use of org.akaza.openclinica.dao.submit.SectionDAO in project OpenClinica by OpenClinica.
the class UrlRewriteServlet method doGet.
/**
* Handles the HTTP <code>GET</code> method.
*
* @param request
* @param response
* @throws ServletException
* @throws java.io.IOException
*/
@Override
public void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException {
try {
String requestURI = request.getRequestURI();
String requestQueryStr = request.getQueryString();
OpenClinicaResource ocResource = null;
String requestOIDStr = null;
String RESTUrlStart = "/ClinicalData/html/view/";
if ((null != requestURI) && (requestURI.contains("/ClinicalData/html/view/"))) {
requestOIDStr = requestURI.substring(requestURI.indexOf(RESTUrlStart) + RESTUrlStart.length(), requestURI.length());
}
ocResource = getOpenClinicaResourceFromURL(requestOIDStr);
if (null != ocResource) {
if (ocResource.isInValid()) {
response.sendError(HttpServletResponse.SC_NOT_FOUND);
//request.setAttribute("errorMsg", ocResource.getMessages().get(0));
errors = new HashMap();
Validator.addError(errors, "error:", ocResource.getMessages().get(0));
request.setAttribute("formMessages", errors);
}
// "/ViewSectionDataEntry"
if ((null != ocResource) && (ocResource.getFormVersionOID() != null)) {
HashMap<String, String> mapQueryParams = getQueryStringParameters(requestQueryStr);
// set the required parameters into request
if (null != ocResource.getEventDefinitionCrfId()) {
request.setAttribute("eventDefinitionCRFId", ocResource.getEventDefinitionCrfId());
}
if (null != ocResource.getEventCrfId()) {
request.setAttribute("ecId", ocResource.getEventCrfId().toString());
}
if (null != ocResource.getStudyEventId()) {
request.setAttribute("eventId", ocResource.getStudyEventId().toString());
}
if (null != ocResource.getStudySubjectID()) {
request.setAttribute("studySubjectId", ocResource.getStudySubjectID().toString());
// request.setAttribute("exitTo", "ViewStudySubject?id=" +
// ocResource.getStudySubjectID());
}
// request.setAttribute("crfVersionId","");
if ((null != mapQueryParams) && (mapQueryParams.size() != 0)) {
if (mapQueryParams.containsKey("tabId")) {
request.setAttribute("tabId", mapQueryParams.get("tabId"));
}
/* else
{
request.setAttribute("tabId", new Integer(1));
}*/
if ((null != ocResource.getStudySubjectID()) && (mapQueryParams.containsKey("exitTo"))) {
request.setAttribute("exitTo", "ViewStudySubject?id=" + ocResource.getStudySubjectID());
}
//@pgawade 16-Aug-2012: fix for issue https://issuetracker.openclinica.com/view.php?id=12343#c55853
//retrieve sectionId from tabId
SectionDAO sdao = new SectionDAO(getDataSource());
if (mapQueryParams.containsKey("tabId")) {
HashMap sectionIdMap = sdao.getSectionIdForTabId(ocResource.getFormVersionID(), Integer.parseInt(mapQueryParams.get("tabId")));
Integer sectionId = null;
if ((sectionIdMap != null) && (sectionIdMap.size() != 0)) {
sectionId = (Integer) sectionIdMap.get("section_id");
}
if (null != sectionId) {
request.setAttribute("sectionId", sectionId);
}
}
/* else{
request.setAttribute("sectionId",1);
}*/
}
//ToDo: Changes to work on to fix #0012507
// else{
// request.setAttribute("crfId", ocResource.getFormID());
// request.setAttribute("crfVersionId", ocResource.getFormVersionID());
// request.setAttribute("module", "?");
// }
forwardPage(Page.VIEW_SECTION_DATA_ENTRY_SERVLET_REST_URL, request, response);
// response.sendRedirect(Page.VIEW_SECTION_DATA_ENTRY_SERVLET.getFileName());
}
}
// implement other RESTful URLs here forwarding to corresponding
// pages of application
// (and associated combinations of mode and format)
} catch (Exception e) {
e.printStackTrace();
}
}
use of org.akaza.openclinica.dao.submit.SectionDAO in project OpenClinica by OpenClinica.
the class CreateFiltersTwoServlet method processRequest.
