From 243a51c61e18fc0f0096a8d012645a05a4c2cd07 Mon Sep 17 00:00:00 2001
From: Etienne Boileau <boileau@uni-heidelberg.de>
Date: Mon, 24 Jun 2024 16:35:19 +0200
Subject: [PATCH] Prepare release

---
 client/src/views/SearchView.vue           | 2 +-
 docker/app_container/Dockerfile           | 2 +-
 docker/app_container/files/entry_point.py | 1 +
 docker/app_container/files/mini_cron.sh   | 7 ++-----
 docker/app_container/files/run_flask.sh   | 9 +++++++--
 server/env_example                        | 4 ++++
 server/pyproject.toml                     | 2 +-
 server/src/scimodom/services/bedtools.py  | 2 ++
 8 files changed, 19 insertions(+), 10 deletions(-)

diff --git a/client/src/views/SearchView.vue b/client/src/views/SearchView.vue
index 74ddf6e1..6acceeab 100644
--- a/client/src/views/SearchView.vue
+++ b/client/src/views/SearchView.vue
@@ -236,7 +236,7 @@ function lazyLoad(event) {
       matchMode: 'in'
     }
   }
-  HTTP.get('/modification', {
+  HTTP.get('/modification/', {
     params: {
       modification: selectedModification.value.key,
       organism: selectedOrganism.value.key,
diff --git a/docker/app_container/Dockerfile b/docker/app_container/Dockerfile
index 8d2fd55c..2397a3fc 100644
--- a/docker/app_container/Dockerfile
+++ b/docker/app_container/Dockerfile
@@ -9,7 +9,7 @@ COPY docker/app_container/files/. /app/
 RUN apt-get update \
     && apt-get install -y bedtools findutils \
     && useradd app \
-    && mkdir -p /uploads /tmp/bedtools /app/venv \
+    && mkdir -p /uploads /app/venv \
     && chown -R app /uploads /install /app/venv \
     && cp -r /install/migrations /install/alembic.ini /app
 
diff --git a/docker/app_container/files/entry_point.py b/docker/app_container/files/entry_point.py
index 6c155d51..cdd80e06 100755
--- a/docker/app_container/files/entry_point.py
+++ b/docker/app_container/files/entry_point.py
@@ -46,4 +46,5 @@ def get_secret(path):
 system("cd /app && /app/mini_cron.sh &")
 system(
     f"exec su - app /app/run_flask.sh {environ.get('HTTP_WORKER_PROCESSES')} {environ.get('HTTP_WORKER_TIMEOUT', 30)}"
+    f" {environ.get('HTTP_REVERSE_PROXY_IPS', '')}"
 )
diff --git a/docker/app_container/files/mini_cron.sh b/docker/app_container/files/mini_cron.sh
index df445a7e..602c1686 100755
--- a/docker/app_container/files/mini_cron.sh
+++ b/docker/app_container/files/mini_cron.sh
@@ -12,11 +12,8 @@ then
     echo 'mini_cron.sh: No $UPLOAD_PATH - aborting.'
     exit 1
 fi
-if [[ -z $BEDTOOLS_TMP_PATH ]]
-then
-    echo 'mini_cron.sh: No $BEDTOOLS_TMP_PATH - aborting.'
-    exit 1
-fi
+
+mkdir -p $BEDTOOLS_TMP_PATH
 
 while [[ 1 = 1 ]]
 do
diff --git a/docker/app_container/files/run_flask.sh b/docker/app_container/files/run_flask.sh
index b08376a4..64ccfc38 100755
--- a/docker/app_container/files/run_flask.sh
+++ b/docker/app_container/files/run_flask.sh
@@ -1,4 +1,4 @@
-#!/bin/bash
+#!/bin/sh
 
 echo '### Activating venv ###'
 . /app/venv/bin/activate
@@ -6,4 +6,9 @@ cd /app
 echo '### Upgrading Database ###'
 alembic upgrade head
 echo '### Starting gunicorn ###'
-exec gunicorn -b 0.0.0.0:8000 -w $1 --timeout $2 'scimodom.app:create_app()'
+extra_opts=''
+if [ "X$3" != X ]
+then
+  extra_opts="--forwarded-allow-ips=$3"
+fi
+exec gunicorn -b 0.0.0.0:8000 -w $1 --timeout $2 $extra_opts 'scimodom.app:create_app()'
diff --git a/server/env_example b/server/env_example
index ca99f0cd..2603f31c 100644
--- a/server/env_example
+++ b/server/env_example
@@ -9,6 +9,10 @@ HTTP_WORKER_TIMEOUT=120
 # Usually you will have a reverse proxy in front to terminate TLS.
 # Use it's name below.
 HTTP_PUBLIC_URL=https://scimodom.my-site.org
+# If we run behind a reverse proxy we need to know it's IP address(es) so that we trust
+# the X-Forwarded-Proto header. Otherwise, we might generate incorrect redirects
+# (http instead of https).
+HTTP_REVERSE_PROXY_IPS=...
 
 # Mail server to use. It must be willing to relay emails
 # for your host/SMTP_FROM_ADDRESS.
diff --git a/server/pyproject.toml b/server/pyproject.toml
index 39b3ddc3..e41de248 100755
--- a/server/pyproject.toml
+++ b/server/pyproject.toml
@@ -33,7 +33,7 @@ dependencies = [
   "Flask-Cors",
   "Flask-JWT-Extended",
   "mysqlclient",
-  "numpy",
+  "numpy<2",
   "pandas",
   "pybedtools",
   "python-dotenv",
diff --git a/server/src/scimodom/services/bedtools.py b/server/src/scimodom/services/bedtools.py
index e1831ee8..3a50b6dd 100644
--- a/server/src/scimodom/services/bedtools.py
+++ b/server/src/scimodom/services/bedtools.py
@@ -1,5 +1,6 @@
 from functools import cache
 import logging
+from os import makedirs
 from pathlib import Path
 from typing import Iterable, Sequence, Any
 
@@ -91,6 +92,7 @@ def _remove_filno(feature, n_fields: int = 9, is_closest: bool = False):
 
 class BedToolsService:
     def __init__(self, tmp_path):
+        makedirs(tmp_path, exist_ok=True)
         pybedtools.helpers.set_tempdir(tmp_path)
 
     def annotate_data_using_ensembl(