive_data[key]:
adapter.add_phenotype(
institute=scout_institute,
case=scout_case,
user=scout_user,
link=f"/{scout_case['owner']}/{scout_case['display_name']}",
hpo_term=archive_term['phenotype_id'],
is_group=key == 'phenotype_groups',
)
def get_case_and_institute(
adapter: MongoAdapter, case_id: str, institute: Optional[str]
) -> (str, str):
"""Fetch the case_id and institute_id
There was an old way to create case ids so we need a special case to handle this.
For old case_id we assume institute-case combo
We check if first part of the case_id is institute, then we know it is the old format
"""
if institute:
return case_id, institute
split_case = case_id.split("-")
institute_id = None
if len(split_case) > 1:
institute_id = split_case[0]
institute_obj = adapter.institute(institute_id)
if institute_obj:
institute_id = institute_obj["_id"]
case_id = split_case[1]
return case_id, institute_id
"""Code for extensions used by flask""" from flask_bootstrap import Bootstrap from flask_debugtoolbar import DebugToolbarExtension from flask_ldap3_login import LDAP3LoginManager from flask_login import LoginManager from authlib.integrations.flask_client import OAuth from flask_mail import Mail from scout.adapter import MongoAdapter from .loqus_extension import LoqusDB from .mongo_extension import MongoDB toolbar = DebugToolbarExtension() bootstrap = Bootstrap() store = MongoAdapter() login_manager = LoginManager() ldap_manager = LDAP3LoginManager() oauth_client = OAuth() mail = Mail() loqusdb = LoqusDB() mongo = MongoDB()