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[protege-owl] Importing several ontologies from stream

Ralf Weinand weinanr at cs.tu-berlin.de
Sun May 4 15:09:12 PDT 2008


Hi Tania,

thanks a lot.
For sure I will remind you... ;-)

Cheers
Ralf


On Thu, May 1, 2008 at 1:38 AM, Tania Tudorache <tudorache at stanford.edu> wrote:
> Hi Ralf,
>
>  I have made the setErrorLevel public. The parser code in the next beta
>  release will be much different than the one in the current release.
>  Please remind me to post an example for importing from streams after we
>  release the new beta.
>
>  Thanks,
>
>
> Tania
>
>
>  Ralf Weinand wrote:
>  > Hi Tania,
>  >
>  > thanks a lot for this hint!
>  > No it works without temp files and repositories! Great!
>  >
>  > The methods
>  > - createARPInvokation(final Reader reader, final String uri)
>  > - setErrorLevel(ARP arp)
>  > are not public so I had to copy them into my class.
>  > maybe you could make them public?
>  >
>  > Anyway, thanks heaps again!
>  >
>  > Ralf
>  >
>  >
>  >
>  >
>  > On Thu, Apr 24, 2008 at 1:51 AM, Tania Tudorache <tudorache at stanford.edu> wrote:
>  >
>  >> Ralf,
>  >>
>  >>  You can do the import from a stream, but not in a straightforward way. Look
>  >> at the method:
>  >>
>  >>  public static void addImport(JenaOWLModel owlModel,
>  >>                                 URI ontologyName,
>  >>                                 String prefixForDefaultNamespace)
>  >>
>  >>  from ProtegeOWLParser.java (I've attached the class code). You can
>  >> basically copy that code in your own method. Make sure that you also add the
>  >> import statement to the importing ontology (see javadoc comment) after you
>  >> do the import. Probably you can get rid of the repository code in the
>  >> method.
>  >>
>  >>  Tania
>  >>
>  >>
>  >>
>  >>
>  >>
>  >>  Ralf Weinand wrote:
>  >>
>  >>
>  >>> Hi Tania,
>  >>>
>  >>> thanks for the hint.
>  >>> I don´t think, that this method is what I need, but I did see another
>  >>> (undocumented) method in RepositoryUtil:
>  >>>
>  >>>
>  >> http://protege.stanford.edu/download/prerelease_javadoc_owl/edu/stanford/smi/protegex/owl/repository/util/RepositoryUtil.html#createImportLocalCopy(edu.stanford.smi.protegex.owl.model.OWLModel,%20java.net.URI,%20java.io.File)
>  >>
>  >>> Can you tell me what it does?
>  >>>
>  >>> Again my problem: i don´t have these ontologies stored physically.
>  >>> I receive them as org.w3c.dom.Element objects so I do not have a
>  >>> physical location (URL).
>  >>> They are just in memory, but I have to import them into one common
>  >>> knowledgebase.
>  >>> That´s why I have to write them temporarily to files and them load the
>  >>> first one and import the others.
>  >>> I´m looking for a better approach.
>  >>>
>  >>> Thanks!
>  >>> Ralf
>  >>>
>  >>>
>  >>>
>  >>> On Wed, Apr 23, 2008 at 3:36 AM, Tania Tudorache <tudorache at stanford.edu>
>  >>>
>  >> wrote:
>  >>
>  >>>
>  >>>> Ralf,
>  >>>>
>  >>>>  There was recently a post that might be relevant. See this thread [1].
>  >>>>
>  >>>>  There is a new utility method,
>  >>>>  RepositoryUtil.loadProjectRepositoriesFromURI(...) that may help. See
>  >>>>  also the Javadoc of this method. You can add as a project repository a
>  >>>>  URL and then do the import with the ontology name (not ontology URL).
>  >>>>  The parser will look at the repositories and get an input stream from
>  >>>>  the repository URL.
>  >>>>
>  >>>>  I haven't tested this yet, but I think it should work.
>  >>>>
>  >>>>  Tania
>  >>>>
>  >>>>  [1]:
>  >>>>
>  >> http://article.gmane.org/gmane.comp.misc.ontology.protege.owl/24368
>  >>
>  >>>>
>  >>>>
>  >>>>  Ralf Weinand wrote:
>  >>>>  > Hi,
>  >>>>  >
>  >>>>  > I am writing a program that receives several ontologies (as strings -
>  >>>>  > or, to be more precise - as RDF/XML serializations).
>  >>>>  > All of these ontologies have to be imported into one common knowledge
>  >>>>  > base to perform some reasoning (also using Jess for SWRL rules).
>  >>>>  > Now I am facing a problem. The first serialization I can simply load
>  >>>>
>  >> via
>  >>
>  >>>>  >
>  >>>>  >             dataflowModel =
>  >>>>  > ProtegeOWL.createJenaOWLModelFromReader(new StringReader(ontology1));
>  >>>>  >
>  >>>>  > But for the rest of the ontologies I have to first write each one
>  >>>>
>  >> into
>  >>
>  >>>>  > a temporary file, take the URI and use this URI
>  >>>>  > to import the ontology via
>  >>>>  >
>  >>>>  >             ImportHelper importHelper = new
>  >>>>
>  >> ImportHelper(dataflowModel);
>  >>
>  >>>>  >
>  >>>>  >             for (int i = 3; i < aArgs.size(); i++)
>  >>>>  >             {
>  >>>>  >                 File sourceModelFile =
>  >>>>  > SemanticUtils.writeOntologyToTempFile(aArgs.get(i));
>  >>>>  >                 importHelper.addImport(sourceModelFile.toURI());
>  >>>>  >             }
>  >>>>  >
>  >>>>  >             importHelper.importOntologies();
>  >>>>  >
>  >>>>  > Isn´t there a mode convenient method to do this?
>  >>>>  > I don´t like the idea of using temp-files.
>  >>>>  >
>  >>>>  > Also, I am facing some problems with this method (some dependencies
>  >>>>  > regarding the order in which I do the imports).
>  >>>>  > Do I have to use a repository manager somehow?
>  >>>>  > Any recommendations?
>  >>>>  >
>  >>>>  > Cheers,
>  >>>>  > Ralf
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