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protege-docker-x11's Introduction

Protégé Desktop Docker running over X11

Desktop version Stanford Ontology IDE

  • Protégé version 5.5 (from latest GIT)

Components

Run (Recommended for easy starting-up)

This will setup all the needed host directory to ensure Protégé configurations being persistent for next run.

./run.sh

Build (Locally build your own image)

./build.sh

Volumes (no action needed - automated mapped in run.sh script)

Three volumes are exposed to host and already defined in "run.sh" script. Hence, you don't need to do anything for the following volumes inside the Docker file and they are mapped to directories under your "$HOME/data-docker/protege_docker_x11".

  • Protégé related files including Logs: ${HOME}/.Protege

  • Protégé Workspace: ${HOME}/Workspace

  • Protégé Plugin (to persist across multiple delete and create of Protégé Docker container) -- This is to keep the installed plug-in libraries to be persistent for next restart/re-create of Container. ${HOME}/protege-x11/plugins

Resources

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Releases

protege-docker-x11's People

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protege-docker-x11's Issues

Can't start

Hi, I am having issues starting the container. Can you help?

protegex       | 11:00:52,471 |-INFO in ch.qos.logback.core.FileAppender[files] - File property is set to [/home/developer/.Protege/logs/protege.log]
protegex       | 11:00:52,471 |-ERROR in ch.qos.logback.core.FileAppender[files] - Failed to create parent directories for [/home/developer/.Protege/logs/protege.log]
protegex       | 11:00:52,472 |-ERROR in ch.qos.logback.core.FileAppender[files] - openFile(/home/developer/.Protege/logs/protege.log,true) call failed. java.io.FileNotFoundException: /home/developer/.Protege/logs/protege.log (No such file or directory)

This is the configuration I'm using:

version: '3'
services:
  protegex:
    image: openkbs/protege-docker-x11
    hostname: protegex
    domainname: mynetwork
    network_mode: mynetwork
    container_name: protegex
    environment:
      - DISPLAY=${DISPLAY:-localhost:0}
      - USER_ID=${USER_ID:-1000}
      - GROUP_ID=${GROUP_ID:-1000}
      - USER_NAME=marin # tried without it
    volumes:
      - protegex-logs:/home/developer/.Protege
      - protegex-workspace:/home/developer/workspace-protege
      - protegex-plugins:/home/developer/protege-x11/plugins
volumes:
  protegex-logs:
  protegex-workspace:
  protegex-plugins:

Can't start

I am running protege with following docker-compose.yml file

  protege:
    image: openkbs/protege-docker-x11

And This is the errors I get

.
.
.
13:19:42,271 |-ERROR in ch.qos.logback.core.FileAppender[files] - Failed to create parent directories for [/home/developer/.Protege/logs/protege.log]
protege_1    | 13:19:42,271 |-ERROR in ch.qos.logback.core.FileAppender[files] - openFile(/home/developer/.Protege/logs/protege.log,true) call failed. java.io.FileNotFoundException: /home/developer/.Protege/logs/protege.log (No such file or directory)
.
.
.
protege_1    | Error starting file:/home/developer/Protege-5.5.0/bundles/protege-editor-core.jar 
protege_1    | org.osgi.framework.BundleException: Activator start error in bundle org.protege.editor.core.application [4].
protege_1    | 	at org.apache.felix.framework.Felix.activateBundle(Felix.java:2276) ~[org.apache.felix.main.jar:na]
protege_1    | 	at org.apache.felix.framework.Felix.startBundle(Felix.java:2144) ~[org.apache.felix.main.jar:na]
protege_1    | 	at org.apache.felix.framework.Felix.setActiveStartLevel(Felix.java:1371) ~[org.apache.felix.main.jar:na]
protege_1    | 	at org.apache.felix.framework.FrameworkStartLevelImpl.run(FrameworkStartLevelImpl.java:308) [org.apache.felix.main.jar:na]
protege_1    | 	at java.lang.Thread.run(Thread.java:745) [na:1.8.0_121]
protege_1    | Caused by: java.awt.AWTError: Can't connect to X11 window server using ':0.0' as the value of the DISPLAY variable.
.
.
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