private void createUpdateElisaList(List<AnalysisItem> resultItems) {
for (AnalysisItem resultItem : resultItems) {
if (resultItem.getIsAccepted()) {
List<Analysis> acceptedAnalysisList = createAnalysisFromElisaAnalysisItem(resultItem);
for (Analysis analysis : acceptedAnalysisList) {
analysis.setStatusId(StatusService.getInstance().getStatusID(AnalysisStatus.Finalized));
analysisUpdateList.add(analysis);
}
}
if (resultItem.getIsRejected()) {
List<Analysis> rejectedAnalysisList = createAnalysisFromElisaAnalysisItem(resultItem);
for (Analysis analysis : rejectedAnalysisList) {
analysis.setStatusId(
StatusService.getInstance().getStatusID(AnalysisStatus.BiologistRejected));
analysisUpdateList.add(analysis);
}
}
}
}
private void addResultSets(Analysis analysis, Result result) {
Sample sample = analysis.getSampleItem().getSample();
Patient patient = sampleHumanDAO.getPatientForSample(sample);
List<DocumentTrack> documents =
documentTrackDAO.getByTypeRecordAndTable(RESULT_REPORT_ID, RESULT_TABLE_ID, result.getId());
if (documents.isEmpty()) {
newResultSet.add(new ResultSet(result, null, null, patient, sample, null, false));
} else {
modifiedResultSet.add(new ResultSet(result, null, null, patient, sample, null, false));
}
}
private void createUpdateList(List<AnalysisItem> analysisItems, boolean areListeners) {
List<String> analysisIdList = new ArrayList<String>();
for (AnalysisItem analysisItem : analysisItems) {
if (!analysisItem.isReadOnly() && analysisItemWillBeUpdated(analysisItem)) {
AnalysisService analysisService = new AnalysisService(analysisItem.getAnalysisId());
Analysis analysis = analysisService.getAnalysis();
NoteService noteService = new NoteService(analysis);
analysis.setSysUserId(currentUserId);
if (!analysisIdList.contains(analysis.getId())) {
if (analysisItem.getIsAccepted()) {
analysis.setStatusId(StatusService.getInstance().getStatusID(AnalysisStatus.Finalized));
analysis.setReleasedDate(new java.sql.Date(Calendar.getInstance().getTimeInMillis()));
analysisIdList.add(analysis.getId());
analysisUpdateList.add(analysis);
}
if (analysisItem.getIsRejected()) {
analysis.setStatusId(
StatusService.getInstance().getStatusID(AnalysisStatus.BiologistRejected));
analysisIdList.add(analysis.getId());
analysisUpdateList.add(analysis);
}
}
createNeededNotes(analysisItem, noteService);
if (areResults(analysisItem)) {
List<Result> results =
createResultFromAnalysisItem(analysisItem, analysisService, noteService);
for (Result result : results) {
resultUpdateList.add(result);
if (areListeners) {
addResultSets(analysis, result);
}
}
}
}
}
}
public void validateQuantifiableItems(AnalysisItem analysisItem, List<ActionError> errors) {
if (analysisItem.isHasQualifiedResult()
&& isBlankOrNull(analysisItem.getQualifiedResultValue())
&& analysisItemWillBeUpdated(analysisItem)) {
errors.add(new ActionError("errors.missing.result.details", new StringBuilder("Result")));
}
// verify that qualifiedResultValue has been entered if required
if (!isBlankOrNull(analysisItem.getQualifiedDictionaryId())) {
String[] qualifiedDictionaryIds =
analysisItem.getQualifiedDictionaryId().replace("[", "").replace("]", "").split(",");
Set<String> qualifiedDictIdsSet = new HashSet<String>(Arrays.asList(qualifiedDictionaryIds));
if (qualifiedDictIdsSet.contains(analysisItem.getResult())
&& isBlankOrNull(analysisItem.getQualifiedResultValue())) {
errors.add(new ActionError("errors.missing.result.details", new StringBuilder("Result")));
}
}
}
/**
* Creates a GPX-formatted file attachment for the given entry.
*
* @param user
* @param entryId
* @param fileName
* @param activityId
* @param track
* @param track
*/
public void createAttachment(
User user, int entryId, String fileName, String title, String activityId, GpsTrack track)
throws DataAccessException, IOException {
Attachment a = new Attachment();
a.setUserName(user.getUserName());
a.setUserId(user.getUserId());
a.setEntryId(entryId);
a.setFileType("map");
a.setFileName(fileName);
a.setActivityId(activityId);
a.setTitle(title);
GpxFormatter formatter = new GpxFormatter();
ByteArrayOutputStream baos = new ByteArrayOutputStream();
List<GpsTrack> tracks = new ArrayList<GpsTrack>();
tracks.add(track);
formatter.format(tracks, baos);
log.debug(new String(baos.toByteArray()));
a.setBytes(baos.toByteArray());
new AttachmentDao().create(a);
}
/**
* Process the specified HTTP request, and create the corresponding HTTP response (or forward to
* another web component that will create it). Return an <code>ActionForward</code> instance
* describing where and how control should be forwarded, or <code>null</code> if the response has
* already been completed.
