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

Example 1 with TissueOrigin

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

the class OicrSampleAliasGeneratorTest method makeTissueFromTissue.

private SampleTissue makeTissueFromTissue() throws Exception {
    SampleTissue parent = (SampleTissue) makeFullTissue();
    parent.setAlias("PROJ_0001_Bn_P_nn_1-1");
    parent.setParent(makeIdentity());
    SampleTissue child = new SampleTissueImpl();
    SampleClass sc = new SampleClassImpl();
    sc.setSampleCategory(SampleTissue.CATEGORY_NAME);
    child.setSampleClass(sc);
    child.setParent(parent);
    child.setTimesReceived(1);
    child.setTubeNumber(1);
    TissueOrigin to = new TissueOriginImpl();
    to.setAlias("Bn");
    child.setTissueOrigin(to);
    TissueType tt = new TissueTypeImpl();
    tt.setAlias("O");
    child.setTissueType(tt);
    return child;
}

Example 2 with TissueOrigin

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

the class OicrSampleAliasGeneratorTest method makeFullTissue.

private Sample makeFullTissue() {
    SampleTissue tissue = makeMinimalTissue();
    TissueOrigin to = new TissueOriginImpl();
    to.setAlias("Bn");
    tissue.setTissueOrigin(to);
    TissueType tt = new TissueTypeImpl();
    tt.setAlias("P");
    tissue.setTissueType(tt);
    tissue.setPassageNumber(32);
    tissue.setTimesReceived(2);
    tissue.setTubeNumber(3);
    return tissue;
}

Example 3 with TissueOrigin

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

the class Dtos method to.

public static TissueOrigin to(TissueOriginDto from) {
    TissueOrigin to = new TissueOriginImpl();
    if (from.getId() != null)
        to.setId(from.getId());
    setString(to::setAlias, from.getAlias());
    setString(to::setDescription, from.getDescription());
    return to;
}

Example 4 with TissueOrigin

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

the class HibernateTissueOriginDaoIT method testGetByAlias.

@Test
public void testGetByAlias() throws Exception {
    String alias = "Test Origin";
    TissueOrigin origin = getTestSubject().getByAlias(alias);
    assertNotNull(origin);
    assertEquals(alias, origin.getAlias());
}

Example 5 with TissueOrigin

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

the class Dtos method toTissueSample.

private static SampleTissue toTissueSample(@Nonnull SampleTissueDto from) {
    SampleTissue to = new SampleTissueImpl();
    to.setPassageNumber(from.getPassageNumber());
    to.setTimesReceived(from.getTimesReceived());
    to.setTubeNumber(from.getTubeNumber());
    to.setRegion(nullifyStringIfBlank(from.getRegion()));
    to.setSecondaryIdentifier(from.getSecondaryIdentifier());
    if (from.getTissueOriginId() != null) {
        TissueOrigin tissueOrigin = new TissueOriginImpl();
        tissueOrigin.setId(from.getTissueOriginId());
        to.setTissueOrigin(tissueOrigin);
    }
    if (from.getTissueTypeId() != null) {
        TissueType tissueType = new TissueTypeImpl();
        tissueType.setId(from.getTissueTypeId());
        to.setTissueType(tissueType);
    }
    if (from.getTissueMaterialId() != null) {
        TissueMaterial tissueMaterial = new TissueMaterialImpl();
        tissueMaterial.setId(from.getTissueMaterialId());
        to.setTissueMaterial(tissueMaterial);
    }
    if (from.getLabId() != null) {
        Lab lab = new LabImpl();
        lab.setId(from.getLabId());
        to.setLab(lab);
    }
    setString(to::setTimepoint, from.getTimepoint());
    return to;
}