public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int itemId = fp.getInt(ITEM_ID);
ItemDAO idao = new ItemDAO(sm.getDataSource());
ItemFormMetadataDAO ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
if (itemId == 0) {
addPageMessage("Please choose an item first.");
forwardPage(Page.ITEM_DETAIL);
return;
}
ItemBean item = (ItemBean) idao.findByPK(itemId);
ArrayList versions = idao.findAllVersionsByItemId(item.getId());
ArrayList versionItems = new ArrayList();
// finds each item metadata for each version
for (int i = 0; i < versions.size(); i++) {
Integer versionId = (Integer) versions.get(i);
CRFVersionBean version = (CRFVersionBean) cvdao.findByPK(versionId.intValue());
if (versionId != null && versionId.intValue() > 0) {
ItemFormMetadataBean imfBean =
ifmdao.findByItemIdAndCRFVersionId(item.getId(), versionId.intValue());
imfBean.setCrfVersionName(version.getName());
CRFBean crf = (CRFBean) cdao.findByPK(version.getCrfId());
imfBean.setCrfName(crf.getName());
versionItems.add(imfBean);
}
}
request.setAttribute(VERSION_ITEMS, versionItems);
request.setAttribute(ITEM_BEAN, item);
forwardPage(Page.ITEM_DETAIL);
}
@Override
public void processRequest() throws Exception {
resetPanel();
panel.setStudyInfoShown(false);
panel.setOrderedData(true);
panel.setSubmitDataModule(false);
panel.setExtractData(false);
panel.setCreateDataset(false);
setToPanel(resword.getString("create_CRF"), respage.getString("br_create_new_CRF_entering"));
setToPanel(
resword.getString("create_CRF_version"), respage.getString("br_create_new_CRF_uploading"));
setToPanel(
resword.getString("revise_CRF_version"), respage.getString("br_if_you_owner_CRF_version"));
setToPanel(
resword.getString("CRF_spreadsheet_template"),
respage.getString("br_download_blank_CRF_spreadsheet_from"));
setToPanel(
resword.getString("example_CRF_br_spreadsheets"),
respage.getString("br_download_example_CRF_instructions_from"));
FormProcessor fp = new FormProcessor(request);
// checks which module the requests are from, manage or admin
String module = fp.getString(MODULE);
request.setAttribute(MODULE, module);
int crfId = fp.getInt(CRF_ID);
if (crfId == 0) {
addPageMessage(respage.getString("please_choose_a_CRF_to_view"));
forwardPage(Page.CRF_LIST);
} else {
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFVersionDAO vdao = new CRFVersionDAO(sm.getDataSource());
CRFBean crf = (CRFBean) cdao.findByPK(crfId);
ArrayList<CRFVersionBean> versions = (ArrayList<CRFVersionBean>) vdao.findAllByCRF(crfId);
crf.setVersions(versions);
// Collection<RuleSetBean> items =
// getRuleSetService().getRuleSetsByCrf(crf);
Collection<TableColumnHolder> items = populate(crf, versions);
TableFacade tableFacade = createTableFacade("rules", request);
tableFacade.setItems(items); // set the items
tableFacade.setExportTypes(response, CSV, JEXCEL);
tableFacade.setStateAttr("restore");
Limit limit = tableFacade.getLimit();
if (limit.isExported()) {
export(tableFacade);
// return null; // In Spring returning null tells the controller
// not to do anything.
}
String html = html(tableFacade);
request.setAttribute("rules", html); // Set the Html in the
// request for the JSP.
