Examples of MoleculeDiff

Examples of org.wymiwyg.rdf.molecules.diff.MoleculeDiff

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      System.out.println("leanifying g2");
      g2 = MoleculeBasedLeanifier.getLeanVersionOf(g2);
    }
    System.out.println("testing g1 of size "+g1.size()+" against g2 of size "+g2.size());
    try {
      MoleculeDiff diff = new MoleculeDiffImpl(
          new ReferenceGroundedDecompositionImpl(
              g1),
          new ReferenceGroundedDecompositionImpl(
              g2));
      File file = File.createTempFile("minimum-failing",".zip");
      diff.serialize(new FileOutputStream(file));
      MoleculeDiff diffRec =  LeanDiffPatch.deserializeDiff(file);
      ReferenceGroundedDecomposition dec2rec = diffRec
          .patch(new ReferenceGroundedDecompositionImpl(
              (g1)));
      Graph g2rec = ReferenceGroundedUtil.reconstructGraph(dec2rec);
      //TODO find out why test 20 fails without this line
      g2rec = JenaUtil.getGraphFromModel(JenaUtil.getModelFromGraph(g2rec), true);
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Examples of org.wymiwyg.rdf.molecules.diff.MoleculeDiff

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      m1.write(new FileOutputStream(File.createTempFile("random-model-1",
          ".nt")), "N-TRIPLE");
      m2.write(new FileOutputStream(File.createTempFile("random-model-1",
          ".nt")), "N-TRIPLE");
      try {
        MoleculeDiff diff = LeanDiffPatch.getDiff(m1, m2);
        File zipFile = File.createTempFile("random-model", ".zip");
        OutputStream diffOut = new FileOutputStream(zipFile);
        diff.serialize(diffOut);
        diffOut.close();
        MoleculeDiff diffRec;// =
        // LeanDiffPatch.deserializeDiff(zipFile);
        {
          InputStream in1 = new FileInputStream(zipFile);
          File tempFile = File.createTempFile(Util
              .createRandomString(5), "dzip");
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Examples of org.wymiwyg.rdf.molecules.diff.MoleculeDiff

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    Model model2 = createFgNodeTestModel2();
    ReferenceGroundedDecomposition dec1 = new ReferenceGroundedDecompositionImpl(
        JenaUtil.getGraphFromModel(model1, true));
    ReferenceGroundedDecomposition dec2 = new ReferenceGroundedDecompositionImpl(
        JenaUtil.getGraphFromModel(model2, true));
    MoleculeDiff diff = new MoleculeDiffImpl(dec1, dec2);
    diff.print(new PrintWriter(System.out, true));
    assertEquals("cross-graph nodset", 1, diff.getCrossGraphFgNodes()
        .size());
    assertEquals("fgnodes only in 1", 0, diff.getFgNodesOnlyIn1().size());
    assertEquals("fgnodes only in 2", 1, diff.getFgNodesOnlyIn2().size());
    assertEquals("molecules only in 1", 1, diff
        .getContextualMoleculesOnlyIn1().size());
    assertEquals("terminal molecules only in 1", 1, diff
        .getTerminalMoleculesOnlyIn1().size());
    assertEquals("molecules only in 2", 1, diff
        .getContextualMoleculesOnlyIn2().size());
    assertEquals("molecules only in 2", 1, diff
        .getTerminalMoleculesOnlyIn2().size());
  }
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Examples of org.wymiwyg.rdf.molecules.diff.MoleculeDiff

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        JenaUtil
            .getGraphFromModel(model1, true));
    ReferenceGroundedDecomposition dec2 = new ReferenceGroundedDecompositionImpl(
        JenaUtil
            .getGraphFromModel(model2, true));
    MoleculeDiff diff = new MoleculeDiffImpl(dec1, dec2, true);
    diff.print(new PrintWriter(System.out, true));
    assertEquals("cross-graph nodset", 1, diff.getCrossGraphFgNodes()
        .size());
    assertEquals("fgnodes only in 1", 0, diff.getFgNodesOnlyIn1().size());
    assertEquals("fgnodes only in 2", 1, diff.getFgNodesOnlyIn2().size());
    assertEquals("molecules only in 1", 0, diff
        .getContextualMoleculesOnlyIn1().size());
  }
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Examples of org.wymiwyg.rdf.molecules.diff.MoleculeDiff

