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Commits on Jul 15, 2009
  1. @egonw
  2. @egonw

    Feature for this RDF-backed version

    egonw authored egonw committed
  3. @egonw

    Compile errors for recent API changes

    egonw authored egonw committed
  4. @egonw

    DBMolecule Id and Name are now roundtripped

    egonw authored egonw committed
  5. @egonw

    Use a local test db, so that I can make an assertion on the database …

    egonw authored egonw committed
    …triple count
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10839 fcb5ba71-d80d-0410-8237-ba3920747fcc
  6. @egonw

    Removed obsolete file

    egonw authored egonw committed
  7. @egonw

    Throw RuntimeException instead of failing: this better distinguishes …

    egonw authored egonw committed
    …between unimplemented tests and actual failing tests
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10836 fcb5ba71-d80d-0410-8237-ba3920747fcc
  8. @egonw

    Worked on adding molecules, but RDF manager does not allow me to add …

    egonw authored egonw committed
    …RDF yet
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10834 fcb5ba71-d80d-0410-8237-ba3920747fcc
  9. @egonw

    Implemented createDatabase and added two matching unit tests

    egonw authored egonw committed
  10. @egonw

    Ignore the autogenerated logs dir, though not sure where that comes f…

    egonw authored egonw committed
    …rom...
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10831 fcb5ba71-d80d-0410-8237-ba3920747fcc
  11. @egonw

    Added test data and setUp method for manager tests

    egonw authored egonw committed
  12. @egonw

    Towards unit testing...

    egonw authored egonw committed
  13. @egonw

    Setting up a test suite

    egonw authored egonw committed
  14. @egonw

    Compile errors for recent API changes

    egonw authored egonw committed
  15. @egonw

    DBMolecule Id and Name are now roundtripped

    egonw authored egonw committed
  16. @egonw

    Added structrdf.getStore() so that we have access to the raw RDF too

    egonw authored egonw committed
  17. @egonw

    Very loosy storage of a molecule: just the name. But it is a start

    egonw authored egonw committed
  18. @egonw

    Worked on adding molecules, but RDF manager does not allow me to add …

    egonw authored egonw committed
    …RDF yet
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10834 fcb5ba71-d80d-0410-8237-ba3920747fcc
  19. @egonw

    Implemented createDatabase and added two matching unit tests

    egonw authored egonw committed
  20. @egonw

    Towards unit testing...

    egonw authored egonw committed
  21. @egonw

    Also extend the IBioclipseManager interface

    egonw authored egonw committed
  22. @egonw

    OK, now properly recognized: apparently it needs a unique interface t…

    egonw authored egonw committed
    …o be loaded correctly.
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10826 fcb5ba71-d80d-0410-8237-ba3920747fcc
  23. @egonw

    Renamed things properly

    egonw authored egonw committed
  24. @egonw

    Template for a RDF-backed structureDB

    egonw authored egonw committed
  25. @egonw

    Added some dependency info

    egonw authored
Commits on Jul 11, 2009
  1. @egonw

    Set up the Pellet plugin and feature (licensed AGPL v3), with links t…

    egonw authored egonw committed
    …o the clarkparsia.com website
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10855 fcb5ba71-d80d-0410-8237-ba3920747fcc
  2. @egonw

    Updated the source files using Pellet explicitly to state that it is …

    egonw authored egonw committed
    …license AGPL v3
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10820 fcb5ba71-d80d-0410-8237-ba3920747fcc
  3. @egonw

    renamed IBioclipseManager.getNameSpace into IBioclipseManager.getMana…

    jonalv authored egonw committed
    …gerName. Fixes bug: #895
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10775 fcb5ba71-d80d-0410-8237-ba3920747fcc
  4. @egonw

    Generalized owl.listClasses() into rdf.isRDFType()

    egonw authored egonw committed
  5. @egonw

    Added helper manager for handling OWL

    egonw authored egonw committed
  6. @egonw

    Factored out a new interface defining the getModel() method, to allow…

    egonw authored egonw committed
    … pellet and rdf managers to work on the stores the both create (which share the new interfaces). In the future, the managers can have a back up route via an RDF serialization.
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@11581 fcb5ba71-d80d-0410-8237-ba3920747fcc
  7. @egonw

    Added support for multiple DOIs:

    egonw authored egonw committed
    * refactored .doi() to return a String[] because the DOI specs allow so many characters
      a 'X'-separated list is impossible
    * added a PublishedClass.doi field
    * added output of DOI info for 'man <MANAGER>'
    
    git-svn-id: https://bioclipse.svn.sourceforge.net/svnroot/bioclipse/bioclipse2/trunk@10869 fcb5ba71-d80d-0410-8237-ba3920747fcc
  8. @egonw

    Added DOI to further literature

    egonw authored egonw committed
  9. @egonw

    Tuned summaries a bit towards RDF

    egonw authored egonw committed
  10. @egonw

    Removed content-types already defined in the net.bioclipse.rdf plugin

    egonw authored egonw committed
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