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Example 91 with SBOLValidationException

use of org.sbolstandard.core2.SBOLValidationException in project libSBOLj by SynBioDex.

the class CombinatorialDesignTest method setupDocument.

@Before
public void setupDocument() throws SBOLValidationException {
    doc.setDefaultURIprefix("http://sbols.org/CRISPR_Example/");
    doc.setComplete(true);
    doc.setCreateDefaults(true);
    String version = "1.0.0";
    // Create ComponentDefinition for cas9_generic protein
    doc.createComponentDefinition("cas9_generic", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefinition for gRNA_generic RNA
    doc.createComponentDefinition("gRNA_generic", version, ComponentDefinition.RNA).addRole(SequenceOntology.SGRNA);
    // Create ComponentDefinition for cas9_gRNA_complex
    doc.createComponentDefinition("cas9_gRNA_complex", version, ComponentDefinition.COMPLEX);
    // Create ComponentDefinition for target gene
    doc.createComponentDefinition("target_gene", version, ComponentDefinition.DNA).addRole(SequenceOntology.PROMOTER);
    // Create ComponentDefinition for target protein
    doc.createComponentDefinition("target", version, ComponentDefinition.PROTEIN);
    // Create ModuleDefinition for CRISPR_Repression_Template
    ModuleDefinition CRISPR_Template = doc.createModuleDefinition("CRISPR_Template", version);
    // Complex Formation Interaction for Cas9m_BFP and gRNA
    Interaction Cas9Complex_Formation = CRISPR_Template.createInteraction("cas9_complex_formation", SystemsBiologyOntology.NON_COVALENT_BINDING);
    Cas9Complex_Formation.createParticipation("cas9_generic", "cas9_generic", SystemsBiologyOntology.REACTANT);
    Cas9Complex_Formation.createParticipation("gRNA_generic", "gRNA_generic", SystemsBiologyOntology.REACTANT);
    Cas9Complex_Formation.createParticipation("cas9_gRNA_complex", "cas9_gRNA_complex", SystemsBiologyOntology.PRODUCT);
    // Production of target from target gene
    Interaction EYFP_production = CRISPR_Template.createInteraction("target_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    EYFP_production.createParticipation("target_gene", "target_gene", SystemsBiologyOntology.PROMOTER);
    EYFP_production.createParticipation("target", "target", SystemsBiologyOntology.PRODUCT);
    // Inhibition of target by cas9m_BFP_gRNA
    Interaction target_generic_gene_inhibition = CRISPR_Template.createInteraction("target_gene_inhibition", SystemsBiologyOntology.INHIBITION);
    target_generic_gene_inhibition.createParticipation("cas9_gRNA_complex", "cas9_gRNA_complex", SystemsBiologyOntology.INHIBITOR);
    target_generic_gene_inhibition.createParticipation("target_gene", "target_gene", SystemsBiologyOntology.PROMOTER);
    // Create Sequence for CRa_U6 promoter
    String CRa_U6_seq_elements = "GGTTTACCGAGCTCTTATTGGTTTTCAAACTTCATTGACTGTGCC" + "AAGGTCGGGCAGGAAGAGGGCCTATTTCCCATGATTCCTTCATAT" + "TTGCATATACGATACAAGGCTGTTAGAGAGATAATTAGAATTAAT" + "TTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGA" + "AAGTAATAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTT" + "AAAATGGACTATCATATGCTTACCGTAACTTGAAATATAGAACCG" + "ATCCTCCCATTGGTATATATTATAGAACCGATCCTCCCATTGGCT" + "TGTGGAAAGGACGAAACACCGTACCTCATCAGGAACATGTGTTTA" + "AGAGCTATGCTGGAAACAGCAGAAATAGCAAGTTTAAATAAGGCT" + "AGTCCGTTATCAACTTGAAAAAGTGGCACCGAGTCGGTGCTTTTT" + "TTGGTGCGTTTTTATGCTTGTAGTATTGTATAATGTTTTT";
