Unable to open essential baseline v6.pprj in Protege

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tmacfarlane
Posts: 8
Joined: 19 Jun 2017, 02:30

I am using a new install and attempted to open the v6.pprj. I get the following error message in the console window. Does the v6 version require a previous version, such as a v5.pprj, as a dependency?

WARNING: unable to load frame: metaproject_Class40006 -- PropertyMapUtil.getFrame()
WARNING: Unknown class: GroupOperation -- Project.loadWidgetDescriptors()
WARNING: Unknown class: PropertyValue -- Project.loadWidgetDescriptors()
WARNING: Unknown class: Server -- Project.loadWidgetDescriptors()
WARNING: Unknown class: Group -- Project.loadWidgetDescriptors()
WARNING: Unknown class: Operation -- Project.loadWidgetDescriptors()
WARNING: Unknown class: Project -- Project.loadWidgetDescriptors()
WARNING: Failed to fix up metaproject to new version. -- edu.stanford.smi.protege.exception.OntologyException: Metaproject Ontology should contain a slot allowedGroupOperation
at edu.stanford.smi.protege.server.metaproject.impl.MetaProjectImpl.getSlot(Unknown Source)
at edu.stanford.smi.protege.server.util.ServerUtil.addPolicyControlledObjectClass(Unknown Source)
at edu.stanford.smi.protege.server.util.ServerUtil.fixMetaProject(Unknown Source)
at edu.stanford.smi.protege.server.Server.initialize(Unknown Source)
at edu.stanford.smi.protege.server.Server.<init>(Unknown Source)
at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
at edu.stanford.smi.protege.server.Server.main(Unknown Source)

SEVERE: server startup failed -- edu.stanford.smi.protege.exception.OntologyException: Metaproject Ontology should contain a class Project
JohnM
Posts: 467
Joined: 17 Feb 2009, 20:19

Hi,

Can you confirm which version of Protege you are using please? It should be under Help > About Protege

Thanks

John
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

Hi -

Following up on John's post (to which we need to know the answer), it would also help to understand more about how far you had got when you get this message.
More specifically, are you setting up a server-based environment or, more simply, opening your repository in Protege client, in stand-alone mode?

The error message suggests that Protege is failing to open the Protege metaproject. This is used by the Protege server to manage its configuration in terms of the repositories that it can serve. Can you tell us a bit more about your installation process, along with the version of Protege that you are using and at what point these messages are reported?

To answer your question, no, the version 6 repository does not require any previous versions to be applied before you can use it. However, if you already have a repository that uses an earlier version of the Essential Meta Model, you can upgrade this to version 6 to take advantage of the latest features of the meta model.

Jonathan
Essential Project Team
tmacfarlane
Posts: 8
Joined: 19 Jun 2017, 02:30

Hi, the install is using Version 3.5 (Build 663). I was opening it from within the protege client and I also tried to open by right-clicking on the file and selecting to open with Protege. Protege just hangs when attempting to open the file and after about 60+ seconds the console shows the final message that I posted in the original statement.

When I attempt to run the protege server (run_protege_server.bat) then this creates the full error message.

C:\Program Files\Protege_3.5>jre\bin\java -Xmx500M -Djava.rmi.server.codebase=file:/c:/program%20files/protege_3.5/protege.jar -Djava.awt.headless=true -Dlog4j.configuration=file:log4j.xml -cp protege.jar;looks.jar;unicode_panel.jar;driver.jar;driver0.jar;driver1.jar edu.stanford.smi.protege.server.Server examples\server\metaproject.pprj
Protege server is starting...
Protege 3.5 Build 663, JVM 1.6.0_01-b06, memory=466M, Windows Vista, encoding=UTF-8, language=en, country=US
Server port = 0, registry port = 1099, compressed stream
Using metaproject from: file:/C:/Program%20Files/Protege_3.5/examples/server/metaproject.pprj
Mon Jun 19 17:22:21 ACT 2017 WARN: Establishing SSL connection without server's identity verification is not recommended. According to MySQL 5.5.45+, 5.6.26+ and 5.7.6+ requirements SSL connection must be established by default if explicit option isn't set. For compliance with existing applications not using SSL the verifyServerCertificate property is set to 'false'. You need either to explicitly disable SSL by setting useSSL=false, or set useSSL=true and provide truststore for server certificate verification.
WARNING: unable to load frame: metaproject_Class40006 -- PropertyMapUtil.getFrame()
WARNING: Unknown class: GroupOperation -- Project.loadWidgetDescriptors()
WARNING: Unknown class: PropertyValue -- Project.loadWidgetDescriptors()
WARNING: Unknown class: Server -- Project.loadWidgetDescriptors()
WARNING: Unknown class: Group -- Project.loadWidgetDescriptors()
WARNING: Unknown class: Operation -- Project.loadWidgetDescriptors()
WARNING: Unknown class: Project -- Project.loadWidgetDescriptors()
WARNING: Failed to fix up metaproject to new version. -- edu.stanford.smi.protege.exception.OntologyException: Metaproject Ontology should contain a slot allowedGroupOperation
at edu.stanford.smi.protege.server.metaproject.impl.MetaProjectImpl.getSlot(Unknown Source)
at edu.stanford.smi.protege.server.util.ServerUtil.addPolicyControlledObjectClass(Unknown Source)
at edu.stanford.smi.protege.server.util.ServerUtil.fixMetaProject(Unknown Source)
at edu.stanford.smi.protege.server.Server.initialize(Unknown Source)
at edu.stanford.smi.protege.server.Server.<init>(Unknown Source)
at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
at edu.stanford.smi.protege.server.Server.main(Unknown Source)

SEVERE: server startup failed -- edu.stanford.smi.protege.exception.OntologyException: Metaproject Ontology should contain a class Project
at edu.stanford.smi.protege.server.metaproject.impl.MetaProjectImpl.getCls(Unknown Source)
at edu.stanford.smi.protege.server.metaproject.impl.MetaProjectImpl.getWrappedInstances(Unknown Source)
at edu.stanford.smi.protege.server.metaproject.impl.MetaProjectImpl.getProjects(Unknown Source)
at edu.stanford.smi.protege.server.Server.getAvailableProjectNames(Unknown Source)
at edu.stanford.smi.protege.server.Server.initializeProjects(Unknown Source)
at edu.stanford.smi.protege.server.Server.initialize(Unknown Source)
at edu.stanford.smi.protege.server.Server.<init>(Unknown Source)
at edu.stanford.smi.protege.server.Server.startServer(Unknown Source)
at edu.stanford.smi.protege.server.Server.main(Unknown Source)
User avatar
jonathan.carter
Posts: 1087
Joined: 04 Feb 2009, 15:44

Hi,

Thanks very much for posting the details of the error messages.

One thing that jumps out is that there is not enough memory available to the environment in this configuration. We should resolve this - even though the specific error message seems to be in a different area.

To add more memory to the Java environment in which Protege is running:
  • For Protege client, increase the maximum memory parameter in the Protege.lax settings (File -> Preferences -> Protege.lax) to increase the memory to 1.5GB (32-bit Java Runtime) or 2GB (64-bit Java Runtime)
  • For Protege server, edit the run_protege_server.bat to increase the -Xmx setting to the above values
The error that is being reported suggests that the Protege server configuration (metaproject.pprj) is missing an important setting. Did you install the meta project that is included in the Protege installer or are you using the meta project that is supplied with the Protege installation?

If you are using the metaproject.pprj that is included in the Essential installation, try opening that in Protege client, making any configuration changes (e.g. the location of your Essential repository Protege project) and then save this. Protege should repair any missing elements.

Jonathan
Essential Project Team
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