Package com.infoclinika.mssharing.model.helper

Examples of com.infoclinika.mssharing.model.helper.DictionaryItem

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    @Override
    public ImmutableSortedSet<DictionaryItem> vendors() {
        return from(vendorRepository.findAll()).transform(new Function<Vendor, DictionaryItem>() {
            @Override
            public DictionaryItem apply(Vendor input) {
                return new DictionaryItem(input.getId(), input.getName());
            }
        }).toImmutableSortedSet(COMPARATOR);
    }
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    @Override
    public ImmutableSortedSet<DictionaryItem> vendorsWithFolderArchiveUploadSupport() {
        return from(vendorRepository.findWithFolderArchiveUploadSupport()).transform(new Function<Vendor, DictionaryItem>() {
            @Override
            public DictionaryItem apply(Vendor input) {
                return new DictionaryItem(input.getId(), input.getName());
            }
        }).toImmutableSortedSet(COMPARATOR);
    }
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    @Override
    public ImmutableSortedSet<DictionaryItem> models(long vendor) {
        return from(instrumentModelRepository.findModelsByVendor(vendor)).transform(new Function<InstrumentModel, DictionaryItem>() {
            @Override
            public DictionaryItem apply(InstrumentModel input) {
                return new DictionaryItem(input.getId(), input.getName());
            }
        }).toImmutableSortedSet(new Comparator<DictionaryItem>() {
            @Override
            public int compare(DictionaryItem o1, DictionaryItem o2) {
                return o1.name.compareTo(o2.name);
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        kate = userManagement.createPersonAndApproveMembership(new UserManagement.PersonInfo(anyStr(), anyStr(), anyStr()), anyStr(), lab, null);
        instrumentManagement.newInstrument(bob, lab, anyInstrumentModel(), new InstrumentManagement.InstrumentDetails(anyStr(), anyStr(), anyStr(), anyStr()));
    }

    private long experiment(long proj, String name, String description) {
        final DictionaryItem type = experimentCreationHelper.experimentTypes().iterator().next();
        final ExperimentCreationHelper.WorkflowTypeItem workflowType = experimentCreationHelper.workflowTypes(type.id).iterator().next();
        DictionaryItem specie = experimentCreationHelper.species().iterator().next();
        final long file = saveFile();
        return studyManagement.newExperiment(bob, proj, lab,
                new StudyManagement.ExperimentInfo(name, description, workflowType.id, specie.id), false,
                new StudyManagement.Restriction(experimentCreationHelper.availableInstrumentModels(bob, null).get(0).id, Optional.<Long>absent()),
                Collections.<StudyManagement.MetaFactor>emptyList(), noFactoredFile(file), new AnalysisBounds(), new ArrayList<Double>());
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    @Test(dependsOnMethods = "testUserCanCreateInstruments")
    public void testUserCanReadInstrumentDetails() {
        final long bob = uc.createLab3AndBob();

        final DictionaryItem vendor = instrumentCreationHelper.vendors().first();
        final DictionaryItem modelItem = instrumentCreationHelper.models(vendor.id).first();
        final Long instrument = instrumentManagement.newInstrument(bob, uc.getLab3(), modelItem.id, instrumentDetails()).get();

        final DetailsReader.InstrumentItem instrumentItem = detailsReader.readInstrument(bob, instrument);

        assertEquals(instrumentItem.model, modelItem.name);
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        final long instrument = createInstrumentByModel(bob, uc.getLab3(), model);
        uc.saveFile(bob, instrument);
        assertNumberOfAvailableInstrumentTypes(bob, 1);

        final Iterable<DictionaryItem> instrumentTypes = experimentCreationHelper.availableInstrumentModels(bob, null);
        final DictionaryItem modelItem = instrumentTypes.iterator().next();

        assertNotNull(modelItem.name);
        assertTrue(modelItem.name.contains(" - "));
    }
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        assertThat(types, isDictionaryOf("Unspecified", "Proteomics", "Metabolomics", "DMPK"));
    }

    @Test
    public void testProteomicsWorkflowTypes() {
        DictionaryItem experimentType = getTypeWithName("Proteomics");
        ImmutableList<ExperimentCreationHelper.WorkflowTypeItem> workflowTypes = helper.workflowTypes(experimentType.id);
        assertThat(workflowTypes, contains(
                workflowType("Unspecified", true),
                workflowType("Label Free Quantitative", true),
                workflowType("MSe", true),
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                workflowType("iTRAQ", true)));
    }

    @Test
    public void testMetabolomicsWorkflowTypes() {
        DictionaryItem experimentType = getTypeWithName("Metabolomics");
        ImmutableList<ExperimentCreationHelper.WorkflowTypeItem> workflowTypes = helper.workflowTypes(experimentType.id);
        assertThat(workflowTypes, contains(
                workflowType("Unspecified", false),
                workflowType("Label Free Differential", true)));
    }
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                workflowType("Label Free Differential", true)));
    }

    @Test
    public void testDMPKWorkflowTypes() {
        DictionaryItem experimentType = getTypeWithName("DMPK");
        ImmutableList<ExperimentCreationHelper.WorkflowTypeItem> workflowTypes = helper.workflowTypes(experimentType.id);
        assertThat(workflowTypes, contains(
                workflowType("Unspecified", false),
                workflowType("Label Free Differential", false)));
    }
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                workflowType("Label Free Differential", false)));
    }

    @Test
    public void testUnspecifiedWorkflowTypes() {
        DictionaryItem experimentType = getTypeWithName("Unspecified");
        ImmutableList<ExperimentCreationHelper.WorkflowTypeItem> workflowTypes = helper.workflowTypes(experimentType.id);
        assertThat(workflowTypes, contains(
                workflowType("Unspecified", true)));
    }
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Related Classes of com.infoclinika.mssharing.model.helper.DictionaryItem

  • com.infoclinika.mssharing.model.internal.helper.InstrumentCreationHelperImpl
  • com.infoclinika.mssharing.model.test.instrument.CreatingInstrumentTest
  • com.infoclinika.mssharing.search.SearcherImplTest
  • com.infoclinika.mssharing.web.demo.SeedDataCreatorTest
  • com.infoclinika.mssharing.web.downloader.BulkDownloadHelper
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