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

Example 1 with Subproject

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

the class Dtos method toDetailedSample.

private static DetailedSample toDetailedSample(@Nonnull DetailedSampleDto from) {
    DetailedSample to = null;
    if (from.getClass() == SampleIdentityDto.class) {
        to = toIdentitySample((SampleIdentityDto) from);
    } else if (from.getClass() == SampleTissueDto.class) {
        to = toTissueSample((SampleTissueDto) from);
    } else if (from instanceof SampleTissueProcessingDto) {
        to = toTissueProcessingSample((SampleTissueProcessingDto) from);
    } else if (from instanceof SampleAliquotDto) {
        to = toAliquotSample((SampleAliquotDto) from);
    } else if (from instanceof SampleStockDto) {
        to = toStockSample((SampleStockDto) from);
    } else {
        to = new DetailedSampleImpl();
    }
    if (from.getSubprojectId() != null) {
        Subproject subproject = new SubprojectImpl();
        subproject.setId(from.getSubprojectId());
        to.setSubproject(subproject);
    }
    if (from.getSampleClassId() != null) {
        SampleClass sampleClass = new SampleClassImpl();
        sampleClass.setId(from.getSampleClassId());
        to.setSampleClass(sampleClass);
    }
    to.setGroupId(nullifyStringIfBlank(from.getGroupId()));
    to.setGroupDescription(nullifyStringIfBlank(from.getGroupDescription()));
    to.setSynthetic(from.getSynthetic());
    to.setCreationDate(LimsUtils.isStringEmptyOrNull(from.getCreationDate()) ? null : parseDate(from.getCreationDate()));
    if (from.getIdentityId() != null) {
        to.setIdentityId(from.getIdentityId());
    }
    to.setNonStandardAlias(from.getNonStandardAlias());
    to.setParent(getParent(from));
    setBigDecimal(to::setVolumeUsed, from.getVolumeUsed());
    setBigDecimal(to::setNgUsed, from.getNgUsed());
    return to;
}

Example 2 with Subproject

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

the class HibernateSubprojectDaoIT method testGetByProjectAndAlias.

@Test
public void testGetByProjectAndAlias() throws Exception {
    Project project = (Project) currentSession().get(ProjectImpl.class, 2L);
    String existingAlias = "Meh";
    Subproject existing = getTestSubject().getByProjectAndAlias(project, existingAlias);
    assertNotNull(existing);
    assertEquals(existingAlias, existing.getAlias());
    assertNull(getTestSubject().getByProjectAndAlias(project, "doesnotexist"));
}

Example 3 with Subproject

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

the class Dtos method to.

public static Subproject to(@Nonnull SubprojectDto from) {
    Subproject to = new SubprojectImpl();
    setLong(to::setId, from.getId(), false);
    setString(to::setAlias, from.getAlias());
    setString(to::setDescription, from.getDescription());
    setBoolean(to::setPriority, from.getPriority(), true);
    setObject(to::setReferenceGenome, ReferenceGenomeImpl::new, from.getReferenceGenomeId());
    setObject(to::setParentProject, ProjectImpl::new, from.getParentProjectId());
    return to;
}

Example 4 with Subproject

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

the class EditProjectController method setupForm.

private ModelAndView setupForm(Project project, ModelMap model) throws IOException {
    if (project.isSaved()) {
        Collection<Subproject> subprojects = subprojectService.listByProjectId(project.getId());
        model.put("subprojects", Dtos.asSubprojectDtos(subprojects));
        model.put("title", "Project " + project.getId());
        MisoWebUtils.addIssues(issueTrackerManager, () -> issueTrackerManager.getIssuesByTag(project.getShortName()), model);
        model.put("projectReportLinks", externalUriBuilder.getUris(project));
    }
    model.put("project", project);
    ObjectMapper mapper = new ObjectMapper();
    model.put("projectDto", mapper.writeValueAsString(Dtos.asDto(project)));
    ObjectNode formConfig = mapper.createObjectNode();
    MisoWebUtils.addJsonArray(mapper, formConfig, "statusOptions", Arrays.asList(StatusType.values()), StatusType::getKey);
    ObjectNode namingConfig = formConfig.putObject("naming");
    addNamingSchemeConfig(namingConfig, "primary", namingSchemeHolder.getPrimary(), project);
    addNamingSchemeConfig(namingConfig, "secondary", namingSchemeHolder.getSecondary(), project);
    model.put("formConfig", mapper.writeValueAsString(formConfig));
    return new ModelAndView("/WEB-INF/pages/editProject.jsp", model);
}

Example 5 with Subproject

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

the class HibernateSubprojectDaoIT method getCreateItem.

@Override
public Subproject getCreateItem() {
    Subproject subproject = new SubprojectImpl();
    subproject.setAlias("Exciting");
    subproject.setPriority(true);
    Project project = (Project) currentSession().get(ProjectImpl.class, 2L);
    subproject.setParentProject(project);
    ReferenceGenome reference = (ReferenceGenome) currentSession().get(ReferenceGenomeImpl.class, 1L);
    subproject.setReferenceGenome(reference);
    User user = (User) currentSession().get(UserImpl.class, 1L);
    subproject.setChangeDetails(user);
    return subproject;
}