Examples with Attribute org.molgenis.data.meta.model.Attribute used on opensource projects

Example 91 with Attribute

use of org.molgenis.data.meta.model.Attribute in project molgenis by molgenis.

the class MappingTargetRepositoryImplTest method beforeMethod.

@BeforeMethod
public void beforeMethod() {
    // POJOs
    EntityType sourceEntityType = entityTypeFactory.create("source");
    targetEntityType = entityTypeFactory.create("target");
    Attribute targetAttribute = attrMetaFactory.create().setName("targetAttribute");
    targetEntityType.addAttribute(targetAttribute);
    entityMappings = singletonList(new EntityMapping("entityMappingID", sourceEntityType, targetEntityType, emptyList()));
    mappingTargets = singletonList(new MappingTarget("mappingTargetID", targetEntityType, entityMappings));
    // Entities
    Entity entityMappingEntity = new DynamicEntity(entityMappingMeta);
    entityMappingEntity.set(EntityMappingMetaData.IDENTIFIER, "entityMappingID");
    entityMappingEntity.set(EntityMappingMetaData.SOURCE_ENTITY_TYPE, "source");
    entityMappingEntity.set(EntityMappingMetaData.TARGET_ENTITY_TYPE, "target");
    entityMappingEntity.set(EntityMappingMetaData.ATTRIBUTE_MAPPINGS, emptyList());
    Entity mappingTargetEntity = new DynamicEntity(mappingTargetMeta);
    mappingTargetEntity.set(IDENTIFIER, "mappingTargetID");
    mappingTargetEntity.set(TARGET, "target");
    entityMappingEntities = singletonList(entityMappingEntity);
    mappingTargetEntity.set(ENTITY_MAPPINGS, entityMappingEntities);
    mappingTargetEntities = singletonList(mappingTargetEntity);
}

Example 92 with Attribute

use of org.molgenis.data.meta.model.Attribute in project molgenis by molgenis.

the class AlgorithmServiceImplTest method testApplyConvertException.

private void testApplyConvertException(String algorithmResult, AttributeType attributeType) {
    AttributeMapping attributeMapping = mock(AttributeMapping.class);
    String algorithm = "algorithm";
    when(attributeMapping.getAlgorithm()).thenReturn(algorithm);
    Attribute targetAttribute = when(mock(Attribute.class).getDataType()).thenReturn(attributeType).getMock();
    when(attributeMapping.getTargetAttribute()).thenReturn(targetAttribute);
    Entity sourceEntity = mock(Entity.class);
    when(jsMagmaScriptEvaluator.eval(algorithm, sourceEntity, 3)).thenReturn(algorithmResult);
    algorithmServiceImpl.apply(attributeMapping, sourceEntity, null);
}

Example 93 with Attribute

use of org.molgenis.data.meta.model.Attribute in project molgenis by molgenis.

the class MappingServiceController method getTagsForAttribute.

private Map<String, List<OntologyTerm>> getTagsForAttribute(String target, MappingProject project) {
    Map<String, List<OntologyTerm>> attributeTagMap = new HashMap<>();
    for (Attribute amd : project.getMappingTarget(target).getTarget().getAtomicAttributes()) {
        EntityType targetMetaData = RunAsSystemAspect.runAsSystem(() -> dataService.getEntityType(target));
        attributeTagMap.put(amd.getName(), newArrayList(ontologyTagService.getTagsForAttribute(targetMetaData, amd).values()));
    }
    return attributeTagMap;
}

Example 94 with Attribute

use of org.molgenis.data.meta.model.Attribute in project molgenis by molgenis.

the class MappingServiceController method addEntityMapping.

