Empty /data/xnat/pipeline folder

[rizwindu]

I'm testing xnat using this docker-compose script. Sorry if my question doesn't make much sense, I'm still learning how this system works.

The /data/xnat/pipeline folder is empty in the default build. As far as I can see, there is no way to set this correctly when setting up XNAT from the war-file.

[johnflavin]

That is correct. Right now this XNAT doesn't come with the pipeline engine.

I'm thinking of ways this could be done. One way is to just download the pipeline engine to a local directory, build it (also locally), and modify docker-compose.yaml to mount that built pipeline engine directory into the xnat-web container. The other way would be to modify tomcat/Dockerfile to do get the xnat-pipeline-engine repo and build it as part of building the image.

I think the first way is probably easiest. Give it a try and let us know how it goes.

[rizwindu]

Thanks for your reply. I was doing some further research into this today and came to the same conclusions that you have mentioned. As a way to improve my knowledge of Docker, tomcat, etc., I'm going to try and modify the tomcat/Dockerfile.

[alvarosan]

Hey @rizwindu , did you try what @johnflavin suggested? Did you get the pipeline-engine running?

[bgeorge0]

Hi @alvarosan - replying from a new GH account. In the end, I didn't get around to making any changes to try and fix the pipeline-engine problem. Hope you have some success if you try yourself.

[alvarosan]

Thanks for the headsup @bgeorge0 . In the end I installed the pipeline-engine manually, this is currently enough for me. As @johnflavin suggested, I downloaded and built the pipeline-engine host side (building from within the container would always fail - I had not much time to further debug why) and mapped the build directory. Next, by inspecting logs/pipeline.log I realized that the pipeline-engine was failing to launch because of a port mismatch, so I set the port explicitly through Administer::Site Administration::Pipeline Settings (e.g. to localhost:8080) and that got things working.

[bkossows]

Hi,
could You please let me know how to disable AutoRun pipeline at all?
B.

[ArnaudC]

Hi,
like alvarosan said, I had to change the pipeline url in Administer::Site Administration::Pipeline Settings.
I didn't used localhost, but the ip given by 'ip addr show docker0' (e.g. to 172.17.1.100:8080).
Also, here is the content of my dockerfile to include the pipeline :

RUN apk add --no-cache wget &&
mkdir ~/pipeline &&
cd ~/pipeline &&
wget http://ci.xnat.org/job/pipeline/job/xnat-pipeline-engine/16/artifact/build/libs/xnat-pipeline-1.7.5.zip &&
unzip -q xnat-pipeline-1.7.5.zip &&
cd ~/pipeline/xnat-pipeline &&
echo -e "xnatUrl=http://localhost:50742\n\
siteName=XNAT\n
adminEmail=[email protected]\n
smtpServer=localhost\n
destination=/data/xnat/pipeline" > ./gradle.properties &&
./gradlew