def populate(
dal: DalClinicalTrials,
num_days: Optional[int] = None,
chunk_size: Optional[int] = 1000,
skip_populated: Optional[bool] = False,
dry_run: Optional[bool] = False,
):
with dal.session_scope() as session: # type: sqlalchemy.orm.Session
studies_chunks = find_recent_studies(
session=session,
num_days=num_days,
chunk_size=chunk_size,
skip_populated=skip_populated,
)
for studies_chunk in studies_chunks:
studies = list(studies_chunk) # type: List[Study]
logger.warning(len(studies))
for study in studies:
logger.info(f"Processing study with ID {study.study_id}")
for location in study.locations:
logger.info(
f"Processing location with ID {location.location_id}")
facility_id = location.facility_id
facility_canonical_id = (
location.facility.facility_canonical_id)
_prefix = "[DRY RUN] " if dry_run else ""
logger.info(
f"{_prefix}IODUing `StudyFacility` with a `study_id`"
f" of '{study.study_id}', `facility_id` of "
f"{facility_id}, and `facility_canonical_id` of "
f"'{facility_canonical_id}'.")
if not dry_run:
dal.iodu_study_facility(
study_id=study.study_id,
facility_id=facility_id,
facility_canonical_id=facility_canonical_id,
)
def find_recent_unmatched_facilities(dal: DalClinicalTrials):
with dal.session_scope() as session: # type: sqlalchemy.orm.Session
query = session.query(Facility)
query = query.join(Facility.studies)
query = query.join(Study.study_dates)
# Filter down to facilities not matched with a canonical facility.
query = query.filter(Facility.facility_canonical_id.is_(None))
# Filter down to studies updated in the last 2 days.
query = query.filter(
StudyDates.last_update_posted > (datetime.date.today() -
datetime.timedelta(days=2)))
query = query.group_by(Facility.facility_id)
facilities_unmatched = query.all()
return facilities_unmatched
def match(dal: DalClinicalTrials, retriever: RetrieverGoogleMaps):
logger.info(
"Retrieving unmatched facilities linked to studies updated in the "
"past 2 days.")
facilities_unmatched = find_recent_unmatched_facilities(dal=dal)
logger.info(
f"Retrieved {len(facilities_unmatched)} unmatched facilities linked "
f"to studies updated in the past 2 days.")
for facility in facilities_unmatched:
logger.info(f"Processing facility {facility}.")
logger.info(f"Matching facility {facility} against a Google Place.")
place_response = find_facility_google_place(retriever=retriever,
facility=facility)
# Skip empty responses.
if not place_response or not place_response.get("candidates"):
logger.warning(
f"No Google Place match found for facility {facility}."
f" Skipping.")
continue
# Retrieving Google Place ID from the first candidate.
google_place_id = place_response["candidates"][0]["place_id"]
logger.info(f"Google Place with ID '{google_place_id}' found matching "
f" facility {facility}.")
with dal.session_scope() as session: # type: sqlalchemy.orm.Session
# noinspection PyTypeChecker
facility_canonical = dal.get_by_attr(
orm_class=FacilityCanonical,
attr_name="google_place_id",
attr_value=google_place_id,
session=session,
) # type: FacilityCanonical
if facility_canonical:
facility_canonical_id = facility_canonical.facility_canonical_id
logger.info(
f"Google Place with ID '{google_place_id}' previously "
f"stored as canonical facility {facility_canonical}.")
else:
logger.info(
f"Google Place with ID '{google_place_id}' not previously "
f"stored as a canonical facility.")
logger.info(
f"Retrieving Google Place details for Google Place with "
f"ID '{google_place_id}'.")
details_response = get_place_details(
google_place_id=google_place_id, retriever=retriever)
if not details_response:
logger.warning(
f"No Google Place details retrieved for Google Place "
f"with ID '{google_place_id}'. Skipping.")
continue
facility_canonical_id = iodu_canonical_facility_from_google(
dal=dal,
google_place_id=google_place_id,
google_response=details_response,
)
logger.info(f"Linking facility {facility} with canonical facility "
f"{facility_canonical}.")
dal.update_attr_value(
orm_class=Facility,
pk=facility.facility_id,
attr_name="facility_canonical_id",
attr_value=facility_canonical_id,
session=session,
)