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Software Updates & Configuring New Database Project

A new project file will need to be created using the raw OWL file located in /app/protégé/data/Protégé_x.x/<PROTÉGÉ INSTANCE>.  See Appendix D for instructions on how to export data from the production database, as well as converting into an OWL File.

  • As long as no changes have been made to the behavior of the startup scripts, the following files and scripts should be copied over from the old Protégé.Server version to the new folder:

run_rmiregistry.sh
run_protege_ server_nci.sh
shutdown_protege_server.sh
codegen.properties
codegen.dat 

  • If you do need to use new scripts, make sure to adjust the memory upwards from the default in the run_protege_server_nci.sh script.  The following table dsisplays how much memory to allocate for each script, per tier.  You will also need to adjust the rmi.registry and rmi.server ports, the hostname and the metaproject location in this same file.  Please view Appendix A for port information for each tier.
  • As long as no changes have been made to the behavior of the startup scripts, navigate to the Protégé.Client folder and transfer the following script:

run_protege_BGT.sh (BiomedGT)  or  run_protege_NCIT.sh (NCIThesaurus)

  • If you do need to use a new script, make sure the Xmx memory is adjusted upwards from the default from the table.
  • As long as no changes have been made to the behavior of the startup scripts,  navigate to the Explanation.Server directory and transfer the following files:

restart_explanation_server.sh
stop_explanation_server.sh 
start_explanation_server.sh (the path to the correct Protege server version will need to modified in this script.  To edit, type 'vi start_explanation_server.sh' to view the script from the vi editor.  Type 'shift + I' and edit the server number to the correct version number.  Press 'esc', then ':wq' to save changes and exit the editor).

  • If you do need to use a new script, utilize the table for the explanation server startup script. There should be no other edits that need to be made.
  • Navigate to the Protégé server, and open the 'codegen.properties' file using a vi editor. To do this, type 'vi codegen.properties".  Once the file is viewable from vi, type "shift + I" to edit.   The code.prefix value can be adjusted, depending on which Protégé Instance is being used (BiomedGT or NCI Thesaurus).  BiomedGT uses a prefix of 'B', while NCI Thesaurus uses 'C'.   Keep the seed number at 100000. Save and exit the file by typing 'esc', then ':wq.
  • Open the  'codegen.dat' file in the vi editor. You will notice a number which represents a code that will be assigned to the concept code created in the database project. Set this number to 101000. Save and exit the file.  
  • Open the Protege client from the dev tier, and click on "Create New Project".  Select OWL/RDF File, and check "Create from existing source".  Click Next.
  • A window will display requesting the address of the source of the OWL file. Navigate to /app/protege/data/Protege_1.4/BiomedGT/ and select BiomedGT-Fixed-wNS-DefaultAndPrefix.owl, and click next. Leave the next two windows to their default values, then click Finish.  Loading the file to the client will take approximately 5-10 minutes.
  • One loaded, the project file can now be converted to an Clark & Parsia OWL/RDF database.   Click File, Convert Project to Format, Clark & Parsia OWL / RDF database.
  • In the database window, enter all requested database info and click finish.   (Please look at the database info for each instance). Conversion can take anywhere up to 2 hours, if a file from production is being used 

     

  • After conversion of the project file, you can verify that the database has been created by utilizing a database GUI tool (DB Visualizer) to view if the table has been created.  Once verified, the project is now ready to be configured from the GUI.
  • Set transitivity by clicking the properties tag, and perform a search for the 'Anatomic_Structure_Has_Location' property. Select, and check the box marked transitive. Repeat the same step for the 'Anatomic_Structure_Is_Physical_Part_Of' property.

   

  • Set the display slots by clicking the NCIEdit tab, and clicking the "F" tab on the very far top right section of the page.  You will now be within the Form Editor section. Set the 'Display Slot' drop down to 'Preferred_Name'.

