Dockerfile to run service

Author: Peter Amstutz

Dockerfile

@@ -0,0 +1,34 @@
+FROM debian:9
+
+# Install passenger
+
+RUN apt-get update && \
+    apt-get install -y dirmngr gnupg && \
+    apt-key adv --keyserver hkp://keyserver.ubuntu.com:80 --recv-keys 561F9B9CAC40B2F7 && \
+    apt-get install -y apt-transport-https ca-certificates && \
+    sh -c 'echo deb https://oss-binaries.phusionpassenger.com/apt/passenger stretch main > /etc/apt/sources.list.d/passenger.list'
+
+RUN apt-get update && \
+    apt-get install -y passenger python-setuptools build-essential python-dev python-pip git && \
+    pip install pip==9.0.3
+
+RUN apt-get install -y libcurl4-openssl-dev libssl1.0-dev
+
+ARG version
+
+COPY dist/wes-service-${version}.tar.gz /root
+
+RUN cd /root && tar xzf wes-service-${version}.tar.gz && \
+    cd wes-service-${version} && \
+    pip install .[arvados]
+
+COPY passenger_wsgi.py /var/www/wes-server/passenger_wsgi.py
+
+EXPOSE 443
+
+WORKDIR /var/www/wes-server/
+RUN chown www-data:www-data -R /var/www
+
+CMD ["passenger", "start", "--environment=production", "--user=www-data", "--port=443", "--ssl", \
+    "--ssl-certificate=/etc/ssl/certs/ssl-cert-wes.pem", \
+    "--ssl-certificate-key=/etc/ssl/private/ssl-cert-wes.key"]

MANIFEST.in

@@ -0,0 +1,2 @@
+include README.pypi.rst
+include wes_service/openapi/workflow_execution_service.swagger.yaml

setup.py

@@ -42,5 +42,5 @@
               "arvados-cwl-runner"
           ]
       },
-      zip_safe=True
+      zip_safe=False
 )

wes-docker.sh

@@ -0,0 +1,10 @@
+#!/bin/sh
+set -e
+#python setup.py sdist
+docker build --build-arg version=2.2 -t commonworkflowlanguage/workflow-service .
+docker run -ti \
+       -v$PWD/config.yml:/var/www/wes-server/config.yml \
+       -v/etc/ssl/certs/ssl-cert-snakeoil.pem:/etc/ssl/certs/ssl-cert-wes.pem \
+       -v/etc/ssl/private/ssl-cert-snakeoil.key:/etc/ssl/private/ssl-cert-wes.key \
+       -v/var/run/docker.sock:/var/run/docker.sock \
+       commonworkflowlanguage/workflow-service

wes_service/__init__.py

@@ -1,19 +1,31 @@
 import argparse
 import sys
+import ruamel.yaml
+import os
+import logging
+
+logging.basicConfig(level=logging.INFO)
 
 import connexion
 import connexion.utils as utils
 from connexion.resolver import Resolver
 
+def setup(args=None):
+    if args is None:
+        args = argparse.Namespace()
 
-def main(argv=sys.argv[1:]):
-    parser = argparse.ArgumentParser(description='Workflow Execution Service')
-    parser.add_argument(
-        "--backend", type=str, default="wes_service.cwl_runner")
-    parser.add_argument("--port", type=int, default=8080)
-    parser.add_argument("--opt", type=str, action="append")
-    parser.add_argument("--debug", action="store_true", default=False)
-    args = parser.parse_args(argv)
+    configfile = "config.yml"
+    if os.path.isfile(configfile):
+        logging.info("Loading %s", configfile)
+        with open(configfile, "r") as f:
+            config = ruamel.yaml.safe_load(f)
+        for c in config:
+            setattr(args, c, config[c])
+
+
+    logging.info("Using config:")
+    for n in args.__dict__:
+        logging.info("  %s: %s", n, getattr(args, n))
 
     app = connexion.App(__name__)
     backend = utils.get_function_from_name(
@@ -26,6 +38,20 @@ def rs(x):
         'openapi/workflow_execution_service.swagger.yaml',
         resolver=Resolver(rs))
 
+    return app
+
+
+def main(argv=sys.argv[1:]):
+    parser = argparse.ArgumentParser(description='Workflow Execution Service')
+    parser.add_argument(
+        "--backend", type=str, default="wes_service.cwl_runner")
+    parser.add_argument("--port", type=int, default=8080)
+    parser.add_argument("--opt", type=str, action="append")
+    parser.add_argument("--debug", action="store_true", default=False)
+    args = parser.parse_args(argv)
+
+    app = setup(args)
+
     app.run(port=args.port, debug=args.debug)