Examples with GenericTopLevel org.sbolstandard.core2.GenericTopLevel used on opensource projects

Example 1 with GenericTopLevel

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

the class RepressionModel method main.

public static void main(String[] args) throws SBOLValidationException, SBOLConversionException, IOException {
    SBOLDocument doc = new SBOLDocument();
    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");
    // try {
    // SBOLWriter.write(doc, "/Users/myers/RepressionModel.rdf");
    // }
    // catch (XMLStreamException | FactoryConfigurationError | CoreIoException e) {
    // e.printStackTrace();
    // }
    // catch (IOException e) {
    // e.printStackTrace();
    // }
    // END of Repression Model construction. Code below uses trivial manipulations to show other major methods in the library.
    ComponentDefinition cas9_generic1 = doc.getComponentDefinition("cas9_generic", version);
    ComponentDefinition cas9_generic2 = doc.getComponentDefinition("cas9_generic", null);
    if (cas9_generic1.equals(cas9_generic2)) {
        System.out.println("Two Cas9 generic protein objects are equal.");
    }
    gRNA_b_gene.getSequenceConstraint("gRNA_b_gene_constraint1");
    CRISPR_Template.setName("C~R*I!S@P#R-based Repression Template");
    if (CRISPR_Template.isSetName()) {
        CRISPR_Template.unsetName();
        CRISPR_Template.setName("CRISPR-based Repression Template");
    }
    CRISPR_Template.setDescription("Authors: S. Kiani, J. Beal, M. Ebrahimkhani, J. Huh, R. Hall, Z. Xie, Y. Li, and R. Weiss" + "Titel: Crispr transcriptional repression devices and layered circuits in mammalian cells" + "Journal: Nature Methods, vol. 11, no. 7, pp. 723–726, 2014.");
    URI gRNA_b_gene_role2 = URI.create("http://identifiers.org/so/SO:0000613");
    gRNA_b_gene.addRole(gRNA_b_gene_role2);
    if (gRNA_b_gene.containsRole(gRNA_b_gene_role2)) {
        gRNA_b_gene.removeRole(gRNA_b_gene_role2);
    }
    gRNA_b_gene.clearRoles();
    if (!gRNA_b_gene.getRoles().isEmpty()) {
        System.out.println("gRNA_b_gene set is not empty.");
    }
    gRNA_b_gene.setRoles(new HashSet<URI>(Arrays.asList(SequenceOntology.PROMOTER)));
    CRP_b.clearSequences();
    CRP_b.addSequence("CRP_b_seq");
    // CRP_b.addSequence(
    // URI.create("http://partsregistry.org/seq/partseq_154")
    // );
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    doc.addNamespace(URI.create(prURI), prPrefix);
    ComponentDefinition pConst = doc.getComponentDefinition("pConst", version);
    pConst.createAnnotation(new QName(prURI, "experience", prPrefix), URI.create("http://parts.igem.org/Part:BBa_J23119:Experience"));
    String myersLabURI = "http://www.async.ece.utah.edu/";
    String myersLabPrefix = "myersLab";
    doc.addNamespace(URI.create(myersLabURI), myersLabPrefix);
    GenericTopLevel datasheet = doc.createGenericTopLevel("datasheet", "1.1", new QName(myersLabURI, "datasheet", myersLabPrefix));
    datasheet.setName("Datasheet for Custom Parameters");
    datasheet.createAnnotation(new QName(myersLabURI, "characterizationData", myersLabPrefix), URI.create(myersLabURI + "/measurement/BBa_J23119"));
    datasheet.createAnnotation(new QName(myersLabURI, "transcriptionRate", myersLabPrefix), 0.75);
    pConst.createAnnotation(new QName(myersLabURI, "datasheet", myersLabPrefix), datasheet.getIdentity());
    ComponentDefinition pConst_alt = (ComponentDefinition) doc.createCopy(pConst, "pConst_alt");
    // pConst_alt.createAnnotation(
    // new QName(prURI, "", prPrefix),
    // URI.create("http://parts.igem.org/Part:BBa_J23100"));
    Sequence pConst_alt_seq = doc.createSequence("pConst_alt_seq", version, "ttgacggctagctcagtcctaggtacagtgctagc", Sequence.IUPAC_DNA);
    pConst_alt.addSequence(pConst_alt_seq);
    SBOLValidate.validateSBOL(doc, true, true, true);
    if (SBOLValidate.getNumErrors() > 0) {
        for (String error : SBOLValidate.getErrors()) {
            System.out.println(error);
        }
        return;
    }
    SBOLWriter.write(doc, (System.out));
    SBOLWriter.write(doc, "RepressionModel.rdf");
}

