XNAT docker-compose with dependency management failed
wenq...@gmail.com
Cloning into 'xnat-docker-compose'...
remote: Enumerating objects: 695, done.
remote: Counting objects: 100% (125/125), done.
remote: Compressing objects: 100% (86/86), done.
remote: Total 695 (delta 58), reused 76 (delta 26), pack-reused 570
Receiving objects: 100% (695/695), 90.72 MiB | 11.00 MiB/s, done.
Resolving deltas: 100% (335/335), done.
ruoqing@ruoqing-pc:~$ cd xnat-docker-compose
ruoqing@ruoqing-pc:~/xnat-docker-compose$ git checkout features/dependency-mgmt
Branch 'features/dependency-mgmt' set up to track remote branch 'features/dependency-mgmt' from 'origin'.
Switched to a new branch 'features/dependency-mgmt'
ruoqing@ruoqing-pc:~/xnat-docker-compose$ ./gradlew composeBuild composeUp
> Task :composeBuild FAILED
xnat-traefik uses an image, skipping
Building xnat-web
dockerfile parse error line 1: FROM requires either one or three arguments
FAILURE: Build failed with an exception.
* What went wrong:
Execution failed for task ':composeBuild'.
> Exit-code 1 when calling docker-compose, stdout:
* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.
* Get more help at https://help.gradle.org
BUILD FAILED in 2s
3 actionable tasks: 3 executed
ruoqing@ruoqing-pc:~/xnat-docker-compose$
wenq...@gmail.com
MAINTAINER Matt Kelsey <kel...@wustl.edu>
ARG XNAT_VERSION=${XNAT_VERSION}
ARG XNAT_ROOT=${XNAT_ROOT}
ARG XNAT_HOME=${XNAT_HOME} ARG XNAT_DATASOURCE_DRIVER=${XNAT_DATASOURCE_DRIVER}
wenq...@gmail.com
> Task :composeBuild
Building xnat-web
> Task :composeBuild FAILED
FAILURE: Build failed with an exception.
* What went wrong:
Execution failed for task ':composeBuild'.
---> 7253c7ce0ab9
Step 2/31 : MAINTAINER Matt Kelsey <kel...@wustl.edu>
---> Using cache
---> a69805dfded9
Step 3/31 : ARG XNAT_VERSION=${XNAT_VERSION}
---> Using cache
---> 4d1e777e8c92
Step 4/31 : ARG XNAT_ROOT=${XNAT_ROOT}
---> Using cache
---> 104b1b5ec1ea
Step 5/31 : ARG XNAT_HOME=${XNAT_HOME}
---> Using cache
---> 6a5ee2fcd8c2
Step 6/31 : ARG XNAT_DATASOURCE_DRIVER=${XNAT_DATASOURCE_DRIVER}
---> Using cache
---> 0217055f373c
Step 7/31 : ARG XNAT_DATASOURCE_URL=${XNAT_DATASOURCE_URL}
---> Using cache
---> 113955d23df6
Step 8/31 : ARG XNAT_DATASOURCE_USERNAME=${XNAT_DATASOURCE_USERNAME}
---> Using cache
---> 21ae47367726
Step 9/31 : ARG XNAT_DATASOURCE_PASSWORD=${XNAT_DATASOURCE_PASSWORD}
---> Using cache
---> f5199c4ac31f
Step 10/31 : ARG XNAT_WEBAPP_FOLDER=${XNAT_WEBAPP_FOLDER}
---> Using cache
---> da6f6074fd54
Step 11/31 : ARG XNAT_EMAIL=${XNAT_EMAIL}
---> Using cache
---> 6eee17d3b7be
Step 12/31 : ARG XNAT_ACTIVEMQ_URL=${XNAT_ACTIVEMQ_URL}
---> Using cache
---> 1cad60e4282a
Step 13/31 : ARG XNAT_ACTIVEMQ_USERNAME=${XNAT_ACTIVEMQ_USERNAME}
---> Using cache
---> f4bb8ffb2c99
Step 14/31 : ARG XNAT_ACTIVEMQ_PASSWORD=${XNAT_ACTIVEMQ_PASSWORD}
---> Using cache
---> 6505a31e8b80
Step 15/31 : ARG XNAT_PROCESSING_URL=http://xnat-web:8080
---> Using cache
---> 0ad7e852c0e1
Step 16/31 : ARG XNAT_SMTP_ENABLED=${XNAT_SMTP_ENABLED}
---> Using cache
---> fe633cf0d36e