request.setAttribute(CRF, crf);
forwardPage(Page.VIEW_CRF);
}
}
public void testStuff() throws Exception {
ArrayList col = (ArrayList) cdao.findAll();
for (int i = 0; i < col.size(); i++) {
CRFBean eb = (CRFBean) col.get(i);
System.out.println(eb.getName());
}
assertNotNull("findAll", col);
}
public void testFindByVersionIdFail() throws Exception {
int crfVersionId = -1;
int crfId = 1;
CRFBean cb = cdao.findByVersionId(crfVersionId);
assertNotNull("bean valid", cb);
assertTrue("bean inactive", !cb.isActive());
}
public void testFindByVersionIdSuccess() throws Exception {
int crfVersionId = 1;
int crfId = 1;
CRFBean cb = cdao.findByVersionId(crfVersionId);
assertNotNull("bean valid", cb);
assertTrue("bean id set", cb.isActive());
assertEquals("correct bean found", cb.getId(), crfId);
}
// testInsert
public void testInsertSuccess() throws Exception {
CRFBean cb = new CRFBean();
cb.setName("test CRF -- please delete");
cb.setStatus(Status.AVAILABLE);
cb.setDescription("test CRF -- please delete");
UserAccountBean ub = new UserAccountBean();
ub.setId(1);
cb.setOwner(ub);
CRFBean cbc = (CRFBean) cdao.create(cb);
assertNotNull("test insert", cbc);
}
private ArrayList<StudyEventDefinitionBean> initDefinitions(StudyBean site) {
ArrayList<StudyEventDefinitionBean> seds = new ArrayList<StudyEventDefinitionBean>();
StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(sm.getDataSource());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
CRFDAO cdao = new CRFDAO(sm.getDataSource());
StudyBean parentStudy =
(StudyBean) new StudyDAO(sm.getDataSource()).findByPK(site.getParentStudyId());
seds = sedDao.findAllByStudy(parentStudy);
int start = 0;
for (StudyEventDefinitionBean sed : seds) {
int defId = sed.getId();
ArrayList<EventDefinitionCRFBean> edcs =
(ArrayList<EventDefinitionCRFBean>)
edcdao.findAllByDefinitionAndSiteIdAndParentStudyId(
defId, site.getId(), parentStudy.getId());
ArrayList<EventDefinitionCRFBean> defCrfs = new ArrayList<EventDefinitionCRFBean>();
// sed.setCrfNum(edcs.size());
for (EventDefinitionCRFBean edcBean : edcs) {
int edcStatusId = edcBean.getStatus().getId();
CRFBean crf = (CRFBean) cdao.findByPK(edcBean.getCrfId());
int crfStatusId = crf.getStatusId();
if (edcStatusId == 5 || edcStatusId == 7 || crfStatusId == 5 || crfStatusId == 7) {
} else {
ArrayList<CRFVersionBean> versions =
(ArrayList<CRFVersionBean>) cvdao.findAllActiveByCRF(edcBean.getCrfId());
edcBean.setVersions(versions);
edcBean.setCrfName(crf.getName());
CRFVersionBean defaultVersion =
(CRFVersionBean) cvdao.findByPK(edcBean.getDefaultVersionId());
edcBean.setDefaultVersionName(defaultVersion.getName());
String sversionIds = edcBean.getSelectedVersionIds();
ArrayList<Integer> idList = new ArrayList<Integer>();
if (sversionIds.length() > 0) {
String[] ids = sversionIds.split("\\,");
for (String id : ids) {
idList.add(Integer.valueOf(id));
}
}
edcBean.setSelectedVersionIdList(idList);
defCrfs.add(edcBean);
++start;
}
}
logger.debug("definitionCrfs size=" + defCrfs.size() + " total size=" + edcs.size());
sed.setCrfs(defCrfs);
sed.setCrfNum(defCrfs.size());
}
return seds;
}
public void testInsertFail() throws Exception {
CRFBean cb = new CRFBean();
cb.setName("test CRF -- please delete");
cb.setStatus(Status.AVAILABLE);
cb.setDescription("test CRF -- please delete");
cb.setOwner(new UserAccountBean());
CRFBean cbc = (CRFBean) cdao.create(cb);
assertNotNull("test insert", cbc);
assertEquals("check primarykey", cb.getId(), 0);
}
public void testUpdateFail() throws Exception {
CRFBean sb = (CRFBean) cdao.findByPK(1000);
String keepName = sb.getName();
sb.setName("new name");
UserAccountBean ub = new UserAccountBean();
ub.setId(2);
sb.setUpdater(ub);
sb.setStatus(Status.AVAILABLE);
sb = (CRFBean) cdao.update(sb);
sb.setName(keepName);
CRFBean sbs = (CRFBean) cdao.update(sb);
