Merge pull request #145 from BIH-CEI/144-hpo

144 hpo

src/phenopacket_mapper/api_requests/__init__.py

@@ -5,10 +5,12 @@
 from .api_request_super_class import APIRequestSuperClass
 from .get import get
 from .orpha_api_request import OrphaAPIRequest
+from .hpo_api_request import HPOAPIRequest
 
 __all__ = [
     "APIRequestSuperClass",
     "get",
     "OrphaAPIRequest",
+    "HPOAPIRequest",
 
 ]

src/phenopacket_mapper/api_requests/hpo_api_request.py

@@ -0,0 +1,27 @@
+from typing import Union
+
+from phenopacket_mapper.data_standards import CodeSystem
+from phenopacket_mapper.api_requests import APIRequestSuperClass
+from phenopacket_mapper.api_requests import get as rest_get
+from phenopacket_mapper.data_standards import Coding, HPO
+
+
+class HPOAPIRequest(APIRequestSuperClass):
+    """A class to request data from the HPO API."""
+
+    api_base_url = "https://ontology.jax.org/api/hp/terms/HP:"
+
+    def __init__(self, hpo_code_system: CodeSystem = HPO) -> None:
+        self.hpo_code_system = hpo_code_system
+
+    def get(self, concept_id: Union[str, int]) -> Coding:
+        """Get details about a concept from the Orphanet API."""
+        json = rest_get(self.api_base_url + str(concept_id), json=True)
+
+        name = json['name']
+
+        return Coding(
+            system=self.hpo_code_system,
+            code=str(concept_id),
+            display=name
+        )

src/phenopacket_mapper/api_requests/orpha_api_request.py

@@ -1,3 +1,5 @@
+from typing import Union
+
 from bs4 import BeautifulSoup
 
 from phenopacket_mapper.data_standards import CodeSystem
@@ -14,7 +16,7 @@ class OrphaAPIRequest(APIRequestSuperClass):
     def __init__(self, orpha_code_system: CodeSystem = ORDO) -> None:
         self.orpha_code_system = orpha_code_system
 
-    def get(self, concept_id: int) -> Coding:
+    def get(self, concept_id: Union[str, int]) -> Coding:
         """Get details about a concept from the Orphanet API."""
         html = rest_get(self.api_base_url + str(concept_id))
 

tests/api_requests/test_hpo_api_request.py

@@ -0,0 +1,7 @@
+from phenopacket_mapper.api_requests.hpo_api_request import HPOAPIRequest
+from phenopacket_mapper.data_standards import Coding, HPO
+
+
+def test_hpo_api_request():
+    hp = HPOAPIRequest()
+    assert hp.get("0000098") == Coding(system=HPO, code="0000098", display="Tall stature")