feat!: add RxClass API fetcher

pyproject.toml

@@ -141,7 +141,7 @@ ignore = [
 # B011 - assert-false
 # INP001 - implicit-namespace-package
 # D103 - missing-docstring-public-function
-"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011", "INP001", "D103"]
+"tests/*" = ["ANN001", "ANN2", "ANN102", "S101", "B011", "INP001", "D103", "D100"]
 
 [tool.ruff.format]
 docstring-code-format = true

src/regbot/fetch/drugsfda.py

@@ -635,7 +635,7 @@ def _get_result(data: dict, normalize: bool) -> Result:
     )
 
 
-def get_drugsfda_results(
+def make_drugsatfda_request(
     url: str, normalize: bool = False, limit: int = 500
 ) -> list[Result] | None:
     """Get Drugs@FDA data given an API query URL.
@@ -677,7 +677,7 @@ def get_anda_results(anda: str, normalize: bool = False) -> list[Result] | None:
     :return: list of Drugs@FDA ``Result``s if successful
     """
     url = f"https://api.fda.gov/drug/drugsfda.json?search=openfda.application_number:ANDA{anda}"
-    return get_drugsfda_results(url, normalize)
+    return make_drugsatfda_request(url, normalize)
 
 
 def get_nda_results(nda: str, normalize: bool = False) -> list[Result] | None:
@@ -689,4 +689,4 @@ def get_nda_results(nda: str, normalize: bool = False) -> list[Result] | None:
     :return: list of Drugs@FDA ``Result``s if successful
     """
     url = f"https://api.fda.gov/drug/drugsfda.json?search=openfda.application_number:NDA{nda}"
-    return get_drugsfda_results(url, normalize)
+    return make_drugsatfda_request(url, normalize)

src/regbot/fetch/rxclass.py

@@ -1,4 +1,4 @@
-"""todo"""
+"""Fetch data from RxClass API."""
 
 import logging
 from collections import namedtuple
@@ -118,46 +118,74 @@ def _missing_(cls, value):  # noqa: ANN001 ANN206
         )
 
 
-def _get_concept(concept_raw: dict) -> DrugConcept:
-    """TODO"""
+def _get_concept(concept_raw: dict, normalize: bool) -> DrugConcept:
     return DrugConcept(
         concept_id=f"rxcui:{concept_raw['rxcui']}",
         name=concept_raw["name"],
-        term_type=TermType[concept_raw["tty"]],
+        term_type=TermType[concept_raw["tty"]] if normalize else concept_raw["tty"],
     )
 
 
-def _get_classification(classification_raw: dict) -> DrugClassification:
-    """TODO"""
+def _get_classification(
+    classification_raw: dict, normalize: bool
+) -> DrugClassification:
     return DrugClassification(
         class_id=classification_raw["classId"],
         class_name=classification_raw["className"],
-        class_type=classification_raw["classType"],
+        class_type=ClassType(classification_raw["classType"].lower())
+        if normalize
+        else classification_raw["classType"],
         class_url=classification_raw.get("classUrl"),
     )
 
 
-def _get_rxclass_entry(drug_info: dict) -> RxClassEntry:
-    """Todo"""
+def _get_relation(raw_value: str | None, normalize: bool) -> str | Relation | None:
+    if raw_value is None:
+        return None
+    if normalize:
+        return Relation(raw_value.lower())
+    return raw_value
+
+
+def _get_relation_source(raw_value: str, normalize: bool) -> str | RelationSource:
+    return RelationSource(raw_value.lower()) if normalize else raw_value
+
+
+def _get_rxclass_entry(drug_info: dict, normalize: bool) -> RxClassEntry:
     return RxClassEntry(
-        concept=_get_concept(drug_info["minConcept"]),
-        drug_classification=_get_classification(drug_info["rxclassMinConceptItem"]),
-        relation=Relation(drug_info["rela"].lower()) if drug_info["rela"] else None,
-        relation_source=RelationSource(drug_info["relaSource"].lower()),
+        concept=_get_concept(drug_info["minConcept"], normalize),
+        drug_classification=_get_classification(
+            drug_info["rxclassMinConceptItem"], normalize
+        ),
+        relation=_get_relation(drug_info.get("rela"), normalize),
+        relation_source=_get_relation_source(drug_info["relaSource"], normalize),
     )
 
 
-def make_rxclass_request(url: str, include_snomedt: bool = False) -> list[RxClassEntry]:
-    """TODO"""
+def make_rxclass_request(
+    url: str, include_snomedt: bool = False, normalize: bool = False
+) -> list[RxClassEntry]:
+    """Issue an API request to RxClass.
+
+    :param url: RxClass API URL to request
+    :param include_snomedct: if ``True``, include class claims provided by SNOMEDCT.
+        These are provided under a different license from the rest of the data and
+        may present publishability issues for data consumers.
+    :param normalize: if ``True``, try to normalize values to controlled enumerations
+        and appropriate Python datatypes
+    :return: processed list of drug class descriptions from RxClass
+    """
     with requests.get(url, timeout=30) as r:
         try:
             r.raise_for_status()
         except RequestException as e:
             _logger.warning("Request to %s returned status code %s", url, r.status_code)
             raise e
         raw_data = r.json()
+    if not raw_data:
+        return []
     processed_results = [
-        _get_rxclass_entry(entry)
+        _get_rxclass_entry(entry, normalize)
         for entry in raw_data["rxclassDrugInfoList"]["rxclassDrugInfo"]
     ]
     if not include_snomedt:
@@ -167,9 +195,23 @@ def make_rxclass_request(url: str, include_snomedt: bool = False) -> list[RxClas
     return processed_results
 
 
-def get_drug_info(drug: str) -> list[RxClassEntry]:
-    """TODO"""
+def get_drug_class_info(
+    drug: str, include_snomedct: bool = False, normalize: bool = False
+) -> list[RxClassEntry]:
+    """Get RxClass-provided drug info.
+
+    See also RxClass getClassByRxNormDrugName API:
+        https://lhncbc.nlm.nih.gov/RxNav/APIs/api-RxClass.getClassByRxNormDrugName.html
+
+    :param drug: RxNorm-provided drug name
+    :param include_snomedct: if ``True``, include class claims provided by SNOMEDCT.
+        These are provided under a different license from the rest of the data and
+        may present publishability issues for data consumers.
+    :param normalize: if ``True``, try to normalize values to controlled enumerations
+        and appropriate Python datatypes
+    :return: list of drug class descriptions from RxClass
+    """
     url = (
         f"https://rxnav.nlm.nih.gov/REST/rxclass/class/byDrugName.json?drugName={drug}"
     )
-    return make_rxclass_request(url)
+    return make_rxclass_request(url, include_snomedct, normalize)