private List<IdValuePair> getTestsForTypeOfSample(TypeOfSample typeOfSample) { List<Test> testList = TypeOfSampleUtil.getTestListBySampleTypeId(typeOfSample.getId(), false); List<IdValuePair> valueList = new ArrayList<IdValuePair>(); for (Test test : testList) { if (test.getOrderable()) { valueList.add(new IdValuePair(test.getId(), TestService.getUserLocalizedTestName(test))); } } return valueList; }
@Test public void sample_save_should_form_panel_to_sample_associations() throws Exception { testService.createOrUpdate(referenceDataTest); panelService.createOrUpdate(referenceDataPanel); us.mn.state.health.lims.test.valueholder.Test savedTest = testDAO.getTestByName("Test Name"); assertEquals("Test Name", savedTest.getTestName()); assertEquals("New", savedTest.getTestSection().getTestSectionName()); Panel savedPanel = panelDAO.getPanelByName("Panel Name"); assertEquals("Panel Name", savedPanel.getPanelName()); referenceDataSample.addTest( new MinimalResource(referenceDataTest.getId(), referenceDataTest.getName())); referenceDataSample.addPanel( new MinimalResource(referenceDataPanel.getId(), referenceDataPanel.getName())); typeOfSampleService.createOrUpdate(referenceDataSample); TypeOfSample savedSample = typeOfSampleDAO.getTypeOfSampleByUUID(sampleUuid); assertEquals("Sample Name", savedSample.getDescription()); assertEquals("Sample Name", savedSample.getLocalAbbreviation()); TypeOfSampleTest sampleTestAssoc = typeOfSampleTestDAO.getTypeOfSampleTestForTest(savedTest.getId()); assertNotNull(sampleTestAssoc); assertEquals(savedTest.getId(), sampleTestAssoc.getTestId()); assertEquals(savedSample.getId(), sampleTestAssoc.getTypeOfSampleId()); TypeOfSamplePanel samplePanelAssoc = typeOfSamplePanelDao.getTypeOfSamplePanelForPanel(savedPanel.getId()); assertNotNull(samplePanelAssoc); assertEquals(savedPanel.getId(), samplePanelAssoc.getPanelId()); assertEquals(savedSample.getId(), samplePanelAssoc.getTypeOfSampleId()); }
private static List<IdValuePair> createSampleTypeList() { TypeOfSampleDAO typeOfSampleDAO = new TypeOfSampleDAOImpl(); List<TypeOfSample> list = typeOfSampleDAO.getTypesForDomainBySortOrder(TypeOfSampleDAO.SampleDomain.HUMAN); List<IdValuePair> filteredList = new ArrayList<IdValuePair>(); for (TypeOfSample type : list) { if (type.isActive()) { filteredList.add(new IdValuePair(type.getId(), type.getLocalizedName())); } } return filteredList; }
private HashMap populateHumanSampleOneMap( Patient patient, Person person, Provider provider, Person providerPerson, Sample sample, SampleHuman sampleHuman, SampleOrganization sampleOrganization, SampleItem sampleItem, List analyses) { HashMap humanSampleOneMap = new HashMap(); List sampleProjects = new ArrayList(); SampleProject sampleProject = null; SampleProject sampleProject2 = null; sampleProjects = sample.getSampleProjects(); if (sampleProjects != null && sampleProjects.size() > 0) { sampleProject = (SampleProject) sampleProjects.get(0); if (sampleProjects.size() > 1) { sampleProject2 = (SampleProject) sampleProjects.get(1); } } if (sample.getAccessionNumber() != null) { humanSampleOneMap.put("accessionNumber", sample.getAccessionNumber()); } else { humanSampleOneMap.put("accessionNumber", ""); } if (patient.getBirthDateForDisplay() != null) { humanSampleOneMap.put("birthDateForDisplay", patient.getBirthDateForDisplay()); } else { humanSampleOneMap.put("birthDateForDisplay", ""); } if (sample.getCollectionDateForDisplay() != null) { humanSampleOneMap.put("collectionDateForDisplay", sample.getCollectionDateForDisplay()); } else { humanSampleOneMap.put("collectionDateForDisplay", ""); } if (sample.getCollectionTimeForDisplay() != null) { humanSampleOneMap.put("collectionTimeForDisplay", sample.getCollectionTimeForDisplay()); } else { // bugzilla 1894 humanSampleOneMap.put( "collectionTimeForDisplay", SystemConfiguration.getInstance().getHumanSampleOneDefaultCollectionTimeForDisplay()); } // bugzilla 1904 if (patient.getChartNumber() != null) { humanSampleOneMap.put("chartNumber", patient.getChartNumber()); } else { humanSampleOneMap.put("chartNumber", ""); } if (person.getCity() != null) { // bugzilla 1766 humanSampleOneMap.put("city", person.getCity().toUpperCase().trim()); } else { humanSampleOneMap.put("city", ""); } if (sample.getClientReference() != null) { humanSampleOneMap.put("clientReference", sample.getClientReference()); } else { humanSampleOneMap.put("clientReference", ""); } if (patient.getExternalId() != null) { humanSampleOneMap.put("externalId", patient.getExternalId()); } else { humanSampleOneMap.put("externalId", ""); } if (person.getFirstName() != null) { humanSampleOneMap.put("firstName", person.getFirstName()); } else { humanSampleOneMap.put("firstName", ""); } if (patient.getGender() != null) { humanSampleOneMap.put("gender", patient.getGender()); } else { humanSampleOneMap.put("gender", ""); } if (person.getLastName() != null) { humanSampleOneMap.put("lastName", person.getLastName()); } else { humanSampleOneMap.put("lastName", ""); } if (person.getMiddleName() != null) { humanSampleOneMap.put("middleName", person.getMiddleName()); } else { humanSampleOneMap.put("middleName", ""); } if (person.getMultipleUnit() != null) { humanSampleOneMap.put("multipleUnit", person.getMultipleUnit()); } else { humanSampleOneMap.put("multipleUnit", ""); } if (sampleOrganization != null && sampleOrganization.getOrganization() != null) { // bugzilla 2069 humanSampleOneMap.put( "organizationLocalAbbreviation", sampleOrganization.getOrganization().getOrganizationLocalAbbreviation()); humanSampleOneMap.put( "organizationNameForDisplay", sampleOrganization.getOrganization().getOrganizationName()); } else { humanSampleOneMap.put("organizationLocalAbbreviation", ""); humanSampleOneMap.put("organizationNameForDisplay", ""); } if (sampleProject != null && sampleProject.getProject() != null) { // bugzilla 2438 humanSampleOneMap.put("projectId", sampleProject.getProject().getLocalAbbreviation()); // bugzilla 1766 since we capitolize project name do this here // for comparison purposes humanSampleOneMap.put( "projectName", sampleProject.getProject().getProjectName().toUpperCase().trim()); } else { humanSampleOneMap.put("projectId", ""); humanSampleOneMap.put("projectName", ""); } if (sampleProject2 != null && sampleProject2.getProject() != null) { // bugzilla 2438 humanSampleOneMap.put("projectId2", sampleProject2.getProject().getLocalAbbreviation()); // bugzilla 1766 since we capitolize project name do this here // for comparison purposes humanSampleOneMap.put( "projectName2", sampleProject2.getProject().getProjectName().toUpperCase().trim()); } else { humanSampleOneMap.put("projectId2", ""); humanSampleOneMap.put("projectName2", ""); } if (providerPerson.getFirstName() != null) { humanSampleOneMap.put("providerFirstName", providerPerson.getFirstName()); } else { humanSampleOneMap.put("providerFirstName", ""); } if (providerPerson.getLastName() != null) { humanSampleOneMap.put("providerLastName", providerPerson.getLastName()); } else { humanSampleOneMap.put("providerLastName", ""); } if (providerPerson.getWorkPhone() != null) { String storedResult = providerPerson.getWorkPhone(); humanSampleOneMap.put("providerWorkPhone", StringUtil.formatPhoneForDisplay(storedResult)); } else { humanSampleOneMap.put("providerWorkPhone", ""); } if (providerPerson.getWorkPhone() != null) { String storedResult = providerPerson.getWorkPhone(); // bugzilla 2442 String extension = StringUtil.formatExtensionForDisplay(storedResult); humanSampleOneMap.put("providerWorkPhoneExtension", StringUtil.trim(extension)); } else { humanSampleOneMap.put("providerWorkPhoneExtension", ""); } if (sample.getReceivedDateForDisplay() != null) { humanSampleOneMap.put("receivedDateForDisplay", sample.getReceivedDateForDisplay()); } else { humanSampleOneMap.put("receivedDateForDisplay", ""); } if (sample.getReferredCultureFlag() != null) { humanSampleOneMap.put("referredCultureFlag", sample.getReferredCultureFlag()); } else { humanSampleOneMap.put("referredCultureFlag", ""); } if (sampleItem.getSourceOfSample() != null) { SourceOfSample sos = (SourceOfSample) sampleItem.getSourceOfSample(); // bugzilla 1766 humanSampleOneMap.put("sourceOfSampleDesc", sos.getDescription().toUpperCase().trim()); // bugzilla 1465 humanSampleOneMap.put("sourceOfSampleId", sos.getId()); } else { humanSampleOneMap.put("sourceOfSampleDesc", ""); // bugzilla 1465 humanSampleOneMap.put("sourceOfSampleId", ""); } if (sampleItem.getSourceOther() != null) { humanSampleOneMap.put("sourceOther", sampleItem.getSourceOther().trim()); } else { humanSampleOneMap.put("sourceOther", ""); } if (person.getState() != null) { humanSampleOneMap.put("state", person.getState()); } else { humanSampleOneMap.put("state", ""); } if (sample.getStickerReceivedFlag() != null) { humanSampleOneMap.put("stickerReceivedFlag", sample.getStickerReceivedFlag()); } else { humanSampleOneMap.put("stickerReceivedFlag", ""); } if (person.getStreetAddress() != null) { humanSampleOneMap.put("streetAddress", person.getStreetAddress().trim()); } else { humanSampleOneMap.put("streetAddress", ""); } if (sampleItem.getTypeOfSample() != null) { TypeOfSample tos = (TypeOfSample) sampleItem.getTypeOfSample(); // bugzilla 1766 humanSampleOneMap.put("typeOfSampleDesc", tos.getDescription().toUpperCase().trim()); // bugzilla 1465 humanSampleOneMap.put("typeOfSampleId", tos.getId()); } else { humanSampleOneMap.put("typeOfSampleDesc", ""); // bugzilla 1465 humanSampleOneMap.put("typeOfSampleId", ""); } if (person.getZipCode() != null) { humanSampleOneMap.put("zipCode", person.getZipCode().trim()); } else { humanSampleOneMap.put("zipCode", ""); } return humanSampleOneMap; }