// < ResourceBundle restext,resword,respage,resexception;
@Override
public void processRequest() throws Exception {
// we can't get to here without an action:
// begin--takes us to specify parameters,
// where the user will select CRF, then section,
// then parameters of the section: a little tricky
// to do entirely with javascript, but can be done.
// possible to set up the CRF-section relationship,
// and then have a screen 3.5 with the parameters?
// criteria--takes us to specify criteria, that is,
// to specify and, or, not and, etc. here we'll take the
// list we just generated online and generate a chain
// of filterobjectbeans, which will in turn,
// generate the SQL add on for the dataset.
String action = request.getParameter("action");
StudyBean studyWithEventDefs = currentStudy;
if (currentStudy.getParentStudyId() > 0) {
studyWithEventDefs = new StudyBean();
studyWithEventDefs.setId(currentStudy.getParentStudyId());
}
if (StringUtil.isBlank(action)) {
// throw an error
} else if ("begin".equalsIgnoreCase(action)) {
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
HashMap events = sedao.findCRFsByStudy(studyWithEventDefs);
// if events are empty -- resend to first filter page with message
if (events.isEmpty()) {
addPageMessage(respage.getString("no_CRF_assigned_pick_another"));
FormProcessor fp = new FormProcessor(request);
FilterDAO fdao = new FilterDAO(sm.getDataSource());
EntityBeanTable table = fp.getEntityBeanTable();
ArrayList filters = (ArrayList) fdao.findAll();
ArrayList filterRows = FilterRow.generateRowsFromBeans(filters);
String[] columns = { resword.getString("filter_name"), resword.getString("description"), resword.getString("created_by"), resword.getString("created_date"), resword.getString("status"), resword.getString("actions") };
table.setColumns(new ArrayList(Arrays.asList(columns)));
table.hideColumnLink(5);
table.addLink(resword.getString("create_new_filter"), "CreateFiltersOne?action=begin");
table.setQuery("CreateFiltersOne", new HashMap());
table.setRows(filterRows);
table.computeDisplay();
request.setAttribute("table", table);
forwardPage(Page.CREATE_FILTER_SCREEN_1);
} else {
// else, send to the following page:
request.setAttribute("events", events);
forwardPage(Page.CREATE_FILTER_SCREEN_3);
}
} else if ("crfselected".equalsIgnoreCase(action)) {
// get the crf id, return to a new page with sections
// and parameters attached, tbh
FormProcessor fp = new FormProcessor(request);
HashMap errors = new HashMap();
int crfId = fp.getInt("crfId");
if (crfId > 0) {
CRFVersionDAO cvDAO = new CRFVersionDAO(sm.getDataSource());
CRFDAO cDAO = new CRFDAO(sm.getDataSource());
SectionDAO secDAO = new SectionDAO(sm.getDataSource());
Collection sections = secDAO.findByVersionId(crfId);
CRFVersionBean cvBean = (CRFVersionBean) cvDAO.findByPK(crfId);
CRFBean cBean = (CRFBean) cDAO.findByPK(cvBean.getCrfId());
request.setAttribute("sections", sections);
session.setAttribute("cBean", cBean);
// for further pages,
session.setAttribute("cvBean", cvBean);
// tbh
forwardPage(Page.CREATE_FILTER_SCREEN_3_1);
} else {
addPageMessage(respage.getString("select_a_CRF_before_picking"));
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
HashMap events = sedao.findCRFsByStudy(studyWithEventDefs);
request.setAttribute("events", events);
forwardPage(Page.CREATE_FILTER_SCREEN_3);