Example 2 with GenericTopLevel

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

the class GettingStartedExample method main.

public static void main(String[] args) throws IOException, SBOLValidationException, SBOLConversionException {
    String prURI = "http://partsregistry.org/";
    String prPrefix = "pr";
    String myersLabURI = "http://www.async.ece.utah.edu/";
    String myersLabPrefix = "myersLab";
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    document.setComplete(true);
    document.setCreateDefaults(true);
    document.addNamespace(URI.create(prURI), prPrefix);
    document.addNamespace(URI.create(myersLabURI), myersLabPrefix);
    // Creating a Top-level SBOL Data Object
    HashSet<URI> types = new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA, URI.create("http://identifiers.org/chebi/CHEBI:4705")));
    ComponentDefinition TetR_promoter = document.createComponentDefinition("BBa_R0040", types);
    ComponentDefinition LacI_repressor = document.createComponentDefinition("BBa_C0012", types);
    ComponentDefinition pIKELeftCassette = document.createComponentDefinition("pIKELeftCassette", types);
    Sequence seq_187 = document.createSequence("partseq_187", "tccctatcagtgatagagattgacatccctatcagtgatagagatactgagcac", Sequence.IUPAC_DNA);
    String element2 = "atggtgaatgtgaaaccagtaacgttatacgatgtcgcagagtatgccggtgtc" + "tcttatcagaccgtttcccgcgtggtgaaccaggccagccacgtttctgcgaaaacgcggga" + "aaaagtggaagcggcgatggcggagctgaattacattcccaaccgcgtggcacaacaactgg" + "cgggcaaacagtcgttgctgattggcgttgccacctccagtctggccctgcacgcgccgtcg" + "caaattgtcgcggcgattaaatctcgcgccgatcaactgggtgccagcgtggtggtgtcgat" + "ggtagaacgaagcggcgtcgaagcctgtaaagcggcggtgcacaatcttctcgcgcaacgcg" + "tcagtgggctgatcattaactatccgctggatgaccaggatgccattgctgtggaagctgcc" + "tgcactaatgttccggcgttatttcttgatgtctctgaccagacacccatcaacagtattat" + "tttctcccatgaagacggtacgcgactgggcgtggagcatctggtcgcattgggtcaccagc" + "aaatcgcgctgttagcgggcccattaagttctgtctcggcgcgtctgcgtctggctggctgg" + "cataaatatctcactcgcaatcaaattcagccgatagcggaacgggaaggcgactggagtgc" + "catgtccggttttcaacaaaccatgcaaatgctgaatgagggcatcgttcccactgcgatgc" + "tggttgccaacgatcagatggcgctgggcgcaatgcgcgccattaccgagtccgggctgcgc" + "gttggtgcggatatctcggtagtgggatacgacgataccgaagacagctcatgttatatccc" + "gccgttaaccaccatcaaacaggattttcgcctgctggggcaaaccagcgtggaccgcttgc" + "tgcaactctctcagggccaggcggtgaagggcaatcagctgttgcccgtctcactggtgaaa" + "agaaaaaccaccctggcgcccaatacgcaaaccgcctctccccgcgcgttggccgattcatt" + "aatgcagctggcacgacaggtttcccgactggaaagcgggcaggctgcaaacgacgaaaact" + "acgctttagtagcttaataa";
    Sequence seq_153 = document.createSequence("partseq_153", element2, Sequence.IUPAC_DNA);
    // Setting and editing optional fields
    TetR_promoter.setName("p(tetR)");
    LacI_repressor.setName("lacI");
    TetR_promoter.setDescription("TetR repressible promoter");
    LacI_repressor.setDescription("lacI repressor from E. coli (+LVA)");
    if (TetR_promoter.isSetName()) {
        TetR_promoter.unsetName();
    }
    TetR_promoter.setName("p(tetR)");
    TetR_promoter.addRole(SequenceOntology.PROMOTER);
