Hi Luca. Thanks for posting.
Let me start by asking you some questions:
Which version of Protege are you using, 3.3.1 or 3.4?
Protege 3.4 has only just been properly released (although we've been testing with the release candidate 1) and we are updating the documentation to reflect some of the changes.
In Protege 3.4, the configuration of the metaproject is slightly different to that which is described in the installation guide.
To set it up (as with Protege 3.3.1) you have to open the metaproject.pprj in Protege. Then you need to define the Essential AM Repository project. This has moved slightly in version 3.4 and Project instances are now found under a Class called PolicyControlledObject.
Make sure that you have the path to the PPRJ file for the Essential repository correctly defined - and it's best to use the fully-qualified path, e.g. /Users/...
You might also need to define a Server instance (again, under the PolicyControlledObject Class) if it's not already there. Make sure that you have the AllowedGroupOperations defined for your Server instance and that you've added your users to the Groups in the User instances.
Is the Protege Server running correctly?
Start the Protege Server from a Terminal window to make sure all is working properly. Run the /Applications/Protege_3.x/run_protege_server.sh file and make sure that there are no errors reported as it starts up. When it has started, you'll see the message:
"Protege server ready to accept connections..."
Check the terminal window when you attempt to connect to the server from the Protege client. If there are any issues with the project configurations in the metaproject, errors will be reported.
e.g. If the database containing the Essential repository is not running, then the project will not be available to the client (assuming that you've converted the project to use the database backend). In this case you'll see an error on the terminal window like:
'WARNING: Missing project at...'
It is important to complete all of the installation steps (e.g. Step 9, Repository Database Configuration) before attempting to open the Essential repository.
Some points to note:
The metaproject is a file not database. This file is used to control the configuration of the Protege server but is always a file-based Protege project, not in the database. The default location for this is /Application/Protege_3.x/examples/server. If you've moved this metaproject.pprj to another location, you need to specify this new location in the run_protege_server.sh script. For simplicity of install, this is why we guide you through using the default metaproject rather than shipping one with our repository.
When you make changes to the metaproject.pprj in Protege, you must restart the server for these to take effect. This includes adding users and changing user rights. In Protege 3.4, some new features have been added that allow you to add users from the client but requires you to enable this capability via a property. It is not available by default.
Dropping the Database containing the Essential Repository will certainly break the Protege project. If you've dropped the table, then you should recreate this by opening the essential_baseline_v1.pprj that you downloaded and converting it to use the database backend again.
The Essential metamodel can be extended and modified and instances can be added as much as you need when the project is running on the database backend. As I mentioned, the metaproject is not stored in the database.
It may be worth having a look at the
Protege Client-Server Tutorial for some extensive documentation on setting up the server. In particular, the new administration tools that come with version 3.4.
Hopefully, this will help resolve the issues that you're having. Please don't hesitate to post back with more details about your configuration and the answers to my questions and we will get this working.
Let us know how you get on
Jonathan