make ena-submission github repo public, remove need for PAT and USERN…

…AME.
loculus-project · Sep 18, 2024 · 59aad25 · 59aad25
1 parent af9849c
commit 59aad25
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Showing 5 changed files with 8 additions and 44 deletions.
diff --git a/ena-submission/config/defaults.yaml b/ena-submission/config/defaults.yaml
@@ -7,9 +7,7 @@ unique_project_suffix: Loculus
 ena_submission_username: fake-user
 ena_submission_password: fake-password
 ena_submission_url: https://wwwdev.ebi.ac.uk/ena/submit/drop-box/submit # TODO(https://github.com/loculus-project/loculus/issues/2425): update in production
-github_username: fake_username
-github_pat: fake_pat
-github_url: https://api.github.com/repos/pathoplexus/ena-submission/contents/test/approved_ena_submission_list.json?ref=main # TODO(https://github.com/loculus-project/loculus/issues/2425): update in production
+github_url: https://raw.githubusercontent.com/pathoplexus/ena-submission/main/test/approved_ena_submission_list.json # TODO(https://github.com/loculus-project/loculus/issues/2425): update in production
 ena_reports_service_url: https://wwwdev.ebi.ac.uk/ena/submit/report # TODO(https://github.com/loculus-project/loculus/issues/2425): update in production
 #ena_checklist: ERC000033 - do not use until all fields are mapped to ENA accepted options
 metadata_mapping:

diff --git a/ena-submission/scripts/trigger_submission_to_ena.py b/ena-submission/scripts/trigger_submission_to_ena.py
@@ -4,7 +4,6 @@
 import base64
 import json
 import logging
-import os
 import time
 from dataclasses import dataclass
 from typing import Any
@@ -13,7 +12,6 @@
 import requests
 import yaml
 from psycopg2.pool import SimpleConnectionPool
-from requests.auth import HTTPBasicAuth
 from submission_db_helper import (
     SubmissionTableEntry,
     add_to_submission_table,
@@ -37,8 +35,6 @@ class Config:
     db_username: str
     db_password: str
     db_host: str
-    github_username: str
-    github_pat: str
     github_url: str
 
 
@@ -102,17 +98,8 @@ def trigger_submission_to_ena(log_level, config_file, input_file=None):
 
     while True:
         # In a loop get approved sequences uploaded to Github and upload to submission_table
-        github_username = os.getenv("GITHUB_USERNAME")
-        if not github_username:
-            github_username = config.github_username
-
-        github_pat = os.getenv("GITHUB_PAT")
-        if not github_pat:
-            github_pat = config.github_pat
-
         response = requests.get(
             config.github_url,
-            auth=HTTPBasicAuth(github_username, github_pat),
             timeout=10,
         )
 
@@ -123,7 +110,7 @@ def trigger_submission_to_ena(log_level, config_file, input_file=None):
             error_msg = f"Failed to retrieve file: {response.status_code}"
             logger.error(error_msg)
         upload_sequences(db_config, sequences_to_upload)
-        time.sleep(30)  # Sleep for 30seconds to not overwhelm github
+        time.sleep(60)  # Sleep for 1min to not overwhelm github
 
 
 if __name__ == "__main__":

diff --git a/kubernetes/loculus/templates/ena-submission-deployment.yaml b/kubernetes/loculus/templates/ena-submission-deployment.yaml
@@ -99,16 +99,6 @@ spec:
                 secretKeyRef:
                   name: ena-submission
                   key: password
-            - name: GITHUB_USERNAME
-              valueFrom:
-                secretKeyRef:
-                  name: github-approval-repo
-                  key: github-username
-            - name: GITHUB_PAT
-              valueFrom:
-                secretKeyRef:
-                  name: github-approval-repo
-                  key: github-pat
           args:
             - snakemake
             - results/triggered

diff --git a/kubernetes/loculus/values.yaml b/kubernetes/loculus/values.yaml
@@ -1483,11 +1483,6 @@ secrets:
       slack-hook: "dummy"
       slack-token: "dummy"
       slack-channel-id: "dummy"
-  github-approval-repo:
-    type: raw
-    data:
-      github-username: "dummy"
-      github-pat: "dummy"
   ena-submission:
     type: raw
     data:
@@ -1564,9 +1559,9 @@ resources:
     limits:
       memory: "3Gi"
 defaultResources:
-    requests:
-      memory: "200Mi"
-      cpu: "20m"
-    limits:
-       memory: "1Gi"
-       cpu: "20m"
+  requests:
+    memory: "200Mi"
+    cpu: "20m"
+  limits:
+    memory: "1Gi"
+    cpu: "20m"
diff --git a/kubernetes/loculus/values_preview_server.yaml b/kubernetes/loculus/values_preview_server.yaml
@@ -22,12 +22,6 @@ secrets:
       slack-hook: 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
       slack-token: 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
       slack-channel-id: 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
-  github-approval-repo:
-    type: sealedsecret
-    clusterWide: "true"
-    encryptedData:
-      github-username: 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
-      github-pat: 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
   ena-submission:
     type: sealedsecret
     clusterWide: "true"