    doc.createSequence("CRa_U6_seq", version, CRa_U6_seq_elements, Sequence.IUPAC_DNA);
    // Create Sequence for gRNA_b coding sequence
    String gRNA_b_elements = "AAGGTCGGGCAGGAAGAGGGCCTATTTCCCATGATTCCTTCATAT" + "TTGCATATACGATACAAGGCTGTTAGAGAGATAATTAGAATTAAT" + "TTGACTGTAAACACAAAGATATTAGTACAAAATACGTGACGTAGA" + "AAGTAATAATTTCTTGGGTAGTTTGCAGTTTTAAAATTATGTTTT" + "AAAATGGACTATCATATGCTTACCGTAACTTGAAAGTATTTCGAT" + "TTCTTGGCTTTATATATCTTGTGGAAAGGACGAAACACCGTACCT" + "CATCAGGAACATGTGTTTAAGAGCTATGCTGGAAACAGCAGAAAT" + "AGCAAGTTTAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGG" + "CACCGAGTCGGTGCTTTTTTT";
    doc.createSequence("gRNA_b_seq", version, gRNA_b_elements, Sequence.IUPAC_DNA);
    // Create Sequence for mKate
    String mKate_seq_elements = "TCTAAGGGCGAAGAGCTGATTAAGGAGAACATGCACATGAAGCTG" + "TACATGGAGGGCACCGTGAACAACCACCACTTCAAGTGCACATCC" + "GAGGGCGAAGGCAAGCCCTACGAGGGCACCCAGACCATGAGAATC" + "AAGGTGGTCGAGGGCGGCCCTCTCCCCTTCGCCTTCGACATCCTG" + "GCTACCAGCTTCATGTACGGCAGCAAAACCTTCATCAACCACACC" + "CAGGGCATCCCCGACTTCTTTAAGCAGTCCTTCCCTGAGGTAAGT" + "GGTCCTACCTCATCAGGAACATGTGTTTTAGAGCTAGAAATAGCA" + "AGTTAAAATAAGGCTAGTCCGTTATCAACTTGAAAAAGTGGCACC" + "GAGTCGGTGCTACTAACTCTCGAGTCTTCTTTTTTTTTTTCACAG" + "GGCTTCACATGGGAGAGAGTCACCACATACGAAGACGGGGGCGTG" + "CTGACCGCTACCCAGGACACCAGCCTCCAGGACGGCTGCCTCATC" + "TACAACGTCAAGATCAGAGGGGTGAACTTCCCATCCAACGGCCCT" + "GTGATGCAGAAGAAAACACTCGGCTGGGAGGCCTCCACCGAGATG" + "CTGTACCCCGCTGACGGCGGCCTGGAAGGCAGAAGCGACATGGCC" + "CTGAAGCTCGTGGGCGGGGGCCACCTGATCTGCAACTTGAAGACC" + "ACATACAGATCCAAGAAACCCGCTAAGAACCTCAAGATGCCCGGC" + "GTCTACTATGTGGACAGAAGACTGGAAAGAATCAAGGAGGCCGAC" + "AAAGAGACCTACGTCGAGCAGCACGAGGTGGCTGTGGCCAGATAC" + "TGCG";
    doc.createSequence("mKate_seq", version, mKate_seq_elements, Sequence.IUPAC_DNA);
    // Create Sequence for CRP_b promoter
    String CRP_b_seq_elements = "GCTCCGAATTTCTCGACAGATCTCATGTGATTACGCCAAGCTACG" + "GGCGGAGTACTGTCCTCCGAGCGGAGTACTGTCCTCCGAGCGGAG" + "TACTGTCCTCCGAGCGGAGTACTGTCCTCCGAGCGGAGTTCTGTC" + "CTCCGAGCGGAGACTCTAGATACCTCATCAGGAACATGTTGGAAT" + "TCTAGGCGTGTACGGTGGGAGGCCTATATAAGCAGAGCTCGTTTA" + "GTGAACCGTCAGATCGCCTCGAGTACCTCATCAGGAACATGTTGG" + "ATCCAATTCGACC";
    doc.createSequence("CRP_b_seq", version, CRP_b_seq_elements, Sequence.IUPAC_DNA);
    // Create ComponentDefinition for a Constitutive Promoter
    doc.createComponentDefinition("pConst", version, ComponentDefinition.DNA).addRole(SequenceOntology.PROMOTER);
    // Create ComponentDefinition for cas9m_BFP coding sequence
    doc.createComponentDefinition("cas9m_BFP_cds", version, ComponentDefinition.DNA).addRole(SequenceOntology.CDS);
    // Create ComponentDefinition for cas9m_BFP gene
    ComponentDefinition cas9m_BFP_gene = doc.createComponentDefinition("cas9m_BFP_gene", version, ComponentDefinition.DNA);
    cas9m_BFP_gene.addRole(SequenceOntology.PROMOTER);
    cas9m_BFP_gene.createSequenceConstraint("cas9m_BFP_gene_constraint", RestrictionType.PRECEDES, "pConst", "cas9m_BFP_cds");
    // Create ComponentDefintion for cas9m_BFP protein
    doc.createComponentDefinition("cas9m_BFP", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefintion for CRa_U6 promoter
    ComponentDefinition CRa_U6 = doc.createComponentDefinition("CRa_U6", version, ComponentDefinition.DNA);
