Examples with WithJsMagmaScriptContext org.molgenis.js.magma.WithJsMagmaScriptContext used on opensource projects

Example 1 with WithJsMagmaScriptContext

use of org.molgenis.js.magma.WithJsMagmaScriptContext in project molgenis by molgenis.

the class RestControllerV2 method updateAttribute.

/**
 * @param entityTypeId The name of the entity to update
 * @param attributeName The name of the attribute to update
 * @param request EntityCollectionBatchRequestV2
 * @param response HttpServletResponse
 */
// getEntities is guaranteed to be not empty
@SuppressWarnings("java:S2259")
@Transactional
@WithJsMagmaScriptContext
@PutMapping("/{entityTypeId}/{attributeName}")
@ResponseStatus(OK)
public synchronized void updateAttribute(@PathVariable("entityTypeId") String entityTypeId, @PathVariable("attributeName") String attributeName, @RequestBody @Valid EntityCollectionBatchRequestV2 request, HttpServletResponse response) {
    final EntityType meta = dataService.getEntityType(entityTypeId);
    try {
        Attribute attr = meta.getAttribute(attributeName);
        if (attr == null) {
            throw new UnknownAttributeException(meta, attributeName);
        }
        if (attr.isReadOnly()) {
            throw createMolgenisDataAccessExceptionReadOnlyAttribute(entityTypeId, attributeName);
        }
        // transform request entities to real Entity objects
        final List<Entity> entities = request.getEntities().stream().filter(e -> e.size() == 2).map(e -> this.restService.toEntity(meta, e)).collect(toList());
        if (entities.size() != request.getEntities().size()) {
            throw createMolgenisDataExceptionIdentifierAndValue();
        }
        // update original entities
        final List<Entity> updatedEntities = new ArrayList<>();
        int count = 0;
        for (Entity entity : entities) {
            Object id = checkForEntityId(entity, count);
            Entity originalEntity = dataService.findOneById(entityTypeId, id);
            if (originalEntity == null) {
                throw new UnknownEntityException(meta, id);
            }
            originalEntity.set(attributeName, entity.get(attributeName));
            updatedEntities.add(originalEntity);
            count++;
        }
        this.dataService.update(entityTypeId, updatedEntities.stream());
        response.setStatus(HttpServletResponse.SC_OK);
    } catch (Exception e) {
        response.setStatus(HttpServletResponse.SC_NO_CONTENT);
        throw e;
    }
}

Example 2 with WithJsMagmaScriptContext

use of org.molgenis.js.magma.WithJsMagmaScriptContext in project molgenis by molgenis.

the class CopyServiceImpl method copy.

@Override
@SuppressWarnings(// Exception types should not be tested using "instanceof" in catch blocks
"java:S1193")
@Transactional(isolation = Isolation.SERIALIZABLE)
@WithJsMagmaScriptContext
public Void copy(List<ResourceIdentifier> resources, @Nullable @CheckForNull String targetPackageId, Progress progress) {
    try {
        ResourceCollection resourceCollection = resourceCollector.get(resources);
        Package targetPackage = getPackage(targetPackageId);
        CopyState state = CopyState.create(targetPackage, progress);
        copyResources(resourceCollection, state);
    } catch (RuntimeException e) {
        if (e instanceof ErrorCoded) {
            throw e;
        } else {
            throw new UnknownCopyFailedException(e);
        }
    }
    return null;
}

Example 3 with WithJsMagmaScriptContext

use of org.molgenis.js.magma.WithJsMagmaScriptContext in project molgenis by molgenis.

the class NegotiatorController method validateNegotiatorExport.