    LacI_repressor.addRole(SequenceOntology.CDS);
    URI TetR_promoter_role2 = URI.create("http://identifiers.org/so/SO:0000613");
    TetR_promoter.addRole(TetR_promoter_role2);
    if (TetR_promoter.containsRole(TetR_promoter_role2)) {
        TetR_promoter.removeRole(TetR_promoter_role2);
    }
    TetR_promoter.clearRoles();
    if (!TetR_promoter.getRoles().isEmpty()) {
        System.out.println("TetR_promoter set is not empty");
    }
    TetR_promoter.setRoles(new HashSet<URI>(Arrays.asList(SequenceOntology.PROMOTER)));
    // Creating and editing references
    TetR_promoter.addSequence(seq_187);
    LacI_repressor.addSequence(seq_153);
    pIKELeftCassette.addSequence(seq_187);
    pIKELeftCassette.clearSequences();
    // Adding the sequence below causes an exception because it cannot be found
    // pIKELeftCassette.addSequence(URI.create("http://partsregistry.org/seq/partseq_154"));
    // Creating Annotations
    TetR_promoter.createAnnotation(new QName(prURI, "experience", prPrefix), URI.create("http://parts.igem.org/Part:BBa_R0040"));
    // Creating Generic TopLevel Object
    GenericTopLevel datasheet = document.createGenericTopLevel("datasheet", "1.0", new QName(myersLabURI, "datasheet", myersLabPrefix));
    datasheet.setName("Datasheet for Custom Parameters");
    datasheet.createAnnotation(new QName(myersLabURI, "characterizationData", myersLabPrefix), URI.create(myersLabURI + "/measurement/Part:BBa_R0040"));
    datasheet.createAnnotation(new QName(myersLabURI, "transcriptionRate", myersLabPrefix), "0.75");
    TetR_promoter.createAnnotation(new QName(myersLabURI, "datasheet", myersLabPrefix), datasheet.getIdentity());
    // Creating and editing Child Objects
    // For pIKELeftCassette, create sequence constraint that says BBa_R0040 precedes BBa_C0012.
    // Note that with CreateDefaults that components get created automatically.
    // The position of the subject Component MUST precede that of the object Component.
    pIKELeftCassette.createSequenceConstraint("pIKELeftCassette_sc", RestrictionType.PRECEDES, TetR_promoter.getDisplayId(), LacI_repressor.getDisplayId());
    if (pIKELeftCassette.getComponent("BBa_R0040") == null) {
        System.out.println("TetR_promoter component is missing");
    }
    if (pIKELeftCassette.getComponent("BBa_C0012") == null) {
        System.out.println("LacI_repressor component is missing");
    }
    // Removing the subject component below causes an exception.
    // pIKELeftCassette.removeComponent(pIKELeftCassette.getComponent("BBa_R0040"));
    // Copying objects
    ComponentDefinition TetR_promoter_copy = (ComponentDefinition) document.createCopy(TetR_promoter, "BBa_K137046");
    Sequence seq = document.createSequence("seq_K137046", "gtgctcagtatctctatcactgatagggatgtcaatctctatcactgatagggactctagtatat" + "aaacgcagaaaggcccacccgaaggtgagccagtgtgactctagtagagagcgttcaccgaca" + "aacaacagataaaacgaaaggc", Sequence.IUPAC_DNA);
    TetR_promoter_copy.addSequence(seq);
    SBOLWriter.write(document, "GettingStartedExample.rdf");
    writeThenRead(document);
}

