If the Protégé 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 the following bullets for details):
star RMI
start explanation server
start Protégé server
Remote login
Use reflection X (or SSH client if running the Protégé 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 with option to periodically save the reasoner state at a desired time frame: ./start_explanation_server.sh --port 8092 --protege-standalone /path/to/database/project/ --persistence <numeric time value>
Run w/out checking for any changes in ontology: ./start_explanation_server.sh --port 8092 --protege-standalone /path/to/database/project/ --no-ontology-sync
Restart explanation server
From /usr/local/protegeqa/NCIThesaurusGroup/Explanation.Server-x.y.z
Run with option to restore to previous saved state of reasoner, as well as to check for any recent changes in the ontology from the previous saved state: ./restart_explanation_server.sh --restore --persistaece
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 Protégé Server
From /usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
Run ./run_protege_server_nci.sh
Shutdown Protégé Server
From /usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
Run ./shutdown_protege_server.sh localhost:2822
Verifying Protégé servers is starting up correctly
From /usr/local/protegeqa/NCIThesaurusGroup/Protege.Server-x.y.z
Run tail -f console.txt
Start Protégé 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 Protégé server
Shut down explanation server
Start Protégé 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 Protégé 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 Protégé server)
Save the Inferred Ontology using the save button on the Inferred Hierarchy section. Give the naming convention 'Thesaurus-Inferred-YYMMDD.owl
Start up Protégé server
Verify Protégé 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: (a) the filename of the baseline and (b) 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 Protégé 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 Protégé 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 Protégé 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 Protégé
Configure Protégé 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 Protégé server is going to be shutdown
Remote login to the host computer using Reflection X
username and password are advertised separately
Shutdown Protégé server
Restart explanation server
Start Protégé 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 Protégé server
Verify Protégé server is running
connect to server from the client
exit the client
Exit console
Exit Reflection X
Classification (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)