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

Example 11 with EventCrf

use of org.akaza.openclinica.domain.datamap.EventCrf 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 12 with EventCrf

use of org.akaza.openclinica.domain.datamap.EventCrf 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 EventCrf

use of org.akaza.openclinica.domain.datamap.EventCrf 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);
}

Example 14 with EventCrf

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

the class ItemProcessor method process.

public void process(SubmissionContainer container) throws Exception {
    logger.info("Executing Item Processor.");
    ArrayList<HashMap> listOfUploadFilePaths = container.getListOfUploadFilePaths();
    DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
    DocumentBuilder db = dbf.newDocumentBuilder();
    InputSource is = new InputSource();
    is.setCharacterStream(new StringReader(container.getRequestBody()));
    Document doc = db.parse(is);
    String itemName;
    String itemValue;
    String groupNodeName = "";
    NodeList instanceNodeList = doc.getElementsByTagName("instance");
    // Instance loop
    for (int i = 0; i < instanceNodeList.getLength(); i = i + 1) {
        Node instanceNode = instanceNodeList.item(i);
        if (instanceNode instanceof Element) {
            NodeList crfNodeList = instanceNode.getChildNodes();
            // Form loop
            for (int j = 0; j < crfNodeList.getLength(); j = j + 1) {
                Node crfNode = crfNodeList.item(j);
                if (crfNode instanceof Element) {
                    CrfVersion crfVersion = container.getEventCrf().getCrfVersion();
                    EventCrf eventCrf = container.getEventCrf();
                    ArrayList<ItemData> itemDataList = new ArrayList<ItemData>();
                    HashMap<Integer, Set<Integer>> groupOrdinalMapping = new HashMap<Integer, Set<Integer>>();
                    NodeList groupNodeList = crfNode.getChildNodes();
                    List<Item> items = itemDao.findAllByCrfVersionId(crfVersion.getCrfVersionId());
                    List<ItemData> itemDatas = itemDataDao.findAllByEventCrf(container.getEventCrf().getEventCrfId());
                    List<ItemGroup> itemGroups = itemGroupDao.findByCrfVersionId(crfVersion.getCrfVersionId());
                    List<ItemGroupMetadata> itemGroupMetadatas = itemGroupMetadataDao.findAllByCrfVersion(crfVersion.getCrfVersionId());
                    List<ItemFormMetadata> itemFormMetadatas = itemFormMetadataDao.findAllByCrfVersion(crfVersion.getCrfVersionId());
                    // Group loop
                    for (int k = 0; k < groupNodeList.getLength(); k = k + 1) {
                        Node groupNode = groupNodeList.item(k);
                        if (groupNode instanceof Element && !groupNode.getNodeName().startsWith("SECTION_")) {
                            groupNodeName = groupNode.getNodeName();
                            ItemGroup itemGroup = lookupItemGroup(groupNodeName, crfVersion, itemGroups);
                            if (itemGroup == null) {
                                logger.error("Failed to lookup item group: '" + groupNodeName + "'.  Continuing with submission.");
                                continue;
                            }
                            if (itemGroup != null && !groupOrdinalMapping.containsKey(itemGroup.getItemGroupId()))
                                groupOrdinalMapping.put(itemGroup.getItemGroupId(), new TreeSet<Integer>());
                            NodeList itemNodeList = groupNode.getChildNodes();
                            // Item loop
                            for (int m = 0; m < itemNodeList.getLength(); m = m + 1) {
                                Node itemNode = itemNodeList.item(m);
                                if (itemNode instanceof Element && !itemNode.getNodeName().endsWith(".HEADER") && !itemNode.getNodeName().endsWith(".SUBHEADER") && !itemNode.getNodeName().equals("OC.REPEAT_ORDINAL") && !itemNode.getNodeName().equals("OC.STUDY_SUBJECT_ID") && !itemNode.getNodeName().equals("OC.STUDY_SUBJECT_ID_CONFIRM")) {
                                    itemName = itemNode.getNodeName().trim();
                                    itemValue = itemNode.getTextContent();
                                    Item item = lookupItem(itemName, crfVersion, items);
                                    if (item == null) {
                                        logger.error("Failed to lookup item: '" + itemName + "'.  Continuing with submission.");
                                        continue;
                                    }
                                    ItemGroupMetadata itemGroupMeta = lookupItemGroupMetadata(item.getItemId(), crfVersion.getCrfVersionId(), itemGroupMetadatas);
                                    ItemFormMetadata itemFormMetadata = lookupItemFormMetadata(item.getItemId(), crfVersion.getCrfVersionId(), itemFormMetadatas);
                                    Integer itemOrdinal = getItemOrdinal(groupNode, itemGroupMeta.isRepeatingGroup(), itemDataList, item);
                                    // Convert space separated Enketo multiselect values to comma separated OC multiselect values
                                    Integer responseTypeId = itemFormMetadata.getResponseSet().getResponseType().getResponseTypeId();
                                    if (responseTypeId == 3 || responseTypeId == 7) {
                                        itemValue = itemValue.replaceAll(" ", ",");
                                    }
                                    if (responseTypeId == 4) {
                                        for (HashMap uploadFilePath : listOfUploadFilePaths) {
                                            if ((boolean) uploadFilePath.containsKey(itemValue) && itemValue != "") {
                                                itemValue = (String) uploadFilePath.get(itemValue);
                                                break;
                                            }
                                        }
                                    }
                                    // Build set of submitted row numbers to be used to find deleted DB rows later
                                    Set<Integer> ordinals = groupOrdinalMapping.get(itemGroup.getItemGroupId());
                                    ordinals.add(itemOrdinal);
                                    groupOrdinalMapping.put(itemGroup.getItemGroupId(), ordinals);
                                    ItemData newItemData = createItemData(item, itemValue, itemOrdinal, eventCrf, container.getStudy(), container.getSubject(), container.getUser());
                                    Errors itemErrors = validateItemData(newItemData, item, responseTypeId);
                                    if (itemErrors.hasErrors()) {
                                        container.getErrors().addAllErrors(itemErrors);
                                        throw new Exception("Item validation error.  Rolling back submission changes.");
                                    } else {
                                        itemDataList.add(newItemData);
                                    }
                                    ItemData existingItemData = lookupItemData(item.getItemId(), eventCrf.getEventCrfId(), itemOrdinal, itemDatas);
                                    if (existingItemData == null) {
                                        // No existing value, create new item.
                                        if (newItemData.getOrdinal() < 0) {
                                            newItemData.setOrdinal(itemDataDao.getMaxGroupRepeat(eventCrf.getEventCrfId(), item.getItemId()) + 1);
                                            groupOrdinalMapping.get(itemGroup.getItemGroupId()).add(newItemData.getOrdinal());
                                        }
                                        itemDataDao.saveOrUpdate(newItemData);
                                        newItemData.setStatus(Status.UNAVAILABLE);
                                        itemDataDao.saveOrUpdate(newItemData);
                                    } else if (existingItemData.getValue().equals(newItemData.getValue())) {
                                    // Existing item. Value unchanged. Do nothing.
                                    } else {
                                        // Existing item. Value changed. Update existing value.
                                        existingItemData.setValue(newItemData.getValue());
                                        existingItemData.setUpdateId(container.getUser().getUserId());
                                        existingItemData.setDateUpdated(new Date());
                                        itemDataDao.saveOrUpdate(existingItemData);
                                    }
                                }
                            }
                        }
                    }
                    // Delete rows that have been removed
                    removeDeletedRows(groupOrdinalMapping, eventCrf, crfVersion, container.getStudy(), container.getSubject(), container.getLocale(), container.getUser());
                }
            }
        }
    }
}