}
} else if ("sectionselected".equalsIgnoreCase(action)) {
// TODO set the crf and the section into session,
// allow for the user to go back and forth,
// set up the questions to be picked,
// allow the user to move on to create_filter_screen_4
FormProcessor fp = new FormProcessor(request);
int sectionId = fp.getInt("sectionId");
if (sectionId > 0) {
SectionDAO secDAO = new SectionDAO(sm.getDataSource());
SectionBean secBean = (SectionBean) secDAO.findByPK(sectionId);
session.setAttribute("secBean", secBean);
ItemFormMetadataDAO ifmDAO = new ItemFormMetadataDAO(sm.getDataSource());
Collection metadatas = ifmDAO.findAllBySectionId(sectionId);
if (metadatas.size() > 0) {
request.setAttribute("metadatas", metadatas);
forwardPage(Page.CREATE_FILTER_SCREEN_3_2);
} else {
CRFVersionBean cvBean = (CRFVersionBean) session.getAttribute("cvBean");
addPageMessage(respage.getString("section_not_have_questions_select_another"));
// SectionDAO secDAO = new SectionDAO(sm.getDataSource());
Collection sections = secDAO.findByVersionId(cvBean.getId());
request.setAttribute("sections", sections);
forwardPage(Page.CREATE_FILTER_SCREEN_3_1);
}
} else {
CRFVersionBean cvBean = (CRFVersionBean) session.getAttribute("cvBean");
addPageMessage(respage.getString("select_section_before_select_question"));
SectionDAO secDAO = new SectionDAO(sm.getDataSource());
Collection sections = secDAO.findByVersionId(cvBean.getId());
request.setAttribute("sections", sections);
forwardPage(Page.CREATE_FILTER_SCREEN_3_1);
}
} else if ("questionsselected".equalsIgnoreCase(action)) {
ArrayList alist = this.extractIdsFromForm();
// and send the user to create_filter_screen_4
if (alist.size() > 0) {
ItemFormMetadataDAO ifmDAO = new ItemFormMetadataDAO(sm.getDataSource());
Collection questions = ifmDAO.findByMultiplePKs(alist);
session.setAttribute("questions", questions);
forwardPage(Page.CREATE_FILTER_SCREEN_4);
} else {
SectionBean secBean = (SectionBean) session.getAttribute("secBean");
addPageMessage(respage.getString("select_questions_before_set_parameters"));
ItemFormMetadataDAO ifmDAO = new ItemFormMetadataDAO(sm.getDataSource());
Collection metadatas = ifmDAO.findAllBySectionId(secBean.getId());
request.setAttribute("metadatas", metadatas);
forwardPage(Page.CREATE_FILTER_SCREEN_3_2);
}
} else if ("validatecriteria".equalsIgnoreCase(action)) {
// TODO look at the criteria and create a list of filterobjectdata
// beans, so that we can create the SQL later on in
// the process.
// also, throw the user back to the process or throw
// them forward into the createServletThree process
FormProcessor fp = new FormProcessor(request);
String logical = fp.getString("logical");
ArrayList questions = (ArrayList) session.getAttribute("questions");
ArrayList filterobjects = new ArrayList();
// (ArrayList)session.getAttribute("filterobjects");
Iterator q_it = questions.iterator();
int arrCnt = 0;
while (q_it.hasNext()) {
ItemFormMetadataBean ifmBean = (ItemFormMetadataBean) q_it.next();
String opString = "operator:" + ifmBean.getId();
String valString = "value:" + ifmBean.getId();
String remString = "remove:" + ifmBean.getId();
if ("remove".equals(fp.getString(remString))) {
logger.info("found the string: " + remString);
// TODO remove the question from from the list,
// redirect to that page again????? <--maybe not?
