def sex(patient, unit, timestamp):
if patient == None:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": "record not found"
})
else:
gender = patient.get("gender")
if gender is None:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": "gender not set"
})
else:
return Right({
"variableValue": {
"value": gender
},
"certitude":
2,
"how":
f"FHIR resource 'Patient' field>'gender' = {gender}"
})
def merge_array(a, b, err):
if a is None:
return Right(b)
elif b is None:
return Right(a)
else:
return Right(a + [elem for elem in b if elem not in a])
def address(pat):
extensions = pat.get("extension", [])
lat = list(
map(
lambda x: x["valueDecimal"],
filter(lambda x: x.get("url", "").lower() == "latitude",
extensions)))
lon = list(
map(
lambda x: x["valueDecimal"],
filter(lambda x: x.get("url", "").lower() == "longitude",
extensions)))
if len(lat) > 1:
return Left("more than one latitudes")
if len(lon) > 1:
return Left("more than one longitudes")
if len(lat) == 0:
if len(lon) == 0:
return Right(None)
else:
return Left("a longitude without a latitude")
elif len(lon) == 0:
return Left("a latitude without a longitude")
else:
return Right({"latitude": lat[0], "longitude": lon[0]})
def query_feature(table, feature):
feature_def = features_dict[table][feature]
ty = feature_def["type"]
if ty == "string":
if "enum" not in feature_def:
return Left("node has type string but has no enum")
else:
return Right({
"feature_name":
feature,
"feature_qualifiers": [{
"operator": "=",
"value": v
} for v in feature_def["enum"]]
})
elif ty == "integer":
if "maximum" not in feature_def or "minimum" not in feature_def:
return Left(
"node has type integer but has no maximum or has no minimum")
else:
return Right({
"feature_name":
feature,
"feature_qualifiers": [{
"operator": "=",
"value": v
} for v in range(feature_def["minimum"],
feature_def["maximum"] + 1)]
})
else:
return Left(f"unsupported node type {ty}")
def handle_records_filtered(records_filtered):
if len(records_filtered) == 0:
from_code = calculation(codes)
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": f"no record found code {from_code}"
})
else:
ts = timestamp.timestamp()
def key(a):
return extract_key(a).rec(
lambda ext_key: diff_func(strtots(ext_key) - ts),
float("inf"))
records_filtered_key = [(a, key(a)) for a in records_filtered]
records_with_key = [
a for a in records_filtered_key if a[1] is not None
]
if len(records_with_key) == 0:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": f"no record found code {from_code}"
})
else:
record = min(records_with_key, key=lambda a: a[1])[0]
return convert_record_to_pds(record, unit, timestamp,
clinical_variable, resource_name)
def merge(a, b, err):
if a is None:
return Right(b)
elif b is None:
return Right(a)
elif a == b:
return Right(a)
else:
return Left(f"err={err} a={a} b={b}")
def func(patient, unit, timestamp):
if patient == None:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": "record not found"
})
else:
extension = patient.get("extension")
if extension is None:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": "extension not found"
})
else:
filtered = filter(lambda x: x["url"] == url, extension)
if len(filtered) == 0:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": f"extension not found url {url}"
})
else:
certitude = 2
value = []
calculation = url
hasValueCodeableConcept = True
for a in filtered:
valueCodeableConcept = a.get("valueCodeableConcept")
if valueCodeableConcept is None:
certitude = 1
calculation += " valueCodeableConcept not found"
else:
hasValueCodeableConcept = True
value.append(valueCodeableConcept)
if len(value) == 0:
certitude = 0
elif not hasValueCodeableConcept:
calculation += " on some extension"
return Right({