    CRa_U6.addRole(SequenceOntology.PROMOTER);
    CRa_U6.addSequence("CRa_U6_seq");
    // Create ComponentDefintion for gRNA_b coding sequence
    ComponentDefinition gRNA_b_nc = doc.createComponentDefinition("gRNA_b_nc", version, ComponentDefinition.DNA);
    gRNA_b_nc.addRole(SequenceOntology.CDS);
    gRNA_b_nc.addSequence("gRNA_b_seq");
    // Create ComponentDefinition for gRNA_b terminator
    doc.createComponentDefinition("gRNA_b_terminator", version, ComponentDefinition.DNA).addRole(SequenceOntology.TERMINATOR);
    // Create ComponentDefinition for gRNA_b gene
    ComponentDefinition gRNA_b_gene = doc.createComponentDefinition("gRNA_b_gene", version, ComponentDefinition.DNA);
    gRNA_b_gene.addRole(SequenceOntology.PROMOTER);
    gRNA_b_gene.createSequenceConstraint("gRNA_b_gene_constraint1", RestrictionType.PRECEDES, "CRa_U6", "gRNA_b_nc");
    gRNA_b_gene.createSequenceConstraint("gRNA_b_gene_constraint2", RestrictionType.PRECEDES, "gRNA_b_nc", "gRNA_b_terminator");
    // Create ComponentDefinition for gRNA_b RNA
    doc.createComponentDefinition("gRNA_b", version, ComponentDefinition.RNA).addRole(SequenceOntology.SGRNA);
    SequenceOntology so = new SequenceOntology();
    URI sgrna = so.getURIbyName("sgRNA");
    // Create ComponentDefinition for cas9m_BFP gRNA_b complex
    doc.createComponentDefinition("cas9m_BFP_gRNA_b", version, ComponentDefinition.COMPLEX);
    // Create ComponentDefinition for mKate coding sequence
    ComponentDefinition mKate_cds = doc.createComponentDefinition("mKate_cds", version, ComponentDefinition.DNA);
    mKate_cds.addRole(SequenceOntology.CDS);
    mKate_cds.addSequence("mKate_seq");
    // Create ComponentDefinition for mKate gene
    ComponentDefinition mKate_gene = doc.createComponentDefinition("mKate_gene", version, ComponentDefinition.DNA);
    mKate_gene.addRole(SequenceOntology.PROMOTER);
    mKate_gene.createSequenceConstraint("mKate_gene_constraint", RestrictionType.PRECEDES, "pConst", "mKate_cds");
    // Create ComponentDefinition for mKate protein
    doc.createComponentDefinition("mKate", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefinition for Gal4VP16 coding sequence
    ComponentDefinition Gal4VP16_cds = doc.createComponentDefinition("Gal4VP16_cds", version, ComponentDefinition.DNA);
    Gal4VP16_cds.addRole(SequenceOntology.CDS);
    // Create ComponentDefintion for Gal4VP16 gene
    ComponentDefinition Gal4VP16_gene = doc.createComponentDefinition("Gal4VP16_gene", version, ComponentDefinition.DNA);
    Gal4VP16_gene.addRole(SequenceOntology.PROMOTER);
    Gal4VP16_gene.createSequenceConstraint("GAL4VP16_gene_constraint", RestrictionType.PRECEDES, "pConst", "Gal4VP16_cds");
    // Create ComponentDefintion for Gal4VP16 protein
    doc.createComponentDefinition("Gal4VP16", version, ComponentDefinition.PROTEIN);
    // Create ComponentDefinition for CRP_b promoter
    ComponentDefinition CRP_b = doc.createComponentDefinition("CRP_b", version, ComponentDefinition.DNA);
    CRP_b.addRole(SequenceOntology.PROMOTER);
    CRP_b.addSequence("CRP_b_seq");
    // Create ComponentDefintiion for EYFP coding sequence
    ComponentDefinition EYFP_cds = doc.createComponentDefinition("EYFP_cds", version, ComponentDefinition.DNA);
    EYFP_cds.addRole(SequenceOntology.CDS);
    // Create ComponentDefinition for EYFP gene
