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

Example 6 with Collection

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

the class VariableComponent method addVariantCollection.

/**
 * Adds the given variant collection to the list of variant collections.
 *
 * @param uriPrefix
 * 			URI prefix for variant collection
 * @param displayId
 * 	        display id for variant collection
 * @param version
 *          version for variant collection
 * @throws SBOLValidationException if the following SBOL validation rule was violated:
 */
public void addVariantCollection(String uriPrefix, String displayId, String version) throws SBOLValidationException {
    URI uri = URIcompliance.createCompliantURI(uriPrefix, displayId, version);
    Collection collection = this.getSBOLDocument().getCollection(uri);
    addVariantCollection(collection.getIdentity());
}

Example 7 with Collection

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

use of org.sbolstandard.core2.Collection in project atlasmap by atlasmap.

the class BaseMarshallerTest method generateCollectionMapping.

protected AtlasMapping generateCollectionMapping() {
    AtlasMapping innerMapping1 = generateAtlasMapping();
    AtlasMapping innerMapping2 = generateAtlasMapping();
    Collection cMapping = (Collection) AtlasModelFactory.createMapping(MappingType.COLLECTION);
    cMapping.setMappings(new Mappings());
    cMapping.getMappings().getMapping().addAll(innerMapping1.getMappings().getMapping());
    cMapping.getMappings().getMapping().addAll(innerMapping2.getMappings().getMapping());
    cMapping.setCollectionType(CollectionType.LIST);
    cMapping.setCollectionSize(new BigInteger("2"));
    cMapping.setAlias("alias");
    cMapping.setDescription("description");
    AtlasMapping mapping = generateAtlasMapping();
    mapping.getMappings().getMapping().clear();
    mapping.getMappings().getMapping().add(cMapping);
    return mapping;
}

Example 9 with Collection

use of org.sbolstandard.core2.Collection in project atlasmap by atlasmap.

the class DefaultAtlasContext method extractCollectionMappings.

private List<Mapping> extractCollectionMappings(DefaultAtlasSession session, BaseMapping baseMapping) throws AtlasException {
    if (LOG.isDebugEnabled()) {
        LOG.debug("Generating Source Mappings from mapping: {}", baseMapping);
    }
    if (!baseMapping.getMappingType().equals(MappingType.COLLECTION)) {
        if (LOG.isDebugEnabled()) {
            LOG.debug("Mapping is not a collection mapping, not cloning: {}", baseMapping);
        }
        return Arrays.asList((Mapping) baseMapping);
    }
    List<Mapping> mappings = new LinkedList<>();
    for (BaseMapping m : ((Collection) baseMapping).getMappings().getMapping()) {
        Mapping mapping = (Mapping) m;
        Field sourceField = mapping.getInputField().get(0);
        boolean sourceIsCollection = AtlasPath.isCollection(sourceField.getPath());
        if (!sourceIsCollection) {
            // just copy it over
            if (LOG.isDebugEnabled()) {
                LOG.debug("Internal mapping's source field is not a collection, not cloning: {}", mapping);
            }
            // output object to be created for our copied firstName value
            for (Field f : mapping.getOutputField()) {
                f.setPath(AtlasPath.overwriteCollectionIndex(f.getPath(), 0));
            }
            mappings.add(mapping);
            continue;
        }
        AtlasModule module = resolveModule(FieldDirection.SOURCE, sourceField);
        int sourceCollectionSize = module.getCollectionSize(session, sourceField);
        if (LOG.isDebugEnabled()) {
            LOG.debug("Internal mapping's source field is a collection. Cloning it for each item ({} clones): {}", sourceCollectionSize, mapping);
        }
        for (int i = 0; i < sourceCollectionSize; i++) {
            Mapping cloneMapping = (Mapping) AtlasModelFactory.cloneMapping(mapping, false);
            for (Field f : mapping.getInputField()) {
                Field clonedField = module.cloneField(f);
                clonedField.setPath(AtlasPath.overwriteCollectionIndex(clonedField.getPath(), i));
                cloneMapping.getInputField().add(clonedField);
            }
            for (Field f : mapping.getOutputField()) {
                Field clonedField = module.cloneField(f);
                if (AtlasPath.isCollection(clonedField.getPath())) {
                    clonedField.setPath(AtlasPath.overwriteCollectionIndex(clonedField.getPath(), i));
                }
                cloneMapping.getOutputField().add(clonedField);
            }
            mappings.add(cloneMapping);
        }
    }
    if (LOG.isDebugEnabled()) {
        LOG.debug("Generated {} mappings from mapping: {}", mappings.size(), baseMapping);
    }
    ((Collection) baseMapping).getMappings().getMapping().clear();
    ((Collection) baseMapping).getMappings().getMapping().addAll(mappings);
    return mappings;
}

Example 10 with Collection

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

the class SBOLReader method parseVariableComponent.

