Help with test setup for testing container pipelines

[tom.g...@gmail.com]

Hi,

I have installed of XNAT + postgres inside a single Docker image to run unittests for some container service pipelines I am developing. I mount in the local docker socket to use for the container service with

docker run -p 80:80 -v /var/run/docker.sock:/var/run/docker.sock tclose/test-xnat

but I keep getting a failure on launch

Did not start.Could not start container cefeea27ee812f8c1a80bb3faf2fc6fb9df06311d8b09d433d1957ce4a5e6b7b: Request error: POST unix://localhost:80/containers/cefeea27ee812f8c1a80bb3faf2fc6fb9df06311d8b09d433d1957ce4a5e6b7b/start: 500

and can't work out why. If anyone is interested in taking a look you can access a snapshot of the XNAT Docker container on Docker Hub at

tclose/test-xnat

and pull the container pipeline I'm trying to test at

tclose/arcana-concatenate-test

Thanks!

[tom.g...@gmail.com]

Am I right in thinking that this is a problem with my XNAT setup, or could it be an issue with my container pipeline?

[tom.g...@gmail.com]

Here is the dockerfile if anyone can spot anything that is missing. My understanding was that all you needed to do was install the docker package and mount in the hosts docker socket, should this work?

I'm able to run the XNAT container and launch the docker workflow using the docker CLI fine so I'm not sure why the XNAT CS isn't able to use it

FROM tomcat:9-jre8-alpine

# User configurable arguments

ARG XNAT_VER=1.8.3

ARG XNAT_CS_PLUGIN_VER=3.1.0

ARG XNAT_BATCH_LAUNCH_PLUGIN_VER=0.5.0

ARG XNAT_ROOT=/data/xnat

ARG XNAT_HOME=/data/xnat/home

ARG JAVA_MS=256m

ARG JAVA_MX=2g

ARG XNAT_DATASOURCE_DRIVER=org.postgresql.Driver

ARG XNAT_DATASOURCE_URL=jdbc:postgresql://localhost:5432/xnat

ARG XNAT_DATASOURCE_USERNAME=xnat

ARG XNAT_DATASOURCE_PASSWORD=xnat

ARG XNAT_HIBERNATE_DIALECT=org.hibernate.dialect.PostgreSQL9Dialect

ARG TOMCAT_XNAT_FOLDER=ROOT

ARG TOMCAT_XNAT_FOLDER_PATH=${CATALINA_HOME}/webapps/${TOMCAT_XNAT_FOLDER}

# Create XNAT config file at $XNAT_HOME/config/xnat-conf.properties

COPY make-xnat-config.sh /usr/local/bin/make-xnat-config.sh

# Install XNAT

RUN apk add --no-cache postgresql postgresql-client supervisor wget vim docker

RUN rm -rf ${CATALINA_HOME}/webapps/*

RUN mkdir -p \

${TOMCAT_XNAT_FOLDER_PATH} \

${XNAT_HOME}/config \

${XNAT_HOME}/logs \

${XNAT_HOME}/plugins \

${XNAT_HOME}/work \

${XNAT_ROOT}/archive \

${XNAT_ROOT}/build \

${XNAT_ROOT}/cache \

${XNAT_ROOT}/ftp \

${XNAT_ROOT}/pipeline \

${XNAT_ROOT}/prearchive

RUN /usr/local/bin/make-xnat-config.sh

RUN rm /usr/local/bin/make-xnat-config.sh

RUN wget --no-verbose --output-document=/tmp/xnat-web-${XNAT_VER}.war https://api.bitbucket.org/2.0/repositories/xnatdev/xnat-web/downloads/xnat-web-${XNAT_VER}.war

RUN unzip -o -d ${TOMCAT_XNAT_FOLDER_PATH} /tmp/xnat-web-${XNAT_VER}.war

RUN rm -f /tmp/xnat-web-${XNAT_VER}.war

RUN wget --output-document ${XNAT_HOME}/plugins/container-service-plugin.jar https://bitbucket.org/xnatdev/container-service/downloads/container-service-${XNAT_CS_PLUGIN_VER}-fat.jar

RUN wget --output-document ${XNAT_HOME}/plugins/batch-launch-plugin.jar https://bitbucket.org/xnatx/xnatx-batch-launch-plugin/downloads/batch-launch-plugin-${XNAT_BATCH_LAUNCH_PLUGIN_VER}.jar

RUN apk del wget

RUN mkdir /var/log/tomcat

ENV XNAT_HOME=${XNAT_HOME} XNAT_DATASOURCE_USERNAME=${XNAT_DATASOURCE_USERNAME} PGPASSWORD=${XNAT_DATASOURCE_PASSWORD}

ENV CATALINA_OPTS="-Xms${JAVA_MS} -Xmx${JAVA_MX} -Dxnat.home=${XNAT_HOME}"

# Add scripts for configuring XNAT database before launching Tomcat

COPY launch-xnat.sh /launch-xnat.sh

COPY XNAT.sql /XNAT.sql

# Skip the new site setup by creating site preferences file

COPY xnat-prefs-init.ini ${XNAT_HOME}/config/prefs-init.ini

# Change the default port to 80 (so that the container service knows where to)

# find it) and expose it

RUN sed -i 's/port="8080"/port="80"/' ${CATALINA_HOME}/conf/server.xml

EXPOSE 80

# Setup Postgres

RUN mkdir /run/postgresql

RUN mkdir /var/lib/postgresql/data

RUN chmod 700 /var/lib/postgresql/data

RUN chown postgres:postgres /run/postgresql /var/lib/postgresql/data

# Create postgres DB

USER postgres

RUN initdb -D /var/lib/postgresql/data

RUN echo -e "\ndatasource.driver = '/tmp'" >> /var/lib/postgresql/data/postgresql.conf

USER root

# Use supervisord to launch postgres and tomcat

COPY supervisord.conf /etc/supervisord.conf

CMD ["/usr/bin/supervisord"]

[tom.g...@gmail.com]

For anyone interested, one of my colleagues got to the bottom of the problem with my setup.

The issue was that I was that I needed to place the archive directory on the Docker Host (i.e. my mac) and mount it into the Docker container running XNAT, and then set the "Docker Server Path Prefix" to the parent of the mounted directory on the Docker Host, e.g.

docker run -p 80:80 -v /Users/tclose/Desktop/xnat-home/archive:/data/xnat/archive -v /var/run/docker.sock:/var/run/docker.sock tclose/test-xnat

"Docker Server Path Prefix"=/Users/tclose/Desktop/xnat-home

[Herrick, Rick]

I’m glad you figured that because I started to reply a couple times but really didn’t have any idea what was going on 😊

 

-- 

Rick Herrick

XNAT Architect/Developer

Computational Imaging Laboratory

Washington University School of Medicine

 

 

From: xnat_di...@googlegroups.com <xnat_di...@googlegroups.com> on behalf of tom.g...@gmail.com <tom.g...@gmail.com>
Date: Wednesday, November 10, 2021 at 10:01 PM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: [XNAT Discussion] Re: Help with test setup for testing container pipelines

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