From 2d8bd871ac91277b0d2924960cfa6371e2d67a61 Mon Sep 17 00:00:00 2001 From: Sally Grindstaff Date: Wed, 16 Aug 2023 15:12:06 -0700 Subject: [PATCH] Update etl clinical command to process KP2023 metadata --- .../id3c/cli/command/etl/__init__.py | 3 + .../id3c/cli/command/etl/clinical.py | 829 +++++++++++++++++- .../id3c/cli/command/etl/redcap_map.py | 3 + 3 files changed, 810 insertions(+), 25 deletions(-) diff --git a/lib/seattleflu/id3c/cli/command/etl/__init__.py b/lib/seattleflu/id3c/cli/command/etl/__init__.py index d4375f0b..8933f5a5 100644 --- a/lib/seattleflu/id3c/cli/command/etl/__init__.py +++ b/lib/seattleflu/id3c/cli/command/etl/__init__.py @@ -92,6 +92,7 @@ def race(races: Optional[Any]) -> list: "indian": "americanIndianOrAlaskaNative", "native": "americanIndianOrAlaskaNative", "alaska native": "americanIndianOrAlaskaNative", + "ai_an": "americanIndianOrAlaskaNative", "asian": "asian", @@ -99,6 +100,7 @@ def race(races: Optional[Any]) -> list: "black or african american": "blackOrAfricanAmerican", "black": "blackOrAfricanAmerican", "black or african-american": "blackOrAfricanAmerican", + "black_aa": "blackOrAfricanAmerican", "nativehawaiian": "nativeHawaiian", "native hawaiian": "nativeHawaiian", @@ -111,6 +113,7 @@ def race(races: Optional[Any]) -> list: "nativehi": "nativeHawaiian", "native_hawaiian": "nativeHawaiian", "ha_pi": "nativeHawaiian", + "nh_opi": "nativeHawaiian", "white": "white", "white or caucasian": "white", diff --git a/lib/seattleflu/id3c/cli/command/etl/clinical.py b/lib/seattleflu/id3c/cli/command/etl/clinical.py index c9c17291..4d37ad5f 100644 --- a/lib/seattleflu/id3c/cli/command/etl/clinical.py +++ b/lib/seattleflu/id3c/cli/command/etl/clinical.py @@ -39,6 +39,7 @@ from . import race, ethnicity from .fhir import * from .clinical_retrospectives import * +from .redcap_map import map_symptom LOG = logging.getLogger(__name__) @@ -108,11 +109,11 @@ def etl_clinical(*, db: DatabaseSession): details = {"type": "retrospective"}) - # PHSKC will be handled differently that other clinical records, converted + # PHSKC and KP2023 will be handled differently that other clinical records, converted # to FHIR format and inserted into receiving.fhir table to be processed # by the FHIR ETL. When time allows, SCH and KP should follow suit. - if site.identifier == 'RetrospectivePHSKC': - fhir_bundle = generate_fhir_bundle(db, record.document) + if site.identifier in ('RetrospectivePHSKC', 'KaiserPermanente2023'): + fhir_bundle = generate_fhir_bundle(db, record.document, site.identifier) insert_fhir_bundle(db, fhir_bundle) else: @@ -194,30 +195,30 @@ def determine_questionnaire_items(record: dict) -> List[dict]: """ Returns a list of FHIR Questionnaire Response answer items """ items: Dict[str, Any] = {} - if record["age"]: + if record.get("age", None): items["age"] = [{ 'valueInteger': (int(record["age"]))}] - if record["race"]: + if record.get("race", None): items["race"] = [] for code in race(record["race"]): items["race"].append({ 'valueCoding': create_coding(f"{SFS}/race", code)}) - if record["ethnicity"]: + if record.get("ethnicity", None): items["ethnicity"] = [{ 'valueBoolean': ethnicity(record["ethnicity"]) }] - if record["if_symptoms_how_long"]: + if record.get("if_symptoms_how_long", None): items["if_symptoms_how_long"] = [{ 'valueString': if_symptoms_how_long(record["if_symptoms_how_long"])}] - if record["vaccine_status"]: + if record.get("vaccine_status", None): items["vaccine_status"] = [{ 'valueString': covid_vaccination_status(record["vaccine_status"])}] - if record["inferred_symptomatic"]: + if record.get("inferred_symptomatic", None): items["inferred_symptomatic"] = [{ 'valueBoolean': inferred_symptomatic(record["inferred_symptomatic"])}] - if record["survey_have_symptoms_now"]: + if record.get("survey_have_symptoms_now", None): items["survey_have_symptoms_now"] = [{ 'valueBoolean': survey_have_symptoms_now(record["survey_have_symptoms_now"])}] - if record["survey_testing_because_exposed"]: + if record.get("survey_testing_because_exposed", None): items["survey_testing_because_exposed"] = [{ 'valueString': survey_testing_because_exposed(record["survey_testing_because_exposed"])}] @@ -231,7 +232,7 @@ def determine_questionnaire_items(record: dict) -> List[dict]: return questionnaire_items -def generate_fhir_bundle(db: DatabaseSession, record: dict) -> Optional[dict]: +def generate_fhir_bundle(db: DatabaseSession, record: dict, site_id: str) -> Optional[dict]: patient_entry, patient_reference = create_patient(record) @@ -240,7 +241,18 @@ def generate_fhir_bundle(db: DatabaseSession, record: dict) -> Optional[dict]: return None specimen_entry, specimen_reference = create_specimen(record, patient_reference) - location_entries, location_references = create_resident_locations(record) + + # PHSKC metadata include address information, while KP2023 metadata only include census tract information + # function create_resident_locations will only return a resource