View Source

Admin Guide Cheat Sheet for Protege NCI Thesaurus

Servers

cbiows501	Production (protegeqa user)
cbvapp-s1005	Stage (protegeadm user)
cbapp-q1001	QA (protegeadm user)
cbvapp-d1012	Dev (protegeadm user)

Related Programs/Services

Reflection X (using "Direct" or xterm over SSH connection).
F-Secure SSH Client
F-Secure SSH Transfer
Username and password advertised separately

Related Directory Structure in the Various Boxes/VMs

Production

/usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
/usr/local/protegeqa/NCIThesaurusGroup/Protege.Client-x.y.z
/usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z
/app/protegeqa/data

Dev, QA, Stage

usr/local/protege/Protege_x.x.x/\[PROTEGE INSTANCE\]/Protege.Server-x.y.z

usr/local/protege/Protege_x.x.x/\[PROTEGE INSTANCE\]/Protege.Client-x.y.z

usr/local/protege/Protege_x.x.x/\[PROTEGE INSTANCE\]/Explanation.Server-x.y.z

Dev, QA, Stage File Directory for Builds

/app/protege/repo

Production Login and Basic Server Operations

If the Protege server is brought down for maintenance, classification, Prompt analysis, and so on, the RMI can continue running. While all the services need to be started (e.g. after a reboot), follow this order (see bullets below for details):
- star RMI
- start explanation server
- start Protege server

Remote login
- Use reflection X (or SSH client if running the Protege client is not required).

Start RMI registry (configure script to use port 2822 in production
- From /usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
- Run ./run_rmiregistry.sh

Shutdown rmiregistry
- Kill from OS (identify with ps -ef | grep rmiregistry)

Start explanation server

From /usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z

Run&nbsp;&nbsp;&nbsp;&nbsp; ./start_explanation_server.sh \-p 8092 \--url jdbc:mysql://cbiows501.nci.nih.gov:3625/NCIt_Demo \-t Thesaurus_Baseline \-U protege \-P \[obtain password from system administrator\]

Restart explanation server
- From /usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z
- Run ./restart_explanation_server.sh

Verifying explanation servers is starting up correctly
- From /usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z
- Run tail -f nohup.out

Shutdown explanation sever
- From /usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z
- Run ./stop_explanation_server.sh
- Note - after a shutdown, the server can't be "restarted", it must be "started" instead.

Start Protege Server
- From /usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
- Run ./run_protege_server_nci.sh

Shutdown Protege Server
- From /usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
- Run ./shutdown_protege_server.sh localhost:2822

Verifying Protege servers is starting up correctly
- From /usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
- Run tail -f console.txt

Start Protege client
- From /usr/local/protegeqa/NCIThesaurusGroup/Protege.Client-x.y.z
- Run ./run_protege_NCIT.sh

