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

Example 6 with Usage

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

the class SBOLReader method parseUsage.

private static Usage parseUsage(SBOLDocument SBOLDoc, NestedDocument<QName> usage, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    String displayId = null;
    String name = null;
    String description = null;
    URI persistentIdentity = null;
    String version = null;
    URI entityURI = null;
    Set<URI> roles = new HashSet<>();
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    List<Annotation> annotations = new ArrayList<>();
    for (NamedProperty<QName> namedProperty : usage.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", usage.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", usage.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", usage.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", usage.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", usage.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", usage.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", usage.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Usage.role)) {
            if (!(namedProperty.getValue() instanceof Literal) || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-12502", usage.getIdentity());
            }
            roles.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else if (namedProperty.getName().equals(Sbol2Terms.Usage.entity)) {
            if (!(namedProperty.getValue() instanceof Literal) || entityURI != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-12502", usage.getIdentity());
            }
            entityURI = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    Usage u = new Usage(usage.getIdentity(), entityURI);
    if (persistentIdentity != null)
        u.setPersistentIdentity(persistentIdentity);
    if (version != null)
        u.setVersion(version);
    if (displayId != null)
        u.setDisplayId(displayId);
    if (name != null)
        u.setName(name);
    if (description != null)
        u.setDescription(description);
    u.setWasDerivedFroms(wasDerivedFroms);
    u.setWasGeneratedBys(wasGeneratedBys);
    if (!annotations.isEmpty())
        u.setAnnotations(annotations);
    if (!roles.isEmpty())
        u.setRoles(roles);
    return u;
}

Example 7 with Usage

use of org.sbolstandard.core2.Usage 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 8 with Usage

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

the class Activity method copy.

void copy(Activity activity) throws SBOLValidationException {
    ((TopLevel) this).copy((TopLevel) activity);
    if (activity.isSetStartedAtTime()) {
        this.setStartedAtTime(activity.getStartedAtTime());
    }
    if (activity.isSetEndedAtTime()) {
        this.setEndedAtTime(activity.getEndedAtTime());
    }
    for (Association association : activity.getAssociations()) {
        String displayId = URIcompliance.findDisplayId(association);
        Association newAssociation = this.createAssociation(displayId, association.getAgentURI());
        newAssociation.copy(association);
    }
    for (Usage usage : activity.getUsages()) {
        String displayId = URIcompliance.findDisplayId(usage);
        Usage newUsage = this.createUsage(displayId, usage.getEntityURI());
        newUsage.copy(usage);
    }
    for (URI wasInformedBy : activity.getWasInformedByURIs()) {
        this.addWasInformedBy(URI.create(wasInformedBy.toString()));
    }
}