From 7fadd2414b20dd3fb158ea6135ff76c82145cc03 Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Wed, 6 Dec 2023 10:59:43 -0500
Subject: [PATCH 1/3] chore: gunicorn logging + gevent worker + increased
 timeout

---
 container.requirements.txt | 1 +
 run.bash                   | 7 ++++++-
 2 files changed, 7 insertions(+), 1 deletion(-)

diff --git a/container.requirements.txt b/container.requirements.txt
index a986da5a..121ada7f 100644
--- a/container.requirements.txt
+++ b/container.requirements.txt
@@ -1,3 +1,4 @@
 gunicorn==21.2.0
+gevent==23.9.1
 pysam>=0.22.0,<0.23.0
 fasta-checksum-utils>=0.3.1,<0.4
diff --git a/run.bash b/run.bash
index b62692db..00373c25 100644
--- a/run.bash
+++ b/run.bash
@@ -6,12 +6,14 @@
 # Start Celery worker with log level dependent on BENTO_DEBUG
 echo "[bento_wes] [entrypoint] Starting celery worker"
 celery_log_level="INFO"
+gunicorn_log_level="info"
 if [[
   "${BENTO_DEBUG}" == "true" ||
   "${BENTO_DEBUG}" == "True" ||
   "${BENTO_DEBUG}" == "1"
 ]]; then
   celery_log_level="DEBUG"
+  gunicorn_log_level="debug"
 fi
 celery --app bento_wes.app worker --loglevel="${celery_log_level}" &
 
@@ -20,6 +22,9 @@ echo "[bento_wes] [entrypoint] Starting gunicorn"
 # using 1 worker, multiple threads
 # see https://stackoverflow.com/questions/38425620/gunicorn-workers-and-threads
 gunicorn bento_wes.app:application \
+  --log-level "${gunicorn_log_level}" \
+  --timeout 660 \
   --workers 1 \
+  --worker-class 'gevent' \
   --threads "$(( 2 * $(nproc --all) + 1))" \
-  --bind "0.0.0.0:${INTERNAL_PORT}"
+  --bind "0.0.0.0:${INTERNAL_PORT}" \

From e55ea19350a4278c3e0a5c4ef79b9f6585578072 Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Wed, 6 Dec 2023 11:04:43 -0500
Subject: [PATCH 2/3] chore: require at least werkzeug 2.2.3

---
 pyproject.toml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pyproject.toml b/pyproject.toml
index 9b93af98..5a89bef2 100644
--- a/pyproject.toml
+++ b/pyproject.toml
@@ -30,7 +30,7 @@ requests = "^2.28.1"
 Flask = "~2.2.5"
 pydantic = "^2.0.2"
 flask-cors = "^4.0.0"
-werkzeug = "~2.2.2"  # debugpy is broken with werkzeug 2.3.x so pin this manually
+werkzeug = "~2.2.3"  # debugpy is broken with werkzeug 2.3.x so pin this manually
 
 [tool.poetry.group.dev.dependencies]
 coverage = "^7.2.2"

From 9074499c1c8130448ead3bf8b6a88de967e410ff Mon Sep 17 00:00:00 2001
From: David Lougheed <david.lougheed@gmail.com>
Date: Wed, 6 Dec 2023 11:08:55 -0500
Subject: [PATCH 3/3] typo

---
 run.bash | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/run.bash b/run.bash
index 00373c25..745e1ee3 100644
--- a/run.bash
+++ b/run.bash
@@ -27,4 +27,4 @@ gunicorn bento_wes.app:application \
   --workers 1 \
   --worker-class 'gevent' \
   --threads "$(( 2 * $(nproc --all) + 1))" \
-  --bind "0.0.0.0:${INTERNAL_PORT}" \
+  --bind "0.0.0.0:${INTERNAL_PORT}"