// questions.remove(arrCnt);
// shouldn't have to remove the above, just do nothing
arrCnt++;
} else {
String operator = fp.getString(opString);
String value = fp.getString(valString);
FilterObjectBean fob = new FilterObjectBean();
fob.setItemId(ifmBean.getId());
fob.setItemName(ifmBean.getHeader() + " " + ifmBean.getLeftItemText() + " " + ifmBean.getRightItemText());
// case operator:
if ("equal to".equalsIgnoreCase(operator)) {
fob.setOperand("=");
} else if ("greater than".equalsIgnoreCase(operator)) {
fob.setOperand(">");
} else if ("less than".equalsIgnoreCase(operator)) {
fob.setOperand("<");
} else if ("greater than or equal".equalsIgnoreCase(operator)) {
fob.setOperand(">=");
} else if ("less than or equal".equalsIgnoreCase(operator)) {
fob.setOperand("<=");
} else if ("like".equalsIgnoreCase(operator)) {
fob.setOperand(" like ");
} else if ("not like".equalsIgnoreCase(operator)) {
fob.setOperand(" not like ");
} else {
fob.setOperand("!=");
}
fob.setValue(value);
filterobjects.add(fob);
}
// end else
//
}
// end while
session.setAttribute("questions", questions);
// TODO where does the connector come into play?
// session.setAttribute("filterobjects",filterobjects);
FilterDAO fDAO = new FilterDAO(sm.getDataSource());
String newSQL = (String) session.getAttribute("newSQL");
ArrayList newExp = (ArrayList) session.getAttribute("newExp");
// human readable explanation
String newNewSQL = fDAO.genSQLStatement(newSQL, logical, filterobjects);
ArrayList newNewExp = fDAO.genExplanation(newExp, logical, filterobjects);
if (arrCnt == questions.size()) {
newNewSQL = newSQL;
newNewExp = newExp;
// don't change anything, if we've removed everything from this
// list
}
logger.info("new SQL Generated: " + newNewSQL);
String sub = fp.getString("submit");
if ("Specify Filter Metadata".equals(sub)) {
// add new params, create the filter object,
// and go to create metadata
FilterBean fb = new FilterBean();
fb.setSQLStatement(newNewSQL + ")");
// adding parens here to finish off other
// statement--might add first part of statement here
// for legibility's sake
// tbh 06-02-2005
session.removeAttribute("newSQL");
// end of the road
session.setAttribute("newFilter", fb);
request.setAttribute("statuses", getStatuses());
forwardPage(Page.CREATE_FILTER_SCREEN_5);
} else {
// replace the 'old' sql with the new sql gathered from the
// session
session.setAttribute("newSQL", newNewSQL);
session.setAttribute("newExp", newNewExp);
// add new params, and go back
StudyEventDAO sedao = new StudyEventDAO(sm.getDataSource());
HashMap events = sedao.findCRFsByStudy(currentStudy);
//
request.setAttribute("events", events);
forwardPage(Page.CREATE_FILTER_SCREEN_3);
}
}
}
use of org.akaza.openclinica.dao.submit.SectionDAO in project OpenClinica by OpenClinica.
the class TableOfContentsServlet method getDisplayBeanWithShownSections.
/**
* A section contains all hidden dynamics will be removed from data entry tab and jump box.
*
* @param ds
* @param displayTableOfContentsBean
* @param dynamicsMetadataService
* @return
*/
public static DisplayTableOfContentsBean getDisplayBeanWithShownSections(DataSource ds, DisplayTableOfContentsBean displayTableOfContentsBean, DynamicsMetadataService dynamicsMetadataService) {
if (displayTableOfContentsBean == null) {
return displayTableOfContentsBean;
}
EventCRFBean ecb = displayTableOfContentsBean.getEventCRF();
SectionDAO sectionDAO = new SectionDAO(ds);
ArrayList<SectionBean> sectionBeans = getSections(ecb, ds);
ArrayList<SectionBean> showSections = new ArrayList<SectionBean>();
if (sectionBeans != null && sectionBeans.size() > 0) {
for (SectionBean s : sectionBeans) {
if (sectionDAO.containNormalItem(s.getCRFVersionId(), s.getId())) {
showSections.add(s);
} else {
//for section contains dynamics, does it contain showing item_group/item?