if address information is present, + # so use create_location_tract_only to process KP2023 location metadata + # ideally would not require site id for this, since it makes it more difficult to incorporate future projects + if site_id == 'RetrospectivePHSKC': + location_entries, location_references = create_resident_locations(record) + elif site_id == 'KaiserPermanente2023': + location_entries, location_references = create_location_tract_only(record) + else: + LOG.warning(f'Function generate_fhir_bundle does not currently create location resource entries for site {site_id}') + encounter_entry, encounter_reference = create_encounter(db, record, patient_reference, location_references) if not encounter_entry: @@ -251,18 +263,26 @@ def generate_fhir_bundle(db: DatabaseSession, record: dict) -> Optional[dict]: specimen_observation_entry = create_specimen_observation_entry(specimen_reference, patient_reference, encounter_reference) - diagnostic_code = create_codeable_concept( - system = f'{SFS}/presence-absence-panel', - code = test_coding(record['site']) - ) - - diagnostic_report_resource_entry = create_diagnostic_report( - record, - patient_reference, - specimen_reference, - diagnostic_code, - create_clinical_result_observation_resource, - ) + # for now, only run these for PHSKC, because otherwise an UnknownSiteError will be raised when test_coding is run. + # it would be better to use information from the record to decide whether to run these steps though. + # create_diagnostic_report returns None if there is no clinical result information, so it doesn't really need + # to be run inside the if statement, but the diagnostic_code parameter is not type annotated as Optional, + # and I don't know whether to require diagnostic_code to run create_diagnostic_report, even if it will return None? + if site_id == 'RetrospectivePHSKC': + diagnostic_code = create_codeable_concept( + system = f'{SFS}/presence-absence-panel', + code = test_coding(record['site']) + ) + + diagnostic_report_resource_entry = create_diagnostic_report( + record, + patient_reference, + specimen_reference, + diagnostic_code, + create_clinical_result_observation_resource, + ) + else: + diagnostic_report_resource_entry = None resource_entries = [ patient_entry, @@ -278,6 +298,13 @@ def generate_fhir_bundle(db: DatabaseSession, record: dict) -> Optional[dict]: if diagnostic_report_resource_entry: resource_entries.append(diagnostic_report_resource_entry) + if site_id == 'KaiserPermanente2023': + # KP2023 includes some types of metadata that PHSKC does not + icd10_condition_entries = create_icd10_conditions_kp2023(record, patient_reference) + symptom_condition_entries = create_symptom_conditions(record, patient_reference, encounter_reference) + immunization_entries = create_immunization_kp2023(record, patient_reference) + resource_entries.extend(icd10_condition_entries + symptom_condition_entries + immunization_entries) + return create_bundle_resource( bundle_id = str(uuid4()), timestamp = datetime.now().astimezone().isoformat(), @@ -285,6 +312,750 @@ def generate_fhir_bundle(db: DatabaseSession, record: dict) -> Optional[dict]: entries = list(filter(None, resource_entries)) ) + +def create_location_tract_only(record: dict) -> Optional[tuple]: + """ + Returns a location entry and location reference for a record containing census tract information + If the record contains address information beyond a census tract, use function create_resident_locations instead + """ + location_type_system = 'http://terminology.hl7.org/CodeSystem/v3-RoleCode' + location_type = create_codeable_concept(location_type_system, 'PTRES') + tract_identifier = record["census_tract"] + + if tract_identifier: + tract_id = create_identifier(f"{SFS}/location/tract", tract_identifier) + tract_location = create_location_resource([location_type], [tract_id]) + tract_entry, tract_reference = create_entry_and_reference(tract_location, "Location") + + # return entry and reference as lists of dicts for consistency with function create_resident_locations + return [tract_entry], [tract_reference] + else: + return None, None + + +def create_immunization_kp2023(record: dict, patient_reference: dict) -> list: + """ Returns a FHIR Immunization resource entry for each immunization recorded """ + immunization_entries = [] + + immunization_columns = [ + { + "date": "date_flu_1", + "name": "flu_type_1" + }, + { + "date": "date_flu_2", + "name": "flu_type_2" + }, + { + "date": "date_covid_1", + "name": None + }, + { + "date": "date_covid_2", + "name": None + }, + { + "date": "date_covid_3", + "name": None + }, + { + "date": "date_covid_4", + "name": None + }, + { + "date": "date_covid_5", + "name": None + }, + { + "date": "date_covid_6", + "name": None + } + ] + + # CVX codes were sourced from here: + # https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=cvx + # and here: + # https://www2a.cdc.gov/vaccines/iis/iisstandards/vaccines.asp?rpt=tradename + cvx_codes = { + 