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

Example 6 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(URI originalIdentity, URI newIdentity) throws SBOLValidationException {
    for (TopLevel topLevel : getTopLevels()) {
        for (URI wasDerivedFrom : topLevel.getWasDerivedFroms()) {
            if (wasDerivedFrom.equals(originalIdentity)) {
                topLevel.removeWasDerivedFrom(originalIdentity);
                topLevel.addWasDerivedFrom(newIdentity);
            }
        }
        for (URI wasGeneratedBy : topLevel.getWasGeneratedBys()) {
            if (wasGeneratedBy.equals(originalIdentity)) {
                topLevel.removeWasGeneratedBy(originalIdentity);
                topLevel.addWasGeneratedBy(newIdentity);
            }
        }
        for (URI attachmentURI : topLevel.getAttachmentURIs()) {
            if (attachmentURI.equals(originalIdentity)) {
                topLevel.removeAttachment(originalIdentity);
                topLevel.addAttachment(newIdentity);
            }
        }
    }
    for (Collection collection : getCollections()) {
        for (URI memberURI : collection.getMemberURIs()) {
            if (memberURI.equals(originalIdentity)) {
                collection.removeMember(originalIdentity);
                collection.addMember(newIdentity);
            }
        }
        updateReferences(collection, originalIdentity, newIdentity);
    }
    for (ComponentDefinition componentDefinition : getComponentDefinitions()) {
        updateReferences(componentDefinition, originalIdentity, newIdentity);
        for (Component component : componentDefinition.getComponents()) {
            if (component.getDefinitionURI().equals(originalIdentity)) {
                component.setDefinition(newIdentity);
                for (MapsTo mapsTo : component.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(newIdentity);
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(component, originalIdentity, newIdentity);
            for (MapsTo mapsTo : component.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (SequenceAnnotation sa : componentDefinition.getSequenceAnnotations()) {
            for (Location loc : sa.getLocations()) {
                updateReferences(loc, originalIdentity, newIdentity);
            }
            updateReferences(sa, originalIdentity, newIdentity);
        }
        for (SequenceConstraint sc : componentDefinition.getSequenceConstraints()) {
            updateReferences(sc, originalIdentity, newIdentity);
        }
        for (URI sequenceURI : componentDefinition.getSequenceURIs()) {
            if (sequenceURI.equals(originalIdentity)) {
                componentDefinition.removeSequence(originalIdentity);
                componentDefinition.addSequence(newIdentity);
            }
        }
    }
    for (ModuleDefinition moduleDefinition : getModuleDefinitions()) {
        updateReferences(moduleDefinition, originalIdentity, newIdentity);
        for (FunctionalComponent functionalComponent : moduleDefinition.getFunctionalComponents()) {
            if (functionalComponent.getDefinitionURI().equals(originalIdentity)) {
                functionalComponent.setDefinition(newIdentity);
                for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                    ComponentDefinition cd = getComponentDefinition(newIdentity);
                    if (cd != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(cd.getPersistentIdentity().toString(), displayId, cd.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(functionalComponent, originalIdentity, newIdentity);
            for (MapsTo mapsTo : functionalComponent.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (Module module : moduleDefinition.getModules()) {
            if (module.getDefinitionURI().equals(originalIdentity)) {
                module.setDefinition(newIdentity);
                for (MapsTo mapsTo : module.getMapsTos()) {
                    ModuleDefinition md = getModuleDefinition(newIdentity);
                    if (md != null) {
                        String displayId = URIcompliance.extractDisplayId(mapsTo.getRemoteURI());
                        URI newURI = URIcompliance.createCompliantURI(md.getPersistentIdentity().toString(), displayId, md.getVersion());
                        mapsTo.setRemote(newURI);
                    }
                }
            }
            updateReferences(module, originalIdentity, newIdentity);
            for (MapsTo mapsTo : module.getMapsTos()) {
                updateReferences(mapsTo, originalIdentity, newIdentity);
            }
        }
        for (Interaction interaction : moduleDefinition.getInteractions()) {
            updateReferences(interaction, originalIdentity, newIdentity);
            for (Participation participation : interaction.getParticipations()) {
                updateReferences(participation, originalIdentity, newIdentity);
            }
        }
        for (URI modelURI : moduleDefinition.getModelURIs()) {
            if (modelURI.equals(originalIdentity)) {
                moduleDefinition.removeModel(originalIdentity);
                moduleDefinition.addModel(newIdentity);
            }
        }
    }
    for (Model model : getModels()) {
        updateReferences(model, originalIdentity, newIdentity);
    }
    for (Attachment attachment : getAttachments()) {
        updateReferences(attachment, originalIdentity, newIdentity);
    }
    for (Implementation implementation : getImplementations()) {
        if (implementation.isSetBuilt() && implementation.getBuiltURI().equals(originalIdentity)) {
            implementation.setBuilt(newIdentity);
        }
        updateReferences(implementation, originalIdentity, newIdentity);
    }
    for (Sequence sequence : getSequences()) {
        updateReferences(sequence, originalIdentity, newIdentity);
    }
    for (GenericTopLevel genericTopLevel : getGenericTopLevels()) {
        updateReferences(genericTopLevel, originalIdentity, newIdentity);
    }
    for (CombinatorialDerivation combinatorialDerivation : getCombinatorialDerivations()) {
        updateReferences(combinatorialDerivation, originalIdentity, newIdentity);
        if (combinatorialDerivation.getTemplateURI().equals(originalIdentity)) {
            combinatorialDerivation.setTemplate(newIdentity);
            ComponentDefinition cd = getComponentDefinition(newIdentity);
            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, originalIdentity, newIdentity);
        }
    }
    for (Activity activity : getActivities()) {
        updateReferences(activity, originalIdentity, newIdentity);
        for (Association association : activity.getAssociations()) {
            if (association.getAgentURI().equals(originalIdentity)) {
                association.setAgent(newIdentity);
            }
            if (association.isSetPlan() && association.getPlanURI().equals(originalIdentity)) {
                association.setPlan(newIdentity);
            }
            updateReferences(association, originalIdentity, newIdentity);
        }
        for (Usage usage : activity.getUsages()) {
            if (usage.getEntityURI().equals(originalIdentity)) {
                usage.setEntity(newIdentity);
            }
            updateReferences(usage, originalIdentity, newIdentity);
        }
    }
    for (Agent agent : getAgents()) {
        updateReferences(agent, originalIdentity, newIdentity);
    }
    for (Plan plan : getPlans()) {
        updateReferences(plan, originalIdentity, newIdentity);
    }
}

