async def get_docs_results(matchengine: MatchEngine, needed_clinical,
needed_extended):
"""
Matching criteria for clinical and extended_attributes values can be set/extended in config.json
:param matchengine:
:param needed_clinical:
:param needed_extended:
:return:
"""
clinical_projection = matchengine.match_criteria_transform.projections[
"clinical"]
clinical_query = MongoQuery({"_id": {"$in": list(needed_clinical)}})
db_calls = list()
db_calls.append(
perform_db_call(matchengine, "clinical", clinical_query,
clinical_projection))
for extended_collection, extended_ids in needed_extended.items():
genomic_query = MongoQuery({"_id": {"$in": list(extended_ids)}})
projection = matchengine.match_criteria_transform.projections[
extended_collection]
db_calls.append(
perform_db_call(matchengine, extended_collection, genomic_query,
projection))
results = await asyncio.gather(*db_calls)
return results
async def get_all_except(matchengine: MatchEngine, protocol_no: str,
trial_matches_by_sample_id: dict) -> list:
"""Return all matches except ones matching current protocol_no"""
# get clinical ids with matches
clinical_ids = {
matchengine.sample_mapping[sample_id]
for sample_id in trial_matches_by_sample_id.keys()
}
# if protocol has been run previously, subtract clinical ids from current run from
# previously run clinical ids for a specific protocol. The remainder are ids
# which were run previously, but not in the current run.
if protocol_no in matchengine.clinical_run_log_entries:
clinical_ids = matchengine.clinical_run_log_entries[
protocol_no] - clinical_ids
query = {
matchengine.match_criteria_transform.match_trial_link_id: protocol_no,
"clinical_id": {
'$in': [clinical_id for clinical_id in clinical_ids]
}
}
projection = {'_id': 1, 'hash': 1, 'clinical_id': 1}
results = await perform_db_call(
matchengine,
collection=matchengine.trial_match_collection,
query=MongoQuery(query),
projection=projection)
return [result for result in results]
async def get_matches_to_disable(matchengine: MatchEngine,
new_matches_hashes: list, protocol_no: str,
sample_id: str) -> list:
"""
Get matches to disable by looking for existing, enabled matches whose
hashes are not present in newly generated matches during current run.
Done for every sample_id
:param matchengine:
:param new_matches_hashes:
:param protocol_no:
:param sample_id:
:return:
"""
query = {
matchengine.match_criteria_transform.match_trial_link_id: protocol_no,
'sample_id': sample_id,
'is_disabled': False,
'hash': {
'$nin': new_matches_hashes
}
}
matches_to_disable_query = MongoQuery(query)
projection = {"hash": 1, "is_disabled": 1}
matches = await asyncio.gather(
perform_db_call(matchengine, matchengine.trial_match_collection,
matches_to_disable_query, projection))
return matches[0]
async def get_all_except(matchengine: MatchEngine,
protocol_no: str,
trial_matches_by_sample_id: dict) -> list:
"""Return all matches except ones matching current protocol_no"""
clinical_ids = {matchengine.sample_mapping[sample_id] for sample_id in trial_matches_by_sample_id.keys()}
if protocol_no in matchengine.clinical_run_log_entries:
clinical_ids = matchengine.clinical_run_log_entries[protocol_no] - clinical_ids
query = {
'protocol_no': protocol_no,
"clinical_id": {
'$in': [clinical_id for clinical_id in clinical_ids]
}
}
projection = {
'_id': 1,
'hash': 1,
'clinical_id': 1
}
results = await perform_db_call(matchengine,
collection=matchengine.trial_match_collection,
query=MongoQuery(query),
projection=projection)
return [result for result in results]
async def get_docs_results(matchengine: MatchEngine, needed_clinical,
needed_genomic):
"""
Matching criteria for clinical and genomic values can be set/extended in config.json
:param matchengine:
:param needed_clinical:
:param needed_genomic:
:return:
"""
genomic_projection = matchengine.match_criteria_transform.genomic_projection
clinical_projection = matchengine.match_criteria_transform.clinical_projection
clinical_query = MongoQuery({"_id": {"$in": list(needed_clinical)}})
genomic_query = MongoQuery({"_id": {"$in": list(needed_genomic)}})
results = await asyncio.gather(
perform_db_call(matchengine, "clinical", clinical_query,
clinical_projection),
perform_db_call(matchengine, "genomic", genomic_query,
genomic_projection))
return results
async def get_existing_matches(matchengine: MatchEngine, new_matches_hashes: list) -> list:
matches_to_not_change_query = MongoQuery({'hash': {'$in': new_matches_hashes}})
projection = {"hash": 1, "is_disabled": 1}
matches = await asyncio.gather(
perform_db_call(matchengine,
matchengine.trial_match_collection,
matches_to_not_change_query,
projection)
)
return matches[0]
async def get_matches_to_disable(matchengine: MatchEngine,
new_matches_hashes: list,
protocol_no: str,
sample_id: str) -> list:
matches_to_disable_query = MongoQuery({'protocol_no': protocol_no,
'sample_id': sample_id,
'is_disabled': False,
'hash': {'$nin': new_matches_hashes}})
projection = {"hash": 1, "is_disabled": 1}
matches = await asyncio.gather(
perform_db_call(matchengine,
matchengine.trial_match_collection,
matches_to_disable_query,
projection)
)
return matches[0]
async def get_existing_matches(matchengine: MatchEngine,
new_matches_hashes: list) -> list:
"""
Get matches in db which have the same hashes as newly found matches.
:param matchengine:
:param new_matches_hashes:
:return:
"""
matches_to_not_change_query = MongoQuery(
{'hash': {
'$in': new_matches_hashes
}})
projection = {"hash": 1, "is_disabled": 1}
matches = await asyncio.gather(
perform_db_call(matchengine, matchengine.trial_match_collection,
matches_to_not_change_query, projection))
return matches[0]