"variableValue": {
"value": value
},
"certitude": certitude,
"how": calculation
})
def one(xs):
if len(xs) == 1:
return Right(xs[0])
elif len(xs) == 0:
return Right(None)
else:
return Left({
"variableValue": {
"value": None
},
"how": "more than one record found",
"certitude": 0
})
def convert_record_to_pds(record, unit, timestamp, clinical_variable,
resource_name):
ts = extract_key(record)
cert = ts.rec(const(2), 1)
vq = record.get("valueQuantity")
if vq is not None:
v = vq["value"]
from_u = vq.get("unit")
if from_u is None:
from_u = vq.get("code")
mv = convert(v, from_u, unit)
if isinstance(mv, Left):
return mv
else:
v = mv.value
else:
v = True
from_u = None
c = calculation_template(clinical_variable, resource_name, timestamp,
record, unit)
return Right({
"variableValue": {
"value":
v,
**({
"unit": unit
} if unit is not None else {
"unit": from_u
} if from_u is not None else {}),
},
"certitude": cert,
"timestamp": maybe.to_python(ts),
"how": c
})
def filter_records(records, codes, resource_name):
records_filtered = []
for record in records:
logger.info(f"filtering record: {record}")
for c in codes:
system = c["system"]
code = c["code"]
is_regex = c["is_regex"]
if resource_name == "MedicationRequest":
code2 = record.get("medication",
{}).get("medicationCodeableConcept")
else:
code2 = record.get("code")
if code2 is None:
return Left({
"error": f"malformated record: no code",
"record": record
})
coding2 = code2.get("coding")
if coding2 is None:
return Left({
"error": f"malformated record: no coding under code",
"record": record
})
for c2 in coding2:
if c2["system"] == system:
if (is_regex and re.search(code, "^" + c2["code"] +
"$")) or c2["code"] == code:
records_filtered.append(record)
return Right(records_filtered)
def calculate_age2(born, timestamp):
try:
today = strtodate(timestamp)
except Exception as e:
return Left({"error": str(e)})
return Right(today.year - born.year -
((today.month, today.day) < (born.month, born.day)))
def get_features_by_identifier(table, identifier):
if table in input_dict:
identifier_dict = input_dict[table]
else:
raise Left(f"Cannot find table {table}, available {input_dict}")
return Right([feature for feature, identifiers in identifier_dict.items() if identifier in identifiers])
def sequence(l):
l2 = []
for x in l:
if isinstance(x, Left):
return x
else:
l2.append(x.value)
return Right(l2)
def update_key(d, ok, nk):
curr_keys = list(d.keys())
if ok in curr_keys:
i = curr_keys.index(ok)
d.insert(i, nk, d.pop(ok))
return Right(())
else:
return Left(f"variable {ok} no longer exists")
def age(patient, unit, timestamp):
if unit is not None and unit != "year":
return Left((f"unsupported unit {unit}", 400))
if patient == None:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": "record not found"
})
else:
if "birthDate" in patient:
birth_date = patient["birthDate"]
date_of_birth = strtodate2(birth_date)
today = timestamp.strftime("%Y-%m-%d")
mage = calculate_age2(date_of_birth, timestamp)
return mage.map(
lambda age: {
"variableValue": {
"value": age,
"unit": "year"
},
"certitude": 2,
"how": {
"request_timestamp": today,
"computed_from": ["request_timestamp", "birthDate"],
"birthDate": {
"computed_from": {
"resourceType": "Patient",
"field": "birthDate"
},
"value": birth_date
}
}
})
else:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": "birthDate not set"
})
def ethnicities(pat):
extensions = pat.get("extension", [])
return Right(
list(
map(
lambda x: x["valueString"],
filter(
lambda x: x.get("url") in ethnicity_urls and "valueString"
in x, extensions))))
def address(patient, unit, timestamp):
if patient == None:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": "record not found"
})
else:
address = patient.get("address")
