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Troubleshooting.md

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This file contains a collection of tips

Common problem when provisioning the devspace

If you have previously used the devspace_openstack_ip, the above command might fail with the message

...
host key for 10.0.51.xxx has changed and you have requested strict checking.\r\nHost key verification failed.\r\n", "unreachable": true}

To fix the issue, remove the entry from ~/.ssh/known_hosts and run the playbook again.

Trigger failure: script not approved

The following error can occur:

org.jenkinsci.plugins.scriptsecurity.scripts.UnapprovedUsageException: script not yet approved for use
    at org.jenkinsci.plugins.scriptsecurity.scripts.ScriptApproval.using(ScriptApproval.java:459)
    at org.jenkinsci.plugins.workflow.cps.CpsFlowDefinition.create(CpsFlowDefinition.java:109)

To fix the issue, go to Trigger > Configure and select Use Groovy Sandbox

Bio-Formats or OMERO-push failure

When the latest Java 8 version is not used, the following error will occur:

Installing JDK jdk-8u121-oth-JPR
Downloading JDK from http://download.oracle.com/otn/java/jdk/8u121-b13/e9e7ea248e2c4826b92b3f075a80e441/jdk-8u121-linux-x64.tar.gz
Oracle now requires Oracle account to download previous versions of JDK. Please specify your Oracle account username/password.
ERROR: Unable to install JDK unless a valid Oracle account username/password is provided in the system configuration.
Finished: FAILURE

To fix the issue:

  • Click on Manage Jenkins > Global Tool Configuration
  • Click on JDK installations...
  • Select the latest JDK 8 using the selection box

Access the OMERO.server logs

  • Log in:ssh omero@devspace_openstack_ip
  • Access the docker container docker exec -ti devspace_omero_1 bash
  • Logs are under /home/omero/workspace/OMERO-server/OMERO.server/var/log

Copy the OMERO.server logs to your local machine

  • Log in:ssh omero@devspace_openstack_ip

  • Copy the logs from the container

    docker cp devspace_omero_1:/home/omero/workspace/OMERO-server/OMERO.server/var/log .

  • Copy the logs to your machine

    scp -Cr omero@devspace_openstack_ip:/home/omero/log /local/path/for/log

Access test-integration logs

  • Follow the same steps as above using the container devspace_testintegration_1
  • Logs are under /home/omero/workspace/OMERO-test-integration/src/dist/var/log

Update scripts

By default the OMERO-push job does not merge the open PRs of ome/scripts. If you need to use non-released version of the scripts you will need to:

  • Fork the ome/scripts repository
  • Edit the merge command of the OMERO-push job and replace --shallow by --update-gitmodules

Give others acces to the devspace

  • Log in ssh omero@devspace_openstack_ip
  • Open .ssh/authorized_keys and add the key(s)

Configure Push jobs

Both BioFormats-push and OMERO-push can be modified to only merge the desired PR Below is an example on how to only include PRs opened against openmicroscopy/openmicroscopy with --training in their description

  • Click on OMERO-push > Configure

  • Go to MERGE_COMMAND and enter

    merge develop -Dnone -Itraining --no-ask --reset --shallow