wip debugging

backend/src/repository/analysis_collection.py

@@ -1,6 +1,7 @@
 """
 Collection with retrieves, creates, and modify analyses.
 """
+import json
 from typing import List
 from uuid import uuid4
 
@@ -107,10 +108,26 @@ def update_analysis_nominator(self, analysis_name: str, nominator: str):
         updated_analysis_document.pop("_id", None)
         return updated_analysis_document
 
-    def update_analysis_sections(self, analysis_name: str, updated_sections: List[Section]):
+    def update_analysis_sections(self, analysis_name: str, updated_sections_json: List):
         """Updates each of the sections and fields within the sections if they exist in the database"""
-        for section in updated_sections:
+        # print("")
+        # print("the original")
+        print(type(updated_sections_json))
+        # print(updated_sections_json)
+        for section_str in updated_sections_json:
+            # print("in loop")
+            # print(section_str)
+            print(type(section_str))
+            print("what is going into the json loads")
+            print(section_str)
+            section_json = json.loads(section_str)
+            print(type(section_json))
+            print("what is the object of the result of json.loads")
+            # print(section_json)
+            section = Section(**section_json)
+            # print(section)
             for field in section.content:
+
                 field_name, field_value = field["fieldName"], field["value"]
                 if "Nominator" == field_name:
                     self.update_analysis_nominator(analysis_name, '; '.join(field_value))

backend/src/routers/analysis_router.py

@@ -8,7 +8,7 @@
 from typing import List, Optional, Union
 
 from fastapi import (
-    APIRouter, BackgroundTasks, Depends, HTTPException, File, status, UploadFile, Form, Response, Security
+    APIRouter, BackgroundTasks, Body, Depends, HTTPException, File, status, UploadFile, Form, Response, Security
 )
 from fastapi.responses import StreamingResponse
 
@@ -111,15 +111,16 @@ def update_event(
 def update_analysis_sections(
     analysis_name: str,
     row_type: SectionRowType,
-    updated_sections: List = Form(...),
+    updated_sections: List[Section] = Body(...),
     # upload_file: UploadFile = File(None),
     repositories=Depends(database),
     authorized=Security(get_authorization, scopes=["write"])  #pylint: disable=unused-argument
 ):
     """Updates the sections that have changes"""
 
     print("UPDATING THE SECTIONS FROM THE SENT")
-    print(updated_sections)
+    print(type(updated_sections))
+
     # print("Upload file exist?")
     # print(upload_file)
     if row_type == SectionRowType.TEXT:

backend/tests/integration/test_analysis_routers.py

@@ -86,7 +86,7 @@ def test_import_analysis_with_phenotips_json(
 def test_update_analysis_sections(client, mock_access_token, mock_repositories, cpam0047_analysis_json):
     """Testing if the update analysis endpoint updates an existing analysis"""
 
-    mock_updated_sections = [{
+    mock_updated_sections =[{
         "header": "Brief",
         "content": [{"fieldName": "Reason", "value": ["the quick brown fox jumps over the lazy dog."]},
                     {"fieldName": "Nominated", "value": ["Lorem ipsum dolor"]}]