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Building and Installing using Jenkins

  1. A new release will be tagged in the github project https://github.com/ncievs/nci-protege5.git
  2. Navigate to Jenkins at https://evs-jenkins.nci.nih.gov/jenkins/job/_default/job/_lower/job/_Protege/
  3. Choose protege_build > Build with Parameters and select the appropriate tag in the BRANCH_OR_TAG selection box and click Build
  4. Review the Console Output for any errors
  5. For Dev, choose protege_deploy_dev > Build with Parameters. You should be presented with the same tag. Click Build
  6. Review the Console Output for any errors
  7. Check the protege dev server and see that the /local/content/protege/protege-server and protege-desktop have been updated
  8. Confirm the service has started by checking /local/content/protege/logs/protserv-console.txt for "Admin server has started at port 9091"

Manual Build

Building a new Protege version on Dev using Ant

  1. A new release will be tagged in the github project https://github.com/ncievs/nci-protegeprotege5.git
  2. Clone the new release into your local environment.a new directory in /local/project.  "git clone https://github.com/ncievs/nci-protege5.git nci-protege-V<tag>"
  3. The clone will create a directory "nci-protege5".   Enter into the scripts subdirectory "cd nci-protege-protege5V<tag>/scripts/"
  4. Run the build script, passing in the version number "./build.sh versionTag <tag> ncievs >> build.log". 
  5. Review the output for errors or build failures: "cat build.
  6. Shutdown the protege server and explanation server (See below)
  7. log | grep FAILURE"
  8. Check the structure of the build.  The following folders and files should be present under <build-location>/nci-protege5/scripts/nci-protege5
    • binaryowl
    • explanation-workbench
    • metaproject
    • nci-protege_<date>.tar.gz
    • nci-protege_<date>.zip
    • owlapi
    • protege
    • protege-server
    • run-protege.sh
    • run-server.sh

Installing the server build

  1. Navigate to the running instance of protege, on Dev this is Navigate to /local/content/protege/scripts/
  2. Move the protegeserver directory to a backup and create an empty folder in its place 
    1. "mv protegeserver protegeserver-bak"
    2. "mkdir protegeserver"
  3. Shutdown the protege server: "./shutdown.sh" 
  4. Archive the previous version of the services, which are these 2 directories in /local/content/protege:
    Repeat the backup step for explanationserver and
    • protegeserver
    • protegedesktop
  5. Copy the new protegeserver into the empty server service directory "cp -r /local/project/nciedittab-dev-1.00v<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 

    /local/project/nciedittab-dev-1.00v<build-location>/nci-protege5/scripts/nci-protege5/protege/protege-desktop/target/protege-5.1.1<version>-SNAPSHOT-platform-independent/Protege-5.1.1<version>-SNAPSHOT /* ./local/content/protege/protegedesktop"

    Copy the explanationserver tarball to the explanationserver folder "cp
  7. From the /local/project/nciedittab-dev-1.00v/nci-protege5/scripts/nci-protege5/pellet/distribution/target/*.gz ./explanationserver/"  and untar itcontent/protege/scripts directory start the protege server: "./run-background.sh".  The server should start almost immediately
  8. Confirm the service has started by checking /Remove previously compiled reasonings from the protegedata/pelletdata folder "rm -rf /local/content/protege/protegedata/pelletdata/*logs/protserv-console.txt for "Admin server has started at port 9091"


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: ????

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. Server is started when you see "Admin server has started at port 9091"
  2. Unzip the protege package in your chosed directory
  3. Run the bat or sh file
  4. 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
  5. Set up Lucene - Go to File/Preferences and choose Lucene as in tne General tab
  6. 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
  7. Optional - restart Protege
  8. Choose File Open from Protege Server.  Enter the credentials and wait.
  9. Profit