if address is None:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": "address not set"
})
else:
# use home type address if available, otherwise, just use the first address
used_addr_dict = None
for addr in address:
if addr['use'] == 'home':
used_addr_dict = addr
break
if not used_addr_dict:
used_addr_dict = address[0]
used_addr_str = '{line}, {city}, {state} {pc}, {country}'.format(
line=','.join(used_addr_dict['line']),
city=used_addr_dict['city'],
state=used_addr_dict['state'],
pc=used_addr_dict['postalCode'],
country=used_addr_dict['country'])
return Right({
"variableValue": {
"value": used_addr_str
},
"certitude":
2,
"how":
f"FHIR resource 'Patient' field>'address' = {used_addr_str}"
})
def get(self, table, key):
FHIR, GEOID, NearestRoad, NearestPoint, Visit = self.get_sub_objects()
FHIR_keys, GEOID_keys, NearestRoad_keys, NearestPoint_keys, Visit_keys = self.get_sub_keys(
FHIR, GEOID, NearestRoad, NearestPoint, Visit)
if key in FHIR_keys:
return Right(self.obj["FHIR"][key])
for name, keys in GEOID_keys.items():
if key in keys:
return Right(GEOID[name])
for name, keys in NearestRoad_keys.items():
if old_key in keys:
return Right(NearestRoad[name])
for name, keys in NearestPoint_keys.items():
if old_key in keys:
return Right(NearestPoint[name])
return Left(f"variable {old_key} no longer exists")
def update_key(self, table, old_key, new_key):
FHIR, GEOID, NearestRoad, NearestPoint, Visit = self.get_sub_objects()
FHIR_keys, GEOID_keys, NearestRoad_keys, NearestPoint_keys, Visit_keys = self.get_sub_keys(
FHIR, GEOID, NearestRoad, NearestPoint, Visit)
if old_key in FHIR_keys:
update_key(self.obj["FHIR"], old_key, new_key)
return Right(())
for name, keys in GEOID_keys.items():
if old_key in keys:
columns = GEOID[name]["columns"]
for column_name, var_name in columns.items():
if var_name == old_key:
columns[column_name] = new_key
return Right(())
for name, keys in NearestRoad_keys.items():
if old_key in keys:
nearest_road = NearestRoad[name]
if old_key == nearest_road["distance_feature_name"]:
nearest_road["distance_feature_name"] = new_key
else:
for attribute_name, feature in nearest_road[
"attributes_to_features_map"].items():
if feature["feature_name"] == old_key:
feature["feature_name"] = new_key
return Right(())
for name, keys in NearestPoint_keys.items():
if old_key in keys:
nearest_point = NearestPoint[name]
if old_key == nearest_point["distance_feature_name"]:
nearest_point["distance_feature_name"] = new_key
else:
for attribute_name, feature in nearest_point[
"attributes_to_features_map"].items():
if feature["feature_name"] == old_key:
feature["feature_name"] = new_key
return Right(())
return Left(f"variable {old_key} no longer exists")
def set_races(pat, races):
extensions = pat.get("extension", [])
pat["extension"] = list(
filter(lambda x: x.get("url") not in race_urls, extensions)) + list(
map(
lambda race: {
"url": race_urls[0],
"extension": [{
"valueString": race
}]
}, races))
return Right(pat)
def set_ethnicities(pat, ethnicities):
extensions = pat.get("extension", [])
pat["extension"] = list(
filter(lambda x: x.get("url") not in ethnicity_urls,
extensions)) + list(
map(
lambda ethnicity: {
"url": ethnicity_urls[0],
"extension": [{
"valueString": ethnicity
}]
}, ethnicities))
return Right(pat)
def age(patient, unit, timestamp):
if unit is not None and unit != "year":
return Left((f"unsupported unit {unit}", 400))
if patient == None:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": "record not found"
})
else:
if "birthDate" in patient:
birth_date = patient["birthDate"]
date_of_birth = strtodate(birth_date)
today = strtodate(timestamp).strftime("%Y-%m-%d")
mage = calculate_age2(date_of_birth, timestamp)
return mage.map(
lambda age: {
