def _get_records(ptid, fhir_plugin_id, timestamp):
url_patient = f"{pds_url_base}/{fhir_plugin_id}/Patient/{ptid}"
url_condition = f"{pds_url_base}/{fhir_plugin_id}/Condition?patient={ptid}"
url_observation = f"{pds_url_base}/{fhir_plugin_id}/Observation?patient={ptid}"
return get(url_patient).bind(lambda patient: get(url_condition).bind(lambda condition: get(url_observation).bind(lambda observation: unbundle(condition).bind(lambda condition_unbundled: unbundle(observation).map(lambda observation_unbundled: bundle([
patient,
*condition_unbundled,
*observation_unbundled
]))))))
def get_patient(patient_id, plugin):
resp = get(pdsdpi_url_base(plugin) + f"/Patient/{patient_id}")
if isinstance(resp, Left) and isinstance(
resp.value[0], dict) and resp.value[0].get("status_code") == 404:
return Right(None)
else:
return resp
def _get_records(ptids, fhir_plugin_id, timestamp):
pt_records = []
for ptid in ptids:
url_patient = f"{pds_url_base}/{fhir_plugin_id}/Patient/{ptid}"
url_condition = f"{pds_url_base}/{fhir_plugin_id}/Condition?patient={ptid}"
url_observation = f"{pds_url_base}/{fhir_plugin_id}/Observation?patient={ptid}"
val = get(url_patient).bind(lambda patient: get(url_condition).bind(
lambda condition: get(url_observation).
bind(lambda observation: unbundle(condition).bind(
lambda condition_unbundled: unbundle(observation).map(
lambda observation_unbundled: bundle([
patient, *condition_unbundled, *observation_unbundled
]))))))
pt_records.append(val)
return list_traversable_either_applicative.sequence(pt_records)
def _get_config(piid=None):
url = f"{pds_url_base}/{pds_config}/config"
if piid is not None:
url += f"/{piid}"
return error_code(
get(url)).map(lambda config: config if piid is None else [config])
def _get_plugin_config_factory_default(piid):
config = get(pdsdpi_url_base(piid) + "/config")
config = config.value
config["piid"] = piid
if "enabled" not in config:
config["enabled"] = True
return config
def _get_config(piid=None):
url = f"{pds_url_base}/{pds_config}/config"
resp = get(url)
if isinstance(resp, Left):
return resp
else:
if piid is not None:
l = list(filter(lambda x : x["piid"] == piid, resp.value))
if len(l) == 0:
return Left(("not found", 404))
else:
return Right(l)
else:
return resp
def profile(patient_id, model_plugin_id, timestamp, body):
phenotype_mapping_plugin_id = body["phenotype_mapping_plugin_id"]
data_provider_plugin_id = body["data_provider_plugin_id"]
custom_units = body.get("custom_units")
url = f"{pds_url_base}/{model_plugin_id}/clinical_feature_variables"
resp1 = get(url, schema=cfv_schema)
if isinstance(resp1, Left):
return resp1.value
clinical_feature_variable_objects = resp1.value
def cfvo_to_cfvo2(cfvo):
cfv = cfvo["clinical_feature_variable"]
cfvo2 = {
"clinical_feature_variable": cfv
}
unit = cfvo.get("unit")
if unit is not None:
cfvo2["unit"] = unit
elif custom_units is not None:
cus = [a for a in custom_units if a["clinical_feature_variable"] == cfv]
if len(cus) > 0:
cfvo2["unit"] = cus[0]["unit"]
return cfvo2
cfvos2 = list(map(cfvo_to_cfvo2, clinical_feature_variable_objects))
url = f"{pds_url_base}/{phenotype_mapping_plugin_id}/mapping?patient_id={patient_id}&data_provider_plugin_id={data_provider_plugin_id}×tamp={timestamp}"
print(f"url = {url}")
resp2 = post(url, json=cfvos2)
if isinstance(resp2, Left):
return resp2.value
value_objects = resp2.value
print(f"value_objects = {value_objects}")
sys.stdout.flush()
profile = [{
**clinical_feature_variable_object, **value_object
} for value_object, clinical_feature_variable_object in zip(value_objects, clinical_feature_variable_objects)]
return profile
def get_condition(patient_id, plugin):
resp = get(pdsdpi_url_base(plugin) + f"/Condition?patient={patient_id}")
return resp.bind(unbundle)
def get_selectors(piid=None):
url = f"{pds_url_base}/{pds_config}/selectors"
resp = get(url)
return resp.value
def _get_selector_config():
url = f"{pds_url_base}/{pds_config}/selectorConfig"
return error_code(get(url))
def _get_custom_units():
url = f"{pds_url_base}/{pds_config}/custom_units"
return get(url)