Examples of org.openbel.framework.core.protonetwork.ProtoNetworkBuilder

Package org.openbel.framework.core.protonetwork

Examples of org.openbel.framework.core.protonetwork.ProtoNetworkBuilder

org.openbel.framework.core.protonetwork.ProtoNetworkBuilder
ProtoNetworkBuilder breaks down a {@link Document} into a proto network thatindividual identifies the following:
- Document header information
- Namespaces
- Which document defines which namespace
- Parameters
- Terms
- Which parameters are defined in which terms and in what order
- Statements
- Which document defines which statement
- Annotation definitions
- Annotation values
- Which statements reference which annotations
@author Anthony Bargnesi {@code }

    /**
     * {@inheritDoc}
     */
    @Override
    public void expandTerms(final Document doc, final ProtoNetwork pn) {
        final ProtoNetworkBuilder pnb = new ProtoNetworkBuilder(doc);
        final StatementTable st = pn.getStatementTable();
        final List<TableStatement> stmts = st.getStatements();
        final Map<Integer, Statement> si = st.getIndexedStatements();


        final List<Statement> expansions = new ArrayList<Statement>();

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     * {@inheritDoc}
     */
    @Override
    public void expandStatements(final Document doc, final ProtoNetwork pn,
            final boolean stmtExpand) {
        final ProtoNetworkBuilder pnb = new ProtoNetworkBuilder(doc);
        final ArrayList<ExpansionRule<Statement>> rules = sizedArrayList(2);
        if (stmtExpand) {
            rules.add(distributedRule);
        } else {
            rules.add(extractRule);

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     * Testcase - Test the successful building of a simple statement {@link ProtoNetwork}.
     */
    @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();

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                "", "", "", "", "");
        Document document = new Document(header, statementGroup);
        document.setDefinitions(asList(speciesDefinition, tissueDefinition));
        document.setNamespaceGroup(namespaceGroup);


        protoNetwork = new ProtoNetworkBuilder(document).buildProtoNetwork();
    }

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                asList("Shrubbery"), "", "", "", "", "");
        Document document = new Document(header, statementGroup);
        document.setDefinitions(asList(speciesDefinition, tissueDefinition));
        document.setNamespaceGroup(namespaceGroup);


        protoNetwork = new ProtoNetworkBuilder(document).buildProtoNetwork();
    }

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        // read in BEL document and compile to proto network
        final File doc = new File(DOC_PATH);
        assertThat("test BEL document cannot be read", doc.canRead(), is(true));
        Stage1Output p1s1 = p1.stage1BELValidation(doc);
        final ProtoNetworkBuilder bldr = new ProtoNetworkBuilder(p1s1.getDocument());
        pn = bldr.buildProtoNetwork();


        // Create system configuration, BELFRAMEWORK_HOME must be set.
        try {
            createSystemConfiguration();
        } catch (IOException e) {

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Related Classes of org.openbel.framework.core.protonetwork.ProtoNetworkBuilder

org.openbel.framework.common.enums.RelationshipType

org.openbel.framework.common.protonetwork.model.AnnotationDefinitionTable.TableAnnotationDefinition

org.openbel.framework.common.protonetwork.model.DocumentTable.DocumentHeader

org.openbel.framework.common.protonetwork.model.NamespaceTable.TableNamespace

org.openbel.framework.common.protonetwork.model.ParameterTable.TableParameter

org.openbel.framework.common.protonetwork.model.StatementAnnotationMapTable.AnnotationPair

org.openbel.framework.common.protonetwork.model.StatementTable.TableStatement

org.openbel.framework.core.compiler.expansion.ExpansionServiceImpl

org.openbel.framework.core.protonetwork.BinaryProtoNetworkIOTest

org.openbel.framework.core.protonetwork.ProtoNetworkBuilderTest

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