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Admin guide cheat sheet for Protégé BiomedGT

Servers

cbiows501         production
cbapp-q1001    qa
cbvapp-d1012 dev (VM)
cbvapp-s1005    stage (VM)

Related Programs/Services

Reflection X (using "Direct" or xterm over SSH connection)
F-Secure SSH Client
F-Secure SSH File Transfer

Username and password advertised separately.

Relevant Directory Structure in the various boxes/VMs

Production

/usr/local/protege/Protege.Server-x.y.z
/usr/local/protege/Protege.Client-x.y.z
/usr/local/protege/Explanation.Server-x.y.z
/app/protégé/data

Dev, QA, Stage

/usr/local/protege/Protégé_x.x.x/\[PROTÉGÉ INSTANCE\]/Protege.Server-x.y.z
/usr/local/protege/Protégé_x.x.x/\[PROTÉGÉ INSTANCE\]/Protege.Client-x.y.z
/usr/local/protege/Protégé_x.x.x/\[PROTÉGÉ INSTANCE\]/Explanation.Server-x.y.z

Dev, QA, Stage SVN files for builds

/app/protege/repo/<protégé release folder>

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. When all the services need to be started (e.g. after a reboot), follow this order (see bullets below for details):

start rmi
start Explanation server
start Protege server

Remote login

Use reflection X (or SSH client if running the Protege client is not required)

Start rmiregistry (configure script to use port 2633 in PROD)

From '/usr/local/protege/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/protege/Explanation.Server-x.y.z
Run ./start_explanation_server.sh --protégé-standalone --port 8090 /path/to/database/project.pprj

Re start Explanation server

From /usr/local/protege/Explanation.Server-x.y.z
Run ./restart_explanation_server.sh

Verifying Explanation servers is starting up correctly

From /usr/local/protege/Explanation.Server-x.y.z
Run tail -f nohup.out

Shutdown Explanation server

From /usr/local/protege/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/protege/Protege.Server-x.y.z
Run ./run_protege_server_nci.sh

Shutdown Protege server

From /usr/local/protege/Protege.Server-x.y.z
Run ./shutdown_protege_server.sh localhost: 2633

Verifying Protege servers is starting up correctly

From /usr/local/protege/Protege.Server-x.y.z
Run tail -f console.txt

Start Protege client

From /usr/local/protege/Protege.Client-x.y.z
Run ./run_protege_BGT.sh

Prompt Accept/Reject cycle

Advertise (email/chat) the server is going to be shut down
Clean up Pre-Merged, and Pre-Reitred 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/protege/data/BiomedGT.pprj
Enable PromptTab 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)
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 next Prompt comparison or publication
- Convert Project to Format -> OWL / RDF Files
  - This creates a new project .pprj and associated OWL file, give it a name with a date suffix, example BiomedGTFile-071128.pprj.
Close project without saving, and exit the client.
In the Reflection X console, navigate to /app/protege/data/ and look for any BiomedGT accept files: (BiomedGT-accept.pprj, .pjrn, .rdf, .rdfs) and remove them from the directory by typing 'rm BiomedGT-accept.pprj' and so on for the other files.
Start Explanation server (always restart explanation server first before the Protégé Server).
For Production tier at the end of the monthi) Reopen Protégé client.
ii) Click 'Project', 'Configure', enable 'OWLClasses Tab'
iii) Click 'Reasoning', 'Classify Taxonomy'
iv) Save the Inferred Ontolgoy using the save button in the Inferred Hierarchy section. Give the naming convention 'BiomedGT-Inferred-YYMMDD.owl'* Startup Protege server.
Verify Protege server is up.
Verify Explanation tab communicates with 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 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 help keep the Protégé server clean and organized.

Database Load from File

Remote login to the host computer using Reflection X.
cd to /usr/local/protege/Protege.Client-x.y.z.
Start protege ("./run_protege_BGT.sh").
Load file from /app/protege/data/(new project).
Convert project to format (Clark & Parsia owl / rdf database).
- initial project BiomedGT.pprj (as opposed to baselines).
Configure project (see below, include Save but don't Exit).
Convert project to format (owl / rdf file) for a file baseline, with date.
Exit Protege without saving (the Save gets done automatically during the conversion).

Configuring 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)

    Enable journaling
    Disable redo/undo
    Set OWL Preferences items:
    Configure URL to the correct explanation server
    Set preferences to read Manchester Syntax
    Disable drag and drop in owl preferences
    Disable test of deprecated classes/properties
    Set Visibility to uncheck all MetaData Items
    Set Reasoning menu items:
    Click on Reasoning menu, and ensure that Clark & Parsia Custom Protégé 3.x Reasoner is selected on the menu list.
    Click on Reasoning menu ? C & P Custom Protégé 3.x Reasoner Details ? ensure Synchronize Changes with Reasoner box is checked ? click OK.
    Set transitivity
    Set display slots to read rdfs:label for NCI Edit tab as well as Property Tag
    Generate Lucene indices from Lucene menu. Ensure both Phonetic and Standard boxes are checked prior to indexing.
    Start explanation server, point to the newly created project. Once the server's up and running, save the project.
    Exit protege
Configure protege server for a project
    Edit run_protege_server_nci.sh

a) to include the proper directory path for the nci_metaproject file - /app/protege/data/metaproject/
b) to use the correct rmi port (use 2633)

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
    Shut down Protege server
    Restart Explanation server
    start protege client
connect to database project
    in    /app/protege/data/
    file    BiomedGT.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 without saving
    start protege server
    verify protege server is running
    connect to the server from the client
    exit the client
    exit terminal
    exit reflection X

Classification (client/server mode)

    From the GUI, enable OWLClassesTab (results are shown there)
    from the OWL menu, select "Classify taxonomy", it takes about 20 minutes
    Once classifications 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.