Examples with Dtos uk.ac.bbsrc.tgac.miso.dto.Dtos used on opensource projects

Example 16 with Dtos

use of uk.ac.bbsrc.tgac.miso.dto.Dtos in project miso-lims by miso-lims.

the class ChangeLogTag method doStartTagInternal.

@Override
protected int doStartTagInternal() throws Exception {
    ChangeLoggable item = (ChangeLoggable) this.item;
    if (item.getChangeLog().isEmpty()) {
        return SKIP_BODY;
    }
    ObjectMapper mapper = new ObjectMapper();
    pageContext.getOut().append(String.format("<br/><h1>Changes</h1><table id='changelog' class='display no-border ui-widget-content'></table><script type='text/javascript'>jQuery(document).ready(function () { ListUtils.createStaticTable('changelog', ListTarget.changelog, {}, %1$s);});</script>", mapper.writeValueAsString(item.getChangeLog().stream().map(Dtos::asDto).collect(Collectors.toList()))));
    return SKIP_BODY;
}

Example 17 with Dtos

use of uk.ac.bbsrc.tgac.miso.dto.Dtos in project miso-lims by miso-lims.

the class BoxRestController method getBoxScan.

/**
 * Gets the Box Scanner scan results (map of box positions and barcodes)
 *
 * @param boxId
 * @param requestData
 * @return a serialized box object containing the Boxable items
 *         linked with each barcode at each position indicated by the scan results. Any errors are returned with a message containing the
 *         type of
 *         error (unable to read at certain positions; multiple items associated with a single barcode; unable to find box scanner), a
 *         message
 *         about the error, the positions that were successfully read (if applicable) and the positions at which the error was triggered
 *         (if
 *         applicable)
 */
@PostMapping(value = "/{boxId}/scan")
@ResponseBody
public ScanResultsDto getBoxScan(@PathVariable(required = true) int boxId, @RequestBody(required = true) ScanRequest requestData) {
    try {
        BoxScanner boxScanner = boxScanners.get(requestData.getScannerName());
        if (boxScanner == null) {
            throw new RestException("Invalid scanner specified", Status.BAD_REQUEST);
        }
        BoxScan scan = boxScanner.getScan();
        if (scan == null) {
            throw new RestException("The scanner did not detect a box!", Status.CONFLICT);
        }
        Map<String, String> barcodesByPosition = scan.getBarcodesMap();
        // Extract the valid barcodes and build a barcode to item map
        Set<String> validBarcodes = barcodesByPosition.values().stream().filter(barcode -> isRealBarcode(scan, barcode)).collect(Collectors.toSet());
        Map<String, BoxableView> boxablesByBarcode = boxService.getViewsFromBarcodeList(validBarcodes).stream().collect(Collectors.toMap(BoxableView::getIdentificationBarcode, Function.identity()));
        // For all the valid barcodes, build a list of DTOs with the updated positions
        List<BoxableDto> items = barcodesByPosition.entrySet().stream().filter(entry -> isRealBarcode(scan, entry.getValue()) && boxablesByBarcode.containsKey(entry.getValue())).map(entry -> {
            BoxableDto dto = Dtos.asDto(boxablesByBarcode.get(entry.getValue()));
            dto.setCoordinates(entry.getKey());
            return dto;
        }).collect(Collectors.toList());
        // Collect all the errors
        List<ErrorMessage> errors = new ArrayList<>();
        // If there's a barcode that wasn't found in the DB, create an error.
        barcodesByPosition.entrySet().stream().filter(entry -> isRealBarcode(scan, entry.getValue()) && !boxablesByBarcode.containsKey(entry.getValue())).map(entry -> {
            ErrorMessage dto = new ErrorMessage();
            dto.setCoordinates(entry.getKey());
            dto.setMessage("Barcode " + entry.getValue() + " not found.");
            return dto;
        }).forEachOrdered(errors::add);
        // If there was a read error, produce an error.
        scan.getReadErrorPositions().stream().map(position -> {
            ErrorMessage dto = new ErrorMessage();
            dto.setCoordinates(position);
            dto.setMessage("Cannot read tube.");
            return dto;
        }).forEachOrdered(errors::add);
        long totalBarcodes = barcodesByPosition.values().stream().filter(barcode -> isRealBarcode(scan, barcode)).count();
        if (validBarcodes.size() != totalBarcodes) {
            ErrorMessage dto = new ErrorMessage();
            dto.message = "Duplicate barcodes detected!";
            errors.add(dto);
        }
        // Build the diffs for this box
        List<DiffMessage> diffs = new ArrayList<>();
        Box box;
        Map<String, BoxableView> boxables;
        try {
            box = boxService.get(boxId);
            boxables = boxService.getBoxContents(boxId).stream().collect(Collectors.toMap(BoxableView::getBoxPosition, Function.identity()));
        } catch (IOException e) {
            throw new RestException("Cannot get the Box: " + e.getMessage(), Status.INTERNAL_SERVER_ERROR);
        }
        if (box.getSize().getRows() != scan.getRowCount() || box.getSize().getColumns() != scan.getColumnCount())
            throw new RestException(String.format("Box is %d×%d, but scanner detected %d×%d.", box.getSize().getRows(), box.getSize().getColumns(), scan.getRowCount(), scan.getColumnCount()), Status.BAD_REQUEST);
        box.getSize().positionStream().map(position -> {
            BoxableView originalItem = boxables.containsKey(position) ? boxables.get(position) : null;
            BoxableView newItem = barcodesByPosition.containsKey(position) && boxablesByBarcode.containsKey(barcodesByPosition.get(position)) ? boxablesByBarcode.get(barcodesByPosition.get(position)) : null;
            if (originalItem != null && newItem != null && !newItem.getIdentificationBarcode().equals(originalItem.getIdentificationBarcode())) {
                DiffMessage dto = new DiffMessage();
                dto.action = "changed";
                dto.modified = Dtos.asDto(newItem);
                dto.original = Dtos.asDto(originalItem);
                return dto;
            } else if (originalItem != null && newItem == null) {
                DiffMessage dto = new DiffMessage();
                dto.action = "removed";
                dto.original = Dtos.asDto(originalItem);
                return dto;
            } else if (originalItem == null && newItem != null) {
                DiffMessage dto = new DiffMessage();
                dto.action = "added";
                dto.modified = Dtos.asDto(newItem);
                return dto;
            } else {
                return null;
            }
        }).filter(Objects::nonNull);
        ScanResultsDto scanResults = new ScanResultsDto();
        scanResults.setEmptyPositions(// 
        barcodesByPosition.entrySet().stream().filter(// 
        entry -> !isRealBarcode(scan, entry.getValue())).map(// 
        Entry::getKey).collect(Collectors.toList()));
        scanResults.setItems(items);
        scanResults.setErrors(errors);
        scanResults.setDiffs(diffs);
        scanResults.setRows(scan.getRowCount());
        scanResults.setColumns(scan.getColumnCount());
        return scanResults;
    } catch (IntegrationException | IOException e) {
        throw new RestException("Error scanning box: " + e.getMessage(), Status.INTERNAL_SERVER_ERROR);
    }
}

