Examples with RestException uk.ac.bbsrc.tgac.miso.webapp.controller.rest.RestException used on opensource projects

Example 1 with RestException

use of uk.ac.bbsrc.tgac.miso.webapp.controller.rest.RestException in project miso-lims by miso-lims.

the class AbstractTypeDataController method bulkCreate.

protected final ModelAndView bulkCreate(Integer quantity, ModelMap model, BiConsumer<ObjectNode, ObjectMapper> configurer) throws IOException {
    if (quantity == null || quantity <= 0) {
        throw new RestException("Must specify quantity to create", Status.BAD_REQUEST);
    }
    ObjectNode config = makeBaseConfig();
    config.put(PageMode.PROPERTY, PageMode.CREATE.getLabel());
    addHotConfig(config, mapper);
    if (configurer != null) {
        configurer.accept(config, mapper);
    }
    addHotAttributes("Create " + pluralType, config, PageMode.CREATE, model);
    model.put("input", mapper.writeValueAsString(Collections.nCopies(quantity, makeDto())));
    return new ModelAndView(newInterface ? NEW_JSP : OLD_JSP, model);
}

Example 2 with RestException

use of uk.ac.bbsrc.tgac.miso.webapp.controller.rest.RestException in project miso-lims by miso-lims.

the class ConstantsController method rebuildConstants.