Prompt Accept/Reject Cycle

Advertise (email/chat) the server is going to be shutdown
Clean up Pre-Merged, and Pre-Retired concepts.
Remote login to the host computer using Reflection X
Shut down Protege server
Shut down explanation server
Start Protege client
Connect to database project by following the path: /app/protegeqa/data/Protege_1.2.3/NCIThesaurus/Thesaurus.pprj
Enable Prompt Tab in menu (in Project --> Configuration dialog)
Compare against previous baseline file / database project (pprj file).
Accept/reject changes
Save concept history (in "save" icon in 'Table View' tab)
Disable PromptTab (in Configuration dialog)
Adjust baseline version in Metadata tab
in the Protege GUI menu, click 'Change' -> 'Clean up Changes Ontology'. Ensure that 'Delete Changes' and 'Archive Changes' remain checked. Click 'OK'. After the process has been completed, click 'Change' -> 'Save Changes Ontology'
Export file for the next Prompt comparison or publication
- Click 'File' -> 'Convert Project to Format' -> 'OWL/RDF Files
  - this creates a new project .pprj file and associated OWL file, give it a name with a date suffix, example: ThesaurusInterim-071120.pprj
Close project without saving, and exit client
In Reflection X console, navigate to /app/protegeqa/data/Protege_x.x.x/NCIThesaurus and look for any Thesaurus accept files: (Thesaurus-accept.pprj, pjrn, .rdf, rdfs) and remove them from the directory by typing 'rm Thesaurus-accept.pprj' and so on for the other files.
Start explanation server (always restart explanation server first before the Protege server)
For production tier at the end of the month:
- Reopen Protege client
- Click 'Project' -> 'Configure' -> enable 'OWL Classes Tab'
- Click 'OWL' --> 'Classify Taxonomy'
- Save the Inferred Ontology using the save button on the Inferred Hierarchy section. Give the naming convention 'Thesaurus-Inferred-YYMMDD.owl
Start up Protege server
Verify Protege server is up
Verify explanation tab communicates with the explanation server
Exit remote program
Advertise that the server is back up
For end-of-the-month publications, after performing a prompt, notify Tracy, John, or Rob of the availability of the new baseline
In the notification include: the filename of the baseline and (ii) the length of the time for the Prompt/export to file to complete.
The raw exports (OWL files only) will be archived in the private FTP site,and the processed exports in the anonymous FTP site. This will keep the Protege server clean and organized.

Database Load from File

Remote login to the host computer using Reflection X
cd to /usr/local/protegeqa/NCIThesaurusGroup/Protege.Client-x.y.z
Start Protege client ('./run_protege_NCIT.sh')
Load file from /app/protegeqa/data/Protege_x.y.z/NCIThesaurus (new project)
Convert project to format (OWL/RDF database)
- initial project - Thesaurus.pprj (as opposed to baselines)

Configure project (see below, include Save, but don't Exit).
Exit Protege without saving (the Save gets done automatically during the conversion)

Configuring a New Project

(already logged-in in the server box)
Enable tabs
- nciedittab
- advanced query
- properties
- metadata
- changes
- explanation tab
Disable extra tabs (OWLClasses, OWLInstances, OWLForms)
Configure URL for explanation service.
Enable journaling
Disable redo/undo
Set OWL Preferences to read 'Manchester Syntax'
Set transitivity
Set display slots to read 'Preferred Name' for the NCI Edit tab as well as Property Tag
Disable drag and drop in 'OWL Preferences'
Disable test of deprecated classes/properties
Set Visibility tab to uncheck all MetaData items
Generate Lucene indices
- Move lucene index from /app/protegeqa/data/Protege_x.y.z/NCIThesaurus to the Proege server directory
Save project
Exit Protege

Configure Protege Server for a Project

Edit run_protege_server_nci.sh
- to include the proper directory path for the nci_metaproject file - /app/protegeqa/data/NCIThesaurusMetaProject/
- to use the correct rmi port (use 2822)

Classification (Standalone Mode)

Advertise the Protege server is going to be shutdown
Remote login to the host computer using Reflection X
- username and password are advertised separately
Shutdown Protege server
Restart explanation server
Start Protege client
Connect to the database project
- in /app/protegeqa/data/Protege_x.y.z/NCIThesaurus
- file Thesaurus.pprj
Enable OWLClassesTab (results are shown there)
From the OWL menu, select 'Classify Taxonomy', it takes about 20 minutes
Once classification is complete, an inferred hierarchy panel and a list panel are displayed
Accept retreeing suggestions in the list panel as per guideline.
Generate table to pass around to editors and mail it
Process table from previous classification (accept/reject)
Close project withtout saving
Start Protege server
Verify Protege server is running
- connect to server from the client
- exit the client
Exit console
Exit Reflection X

Classfication (Client/Server) Mode

From the client GUI, enable OWLClassesTab (results are shown there)
From the OWL menu, select 'Classify Taxonomy' it takes about 20 minutes
Once classification is complete, an inferred hierarchy panel and a list panel are displayed.
Accept retreeing suggestions in the list panel as per guideline
Generate table to pass around to editors and mail it
Process table from previous classification (accept/reject)
Close project without saving
Exit the client.