feat(ingest): Add slack_hook to ingest, send notification when reinge…

…st wants to change grouping and revoke old groups. (#2392)

* Add slack_hook to ingest, send notification when reingest wants to change grouping and revoke old groups.

ingest/Snakefile

@@ -11,6 +11,7 @@ for key, value in defaults.items():
     if not key in config:
         config[key] = value
 
+config["slack_hook"] = os.getenv("SLACK_HOOK")
 # Infer whether nucleotide sequences are segmented
 config["segmented"] = len(config["nucleotide_sequences"]) > 1
 

ingest/scripts/prepare_files.py

@@ -7,13 +7,16 @@
 
 import click
 import orjsonl
+import requests
 import yaml
 
 
 @dataclass
 class Config:
     segmented: str
     nucleotide_sequences: list[str]
+    slack_hook: str
+    backend_url: str
 
 
 logger = logging.getLogger(__name__)
@@ -37,6 +40,24 @@ def ids_to_add(fasta_id, config) -> set[str]:
     return {fasta_id}
 
 
+def notify(config: Config, text: str):
+    """Send slack notification with revocation details"""
+    if config.slack_hook:
+        requests.post(config.slack_hook, data=json.dumps({"text": text}), timeout=10)
+    logger.warn(text)
+
+
+def revocation_notification(config: Config, to_revoke: dict[str, dict[str, str]]):
+    """Send slack notification with revocation details"""
+    text = (
+        f"{config.backend_url}: Ingest pipeline wants to add the following sequences"
+        f" which will lead to revocations: {to_revoke}. "
+        "If you agree with this run the regroup_and_revoke rule in the ingest pod:"
+        " `kubectl exec -it INGEST_POD_NAME -- snakemake regroup_and_revoke`."
+    )
+    notify(config, text)
+
+
 @click.command()
 @click.option("--config-file", required=True, type=click.Path(exists=True))
 @click.option("--metadata-path", required=True, type=click.Path(exists=True))
@@ -102,10 +123,14 @@ def main(
         metadata_revise.append(revise_record)
         revise_ids.update(ids_to_add(fasta_id, config))
 
+    found_seq_to_revoke = False
     for fasta_id in to_revoke:
         metadata_submit_prior_to_revoke.append(metadata[fasta_id])
         submit_prior_to_revoke_ids.update(ids_to_add(fasta_id, config))
 
+    if found_seq_to_revoke:
+        revocation_notification(config, to_revoke)
+
     def write_to_tsv(data, filename):
         if not data:
             Path(filename).touch()

kubernetes/loculus/templates/ingest-deployment.yaml

@@ -43,6 +43,11 @@ spec:
                 secretKeyRef:
                   name: ingest-ncbi
                   key: api-key
+            - name: SLACK_HOOK
+              valueFrom:
+                secretKeyRef:
+                  name: slack-notifications
+                  key: slack-hook
           args:
             - snakemake
             - results/approved