/**
 * Adds a new {@link EntityMapping} to an existing {@link MappingTarget}
 *
 * @param target           the name of the {@link MappingTarget}'s entity to add a source entity to
 * @param source           the name of the source entity of the newly added {@link EntityMapping}
 * @param mappingProjectId the ID of the {@link MappingTarget}'s {@link MappingProject}
 * @return redirect URL for the mapping project
 */
@PostMapping("/addEntityMapping")
public String addEntityMapping(@RequestParam String mappingProjectId, String target, String source) {
    EntityType sourceEntityType = dataService.getEntityType(source);
    EntityType targetEntityType = dataService.getEntityType(target);
    Iterable<Attribute> attributes = targetEntityType.getAtomicAttributes();
    MappingProject project = mappingService.getMappingProject(mappingProjectId);
    if (hasWritePermission(project)) {
        EntityMapping mapping = project.getMappingTarget(target).addSource(sourceEntityType);
        mappingService.updateMappingProject(project);
        autoGenerateAlgorithms(mapping, sourceEntityType, targetEntityType, attributes, project);
    }
    return "redirect:" + getMappingServiceMenuUrl() + "/mappingproject/" + mappingProjectId;
}

Example 95 with Attribute

use of org.molgenis.data.meta.model.Attribute in project molgenis by molgenis.

the class MappingServiceController method attributeMappingFeedback.

@PostMapping("/attributemappingfeedback")
public String attributeMappingFeedback(@RequestParam() String mappingProjectId, @RequestParam() String target, @RequestParam() String source, @RequestParam() String targetAttribute, @RequestParam() String algorithm, Model model) {
    MappingProject project = mappingService.getMappingProject(mappingProjectId);
    MappingTarget mappingTarget = project.getMappingTarget(target);
    EntityMapping entityMapping = mappingTarget.getMappingForSource(source);
    AttributeMapping algorithmTest;
    if (entityMapping.getAttributeMapping(targetAttribute) == null) {
        algorithmTest = entityMapping.addAttributeMapping(targetAttribute);
        algorithmTest.setAlgorithm(algorithm);
    } else {
        algorithmTest = entityMapping.getAttributeMapping(targetAttribute);
        algorithmTest.setAlgorithm(algorithm);
    }
    try {
        Collection<String> sourceAttributeNames = algorithmService.getSourceAttributeNames(algorithm);
        if (!sourceAttributeNames.isEmpty()) {
            List<Attribute> sourceAttributes = sourceAttributeNames.stream().map(attributeName -> {
                EntityType sourceEntityType = entityMapping.getSourceEntityType();
                return sourceEntityType.getAttribute(attributeName);
            }).filter(Objects::nonNull).collect(Collectors.toList());
            model.addAttribute("sourceAttributes", sourceAttributes);
        }
    } catch (Exception e) {
        throw new RuntimeException(e);
    }
    model.addAttribute("mappingProjectId", mappingProjectId);
    model.addAttribute("target", target);
    model.addAttribute("source", source);
    model.addAttribute("targetAttribute", dataService.getEntityType(target).getAttribute(targetAttribute));
    FluentIterable<Entity> sourceEntities = FluentIterable.from(() -> dataService.findAll(source).iterator()).limit(10);
    ImmutableList<AlgorithmResult> algorithmResults = sourceEntities.transform(sourceEntity -> {
        try {
            return AlgorithmResult.createSuccess(algorithmService.apply(algorithmTest, sourceEntity, sourceEntity.getEntityType()), sourceEntity);
        } catch (Exception e) {
            return AlgorithmResult.createFailure(e, sourceEntity);
        }
    }).toList();
    model.addAttribute("feedbackRows", algorithmResults);
    long missing = algorithmResults.stream().filter(r -> r.isSuccess() && r.getValue() == null).count();
    long success = algorithmResults.stream().filter(AlgorithmResult::isSuccess).count() - missing;
    long error = algorithmResults.size() - success - missing;
    model.addAttribute("success", success);
    model.addAttribute("missing", missing);
    model.addAttribute("error", error);
    model.addAttribute("dataexplorerUri", menuReaderService.getMenu().findMenuItemPath(DataExplorerController.ID));
    return VIEW_ATTRIBUTE_MAPPING_FEEDBACK;
}