Protégé Server Build Procedures

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This procedural guide is meant for use in performing a new Protégé server build for both the NCI Thesaurus and BiomedGT instances. Protégé server builds can be performed either manually, or via automated run scripts. Generally, using the automated scripts would be less time-consuming. However, it is recommended that going through the manual process (at least once) be performed to understand the concepts and the workflow of a Protege build. Doing so will facilitate troubleshooting any future problems during a build.

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• Explanation Server - The Explanation server is also an open-source application developed by the Clark & Parsia group in the Washington D.C. area. The server makes a connection to a specified Protege database, and classifies all concepts. The server will then allow users to pull up and view any concept's super-concepts as well as sub-concepts.

• Protégé Client (Editor) - The Protégé Client is the editing tool which the editors utilize to create, update, or view the various concept and concept property data. Data can be accessed from the database via the Protégé Server.   The editors have the client running on their Windows workstations.

Steps for Jenkins build

There are 2 parts to the Jenkins build, the compilation and the deployment.  Navigate to https://evs-jenkins.nci.nih.gov and find "default >> lower >> protege".  Select "protege-build" and select the tag given to you by the developers.  The build will take 10-15 minutes.  At the conclusion, go to "protege_deploy_dev" and deploy the tag you just built.

Steps to complete a Manual Protégé Server Build Process for Dev, QA, and Stage Tiers

You will need tier-specific info for Dev, QA, Stage before commencing the build. Production-tier information is separated, since the information is a bit different than the other tiers.

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• Connect with the database project on the server.   The database project should have the following naming convention: <PROTEGE INSTANCE>-YYMMDD-DB.pprj.

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• To run from the Windows GUI: Create the following folder structure: gforge<YYMMDD><VERSION>nciscn<YYMMDD><VERSION>/protegegui/. From this location, right click, select 'SVN Checkout'. A window will appear asking for the source and target of files. Protégé files are located in GForgeNCI SVN, and can be checked out from: Code Blockhttps://gforgencisvn.nci.nih.gov/svnrootsvn/protegegui

• To run from command prompt on the server, navigate to /app/protégé/repo, and create the following directory

  gforge<YYMMDD><VERSION>

  ncisvn<YYMMDD><VERSION>/protegegui/

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  and run

  : Code Blocksvn co [https://gforge.nci.nih.gov/svnroot/protegegui

  the svn checkout:

  
  

svn co https://gforgencisvn.nci.nih.gov/svnrootsvn/protegegui/collaborativedevterminologytools/scripts/trunk/

• There may be instances where you will need to modify a few targets within the branches tag to reflect changes in other projects. In this case, you must verify that the proper 'svn-url.properties file is being referenced in the build.xml file. Each build will hold 2 separate svn-url.properties files.

   

  One is usually the default, which builds from the trunk folder. There is also a customized file that will build from the branches folders. Example code snippets are below for each file:

  Code Block

  svn-url-trunk.properties (default) 'ncitab.url=$nci.base.url/protegegui/*trunk*' ncitab.project=$projects/ncitab nciconcepthistory.url=$nci.base.url/protegehistory/NCIConceptHistory/*trunk* nciconcepthistory.project=$projects/nciprojecthistory ncievshistory.url=$nci.base.url/protegehistory/NCIEVSHistory/*trunk* ncievshistory.project=$projects/ncievshistory classification.url=$nci.base.url/classification/*trunk* classification.project=$projects/classification *svn-url-1.4.properties (customized)* ncitab.url=$nci.base.url/*nci-branches/1.4*/protegegui ncitab.project=$projects/ncitab nciconcepthistory.url=$nci.base.url/*nci-branches/1.4*/NCIConceptHistory nciconcepthistory.project=$projects/nciconcepthistory ncievshistory.url=$nci.base.url*/nci-branches/1.4*/NCIEVSHistory ncievshistory.project=$projects/ncievshistory classification.url=$nci.base.url/*nci-branches/1.4*/classification classification.project=$projects/classification

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• Navigate to <PATH>/trunk and open the 'localbuild.properties' file and modify the 'PromptNCIPlugins.properties settings' section within the file. This info represents the tier's database connection information, and will need to be set before running the ant build commands. To edit the file using a Unix VI editor within the server console, type 'vi local.properties'. The file should now be displayed in the console. ype 'Shift + I (eye)' to enable editing, and utilize the arrow keys to navigate to the PromptNCIPlugins.properties section, and fill in the default database connection values with tier-specific values. Upon completion, type 'esc' to move out of editing mode, and type ':wq' to overwrite, save changes, and exit the file back to the console prompt.

• Within the same directory, open the 'vesrionversion.info' file and modify the current version to the latest version (if necessary)   following the same steps as above.   By default, the version number will display as 1.1.0.   Save changes following the instructions above. 

Protege Server Build Ant Commands

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• Run 'ant archive' to create zip files for each of the Protégé packages. The process will also create an ncibuilder.zip file. This file contains all files for the entire project. The file will be created at <PATH> /trunk/build/archive. 

• Transfer the folders to usr/local/protégé/Protégé_x.x/<PROTÉGÉ INSTANCE> on the server machine. A copy of the client folder should also be saved on your local machine, to test a successful connection to the server after the build.

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If the build involves software updates that include any database code or schema changes, skip to the 'Protege Software Updates & Configuring New Database Project' section. For builds that will only require software updates connecting to an existing database project, please follow the 'Protege Software Updates' section.