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;
}
@Test
public void sample_save_should_form_test_to_sample_associations() throws Exception {
testService.createOrUpdate(referenceDataTest);
us.mn.state.health.lims.test.valueholder.Test savedTest = testDAO.getTestByName("Test Name");
assertEquals("Test Name", savedTest.getTestName());
assertEquals("New", savedTest.getTestSection().getTestSectionName());
referenceDataSample.addTest(
new MinimalResource(referenceDataTest.getId(), referenceDataTest.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());
}
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;
}
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;
}
private ReferralItem getReferralItem(Referral referral) {
boolean allReferralResultsHaveResults = true;
List<ReferralResult> referralResults =
referralResultDAO.getReferralResultsForReferral(referral.getId());
for (ReferralResult referralResult : referralResults) {
if (referralResult.getResult() == null
|| GenericValidator.isBlankOrNull(referralResult.getResult().getValue())) {
allReferralResultsHaveResults = false;
break;
}
}
if (allReferralResultsHaveResults) {
return null;
}
ReferralItem referralItem = new ReferralItem();
AnalysisService analysisService = new AnalysisService(referral.getAnalysis());
referralItem.setCanceled(false);
referralItem.setReferredResultType("N");
referralItem.setAccessionNumber(analysisService.getOrderAccessionNumber());
TypeOfSample typeOfSample = analysisService.getTypeOfSample();
referralItem.setSampleType(typeOfSample.getLocalizedName());
referralItem.setReferringTestName(
TestService.getUserLocalizedTestName(analysisService.getAnalysis().getTest()));
List<Result> resultList = analysisService.getResults();
String resultString = "";
if (!resultList.isEmpty()) {
Result result = resultList.get(0);
resultString = getAppropriateResultValue(resultList);
referralItem.setInLabResultId(result.getId());
}
referralItem.setReferralId(referral.getId());
if (!referralResults.isEmpty()) {
referralResults = setReferralItemForNextTest(referralItem, referralResults);
if (!referralResults.isEmpty()) {
referralItem.setAdditionalTests(getAdditionalReferralTests(referralResults));
}
}
referralItem.setReferralResults(resultString);
referralItem.setReferralDate(DateUtil.convertTimestampToStringDate(referral.getRequestDate()));
referralItem.setReferredSendDate(getSendDateOrDefault(referral));
referralItem.setReferrer(referral.getRequesterName());
referralItem.setReferralReasonId(referral.getReferralReasonId());
referralItem.setTestSelectionList(getTestsForTypeOfSample(typeOfSample));
referralItem.setReferralId(referral.getId());
if (referral.getOrganization() != null) {
referralItem.setReferredInstituteId(referral.getOrganization().getId());
}
String notes = analysisService.getNotesAsString(true, true, "<br/>", false);
if (notes != null) {
referralItem.setPastNotes(notes);
}
return referralItem;
}