Examples with StudySubject org.akaza.openclinica.domain.datamap.StudySubject used on opensource projects

Example 11 with StudySubject

use of org.akaza.openclinica.domain.datamap.StudySubject in project OpenClinica by OpenClinica.

the class GenerateClinicalDataServiceImpl method listStudySubjects.

private List<StudySubject> listStudySubjects(String studySubjectOID) {
    ArrayList<StudySubject> studySubjs = new ArrayList<StudySubject>();
    StudySubject studySubj = getStudySubjectDao().findByColumnName(studySubjectOID, "ocOid");
    studySubjs.add(studySubj);
    return studySubjs;
}

Example 12 with StudySubject

use of org.akaza.openclinica.domain.datamap.StudySubject in project OpenClinica by OpenClinica.

the class EnketoUrlService method getEditUrl.

public String getEditUrl(String subjectContextKey, PFormCacheSubjectContextEntry subjectContext, String studyOid, FormLayout formLayout, StudyEvent studyEvent, String flavor) throws Exception {
    Study study = enketoCredentials.getParentStudy(studyOid);
    studyOid = study.getOc_oid();
    String editURL = null;
    StudyEventDefinition eventDef;
    StudySubject subject;
    String goTo = null;
    if (subjectContext.getItemName() != null) {
        goTo = (subjectContext.isItemInRepeatingGroup()) ? "//" + subjectContext.getItemRepeatGroupName() + "[" + subjectContext.getItemRepeatOrdinal() + "]//" + subjectContext.getItemName() : "//" + subjectContext.getItemName();
    }
    if (studyEvent == null) {
        // Lookup relevant data
        eventDef = studyEventDefinitionDao.findByStudyEventDefinitionId(subjectContext.getStudyEventDefinitionId());
        subject = studySubjectDao.findByOcOID(subjectContext.getStudySubjectOid());
        studyEvent = studyEventDao.fetchByStudyEventDefOIDAndOrdinal(eventDef.getOc_oid(), Integer.valueOf(subjectContext.getOrdinal()), subject.getStudySubjectId());
    } else {
        eventDef = studyEvent.getStudyEventDefinition();
        subject = studyEvent.getStudySubject();
    }
    if (formLayout == null) {
        formLayout = formLayoutDao.findByOcOID(subjectContext.getFormLayoutOid());
    }
    EventCrf eventCrf = eventCrfDao.findByStudyEventIdStudySubjectIdFormLayoutId(studyEvent.getStudyEventId(), subject.getStudySubjectId(), formLayout.getFormLayoutId());
    CrfVersion crfVersion = eventCrf.getCrfVersion();
    // Load populated instance
    String populatedInstance = populateInstance(crfVersion, formLayout, eventCrf, studyOid, flavor);
    // Call Enketo api to get edit url
    EnketoAPI enketo = new EnketoAPI(EnketoCredentials.getInstance(studyOid));
    // Build redirect url
    String redirectUrl = getRedirectUrl(subject.getOcOid(), studyOid);
    boolean markComplete = true;
    if (eventCrf.getStatusId() == Status.UNAVAILABLE.getCode()) {
        markComplete = false;
    }
    // Return Enketo URL
    List<FormLayoutMedia> mediaList = formLayoutMediaDao.findByEventCrfId(eventCrf.getEventCrfId());
    EnketoURLResponse eur = enketo.getEditURL(formLayout, flavor, populatedInstance, subjectContextKey, redirectUrl, markComplete, studyOid, mediaList, goTo);
    editURL = eur.getEdit_url();
    int hashIndex = editURL.lastIndexOf("#");
    String part1 = "";
    String part2 = "";
    if (hashIndex != -1) {
        part1 = editURL.substring(0, hashIndex);
        part2 = editURL.substring(hashIndex);
        editURL = part1 + "&ecid=" + subjectContextKey + part2;
    } else {
        editURL = editURL + "&ecid=" + subjectContextKey;
    }
    logger.debug("Generating Enketo edit url for form: " + editURL);
    return editURL;
}

Example 13 with StudySubject

use of org.akaza.openclinica.domain.datamap.StudySubject in project OpenClinica by OpenClinica.

the class OpenRosaSubmissionController method markComplete.

