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

Example 1 with SampleQC

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

the class BulkSampleQCIT method testAddQc.

@Test
public void testAddQc() throws Exception {
    // Goal: ensure a sample QC can be added
    BulkQCPage page = getAddPage(Arrays.asList(2201L), 1);
    HandsOnTable table = page.getTable();
    Map<String, String> attrs = Maps.newLinkedHashMap();
    attrs.put(QcColumns.DATE, "2018-07-10");
    attrs.put(QcColumns.TYPE, "test edit qc");
    attrs.put(QcColumns.RESULT, "32.6");
    fillRow(table, 0, attrs);
    assertFalse(table.isWritable(QcColumns.SAMPLE_ALIAS, 0));
    assertFalse(table.isWritable(QcColumns.UNITS, 0));
    assertColumnValues(table, 0, attrs, "pre-save");
    assertTrue(page.save(false));
    SampleQC saved = getLatestQc();
    assertQCAttributes(attrs, saved);
}

Example 2 with SampleQC

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

the class BulkSampleQCIT method testEditQc.

@Test
public void testEditQc() throws Exception {
    // Goal: ensure a sample QC can be edited
    BulkQCPage page = getEditPage(Arrays.asList(2201L));
    HandsOnTable table = page.getTable();
    Map<String, String> attrs = Maps.newLinkedHashMap();
    attrs.put(QcColumns.DATE, "2018-07-10");
    attrs.put(QcColumns.RESULT, "32.6");
    fillRow(table, 0, attrs);
    assertFalse(table.isWritable(QcColumns.SAMPLE_ALIAS, 0));
    assertFalse(table.isWritable(QcColumns.UNITS, 0));
    assertFalse(table.isWritable(QcColumns.TYPE, 0));
    assertColumnValues(table, 0, attrs, "pre-save");
    assertTrue(page.save(false));
    SampleQC saved = getLatestQc();
    assertQCAttributes(attrs, saved);
}

Example 3 with SampleQC

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

the class BulkSampleQCIT method testAutoUpdateVolume.

@Test
public void testAutoUpdateVolume() throws Exception {
    // Goal: ensure that volume and volume units are updated by the QC
    BulkQCPage page = getAddPage(Arrays.asList(2201L), 1);
    HandsOnTable table = page.getTable();
    Map<String, String> attrs = Maps.newLinkedHashMap();
    attrs.put(QcColumns.DATE, "2018-07-10");
    attrs.put(QcColumns.TYPE, "update volume qc");
    attrs.put(QcColumns.RESULT, "10.43");
    fillRow(table, 0, attrs);
    assertFalse(table.isWritable(QcColumns.SAMPLE_ALIAS, 0));
    assertFalse(table.isWritable(QcColumns.UNITS, 0));
    assertColumnValues(table, 0, attrs, "pre-save");
    assertTrue(page.save(false));
    SampleQC saved = getLatestQc();
    assertQCAttributes(attrs, saved);
    assertEquals(String.format("Expected volume to be updated to %s, instead got %f", "10.43", saved.getSample().getVolume()), 0, saved.getSample().getVolume().compareTo(new BigDecimal("10.43")));
    assertEquals(String.format("Expected volume units to be updated to %s, instead got %s", VolumeUnit.MICROLITRES.getUnits(), saved.getSample().getVolumeUnits().getUnits()), VolumeUnit.MICROLITRES, saved.getSample().getVolumeUnits());
}

Example 4 with SampleQC

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

the class Dtos method to.

public static QC to(@Nonnull QcDto dto) {
    QC to;
    switch(dto.getQcTarget()) {
        case "Library":
            LibraryQC newLibraryQc = new LibraryQC();
            Library ownerLibrary = new LibraryImpl();
            ownerLibrary.setId(dto.getEntityId());
            newLibraryQc.setLibrary(ownerLibrary);
            to = newLibraryQc;
            break;
        case "Sample":
            SampleQC newSampleQc = new SampleQC();
            Sample ownerSample = new SampleImpl();
            ownerSample.setId(dto.getEntityId());
            newSampleQc.setSample(ownerSample);
            to = newSampleQc;
            break;
        case "Pool":
            PoolQC newPoolQc = new PoolQC();
            Pool ownerPool = new PoolImpl();
            ownerPool.setId(dto.getEntityId());
            newPoolQc.setPool(ownerPool);
            to = newPoolQc;
            break;
        case "Container":
            ContainerQC newContainerQc = new ContainerQC();
            SequencerPartitionContainer ownerContainer = new SequencerPartitionContainerImpl();
            ownerContainer.setId(dto.getEntityId());
            newContainerQc.setContainer(ownerContainer);
            to = newContainerQc;
            break;
        case "Requisition":
            RequisitionQC newRequisitionQc = new RequisitionQC();
            Requisition ownerRequisition = new Requisition();
            ownerRequisition.setId(dto.getEntityId());
            newRequisitionQc.setRequisition(ownerRequisition);
            to = newRequisitionQc;
            break;
        default:
            throw new IllegalArgumentException("No such QC target: " + dto.getQcTarget());
    }
    if (dto.getId() != null) {
        to.setId(dto.getId());
    }
    to.setDate(parseDate(dto.getDate()));
    setBigDecimal(to::setResults, dto.getResults());
    setObject(to::setType, QcType::new, dto.getQcTypeId());
    to.setDescription(dto.getDescription());
    setObject(to::setInstrument, InstrumentImpl::new, dto.getInstrumentId());
    setObject(to::setKit, KitDescriptor::new, dto.getKitDescriptorId());
    setString(to::setKitLot, dto.getKitLot());
    addQcControlRuns(dto.getControls(), to, QcTarget.valueOf(dto.getQcTarget()));
    return to;
}

Example 5 with SampleQC

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

the class DefaultQualityControlService method saveControlRuns.

private void saveControlRuns(long savedId, QC from, QcTargetStore handler) throws IOException {
    QC to = get(from.getEntity().getQcTarget(), from.getId());
    List<QcControlRun> toDelete = new ArrayList<>();
    for (QcControlRun toControl : to.getControls()) {
        if (!toControl.isSaved()) {
            // newly created QC
            continue;
        }
        QcControlRun fromControl = from.getControls().stream().filter(fc -> fc.getId() == toControl.getId()).findFirst().orElse(null);
        if (fromControl == null) {
            toDelete.add(toControl);
        } else {
            toControl.setControl(fromControl.getControl());
            toControl.setLot(fromControl.getLot());
            toControl.setQcPassed(fromControl.isQcPassed());
            handler.updateControlRun(toControl);
        }
    }
    for (QcControlRun control : toDelete) {
        handler.deleteControlRun(control);
    }
    for (QcControlRun fromControl : from.getControls()) {
        if (!fromControl.isSaved()) {
            switch(to.getType().getQcTarget()) {
                case Container:
                    ((ContainerQcControlRun) fromControl).setQc((ContainerQC) to);
                    break;
                case Library:
                    ((LibraryQcControlRun) fromControl).setQc((LibraryQC) to);
                    break;
                case Pool:
                    ((PoolQcControlRun) fromControl).setQc((PoolQC) to);
                    break;
                case Sample:
                    ((SampleQcControlRun) fromControl).setQc((SampleQC) to);
                    break;
                default:
                    throw new IllegalArgumentException("Unhandled QC target: " + to.getType().getQcTarget());
            }
            handler.createControlRun(fromControl);
        }
    }
}