Example 3 with GenericTopLevel

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

the class SBOLReader method parseActivity.

@SuppressWarnings("unchecked")
private static Activity parseActivity(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    String displayId = null;
    String name = null;
    String description = null;
    URI persistentIdentity = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> attachments = new HashSet<>();
    DateTime startedAtTime = null;
    DateTime endedAtTime = null;
    Set<URI> wasInformedBys = new HashSet<>();
    Set<Association> qualifiedAssociations = new HashSet<>();
    Set<Usage> qualifiedUsages = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
            if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10203", topLevel.getIdentity());
            }
            persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
            if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10206", topLevel.getIdentity());
            }
            version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || displayId != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", topLevel.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
            if (!(namedProperty.getValue() instanceof Literal) || name != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", topLevel.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || description != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", topLevel.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10208", topLevel.getIdentity());
            }
            wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10221", topLevel.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.TopLevel.hasAttachment)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
                attachments.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Attachment.Attachment)) {
                    Attachment attachment = parseAttachment(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
                    attachments.add(attachment.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Activity.startedAtTime)) {
            if (!(namedProperty.getValue() instanceof Literal) || startedAtTime != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-12402", topLevel.getIdentity());
            }
            DateTimeFormatter fmt = ISODateTimeFormat.dateTime();
            try {
                startedAtTime = fmt.parseDateTime(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            } catch (IllegalArgumentException e) {
                throw new SBOLValidationException("sbol-12402", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Activity.endedAtTime)) {
            if (!(namedProperty.getValue() instanceof Literal) || endedAtTime != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-12403", topLevel.getIdentity());
            }
            DateTimeFormatter fmt = ISODateTimeFormat.dateTime();
            try {
                endedAtTime = fmt.parseDateTime(((Literal<QName>) namedProperty.getValue()).getValue().toString());
            } catch (IllegalArgumentException e) {
                throw new SBOLValidationException("sbol-12403", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Activity.wasInformedBy)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-12406", topLevel.getIdentity());
                }
                wasInformedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Activity.Activity)) {
                    Activity activity = parseActivity(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    wasInformedBys.add(activity.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-12406", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-12406", topLevel.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Activity.qualifiedAssociation)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Association.Association)) {
                    throw new SBOLValidationException("sbol-12404", topLevel.getIdentity());
                }
                qualifiedAssociations.add(parseAssociation(SBOLDoc, ((NestedDocument<QName>) namedProperty.getValue()), nested));
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                NestedDocument<QName> nestedDocument = nested.get(uri);
                if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Association.Association)) {
                    throw new SBOLValidationException("sbol-12404", topLevel.getIdentity());
                }
                qualifiedAssociations.add(parseAssociation(SBOLDoc, nestedDocument, nested));
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.Activity.qualifiedUsage)) {
            if (namedProperty.getValue() instanceof NestedDocument) {
                NestedDocument<QName> nestedDocument = ((NestedDocument<QName>) namedProperty.getValue());
                if (nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Usage.Usage)) {
                    throw new SBOLValidationException("sbol-12405", topLevel.getIdentity());
                }
                qualifiedUsages.add(parseUsage(SBOLDoc, ((NestedDocument<QName>) namedProperty.getValue()), nested));
            } else {
                URI uri = (URI) ((Literal<QName>) namedProperty.getValue()).getValue();
                NestedDocument<QName> nestedDocument = nested.get(uri);
                if (nestedDocument == null || nestedDocument.getType() == null || !nestedDocument.getType().equals(Sbol2Terms.Usage.Usage)) {
                    throw new SBOLValidationException("sbol-12405", topLevel.getIdentity());
                }
                qualifiedUsages.add(parseUsage(SBOLDoc, nestedDocument, nested));
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    // GenericTopLevel t = SBOLDoc.createGenericTopLevel(topLevel.getIdentity(), topLevel.getType());
    Activity t = new Activity(topLevel.getIdentity());
    if (persistentIdentity != null)
        t.setPersistentIdentity(persistentIdentity);
    if (version != null)
        t.setVersion(version);
    if (displayId != null)
        t.setDisplayId(displayId);
    if (name != null)
        t.setName(name);
    if (description != null)
        t.setDescription(description);
    t.setWasDerivedFroms(wasDerivedFroms);
    t.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        t.setAnnotations(annotations);
    if (startedAtTime != null)
        t.setStartedAtTime(startedAtTime);
    if (endedAtTime != null)
        t.setEndedAtTime(endedAtTime);
    if (!qualifiedAssociations.isEmpty())
        t.setAssociations(qualifiedAssociations);
    if (!qualifiedUsages.isEmpty())
        t.setUsages(qualifiedUsages);
    if (!wasInformedBys.isEmpty())
        t.setWasInformedBys(wasInformedBys);
    if (!attachments.isEmpty())
        t.setAttachments(attachments);
    Activity oldA = SBOLDoc.getActivity(topLevel.getIdentity());
    if (oldA == null) {
        SBOLDoc.addActivity(t);
    } else {
        if (!t.equals(oldA)) {
            throw new SBOLValidationException("sbol-10202", t);
        }
    }
    return t;
}

Example 4 with GenericTopLevel

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

the class SBOLDocument method updateReferences.

