From 129197b89817cbc1f484e06f6d398b3fd0f57068 Mon Sep 17 00:00:00 2001
From: bistline <bistline@broadinstitute.org>
Date: Thu, 30 Jan 2025 13:32:20 -0500
Subject: [PATCH 1/2] adding STDOUT logging handler

---
 ingest/monitor.py              |  3 +++
 scripts/vault-gsm-migration.sh | 15 +++++++++++++--
 2 files changed, 16 insertions(+), 2 deletions(-)

diff --git a/ingest/monitor.py b/ingest/monitor.py
index 21f9e737..1ba98df9 100644
--- a/ingest/monitor.py
+++ b/ingest/monitor.py
@@ -1,5 +1,6 @@
 import logging
 import os
+import sys
 from contextlib import nullcontext
 
 # General docs for Sentry:
@@ -41,6 +42,8 @@ def setup_logger(logger_name, log_file, level=logging.DEBUG, format="default"):
         logger.propagate = True
     logger.setLevel(level)
     logger.addHandler(handler)
+    # also log to STDOUT to pass to cloud logging
+    logger.addHandler(logging.StreamHandler(sys.stdout))
     return logger
 
 
diff --git a/scripts/vault-gsm-migration.sh b/scripts/vault-gsm-migration.sh
index 04e9536b..14709bc2 100755
--- a/scripts/vault-gsm-migration.sh
+++ b/scripts/vault-gsm-migration.sh
@@ -38,7 +38,8 @@ function main {
   BASEPATH="secret/kdux/scp/development/$(whoami)"
   VAULT_SECRET=""
   ROLLBACK="false"
-  while getopts "t:p:b:s:rh" OPTION; do
+  NAME_OVERRIDE=""
+  while getopts "t:p:b:s:n:rh" OPTION; do
     case $OPTION in
       t)
         VAULT_TOKEN="$OPTARG"
@@ -55,6 +56,10 @@ function main {
         VAULT_SECRET="$OPTARG"
         echo "setting VAULT_SECRET to $VAULT_SECRET"
         ;;
+      n)
+        NAME_OVERRIDE="$OPTARG"
+        echo "using $NAME_OVERRIDE as GSM secret name"
+        ;;
       r)
         ROLLBACK="true"
         ;;
@@ -78,7 +83,12 @@ function main {
 
   # set up for GSM secret based on existing vault path
   # changes / to -, e.g. mongo/hostname becomes mongo-hostname
-  GSM_SECRET_NAME=$(echo "$VAULT_SECRET" | sed 's/\//\-/g')
+  GSM_SECRET_NAME=$(echo "$VAULT_SECRET" | sed 's/[/_]/\-/g')
+
+  # use name override if specified
+  if [[ -n "$NAME_OVERRIDE" ]]; then
+    GSM_SECRET_NAME="$NAME_OVERRIDE"
+  fi
 
   if [[ "$ROLLBACK" = "true" ]]; then
     echo "Rolling back GSM migration"
@@ -109,6 +119,7 @@ USAGE:
   -s VAULT_SECRET set the name of the requested secret in vault to copy (no default)
 
   [OPTIONS]
+  -n GSM_NAME     set the name of the new GSM secret, otherwise defaults to old name with special chars converted to -
   -p PROJECT      set the GCP project in which to create secrets (defaults to '$(gcloud info --format="value(config.project)")')
   -b BASEPATH     set the base vault path for retrieving secrets (defaults to 'secret/kdux/scp/development/$(whoami)')
   -r              roll back migration and delete scp-ingest-pipeline secret in GSM

From 22786522fb390e97f847355be12887477557350e Mon Sep 17 00:00:00 2001
From: bistline <bistline@broadinstitute.org>
Date: Thu, 30 Jan 2025 13:49:46 -0500
Subject: [PATCH 2/2] fixing typo

---
 ingest/de.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/ingest/de.py b/ingest/de.py
index b214eab0..a6f0de32 100644
--- a/ingest/de.py
+++ b/ingest/de.py
@@ -367,7 +367,7 @@ def write_de_result(adata, group, annotation, rank_key, cluster_name, extra_para
             clean_group = DifferentialExpression.sanitize_string(group)
             out_file = f'{cluster_name}--{clean_annotation}--{clean_group}--{annot_scope}--{method}.tsv'
             DifferentialExpression.de_logger.info(
-                f"Writing DE output for {clean_group} vs restq"
+                f"Writing DE output for {clean_group} vs rest"
             )
         elif de_type == "pairwise":
             # rank_genes_groups accepts a list. For SCP pairwise, should be a list with one item