assertNotNull("test update", sbs);
assertEquals("check primarykey", sb.getId(), 0);
}
// testUpdate
public void testUpdateSuccess() throws Exception {
CRFBean sb = (CRFBean) cdao.findByPK(1);
String keepName = sb.getName();
sb.setName("new name");
UserAccountBean ub = new UserAccountBean();
ub.setId(1);
sb.setUpdater(ub);
sb.setStatus(Status.AVAILABLE);
sb = (CRFBean) cdao.update(sb);
sb.setName(keepName);
CRFBean sbs = (CRFBean) cdao.update(sb);
assertNotNull("test update", sbs);
}
public ArrayList findAllActiveByCRF(CRFBean crf) {
HashMap variables = new HashMap();
this.setTypesExpected();
this.setTypeExpected(14, TypeNames.INT); // crf_version_id
this.setTypeExpected(15, TypeNames.STRING); // version name
variables.put(new Integer(1), new Integer(crf.getId()));
String sql = digester.getQuery("findAllActiveByCRF");
ArrayList alist = this.select(sql, variables);
ArrayList al = new ArrayList();
Iterator it = alist.iterator();
while (it.hasNext()) {
HashMap hm = (HashMap) it.next();
ItemBean eb = (ItemBean) this.getEntityFromHashMap(hm);
Integer versionId = (Integer) hm.get("crf_version_id");
String versionName = (String) hm.get("cvname");
ItemFormMetadataBean imf = new ItemFormMetadataBean();
imf.setCrfVersionName(versionName);
// logger.info("versionName" + imf.getCrfVersionName());
imf.setCrfVersionId(versionId.intValue());
eb.setItemMeta(imf);
al.add(eb);
}
return al;
}
@Override
public void processRequest() throws Exception {
FormProcessor fp = new FormProcessor(request);
int studySubId = fp.getInt(STUDY_SUB_ID, true);
int eventCRFId = fp.getInt(EVENT_CRF_ID);
String action = request.getParameter("action");
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
StudySubjectDAO subdao = new StudySubjectDAO(sm.getDataSource());
EventCRFDAO ecdao = new EventCRFDAO(sm.getDataSource());
StudyDAO sdao = new StudyDAO(sm.getDataSource());
if (eventCRFId == 0) {
addPageMessage(respage.getString("please_choose_an_event_CRF_to_delete"));
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
} else {
EventCRFBean eventCRF = (EventCRFBean) ecdao.findByPK(eventCRFId);
StudySubjectBean studySub = (StudySubjectBean) subdao.findByPK(studySubId);
request.setAttribute("studySub", studySub);
// construct info needed on view event crf page
CRFDAO cdao = new CRFDAO(sm.getDataSource());
CRFVersionDAO cvdao = new CRFVersionDAO(sm.getDataSource());
int crfVersionId = eventCRF.getCRFVersionId();
CRFBean cb = cdao.findByVersionId(crfVersionId);
eventCRF.setCrf(cb);
CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(crfVersionId);
eventCRF.setCrfVersion(cvb);
// then get the definition so we can call
// DisplayEventCRFBean.setFlags
int studyEventId = eventCRF.getStudyEventId();
StudyEventBean event = (StudyEventBean) sedao.findByPK(studyEventId);
int studyEventDefinitionId = sedao.getDefinitionIdFromStudyEventId(studyEventId);
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(sm.getDataSource());
StudyEventDefinitionBean sed =
(StudyEventDefinitionBean) seddao.findByPK(studyEventDefinitionId);
event.setStudyEventDefinition(sed);
request.setAttribute("event", event);
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(sm.getDataSource());
StudyBean study = (StudyBean) sdao.findByPK(studySub.getStudyId());
EventDefinitionCRFBean edc =
edcdao.findByStudyEventDefinitionIdAndCRFId(study, studyEventDefinitionId, cb.getId());
DisplayEventCRFBean dec = new DisplayEventCRFBean();
dec.setEventCRF(eventCRF);
dec.setFlags(eventCRF, ub, currentRole, edc.isDoubleEntry());
// find all item data
ItemDataDAO iddao = new ItemDataDAO(sm.getDataSource());
dnDao = new DiscrepancyNoteDAO(sm.getDataSource());
ArrayList<ItemDataBean> itemData = iddao.findAllByEventCRFId(eventCRF.getId());
request.setAttribute("items", itemData);
if ("confirm".equalsIgnoreCase(action)) {
request.setAttribute("displayEventCRF", dec);
