Cleanup, logging, python version upgrage for docker, exception handling

Author: dashrath-chauhan

Dockerfile

@@ -1,4 +1,4 @@
-FROM python:3.11-slim
+FROM python:3.13-slim
 
 WORKDIR /app
 

app/services/epmc_client.py

@@ -1,14 +1,17 @@
+import logging
 import requests
 import pandas as pd
 import json
 import app.constants.api as api_constants
 
+logger = logging.getLogger(__name__)
+
 
 def get_json(endpoint):
     """
     Generic GET → JSON helper (same as pypi_client.get_json).
     """
-    print(f"Calling API: {endpoint}")
+    logger.debug("Calling API: %s", endpoint)
     resp = requests.get(endpoint, timeout=30)
     resp.raise_for_status()
     return resp.json()
@@ -25,7 +28,7 @@ def get_all_paginated(endpoint, limit=1000):
 
     while True:
         params = {"limit": limit, "skip": skip}
-        print(f"Calling API: {endpoint} params={params}")
+        logger.debug("Calling API: %s params=%s", endpoint, params)
         resp = requests.get(endpoint, params=params, timeout=30)
         resp.raise_for_status()
         data = resp.json()

app/services/github_client.py

@@ -1,3 +1,4 @@
+import logging
 import requests
 import pandas as pd
 import numpy as np
@@ -6,13 +7,15 @@
 
 import app.constants.api as api_constants
 
+logger = logging.getLogger(__name__)
+
 
 def get_json(endpoint: str, token: Optional[str] = None):
     headers = {}
     if token:
         headers["Authorization"] = f"token {token}"
 
-    print(f"Calling API: {endpoint}")
+    logger.debug("Calling API: %s", endpoint)
     resp = requests.get(endpoint, headers=headers, timeout=30)
     resp.raise_for_status()
     return resp.json()

app/services/pypi_client.py

@@ -1,7 +1,11 @@
+import logging
 import requests
 import app.constants.api as api_constants
 import pandas as pd
 
+logger = logging.getLogger(__name__)
+
+
 def get_json(endpoint):
     """
     Function to get JSON response from API for get_json
@@ -10,7 +14,7 @@ def get_json(endpoint):
     Returns:
         dict: JSON response from the API
     """
-    print(f"Calling API: {endpoint}")
+    logger.debug("Calling API: %s", endpoint)
     resp = requests.get(endpoint, timeout=30)
     resp.raise_for_status()
     return resp.json()

app/services/service_map_client.py

@@ -1,7 +1,10 @@
+import logging
 import requests
 import pandas as pd
 from typing import Optional
 
+logger = logging.getLogger(__name__)
+
 BASE_URL = "https://implementation-registry.ga4gh.org/api"
 STANDARDS_ENDPOINT = f"{BASE_URL}/standards"
 SERVICES_ENDPOINT = f"{BASE_URL}/services"
@@ -12,7 +15,7 @@ def get_json(endpoint: str, token: Optional[str] = None):
     if token:
         headers["Authorization"] = f"token {token}"
 
-    print(f"Calling API: {endpoint}")
+    logger.debug("Calling API: %s", endpoint)
     resp = requests.get(endpoint, headers=headers, timeout=30)
     resp.raise_for_status()
     return resp.json()