88: { + "system": "http://hl7.org/fhir/sid/cvx", + "code": "88", + "display": "influenza, unspecified formulation", + }, + 158: { + "system": "http://hl7.org/fhir/sid/cvx", + "code": "158", + "display": "influenza, injectable, quadrivalent, contains preservative" + }, + 205: { + "system": "http://hl7.org/fhir/sid/cvx", + "code": "205", + "display": "influenza, seasonal vaccine, quadrivalent, adjuvanted, 0.5mL dose, preservative free" + }, + 150: { + "system": "http://hl7.org/fhir/sid/cvx", + "code": "150", + "display": "influenza, injectable, quadrivalent, preservative free" + }, + 185: { + "system": "http://hl7.org/fhir/sid/cvx", + "code": "185", + "display": "seasonal, quadrivalent, recombinant, injectable influenza vaccine, preservative free" + }, + 149: { + "system": "http://hl7.org/fhir/sid/cvx", + "code": "149", + "display": "influenza, live, intranasal, quadrivalent" + }, + 197: { + "system": "http://hl7.org/fhir/sid/cvx", + "code": "197", + "display": "influenza, high-dose seasonal, quadrivalent, 0.7mL dose, preservative free" + }, + 213: { + "system": "http://hl7.org/fhir/sid/cvx", + "code": "213", + "display": "sars-cov-2 (covid-19) vaccine, unspecified" + }, + } + + flu_vaccine_mapper = { + "unknown": 88, + "afluria quadrivalent": 158, + "fluad quadrivalent": 205, + "fluarix quadrivalent": 150, + "flublok quadrivalent": 185, + # "flucelvax quadrivalent" - not known whether with or without preservative + # "flulaval quadrivalent" - not known whether with or without preservative + "flumist quadrivalent": 149, + "fluzone high-dose quadrivlanet": 197, #assuming not the southern hemisphere? + # "fluzone quadrivalent" - not known whether with or without preservative, or whether pediatric + } + + for column_map in immunization_columns: + # if there is no date, do not create a resource entry + # is this a good assumption? what if there is a flu vaccine name but no date? + if not record[column_map['date']]: + continue + + # assign date. should be in ISO format after id3c clinical parse-kp2023 + immunization_date = record[column_map['date']] + + # assign name and code for flu vaccines + if 'flu' in column_map['date']: + if record[column_map['name']]: + # assign and format vaccine name + vaccine_name = record[column_map['name']].lower() + else: + # if there is a date but no vaccine name, assign the name as 'unknown' which will map to unspecified flu vaccine + vaccine_name = 'unknown' # should we throw a warning here? + + # Validate vaccine name and determine CVX code + vaccine_code = None + if vaccine_name in flu_vaccine_mapper: + vaccine_code = cvx_codes[flu_vaccine_mapper[vaccine_name]] if flu_vaccine_mapper[vaccine_name] else None + else: + raise UnknownVaccine (f"Unknown vaccine «{vaccine_name}».") # we already standardize vaccine names in parse-kp2023, so this is just for extra safety + + # assign name and code for covid vaccines + elif 'covid' in column_map['date']: + vaccine_code = cvx_codes[213] # covid vaccines are not specified in this study, so assign code for unspecified covid-19 vaccine + + if vaccine_code: + immunization_identifier_hash = generate_hash(f"{record['mrn']}{vaccine_code['code']}{immunization_date}".lower()) + immunization_identifier = create_identifier(f"{SFS}/immunization", immunization_identifier_hash) + + immunization_resource = create_immunization_resource( + patient_reference = patient_reference, + immunization_identifier = [immunization_identifier], + immunization_date = immunization_date, + immunization_status = "completed", + vaccine_code = vaccine_code, + ) + + immunization_entries.append(create_resource_entry( + resource = immunization_resource, + full_url = generate_full_url_uuid() + )) + + return immunization_entries + + +def create_symptom_conditions(record: dict, patient_reference: dict, encounter_reference: dict) -> list: + """ Returns a FHIR Condition resource for each symptom present in a record """ + + condition_entries = [] + + for symptom in record['symptom']: + mapped_symptom_name = map_symptom(symptom) + onset_date = record['date_symptom_onset'] + symptom_code = { + "system": f"{SFS}/symptom", + "code": mapped_symptom_name + } + + condition_resource = create_condition_resource(mapped_symptom_name, + patient_reference, + onset_date, + symptom_code, + encounter_reference + ) + + condition_entries.append(create_resource_entry( + resource = condition_resource, + full_url = generate_full_url_uuid() + )) + + return condition_entries + + +def create_icd10_conditions_kp2023(record:dict, patient_reference: dict) -> list: + """ + Create a condition resource for each ICD-10 code, following the FHIR format + (http://www.hl7.org/implement/standards/fhir/condition.html) + """ + # todo: raise unknown icd10 error if icd10 code not in mapper + + condition_entries = [] + + icd10_codes = { + "I25": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "I25", + "display": "chronic ischemic heart disease" + }, + "I50": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "I50", + "display": "heart