Package org.openbel.framework.common.model

Examples of org.openbel.framework.common.model.Namespace

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        err.println("testImproperListUsage");

        // Test that SemanticServiceImpl#checkListUsage() fails
        // on improper uses of the LIST function type.

        final Namespace meshd =
                new Namespace("MESHD", "http://resource.belframework.org/" +
                        "belframework/1.0/namespace/mesh-diseases.belns");
        final Namespace go =
                new Namespace(
                        "GO",
                        "http://resource.belframework.org/"
                                +
                                "belframework/1.0/namespace/go-biological-processes-names.belns");
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     * {@code p(HGNC:AKT1)}
     * </p>
     */
    @Test
    public void testTermIdentityEquivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");

        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
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    /**
     * Test mismatched {@link Object object types}.
     */
    @Test
    public void testMismatchedTypeUnequivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");

        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
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     * {@code p(HGNC:AKT1)}
     * </p>
     */
    @Test
    public void testExactMatchEquivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");
        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term1 = new EquivalentTerm(PROTEIN_ABUNDANCE,
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     * {@code g(HGNC:AKT1)}
     * </p>
     */
    @Test
    public void testMismatchedFunctionUnequivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");
        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
        EquivalentTerm term1 = new EquivalentTerm(PROTEIN_ABUNDANCE,
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     * {@code ALL_FUNCTIONS(EGID:207)}
     * </p>
     */
    @Test
    public void testMismatchedArgumentCardinalityUnequivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");
        final Namespace egid =
                new Namespace(
                        "EGID",
                        "http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns");

        for (final FunctionEnum f : values()) {
            EquivalentParameter param1 =
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     * the UUID in isolation.
     * </p>
     */
    @Test
    public void testDifferentParameterUUIDSUnequivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");

        // different parameter uuids, not equivalent
        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
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     * {@code p(HGNC:AKT2) with UUID 9be88c14-6311-4452-a911-9f02abcf6a1e}
     * </p>
     */
    @Test
    public void testDifferentParameterValuesUnequivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");

        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
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     * {@code p(EGID:207) with UUID a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f}
     * </p>
     */
    @Test
    public void testDifferentNamespacesSameUUIDSEquivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");
        final Namespace egid =
                new Namespace(
                        "EGID",
                        "http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns");

        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
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     * {@code p(EGID:257) with UUID aae305e5-bb6d-4e75-ac0b-85a76e1e8e09}
     * </p>
     */
    @Test
    public void testDifferentNamespacesDifferentValuesUnequivalent() {
        final Namespace hgnc =
                new Namespace(
                        "HGNC",
                        "http://resource.belframework.org/belframework/1.0/namespace/hgnc-approved-symbols.belns");
        final Namespace egid =
                new Namespace(
                        "EGID",
                        "http://resource.belframework.org/belframework/1.0/namespace/entrez-gene-ids-hmr.belns");

        EquivalentParameter param1 = new EquivalentParameter(hgnc, "AKT1",
                SkinnyUUID.fromString("a32fd1cb-7d97-44ee-a0d0-db16c2a93b3f"));
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Related Classes of org.openbel.framework.common.model.Namespace

  • org.openbel.framework.api.DefaultSpeciesDialect
  • org.openbel.framework.api.Namespaces
  • org.openbel.framework.api.Resolver
  • org.openbel.framework.common.bel.converters.BELDocumentConverter
  • org.openbel.framework.common.bel.converters.BELNamespaceDefinitionConverter
  • org.openbel.framework.common.bel.converters.BELStatementConverter
  • org.openbel.framework.common.bel.parser.BELStatementParser
  • org.openbel.framework.common.InvalidArgument
  • org.openbel.framework.common.NamespaceTest
  • org.openbel.framework.common.protonetwork.model.StatementTable
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