Add Medication and Allergy CDA fields (#51)

* Add medication and allergy extractors * finishing medication and allergies * Added validation and add_to method for medications * added allergies to cda * Tweaked allergy parsing and refactored meds parsing function * Fixed tuple typing error in 3.8 * Added more test conditions for allergy entries * Bug fixes, logging, and added meds and allergies to clindoc use case function body * Updated tests * Update example use and added more example cda --------- Co-authored-by: jennferjiangkells <[email protected]>
dotimplement · Aug 5, 2024 · 3d661a3 · 3d661a3
1 parent 3471ff0
commit 3d661a3
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diff --git a/example_use.py b/example_use.py
@@ -1,7 +1,14 @@
 import healthchain as hc
+import logging
 
 from healthchain.models.data.ccddata import CcdData
-from healthchain.models.data.concept import ProblemConcept
+from healthchain.models.data.concept import (
+    AllergyConcept,
+    Concept,
+    MedicationConcept,
+    ProblemConcept,
+    Quantity,
+)
 from healthchain.use_cases import ClinicalDecisionSupport
 from healthchain.data_generators import CdsDataGenerator
 from healthchain.models import Card, CdsFhirData, CDSRequest
@@ -17,6 +24,10 @@
 load_dotenv()
 
 
+log = logging.getLogger("healthchain")
+log.setLevel(logging.DEBUG)
+
+
 @hc.sandbox
 class MyCoolSandbox(ClinicalDecisionSupport):
     def __init__(self, testing=True):
@@ -56,31 +67,66 @@ def my_service(self, request: CDSRequest) -> List[Card]:
 
 @hc.sandbox
 class NotereaderSandbox(ClinicalDocumentation):
-    def __init__(self, testing=True):
-        self.testing = testing
+    def __init__(self):
+        self.overwrite = True
 
     @hc.ehr(workflow="sign-note-inpatient")
     def load_data_in_client(self) -> CcdData:
         # data = self.data_generator.generate()
         # return data
 
-        with open("./resources/epic_cda.xml", "r") as file:
+        with open("./resources/uclh_cda.xml", "r") as file:
             xml_string = file.read()
 
         return CcdData(cda_xml=xml_string)
 
     @hc.api
     def my_service(self, ccd_data: CcdData) -> CcdData:
-        # if self.testing:
-        #     result = "test"
+        print(ccd_data.problems)
+        print(ccd_data.medications)
+        print(ccd_data.allergies)
 
         new_problem = ProblemConcept(
             code="38341003",
             code_system="2.16.840.1.113883.6.96",
             code_system_name="SNOMED CT",
             display_name="Hypertension",
         )
-        ccd_data.problems = [new_problem]
+        new_other_problem = ProblemConcept(
+            code="12341",
+            code_system="2.16.840.1.113883.6.96",
+            code_system_name="SNOMED CT",
+            display_name="Diabetes",
+        )
+        new_allergy = AllergyConcept(
+            code="70618",
+            code_system="2.16.840.1.113883.6.96",
+            code_system_name="SNOMED CT",
+            display_name="Allergy to peanuts",
+        )
+        another_allergy = AllergyConcept(
+            code="12344",
+            code_system="2.16.840.1.113883.6.96",
+            code_system_name="SNOMED CT",
+            display_name="CATS",
+        )
+        new_medication = MedicationConcept(
+            code="197361",
+            code_system="2.16.840.1.113883.6.88",
+            code_system_name="RxNorm",
+            display_name="Lisinopril 10 MG Oral Tablet",
+            dosage=Quantity(value=10, unit="mg"),
+            route=Concept(
+                code="26643006",
+                code_system="2.16.840.1.113883.6.96",
+                code_system_name="SNOMED CT",
+                display_name="Oral",
+            ),
+        )
+        ccd_data.problems = [new_problem, new_other_problem]
+        ccd_data.allergies = [new_allergy, another_allergy]
+        ccd_data.medications = [new_medication]
+
         print(ccd_data.note)
 
         return ccd_data