    ComponentDefinition EYFP_gene = doc.createComponentDefinition("EYFP_gene", version, ComponentDefinition.DNA);
    EYFP_gene.addRole(SequenceOntology.PROMOTER);
    EYFP_gene.createSequenceConstraint("EYFP_gene_constraint", RestrictionType.PRECEDES, "CRP_b", "EYFP_cds");
    // Create ComponentDefintiion for EYFP protein
    doc.createComponentDefinition("EYFP", version, ComponentDefinition.PROTEIN);
    // Create ModuleDefintion for CRISPR Repression
    ModuleDefinition CRPb_circuit = doc.createModuleDefinition("CRPb_characterization_circuit", version);
    // Create the FunctionalComponents for the ModuleDefinition CRISPR_Repression
    CRPb_circuit.createFunctionalComponent("cas9m_BFP", AccessType.PRIVATE, "cas9m_BFP", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("cas9m_BFP_gene", AccessType.PRIVATE, "cas9m_BFP_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("gRNA_b", AccessType.PRIVATE, "gRNA_b", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("gRNA_b_gene", AccessType.PRIVATE, "gRNA_b_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("mKate", AccessType.PRIVATE, "mKate", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("mKate_gene", AccessType.PRIVATE, "mKate_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("Gal4VP16", AccessType.PRIVATE, "Gal4VP16", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("Gal4VP16_gene", AccessType.PRIVATE, "Gal4VP16_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("EYFP", AccessType.PRIVATE, "EYFP", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("EYFP_gene", AccessType.PRIVATE, "EYFP_gene", version, DirectionType.NONE);
    CRPb_circuit.createFunctionalComponent("cas9m_BFP_gRNA_b", AccessType.PRIVATE, "cas9m_BFP_gRNA_b", version, DirectionType.NONE);
    /* Production of mKate from the mKate gene */
    Interaction mKate_production = CRPb_circuit.createInteraction("mKate_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    mKate_production.createParticipation("mKate", "mKate", SystemsBiologyOntology.PRODUCT);
    mKate_production.createParticipation("mKate_gene", "mKate_gene", SystemsBiologyOntology.PROMOTER);
    // Production of GAL4VP16 from the GAL4VP16 gene
    Interaction GAL4VP16_production = CRPb_circuit.createInteraction("Gal4VP16_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    GAL4VP16_production.createParticipation("Gal4VP16_gene", "Gal4VP16_gene", SystemsBiologyOntology.PROMOTER);
    GAL4VP16_production.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.PRODUCT);
    // Production of cas9m_BFP from the cas9m_BFP gene
    Interaction cas9m_BFP_production = CRPb_circuit.createInteraction("cas9m_BFP_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    cas9m_BFP_production.createParticipation("cas9m_BFP_gene", "cas9m_BFP_gene", SystemsBiologyOntology.PROMOTER);
    cas9m_BFP_production.createParticipation("cas9m_BFP", "cas9m_BFP", SystemsBiologyOntology.PRODUCT);
    // Production of gRNA_b from the gRNA_b gene
    Interaction gRNA_b_production = CRPb_circuit.createInteraction("gRNA_b_production", SystemsBiologyOntology.GENETIC_PRODUCTION);
    gRNA_b_production.createParticipation("gRNA_b_gene", "gRNA_b_gene", SystemsBiologyOntology.PROMOTER);
    gRNA_b_production.createParticipation("gRNA_b", "gRNA_b", SystemsBiologyOntology.PRODUCT);