Example 18 with Dtos

use of uk.ac.bbsrc.tgac.miso.dto.Dtos in project miso-lims by miso-lims.

the class LabRestController method updateLab.

@PutMapping(value = "/{id}", headers = { "Content-type=application/json" })
@ResponseBody
public LabDto updateLab(@PathVariable("id") Long id, @RequestBody LabDto labDto, UriComponentsBuilder uriBuilder) throws IOException {
    LabDto updated = RestUtils.updateObject("Lab", id, labDto, Dtos::to, labService, Dtos::asDto);
    constantsController.refreshConstants();
    return updated;
}

Example 19 with Dtos

use of uk.ac.bbsrc.tgac.miso.dto.Dtos in project miso-lims by miso-lims.

the class RunRestController method getPotentialExperiments.

@GetMapping("/{runId}/potentialExperiments")
@ResponseBody
public List<StudiesForExperiment> getPotentialExperiments(@PathVariable long runId) throws IOException {
    Run run = getRun(runId);
    RunDto runDto = Dtos.asDto(run);
    InstrumentModelDto instrumentModelDto = Dtos.asDto(run.getSequencer().getInstrumentModel());
    Map<Library, List<Partition>> libraryGroups = getLibraryGroups(run);
    return libraryGroups.entrySet().stream().map(group -> new Pair<>(group.getKey(), group.getValue().stream().map(partition -> Dtos.asDto(partition, indexChecker)).map(partitionDto -> new RunPartitionDto(runDto, partitionDto)).collect(Collectors.toList()))).map(group -> {
        StudiesForExperiment result = new StudiesForExperiment();
        result.experiment = new ExperimentDto();
        result.experiment.setLibrary(Dtos.asDto(group.getKey(), false));
        result.experiment.setInstrumentModel(instrumentModelDto);
        result.experiment.setPartitions(group.getValue());
        result.studies = group.getKey().getSample().getProject().getStudies().stream().map(Dtos::asDto).collect(Collectors.toList());
        return result;
    }).collect(Collectors.toList());
}

Example 20 with Dtos

use of uk.ac.bbsrc.tgac.miso.dto.Dtos in project miso-lims by miso-lims.

the class SampleClassRestController method createSampleClass.

@PostMapping(headers = { "Content-type=application/json" })
@ResponseStatus(HttpStatus.CREATED)
@ResponseBody
public SampleClassDto createSampleClass(@RequestBody SampleClassDto sampleClassDto) throws IOException {
    return RestUtils.createObject("Sample Class", sampleClassDto, Dtos::to, sampleClassService, sampleClass -> {
        SampleClassDto dto = Dtos.asDto(sampleClass);
        constantsController.refreshConstants();
        return dto;
    });
}