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

Example 1 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 = new Collection();
    cMapping.getMappings().getMapping().addAll(innerMapping1.getMappings().getMapping());
    cMapping.getMappings().getMapping().addAll(innerMapping2.getMappings().getMapping());
    cMapping.setCollectionType(CollectionType.LIST);
    AtlasMapping mapping = generateAtlasMapping();
    mapping.getMappings().getMapping().clear();
    mapping.getMappings().getMapping().add(cMapping);
    return mapping;
}

Example 2 with Collection

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

the class DefaultAtlasContextTest method testProcess.

@Test
public void testProcess() throws AtlasException {
    DefaultAtlasSession session = mock(DefaultAtlasSession.class);
    when(session.getAtlasContext()).thenReturn(context);
    Head head = mock(Head.class);
    when(session.head()).thenReturn(head);
    when(head.setMapping(any(Mapping.class))).thenReturn(head);
    when(head.setLookupTable(any(LookupTable.class))).thenReturn(head);
    Field headField = mock(ConstantField.class);
    when(head.getSourceField()).thenReturn(headField);
    Audits audits = mock(Audits.class);
    when(session.getAudits()).thenReturn(audits);
    Validations validations = mock(Validations.class);
    when(session.getValidations()).thenReturn(validations);
    AtlasMapping mapping = mock(AtlasMapping.class);
    when(session.getMapping()).thenReturn(mapping);
    when(session.hasErrors()).thenReturn(true);
    context.process(session);
    when(session.hasErrors()).thenReturn(false);
    Mappings mappings = mock(Mappings.class);
    when(mapping.getMappings()).thenReturn(mappings);
    List<BaseMapping> baseMappings = new ArrayList<>();
    Collection baseMapping = mock(Collection.class);
    when(baseMapping.getMappingType()).thenReturn(MappingType.COLLECTION);
    baseMappings.add(baseMapping);
    when(mappings.getMapping()).thenReturn(baseMappings);
    Mappings subMappings = mock(Mappings.class);
    when(baseMapping.getMappings()).thenReturn(subMappings);
    List<BaseMapping> baseMappingList = new ArrayList<>();
    Mapping mappingElement1 = mock(Mapping.class);
    List<Field> sourceFieldList = new ArrayList<>();
    ConstantField sourceField = mock(ConstantField.class);
    sourceFieldList.add(sourceField);
    when(sourceField.getPath()).thenReturn("contact.firstName");
    when(mappingElement1.getInputField()).thenReturn(sourceFieldList);
    List<Field> outputFieldList = new ArrayList<>();
    Field outputField = mock(Field.class);
    outputFieldList.add(outputField);
    when(outputField.getPath()).thenReturn("contact.firstName");
    when(mappingElement1.getOutputField()).thenReturn(outputFieldList);
    when(mappingElement1.getMappingType()).thenReturn(MappingType.ALL);
    baseMappingList.add(mappingElement1);
    when(subMappings.getMapping()).thenReturn(baseMappingList);
    Mapping mappingElement2 = mock(Mapping.class);
    when(mappingElement2.getMappingType()).thenReturn(MappingType.ALL);
    baseMappingList.add(mappingElement2);
    List<Field> sourceFieldList2 = new ArrayList<>();
    ConstantField sourceField2 = mock(ConstantField.class);
    sourceFieldList2.add(sourceField2);
    when(sourceField2.getPath()).thenReturn("contact[1]");
    when(mappingElement2.getInputField()).thenReturn(sourceFieldList2);
    ConstantModule mockConstantModule = mock(ConstantModule.class);
    when(mockConstantModule.getCollectionSize(any(AtlasInternalSession.class), any(Field.class))).thenReturn(1);
    ConstantField clonedField = mock(ConstantField.class);
    when(clonedField.getPath()).thenReturn("cloned[1]");
    when(mockConstantModule.cloneField(any(Field.class))).thenReturn(clonedField);
    List<Field> mockSourceFieldList = new ArrayList<>();
    ConstantField mockSourceField = mock(ConstantField.class);
    mockSourceFieldList.add(mockSourceField);
    when(mockSourceField.getPath()).thenReturn("source[1]");
    when(mappingElement2.getInputField()).thenReturn(mockSourceFieldList);
    List<Field> mockOutputFieldList = new ArrayList<>();
    ConstantField mockOutputField = mock(ConstantField.class);
    mockOutputFieldList.add(mockOutputField);
    when(mockOutputField.getPath()).thenReturn("output[1]");
    when(mappingElement2.getOutputField()).thenReturn(mockOutputFieldList);
    context.getSourceModules().put(DefaultAtlasContext.CONSTANTS_DOCUMENT_ID, mockConstantModule);
    context.process(session);
}

Example 3 with Collection

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

the class AtlasModuleSupportTest method testListTargetPathsListOfBaseMapping.

