@RequestMapping(value = "bloodTypingRuleSummary", method = RequestMethod.GET)
public ModelAndView getBloodTypingRuleSummary(
HttpServletRequest request, @RequestParam(value = "bloodTypingRuleId") Integer ruleId) {
ModelAndView mv = new ModelAndView("admin/bloodTypingRuleSummary");
BloodTestingRuleViewModel bloodTypingRule;
bloodTypingRule =
new BloodTestingRuleViewModel(bloodTestingRepository.getBloodTestingRuleById(ruleId));
mv.addObject("bloodTypingRule", bloodTypingRule);
mv.addObject("refreshUrl", getUrl(request));
List<BloodTest> bloodTypingTests = bloodTestingRepository.getBloodTypingTests();
mv.addObject("bloodTypingTests", bloodTypingTests);
mv.addObject("bloodTypingTestsMap", getBloodTypingTestsAsMap(bloodTypingTests));
return mv;
}
@RequestMapping(value = "saveNewBloodTypingRule", method = RequestMethod.POST)
public @ResponseBody Map<String, Object> saveNewBloodTypingRule(
HttpServletRequest request,
HttpServletResponse response,
@RequestParam("newBloodTypingRule") String newBloodTypingRuleAsJsonStr) {
Map<String, Object> m = new HashMap<String, Object>();
ObjectMapper mapper = new ObjectMapper();
boolean success = false;
try {
Map<String, Object> newBloodTypingRuleAsMap;
newBloodTypingRuleAsMap = mapper.readValue(newBloodTypingRuleAsJsonStr, HashMap.class);
bloodTestingRepository.saveNewBloodTypingRule(newBloodTypingRuleAsMap);
success = true;
} catch (JsonParseException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (JsonMappingException e) {
// TODO Auto-generated catch block
e.printStackTrace();
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
}
if (!success) response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
return m;
}
@RequestMapping(value = "deleteBloodTypingRule", method = RequestMethod.POST)
public @ResponseBody Map<String, Object> deleteBloodTypingRule(
HttpServletRequest request, @RequestParam(value = "bloodTypingRuleId") Integer ruleId) {
Map<String, Object> m = new HashMap<String, Object>();
bloodTestingRepository.deleteBloodTestingRule(ruleId);
return m;
}
public List<BloodTestViewModel> getBloodTestsOnPlate() {
List<BloodTestViewModel> tests = new ArrayList<BloodTestViewModel>();
for (BloodTest rawBloodTest :
bloodTestingRepository.getBloodTestsOfType(BloodTestType.BASIC_BLOODTYPING)) {
tests.add(new BloodTestViewModel(rawBloodTest));
}
return tests;
}
@RequestMapping(value = "/bloodTypingWorksheetGenerator", method = RequestMethod.GET)
public ModelAndView getBloodTypingWorksheet(HttpServletRequest request) {
ModelAndView mv = new ModelAndView("bloodtesting/bloodTypingWorksheetForm");
Map<String, Object> tips = new HashMap<String, Object>();
utilController.addTipsToModel(tips, "bloodtyping.plate.step1");
mv.addObject("tips", tips);
mv.addObject("plate", bloodTestingRepository.getPlate("bloodtyping"));
mv.addObject("refreshUrl", "bloodTypingWorksheetGenerator.html");
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 = "/getBloodTypingStatusForCollections", method = RequestMethod.GET)
public ModelAndView getBloodTypingStatusForCollections(
HttpServletRequest request,
HttpServletResponse response,
@RequestParam(value = "collectionIds") String collectionIdsParam) {
ModelAndView mv = new ModelAndView();
String[] collectionIds = collectionIdsParam.split(",");
Map<String, Object> results =
bloodTestingRepository.getAllTestsStatusForCollections(Arrays.asList(collectionIds));
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"));
// depend on the getBloodTypingTestStatus() method to return collections, blood typing output as
// a linked hashmap so that iteration is done in the same order as the collections in the well
mv.addObject("collections", results.get("collections"));
mv.addObject("bloodTypingOutput", results.get("bloodTestingResults"));
mv.addObject("success", true);
mv.setViewName("bloodtesting/bloodTypingResultsForCollections");
return mv;
}
@RequestMapping(value = "/saveAdditionalBloodTypingTests", method = RequestMethod.POST)
public @ResponseBody Map<String, Object> saveAdditionalBloodTypingTests(
HttpServletRequest request,
HttpServletResponse response,
@RequestParam(value = "collectionId") String collectionId,
@RequestParam(value = "saveTestsData") String saveTestsDataStr,
@RequestParam(value = "saveUninterpretableResults") boolean saveUninterpretableResults) {
Map<String, Object> m = new HashMap<String, Object>();
try {
Map<Long, Map<Long, String>> bloodTypingTestResultsMap =
new HashMap<Long, Map<Long, String>>();
Map<Long, String> saveTestsDataWithLong = new HashMap<Long, String>();