Step 17/31 : ARG XNAT_SMTP_HOSTNAME=${XNAT_SMTP_HOSTNAME}
---> Using cache
---> 589c98c5dcbf
Step 18/31 : ARG XNAT_SMTP_PORT=${XNAT_SMTP_PORT}
---> Using cache
---> 97bd66225727
Step 19/31 : ARG XNAT_SMTP_AUTH=${XNAT_SMTP_AUTH}
---> Using cache
---> bc40eab0c57a
Step 20/31 : ARG XNAT_SMTP_USERNAME=${XNAT_SMTP_USERNAME}
---> Using cache
---> 5a8106370fdb
Step 21/31 : ARG XNAT_SMTP_PASSWORD=${XNAT_SMTP_PASSWORD}
---> Using cache
---> 95003a1f3398
Step 22/31 : ARG XNAT_PIPELINE_ARCHIVE=xnat-pipeline-${XNAT_VERSION}.zip
---> Using cache
---> f8ce97031ea0
Step 23/31 : ARG XNAT_PIPELINE_URL=https://ci.xnat.org/job/pipeline/job/xnat-pipeline-engine/lastSuccessfulReleaseBuild/artifact/build/libs/${XNAT_PIPELINE_ARCHIVE}
---> Using cache
---> ebd321f6f379
Step 24/31 : ADD make-xnat-config.sh /usr/local/bin/make-xnat-config.sh
---> Using cache
---> 1ad50d174e25
Step 25/31 : ADD wait-for-postgres.sh /usr/local/bin/wait-for-postgres.sh
---> Using cache
---> ff4d208e27c5
Step 26/31 : ADD ${XNAT_PATH} /webapps
---> Using cache
---> 4b23c69d3db6
Step 27/31 : RUN apk add --no-cache postgresql-client wget && rm -rf ${CATALINA_HOME}/webapps/* && mkdir -p ${CATALINA_HOME}/webapps/${XNAT_WEBAPP_FOLDER} ${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 ${XNAT_ROOT}/prearchive && /usr/local/bin/make-xnat-config.sh && rm /usr/local/bin/make-xnat-config.sh
---> Running in 6bf8490d0098
/bin/sh: 1: apk: not found
* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.
* Get more help at https://help.gradle.org
3 actionable tasks: 1 executed, 2 up-to-date
ruoqing@ruoqing-pc:~/xnat-docker-compose$
Herrick, Rick
Sorry Renjie, this was my bad. I missed pushing a commit to that branch. I just tested that commit with this command:
$ ./gradlew -PenvFile=test-vars.env fullStackComposeBuild fullStackComposeUp
After a couple minutes I had a fresh new XNAT running on http://localhost.
--
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 wenq...@gmail.com <wenq...@gmail.com>
Date: Thursday, June 3, 2021 at 6:30 PM
To: xnat_discussion <xnat_di...@googlegroups.com>
Subject: [XNAT Discussion] Re: XNAT docker-compose with dependency management failed
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wenq...@gmail.com
Will use 172.21.0.1 (network xnat-services) as host of xnat-web
More forwarded TCP ports for service 'xnat-web:8000 [[HostIp:0.0.0.0, HostPort:8000], [HostIp:::, HostPort:8000]]'. Will use the first one.
More forwarded TCP ports for service 'xnat-web:8104 [[HostIp:0.0.0.0, HostPort:8104], [HostIp:::, HostPort:8104]]'. Will use the first one.
More forwarded TCP ports for service 'xnat-web:8144 [[HostIp:0.0.0.0, HostPort:8144], [HostIp:::, HostPort:8144]]'. Will use the first one.
psql: could not connect to server: Connection refused
Is the server running on host "xnat-db" (172.21.0.2) and accepting
TCP/IP connections on port 5432?
Postgres is unavailable - sleeping
psql: could not connect to server: Connection timed out
Is the server running on host "xnat-db" (23.202.231.169) and accepting
TCP/IP connections on port 5432?