/**
 * Validates a {@link NegotiatorRequest}.
 *
 * <p>Used by the data explorer to verify the request. Since the data explorer does not allow
 * filtering on more than one repository, this endpoint does *NOT* support providing biobankRsql.
 *
 * <ul>
 *   <li>Checks if disabled collections are selected.
 *   <li>Checks if at least one collection is left after filtering out the disabled ones.
 * </ul>
 *
 * @param request the request to validate
 * @return ExportValidationResponse
 * @throws MolgenisDataException if the negotiator is not configured for this entity type
 */
@PostMapping("/validate")
@ResponseBody
@WithJsMagmaScriptContext
public ExportValidationResponse validateNegotiatorExport(@RequestBody NegotiatorRequest request) {
    if (request.getBiobankRsql() != null || request.getBiobankId() != null) {
        throw new IllegalArgumentException("Cannot verify requests with biobank filters.");
    }
    boolean isValidRequest = true;
    String message = "";
    List<String> enabledCollectionsLabels;
    List<String> disabledCollectionLabels;
    Optional<NegotiatorEntityConfig> entityConfigOptional = getNegotiatorEntityConfig(request.getEntityId());
    if (entityConfigOptional.isPresent()) {
        NegotiatorEntityConfig entityConfig = entityConfigOptional.get();
        LOG.info("Validating negotiator request\n\n{}", request);
        List<Entity> collectionEntities = getCollectionEntities(request);
        List<Entity> disabledCollections = getDisabledCollections(collectionEntities, entityConfig);
        Function<Entity, String> getLabel = entity -> entity.getLabelValue().toString();
        disabledCollectionLabels = disabledCollections.stream().map(getLabel).collect(toList());
        enabledCollectionsLabels = collectionEntities.stream().filter(e -> !disabledCollections.contains(e)).map(getLabel).collect(toList());
        if (!disabledCollections.isEmpty()) {
            message = messageSource.getMessage("dataexplorer_directory_disabled", new Object[] { disabledCollections.size(), collectionEntities.size() }, getLocale());
        }
        if (collectionEntities.isEmpty() || (collectionEntities.size() == disabledCollections.size())) {
            isValidRequest = false;
            message = messageSource.getMessage("dataexplorer_directory_no_rows", new Object[] {}, getLocale());
        }
    } else {
        throw new MolgenisDataException(messageSource.getMessage("dataexplorer_directory_no_config", new Object[] {}, getLocale()));
    }
    return ExportValidationResponse.create(isValidRequest, message, enabledCollectionsLabels, disabledCollectionLabels);
}

Example 4 with WithJsMagmaScriptContext

use of org.molgenis.js.magma.WithJsMagmaScriptContext in project molgenis by molgenis.

the class MappingServiceController method attributeMappingFeedback.

@WithJsMagmaScriptContext
@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(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));
    Stream<Entity> sourceEntities = dataService.findAll(source).limit(10);
    List<AlgorithmResult> algorithmResults = sourceEntities.map(sourceEntity -> {
        try {
            algorithmService.bind(sourceEntity);
            return AlgorithmResult.createSuccess(algorithmService.apply(algorithmTest), sourceEntity);
        } catch (Exception e) {
            return AlgorithmResult.createFailure(e, sourceEntity);
        }
    }).collect(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.findMenuItemPath(DataExplorerController.ID));
    return VIEW_ATTRIBUTE_MAPPING_FEEDBACK;
}

Example 5 with WithJsMagmaScriptContext

use of org.molgenis.js.magma.WithJsMagmaScriptContext in project molgenis by molgenis.

the class MappingServiceImpl method applyMappings.

@Override
@Transactional
@WithJsMagmaScriptContext
public long applyMappings(String mappingProjectId, String entityTypeId, Boolean addSourceAttribute, String packageId, String label, Progress progress) {
    MappingProject mappingProject = getMappingProject(mappingProjectId);
    MappingTarget mappingTarget = mappingProject.getMappingTargets().get(0);
    progress.setProgressMax(calculateMaxProgress(mappingTarget));
    progress.progress(0, format("Checking target repository [%s]...", entityTypeId));
    EntityType targetMetadata = createTargetMetadata(mappingTarget, entityTypeId, packageId, label, addSourceAttribute);
    Repository<Entity> targetRepo = getTargetRepository(entityTypeId, targetMetadata);
    return applyMappingsInternal(mappingTarget, targetRepo, progress);
}