ObjectMapper mapper = new ObjectMapper();
Map<String, String> saveTestsData = mapper.readValue(saveTestsDataStr, HashMap.class);
for (String testIdStr : saveTestsData.keySet()) {
saveTestsDataWithLong.put(Long.parseLong(testIdStr), saveTestsData.get(testIdStr));
}
bloodTypingTestResultsMap.put(Long.parseLong(collectionId), saveTestsDataWithLong);
Map<String, Object> results =
bloodTestingRepository.saveBloodTestingResults(
bloodTypingTestResultsMap, saveUninterpretableResults);
Map<Long, Object> errorMap = (Map<Long, Object>) results.get("errors");
System.out.println(errorMap);
if (errorMap != null && !errorMap.isEmpty()) {
response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
Map<Long, String> errorsForCollection =
(Map<Long, String>) errorMap.get(Long.parseLong(collectionId));
if (errorsForCollection != null
&& errorsForCollection.size() == 1
&& errorsForCollection.containsKey((long) -1)) m.put("uninterpretable", true);
else m.put("invalidResults", true);
}
} catch (Exception ex) {
ex.printStackTrace();
response.setStatus(HttpServletResponse.SC_BAD_REQUEST);
}
return m;
}
public void updateLabSetup(Map<String, String> params) {
Map<String, String> configProperties = new HashMap<String, String>();
BloodTypingMechanism bloodTypingMechanism =
BloodTypingMechanism.valueOf(params.get("bloodTypingMechanism"));
switch (bloodTypingMechanism) {
case BLOODTYPING_TEST_RESULTS_ELISA:
configProperties.put(
"bloodTypingContext", BloodTestContext.RECORD_BLOOD_TYPING_TESTS.toString());
bloodTestingRepository.activateTests(BloodTestContext.RECORD_BLOOD_TYPING_TESTS);
bloodTestingRepository.deactivateTests(BloodTestContext.RECORD_BLOOD_TYPING_OUTCOMES);
configProperties.put("bloodTypingElisa", "true");
configProperties.put("bloodTypingWorksheets", "false");
break;
case BLOODTYPING_TEST_RESULTS_WORKSHEETS:
configProperties.put(
"bloodTypingContext", BloodTestContext.RECORD_BLOOD_TYPING_TESTS.toString());
bloodTestingRepository.activateTests(BloodTestContext.RECORD_BLOOD_TYPING_TESTS);
bloodTestingRepository.deactivateTests(BloodTestContext.RECORD_BLOOD_TYPING_OUTCOMES);
configProperties.put("bloodTypingElisa", "false");
configProperties.put("bloodTypingWorksheets", "true");
break;
case BLOODTYPING_OUTCOMES_WORKSHEETS:
configProperties.put(
"bloodTypingContext", BloodTestContext.RECORD_BLOOD_TYPING_OUTCOMES.toString());
bloodTestingRepository.activateTests(BloodTestContext.RECORD_BLOOD_TYPING_OUTCOMES);
bloodTestingRepository.deactivateTests(BloodTestContext.RECORD_BLOOD_TYPING_TESTS);
configProperties.put("bloodTypingElisa", "false");
configProperties.put("bloodTypingWorksheets", "true");
break;
}
configProperties.put("bloodTypingMechanism", bloodTypingMechanism.toString());
TTIMechanism ttiMechanism = TTIMechanism.valueOf(params.get("ttiMechanism"));
switch (ttiMechanism) {
case TTI_ELISA:
configProperties.put("ttiElisa", "true");
configProperties.put("ttiWorksheets", "false");
configProperties.put("recordMachineReadingsForTTI", "true");
break;
case TTI_WORKSHEETS:
configProperties.put("ttiElisa", "false");
configProperties.put("ttiWorksheets", "true");
configProperties.put("recordMachineReadingsForTTI", "false");
break;
}
if (configProperties.get("ttiWorksheets").equals("false")
&& configProperties.get("bloodTypingWorksheets").equals("false")) {
configProperties.put("useWorksheets", "false");
} else {
configProperties.put("useWorksheets", "true");
}
configProperties.put("ttiMechanism", ttiMechanism.toString());
configProperties.put("recordUsage", params.get("recordUsage"));
if (params.get("recordUsage").equals("false")) configProperties.put("usageTabEnabled", "false");
else configProperties.put("usageTabEnabled", "true");
CrossmatchProcedure crossmatchProcedure =
CrossmatchProcedure.valueOf(params.get("crossmatchProcedure"));
switch (crossmatchProcedure) {
case CROSSMATCH_NOT_DONE:
configProperties.put("showCrossmatchConfirmation", "false");
configProperties.put("allowSkipCrossmatch", "true");
break;
case CROSSMATCH_DONE_CAN_SKIP:
configProperties.put("showCrossmatchConfirmation", "true");
configProperties.put("allowSkipCrossmatch", "true");
break;
case CROSSMATCH_DONE_CANNOT_SKIP:
configProperties.put("showCrossmatchConfirmation", "true");
configProperties.put("allowSkipCrossmatch", "false");
break;
}
configProperties.put("crossmatchProcedure", crossmatchProcedure.toString());
genericConfigRepository.updateConfigProperties("labsetup", configProperties);
}
@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;
}