failure" + }, + "J41": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "J41", + "display": "simple and mucopurulent chronic bronchitis" + }, + "J42": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "J42", + "display": "unspecified chronic bronchitis" + }, + "J44": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "J44", + "display": "other chronic obstructive pulmonary disease" + }, + "J45": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "J45", + "display": "asthma" + }, + "J47": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "J47", + "display": "bronchiectasis" + }, + "J80": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "J80", + "display": "acute respiratory distress syndrome" + }, + "E11": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "E11", + "display": "type 2 diabetes mellitus" + }, + "Z51.1": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "Z51.1", + "display": "encounter for antineoplastic chemotherapy and immunotherapy" + }, + "Z94": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "Z94", + "display": "transplanted organ and tissue status" + }, + "B18": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "B18", + "display": "chronic viral hepatitis" + }, + "K70": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "K70", + "display": "alcoholic liver disease" + }, + "C00": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C00", + "display": "malignant neoplasm of lip" + }, + "C01": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C01", + "display": "malignant neoplasm of base of tongue" + }, + "C02": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C02", + "display": "malignant neoplasm of other and unspecified parts of tongue" + }, + "C03": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C03", + "display": "malignant neoplasm of gum" + }, + "C04": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C04", + "display": "malignant neoplasm of floor of mouth" + }, + "C05": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C05", + "display": "malignant neoplasm of palate" + }, + "C06": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C06", + "display": "malignant neoplasm of other and unspecified parts of mouth" + }, + "C07": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C07", + "display": "malignant neoplasm of parotid gland" + }, + "C08": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C08", + "display": "malignant neoplasm of other and unspecified major salivary glands" + }, + "C09": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C09", + "display": "malignant neoplasm of tonsil" + }, + "C10": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C10", + "display": "malignant neoplasm of oropharynx" + }, + "C11": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C11", + "display": "malignant neoplasm of nasopharynx" + }, + "C12": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C12", + "display": "malignant neoplasm of pyriform sinus" + }, + "C13": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C13", + "display": "malignant neoplasm of hypopharynx" + }, + "C14": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C14", + "display": "malignant neoplasm of other and ill-defined sites in the lip, oral cavity and pharynx" + }, + "C15": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C15", + "display": "malignant neoplasm of esophagus" + }, + "C16": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C16", + "display": "malignant neoplasm of stomach" + }, + "C17": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C17", + "display": "malignant neoplasm of small intestine" + }, + "C18": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C18", + "display": "malignant neoplasm of colon" + }, + "C19": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C19", + "display": "malignant neoplasm of rectosigmoid junction" + }, + "C20": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C20", + "display": "malignant neoplasm of rectum" + }, + "C21": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C21", + "display": "malignant neoplasm of anus and anal canal" + }, + "C22": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C22", + "display": "malignant neoplasm of liver and intrahepatic bile ducts" + }, + "C23": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C23", + "display": "malignant neoplasm of gallbladder" + }, + "C24": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C24", + "display": "malignant neoplasm of other and unspecified parts of biliary tract" + }, + "C25": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C25", + "display": "malignant neoplasm of pancreas" + }, + "C26": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C26", + "display": "malignant neoplasm of other and ill-defined digestive organs" + }, + "C30": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C30", + "display": "malignant neoplasm of nasal cavity and middle