diff --git a/ingest/scripts/submit_to_loculus.py b/ingest/scripts/submit_to_loculus.py index 3a1c13095..3aee63332 100644 --- a/ingest/scripts/submit_to_loculus.py +++ b/ingest/scripts/submit_to_loculus.py @@ -3,11 +3,12 @@ import requests import logging -BRANCH="mpox-with-processing" +BRANCH="main" GROUP_NAME="insdc_ingest_group" USERNAME="insdc_ingest_user" PASSWORD="insdc_ingest_user" -KEYCLOAK_TOKEN_URL=f"https://authentication.{BRANCH}.preview.k3s.loculus.org/realms/loculusRealm/protocol/openid-connect/token" +BACKEND_URL=f"https://backend-{BRANCH}.loculus.org" +KEYCLOAK_TOKEN_URL=f"https://authentication-{BRANCH}.loculus.org/realms/loculusRealm/protocol/openid-connect/token" KEYCLOAK_CLIENT_ID="test-cli" # Apparently required to be exactly this ORGANISM="mpox" @@ -35,7 +36,7 @@ def get_jwt(username, password): def create_group(group_name): # Create the ingest group - url = f"https://backend.{BRANCH}.preview.k3s.loculus.org/groups" + url = f"{BACKEND_URL}/groups" token = get_jwt(USERNAME, PASSWORD) group_name = group_name @@ -45,7 +46,7 @@ def create_group(group_name): } data = { - "groupName": group_name + "groupName": group_name, } response = requests.post(url, json=data, headers=headers) @@ -64,7 +65,7 @@ def submit(metadata, sequences): jwt = get_jwt(USERNAME, PASSWORD) # Endpoint URL - url = f'https://backend.{BRANCH}.preview.k3s.loculus.org/{ORGANISM}/submit' + url = f'{BACKEND_URL}/{ORGANISM}/submit' # Headers with Bearer Authentication headers = { @@ -79,7 +80,8 @@ def submit(metadata, sequences): # Query parameters params = { - 'groupName': GROUP_NAME + 'groupName': GROUP_NAME, + "dataUseTermsType": "OPEN", } # POST request @@ -96,12 +98,12 @@ def approve(): """ Get sequences that were preprocessed successfully and approve them. 1. Get the ids of the sequences that were preprocessed successfully - /ORGANISM/get-sequences-of-user + /ORGANISM/get-sequences 2. Approve the sequences """ jwt = get_jwt(USERNAME, PASSWORD) - url = f'https://backend.{BRANCH}.preview.k3s.loculus.org/{ORGANISM}/get-sequences-of-user' + url = f'{BACKEND_URL}/{ORGANISM}/get-sequences' # Headers with Bearer Authentication @@ -125,7 +127,7 @@ def approve(): payload = {"accessionVersions": to_approve} - url = f'https://backend.{BRANCH}.preview.k3s.loculus.org/{ORGANISM}/approve-processed-data' + url = f'{BACKEND_URL}/{ORGANISM}/approve-processed-data' response = requests.post(url, headers=headers, json=payload) response.raise_for_status()