// @RequestMapping(value = "/{studyOID}/fieldsubmission/complete", method = RequestMethod.POST)
public ResponseEntity<String> markComplete(HttpServletRequest request, HttpServletResponse response, @PathVariable("studyOID") String studyOID, @RequestParam(FORM_CONTEXT) String ecid) throws Exception {
    HashMap<String, String> subjectContext = null;
    PFormCache cache = PFormCache.getInstance(context);
    subjectContext = cache.getSubjectContext(ecid);
    int studyEventDefinitionID = Integer.valueOf(subjectContext.get("studyEventDefinitionID"));
    int userAccountID = Integer.valueOf(subjectContext.get("userAccountID"));
    String studySubjectOID = subjectContext.get("studySubjectOID");
    String formLayoutOID = subjectContext.get("formLayoutOID");
    int studyEventOrdinal = Integer.valueOf(subjectContext.get("studyEventOrdinal"));
    UserAccount userAccount = userAccountDao.findById(userAccountID);
    StudySubject studySubject = studySubjectDao.findByOcOID(studySubjectOID);
    Study study = studyDao.findByOcOID(studyOID);
    StudyEventDefinition sed = studyEventDefinitionDao.findById(studyEventDefinitionID);
    FormLayout formLayout = formLayoutDao.findByOcOID(formLayoutOID);
    CrfVersion crfVersion = crfVersionDao.findAllByCrfId(formLayout.getCrf().getCrfId()).get(0);
    StudyEvent studyEvent = studyEventDao.fetchByStudyEventDefOIDAndOrdinalTransactional(sed.getOc_oid(), studyEventOrdinal, studySubject.getStudySubjectId());
    EventCrf eventCrf = eventCrfDao.findByStudyEventIdStudySubjectIdFormLayoutId(studyEvent.getStudyEventId(), studySubject.getStudySubjectId(), formLayout.getFormLayoutId());
    if (eventCrf == null) {
        eventCrf = createEventCrf(formLayout, studyEvent, studySubject, userAccount);
        List<Item> items = itemDao.findAllByCrfVersion(crfVersion.getCrfVersionId());
        createItemData(items.get(0), "", eventCrf, userAccount);
    }
    eventCrf.setStatusId(org.akaza.openclinica.domain.Status.UNAVAILABLE.getCode());
    eventCrf.setUserAccount(userAccount);
    eventCrf.setUpdateId(userAccount.getUserId());
    eventCrf.setDateUpdated(new Date());
    eventCrfDao.saveOrUpdate(eventCrf);
    List<EventCrf> eventCrfs = eventCrfDao.findByStudyEventIdStudySubjectId(studyEvent.getStudyEventId(), studySubject.getOcOid());
    List<EventDefinitionCrf> eventDefinitionCrfs = eventDefinitionCrfDao.findAvailableByStudyEventDefStudy(sed.getStudyEventDefinitionId(), study.getStudyId());
    int count = 0;
    for (EventCrf evCrf : eventCrfs) {
        if (evCrf.getStatusId() == org.akaza.openclinica.domain.Status.UNAVAILABLE.getCode() || evCrf.getStatusId() == org.akaza.openclinica.domain.Status.DELETED.getCode() || evCrf.getStatusId() == org.akaza.openclinica.domain.Status.AUTO_DELETED.getCode()) {
            for (EventDefinitionCrf eventDefinitionCrf : eventDefinitionCrfs) {
                if (eventDefinitionCrf.getCrf().getCrfId() == evCrf.getFormLayout().getCrf().getCrfId()) {
                    count++;
                    break;
                }
            }
        }
    }
    if (count == eventDefinitionCrfs.size()) {
        studyEvent.setSubjectEventStatusId(SubjectEventStatus.COMPLETED.getCode());
        studyEvent.setUserAccount(userAccount);
        studyEventDao.saveOrUpdate(studyEvent);
    } else if (studyEvent.getSubjectEventStatusId() == SubjectEventStatus.SCHEDULED.getCode()) {
        studyEvent.setSubjectEventStatusId(SubjectEventStatus.DATA_ENTRY_STARTED.getCode());
        studyEvent.setUserAccount(userAccount);
        studyEventDao.saveOrUpdate(studyEvent);
    }
    String responseMessage = "<OpenRosaResponse xmlns=\"http://openrosa.org/http/response\">" + "<message>success</message>" + "</OpenRosaResponse>";
    return new ResponseEntity<String>(responseMessage, HttpStatus.CREATED);
}

Example 14 with StudySubject

use of org.akaza.openclinica.domain.datamap.StudySubject in project OpenClinica by OpenClinica.

the class EventProcessor method process.