// TODO: need to update persistentIdentities too
private void updateReferences(HashMap<URI, URI> uriMap) throws SBOLValidationException {
    for (TopLevel topLevel : getTopLevels()) {
        for (URI wasDerivedFrom : topLevel.getWasDerivedFroms()) {
            if (uriMap.get(wasDerivedFrom) != null) {
                topLevel.removeWasDerivedFrom(wasDerivedFrom);
                topLevel.addWasDerivedFrom(uriMap.get(wasDerivedFrom));
            }
        }
        for (URI wasGeneratedBy : topLevel.getWasGeneratedBys()) {
            if (uriMap.get(wasGeneratedBy) != null) {
                topLevel.removeWasGeneratedBy(wasGeneratedBy);
                topLevel.addWasGeneratedBy(uriMap.get(wasGeneratedBy));
            }
        }
        for (URI attachmentURI : topLevel.getAttachmentURIs()) {
            if (uriMap.get(attachmentURI) != null) {
                topLevel.removeAttachment(attachmentURI);
                topLevel.addAttachment(uriMap.get(attachmentURI));
            }
        }
    }
    for (Collection collection : getCollections()) {
        for (URI memberURI : collection.getMemberURIs()) {
            if (uriMap.get(memberURI) != null) {
                collection.removeMember(memberURI);
                collection.addMember(uriMap.get(memberURI));
            }
        }
        updateReferences(collection, uriMap);
    }
    for (ComponentDefinition componentDefinition : getComponentDefinitions()) {
        updateReferences(componentDefinition, uriMap);
        for (Component component : componentDefinition.getComponents()) {
            if (uriMap.get(component.getDefinitionURI()) != null) {
                component.setDefinition(uriMap.get(component.getDefinitionURI()));
                for (MapsTo mapsTo : component.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(component.getDefinitionURI());
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(component, uriMap);
            for (MapsTo mapsTo : component.getMapsTos()) {
                updateReferences(mapsTo, uriMap);
            }
        }
        for (SequenceAnnotation sa : componentDefinition.getSequenceAnnotations()) {
            for (Location loc : sa.getLocations()) {
                updateReferences(loc, uriMap);
            }
            updateReferences(sa, uriMap);
        }
        for (SequenceConstraint sc : componentDefinition.getSequenceConstraints()) {
            updateReferences(sc, uriMap);
        }
        for (URI sequenceURI : componentDefinition.getSequenceURIs()) {
            if (uriMap.get(sequenceURI) != null) {
                componentDefinition.removeSequence(sequenceURI);
                componentDefinition.addSequence(uriMap.get(sequenceURI));
            }
        }
    }
    for (ModuleDefinition moduleDefinition : getModuleDefinitions()) {
        updateReferences(moduleDefinition, uriMap);
        for (FunctionalComponent functionalComponent : moduleDefinition.getFunctionalComponents()) {
            if (uriMap.get(functionalComponent.getDefinitionURI()) != null) {
                functionalComponent.setDefinition(uriMap.get(functionalComponent.getDefinitionURI()));
                for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(functionalComponent.getDefinitionURI());
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(functionalComponent, uriMap);
            for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                updateReferences(mapsTo, uriMap);
            }
        }
        for (Module module : moduleDefinition.getModules()) {
            if (uriMap.get(module.getDefinitionURI()) != null) {
                module.setDefinition(uriMap.get(module.getDefinitionURI()));
                for (MapsTo mapsTo : module.getMapsTos()) {