"variableValue": {
"value": age,
"units": "year"
},
"certitude":
2,
"how":
f"Current date '{today}' minus patient's birthdate (FHIR resource 'Patient' field>'birthDate' = '{birth_date}')"
})
else:
return Right({
"variableValue": {
"value": None
},
"certitude": 0,
"how": "birthDate not set"
})
def update_value(self, table, key, new_value):
FHIR, GEOID, NearestRoad, NearestPoint, Visit = self.get_sub_objects()
FHIR_keys, GEOID_keys, NearestRoad_keys, NearestPoint_keys, Visit_keys = self.get_sub_keys(
FHIR, GEOID, NearestRoad, NearestPoint, Visit)
if key in FHIR_keys:
self.obj["FHIR"][key] = new_value
return Right(())
for name, keys in GEOID_keys.items():
if key in keys:
GEOID[name] = new_value
return Right(())
for name, keys in NearestRoad_keys.items():
if key in keys:
NearestRoad[name] = new_value
return Right(())
for name, keys in NearestPoint_keys.items():
if key in keys:
NearestPoint[name] = new_value
return Right(())
return Left(f"variable {key} no longer exists")
def set_addresses(pat, addresses):
pat["address"] = list(
map(
lambda address: {
"extension": [{
"url":
None,
"extension": [{
"url": "latitude",
"valueDecimal": address["latitude"]
}, {
"url": "longitude",
"valueDecimal": address["longitude"]
}]
}]
}, addresses))
return Right(pat)
def handle_requests(requests):
rescs = []
for request in requests:
method = request["method"]
url = request["url"]
result = urlsplit(url)
pcs = result.path.split("/")
qcs = map(lambda x: x.split("="), result.query.split("&"))
if pcs[1] == "Patient":
rescs.append(_get_patient(pcs[2]))
else:
patient_id = None
for qc in qcs:
if qc[0] == "patient":
patient_id = qc[1]
rescs.append(_get_resource(pcs[1], patient_id))
return Right(bundle(rescs, "batch-response"))
def handle_src_and_tgt_features(src_features, tgt_features):
edge_property_value = []
for src_feature in src_features:
for tgt_feature in tgt_features:
edge = co_occurrence_feature_edge(conn, table, year,
cohort_features, src_feature,
tgt_feature)
if isinstance(edge, Right):
edge_property_value.append({
"src_feature": src_feature,
"tgt_feature": tgt_feature,
"p_value": edge.value
})
else:
return edge
if len(edge_property_value) == 0:
return Left("no edge found")
else:
return Right(edge_property_value)
def validateTable(ctx, tablename, tfname, kvp):
with open(tfname, "r", newline="", encoding="utf-8") as tfi:
reader = csv.reader(tfi)
header = next(reader)
n = len(header)
i = 0
for row in reader:
n2 = len(row)
if n2 != n:
return Left(f"row {i} number of items, expected {n}, encountered {n2}")
i += 1
seen = set()
dups = []
for x in header:
if x in seen:
dups.append(x)
else:
seen.add(x)
if len(dups) > 0:
return Left(f"duplicate header(s) in upload {dups}")
header2 = list(kvp.keys())
i2 = [a for a in header if a in header2]
if len(i2) > 0:
return Left(f"duplicate header(s) in input {i2}")
conn = connect(user=ctx["dbuser"], password=ctx["dbpass"], host=ctx["dbhost"], dbname=ctx["dbname"])
cursor = conn.cursor()
try:
cursor.execute('''
select column_name, data_type
from information_schema.columns
where table_schema NOT IN ('information_schema', 'pg_catalog') and table_name=%s
order by table_schema, table_name
''', (tablename,))
rows = cursor.fetchall()
header3 = list(map(lambda r:r[0], rows))
d2 = [a for a in header + header2 if a not in header3]
if len(d2) > 0:
return Left(f"undefined header(s) in input {d2} available {header3}")
return Right(())
finally:
cursor.close()
conn.close()
def error_code(result):
return result.rec(
lambda err: Left(("not found", 404)
if err[0]["status_code"] == 404 else err),
lambda config: Right(config))
def cfvo_to_cfvo2(cfvo):
cfvo2 = {**cfvo}
return Right(cfvo2)
def set_gender(pat, gender):
pat["gender"] = gender
return Right(pat)