    // Activation of EYFP production by GAL4VP16
    Interaction EYFP_Activation = CRPb_circuit.createInteraction("EYFP_Activation", SystemsBiologyOntology.STIMULATION);
    EYFP_Activation.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.STIMULATOR);
    EYFP_Activation.createParticipation("EYFP_gene", "EYFP_gene", SystemsBiologyOntology.PROMOTER);
    // Degradation of mKate
    Interaction mKate_deg = CRPb_circuit.createInteraction("mKate_deg", SystemsBiologyOntology.DEGRADATION);
    mKate_deg.createParticipation("mKate", "mKate", SystemsBiologyOntology.REACTANT);
    // Degradation of GAL4VP16
    Interaction GAL4VP16_deg = CRPb_circuit.createInteraction("Gal4VP16_deg", SystemsBiologyOntology.DEGRADATION);
    GAL4VP16_deg.createParticipation("Gal4VP16", "Gal4VP16", SystemsBiologyOntology.REACTANT);
    // Degradation of cas9m_BFP
    Interaction cas9m_BFP_deg = CRPb_circuit.createInteraction("cas9m_BFP_deg", SystemsBiologyOntology.DEGRADATION);
    cas9m_BFP_deg.createParticipation("cas9m_BFP", "cas9m_BFP", SystemsBiologyOntology.REACTANT);
    // Degradation of gRNA_b
    Interaction gRNA_b_deg = CRPb_circuit.createInteraction("gRNA_b_deg", SystemsBiologyOntology.DEGRADATION);
    gRNA_b_deg.createParticipation("gRNA_b", "gRNA_b", SystemsBiologyOntology.REACTANT);
    // Degradation of EYFP
    Interaction EYFP_deg = CRPb_circuit.createInteraction("EYFP_deg", SystemsBiologyOntology.DEGRADATION);
    EYFP_deg.createParticipation("EYFP", "EYFP", SystemsBiologyOntology.REACTANT);
    // Degradation of cas9m_BFP_gRNA_b
    Interaction cas9m_BFP_gRNA_b_deg = CRPb_circuit.createInteraction("cas9m_BFP_gRNA_b_deg", SystemsBiologyOntology.DEGRADATION);
    cas9m_BFP_gRNA_b_deg.createParticipation("cas9m_BFP_gRNA_b", "cas9m_BFP_gRNA_b", SystemsBiologyOntology.REACTANT);
    // Create Template Module
    Module Template_Module = CRPb_circuit.createModule("CRISPR_Template", "CRISPR_Template", version);
    // Add MapsTos to Template Module
    Template_Module.createMapsTo("cas9m_BFP_map", RefinementType.USELOCAL, "cas9m_BFP", "cas9_generic");
    Template_Module.createMapsTo("gRNA_b_map", RefinementType.USELOCAL, "gRNA_b", "gRNA_generic");
    Template_Module.createMapsTo("cas9m_BFP_gRNA_map", RefinementType.USELOCAL, "cas9m_BFP_gRNA_b", "cas9_gRNA_complex");
    Template_Module.createMapsTo("EYFP_map", RefinementType.USELOCAL, "EYFP", "target");
    Template_Module.createMapsTo("EYFP_gene_map", RefinementType.USELOCAL, "EYFP_gene", "target_gene");
    // Create CombinatorialDerivations
    CombinatorialDerivation Combinatorial_Derivation = doc.createCombinatorialDerivation("combDev", version, "Gal4VP16", version);
    Combinatorial_Derivation.setStrategy(StrategyType.SAMPLE);
    SBOLValidate.validateSBOL(doc, true, true, true);
    if (SBOLValidate.getNumErrors() > 0) {
        for (String error : SBOLValidate.getErrors()) {
            System.out.println(error);
        }
        fail();
    }
}
Also used : SequenceOntology(org.sbolstandard.core2.SequenceOntology) ModuleDefinition(org.sbolstandard.core2.ModuleDefinition) Interaction(org.sbolstandard.core2.Interaction) Module(org.sbolstandard.core2.Module) URI(java.net.URI) CombinatorialDerivation(org.sbolstandard.core2.CombinatorialDerivation) ComponentDefinition(org.sbolstandard.core2.ComponentDefinition) Before(org.junit.Before)

