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. Give the Project name the following naming convention: <PROTEGE INSTANCE>-YYMMDD-DB.pprj.  Note that the JDBC URL must be in the following format: jdbc:mysql://<databasehostname>:<port>/<database name>  (Please look at the database info for each instance and tier). Give the table name the following naming convention: <PROTEGE-INSTANCE>_<YYMMDD>_<tier>_<release number>.  Conversion can take anywhere up to 2.5 hours.

• 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 client.

• 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 'rdfs:label'.

• 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 'rdfs:label'.  Next, click on the owl:ObjectProperty on the left hand menu, and set its display slot drop down field to 'rdfs:label' 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. The correct port per tier can be determined from the tier-specific info page.

• 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 Widgets 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 both the 'Phonetic Indexer' and the 'Standard Indexer', and and select 'OK'.  After indexing has completed, a new lucene folder will be stored in the same directory as your database project file.

• At this point, if a previous version of the Protege and Explanation servers are running, they will need to be shutdown. For best practices, the RMI registry will need to be shutdown as well. Advertise via email that the tier's current Protege instance will be brought down.  To shutdown, open another reflection X window to the same server.  Type 'ps -ef | grep server' to see view the current protege processes running.  If both explanation and Protege servers are running, shutdown the explanation server first. 

• Type 'cd /usr/local/protege/Protege_x.x/<PROTEGE INSTANCE>Explanation.Server-x.x.x.  Type './stop_explanation_server.sh'.  Next, do a 'ps -ef | grep server' to see if the explanation server was killed.

• Navigate to the previous version Protege server folder by typing 'cd ../Protege.Server-x.x.x'.  Once in the directory, type './shutdown_protege_server.sh localhost:<server port>. A message will appear on the console that the server has been shut down.  The RMI registry is also shutdown from this directory.  Unfortunately, there is no script to shutdown the RMI registry, however, can be killed manually.  To determine which port you want to kill, refer to the tier-specific info page.  Once the correct port has been determined, type 'ps -ef | grep rmi' to figure out which process ID is running the port that needs to be killed.  To kill the process, type 'KILL -9 <RMI Process ID>.  Once executed, type ps -ef | grep rmi again to see if the process has been terminated.

• Now that the all servers from the previous version have been shutdown, the explanation servers for the latest version must now be restarted. Navigate to the latest version's explanation server folder by typing 'cd /usr/local/protege.Protege_x.x/<PROTEGE INSTANCE>/Explanation.Server-x.x.x.

• Once in the directory, type './start_explanation_server.sh --protege-standalone --port <port number> /app/protege/data/Protege_x.x/<PROTEGE INSTANCE>/<DB PROEJCT NAME>.pprj.  After the server has initiated start up, 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' processes all complete, and a "Server started, listening on port xxxx" message.

• Once the server is up and running, go back to the client GUI, click on the 'Reasoning' menu, and ensure that "Clark&Parsia Custom Protege 3.x Reasoner" is selected on the menu list. Click on the 'Reasoning menu again, and scroll down to "Clark&Parsia Custom Protege 3.x Reasoner Details" and ensure that the 'Synchronize Changes with Reasoner' box is checked.  Click 'OK'.

• Click File,  Save 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: BiomedGT-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 display project name and set the correct path to your project files. 
  
  
• Within the nci_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.

• 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.
  

• Once tested, the client can now be posted up on the GForge website to be downloaded by users.