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

Example 26 with SampleClass

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

the class DefaultSampleClassService method collectValidationErrors.

@Override
protected void collectValidationErrors(SampleClass object, SampleClass beforeChange, List<ValidationError> errors) throws IOException {
    long usage = beforeChange == null ? 0L : sampleClassDao.getUsage(beforeChange);
    if (beforeChange == null && SampleIdentity.CATEGORY_NAME.equals(object.getSampleCategory()) && list().stream().anyMatch(sampleClass -> SampleIdentity.CATEGORY_NAME.equals(sampleClass.getSampleCategory()))) {
        errors.add(new ValidationError("sampleCategory", "There can be only one identity class"));
    }
    if (usage > 0L) {
        if (ValidationUtils.isSetAndChanged(SampleClass::getSampleCategory, object, beforeChange)) {
            errors.add(new ValidationError("sampleCategory", String.format("Cannot change because this sample class is already used by %d samples", usage)));
        }
    }
    if (!SampleClass.CATEGORIES.contains(object.getSampleCategory())) {
        errors.add(new ValidationError("sampleCategory", "Invalid category"));
    } else if (object.getSampleSubcategory() != null && !SampleClass.SUBCATEGORIES.get(object.getSampleCategory()).contains(object.getSampleSubcategory())) {
        errors.add(new ValidationError("sampleSubcategory", "Invalid subcategory"));
    }
    if (beforeChange == null && !object.getChildRelationships().isEmpty()) {
        errors.add(new ValidationError("Cannot specify child relationships for new sample class"));
    }
    validateParentRelationships(object, errors);
    if (object.isArchived()) {
        if (object.getParentRelationships().stream().anyMatch(relationship -> relationship.isArchived())) {
            errors.add(new ValidationError("archived", "Cannot archive class due to unarchived parent relationships"));
        }
        if (object.getChildRelationships().stream().anyMatch(relationship -> relationship.isArchived())) {
            errors.add(new ValidationError("archived", "Cannot archive class due to unarchived child relationships"));
        }
    }
}

Example 27 with SampleClass

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

the class DefaultSampleClassService method inferParentFromChild.

@Override
public SampleClass inferParentFromChild(long childClassId, String childCategory, String parentCategory) throws IOException {
    SampleClass childClass = getNotNullClass(childClassId);
    if (!childClass.getSampleCategory().equals(childCategory)) {
        throw new IllegalArgumentException(String.format("Sample class %s is not a valid %s class.", childClassId, childCategory));
    }
    List<SampleClass> parentClasses = sampleValidRelationshipService.getAll().stream().filter(relationship -> !relationship.isArchived() && !relationship.getParent().isArchived() && relationship.getChild().getId() == childClass.getId() && relationship.getParent().getSampleCategory().equals(parentCategory)).map(SampleValidRelationship::getParent).collect(Collectors.toList());
    return singleResult(parentClasses, childClass, parentCategory);
}

Example 28 with SampleClass

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

the class OicrSampleAliasGeneratorTest method makeAliquotFromStock.

private SampleAliquot makeAliquotFromStock() throws Exception {
    DetailedSample lcm = makeLcmTube();
    lcm.setAlias("PROJ_0001_nn_n_nn_1-1_LCM02");
    SampleStock stock = new SampleStockImpl();
    stock.setParent(lcm);
    SampleClass stockSc = new SampleClassImpl();
    stockSc.setSampleCategory(SampleStock.CATEGORY_NAME);
    stockSc.setSuffix("R_S");
    stock.setSampleClass(stockSc);
    stock.setSiblingNumber(4);
    stock.setAlias("PROJ_0001_nn_n_nn_1-1_R_S4");
    SampleAliquot aliquot = new SampleAliquotImpl();
    aliquot.setParent(stock);
    SampleClass aliquotSc = new SampleClassImpl();
    aliquotSc.setSuffix("R_");
    aliquotSc.setSampleCategory(SampleAliquot.CATEGORY_NAME);
    aliquot.setSampleClass(aliquotSc);
    aliquot.setSiblingNumber(12);
    return aliquot;
}

Example 29 with SampleClass

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

the class OicrSampleAliasGeneratorTest method makeLcmTube.

private SampleTissuePiece makeLcmTube() {
    SampleTissuePiece lcmTube = new SampleTissuePieceImpl();
    SampleTissue tissue = makeMinimalTissue();
    tissue.setAlias("PROJ_0001_nn_n_nn_1-1");
    lcmTube.setParent(tissue);
    lcmTube.setSiblingNumber(2);
    SampleClass sc = new SampleClassImpl();
    sc.setSampleCategory(SampleTissueProcessing.CATEGORY_NAME);
    sc.setSuffix("LCM");
    lcmTube.setSampleClass(sc);
    return lcmTube;
}

Example 30 with SampleClass

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

the class OicrSampleAliasGeneratorTest method makeIdentity.

private SampleIdentity makeIdentity() {
    SampleIdentity identity = new SampleIdentityImpl();
    identity.setId(1L);
    identity.setAlias("PROJ_0001");
    SampleClass sc = new SampleClassImpl();
    sc.setSampleCategory(SampleIdentity.CATEGORY_NAME);
    identity.setSampleClass(sc);
    Project proj = new ProjectImpl();
    proj.setId(1L);
    proj.setAlias("PROJ");
    proj.setShortName("PROJ");
    identity.setProject(proj);
    return identity;
}