*
* @param mapping The ActionMapping used to select this instance
* @param form The optional ActionForm bean for this request (if any)
* @param request The HTTP request we are processing
* @param response The HTTP response we are creating
* @exception Exception if business logic throws an exception
*/
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
// Extract attributes we will need
MessageResources messages = getResources(request);
// save errors
ActionMessages errors = new ActionMessages();
// START check for login (security)
if (!SecurityService.getInstance().checkForLogin(request.getSession(false))) {
return (mapping.findForward("welcome"));
}
// END check for login (security)
// START get id of current project from either request, attribute, or cookie
// id of project from request
String projectId = null;
projectId = request.getParameter("projectViewId");
// check attribute in request
if (projectId == null) {
projectId = (String) request.getAttribute("projectViewId");
}
// id of project from cookie
if (projectId == null) {
projectId = StandardCode.getInstance().getCookie("projectViewId", request.getCookies());
}
// default project to last if not in request or cookie
if (projectId == null) {
List results = ProjectService.getInstance().getProjectList();
ListIterator iterScroll = null;
for (iterScroll = results.listIterator(); iterScroll.hasNext(); iterScroll.next()) {}
iterScroll.previous();
Project p = (Project) iterScroll.next();
projectId = String.valueOf(p.getProjectId());
}
Integer id = Integer.valueOf(projectId);
// END get id of current project from either request, attribute, or cookie
// get project to edit
Project p = ProjectService.getInstance().getSingleProject(id);
// get this project's sources
Set sources = p.getSourceDocs();
// for each source add each sources' Tasks
List totalLinTasks = new ArrayList();
// for each source
for (Iterator sourceIter = sources.iterator(); sourceIter.hasNext(); ) {
SourceDoc sd = (SourceDoc) sourceIter.next();
// for each target of this source
for (Iterator linTargetIter = sd.getTargetDocs().iterator(); linTargetIter.hasNext(); ) {
TargetDoc td = (TargetDoc) linTargetIter.next();
// for each lin Task of this target
for (Iterator linTaskIter = td.getLinTasks().iterator(); linTaskIter.hasNext(); ) {
LinTask lt = (LinTask) linTaskIter.next();
if (lt.getPersonName() != null
&& lt.getDueDateDate() != null
&& (lt.getTaskName().equalsIgnoreCase("Translation")
|| lt.getTaskName().equalsIgnoreCase("Editing")
|| lt.getTaskName().trim().equalsIgnoreCase("Proofreading")
|| lt.getTaskName().equalsIgnoreCase("Proofreading / Linguistic QA"))) {
totalLinTasks.add(lt);
}
System.out.println(
sd.getLanguage() + "--------" + td.getLanguage() + "---------" + lt.getTaskName());
}
}
}
// Sort by task (orderNum), then source (language), then target (language)
Collections.sort(totalLinTasks, CompareTaskLin.getInstance());
Collections.sort(totalLinTasks, CompareTaskLanguages.getInstance());
// array for display in jsp
LinTask[] linTasksArray = (LinTask[]) totalLinTasks.toArray(new LinTask[0]);
for (int i = 0; i < totalLinTasks.size(); i++) {
request.setAttribute(projectId, log);
}
// place all Tasks for this project into the form for display
DynaValidatorForm qvg = (DynaValidatorForm) form;
// HERE down is standard and does not need to change when adding task blocks
// place this project into request for further display in jsp page
request.setAttribute("project", p);
// add this project id to cookies; this will remember the last project
response.addCookie(StandardCode.getInstance().setCookie("projectViewId", projectId));
// add tab location to cookies; this will remember which tab we are at
response.addCookie(StandardCode.getInstance().setCookie("projectViewTab", "Team"));
// an update of totals may be required
// Forward control to the specified success URI
return (mapping.findForward("Success"));
}
private List<Analysis> createAnalysisFromElisaAnalysisItem(AnalysisItem analysisItem) {
List<Analysis> analysisList = new ArrayList<Analysis>();
Analysis analysis = new Analysis();
if (!isBlankOrNull(analysisItem.getMurexResult())) {
analysis = getAnalysisFromId(analysisItem.getMurexAnalysisId());
analysisList.add(analysis);
}
if (!isBlankOrNull(analysisItem.getBiolineResult())) {
analysis = getAnalysisFromId(analysisItem.getBiolineAnalysisId());
analysisList.add(analysis);
}
if (!isBlankOrNull(analysisItem.getIntegralResult())) {
analysis = getAnalysisFromId(analysisItem.getIntegralAnalysisId());
analysisList.add(analysis);
}
if (!isBlankOrNull(analysisItem.getVironostikaResult())) {
analysis = getAnalysisFromId(analysisItem.getVironostikaAnalysisId());
analysisList.add(analysis);
}
if (!isBlankOrNull(analysisItem.getGenieIIResult())) {
analysis = getAnalysisFromId(analysisItem.getGenieIIAnalysisId());
analysisList.add(analysis);
}
if (!isBlankOrNull(analysisItem.getGenieII10Result())) {
analysis = getAnalysisFromId(analysisItem.getGenieII10AnalysisId());
analysisList.add(analysis);
}
if (!isBlankOrNull(analysisItem.getGenieII100Result())) {
analysis = getAnalysisFromId(analysisItem.getGenieII100AnalysisId());
analysisList.add(analysis);
}
if (!isBlankOrNull(analysisItem.getWesternBlot1Result())) {
analysis = getAnalysisFromId(analysisItem.getWesternBlot1AnalysisId());
analysisList.add(analysis);
}
if (!isBlankOrNull(analysisItem.getWesternBlot2Result())) {
analysis = getAnalysisFromId(analysisItem.getWesternBlot2AnalysisId());
analysisList.add(analysis);
}
if (!isBlankOrNull(analysisItem.getP24AgResult())) {
analysis = getAnalysisFromId(analysisItem.getP24AgAnalysisId());
analysisList.add(analysis);
}
if (!isBlankOrNull(analysisItem.getInnoliaResult())) {
analysis = getAnalysisFromId(analysisItem.getInnoliaAnalysisId());
analysisList.add(analysis);
}
analysisList.add(analysis);
return analysisList;
}
