Merge pull request #427 from mboudet/dev

Update Flask (and the rest)

.github/workflows/lint_test.yml

@@ -8,7 +8,7 @@ jobs:
       uses: actions/checkout@v2
     - uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Install flake8
       run: pip install flake8
     - name: Flake8
@@ -33,7 +33,7 @@ jobs:
       uses: actions/checkout@v2
     - uses: actions/setup-python@v1
       with:
-        python-version: 3.8
+        python-version: 3.11
     - name: Update apt cache
       run: sudo apt-get update
     - name: Install python-ldap deps

Makefile

@@ -106,9 +106,9 @@ serve-askomics: check-venv build-config create-user
 	@echo 'Serving AskOmics...'
 	. $(ACTIVATE)
 ifeq ($(MODE), dev)
-	FLASK_ENV=development FLASK_APP=app flask run --host=$(HOST) --port $(PORT)
+	FLASK_DEBUG=development FLASK_APP=app flask run --host=$(HOST) --port $(PORT)
 else
-	FLASK_ENV=production FLASK_APP=app gunicorn --timeout $(TIMEOUT) -w $(WORKERS) -b $(HOST):$(PORT) app
+	FLASK_APP=app gunicorn --timeout $(TIMEOUT) -w $(WORKERS) -b $(HOST):$(PORT) app
 endif
 
 serve-celery: check-venv build-config create-user

Pipfile

@@ -4,21 +4,20 @@ verify_ssl = true
 name = "pypi"
 
 [packages]
-werkzeug = "==0.16.1"
-flask = "<2"
-flask-reverse-proxy-fix = "*"
+werkzeug = "*"
+flask = "<3"
 validate-email = "*"
 gunicorn = "*"
 python-magic = "*"
 rdflib = "*"
 sparqlwrapper = "*"
 requests = "*"
-celery = "==5.0.5"
+celery = "*"
 redis = "*"
 watchdog = "*"
 gitpython = "*"
-biopython = "*"
-bcbio-gff = "*"
+biopython = "==1.81"
+bcbio-gff = "==0.7.0"
 bioblend = "*"
 pysam = "*"
 pybedtools = "*"
@@ -29,7 +28,7 @@ tld = "*"
 argh = "*"
 python-ldap = "*"
 python-dateutil = "*"
-markupsafe = "==2.0.1"
+markupsafe = "*"
 
 [dev-packages]
 pytest = "*"

askomics/app.py

@@ -7,6 +7,7 @@
 """
 
 import configparser
+import os
 
 from askomics.api.admin import admin_bp
 from askomics.api.auth import auth_bp
@@ -20,14 +21,13 @@
 from askomics.api.results import results_bp
 from askomics.api.galaxy import galaxy_bp
 from askomics.api.ontology import onto_bp
+from askomics.middleware import PrefixMiddleware
 
 from celery import Celery
 from kombu import Exchange, Queue
 
 from flask import Flask
 
-from flask_reverse_proxy_fix.middleware import ReverseProxyPrefixFix
-
 from pkg_resources import get_distribution
 
 import sentry_sdk
@@ -109,14 +109,16 @@ def create_app(config='config/askomics.ini', app_name='askomics', blueprints=Non
         for blueprint in blueprints:
             app.register_blueprint(blueprint)
 
-        if app.config['ENV'] == "production":
+        is_gunicorn = "gunicorn" in os.environ.get("SERVER_SOFTWARE", "")
+
+        if is_gunicorn:
             log_level = 10 if app.config['DEBUG'] else 20
             gunicorn_logger = logging.getLogger('gunicorn.error')
             app.logger.handlers = gunicorn_logger.handlers
             app.logger.setLevel(log_level)
 
     if proxy_path:
-        ReverseProxyPrefixFix(app)
+        app.wsgi_app = PrefixMiddleware(app.wsgi_app, prefix=proxy_path.rstrip("/"))
 
     return app
 

askomics/middleware.py

@@ -0,0 +1,13 @@
+class PrefixMiddleware(object):
+
+    def __init__(self, app, prefix=''):
+        self.app = app
+        self.prefix = prefix
+
+    def __call__(self, environ, start_response):
+        if self.prefix is not None:
+            environ['SCRIPT_NAME'] = self.prefix
+            path_info = environ['PATH_INFO']
+            if path_info.startswith(self.prefix):
+                environ['PATH_INFO'] = path_info[len(self.prefix):]
+        return self.app(environ, start_response)

docker/Dockerfile

@@ -1,4 +1,4 @@
-FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.13 AS builder
+FROM quay.io/askomics/flaskomics-base:4.6.0-alpine3.19 AS builder
 MAINTAINER "Xavier Garnier <[email protected]>"
 
 COPY . /askomics
@@ -7,7 +7,7 @@ WORKDIR /askomics
 RUN make clean-config fast-install build
 
 # Final image
-FROM alpine:3.13
+FROM alpine:3.19
 
 WORKDIR /askomics
 RUN apk add --no-cache make python3 bash git libc-dev libstdc++ nodejs-current npm openldap-dev

docker/DockerfileCelery

@@ -1,4 +1,4 @@
-FROM quay.io/askomics/flaskomics-base:4.0.0-alpine3.13 AS builder
+FROM quay.io/askomics/flaskomics-base:4.6.0-alpine3.19 AS builder
 MAINTAINER "Xavier Garnier <[email protected]>"
 
 COPY . /askomics
@@ -7,7 +7,7 @@ WORKDIR /askomics
 RUN make clean-config fast-install
 
 # Final image
-FROM alpine:3.13
+FROM alpine:3.19
 
 WORKDIR /askomics
 RUN apk add --no-cache make python3 bash git libc-dev libstdc++ openldap-dev