public ProcessorEnum process(SubmissionContainer container) throws Exception {
    logger.info("Executing Event Processor.");
    Errors errors = container.getErrors();
    StudySubject studySubject = container.getSubject();
    StudyEventDefinition studyEventDefinition = studyEventDefinitionDao.findByStudyEventDefinitionId(Integer.valueOf(container.getSubjectContext().get("studyEventDefinitionID")));
    FormLayout formLayout = formLayoutDao.findByOcOID(container.getSubjectContext().get("formLayoutOID"));
    container.setFormLayout(formLayout);
    CrfVersion crfVersion = crfVersionDao.findAllByCrfId(formLayout.getCrf().getCrfId()).get(0);
    container.setCrfVersion(crfVersion);
    boolean isAnonymous = false;
    if (container.getSubjectContext().get("studySubjectOID") == null)
        isAnonymous = true;
    // Create study event if it doesn't exist
    if (isAnonymous)
        processAnonymous(container, errors, studySubject, studyEventDefinition);
    else
        processParticipant(container, errors, studySubject, studyEventDefinition);
    // TODO: May need to move this to a new processor that runs at the end
    // Update the EventCrf and StudyEvent to the proper status.
    // Don't do it in the initial save so it will have the expected audit trail entries.
    Study study = null;
    if (container.getSubjectContext().get("studyOID") != null)
        study = studyDao.findByOcOID(container.getSubjectContext().get("studyOID"));
    else
        study = container.getStudy();
    container.setEventCrf(updateEventCrf(container.getEventCrf(), study, studySubject, container.getUser(), isAnonymous));
    container.setStudyEvent(updateStudyEvent(container.getStudyEvent(), studyEventDefinition, study, studySubject, container.getUser(), isAnonymous));
    return ProcessorEnum.PROCEED;
}

Example 15 with StudySubject

use of org.akaza.openclinica.domain.datamap.StudySubject in project OpenClinica by OpenClinica.

the class StudyEventController method completeParticipantEvent.

/**
	 * @api {put} /pages/auth/api/v1/studyevent/studysubject/{studySubjectOid}/studyevent/{studyEventDefOid}/ordinal/{ordinal}/complete Complete a Participant Event
	 * @apiName completeParticipantEvent
	 * @apiPermission Authenticate using api-key. admin
	 * @apiVersion 1.0.0
	 * @apiParam {String} studySubjectOid Study Subject OID.
	 * @apiParam {String} studyEventDefOid Study Event Definition OID.
	 * @apiParam {Integer} ordinal Ordinal of Study Event Repetition.
	 * @apiGroup Form
	 * @apiHeader {String} api_key Users unique access-key.
	 * @apiDescription Completes a participant study event.
	 * @apiErrorExample {json} Error-Response:
	 *                  HTTP/1.1 403 Forbidden
	 *                  {
	 *                  "code": "403",
	 *                  "message": "Request Denied.  Operation not allowed."
	 *                  }
	 * @apiSuccessExample {json} Success-Response:
	 *                    HTTP/1.1 200 OK
	 *                    {
	 *                    "code": "200",
	 *                    "message": "Success."
	 *                    }
	 */
@RequestMapping(value = "/studysubject/{studySubjectOid}/studyevent/{studyEventDefOid}/ordinal/{ordinal}/complete", method = RequestMethod.PUT)
@ResponseBody
public Map<String, String> completeParticipantEvent(HttpServletRequest request, @PathVariable("studySubjectOid") String studySubjectOid, @PathVariable("studyEventDefOid") String studyEventDefOid, @PathVariable("ordinal") Integer ordinal) throws Exception {
    StudySubject subject = studySubjectDao.findByOcOID(studySubjectOid);
    StudyEvent studyEvent = studyEventDao.fetchByStudyEventDefOIDAndOrdinal(studyEventDefOid, ordinal, subject.getStudySubjectId());
    StudyEventDefinition studyEventDefinition = studyEventDefinitionDao.findByStudyEventDefinitionId(studyEvent.getStudyEventDefinition().getStudyEventDefinitionId());
    Study study = studyEventDefinition.getStudy();
    Map<String, String> response = new HashMap<String, String>();
    // Verify this request is allowed.
    if (!mayProceed(study)) {
        response.put("code", String.valueOf(HttpStatus.FORBIDDEN.value()));
        response.put("message", "Request Denied.  Operation not allowed.");
        return response;
    }
    // Get list of eventCRFs
    // By this point we can assume all Participant forms have been submitted at least once and have an event_crf entry.
    // Non-Participant forms may not have an entry.
    List<EventDefinitionCrf> eventDefCrfs = eventDefinitionCrfDao.findByStudyEventDefinitionId(studyEventDefinition.getStudyEventDefinitionId());
    List<EventCrf> eventCrfs = eventCrfDao.findByStudyEventIdStudySubjectId(studyEvent.getStudyEventId(), studySubjectOid);
    try {
        completeData(studyEvent, eventDefCrfs, eventCrfs);
    } catch (Exception e) {
        // Transaction has been rolled back due to an exception.
        logger.error("Error encountered while completing Study Event: " + e.getMessage());
        logger.error(ExceptionUtils.getStackTrace(e));
        response.put("code", String.valueOf(HttpStatus.INTERNAL_SERVER_ERROR.value()));
        response.put("message", "Error encountered while completing participant event.");
        return response;
    }
    response.put("code", String.valueOf(HttpStatus.OK.value()));
    response.put("message", "Success.");
    return response;
//return new ResponseEntity<String>("<message>Success</message>", org.springframework.http.HttpStatus.OK);
}