feat: initial commit

compose.yml

@@ -76,3 +76,22 @@ services:
     depends_on:
       api:
         condition: service_healthy
+
+# TODO: fix this
+  algo-test-runner:
+      image: "python:3.11-slim"
+      env_file:
+        - tests/algorithm/algo.env
+      environment:
+        DB_URI: "postgresql+psycopg2://postgres:pw@db:5432/postgres"
+        API_URL: "http://api:8080"
+      command: sh -c "pip install pandas && python scripts/seed_db.py"
+      volumes:
+        - ./tests/algorithm/scripts:/scripts
+      depends_on:
+        db:
+          condition: service_healthy
+        api:
+          condition: service_healthy
+      profiles:
+        - algo-test

tests/algorithm/README.md

@@ -0,0 +1,45 @@
+# Record Linkage Algorithm Testing
+
+This repository contains a project to test the effectiveness of the RecordLinker algorithm.
+
+## Prerequisites
+
+Before getting started, ensure you have the following installed:
+
+- [Docker](https://docs.docker.com/engine/install/)
+- [Docker Compose](https://docs.docker.com/compose/install/)
+
+## Setup
+
+Before getting started, ensure you have the following installed:
+
+- [Docker](https://docs.docker.com/engine/install/)
+- [Docker Compose](https://docs.docker.com/compose/install/)
+
+<!-- ## Steup
+
+1. Build the Docker images:
+
+    ```bash
+    docker compose --profile algo-test build
+    ```
+
+2. Configure environment variables
+
+    ```bash
+    edit tests/algorithm/algo.env
+    ```
+    Edit the environment variables to set the seed csv file used
+
+## Running Algorithm Tests
+
+1. Run the Synthea tests
+
+    ```bash
+    docker compose --profile algo-test run --rm algo-test-runner python scripts/seed_db.py  #TODO: script name
+    ```
+
+2. Analyze the results
+
+    The results of the algorithm tests will be available in the `tmp/results` directory. -->
+

tests/algorithm/algo.env

@@ -0,0 +1,3 @@
+SEED_CSV_FILE=
+DB_URI="tests"
+API_URL="api estst"

tests/algorithm/scripts/seed_db.py

@@ -0,0 +1,61 @@
+import sys
+import os
+import requests
+import pandas as pd
+
+
+def seed_database(api_url, csv_file):
+    # # Load the CSV data
+    df = pd.read_csv(csv_file)
+
+    cluster_group = []
+
+    for _, row in df.iterrows():
+        # Convert the row to a dictionary
+        record_data = row.to_dict()
+
+        # convert row to a pii_record
+        pii_record = {
+            "external_id": record_data['ID'],
+            "birth_date": record_data['BIRTHDATE'],
+            "sex": record_data['GENDER'],
+            "address": [
+                {
+                    "line": [record_data['ADDRESS']],
+                    "city": record_data['CITY'],
+                    "state": record_data['STATE'],
+                    "county": record_data['COUNTY'],
+                    "postal_code": str(record_data['ZIP'])
+                }
+            ],
+            "name": [
+                {
+                "given": [record_data['FIRST']],
+                "family": record_data['LAST']
+                }
+            ],
+            "ssn": record_data['SSN'],
+            "race": record_data['RACE']
+        }
+
+        # nesting for the seeding api request
+        cluster = {"records": [pii_record]}
+        cluster_group.append(cluster)
+
+    # # make request to api to seed the db
+    # try:
+    #     response = requests.post(api_url, json=pii_record)
+    #     response.raise_for_status()  # Raise an error for bad status codes
+    #     print(f"Successfully posted record {pii_record['external_id']}: {response.status_code}")
+    # except requests.exceptions.RequestException as e:
+    #     print(f"Failed to post record {pii_record['external_id']}: {e}")
+
+if __name__ == "__main__":
+    if len(sys.argv) != 2:
+        print("Usage: python seed_db.py <seedfile.csv>")
+        sys.exit(1)
+
+    csv_file = sys.argv[1]
+
+
+    seed_database("http://localhost:8080/", csv_file)

tests/algorithm/scripts/test.py

@@ -0,0 +1 @@
+print("Heloo World")