private void rebuildConstants() {
    try {
        ObjectMapper mapper = new ObjectMapper();
        ObjectNode node = mapper.createObjectNode();
        node.put("docsVersion", getDocsVersion());
        node.put("isDetailedSample", detailedSample);
        node.put("automaticBarcodes", autoGenerateIdBarcodes);
        node.put("boxScannerEnabled", boxScannerEnabled);
        node.put("newOptionSopUrl", newOptionSopUrl);
        final Collection<SampleValidRelationship> relationships = sampleValidRelationshipService.getAll();
        addJsonArray(mapper, node, "libraryDesigns", libraryDesignService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "libraryTypes", libraryTypeService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "librarySelections", librarySelectionService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "libraryStrategies", libraryStrategyService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "libraryDesignCodes", libraryDesignCodeService.list(), Dtos::asDto);
        Set<Long> activePlatforms = sequencerService.list().stream().filter(Instrument::isActive).map(sequencer -> sequencer.getInstrumentModel().getId()).collect(Collectors.toSet());
        addJsonArray(mapper, node, "instrumentModels", instrumentModelService.list(), platform -> {
            InstrumentModelDto dto = Dtos.asDto(platform);
            dto.setActive(activePlatforms.contains(platform.getId()));
            return dto;
        });
        addJsonArray(mapper, node, "kitDescriptors", kitService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "sampleClasses", sampleClassService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "sampleValidRelationships", relationships, Dtos::asDto);
        addJsonArray(mapper, node, "detailedQcStatuses", detailedQcStatusService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "subprojects", subprojectService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "labs", labService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "tissueOrigins", tissueOriginService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "tissueTypes", tissueTypeService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "tissueMaterials", tissueMaterialService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "tissuePieceTypes", tissuePieceTypeService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "stains", stainService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "targetedSequencings", targetedSequencingService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "samplePurposes", samplePurposeService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "sequencingParameters", sequencingParametersService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "printerBackends", Arrays.asList(Backend.values()), Dtos::asDto);
        addJsonArray(mapper, node, "printerDrivers", Arrays.asList(Driver.values()), Dtos::asDto);
        addJsonArray(mapper, node, "boxSizes", boxSizeService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "boxUses", boxUseService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "studyTypes", studyTypeService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "sampleCategories", SampleClass.CATEGORIES, Function.identity());
        createMap(mapper, node, "sampleSubcategories", SampleClass.SUBCATEGORIES);
        addJsonArray(mapper, node, "submissionAction", Arrays.asList(SubmissionActionType.values()), SubmissionActionType::name);
        addJsonArray(mapper, node, "containerModels", containerModelService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "poreVersions", containerService.listPoreVersions(), Dtos::asDto);
        addJsonArray(mapper, node, "spikeIns", librarySpikeInService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "attachmentCategories", attachmentCategoryService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "runPurposes", runPurposeService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "sequencingControlTypes", sequencingControlTypeService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "scientificNames", scientificNameService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "pipelines", pipelineService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "runLibraryQcStatuses", runLibraryQcStatusService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "worksetCategories", worksetCategoryService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "worksetStages", worksetStageService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "metrics", metricService.list(), MetricDto::from);
        addJsonArray(mapper, node, "metricSubcategories", metricSubcategoryService.list(), MetricSubcategoryDto::from);
        addJsonArray(mapper, node, "assays", assayService.list(), AssayDto::from);
        addJsonArray(mapper, node, "assayTests", assayTestService.list(), AssayTestDto::from);
        addJsonArray(mapper, node, "sampleSheetFormats", Arrays.asList(SampleSheet.values()), SampleSheet::name);
        Collection<IndexFamily> indexFamilies = indexFamilyService.list();
        addJsonArray(mapper, node, "indexFamilies", indexFamilies, Dtos::asDto);
        addJsonArray(mapper, node, "qcTypes", qcService.listQcTypes(), Dtos::asDto);
        addJsonArray(mapper, node, "qcTargets", Arrays.asList(QcTarget.values()), Dtos::asDto);
        addJsonArray(mapper, node, "concentrationUnits", Arrays.asList(ConcentrationUnit.values()), Dtos::asDto);
        addJsonArray(mapper, node, "volumeUnits", Arrays.asList(VolumeUnit.values()), Dtos::asDto);
        addJsonArray(mapper, node, "partitionQcTypes", partitionQcTypeService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "referenceGenomes", referenceGenomeService.list(), Dtos::asDto);
        addJsonArray(mapper, node, "spreadsheetFormats", Arrays.asList(SpreadSheetFormat.values()), Dtos::asDto);
        addJsonArray(mapper, node, "sampleSpreadsheets", Arrays.asList(SampleSpreadSheets.values()), Dtos::asDto);
        addJsonArray(mapper, node, "librarySpreadsheets", Arrays.asList(LibrarySpreadSheets.values()), Dtos::asDto);
        addJsonArray(mapper, node, "libraryAliquotSpreadsheets", Arrays.asList(LibraryAliquotSpreadSheets.values()), Dtos::asDto);
        addJsonArray(mapper, node, "poolSpreadsheets", Arrays.asList(PoolSpreadSheets.values()), Dtos::asDto);
        addJsonArray(mapper, node, "partitionSpreadsheets", Arrays.asList(PartitionSpreadsheets.values()), Dtos::asDto);
        addJsonArray(mapper, node, "runLibrarySpreadsheets", Arrays.asList(RunLibrarySpreadsheets.values()), Dtos::asDto);
        addJsonArray(mapper, node, "workflows", Arrays.asList(WorkflowName.values()), Dtos::asDto);
        addJsonArray(mapper, node, "printableFields", Arrays.asList(PrintableField.values()), PrintableField::name);
        ArrayNode platformTypes = node.putArray("platformTypes");
        Collection<PlatformType> activePlatformTypes = instrumentModelService.listActivePlatformTypes();
        for (PlatformType platformType : PlatformType.values()) {
            ObjectNode dto = platformTypes.addObject();
            dto.put("name", platformType.name());
            dto.put("key", platformType.getKey());
            dto.put("containerName", platformType.getContainerName());
            dto.put("active", activePlatformTypes.contains(platformType));
            dto.put("partitionName", platformType.getPartitionName());
            dto.put("pluralPartitionName", platformType.getPluralPartitionName());
        }
        ArrayNode sampleTypes = node.putArray("sampleTypes");
        for (SampleType sampleType : sampleTypeService.list()) {
            if (!sampleType.isArchived()) {
                sampleTypes.add(sampleType.getName());
            }
        }
        ArrayNode donorSexes = node.putArray("donorSexes");
        for (String label : DonorSex.getLabels()) {
            donorSexes.add(label);
        }
        ArrayNode consentLevels = node.putArray("consentLevels");
        for (ConsentLevel level : ConsentLevel.values()) {
            consentLevels.add(level.getLabel());
        }
        ArrayNode strStatuses = node.putArray("strStatuses");
        for (String label : StrStatus.getLabels()) {
            strStatuses.add(label);
        }
        ArrayNode dilutionFactors = node.putArray("dilutionFactors");
        for (String label : DilutionFactor.getLabels()) {
            dilutionFactors.add(label);
        }
        ArrayNode illuminaChemistry = node.putArray("illuminaChemistry");
        for (IlluminaChemistry chemistry : IlluminaChemistry.values()) {
            illuminaChemistry.add(chemistry.name());
        }
        addIlluminaExperimentTypes(node);
        addHealthTypes(node);
        addIlluminaWorkflowTypes(node);
        addInstrumentTypes(node);
        addDataManglingPolicies(node);
        addMetricCategories(node);
        addThresholdTypes(node);
        ObjectNode warningsNode = mapper.createObjectNode();
        warningsNode.put("consentRevoked", "CONSENT REVOKED");
        warningsNode.put("duplicateIndices", indexChecker.getErrorMismatchesMessage());
        warningsNode.put("nearDuplicateIndices", indexChecker.getWarningMismatchesMessage());
        warningsNode.put("lowQualityLibraries", "Low Quality Libraries");
        warningsNode.put("missingIndex", "MISSING INDEX");
        warningsNode.put("negativeVolume", "Negative Volume");
        node.set("warningMessages", warningsNode);
        node.put("errorEditDistance", indexChecker.getErrorMismatches());
        node.put("warningEditDistance", indexChecker.getWarningMismatches());
        node.put("genomeFolder", genomeFolder);
        // Save the regenerated file in cache.
        constantsJs = "Constants = " + mapper.writeValueAsString(node) + ";";
        constantsTimestamp.set(System.currentTimeMillis() / 1000.0);
    } catch (IOException e) {
        throw new RestException(e);
    }
}