     

  • Next, click the Properties tab, and click the "F" tab on the very right.  Click 'OK'  for the forms dialogue box.  On the left hand menu, click on 'owl:DatatypeProperty, and set it's display slot drop down to 'Preferred_Name'.  Next, click on the owl:ObjectProperty on the left hand menu, and set its display slot drop down field to 'Preferred_Name' as well.

  • Click 'OWL' on the menu tab, and select 'preferences'.  On the General tab, Disable the drag and drop feature, and set the explanation server URL to 'http://<Protege Server Address>:<port>/explain

  • In the Tests tab, disable test of deprecated classes/properties.  This should be the fifth entry down. 

  • Click on the visibility tab from the window, and disable all the boxes in the MetaClasses section.  Close the window.
  • Click 'Project' on the menu bar, and select 'configure'. On the Tab Widgetss tab, enable only the following boxes from the Widgets tab and put in the following order:

     NCIEditTab
     LuceneQueryPlugin
     OWLPropertiesTab
     OWLMetadataTag
     ChangesTab
     ExplanationTab
     WorkflowTab
 

  • Click on the 'options' tab and enable journaling and disable redo/undo. 
  • From the menu bar, select 'LuceneQueryPlugin" and select 'Index Ontologies. A window will pop up.  Check 'Use Phonetic Indexer' and select 'OK'.  After indexing has completed, a new lucene folder will be stored in the same directory as your database project file. Overwrite the old lucene folder with the new lucene folder in /app/protégé/data/.

  • Click File, Save Project As.  Name it with the current date and "DB".  Example: Thesaurus-yymmdd-DB.pprj.  This act of saving will create an Annotations project in the same directory as the main project. 
  • Select File, Convert Project to File.  Store in app/protégé/data/Protégé_x.x/<PROTÉGÉ INSTANCE> labeled with the current date and "file". Example: Thesaurus-yymmdd-file.pprj.  Set the Language drop-down field to 'XML/RDF ABREV'.  You will notice a small dialogue box displaying the conversion progress.  This step may take approximately 30 minutes depending on the size of the database project. Once completed, the dialogue box should disappear, and the client should display the new file project. 
  • Close the project WITHOUT saving the file project, however, leave the Protégé client open.
  • Open the nci_metaproject.pprj located at /app/protégé/data/<PROTÉGÉ INSTACE>/Meta/.  Click on the project tab underneath the SYSTEM-CLASS tab on the left-hand side menu.  Select the 'Instances' tab at the top of the page. You will notice an 'Instance Browser' section, and an 'Instance Editor' section. The instance browser specifies the display name of your project, and the Instance Editor specifies the path of your database project.  Click on the dispay project name and set the correct path to your project files. 

  • Within the metaproject, the changes ontology projects (annotation files) should also not be made visible to users when trying to access a project on the server.  To configure the project display list, please view the DisplayInList setup instructions.
  • Within the shell console, navigate to usr/local/protégé/Protégé_1.3/<PROTÉGÉ INSTANCE>/Explanation.Server-x.x.x and run ./start_explanation_server.sh -p <port> --url jdbc:mysql://<database server address>:<port>/<database name> -t <table_name> -U <db_username> -P <db_password>.   
  • After the server has initiated startup, type 'tail -f nohup.out' to view start up status.  Within the nohup.out file, the explanation server has started when you see "Jena, Classification, and Extracting' all have been initialized, and finally a "Server started, listening on port xxxx" message.
  • Verify that the port numbers in the run_protege_server_nci.sh script correspond to the port numbers in run_rmiregistry.sh. Please refer to Appendix A for tier specific port numbers. 
  •  Restart the RMI registry by running run_rmiregistry.sh.  Type 'ps -ef | grep rmi' to see if the rmi process has started.
  •  Restart the Protégé Server, using the run_protege_server_nci.sh script. The console will indicate that the server has started and is ready to accept connections.
  • Connect to the server via Protégé client to confirm that the project is viewable from the GUI:  run_protege_<PROTÉGÉ INSTANCE>.sh.  Enter proper login information.
     
     
  • Select the desired proeject from the project display window. 
  • The client should now display the database project file, accesed via the Protege server.
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