// TODO: FIX COMMENTED SECTION
@SuppressWarnings("unchecked")
private static VariableComponent parseVariableComponent(SBOLDocument SBOLDoc, NestedDocument<QName> variableComponent, Map<URI, NestedDocument<QName>> nested) throws SBOLValidationException {
    String displayId = null;
    String name = null;
    String description = null;
    URI persistentIdentity = null;
    String version = null;
    List<Annotation> annotations = new ArrayList<>();
    URI variable = null;
    OperatorType operator = null;
    HashSet<URI> variants = new HashSet<>();
    HashSet<URI> variantCollections = new HashSet<>();
    HashSet<URI> variantDerivations = new HashSet<>();
    Set<URI> wasDerivedFroms = new HashSet<>();
    Set<URI> wasGeneratedBys = new HashSet<>();
    for (NamedProperty<QName> namedProperty : variableComponent.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", variableComponent.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", variableComponent.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", variableComponent.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", variableComponent.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", variableComponent.getIdentity());
            }
            description = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
        } else if (namedProperty.getName().equals(Sbol2Terms.VariableComponent.hasVariable)) {
            if (!(namedProperty.getValue() instanceof Literal) || variable != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-13004", variableComponent.getIdentity());
            }
            variable = URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString());
        } else if (namedProperty.getName().equals(Sbol2Terms.VariableComponent.hasVariants)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-13007", variableComponent.getIdentity());
                }
                variants.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.ComponentDefinition.ComponentDefinition)) {
                    ComponentDefinition cd = parseComponentDefinition(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    variants.add(cd.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-13007", variableComponent.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-13007", variableComponent.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.VariableComponent.hasVariantCollections)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-13009", variableComponent.getIdentity());
                }
                variantCollections.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Collection.Collection)) {
                    Collection cd = parseCollection(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    variantCollections.add(cd.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-13009", variableComponent.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-13009", variableComponent.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.VariableComponent.hasVariantDerivations)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-13013", variableComponent.getIdentity());
                }
                variantDerivations.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof IdentifiableDocument) {
                if (((IdentifiableDocument<QName>) namedProperty).getType().equals(Sbol2Terms.Collection.Collection)) {
                    CombinatorialDerivation cd = parseCombinatorialDerivation(SBOLDoc, (IdentifiableDocument<QName>) namedProperty.getValue(), nested);
                    variantDerivations.add(cd.getIdentity());
                } else {
                    throw new SBOLValidationException("sbol-13013", variableComponent.getIdentity());
                }
            } else {
                throw new SBOLValidationException("sbol-13013", variableComponent.getIdentity());
            }
        } else if (namedProperty.getName().equals(Sbol2Terms.VariableComponent.hasOperator)) {
            if (!(namedProperty.getValue() instanceof Literal) || operator != null || (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI))) {
                throw new SBOLValidationException("sbol-13002", variableComponent.getIdentity());
            }
            String operatorTypeStr = ((Literal<QName>) namedProperty.getValue()).getValue().toString();
            try {
                operator = OperatorType.convertToOperatorType(URI.create(operatorTypeStr));
            } catch (SBOLValidationException e) {
                throw new SBOLValidationException("sbol-13003", variableComponent.getIdentity());
            }
        } 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", variableComponent.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", variableComponent.getIdentity());
            }
            wasGeneratedBys.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
        } else {
            annotations.add(new Annotation(namedProperty));
        }
    }
    VariableComponent c = new VariableComponent(variableComponent.getIdentity(), operator, variable);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (version != null)
        c.setVersion(version);
    if (displayId != null)
        c.setDisplayId(displayId);
    if (!variants.isEmpty())
        c.setVariants(variants);
    if (!variantCollections.isEmpty())
        c.setVariantCollections(variantCollections);
    if (!variantDerivations.isEmpty())
        c.setVariantDerivations(variantDerivations);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    return c;
}