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();
}
}
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());
}
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="));
}
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));
}
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!");
}
}
}
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