Example 7 with GenericTopLevel

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

the class GenericTopLevel method copy.

// /**
// * @param newDisplayId
// * @return
// */
// public GenericTopLevel copy(String newDisplayId) {
// GenericTopLevel cloned = (GenericTopLevel) this.deepCopy();
// cloned.updateCompliantURI(newDisplayId);
// return cloned;
// }
// 
// /**
// * Get a deep copy of the object first, and set its major version to the specified value, and minor version to "0".
// * @param newVersion
// * @return the copied {@link ComponentDefinition} instance with the specified major version.
// */
// public GenericTopLevel newVersion(String newVersion) {
// GenericTopLevel cloned = (GenericTopLevel) super.newVersion(newVersion);
// cloned.updateVersion(newVersion);
// return cloned;
// }
/* (non-Javadoc)
	 * @see org.sbolstandard.core2.abstract_classes.TopLevel#copy(java.lang.String, java.lang.String, java.lang.String)
	 */
/**
 * @throws SBOLValidationException if an SBOL validation rule violation occurred in
 * any of the following methods:
 * <ul>
 * <li>{@link #deepCopy()},</li>
 * <li>{@link URIcompliance#createCompliantURI(String, String, String)},</li>
 * <li>{@link #setDisplayId(String)},</li>
 * <li>{@link #setVersion(String)},</li>
 * <li>{@link #setWasDerivedFrom(URI)}, or</li>
 * <li>{@link #setIdentity(URI)}.</li>
 * </ul>
 */
@Override
GenericTopLevel copy(String URIprefix, String displayId, String version) throws SBOLValidationException {
    GenericTopLevel cloned = this.deepCopy();
    cloned.setPersistentIdentity(createCompliantURI(URIprefix, displayId, ""));
    cloned.setDisplayId(displayId);
    cloned.setVersion(version);
    URI newIdentity = createCompliantURI(URIprefix, displayId, version);
    if (!this.getIdentity().equals(newIdentity)) {
        cloned.addWasDerivedFrom(this.getIdentity());
    } else {
        cloned.setWasDerivedFroms(this.getWasDerivedFroms());
    }
    cloned.setIdentity(newIdentity);
    return cloned;
}

Example 8 with GenericTopLevel

use of org.sbolstandard.core2.GenericTopLevel 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="));
}

Example 9 with GenericTopLevel

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

the class GenericTopLevelOutput method main.

public static void main(String[] args) throws Exception {
    String myAppURI = "http://www.myapp.org/";
    String myAppPrefix = "myapp";
    String prURI = "http://www.partsregistry.org/";
    SBOLDocument document = new SBOLDocument();
    document.addNamespace(URI.create(myAppURI + "/"), myAppPrefix);
    document.setDefaultURIprefix(prURI);
    document.setTypesInURIs(true);
    GenericTopLevel topLevel = document.createGenericTopLevel("datasheet1", "", new QName("http://www.myapp.org", "Datasheet", myAppPrefix));
    topLevel.setName("Datasheet 1");
    topLevel.createAnnotation(new QName(myAppURI, "characterizationData", myAppPrefix), URI.create(myAppURI + "/measurement/1"));
    topLevel.createAnnotation(new QName(myAppURI, "transcriptionRate", myAppPrefix), "1");
    ComponentDefinition promoter = document.createComponentDefinition("BBa_J23119", "", new HashSet<URI>(Arrays.asList(ComponentDefinition.DNA)));
    promoter.addRole(SequenceOntology.PROMOTER);
    promoter.setName("J23119");
    promoter.setDescription("Constitutive promoter");
    promoter.createAnnotation(new QName(myAppURI, "datasheet", myAppPrefix), topLevel.getIdentity());
    promoter.addWasDerivedFrom(URI.create("http://www.partsregistry.org/Part:BBa_J23119"));
    SBOLWriter.write(document, (System.out));
}