Merge branch 'main' of https://github.com/sennetconsortium/ingest-api

ingest-api-spec.yaml

@@ -595,6 +595,19 @@ paths:
                   error:
                     type: string
 
+  /metadata/data-provider-groups:
+    get:
+      tags:
+        - metadata
+      summary: Returns an array of nested objects containing information pertaining to all Data Provider groups.
+      responses:
+        "200":
+          description: The JSON containing an array of data provider group information
+        "401":
+          description: User's token is not valid
+        "500":
+          description: An unexpected error occurred
+
   /sources/bulk/validate:
     post:
       tags:
@@ -839,4 +852,4 @@ paths:
         "401":
           description: User's token is not valid
         "500":
-          description: An unexpected error occured
+          description: An unexpected error occurred

src/lib/services.py

@@ -235,7 +235,7 @@ def bulk_update_entities(
                 )
                 results[uuid] = {
                     "success": res.ok,
-                    "data": res.json() if res.ok else res.json().get("error"),
+                    "data": res.json() if res.ok else error_msg(res.json())
                 }
             except requests.exceptions.RequestException as e:
                 logger.error(f"Failed to update entity {uuid}: {e}")
@@ -322,7 +322,7 @@ def bulk_create_entities(
                 results.append(
                     {
                         "success": res.ok,
-                        "data": res.json() if res.ok else res.json().get("error"),
+                        "data": res.json() if res.ok else error_msg(res.json())
                     }
                 )
             except requests.exceptions.RequestException as e:
@@ -336,3 +336,24 @@ def bulk_create_entities(
                 time.sleep(throttle)
 
     return results
+
+
+def error_msg(json_res: dict) -> str:
+    """Get the error message from the json response.
+
+    Parameters
+    ----------
+    json_res : dict
+        The json response from the request.
+
+    Returns
+    -------
+    str
+        The error message from the json response.
+    """
+    if "error" in json_res:
+        return json_res["error"]
+    if "message" in json_res:
+        return json_res["message"]
+
+    return str(json_res)

src/routes/metadata/__init__.py

@@ -2,6 +2,7 @@
 import logging
 import os
 import time
+from http.client import HTTPException
 from uuid import uuid4
 
 from atlas_consortia_commons.decorator import (
@@ -19,7 +20,8 @@
     rest_server_err,
 )
 from atlas_consortia_commons.string import equals
-from flask import Blueprint, jsonify
+from flask import Blueprint, jsonify, Response, current_app
+from hubmap_commons.hm_auth import AuthHelper
 from rq.job import Job, JobStatus, NoSuchJobError
 
 from jobs import (
@@ -177,6 +179,26 @@ def register_metadata_upload(body: dict, token: str, user: User):
     return jsonify({"job_id": job_id, "status": display_status}), 202
 
 
+# Fetch all Data Provider groups through Hubmap Commons
+# Returns an Array of nested objects containing all groups
+@metadata_blueprint.route('/metadata/data-provider-groups', methods=['GET'])
+@require_valid_token()
+def get_all_data_provider_groups(token: str, user: User):
+    try:
+        auth_helper_instance = AuthHelper.instance()
+        group_list = auth_helper_instance.getHuBMAPGroupInfo()
+        return_list = []
+        for group_info in group_list.keys():
+            if group_list[group_info]['data_provider'] == True:
+                return_list.append(group_list[group_info])
+        return jsonify({'groups': return_list}), 200
+    except HTTPException as hte:
+        return Response(hte.get_description(), hte.get_status_code())
+    except Exception as e:
+        logger.error(e, exc_info=True)
+        return Response("Unexpected error while fetching group list: " + str(e) + "  Check the logs", 500)
+
+
 def check_metadata_upload():
     """Checks the uploaded file.