Example 92 with SBOLValidationException

use of org.sbolstandard.core2.SBOLValidationException in project libSBOLj by SynBioDex.

the class VariableComponent method addVariantDerivation.

/**
 * Adds the given variant derivation to the list of variant derivations.
 *
 * @param uriPrefix
 * 			URI prefix for variant derivation
 * @param displayId
 *          display id for variant derivation
 * @param version
 *          version for variant derivation
 * @throws SBOLValidationException if the following SBOL validation rule was violated:
 */
public void addVariantDerivation(String uriPrefix, String displayId, String version) throws SBOLValidationException {
    URI uri = URIcompliance.createCompliantURI(uriPrefix, displayId, version);
    CombinatorialDerivation combinatorialDerivation = this.getSBOLDocument().getCombinatorialDerivation(uri);
    addVariantDerivation(combinatorialDerivation.getIdentity());
}
Also used : URI(java.net.URI) URIcompliance.createCompliantURI(org.sbolstandard.core2.URIcompliance.createCompliantURI)

Example 93 with SBOLValidationException

use of org.sbolstandard.core2.SBOLValidationException in project libSBOLj by SynBioDex.

the class GenericTopLevelTest method test_toString.

@Test
public void test_toString() throws SBOLValidationException {
    GenericTopLevel topLevel = doc.createGenericTopLevel("random_sheet1", "", new QName("http://partsregistry.org/", "Random_Sheet", "pr"));
    assertTrue(doc.getGenericTopLevel(topLevel.getIdentity()).toString().length() != 0);
    assertNotNull(topLevel.toString());
    assertTrue(topLevel.toString().contains("displayId=random_sheet1"));
    assertTrue(!topLevel.toString().contains("name="));
}
Also used : QName(javax.xml.namespace.QName) GenericTopLevel(org.sbolstandard.core2.GenericTopLevel) Test(org.junit.Test)

Example 94 with SBOLValidationException

use of org.sbolstandard.core2.SBOLValidationException in project libSBOLj by SynBioDex.

the class ModuleDefinitionTest method test_moduleDefinitionDeepCopy.

@Test
public void test_moduleDefinitionDeepCopy() throws SBOLValidationException {
    SBOLDocument doc_copy = new SBOLDocument();
    doc_copy.setDefaultURIprefix("http://sbols.org/CRISPR_Example/");
    doc_copy.setComplete(false);
    doc_copy.setCreateDefaults(true);
    doc_copy.createCopy(geneticToggleSwitch);
    ModuleDefinition TetRInverter_copy = doc_copy.getModuleDefinition("geneticToggleSwitch", "");
    assertTrue(TetRInverter_copy.getModule("TetRInverter").equals(TetRInverter));
    assertTrue(doc_copy.createRecursiveCopy(geneticToggleSwitch).equals(doc));
}
Also used : ModuleDefinition(org.sbolstandard.core2.ModuleDefinition) SBOLDocument(org.sbolstandard.core2.SBOLDocument) Test(org.junit.Test)

Example 95 with SBOLValidationException

use of org.sbolstandard.core2.SBOLValidationException in project libSBOLj by SynBioDex.

the class TestCircularModules method main.

// Check if an SBOLValidationException is thrown in every run, and check if it throws the right exception.
/**
 * Tests circular reference between ModuleDefinition and Module (validation rules 11704 and 11705).
 * @param args
 * @throws Exception
 */
public static void main(String[] args) throws Exception {
    ModuleDefModuleTree tree = new ModuleDefModuleTree(maxDepth, numOfModules);
    tree.setRandomSeed(12);
    for (int i = 0; i < numOfRuns; i++) {
        boolean exceptionCaught = false;
        // String expectedError = null;
        try {
            tree.generateModel();
        } catch (SBOLValidationException e) {
            exceptionCaught = true;
            if (!e.getMessage().contains(tree.getExpectedError())) {
                throw new Exception("Unexpected exception!");
            }
        }
        if (!exceptionCaught) {
            throw new Exception("Exception NOT caught!");
        }
    }
}
Also used : SBOLValidationException(org.sbolstandard.core2.SBOLValidationException) SBOLValidationException(org.sbolstandard.core2.SBOLValidationException)

Aggregations

URI (java.net.URI)81 URIcompliance.createCompliantURI (org.sbolstandard.core2.URIcompliance.createCompliantURI)75 QName (javax.xml.namespace.QName)36 HashSet (java.util.HashSet)35 ArrayList (java.util.ArrayList)31 Literal (org.sbolstandard.core.datatree.Literal)30 StringifyQName (org.sbolstandard.core.io.json.StringifyQName)30 IdentifiableDocument (org.sbolstandard.core.datatree.IdentifiableDocument)17 Test (org.junit.Test)16 NestedDocument (org.sbolstandard.core.datatree.NestedDocument)13 ComponentDefinition (org.sbolstandard.core2.ComponentDefinition)9 SBOLDocument (org.sbolstandard.core2.SBOLDocument)9 ModuleDefinition (org.sbolstandard.core2.ModuleDefinition)6 Sequence (org.sbolstandard.core2.Sequence)5 Interaction (org.sbolstandard.core2.Interaction)4 GenericTopLevel (org.sbolstandard.core2.GenericTopLevel)3 MapsTo (org.sbolstandard.core2.MapsTo)3 Set (java.util.Set)2 Annotation (org.sbolstandard.core2.Annotation)2 GenericLocation (org.sbolstandard.core2.GenericLocation)2