forwardPage(Page.DELETE_EVENT_CRF);
} else {
logger.info("submit to delete the event CRF from event");
// OC-6303 Deleting Event CRF resets Show / Hide logic
// delete records from DynamicItemForm and DynamicItemGroup
getDynamicsItemFormMetadataDao().delete(eventCRFId);
getDynamicsItemGroupMetadataDao().delete(eventCRFId);
eventCRF.setOldStatus(eventCRF.getStatus());
eventCRF.setStatus(Status.RESET);
eventCRF.setUpdater(ub);
ecdao.update(eventCRF);
for (ItemDataBean itemdata : itemData) {
// OC-6343 Rule behaviour must be reset if an Event CRF is deleted
// delete the records from ruleActionRunLogDao
getRuleActionRunLogDao().delete(itemdata.getId());
// OC-6344 Notes & Discrepancies must be set to "closed" when event CRF is deleted
// parentDiscrepancyNoteList is the list of the parent DNs records only
ArrayList<DiscrepancyNoteBean> parentDiscrepancyNoteList =
getDnDao().findParentNotesOnlyByItemData(itemdata.getId());
for (DiscrepancyNoteBean parentDiscrepancyNote : parentDiscrepancyNoteList) {
if (parentDiscrepancyNote.getResolutionStatusId()
!= 4) { // if the DN's resolution status is not set to Closed
String description = resword.getString("dn_auto-closed_description");
String detailedNotes = resword.getString("dn_auto_closed_detailed_notes");
// create new DN record , new DN Map record , also update the parent record
createDiscrepancyNoteBean(
description, detailedNotes, itemdata.getId(), study, ub, parentDiscrepancyNote);
}
}
iddao = new ItemDataDAO(sm.getDataSource());
ifmdao = new ItemFormMetadataDAO(sm.getDataSource());
ItemDataBean idBean = (ItemDataBean) iddao.findByPK(itemdata.getId());
ItemFormMetadataBean ifmBean =
ifmdao.findByItemIdAndCRFVersionId(idBean.getItemId(), crfVersionId);
// Updating Dn_item_data_map actovated column into false for the existing DNs
ArrayList<DiscrepancyNoteBean> dnBeans =
getDnDao().findExistingNotesForItemData(itemdata.getId());
if (dnBeans.size() != 0) {
DiscrepancyNoteBean dnBean = new DiscrepancyNoteBean();
dnBean.setEntityId(itemdata.getId());
dnBean.setActivated(false);
getDnDao().updateDnMapActivation(dnBean);
}
// Default Values are not addressed
itemdata.setValue("");
itemdata.setOldStatus(itemdata.getStatus());
itemdata.setOwner(ub);
itemdata.setStatus(Status.AVAILABLE);
itemdata.setUpdater(ub);
iddao.updateUser(itemdata);
iddao.update(itemdata);
}
// OC-6291 event_crf status change
eventCRF.setOldStatus(eventCRF.getStatus());
eventCRF.setStatus(Status.AVAILABLE);
eventCRF.setUpdater(ub);
ecdao.update(eventCRF);
if (event.getSubjectEventStatus().isCompleted()
|| event.getSubjectEventStatus().isSigned()) {
event.setSubjectEventStatus(SubjectEventStatus.DATA_ENTRY_STARTED);
event.setUpdater(ub);
sedao = new StudyEventDAO(sm.getDataSource());
sedao.update(event);
}
String emailBody =
respage.getString("the_event_CRF")
+ cb.getName()
+ respage.getString("has_been_deleted_from_the_event")
+ event.getStudyEventDefinition().getName()
+ ". "
+ respage.getString("has_been_deleted_from_the_event_cont");
addPageMessage(emailBody);
// sendEmail(emailBody);
request.setAttribute("id", new Integer(studySubId).toString());
forwardPage(Page.VIEW_STUDY_SUBJECT_SERVLET);
}
}
}
public void testFindByPKFail() throws Exception {
CRFBean sb = (CRFBean) cdao.findByPK(-1);
assertNotNull("findbypk", sb);
assertTrue("inactive object", !sb.isActive());
}
// testFindByPK
public void testFindByPKSuccess() throws Exception {
CRFBean sb = (CRFBean) cdao.findByPK(1);
assertNotNull("findbypk", sb);
assertTrue("active object", sb.isActive());
assertEquals("correct object", sb.getId(), 1);
}
/**
* @api {get} /rest2/openrosa/:studyOID/formList Get Form List
* @apiName getFormList
* @apiPermission admin
* @apiVersion 1.0.0
* @apiParam {String} studyOID Study Oid.
* @apiGroup Form
* @apiDescription Retrieves a listing of the available OpenClinica forms.
