IRONN-210 One-off script to adjust the withdrawal dates for a group o… (

#4350)

…f patients

based on a spreadsheet supplied by the research team (see comments
inline). https://movember.atlassian.net/browse/IRONN-210

---------

Co-authored-by: Paul Bugni <pbugni@u.washington.edu>

portal/migrations/scripts/update_withdraw_date.py

@@ -0,0 +1,107 @@
+import csv
+import requests
+from datetime import datetime
+
+'''
+This is a one-off script to adjust the withdrawal dates for a group of
+patients, based on a spreadsheet supplied by the research team.
+If a row doesn't have a date in the 'Medidata_OFFSDT' column, the record
+won't be touched, and this script will indicate that.
+This is a clean-up task for 
+https://movember.atlassian.net/browse/IRONN-210 .
+
+Input file format:
+user_id,value,name,research_study_id,acceptance_date,Medidata_OFFSDT,,Done
+986,170-02-xxx,Duke Comprehensive Cancer Center,0,11/09/2023,8/30/2023,,
+2740,170-02-yyy,Duke asdf,0,11/09/2023,8/1/2023,,
+3442,170-02-zzz,Duke asdf,1,11/09/2023,2/10/2021,,
+8888,170-02-uuu,Duke asdf,0,11/09/2023,not withdrawn,,
+'''
+
+# To run this, edit the values here, and then run w/out args.
+my_token = "abc123"
+serversansslash = "https://eproms-test.cirg.washington.edu"
+inputfile = "new_withdraw_dates.csv"
+
+# Function to convert date format from 'M/D/YYYY' to 'YYYY-MM-DDT00:00:00+00:00'
+def convert_date_format(date_str):
+    try:
+        date_obj = datetime.strptime(date_str, '%m/%d/%Y')
+        new_date_str = datetime.strftime(date_obj, '%Y-%m-%dT00:00:00+00:00')
+        return new_date_str
+    except ValueError:
+        return None
+
+# Function to process the csv file
+def process_csv(file_path):
+    with open(file_path, mode='r', encoding='utf-8-sig') as csvfile:
+        reader = csv.DictReader(csvfile)
+        for row in reader:
+            user_id_data = row['user_id']
+            research_study_id_data = int(row['research_study_id'])
+            new_date_data = convert_date_format(row['Medidata_OFFSDT'])
+            if not new_date_data:
+                print(f"Date format error for user_id {user_id_data}; the string was '{row['Medidata_OFFSDT']}'")
+                continue
+
+            print(f"Processing user_id {user_id_data}")
+            headers = {
+                'Authorization': f'Bearer {my_token}'
+            }
+
+            # First API call
+            response = requests.get(
+                f"{serversansslash}/api/user/{user_id_data}/consent",
+                headers=headers
+            )
+
+            if response.status_code == 200:
+                response_text = response.text
+                #print(f"For user_id {user_id_data}, response.text:{response_text}")
+                cas = response.json()
+                consent_agreements = cas['consent_agreements']
+                #consent_agreements = response.json
+                # Find the matching consent agreement
+                matching_agreement = next(
+                    #(item for item in consent_agreements if item["research_study_id"] == 0 and item["status"] == "suspended"),
+                    (item for item in consent_agreements if item["research_study_id"] == research_study_id_data and item["status"] == "suspended"),
+                    None
+                )
+
+                if matching_agreement:
+                    org_id_data = matching_agreement['organization_id']
+                    json_data = {
+                        "organization_id": org_id_data,
+                        "acceptance_date": new_date_data,
+                        "research_study_id": research_study_id_data 
+                    }
+
+                    # Second API call
+                    response = requests.post(
+                        f"{serversansslash}/api/user/{user_id_data}/consent/withdraw",
+                        headers={**headers, 'Content-Type': 'application/json'},
+                        json=json_data
+                    )
+
+                    if response.status_code != 200:
+                        print(f"Error {response.status_code} for POST {serversansslash}/api/user/{user_id_data}/consent with data {json_data}")
+                        continue
+
+                    # Third API call
+                    response = requests.get(
+                        #f"{serversansslash}/api/patient/{user_id_data}/timeline?substudy=true&research_study_id=1&purge=true",
+                        f"{serversansslash}/api/patient/{user_id_data}/timeline?substudy=true&research_study_id={research_study_id_data}&purge=true",
+                        headers=headers
+                    )
+
+                    if response.status_code == 200:
+                        print(f"Successfully processed user_id {user_id_data}")
+                    else:
+                        print(f"Error {response.status_code} for GET {serversansslash}/api/patient/{user_id_data}/timeline")
+                else:
+                    print(f"Error: More than one or no matching consent agreements found for user_id {user_id_data}")
+            else:
+                print(f"Error {response.status_code} for GET {serversanslash}/api/user/{user_id_data}/consent")
+
+process_csv(inputfile)
+