Dockerfile: finish stretch→buster upgrade, python3

Author: mr-c

Dockerfile

@@ -1,41 +1,41 @@
 FROM debian:buster
 
 # Package signing keys for Docker Engine and Phusion Passenger
-ADD keys/58118E89F3A912897C070ADBF76221572C52609D.asc keys/561F9B9CAC40B2F7.asc /tmp/
+ADD keys/58118E89F3A912897C070ADBF76221572C52609D.asc keys/561F9B9CAC40B2F7.asc keys/docker-archive-keyring.gpg /tmp/
 
 # Install passenger
 
 RUN apt-get update && \
     apt-get install -y dirmngr gnupg && \
     apt-key add --no-tty /tmp/561F9B9CAC40B2F7.asc && \
     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'
+    sh -c 'echo deb https://oss-binaries.phusionpassenger.com/apt/passenger buster main > /etc/apt/sources.list.d/passenger.list'
 
 RUN apt-get update && \
     apt-get install -y --no-install-recommends passenger python3-setuptools build-essential python3-dev python3-pip git && \
-    pip3 install pip==9.0.3
+    pip3 install pip==21.1.3
 
-RUN apt-get install -y --no-install-recommends libcurl4-openssl-dev libssl1.0-dev
-
-RUN apt-key add --no-tty /tmp/58118E89F3A912897C070ADBF76221572C52609D.asc
+RUN apt-get install -y --no-install-recommends libcurl4-openssl-dev libssl-dev
 
+RUN mv /tmp/docker-archive-keyring.gpg /usr/share/keyrings/docker-archive-keyring.gpg
 RUN mkdir -p /etc/apt/sources.list.d && \
-    echo deb https://apt.dockerproject.org/repo debian-stretch main > /etc/apt/sources.list.d/docker.list && \
+    echo \
+        "deb [arch=amd64 signed-by=/usr/share/keyrings/docker-archive-keyring.gpg] https://download.docker.com/linux/debian \
+        buster stable" > /etc/apt/sources.list.d/docker.list && \
     apt-get update && \
-    apt-get -yq --no-install-recommends install docker-engine=17.05.0~ce-0~debian-stretch && \
+    apt-get -yq --no-install-recommends install docker-ce=5:20.10.7~3-0~debian-buster docker-ce-cli containerd.io && \
     apt-get clean
 
 ARG arvversion
 COPY dist/arvados-cwl-runner-${arvversion}.tar.gz /root
-RUN cd /root && pip install arvados-cwl-runner-${arvversion}.tar.gz
+RUN cd /root && pip3 install arvados-cwl-runner-${arvversion}.tar.gz
 
 ARG version
 COPY dist/wes_service-${version}-*.whl /root
-RUN cd /root && pip install $(ls wes_service-${version}-*.whl)[arvados]
-
+RUN cd /root && pip3 install $(ls wes_service-${version}-*.whl)[arvados] connexion[swagger-ui]
 COPY passenger_wsgi.py /var/www/wes-server/passenger_wsgi.py
 
 WORKDIR /var/www/wes-server/
 RUN chown www-data:www-data -R /var/www && adduser www-data docker
 
-CMD ["passenger", "start", "--environment=production", "--user=www-data"]
+CMD ["passenger", "start", "--environment=production", "--user=www-data", "--python=python3"]

keys/docker-archive-keyring.gpg

@@ -29,7 +29,6 @@
     install_requires=[
         "connexion >= 2.0.2, < 3",
         "ruamel.yaml >= 0.15.78, <= 0.16.5",
-        "schema-salad < 6",
     ],
     entry_points={
         "console_scripts": [

setup.py

@@ -1,8 +1,8 @@
 #!/bin/sh
-set -e
+set -ex
 python setup.py sdist
-docker build --build-arg version=2.3 -t commonworkflowlanguage/workflow-service .
-docker run -ti \
+docker build --build-arg version=4.0 --build-arg arvversion=2.2.1 -t commonworkflowlanguage/workflow-service .
+docker run -ti -p 127.0.0.1:3000:3000/tcp \
        -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 \

wes-docker.sh

@@ -14,7 +14,7 @@
 
 def setup(args=None):
     if args is None:
-        args = argparse.Namespace()
+        args = get_parser().parse_args([])  # grab the defaults
 
     configfile = "config.yml"
     if os.path.isfile(configfile):
@@ -43,7 +43,7 @@ def rs(x):
     return app
 
 
-def main(argv=sys.argv[1:]):
+def get_parser() -> argparse.Namespace:
     parser = argparse.ArgumentParser(description="Workflow Execution Service")
     parser.add_argument(
         "--backend",
@@ -61,7 +61,11 @@ def main(argv=sys.argv[1:]):
     )
     parser.add_argument("--debug", action="store_true", default=False)
     parser.add_argument("--version", action="store_true", default=False)
-    args = parser.parse_args(argv)
+    return parser
+
+
+def main(argv=sys.argv[1:]):
+    args = get_parser.parse_args(argv)
 
     if args.version:
         pkg = pkg_resources.require("wes_service")