Example 15 with EventCrf

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

the class EventProcessor method createEventCrf.

private EventCrf createEventCrf(CrfVersion crfVersion, StudyEvent studyEvent, StudySubject studySubject, UserAccount user) {
    EventCrf eventCrf = new EventCrf();
    Date currentDate = new Date();
    eventCrf.setAnnotations("");
    eventCrf.setDateCreated(currentDate);
    eventCrf.setCrfVersion(crfVersion);
    eventCrf.setInterviewerName("");
    eventCrf.setDateInterviewed(null);
    eventCrf.setUserAccount(user);
    eventCrf.setStatusId(Status.AVAILABLE.getCode());
    // setCompletionStatusId(1);
    eventCrf.setCompletionStatus(completionStatusDao.findByCompletionStatusId(1));
    eventCrf.setStudySubject(studySubject);
    eventCrf.setStudyEvent(studyEvent);
    eventCrf.setValidateString("");
    eventCrf.setValidatorAnnotations("");
    eventCrf.setUpdateId(user.getUserId());
    eventCrf.setDateUpdated(new Date());
    eventCrf.setValidatorId(0);
    eventCrf.setOldStatusId(0);
    eventCrf.setSdvUpdateId(0);
    eventCrfDao.saveOrUpdate(eventCrf);
    eventCrf = eventCrfDao.findByStudyEventIdStudySubjectIdCrfVersionId(studyEvent.getStudyEventId(), studySubject.getStudySubjectId(), crfVersion.getCrfVersionId());
    logger.debug("*********CREATED EVENT CRF");
    return eventCrf;
}