@Test
public void testListTargetPathsListOfBaseMapping() {
    List<BaseMapping> mappings = null;
    assertEquals(0, AtlasModuleSupport.listTargetPaths(mappings).size());
    mappings = new ArrayList<>();
    assertEquals(0, AtlasModuleSupport.listTargetPaths(mappings).size());
    Mapping mapping = new Mapping();
    Field field = new MockField();
    field.setPath("MockPath");
    mapping.getOutputField().add(field);
    mappings.add(mapping);
    assertEquals(1, AtlasModuleSupport.listTargetPaths(mappings).size());
    Collection collection = null;
    mappings.add(collection);
    assertEquals(1, AtlasModuleSupport.listTargetPaths(mappings).size());
    collection = new Collection();
    mappings.add(collection);
    assertEquals(1, AtlasModuleSupport.listTargetPaths(mappings).size());
    Mappings mapings = new Mappings();
    collection.setMappings(mapings);
    assertEquals(1, AtlasModuleSupport.listTargetPaths(mappings).size());
}

Example 4 with Collection

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

the class CollectionOutput method main.

/**
 * @param args
 * @throws SBOLValidationException see SBOL validation rule violation at {@link Collection#addMember(URI)}
 * @throws SBOLConversionException
 */
public static void main(String[] args) throws SBOLValidationException, SBOLConversionException {
    SBOLDocument document = new SBOLDocument();
    document.setDefaultURIprefix("http://parts.igem.org/Promoters/Catalog");
    document.setTypesInURIs(false);
    Collection col = document.createCollection("Anderson", "");
    col.setName("Anderson promoters");
    col.setDescription("The Anderson promoter collection");
    col.addMember(URI.create("http://partsregistry.org/Part:BBa_J23119"));
    col.addMember(URI.create("http://partsregistry.org/Part:BBa_J23118"));
    SBOLWriter.write(document, (System.out));
}

Example 5 with Collection

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

the class SBOLReader method parseCollection.

/**
 * @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 Collection#Collection(URI)}, </li>
 * 		<li>{@link Collection#setDisplayId(String)}, </li>
 * 		<li>{@link Collection#setVersion(String)}, </li>
 * 		<li>{@link Collection#setMembers(Set)}, </li>
 * 		<li>{@link Collection#setWasDerivedFrom(URI)}, </li>
 * 		<li>{@link Identified#setAnnotations(List)}, or</li>
 * 		<li>{@link SBOLDocument#addCollection(Collection)}.</li>
 * 	</ul>
 * </li>
 * </ul>
 */
@SuppressWarnings({ "rawtypes", "unchecked" })
private static Collection parseCollection(SBOLDocument SBOLDoc, IdentifiableDocument<QName> topLevel, Map<URI, NestedDocument<QName>> nested) 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<>();
    Set<URI> members = 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.Collection.hasMembers)) {
            if (namedProperty.getValue() instanceof Literal) {
                if (!(((Literal<QName>) namedProperty.getValue()).getValue() instanceof URI)) {
                    throw new SBOLValidationException("sbol-12102", topLevel.getIdentity());
                }
                members.add(URI.create(((Literal<QName>) namedProperty.getValue()).getValue().toString()));
            } else if (namedProperty.getValue() instanceof NestedDocument) {
                if (((IdentifiableDocument) namedProperty).getType().equals(Sbol2Terms.Collection.Collection))
                    parseCollection(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.ModuleDefinition.ModuleDefinition))
                    parseModuleDefinition(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Model.Model))
                    parseModel(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Sequence.Sequence))
                    parseSequence(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.ComponentDefinition.ComponentDefinition))
                    parseComponentDefinition(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.CombinatorialDerivation.CombinatorialDerivation))
                    parseCombinatorialDerivation(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Implementation.Implementation))
                    parseImplementation(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Attachment.Attachment))
                    parseAttachment(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Activity.Activity))
                    parseActivity(SBOLDoc, (IdentifiableDocument) namedProperty, nested);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Agent.Agent))
                    parseAgent(SBOLDoc, (IdentifiableDocument) namedProperty);
                else if (((IdentifiableDocument) namedProperty).equals(Sbol2Terms.Plan.Plan))
                    parsePlan(SBOLDoc, (IdentifiableDocument) namedProperty);
                else
                    parseGenericTopLevel(SBOLDoc, (IdentifiableDocument) namedProperty);
            } else {
                throw new SBOLValidationException("sbol-12102", topLevel.getIdentity());
            }
        } 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));
        }
    }
    Collection c = new Collection(topLevel.getIdentity());
    if (displayId != null)
        c.setDisplayId(displayId);
    if (version != null)
        c.setVersion(version);
    if (persistentIdentity != null)
        c.setPersistentIdentity(persistentIdentity);
    if (!members.isEmpty())
        c.setMembers(members);
    if (name != null)
        c.setName(name);
    if (description != null)
        c.setDescription(description);
    c.setWasDerivedFroms(wasDerivedFroms);
    c.setWasGeneratedBys(wasGeneratedBys);
    c.setAttachments(attachments);
    if (!annotations.isEmpty())
        c.setAnnotations(annotations);
    Collection oldC = SBOLDoc.getCollection(topLevel.getIdentity());
    if (oldC == null) {
        SBOLDoc.addCollection(c);
    } else {
        if (!c.equals(oldC)) {
            throw new SBOLValidationException("sbol-10202", c);
        }
    }
    return c;
}