@RequestMapping(value = "/showCollectionSummaryForTesting", method = RequestMethod.GET)
public ModelAndView showCollectionSummaryForTesting(
HttpServletRequest request,
HttpServletResponse response,
@RequestParam(value = "collectionId") String collectionId) {
ModelAndView mv = new ModelAndView();
collectionId = collectionId.trim();
Long collectedSampleId = Long.parseLong(collectionId);
CollectedSample collectedSample =
collectedSampleRepository.findCollectedSampleById(collectedSampleId);
mv.addObject("collection", new CollectedSampleViewModel(collectedSample));
mv.addObject("collectionId", collectedSample.getId());
mv.addObject("collectionFields", utilController.getFormFieldsForForm("collectedSample"));
mv.setViewName("bloodtesting/collectionSummaryForBloodTesting");
mv.addObject("refreshUrl", getUrl(request));
return mv;
}
@RequestMapping(value = "/showBloodTypingResultsForCollection", method = RequestMethod.GET)
public ModelAndView showBloodTypingResultsForCollection(
HttpServletRequest request,
HttpServletResponse response,
@RequestParam(value = "collectionId") String collectionId) {
ModelAndView mv = new ModelAndView();
collectionId = collectionId.trim();
Long collectedSampleId = Long.parseLong(collectionId);
CollectedSample collectedSample =
collectedSampleRepository.findCollectedSampleById(collectedSampleId);
BloodTestingRuleResult ruleResult =
bloodTestingRepository.getAllTestsStatusForCollection(collectedSampleId);
mv.addObject("collection", new CollectedSampleViewModel(collectedSample));
mv.addObject("collectionId", collectedSample.getId());
mv.addObject("bloodTypingOutputForCollection", ruleResult);
mv.addObject("collectionFields", utilController.getFormFieldsForForm("collectedSample"));
List<BloodTest> bloodTypingTests = bloodTestingRepository.getBloodTypingTests();
Map<String, BloodTest> bloodTypingTestsMap = new LinkedHashMap<String, BloodTest>();
for (BloodTest bloodTypingTest : bloodTypingTests) {
bloodTypingTestsMap.put(bloodTypingTest.getId().toString(), bloodTypingTest);
}
mv.addObject("allBloodTypingTests", bloodTypingTestsMap);
List<BloodTest> allBloodTypingTests = bloodTestingRepository.getBloodTypingTests();
Map<String, BloodTest> allBloodTypingTestsMap = new TreeMap<String, BloodTest>();
for (BloodTest bloodTypingTest : allBloodTypingTests) {
allBloodTypingTestsMap.put(bloodTypingTest.getId().toString(), bloodTypingTest);
}
mv.addObject("allBloodTypingTests", allBloodTypingTestsMap);
mv.setViewName("bloodtesting/bloodTypingSummaryCollection");
mv.addObject("refreshUrl", getUrl(request));
return mv;
}
@RequestMapping(value = "/addCollectionsToBloodTypingPlate")
public ModelAndView addCollectionsToBloodTypingPlate(
HttpServletRequest request,
HttpServletResponse response,
@RequestParam(value = "collectionNumbers[]") List<String> collectionNumbers) {
// here the key of the map corresponds to the index of the
// collection number in the parameter collectionNumbers
// corresponding to the collected sample in the value of the map
List<CollectedSample> collections =
collectedSampleRepository.verifyCollectionNumbers(collectionNumbers);
int numErrors = 0;
int numValid = 0;
for (CollectedSample c : collections) {
if (c == null) numErrors++;
else numValid++;
}
ModelAndView mv = new ModelAndView();
mv.addObject("collections", collections);
mv.addObject("collectionNumbers", StringUtils.join(collectionNumbers, ","));
mv.addObject("plate", bloodTestingRepository.getPlate("bloodtyping"));
Map<String, Object> tips = new HashMap<String, Object>();
if (numErrors > 0 || numValid == 0) {
mv.addObject("success", false);
mv.setViewName("bloodtesting/bloodTypingWorksheetForm");
mv.addObject("refreshUrl", "bloodTypingWorksheetGenerator.html");
utilController.addTipsToModel(tips, "bloodtyping.plate.step1");
response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
mv.addObject("errorMessage", "Please fix the errors noted. Some collections do not exist.");
} else {
// this is a map with id of the collected sample as the key
Map<Long, CollectedSample> collectionMap = new HashMap<Long, CollectedSample>();
for (CollectedSample c : collections) {
collectionMap.put(c.getId(), c);
}
mv.addObject("collectionMap", collectionMap);
// no errors but the user should be warned if there are any collections for which testing
// partly done
