Package org.openbel.framework.common.protonetwork.model

Examples of org.openbel.framework.common.protonetwork.model.ProtoNetwork

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        File pn = binaryProtoNetworkDescriptor.getProtoNetwork();
        ObjectInputStream ois = null;
        try {
            ois = new ObjectInputStream(new FileInputStream(pn));

            ProtoNetwork network = new ProtoNetwork();
            network.readExternal(ois);
            return network;
        } catch (FileNotFoundException e) {
            final String msg = "Cannot find binary proto-network for path";
            throw new ProtoNetworkError(pn.getAbsolutePath(), msg, e);
        } catch (IOException e) {
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    private List<SkinnyUUID> uuids;
    private BucketEquivalencer be;

    @Before
    public void setUp() {
        pn = new ProtoNetwork();
        er = new TestEquivResource();
        uuids = new ArrayList<SkinnyUUID>(1000);
        TableNamespace ns1 = new TableNamespace("namespace1");
        TableNamespace ns2 = new TableNamespace("namespace2");
        MockEquivLookup lookup1 = new MockEquivLookup();
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    @Test
    @Ignore
    public void testSimpleStatementProtoNetworkBuilding() {
        ProtoNetworkBuilder protoNetworkBuilder =
                new ProtoNetworkBuilder(document);
        ProtoNetwork protoNetwork = protoNetworkBuilder.buildProtoNetwork();

        //Test extracted symbols
        NamespaceTable namespaceTable = protoNetwork.getNamespaceTable();
        ParameterTable parameterTable = protoNetwork.getParameterTable();
        TermTable termTable = protoNetwork.getTermTable();
        Namespace hgncNs =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/ns/hgnc-approved-symbols.belns");

        //check eg default namespace and hgnc specified namespace
        assertEquals(3, namespaceTable.getNamespaces().size());
        assertEquals(11, parameterTable.getTableParameters().size());

        assertEquals(9, termTable.getTermValues().size());
        assertTrue(parameterTable.getTableParameters().contains(
                new TableParameter(new TableNamespace(hgncNs), "AIFM1")));
        assertTrue(termTable.getTermValues().contains("proteinAbundance(#)"));
        assertTrue(termTable.getTermValues().contains("geneAbundance(#)"));

        //Test extracted statements
        StatementTable statementTable = protoNetwork.getStatementTable();

        assertEquals(6, statementTable.getStatements().size());
    }
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            protoNetworkDescriptor =
                    protoNetworkExternalizer.writeProtoNetwork(protoNetwork,
                            System.getProperty("user.dir"));

            // test read
            ProtoNetwork serializedProtoNetwork =
                    protoNetworkExternalizer
                            .readProtoNetwork(protoNetworkDescriptor);

            Assert.assertEquals(protoNetwork, serializedProtoNetwork);
        } catch (ProtoNetworkError e) {
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                new NamespaceGroup(URL, null),
                parse("m(AKT1) =| p(AKT2)"),
                parse("cat(g(AKT2)) -| p(PARP1)"));

        // merge in different orders
        ProtoNetwork ab = merge(a, b);
        ProtoNetwork ba = merge(b, a);

        network_asserts(ab, ba);
    }
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                new NamespaceGroup(URL, null),
                parse("m(AKT1)"),
                parse("g(AKT2)"));

        // merge in different orders
        ProtoNetwork ab = merge(a, b);
        ProtoNetwork ba = merge(b, a);

        network_asserts(ab, ba);
    }
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                new NamespaceGroup(URL, null),
                parse("m(AKT1) => (g(PARP1) -| p(AKT2))"),
                parse("g(AKT2) -> (r(AKT1) => p(PARP1))"));

        // merge in different orders
        ProtoNetwork ab = merge(a, b);
        ProtoNetwork ba = merge(b, a);

        network_asserts(ab, ba);
    }
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     * @return merged {@link ProtoNetwork}
     */
    private ProtoNetwork merge(Document a, Document b) {
        ExpansionService es = new ExpansionServiceImpl();
        ProtoNetworkBuilder builder = new ProtoNetworkBuilder(a);
        ProtoNetwork networkA = builder.buildProtoNetwork();
        es.expandTerms(a, networkA);
        builder = new ProtoNetworkBuilder(b);
        ProtoNetwork n2 = builder.buildProtoNetwork();
        es.expandTerms(b, n2);
        ProtoNetworkMerger merger = new ProtoNetworkMerger();
        merger.merge(networkA, n2);
        return networkA;
    }
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            if (pedantic) {
                bail(SEMANTIC_VERIFICATION_FAILURE);
            }
        }

        ProtoNetwork pn = stage5(document);

        if (!stage6(document, pn)) {
            if (pedantic) {
                bail(STATEMENT_EXPANSION_FAILURE);
            }
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        bldr.append("Building proto-network for ");
        bldr.append(document.getName());
        stageOutput(bldr.toString());

        long t1 = currentTimeMillis();
        ProtoNetwork ret = p1.stage5Building(document);
        long t2 = currentTimeMillis();

        bldr.setLength(0);
        markTime(bldr, t1, t2);
        markEndStage(bldr);
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Related Classes of org.openbel.framework.common.protonetwork.model.ProtoNetwork

  • org.openbel.framework.common.protonetwork.model.NamespaceTable.TableNamespace
  • org.openbel.framework.common.protonetwork.model.ParameterTable.TableParameter
  • org.openbel.framework.compiler.PhaseTwoImpl
  • org.openbel.framework.core.compiler.PhaseOneIntegrationTest
  • org.openbel.framework.core.equivalence.BucketEquivalencerTest
  • org.openbel.framework.core.protonetwork.BinaryProtoNetworkExternalizer
  • org.openbel.framework.core.protonetwork.BinaryProtoNetworkIOTest
  • org.openbel.framework.core.protonetwork.ProtoNetworkBuilderTest
  • org.openbel.framework.core.protonetwork.ProtoNetworkMerge_CommutativeTest
  • org.openbel.framework.tools.PhaseFourApplication
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