initial commit

fhir_utils/fhir/patient/parsers.py

@@ -0,0 +1,45 @@
+
+
+def fhir_to_dict(fhir_json: str, source: str) -> dict:
+    # Extract identifiers
+    identifiers = []
+    for identifier in fhir_json["identifier"]:
+        identifiers.append({"code": identifier["type"]["coding"][0]["code"],
+                            "value": identifier["value"]})
+
+    # Extract extensions
+    parents = []
+    race_ethnicity = {"race":"", "indigenous_ethnicity":""}
+
+    # TODO: add case for other extensions
+    for extension in fhir_json["extension"]:
+        match  extension["extension"][0]["url"]:
+            case "relationship":
+                parents.append({"code": extension["extension"][0]["valueCode"],
+                                "name": extension["extension"][1]["valueHumanName"]["text"]
+                                })
+            case "race":
+                race_ethnicity.update({"race": extension["extension"][0]["valueCodeableConcept"]["coding"][0]["code"]})
+            case _:
+                pass
+
+    return {"data": {"active": fhir_json["active"] if "active" in fhir_json.keys() else "",
+                     "address": fhir_json["address"] if "address" in fhir_json.keys() else "",
+                     "birth_city": "",
+                     "birth_country": "",
+                     "birth_date": fhir_json["birthDate"] if "birthDate" in fhir_json.keys() else "",
+                     "deceased": fhir_json["deceasedBoolean"] if "deceasedBoolean" in fhir_json.keys() else "",
+                     "gender": fhir_json["gender"] if "gender" in fhir_json.keys() else "",
+                     "identifiers": identifiers,
+                     "name": fhir_json["name"][0]["text"] if "name" in fhir_json.keys() else "",
+                     "nationality": "",
+                     "naturalization": "",
+                     "parents": parents,
+                     "protected_person": "",
+                     "race_ethnicity": race_ethnicity,
+                     "register_quality": "",
+                     "self.telecom":  fhir_json["telecom"] if "telecom" in fhir_json.keys() else ""
+                    },
+            "source": source
+            }
+

fhir_utils/fhir/patient/resource.py

@@ -0,0 +1,37 @@
+# -*- coding: utf-8 -*-
+
+class Patient:
+
+    elements_required = ["active", "birthCountry", "birthDate", "gender", "identifier", "name"]
+
+    def __init__(self, patient: dict, source: str):
+
+        #verify
+
+        # verify if all required elements are in patient
+        elements_required_missing = []
+        for key in elements_required:
+            if key not in patient:
+                elements_required_missing.append(key)
+        if len(elements_required_missing) > 0:
+                raise f"Missing required element(s): {elements_required_missing}"
+
+
+        self.source = source
+        self.active = None
+        self.address =  None
+        self.birth_city =  None
+        self.birth_country =  None
+        self.birth_date =  None
+        self.deceased =  None
+        self.gender =  None
+        self.identifier =  None
+        self.name =  None
+        self.nationality =  None
+        self.naturalization =  None
+        self.parents =  None
+        self.protected_person =  None
+        self.race_ethnicity =  None
+        self.register_quality =  None
+        self.telecom =  None
+

run.py

@@ -0,0 +1,10 @@
+from fhir_utils.utils import json_to_dict
+from fhir_utils.fhir.patient.parsers import fhir_to_dict
+
+patient = json_to_dict("/home/thiagotrabach/tmp/patient_sample.json")
+
+patient_clean = fhir_to_dict(patient, "vitacare")
+
+print(patient_clean)
+
+