Map<Long, BloodTestingRuleResult> collectionsWithBloodTypingTests =
collectedSampleRepository.filterCollectionsWithBloodTypingResults(collections);
mv.addObject("collectionsWithBloodTypingTests", collectionsWithBloodTypingTests);
Map<String, BloodTest> bloodTypingTestsMap = new HashMap<String, BloodTest>();
for (BloodTest bloodTypingTest : bloodTestingRepository.getBloodTypingTests()) {
bloodTypingTestsMap.put(bloodTypingTest.getId().toString(), bloodTypingTest);
}
mv.addObject("bloodTypingTests", bloodTypingTestsMap);
mv.addObject("success", true);
mv.setViewName("bloodtesting/bloodTypingWells");
mv.addObject("refreshUrl", getUrl(request));
mv.addObject("changeCollectionsUrl", "bloodTypingWorksheetGenerator.html");
utilController.addTipsToModel(tips, "bloodtyping.plate.step2");
mv.addObject("bloodTestsOnPlate", getBloodTestsOnPlate());
mv.addObject("bloodTypingConfig", genericConfigRepository.getConfigProperties("bloodTyping"));
}
mv.addObject("tips", tips);
return mv;
}
@SuppressWarnings("unchecked")
@RequestMapping(value = "/saveBloodTypingTests", method = RequestMethod.POST)
public ModelAndView saveBloodTypingTests(
HttpServletRequest request,
HttpServletResponse response,
@RequestParam(value = "bloodTypingTests") String bloodTypingTests,
@RequestParam(value = "collectionNumbers[]") List<String> collectionNumbers,
@RequestParam(value = "refreshUrl") String refreshUrl,
@RequestParam(value = "saveUninterpretableResults") boolean saveUninterpretableResults) {
ModelAndView mv = new ModelAndView();
List<CollectedSample> collections =
collectedSampleRepository.verifyCollectionNumbers(collectionNumbers);
mv.addObject("collectionNumbers", StringUtils.join(collectionNumbers, ","));
mv.addObject("collections", collections);
Map<Long, Map<Long, String>> bloodTypingTestResults = parseBloodTestResults(bloodTypingTests);
Map<Long, Map<Long, String>> errorMap = null;
mv.addObject("bloodTypingTestResults", bloodTypingTestResults);
boolean success = true;
Map<String, Object> results = null;
try {
results =
bloodTestingRepository.saveBloodTestingResults(
bloodTypingTestResults, saveUninterpretableResults);
if (results != null) errorMap = (Map<Long, Map<Long, String>>) results.get("errors");
} catch (Exception ex) {
ex.printStackTrace();
success = false;
}
if (errorMap != null && !errorMap.isEmpty()) success = false;
Map<String, Object> tips = new HashMap<String, Object>();
System.out.println(errorMap);
if (success) {
List<BloodTest> allBloodTypingTests = bloodTestingRepository.getBloodTypingTests();
Map<String, BloodTest> allBloodTypingTestsMap = new HashMap<String, BloodTest>();
for (BloodTest allBloodTypingTest : allBloodTypingTests) {
allBloodTypingTestsMap.put(allBloodTypingTest.getId().toString(), allBloodTypingTest);
}
mv.addObject("allBloodTypingTests", allBloodTypingTestsMap);
mv.addObject("collectionFields", utilController.getFormFieldsForForm("collectedSample"));
mv.addObject("collectionsByCollectionId", results.get("collections"));
List<String> collectionIds = new ArrayList<String>();
for (CollectedSample collection : collections) {
collectionIds.add(collection.getId().toString());
}
mv.addObject("collectionIds", StringUtils.join(collectionIds, ","));
mv.addObject("bloodTypingOutput", results.get("bloodTestingResults"));
mv.addObject("success", success);
mv.setViewName("bloodtesting/bloodTypingWellsSuccess");
} else {
// errors found
mv.addObject("plate", bloodTestingRepository.getPlate("bloodtyping"));
mv.addObject("errorMap", errorMap);
mv.addObject("bloodTypingTests", bloodTypingTests);
mv.addObject("success", success);
mv.addObject("refreshUrl", refreshUrl);
mv.addObject("changeCollectionsUrl", "bloodTypingWorksheetGenerator.html");
mv.addObject(
"collectionsWithUninterpretableResults",
results.get("collectionsWithUninterpretableResults"));
mv.addObject("collectionsByCollectionId", results.get("collections"));
utilController.addTipsToModel(tips, "bloodtyping.plate.step2");
mv.addObject("bloodTestsOnPlate", getBloodTestsOnPlate());
mv.addObject("bloodTypingConfig", genericConfigRepository.getConfigProperties("bloodTyping"));
mv.addObject(
"errorMessage",
"There were errors adding tests. Please verify the results in the wells highlighted in red.");
mv.setViewName("bloodtesting/bloodTypingWellsError");
response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
}
return mv;
}