Example 3 with RestException

use of uk.ac.bbsrc.tgac.miso.webapp.controller.rest.RestException in project miso-lims by miso-lims.

the class AsyncOperationManager method validateBulkUpdate.

private <T, R extends Identifiable> List<R> validateBulkUpdate(String type, List<T> dtos, Function<T, R> toObject, ThrowingFunction<Long, R, IOException> getItem) throws IOException {
    List<R> items = new ArrayList<>();
    for (T dto : dtos) {
        if (dto == null) {
            throw new RestException(String.format("Cannot save null %s", type), Status.BAD_REQUEST);
        }
        R item = toObject.apply(dto);
        if (!item.isSaved()) {
            throw new RestException("Cannot update unsaved item", Status.BAD_REQUEST);
        } else if (getItem.apply(item.getId()) == null) {
            throw new RestException(String.format("No %s found with ID: %d", type, item.getId()), Status.BAD_REQUEST);
        }
        items.add(item);
    }
    return items;
}

Example 4 with RestException

use of uk.ac.bbsrc.tgac.miso.webapp.controller.rest.RestException in project miso-lims by miso-lims.

the class EditSampleController method createBulkSamples.

/**
 * Used to create new samples.
 * <ul>
 * <li>Detailed Sample: create new samples of a given sample class. Root identities will be found or created.</li>
 * <li>Plain Sample: create new samples.</li>
 * </ul>
 * Sends Dtos objects which will then be used for editing in grid.
 */
@PostMapping(value = "/bulk/new")
public ModelAndView createBulkSamples(@RequestParam Map<String, String> form, ModelMap model) throws IOException {
    Integer quantity = getIntegerInput("quantity", form, true);
    String targetCategory = getStringInput("targetCategory", form, isDetailedSampleEnabled());
    Long projectId = getLongInput("projectId", form, false);
    Long boxId = getLongInput("boxId", form, false);
    if (quantity == null || quantity <= 0)
        throw new RestException("Must specify quantity of samples to create", Status.BAD_REQUEST);
    final SampleDto template;
    if (isDetailedSampleEnabled()) {
        // create new detailed samples
        confirmClassesExist(targetCategory);
        template = getCorrectDetailedSampleDto(targetCategory);
    } else {
        template = new SampleDto();
    }
    final Project project;
    if (projectId == null) {
        project = null;
    } else {
        project = projectService.get(projectId);
        template.setProjectId(projectId);
    }
    if (boxId != null) {
        template.setBox(Dtos.asDto(boxService.get(boxId), true));
    }
    Set<Group> recipientGroups = authorizationManager.getCurrentUser().getGroups();
    return new BulkCreateSampleBackend(template.getClass(), template, quantity, project, targetCategory, recipientGroups).create(model);
}