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  public void testMergedSplittedFgNodes() {
    Model m1 = ModelFactory.createDefaultModel();
    Model m2 = ModelFactory.createDefaultModel();
    m1.read(getClass().getResource("splitted-fg-node.n3").toString(), "N3");
    m2.read(getClass().getResource("merged-fg-node.n3").toString(), "N3");
    MoleculeDiff diff = new MoleculeDiffImpl(m1, m2, true);
    diff.print(new PrintWriter(System.out, true));
    assertEquals("molecules only in 1", 0, diff
        .getContextualMoleculesOnlyIn1().size());
    assertEquals("t-molecules only in 1", 2, diff
        .getTerminalMoleculesOnlyIn1().size());
    assertEquals("molecules only in 2", 1, diff
        .getTerminalMoleculesOnlyIn2().size());
  }
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Examples of org.wymiwyg.rdf.molecules.diff.MoleculeDiff

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    m1.read(getClass().getResource("person.n3").toString(), "N3");
    m2
        .read(
            getClass().getResource("person-plus-1-ifp.n3")
                .toString(), "N3");
    MoleculeDiff diff = new MoleculeDiffImpl(m1, m2, true);
    diff.print(new PrintWriter(System.out, true));
    assertEquals("molecules only in 1", 0, diff
        .getTerminalMoleculesOnlyIn1().size());
    assertEquals("molecules only in 2", 0, diff
        .getTerminalMoleculesOnlyIn2().size());
  }
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Examples of org.wymiwyg.rdf.molecules.diff.MoleculeDiff

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    Model m1 = ModelFactory.createDefaultModel();
    Model m2 = ModelFactory.createDefaultModel();
    m1.read(getClass().getResource("person.n3").toString(), "N3");
    m2.read(getClass().getResource("person-plus-another-person.n3")
        .toString(), "N3");
    MoleculeDiff diff = new MoleculeDiffImpl(m1, m2, true);
    diff.print(new PrintWriter(System.out, true));
    assertEquals("terminal molecules only in 1", 0, diff
        .getTerminalMoleculesOnlyIn1().size());
    assertEquals("terminal molecules only in 2", 1, diff
        .getTerminalMoleculesOnlyIn2().size());
    assertEquals("used common fg-nodes", 0, diff
        .getCommonFgNodesInDiffMolecules().size());
  }
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Examples of org.wymiwyg.rdf.molecules.diff.MoleculeDiff

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     */
    m2
        .read(
            getClass().getResource("person-plus-1-ifp.n3")
                .toString(), "N3");
    MoleculeDiff diff = new MoleculeDiffImpl(m1, m2, true);
    diff.print(new PrintWriter(System.out, true));
    assertEquals("molecules only in 1", 0, diff
        .getContextualMoleculesOnlyIn1().size());
    assertEquals("molecules only in 2", 0, diff
        .getContextualMoleculesOnlyIn2().size());
  }
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Examples of org.wymiwyg.rdf.molecules.diff.MoleculeDiff

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          .getFileFormat());

    } catch (MalformedURLException e) {
      throw new RuntimeException(e);
    }
    MoleculeDiff diff;
    try {
      diff = LeanDiffPatch.deserializeDiff(arguments.getDiffPath());
    } catch (IOException e) {
      log.error("Failure reading diff", e);
      return;
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Examples of org.wymiwyg.rdf.molecules.diff.MoleculeDiff

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      model2.read(arguments.getModel2Path().toURL().toString(), arguments
          .getFileFormat());
    } catch (MalformedURLException e) {
      throw new RuntimeException(e);
    }
    MoleculeDiff diff;
    File ontologyFile = arguments.getModelOntologyPath();
    if (ontologyFile != null) {
      Model ontology = ModelFactory.createDefaultModel();
      try {
        ontology.read(ontologyFile.toURL().toString(), arguments
            .getFileFormat());
      } catch (MalformedURLException e) {
        throw new RuntimeException(e);
      }
      diff = new MoleculeDiffImpl(model1, model2, ontology, arguments
          .getUseDefaultOntology());
    } else {

      diff = new MoleculeDiffImpl(model1, model2, arguments
          .getUseDefaultOntology());
    }
    if (arguments.getDiffPath() != null) {
      try {
        diff.serialize(arguments.getDiffPath());
      } catch (IOException e) {
        log.error("Failed serializing diff", e);
      }
    }
    if (arguments.getOutputDiff()) {
      diff.print(new PrintWriter(System.out, true));
    }
  }
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