                    ModuleDefinition md = getModuleDefinition(module.getDefinitionURI());
                    if (md != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(md.getPersistentIdentity().toString(), displayId, md.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(module, uriMap);
            for (MapsTo mapsTo : module.getMapsTos()) {
                updateReferences(mapsTo, uriMap);
            }
        }
        for (Interaction interaction : moduleDefinition.getInteractions()) {
            updateReferences(interaction, uriMap);
            for (Participation participation : interaction.getParticipations()) {
                updateReferences(participation, uriMap);
            }
        }
        for (URI modelURI : moduleDefinition.getModelURIs()) {
            if (uriMap.get(modelURI) != null) {
                moduleDefinition.removeModel(modelURI);
                moduleDefinition.addModel(uriMap.get(modelURI));
            }
        }
    }
    for (Model model : getModels()) {
        updateReferences(model, uriMap);
    }
    for (Sequence sequence : getSequences()) {
        updateReferences(sequence, uriMap);
    }
    for (Attachment attachment : getAttachments()) {
        updateReferences(attachment, uriMap);
    }
    for (Implementation implementation : getImplementations()) {
        if (implementation.isSetBuilt()) {
            URI built = implementation.getBuiltURI();
            if (uriMap.get(built) != null) {
                implementation.setBuilt(uriMap.get(built));
            }
        }
        updateReferences(implementation, uriMap);
    }
    for (GenericTopLevel genericTopLevel : getGenericTopLevels()) {
        updateReferences(genericTopLevel, uriMap);
    }
    for (CombinatorialDerivation combinatorialDerivation : getCombinatorialDerivations()) {
        updateReferences(combinatorialDerivation, uriMap);
        if (uriMap.get(combinatorialDerivation.getTemplateURI()) != null) {
            combinatorialDerivation.setTemplate(uriMap.get(combinatorialDerivation.getTemplateURI()));
            ComponentDefinition cd = getComponentDefinition(combinatorialDerivation.getTemplateURI());
            if (cd != null) {
                for (VariableComponent variableComponent : combinatorialDerivation.getVariableComponents()) {
                    String displayId = URIcompliance.extractDisplayId(variableComponent.getVariableURI());
                    URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                    variableComponent.setVariable(newURI);
                }
            }
        }
        for (VariableComponent variableComponent : combinatorialDerivation.getVariableComponents()) {
            updateReferences(variableComponent, uriMap);
        }
    }
    for (Activity activity : getActivities()) {
        updateReferences(activity, uriMap);
        for (Association association : activity.getAssociations()) {
            if (uriMap.get(association.getAgentURI()) != null) {
                association.setAgent(uriMap.get(association.getAgentURI()));
            }
            if (uriMap.get(association.getPlanURI()) != null) {
                association.setPlan(uriMap.get(association.getPlanURI()));
            }
            updateReferences(association, uriMap);
        }
        for (Usage usage : activity.getUsages()) {
            if (uriMap.get(usage.getEntityURI()) != null) {
                usage.setEntity(uriMap.get(usage.getEntityURI()));
            }
            updateReferences(usage, uriMap);
        }
    }
    for (Agent agent : getAgents()) {
        updateReferences(agent, uriMap);
    }
    for (Plan plan : getPlans()) {
        updateReferences(plan, uriMap);
    }
}

