fhir-reada 0.1.0__py3-none-any.whl → 0.1.2__py3-none-any.whl

fhir_reada/__init__.py

@@ -1 +1 @@
-__version__ = "0.1.0"
+__version__ = "0.1.2"

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-0.1.2.dist-info/METADATA

@@ -0,0 +1,86 @@
+Metadata-Version: 2.1
+Name: fhir-reada
+Version: 0.1.2
+Summary: A FHIR cohort extractor and de-identification tool for clinical research.
+Author-email: Tobenna Oduah <tjlite81@gmail.com>
+License: MIT
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: requests
+Requires-Dist: python-dateutil
+
+# FHIR-READA
+
+**FHIR Research Extractor And De-identified Analyzer**
+
+A Python CLI tool for extracting, de-identifying, and exporting patient data from FHIR servers — built for research teams, clinicians, and medical institutions.
+
+---
+
+## 🔍 Features
+
+- Filter patients by age range and diagnosis  
+- Extract from any FHIR-compliant server  
+- Fetch Conditions and Observations  
+- Automatically de-identify patient IDs  
+- Export results to CSV  
+- Easy-to-use CLI with flexible filters
+
+---
+
+## 💻 Installation
+
+**From PyPI**
+
+```bash
+pip install fhir-reada
+```
+
+**From Source (for development or testing)**
+
+```bash
+git clone https://github.com/TOduah/fhir-reada.git
+cd fhir-reada
+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
+```
+
+---
+
+## ⚙️ CLI Options
+
+| Option         | Description                                          |
+|----------------|------------------------------------------------------|
+| `--url`        | FHIR base URL (e.g. `https://hapi.fhir.org/baseR4`) |
+| `--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`)       |
+| `--out`        | Output filename for CSV export                      |
+
+---
+
+## 🏥 Who Is This For?
+
+- Research institutions running clinical studies  
+- Hospital data science or IT departments  
+- Medical schools teaching FHIR and analytics  
+- Independent developers working with public or private FHIR APIs
+
+---
+
+## 📄 License
+
+This project is licensed under the [MIT License](LICENSE).
+
+---
+
+## 💬 Author
+
+Built by [Tobenna Oduah](https://github.com/toduah).

fhir_reada-0.1.2.dist-info/RECORD

@@ -0,0 +1,12 @@
+fhir_reada/__init__.py,sha256=K5SiDdEGYMpdqXThrqwTqECJJBOQNTQDrnpc2K5mzKs,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=O-W4vGH6XUAnZXsXYfqgz5Nu89mZ78zJbkj6CSKL-rg,1157
+fhir_reada/exporter.py,sha256=FU19ArPFrcHadm7oL4T0h1tGwbyB2XjwnTM4ctAVdNI,360
+fhir_reada/fhir_connector.py,sha256=CDGWwj6Pxw2g-4YU3DgftmQp0lwzmyx_6FAbN32GZNk,1423
+fhir_reada-0.1.2.dist-info/LICENSE,sha256=sb_e78Fe7Dk6yq7gU0w6bytrGEinwYKP527HSihtlio,1111
+fhir_reada-0.1.2.dist-info/METADATA,sha256=fiDNbsi5mN0rokMpMtoCz8kJzVdvPn4uONLGHW7iYN4,2204
+fhir_reada-0.1.2.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
+fhir_reada-0.1.2.dist-info/entry_points.txt,sha256=WGQ4P92SzyjFFTLUZlo6lSqQumr4MvfF05eOXhpgcpQ,51
+fhir_reada-0.1.2.dist-info/top_level.txt,sha256=vJum_GABH4sFXP_XWV47DC7L7Yun_8h21vM5L8pdZ_0,11
+fhir_reada-0.1.2.dist-info/RECORD,,

fhir_reada-0.1.0.dist-info/METADATA

@@ -1,10 +0,0 @@
-Metadata-Version: 2.1
-Name: fhir-reada
-Version: 0.1.0
-Summary: A FHIR cohort extractor and de-identification tool for clinical research.
-Author-email: Tobenna Oduah <tjlite81@gmail.com>
-License: MIT
-License-File: LICENSE
-Requires-Dist: requests
-Requires-Dist: python-dateutil
-

fhir_reada-0.1.0.dist-info/RECORD

@@ -1,12 +0,0 @@
-fhir_reada/__init__.py,sha256=Pru0BlFBASFCFo7McHdohtKkUtgMPDwbGfyUZlE2_Vw,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-0.1.0.dist-info/LICENSE,sha256=sb_e78Fe7Dk6yq7gU0w6bytrGEinwYKP527HSihtlio,1111
-fhir_reada-0.1.0.dist-info/METADATA,sha256=GWZjuwC_yHKzHkf8kgyYIpQgVa1zdln9PyYGsv4bwtU,287
-fhir_reada-0.1.0.dist-info/WHEEL,sha256=iAkIy5fosb7FzIOwONchHf19Qu7_1wCWyFNR5gu9nU0,91
-fhir_reada-0.1.0.dist-info/entry_points.txt,sha256=WGQ4P92SzyjFFTLUZlo6lSqQumr4MvfF05eOXhpgcpQ,51
-fhir_reada-0.1.0.dist-info/top_level.txt,sha256=vJum_GABH4sFXP_XWV47DC7L7Yun_8h21vM5L8pdZ_0,11
-fhir_reada-0.1.0.dist-info/RECORD,,