* @apiParamExample {json} Request-Example: { "studyOid": "S_SAMPLTE", }
* @apiSuccessExample {xml} Success-Response: HTTP/1.1 200 OK { <xforms
* xmlns="http://openrosa.org/xforms/xformsList"> <xform> <formID>F_FIRSTFORM_1</formID>
* <name>First Form</name> <majorMinorVersion>1</majorMinorVersion> <version>1</version>
* <hash>8678370cd92814d4e3216d58d821403f</hash>
* <downloadUrl>http://oc1.openclinica.com/OpenClinica-web/rest2/openrosa/S_SAMPLTE/formXml?
* formId=F_FIRSTFORM_1</downloadUrl> </xform> <xform> <formID>F_SECONDFORM_1</formID>
* <name>Second Form</name> <majorMinorVersion>1</majorMinorVersion> <version>1</version>
* <hash>7ee60d1c6516b730bbe9bdbd7cad942f</hash>
* <downloadUrl>http://oc1.openclinica.com/OpenClinica-web/rest2/openrosa/S_SAMPLTE/formXml?
* formId=F_SECONDFORM_1</downloadUrl> </xform> </xforms>
*/
@GET
@Path("/{studyOID}/formList")
@Produces(MediaType.TEXT_XML)
public String getFormList(
@Context HttpServletRequest request,
@Context HttpServletResponse response,
@PathParam("studyOID") String studyOID,
@QueryParam("formID") String crfOID,
@RequestHeader("Authorization") String authorization,
@Context ServletContext context)
throws Exception {
if (!mayProceedPreview(studyOID)) return null;
StudyDAO sdao = new StudyDAO(getDataSource());
StudyBean study = sdao.findByOid(studyOID);
CRFDAO cdao = new CRFDAO(getDataSource());
Collection<CRFBean> crfs = cdao.findAll();
CRFVersionDAO cVersionDao = new CRFVersionDAO(getDataSource());
Collection<CRFVersionBean> crfVersions = cVersionDao.findAll();
CrfVersionMediaDao mediaDao =
(CrfVersionMediaDao)
SpringServletAccess.getApplicationContext(context).getBean("crfVersionMediaDao");
try {
XFormList formList = new XFormList();
for (CRFBean crf : crfs) {
for (CRFVersionBean version : crfVersions) {
if (version.getCrfId() == crf.getId()) {
XForm form = new XForm(crf, version);
// TODO: Need to generate hash based on contents of
// XForm. Will be done in a later story.
// TODO: For now all XForms get a date based hash to
// trick Enketo into always downloading
// TODO: them.
Calendar cal = Calendar.getInstance();
cal.setTime(new Date());
form.setHash(DigestUtils.md5Hex(String.valueOf(cal.getTimeInMillis())));
String urlBase =
getCoreResources().getDataInfo().getProperty("sysURL").split("/MainMenu")[0];
form.setDownloadURL(
urlBase + "/rest2/openrosa/" + studyOID + "/formXml?formId=" + version.getOid());
List<CrfVersionMedia> mediaList = mediaDao.findByCrfVersionId(version.getId());
if (mediaList != null && mediaList.size() > 0) {
form.setManifestURL(
urlBase + "/rest2/openrosa/" + studyOID + "/manifest?formId=" + version.getOid());
}
formList.add(form);
}
}
}
// Create the XML formList using a Castor mapping file.
XMLContext xmlContext = new XMLContext();
Mapping mapping = xmlContext.createMapping();
mapping.loadMapping(getCoreResources().getURL("openRosaFormListMapping.xml"));
xmlContext.addMapping(mapping);
Marshaller marshaller = xmlContext.createMarshaller();
StringWriter writer = new StringWriter();
marshaller.setWriter(writer);
marshaller.marshal(formList);
// Set response headers
Calendar cal = Calendar.getInstance(TimeZone.getTimeZone("GMT"));
Date currentDate = new Date();
cal.setTime(currentDate);
SimpleDateFormat format = new SimpleDateFormat("E, dd MMM yyyy HH:mm:ss zz");
format.setCalendar(cal);
response.setHeader("Content-Type", "text/xml; charset=UTF-8");
response.setHeader("Date", format.format(currentDate));
response.setHeader("X-OpenRosa-Version", "1.0");
return writer.toString();
} catch (Exception e) {
LOGGER.error(e.getMessage());
LOGGER.error(ExceptionUtils.getStackTrace(e));
return "<Error>" + e.getMessage() + "</Error>";
}
}