ear" + }, + "C31": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C31", + "display": "malignant neoplasm of accessory sinuses" + }, + "C32": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C32", + "display": "malignant neoplasm of larynx" + }, + "C33": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C33", + "display": "malignant neoplasm of trachea" + }, + "C34": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C34", + "display": "malignant neoplasm of bronchus and lung" + }, + "C37": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C37", + "display": "malignant neoplasm of thymus" + }, + "C38": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C38", + "display": "malignant neoplasm of heart, mediastinum and pleura" + }, + "C39": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C39", + "display": "malignant neoplasm of other and ill-defined sites in the respiratory system and intrathoracic organs" + }, + "C40": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C40", + "display": "malignant neoplasm of bone and articular cartilage of limbs" + }, + "C41": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C41", + "display": "malignant neoplasm of bone and articular cartilage of other and unspecified sites" + }, + "C43": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C43", + "display": "malignant melanoma of skin" + }, + "C44": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C44", + "display": "other and unspecified malignant neoplasm of skin" + }, + "C45": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C45", + "display": "mesothelioma" + }, + "C46": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C46", + "display": "kaposi's sarcoma" + }, + "C47": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C47", + "display": "malignant neoplasm of peripheral nerves and autonomic nervous system" + }, + "C48": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C48", + "display": "malignant neoplasm of retroperitoneum and peritoneum" + }, + "C49": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C49", + "display": "malignant neoplasm of other connective and soft tissue" + }, + "C4A": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C4A", + "display": "merkel cell carcinoma" + }, + "C50": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C50", + "display": "malignant neoplasms of breast" + }, + "C51": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C51", + "display": "malignant neoplasm of vulva" + }, + "C52": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C52", + "display": "malignant neoplasm of vagina" + }, + "C53": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C53", + "display": "malignant neoplasm of cervix uteri" + }, + "C54": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C54", + "display": "malignant neoplasm of corpus uteri" + }, + "C55": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C55", + "display": "malignant neoplasm of uterus, part unspecified" + }, + "C56": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C56", + "display": "malignant neoplasm of ovary" + }, + "C57": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C57", + "display": "malignant neoplasm of other and unspecified female genital organs" + }, + "C58": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C58", + "display": "malignant neoplasm of placenta" + }, + "C60": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C60", + "display": "malignant neoplasm of penis" + }, + "C61": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C61", + "display": "malignant neoplasm of prostate" + }, + "C62": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C62", + "display": "malignant neoplasm of testis" + }, + "C63": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C63", + "display": "malignant neoplasm of other and unspecified male genital organs" + }, + "C64": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C64", + "display": "malignant neoplasm of kidney, except renal pelvis" + }, + "C65": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C65", + "display": "malignant neoplasm of renal pelvis" + }, + "C66": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C66", + "display": "malignant neoplasm of ureter" + }, + "C67": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C67", + "display": "malignant neoplasm of bladder" + }, + "C68": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C68", + "display": "malignant neoplasm of other and unspecified urinary organs" + }, + "C69": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C69", + "display": "malignant neoplasm of eye and adnexa" + }, + "C70": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C70", + "display": "malignant neoplasm of meninges" + }, + "C71": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C71", + "display": "malignant neoplasm of brain" + }, + "C72": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C72", + "display": "malignant neoplasm of spinal