Example 5 with GenericTopLevel

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

the class SBOLReader method parseGenericTopLevel.

/**
 * @param SBOLDoc
 * @param topLevel
 * @return
 * @throws SBOLValidationException if either of the following conditions is satisfied:
 * <ul>
 * <li>any of the following SBOL validation rules was violated:
 * 10202, 10203, 10204, 10206, 10208, 10212, 10213, 12102; or</li>
 * <li>an SBOL validation rule violation occurred in the following constructor or methods:
 * 	<ul>
 * 		<li>{@link GenericTopLevel#GenericTopLevel(URI, QName)}, </li>
 * 		<li>{@link GenericTopLevel#setDisplayId(String)}, </li>
 * 		<li>{@link GenericTopLevel#setVersion(String)}, </li>
 * 		<li>{@link GenericTopLevel#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addGenericTopLevel(GenericTopLevel)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings("unchecked")
private static GenericTopLevel parseGenericTopLevel(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel) throws SBOLValidationException {
    // URIcompliance.extractDisplayId(topLevel.getIdentity());
    String displayId = null;
    String name = null;
    String description = null;
    // URI.create(URIcompliance.extractPersistentId(topLevel.getIdentity()));
    URI persistentIdentity = null;
    String version = null;
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    Set<URI> attachments = new HashSet<>();
    QName type = topLevel.getType();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : topLevel.getProperties()) {
        if (namedProperty.getName().equals(Sbol2Terms.Description.type)) {
            String typeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            String nameSpace = URIcompliance.extractNamespace(URI.create(typeStr));
            String localPart = URIcompliance.extractDisplayId(URI.create(typeStr));
            String prefix = null;
            if (nameSpace == null) {
                if (typeStr.lastIndexOf('/') > typeStr.lastIndexOf('#')) {
                    if (typeStr.lastIndexOf('/') > typeStr.lastIndexOf(':')) {
                        nameSpace = typeStr.substring(0, typeStr.lastIndexOf('/') + 1);
                        localPart = typeStr.substring(typeStr.lastIndexOf('/') + 1);
                    } else {
                        nameSpace = typeStr.substring(0, typeStr.lastIndexOf(':') + 1);
                        localPart = typeStr.substring(typeStr.lastIndexOf(':') + 1);
                    }
                } else if (typeStr.lastIndexOf('#') > typeStr.lastIndexOf(':')) {
                    nameSpace = typeStr.substring(0, typeStr.lastIndexOf('#') + 1);
                    localPart = typeStr.substring(typeStr.lastIndexOf('#') + 1);
                } else {
                    nameSpace = typeStr.substring(0, typeStr.lastIndexOf(':') + 1);
                    localPart = typeStr.substring(typeStr.lastIndexOf(':') + 1);
                }
                prefix = SBOLDoc.getNamespacePrefix(URI.create(nameSpace));
                if (prefix == null) {
                    prefix = "ns0";
                    int prefixCnt = 0;
                    while (SBOLDoc.getNamespace(prefix) != null) {
                        prefixCnt++;
                        prefix = "ns" + prefixCnt;
                    }
                    SBOLDoc.addNamespace(new QName(nameSpace, localPart, prefix));
                }
            } else {
                prefix = SBOLDoc.getNamespacePrefix(URI.create(nameSpace));
            }
            if (!nameSpace.equals(Sbol2Terms.sbol2.getNamespaceURI()))
                type = new QName(nameSpace, localPart, prefix);
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.persistentIdentity)) {
            if (!(namedProperty.getValue() instanceof Literal) || persistentIdentity != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10203", topLevel.getIdentity());
            }
            persistentIdentity = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.version)) {
            if (!(namedProperty.getValue() instanceof Literal) || version != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10206", topLevel.getIdentity());
            }
            version = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.displayId)) {
            if (!(namedProperty.getValue() instanceof Literal) || displayId != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10204", topLevel.getIdentity());
            }
            displayId = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.title)) {
            if (!(namedProperty.getValue() instanceof Literal) || name != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10212", topLevel.getIdentity());
            }
            name = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.description)) {
            if (!(namedProperty.getValue() instanceof Literal) || description != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof String))) {
                throw new SBOLValidationException("sbol-10213", topLevel.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasDerivedFrom)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10208", topLevel.getIdentity());
            }
            wasDerivedFroms.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Identified.wasGeneratedBy)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-10221", topLevel.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.TopLevel.hasAttachment)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
                attachments.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Attachment.Attachment)) {
                    Attachment attachment = parseAttachment(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue());
                    attachments.add(attachment.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-XXXXX", topLevel.getIdentity());
            }
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    // GenericTopLevel t = SBOLDoc.createGenericTopLevel(topLevel.getIdentity(), topLevel.getType());
    GenericTopLevel t = new GenericTopLevel(topLevel.getIdentity(), type);
    if (persistentIdentity != null)
        t.setPersistentIdentity(persistentIdentity);
    if (version != null)
        t.setVersion(version);
    if (displayId != null)
        t.setDisplayId(displayId);
    if (name != null)
        t.setName(name);
    if (description != null)
        t.setDescription(description);
    t.setWasDerivedFroms(wasDerivedFroms);
    t.setWasGeneratedBys(wasGeneratedBys);
    t.setAttachments(attachments);
    if (!annotations.isEmpty())
        t.setAnnotations(annotations);
    GenericTopLevel oldG = SBOLDoc.getGenericTopLevel(topLevel.getIdentity());
    if (oldG == null) {
        SBOLDoc.addGenericTopLevel(t);
    } else {
        if (!t.equals(oldG)) {
            throw new SBOLValidationException("sbol-10202", t);
        }
    }
    return t;
}