fhir-reada 0.1.1__py3-none-any.whl → 0.1.3__py3-none-any.whl

fhir_reada/__init__.py

@@ -1 +1 @@
-__version__ = "0.1.1"
+__version__ = "0.1.3"

fhir_reada/cli.py

@@ -28,8 +28,11 @@ def run_cli(url, min_age, max_age, diagnosis, output_file):
 
     print("De-identifying and exporting to CSV...")
     deidentified = [deidentify_patient_bundle(b) for b in bundles]
-    export_to_csv(deidentified, filename=output_file)
-    print(f"Exported to {output_file}")
+    if deidentified:
+        export_to_csv(deidentified, filename=output_file)
+        print(f"✅ Exported to {output_file}")
+    else:
+        print("⚠️ No data to export; file was not created.")
 
 def main():
     parser = argparse.ArgumentParser(description="FHIR Cohort Extractor")

fhir_reada/deid_utils.py

@@ -1,4 +1,18 @@
 from hashlib import sha256
+from datetime import datetime
+
+def get_birth_year_and_age(birth_date_str):
+    try:
+        birth = datetime.strptime(birth_date_str, "%Y-%m-%d")
+        today = datetime.today()
+        age = today.year - birth.year - ((today.month, today.day) < (birth.month, birth.day))
+        birth_year = birth.year
+        return (
+            "90+" if age >= 90 else str(birth_year),
+            "90+" if age >= 90 else str(age)
+        )
+    except Exception:
+        return ("UNKNOWN", "UNKNOWN")
 
 def deidentify_patient_bundle(bundle):
     patient = bundle["patient"]
@@ -6,12 +20,15 @@ def deidentify_patient_bundle(bundle):
     observations = bundle["observations"]
 
     patient_id = patient.get("id", "")
-    pseudo_id = sha256(patient_id.encode()).hexdigest()[:10]
+    pseudo_id = sha256(patient_id.encode()).hexdigest()
+
+    birth_year, age = get_birth_year_and_age(patient.get("birthDate"))
 
     return {
         "id": pseudo_id,
         "gender": patient.get("gender"),
-        "birthDate": patient.get("birthDate"),
+        "birthYear": birth_year,
+        "age": age,
         "conditions": "; ".join(conditions) if conditions else "None",
         "observations": "; ".join(observations) if observations else "None"
     }

{fhir_reada-0.1.1.dist-info → fhir_reada-0.1.3.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: fhir-reada
-Version: 0.1.1
+Version: 0.1.3
 Summary: A FHIR cohort extractor and de-identification tool for clinical research.
 Author-email: Tobenna Oduah <tjlite81@gmail.com>
 License: MIT
@@ -49,7 +49,7 @@ pip install -e .
 ## 🚀 Usage (CLI)
 
 ```bash
-fhir-reada --url https://hapi.fhir.org/baseR4 --min-age 25 --max-age 40 --diagnosis diabetes --out output.csv
+fhir-reada --url https://r4.smarthealthit.org  --min-age 25 --max-age 40 --diagnosis diabetes --out output.csv
 ```
 
 ---
@@ -58,7 +58,7 @@ fhir-reada --url https://hapi.fhir.org/baseR4 --min-age 25 --max-age 40 --diagno
 
 | Option         | Description                                          |
 |----------------|------------------------------------------------------|
-| `--url`        | FHIR base URL (e.g. `https://hapi.fhir.org/baseR4`) |
+| `--url`        | FHIR base URL (e.g. `https://r4.smarthealthit.org`) |
 | `--min-age`    | Minimum age for cohort (e.g. `25`)                  |
 | `--max-age`    | Maximum age for cohort (e.g. `40`)                  |
 | `--diagnosis`  | Diagnosis keyword (optional, e.g. `diabetes`)       |

fhir_reada-0.1.3.dist-info/RECORD

@@ -0,0 +1,12 @@
+fhir_reada/__init__.py,sha256=R5TtpJu7Qu6sOarfDpp-5Oyy8Pi2Ir3VewCvsCQiAgo,21
+fhir_reada/cli.py,sha256=-G3oQnXhukBWkS6QS8WkNeJG0Llk61b7_EThh4vyWQM,1860
+fhir_reada/cohort_builder.py,sha256=92XcLJJZfAZWdUVJBCZ3fPlPNY6AZ-8GPOQSEixO9YM,970
+fhir_reada/deid_utils.py,sha256=O-W4vGH6XUAnZXsXYfqgz5Nu89mZ78zJbkj6CSKL-rg,1157
+fhir_reada/exporter.py,sha256=FU19ArPFrcHadm7oL4T0h1tGwbyB2XjwnTM4ctAVdNI,360
+fhir_reada/fhir_connector.py,sha256=CDGWwj6Pxw2g-4YU3DgftmQp0lwzmyx_6FAbN32GZNk,1423
+fhir_reada-0.1.3.dist-info/LICENSE,sha256=sb_e78Fe7Dk6yq7gU0w6bytrGEinwYKP527HSihtlio,1111
+fhir_reada-0.1.3.dist-info/METADATA,sha256=jMUQAsRnpCSxAARR-g3JdFCkBNhMTSPrUj7mT3BS0Aw,2205
+fhir_reada-0.1.3.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
+fhir_reada-0.1.3.dist-info/entry_points.txt,sha256=WGQ4P92SzyjFFTLUZlo6lSqQumr4MvfF05eOXhpgcpQ,51
+fhir_reada-0.1.3.dist-info/top_level.txt,sha256=vJum_GABH4sFXP_XWV47DC7L7Yun_8h21vM5L8pdZ_0,11
+fhir_reada-0.1.3.dist-info/RECORD,,

fhir_reada-0.1.1.dist-info/RECORD

@@ -1,12 +0,0 @@
-fhir_reada/__init__.py,sha256=8oAxKUG747GUokmxjkrWejyJa5yPNEsoJDlXxoedxTw,21
-fhir_reada/cli.py,sha256=ee-qaFbC9rnRinxDY55CsrAN2jtRApMh_OcU4yyYMVg,1749
-fhir_reada/cohort_builder.py,sha256=92XcLJJZfAZWdUVJBCZ3fPlPNY6AZ-8GPOQSEixO9YM,970
-fhir_reada/deid_utils.py,sha256=ZCNrEUm_oq6VrAgGovAwUaIavvyhOBJrU4XNqHAeghA,577
-fhir_reada/exporter.py,sha256=FU19ArPFrcHadm7oL4T0h1tGwbyB2XjwnTM4ctAVdNI,360
-fhir_reada/fhir_connector.py,sha256=CDGWwj6Pxw2g-4YU3DgftmQp0lwzmyx_6FAbN32GZNk,1423
-fhir_reada-0.1.1.dist-info/LICENSE,sha256=sb_e78Fe7Dk6yq7gU0w6bytrGEinwYKP527HSihtlio,1111
-fhir_reada-0.1.1.dist-info/METADATA,sha256=U8DUGfz8C7cTXqK0qXravIUh0otPMkVwp82Qe6EogCM,2204
-fhir_reada-0.1.1.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
-fhir_reada-0.1.1.dist-info/entry_points.txt,sha256=WGQ4P92SzyjFFTLUZlo6lSqQumr4MvfF05eOXhpgcpQ,51
-fhir_reada-0.1.1.dist-info/top_level.txt,sha256=vJum_GABH4sFXP_XWV47DC7L7Yun_8h21vM5L8pdZ_0,11
-fhir_reada-0.1.1.dist-info/RECORD,,