[kepler-dev] [Bug 4740] New: Create Ontology_Catalog sql table in the CORE persistent database

[bugzilla-daemon at ecoinformatics.org]

http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4740

           Summary: Create Ontology_Catalog sql table in the CORE
                    persistent database
           Product: Kepler
           Version: 1.x dev
          Platform: All
        OS/Version: All
            Status: NEW
          Severity: normal
          Priority: P2
         Component: core
        AssignedTo: aschultz at nceas.ucsb.edu
        ReportedBy: aschultz at nceas.ucsb.edu
         QAContact: kepler-dev at kepler-project.org
                CC: swriddle at gmail.com


I ran into our old friend, the "Cannot Find Ontology" error.  After much time
trying to debug through the OntologyConfiguration and OntologyCatalog classes I
discovered that the way the owl files are being accessed is very fragile and
thus causes this error (which I was finally able to reproduce by ant
clean-cache).  The issue is how the absolute paths are being created to find
the owl files.  I would suggest we create a database table in the persistent
core database that has four columns: ID, NAME, PATH, and LIBRARY.   The PATH is
the fully qualified absolute path to the OWL file on the system that Kepler is
running on (so we don't have to keep trying to figure out what the absolute
path is in the Java code every time we want to get to the owl file).

The new catalog system would work like this:
1.) Default owl files (that are shipped with Kepler) are defined in Java code
and inserted into the table the first time Kepler is started using the fully
qualified absolute path for whatever system Kepler is running on
2.) Tagging (or other modules) can then add ontologies to the sql table (thus
not having to overwrite the ontology_catalog.xml file directly as is done now)
3.) The user can then edit the the catalog through a gui interface (as opposed
to editing the ontology_catalog.xml file as is done now)

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