Examples with QcTarget uk.ac.bbsrc.tgac.miso.core.data.qc.QcTarget used on opensource projects

Example 1 with QcTarget

use of uk.ac.bbsrc.tgac.miso.core.data.qc.QcTarget in project miso-lims by miso-lims.

the class DefaultQualityControlService method startBulkOperation.

private BulkQcSaveOperation startBulkOperation(List<QC> items, ThrowingFunction<QC, QC, IOException> action) throws IOException {
    QcTarget qcTarget = qcTypeService.get(items.get(0).getType().getId()).getQcTarget();
    BulkQcSaveOperation operation = new BulkQcSaveOperation(qcTarget, items, authorizationManager.getCurrentUser());
    // Authentication is tied to the thread, so use this same auth in the new thread
    Authentication auth = SecurityContextHolder.getContextHolderStrategy().getContext().getAuthentication();
    Thread thread = new Thread(() -> {
        SecurityContextHolder.getContextHolderStrategy().getContext().setAuthentication(auth);
        try {
            transactionTemplate.execute(new TransactionCallbackWithoutResult() {

                @Override
                protected void doInTransactionWithoutResult(TransactionStatus status) {
                    while (operation.hasMore()) {
                        try {
                            QC item = operation.getNextItem();
                            QC saved = action.apply(item);
                            operation.addSuccess(saved.getId());
                        } catch (ValidationException e) {
                            operation.addFailure(e);
                            status.setRollbackOnly();
                        } catch (Exception e) {
                            operation.setFailed(e);
                            status.setRollbackOnly();
                        }
                    }
                }
            });
        } catch (Exception e) {
            // Exception during transaction commit
            operation.setFailed(e);
        }
        if (operation.isFailed()) {
            Exception exception = operation.getException();
            if (!(exception instanceof BulkValidationException)) {
                LoggerFactory.getLogger(DefaultQualityControlService.class).error("Bulk save failed", exception);
            }
        }
        operation.setComplete();
    });
    thread.start();
    return operation;
}

Example 2 with QcTarget

use of uk.ac.bbsrc.tgac.miso.core.data.qc.QcTarget in project miso-lims by miso-lims.

the class AsyncOperationManager method startAsyncBulkQcUpdate.

public <T, R extends Identifiable> ObjectNode startAsyncBulkQcUpdate(List<QcDto> dtos) throws IOException {
    final QcTarget qcTarget = getQcTarget(dtos.get(0).getQcTarget());
    List<QC> items = validateBulkUpdate("QC", dtos, Dtos::to, id -> qualityControlService.get(qcTarget, id));
    BulkSaveOperation<QC> operation = qualityControlService.startBulkUpdate(items);
    String uuid = addAsyncOperation(operation);
    return makeRunningProgress(uuid, operation);
}

Example 3 with QcTarget

use of uk.ac.bbsrc.tgac.miso.core.data.qc.QcTarget in project miso-lims by miso-lims.

the class QcController method editBulkFrom.

@PostMapping("/bulk/editFrom/{qcTarget}")
public ModelAndView editBulkFrom(@PathVariable("qcTarget") String qcTargetLabel, @RequestParam Map<String, String> form, ModelMap model) throws IOException {
    QcTarget qcTarget = getQcTarget(qcTargetLabel);
    String entityIds = getStringInput("entityIds", form, true);
    int addControls = getIntegerInput("addControls", form, true);
    return new BulkQcEditTable(qcTarget, qcService, instrumentService, addControls).display(entityIds, model);
}

Example 4 with QcTarget

use of uk.ac.bbsrc.tgac.miso.core.data.qc.QcTarget in project miso-lims by miso-lims.

the class QcController method addBulk.

@PostMapping("/bulk/addFrom/{qcTarget}")
public ModelAndView addBulk(@PathVariable("qcTarget") String qcTargetLabel, @RequestParam Map<String, String> form, ModelMap model) throws IOException {
    QcTarget qcTarget = getQcTarget(qcTargetLabel);
    String entityIds = getStringInput("entityIds", form, true);
    int copies = getIntegerInput("copies", form, true);
    int controls = getIntegerInput("controls", form, true);
    return new BulkQcAddTable(qcTarget, qcService, instrumentService, copies, controls).display(entityIds, model);
}

Example 5 with QcTarget

use of uk.ac.bbsrc.tgac.miso.core.data.qc.QcTarget in project miso-lims by miso-lims.

the class HibernateQcTypeDaoIT method testListByNameAndTarget.

@Test
public void testListByNameAndTarget() throws Exception {
    String name = "QuBit";
    QcTarget target = QcTarget.Library;
    List<QcType> qcTypes = dao.listByNameAndTarget(name, target);
    assertNotNull(qcTypes);
    assertEquals(1, qcTypes.size());
    assertEquals(name, qcTypes.get(0).getName());
    assertEquals(target, qcTypes.get(0).getQcTarget());
}