Initial checkin med admin tab

gen3_tracker/meta/cli.py

@@ -103,7 +103,7 @@ def render_graph(config: Config, directory_path: str, output_path: str, browser:
 @meta.command("dataframe")
 @click.argument('data_type',
                 required=True,
-                type=click.Choice(['Specimen', 'DocumentReference', 'ResearchSubject']),
+                type=click.Choice(['Specimen', 'DocumentReference', 'ResearchSubject', "MedicationAdministration"]),
                 default=None)
 @click.argument("directory_path",
                 type=click.Path(exists=True, file_okay=False),

gen3_tracker/meta/dataframer.py

@@ -504,6 +504,28 @@ def flattened_research_subjects(self) -> Generator[dict, None, None]:
 
             yield flat_research_subject
 
+
+    def flattened_medication_administrations(self) -> Generator[dict, None, None]:
+
+         # get all MedicationAdministrations
+         cursor = self.connect()
+         cursor.execute(
+             "SELECT * FROM resources where resource_type = ?", ("MedicationAdministration",)
+         )
+
+         # get research subject and associated .subject patient
+         for _, _, raw_medication_administration in cursor.fetchall():
+             medication_administration = json.loads(raw_medication_administration)
+             flat_medication_administration = SimplifiedResource.build(
+                 resource=medication_administration
+             ).simplified
+
+             patient = get_subject(self, medication_administration)
+             flat_medication_administration.update(patient)
+
+             yield flat_medication_administration
+
+
     def flattened_document_references(self) -> Generator[dict, None, None]:
         """generator that yields document references populated
         with DocumentReference.subject fields and Observation codes through Observation.focus
@@ -607,6 +629,8 @@ def create_dataframe(
         df = pd.DataFrame(db.flattened_document_references())
     elif data_type == "ResearchSubject":
         df = pd.DataFrame(db.flattened_research_subjects())
+    elif data_type == "MedicationAdministration":
+        df = pd.DataFrame(db.flattened_medication_administrations())
     elif data_type == "Specimen":
         df = pd.DataFrame(db.flattened_specimens())
     else:

gen3_tracker/meta/entities.py

@@ -405,6 +405,35 @@ def values(self) -> dict:
         return _values
 
 
+class SimplifiedMedicationAdministration(SimplifiedFHIR):
+    @computed_field
+    @property
+    def values(self) -> dict:
+        """Return a dictionary of 'value':value."""
+        _values = super().values
+        # Plucking out fields that didn't get picked up by default class simplifier.'
+        dose_value = self.resource.get("dosage", {}).get("dose", {}).get("value", None)
+        if dose_value:
+            _values["total_dosage"] = dose_value
+        occurenceTiming = self.resource.get("occurenceTiming", {}).get("repeat", {}).get("boundsRange")
+        if occurenceTiming:
+            low = occurenceTiming.get("low", {}).get("value")
+            _values["index_date_start_days"] = low if low else None
+            high = occurenceTiming.get("high", {}).get("value")
+            _values["index_date_end_days"] = high if high else None
+        for notes in self.resource.get("note", []):
+            note = notes.get("value", None)
+            if note:
+                # Probably best to concat notes together
+                _values["notes"] = _values["notes"] + "; " + note
+        for identifier in self.resource.get("identifier", []):
+            system = identifier.get("system", None)
+            if system:
+                if system.split("/")[-1] == "regimen":
+                    _values["regimen_id"] = identifier["value"]
+        return _values
+
+
 class SimplifiedCondition(SimplifiedFHIR):
     @computed_field
     @property
@@ -440,4 +469,6 @@ def build(resource: dict) -> SimplifiedFHIR:
             return SimplifiedDocumentReference(resource=resource)
         if resource_type == "Condition":
             return SimplifiedCondition(resource=resource)
+        if resource_type == "MedicationAdministration":
+            return SimplifiedMedicationAdministration(resource=resource)
         return SimplifiedFHIR(resource=resource)