cord, cranial nerves and other parts of central nervous system" + }, + "C73": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C73", + "display": "malignant neoplasm of thyroid gland" + }, + "C74": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C74", + "display": "malignant neoplasm of adrenal gland" + }, + "C75": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C75", + "display": "malignant neoplasm of other endocrine glands and related structures" + }, + "C76": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C76", + "display": "malignant neoplasm of other and ill-defined sites" + }, + "C77": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C77", + "display": "secondary and unspecified malignant neoplasm of lymph nodes" + }, + "C78": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C78", + "display": "secondary malignant neoplasm of respiratory and digestive organs" + }, + "C79": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C79", + "display": "secondary malignant neoplasm of other and unspecified sites" + }, + "C7A": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C7A", + "display": "malignant neuroendocrine tumors" + }, + "C7B": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C7B", + "display": "secondary neuroendocrine tumors" + }, + "C80": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C80", + "display": "malignant neoplasm without specification of site" + }, + "C81": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C81", + "display": "hodgkin lymphoma" + }, + "C82": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C82", + "display": "follicular lymphoma" + }, + "C83": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C83", + "display": "non-follicular lymphoma" + }, + "C84": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C84", + "display": "mature t/nk-cell lymphomas" + }, + "C85": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C85", + "display": "other specified and unspecified types of non-hodgkin lymphoma" + }, + "C86": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C86", + "display": "other specified types of t/nk-cell lymphoma" + }, + "C88": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C88", + "display": "malignant immunoproliferative diseases and certain other b-cell lymphomas" + }, + "C90": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C90", + "display": "multiple myeloma and malignant plasma cell neoplasms" + }, + "C91": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C91", + "display": "lymphoid leukemia" + }, + "C92": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C92", + "display": "myeloid leukemia" + }, + "C93": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C93", + "display": "monocytic leukemia" + }, + "C94": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C94", + "display": "other leukemias of specified cell type" + }, + "C95": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C95", + "display": "leukemia of unspecified cell type" + }, + "C96": { + "system": "http://hl7.org/fhir/sid/icd-10", + "code": "C96", + "display": "other and unspecified malignant neoplasms of lymphoid, hematopoietic and related tissue" + } + } + + for icd10_code in record['icd10']: + condition_resource = create_condition_resource(icd10_code, + patient_reference, + None, + icd10_codes[icd10_code] + ) + + condition_entries.append(create_resource_entry( + resource = condition_resource, + full_url = generate_full_url_uuid() + )) + + return condition_entries + + def test_coding(site_name: str) -> str: """ Given a *site_name*, returns the code associated with the external test run @@ -323,6 +1094,7 @@ def site_identifier(site_name: str) -> str: "SCH": "RetrospectiveChildrensHospitalSeattle", "KP": "KaiserPermanente", "PHSKC": "RetrospectivePHSKC", + "KP2023": "KaiserPermanente2023" } if site_name not in site_map: raise UnknownSiteError(f"Unknown site name «{site_name}»") @@ -973,3 +1745,10 @@ def mark_processed(db, clinical_id: int, entry: Mapping) -> None: set processing_log = processing_log || %(log_entry)s where clinical_id = %(clinical_id)s """, data) + +class UnknownVaccine(ValueError): + """ + Raised by :function: `create_immunization` if it finds a vaccine + name that is not among a set of mapped values + """ + pass diff --git a/lib/seattleflu/id3c/cli/command/etl/redcap_map.py b/lib/seattleflu/id3c/cli/command/etl/redcap_map.py index 24bee660..5fac44dc 100644 --- a/lib/seattleflu/id3c/cli/command/etl/redcap_map.py +++ b/lib/seattleflu/id3c/cli/command/etl/redcap_map.py @@ -81,11 +81,14 @@ def map_symptom(symptom_name: str) -> Optional[str]: 'rash': 'rash', 'breathe': 'increasedTroubleBreathing', 'increased trouble with breathing': 'increasedTroubleBreathing', + 'sob': 'increasedTroubleBreathing', 'eye': 'eyePain', 'smell_taste': 'lossOfSmellOrTaste', 'other': 'other', 'none': 'none', 'none of the above': 'none', + 'unk': 'none', + 'no_answer': 'none' } if symptom_name.lower() not in symptom_map: