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Building a new Protege version on Dev

  1. A new release will be tagged in the github project https://github.com/ncievs/nci-protege.git
  2. Clone the new release into your local build directory.
  3. The clone will create a directory "nci-protege5".   Enter into the scripts subdirectory "cd nci-protege5/scripts/"
  4. Run the build script, passing in the version number "./build.sh versionTag ncievs >> build.log".
  5. Review the output for errors or build failures: "cat build.log | grep FAILURE"
  6. Check the structure of the build.  The following folders and files should be present under <build-location>/nci-protege5/scripts/nci-protege5
    • metaproject
    • nci-protege_<date>.tar.gz
    • nci-protege_<date>.zip
    • owlapi
    • pellet
    • protege
    • protege-client
    • protege-server
    • run-protege.sh
    • run-server.sh

Installing the build

  1. Navigate to the running instance of protege, likely in /local/content/protege/scripts/
  2. Shutdown the explanation server:  “./pellet server --config /local/content/protege/protegedata/configdata/server.properties stop"
  3. Shutdown the protege server: "./shutdown.sh" 
  4. Archive the previous version of the services, which are these 3 directories:
    • explanationserver
    • protegeserver
    • protegedesktop
  5. Copy the new protegeserver into the service directory "cp -r <build-location>/nci-protege5/scripts/nci-protege5/protege-server/target/server-distribution/server /local/content/protege/protegeserver"
  6. Copy the new protegedesktop into the empty desktop directory "cp -r 

    <build-location>/nci-protege5/scripts/nci-protege5/protege/protege-desktop/target/protege-5.1.1-SNAPSHOT-platform-independent/Protege-5.1.1-SNAPSHOT /local/content/protege/protegedesktop"

  7. Create a new explanationserver directory "mkdir explanationserver"

  8. Untar the explanationserver tarball to the server folder 
    • Unpack "tar -xf <build-location>/nci-protege5/scripts/nci-protege5/pellet/distribution/target/*.gz /local/content/protege/pellet-2.4.0-SNAPSHOT" 
    • rename "mv pellet-2.4.0-SNAPSHOT explanationserver"
  9. Remove previously compiled reasonings from the protegedata/pelletdata folder "rm -rf /local/content/protege/protegedata/pelletdata/*"
  10. From the /local/content/protege/scripts directory start the protege server: "./run-background.sh".  The server should start almost immediately
  11. Confirm the service has started by checking /local/content/protege/logs/protserv-console.txt for "Admin server has started at port 9091"
  12. Start the explanation server “./pellet server --config /local/content/protege/protegedata/configdata/server.properties start".  The service can take half an hour or more to start.
  13. Confirm the service has started by checking /local/content/protege/logs/pellet-console.txt for "Listening at: https://<server>.nci.nih.gov:18080"

Shutdown/Startup of Services

There are two services supporting Protege - the main protege server and the explanation server.  The main server should be shutdown before the explanation server.  When starting, the explanation server should be started before the protege server.

Shutdown

  1. Navigate to /local/content/protege/scripts/
  2. To shutdown the protegeserver: "./shutdown.sh" 
  3. To shutdown the explanation server:  “./pellet server --config /local/content/protege/protegedata/configdata/server.properties stop"

Startup

  1. Navigate to /local/content/protege/scripts/
  2. To startup protege server: "./run-background.sh"
  3. Do "tail ../logs/protserv-console.txt" to check that the protege server is running.
  4. To startup explanation server: “./pellet server --config /local/content/protege/protegedata/configdata/server.properties start"
  5. Do "tail ../logs/pellet-console.txt" to check that the explanation server is running.

Packaging Server for Deployment to Upper Tier

  1. Navigate to /tmp/protege and remove any files and folders there
  2. Copy up server directory -  cp -R /local/content/protege/protegeserver .
  3. Copy up explanation server - cp -R /local/content/protege/explanationserver .
  4. Package into tarball with version number - tar -cvzf protege-server-deployment-1.00v.tar.gz explanationserver protegeserver
  5. Copy tarball to /priv-file-repo/protege/deployment
  6. Move any previous versions to /priv-file-repo/protege/archive/deployment-package

Packaging Client for Deployment

  1. Navigate to /local/project/protegeClientPackage
  2. Remove and previous zip files and client directories but leave java and the run scripts
  3. Create directory nci-protege5_V2.1.00v
  4. Copy in the desktop client "cp r /local/content/protege/protegedesktop/* ./nci-protege5_V2.1.00v"
  5. Copy the jre and run scripts into the new directory

    1. cp -r ./jre1.8.0_102 ./nci-protege5_V2.1.00v/

    2. cp run.* ./nci-protege5_V2.1.00v/

  6. Create a zip "zip -r nci-protege5_V2.1.00v.zip nci-protege5_V2.1.00v"

  7. Copy the zip to your local machine, unzip and test

  8. Put zip on sFTP under evs/Protege/Protege-2.0

Deployment

  1. Unzip the protege package in your chosed directory
  2. Run the bat or sh file
  3. Do NOT immediate accept download of plugins.  
    1. Go to Launcher/Preferences then the plugins tab.  Make sure you are pointed to the correct plugins location.
    2. Go to File/Check for plugins and select all plugins
    3. Restart protege
  4. Set up Lucene - Go to File/Preferences and choose Lucene as in tne General tab
  5. Set up Pellet - Go to File/Preferences, the Reasoner tab and the Pellet sub-tab.  
    1. Select Remote as the reasoner type
    2. Enter the server address for pellet
  6. Optional - restart Protege
  7. Choose File Open from Protege Server.  Enter the credentials and wait.
  8. Profit
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