if (dynamicsMetadataService.hasShowingDynGroupInSection(s.getId(), s.getCRFVersionId(), ecb.getId())) {
showSections.add(s);
} else {
if (dynamicsMetadataService.hasShowingDynItemInSection(s.getId(), s.getCRFVersionId(), ecb.getId())) {
showSections.add(s);
}
}
}
}
displayTableOfContentsBean.setSections(showSections);
}
return displayTableOfContentsBean;
}
use of org.akaza.openclinica.dao.submit.SectionDAO in project OpenClinica by OpenClinica.
the class TableOfContentsServlet method getDisplayBean.
public static DisplayTableOfContentsBean getDisplayBean(EventCRFBean ecb, DataSource ds, StudyBean currentStudy) {
DisplayTableOfContentsBean answer = new DisplayTableOfContentsBean();
answer.setEventCRF(ecb);
// get data
StudySubjectDAO ssdao = new StudySubjectDAO(ds);
StudySubjectBean ssb = (StudySubjectBean) ssdao.findByPK(ecb.getStudySubjectId());
answer.setStudySubject(ssb);
StudyEventDAO sedao = new StudyEventDAO(ds);
StudyEventBean seb = (StudyEventBean) sedao.findByPK(ecb.getStudyEventId());
answer.setStudyEvent(seb);
SectionDAO sdao = new SectionDAO(ds);
ArrayList sections = getSections(ecb, ds);
answer.setSections(sections);
// get metadata
StudyEventDefinitionDAO seddao = new StudyEventDefinitionDAO(ds);
StudyEventDefinitionBean sedb = (StudyEventDefinitionBean) seddao.findByPK(seb.getStudyEventDefinitionId());
answer.setStudyEventDefinition(sedb);
CRFVersionDAO cvdao = new CRFVersionDAO(ds);
CRFVersionBean cvb = (CRFVersionBean) cvdao.findByPK(ecb.getCRFVersionId());
answer.setCrfVersion(cvb);
CRFDAO cdao = new CRFDAO(ds);
CRFBean cb = (CRFBean) cdao.findByPK(cvb.getCrfId());
answer.setCrf(cb);
StudyBean studyForStudySubject = new StudyDAO(ds).findByStudySubjectId(ssb.getId());
EventDefinitionCRFDAO edcdao = new EventDefinitionCRFDAO(ds);
EventDefinitionCRFBean edcb = edcdao.findByStudyEventDefinitionIdAndCRFId(studyForStudySubject, sedb.getId(), cb.getId());
answer.setEventDefinitionCRF(edcb);
answer.setAction(getActionForStage(ecb.getStage()));
return answer;
}
use of org.akaza.openclinica.dao.submit.SectionDAO in project OpenClinica by OpenClinica.
the class FormBeanUtil method createDisplaySectionBWithFormGroupsForPrint.
public DisplaySectionBean createDisplaySectionBWithFormGroupsForPrint(int sectionId, int crfVersionId, DataSource dataSource, int eventCRFDefId, EventCRFBean eventCrfBean, ServletContext context) {
DisplaySectionBean displaySectionBean = new DisplaySectionBean();
ItemGroupDAO formGroupDAO = new ItemGroupDAO(dataSource);
ItemGroupMetadataDAO igMetaDAO = new ItemGroupMetadataDAO(dataSource);
ItemDAO itemDao = new ItemDAO(dataSource);
ItemFormMetadataDAO metaDao = new ItemFormMetadataDAO(dataSource);
SectionDAO sectionDao = new SectionDAO(dataSource);
// Give the DisplaySectionBean a legitimate SectionBean
SectionBean secBean = (SectionBean) sectionDao.findByPK(sectionId);
displaySectionBean.setSection(secBean);
// changed from: findGroupBySectionId
List<ItemGroupBean> itemGroupBeans = formGroupDAO.findLegitGroupAllBySectionId(sectionId);
// all items associated with the section, including those not in a group
List<ItemFormMetadataBean> allMetas = new ArrayList<ItemFormMetadataBean>();
try {
allMetas = metaDao.findAllBySectionId(sectionId);
} catch (OpenClinicaException oce) {
logger.info("oce.getOpenClinicaMessage() = " + oce.getOpenClinicaMessage());
}
// Sort these items according to their position on the CRF; their
// ordinal
Collections.sort(allMetas);
// The DisplayItemGroupBean(s) for "nongrouped" items
List<DisplayItemGroupBean> nonGroupBeans = null;
// if(itemGroupBeans.isEmpty()) return displaySectionBean;
// Find out whether there are any checkboxes/radios/select elements
// and if so, get any null values
// associated with them
List<String> nullValuesList = new ArrayList<String>();
boolean itemsHaveChecksRadios = itemsIncludeChecksRadiosSelects(allMetas);
if (itemsHaveChecksRadios && eventCRFDefId > 0) {
// method returns null values as a List<String>
nullValuesList = this.getNullValuesByEventCRFDefId(eventCRFDefId, dataSource);
}
// Get the items associated with each group
List<ItemBean> itBeans;
List<DisplayItemBean> displayItems;
List<DisplayItemGroupBean> displayFormBeans = new ArrayList<DisplayItemGroupBean>();
DisplayItemGroupBean displayItemGBean;
for (ItemGroupBean itemGroup : itemGroupBeans) {
//TODO:fix me!