Postgres is unavailable - sleeping
psql: could not connect to server: Connection timed out
Is the server running on host "xnat-db" (23.221.222.250) and accepting
TCP/IP connections on port 5432?
Postgres is unavailable - sleeping
psql: could not connect to server: Connection refused
Is the server running on host "xnat-db" (23.221.222.250) and accepting
TCP/IP connections on port 5432?
Postgres is unavailable - sleeping
psql: could not connect to server: Connection timed out
Is the server running on host "xnat-db" (23.221.222.250) and accepting
TCP/IP connections on port 5432?
Postgres is unavailable - sleeping
psql: could not connect to server: Connection timed out
Is the server running on host "xnat-db" (23.221.222.250) and accepting
TCP/IP connections on port 5432?
Postgres is unavailable - sleeping
psql: could not connect to server: Connection timed out
Is the server running on host "xnat-db" (23.202.231.169) and accepting
TCP/IP connections on port 5432?
Postgres is unavailable - sleeping
psql: could not connect to server: Connection timed out
Is the server running on host "xnat-db" (23.202.231.169) and accepting
TCP/IP connections on port 5432?
Postgres is unavailable - sleeping
Stopping xnat-activemq ...
Stopping xnat-web ...
Stopping xnat-pacs ...
Stopping xnat-traefik ...
Stopping xnat-activemq ... done
Stopping xnat-traefik ... done
Stopping xnat-web ... done
Stopping xnat-pacs ... done
Removing xnat-smtp ...
Removing xnat-db ...
Removing xnat-activemq ...
Removing xnat-web ...
Removing xnat-pacs ...
Removing xnat-traefik ...
Removing xnat-pacs ... done
Removing xnat-db ... done
Removing xnat-traefik ... done
Removing xnat-smtp ... done
Removing xnat-web ... done
Removing xnat-activemq ... done
Going to remove xnat-smtp, xnat-db, xnat-activemq, xnat-web, xnat-pacs, xnat-traefik
> Task :fullStackComposeUp FAILED
FAILURE: Build failed with an exception.
* What went wrong:
> TCP socket on 172.21.0.1:8000 of 'xnat-web' is still failing. Logs:
* Try:
Run with --stacktrace option to get the stack trace. Run with --info or --debug option to get more log output. Run with --scan to get full insights.
* Get more help at https://help.gradle.org
4 actionable tasks: 2 executed, 2 up-to-date
ruoqing@ruoqing-pc:~/xnat-docker-compose$
Herrick, Rick
Sorry for not responding earlier, I was on vacation last week.
If I had to guess, I’d say that something is already running on port 8000 on your host machine. You can check with the following command (or something like it: this works on OSX and Ubuntu 20.04, not sure how you’d do this on Windows):
lsof -i :8000
If you can’t do anything about whatever’s blocking that port (or nothing seems to be blocking it), you can also just remove that port mapping. That’s used to connect to Java/Tomcat/XNAT for debugging purposes. If you’re not debugging then you don’t need to map it, so you could remove it. You just need to edit docker-compose.yml to remove references to port 8000. There are only two lines to remove or comment out:
xnat-web:
container_name: xnat-web
<snip>
ports:
- "8000:8000" <- delete this line
- "8104:8104"
- "8144:8144"
<snip>
environment:
CATALINA_OPTS: "-Xms${XNAT_MIN_HEAP} -Xmx${XNAT_MAX_HEAP} -Dxnat.home=${XNAT_HOME} -agentlib:jdwp=transport=dt_socket,server=y,suspend=n,address=0.0.0.0:8000" <- remove the highlight bit here
PGPASSWORD: "${XNAT_DATASOURCE_PASSWORD}"
XNAT_HOME: "${XNAT_HOME}"
Presuming that ports 8104 and 8144 aren’t blocked by some other process, that should get the xnat-web container up and running.
--
Rick Herrick
Sr. Programmer/Analyst
Neuroinformatics Research Group
Washington University School of Medicine
Phone: +1 (314) 273-1645
To view this discussion on the web visit https://groups.google.com/d/msgid/xnat_discussion/bd65d386-7ec2-49e1-aa3f-41e6718e5145n%40googlegroups.com.