itBeans = itemDao.findAllItemsByGroupIdForPrint(itemGroup.getId(), crfVersionId, sectionId);
logger.debug("just ran find all by group id " + itemGroup.getId() + " found " + itBeans.size() + " item beans");
//TODO:fix me add item_form_metadata.section_id to the query
List<ItemGroupMetadataBean> metadata = igMetaDAO.findMetaByGroupAndSectionForPrint(itemGroup.getId(), crfVersionId, sectionId);
if (!metadata.isEmpty()) {
// for a given crf version, all the items in the same group
// have the same group metadata info
// so we can get one of the metadata and set the metadata for
// the group
ItemGroupMetadataBean meta = metadata.get(0);
itemGroup.setMeta(meta);
}
displayItems = getDisplayBeansFromItemsForPrint(itBeans, dataSource, eventCrfBean, sectionId, nullValuesList, context, crfVersionId);
displayItemGBean = this.createDisplayFormGroup(displayItems, itemGroup);
displayFormBeans.add(displayItemGBean);
}
// We still have to sort these display item group beans on their
// ItemGroupMetadataBean?
// then number their ordinals accordingly
Collections.sort(displayFormBeans, new Comparator<DisplayItemGroupBean>() {
public int compare(DisplayItemGroupBean displayItemGroupBean, DisplayItemGroupBean displayItemGroupBean1) {
return displayItemGroupBean.getGroupMetaBean().compareTo(displayItemGroupBean1.getGroupMetaBean());
}
});
// Now provide the display item group beans with an ordinal
int digOrdinal = 0;
for (DisplayItemGroupBean digBean : displayFormBeans) {
digBean.setOrdinal(++digOrdinal);
}
// find out whether there are any ungrouped items by comparing the
// number of
// grouped items to allMetas.size()
// List<DisplayItemGroupBean> nonGroupBeans=null;
int tempCount = 0;
for (DisplayItemGroupBean groupBean : displayFormBeans) {
tempCount += groupBean.getItems().size();
}
if (tempCount < allMetas.size()) {
nonGroupBeans = createGroupBeansForNongroupedItems(allMetas, displayFormBeans, sectionId, dataSource, nullValuesList, eventCrfBean, context);
}
if (nonGroupBeans != null) {
displayFormBeans.addAll(nonGroupBeans);
}
// sort the list according to the ordinal of the contained
// DisplayItemGroupBeans
Collections.sort(displayFormBeans, new Comparator<DisplayItemGroupBean>() {
public int compare(DisplayItemGroupBean disFormGroupBean, DisplayItemGroupBean disFormGroupBean1) {
Integer compInt = disFormGroupBean1.getOrdinal();
Integer compInt2 = disFormGroupBean.getOrdinal();
return compInt2.compareTo(compInt);
}
});
displaySectionBean.setDisplayFormGroups(displayFormBeans);
return displaySectionBean;
}
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