package org.akaza.openclinica.web.crfdata;
import org.akaza.openclinica.bean.admin.CRFBean;
import org.akaza.openclinica.bean.core.DataEntryStage;
import org.akaza.openclinica.bean.core.ItemDataType;
import org.akaza.openclinica.bean.core.NullValue;
import org.akaza.openclinica.bean.core.ResponseType;
import org.akaza.openclinica.bean.core.Status;
import org.akaza.openclinica.bean.core.SubjectEventStatus;
import org.akaza.openclinica.bean.login.UserAccountBean;
import org.akaza.openclinica.bean.managestudy.EventDefinitionCRFBean;
import org.akaza.openclinica.bean.managestudy.StudyBean;
import org.akaza.openclinica.bean.managestudy.StudyEventBean;
import org.akaza.openclinica.bean.managestudy.StudyEventDefinitionBean;
import org.akaza.openclinica.bean.managestudy.StudySubjectBean;
import org.akaza.openclinica.bean.submit.CRFVersionBean;
import org.akaza.openclinica.bean.submit.DisplayItemBean;
import org.akaza.openclinica.bean.submit.DisplayItemBeanWrapper;
import org.akaza.openclinica.bean.submit.EventCRFBean;
import org.akaza.openclinica.bean.submit.ItemBean;
import org.akaza.openclinica.bean.submit.ItemDataBean;
import org.akaza.openclinica.bean.submit.ItemFormMetadataBean;
import org.akaza.openclinica.bean.submit.ItemGroupBean;
import org.akaza.openclinica.bean.submit.ResponseOptionBean;
import org.akaza.openclinica.bean.submit.crfdata.FormDataBean;
import org.akaza.openclinica.bean.submit.crfdata.ImportItemDataBean;
import org.akaza.openclinica.bean.submit.crfdata.ImportItemGroupDataBean;
import org.akaza.openclinica.bean.submit.crfdata.ODMContainer;
import org.akaza.openclinica.bean.submit.crfdata.StudyEventDataBean;
import org.akaza.openclinica.bean.submit.crfdata.SubjectDataBean;
import org.akaza.openclinica.bean.submit.crfdata.SummaryStatsBean;
import org.akaza.openclinica.bean.submit.crfdata.UpsertOnBean;
import org.akaza.openclinica.control.form.DiscrepancyValidator;
import org.akaza.openclinica.control.form.FormDiscrepancyNotes;
import org.akaza.openclinica.control.form.Validator;
import org.akaza.openclinica.control.submit.ImportCRFInfoContainer;
import org.akaza.openclinica.dao.admin.CRFDAO;
import org.akaza.openclinica.dao.managestudy.EventDefinitionCRFDAO;
import org.akaza.openclinica.dao.managestudy.StudyDAO;
import org.akaza.openclinica.dao.managestudy.StudyEventDAO;
import org.akaza.openclinica.dao.managestudy.StudyEventDefinitionDAO;
import org.akaza.openclinica.dao.managestudy.StudySubjectDAO;
import org.akaza.openclinica.dao.submit.CRFVersionDAO;
import org.akaza.openclinica.dao.submit.EventCRFDAO;
import org.akaza.openclinica.dao.submit.ItemDAO;
import org.akaza.openclinica.dao.submit.ItemDataDAO;
import org.akaza.openclinica.dao.submit.ItemFormMetadataDAO;
import org.akaza.openclinica.dao.submit.ItemGroupDAO;
import org.akaza.openclinica.exception.OpenClinicaException;
import org.akaza.openclinica.i18n.util.ResourceBundleProvider;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.math.BigDecimal;
import java.text.MessageFormat;
import java.text.ParseException;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Locale;
import java.util.ResourceBundle;
import javax.servlet.http.HttpServletRequest;
import javax.sql.DataSource;
public class ImportCRFDataService {
protected final Logger logger = LoggerFactory.getLogger(getClass().getName());
private final DataSource ds;
private ItemDataDAO itemDataDao;
public static ResourceBundle respage;
public ImportCRFDataService(DataSource ds, Locale locale) {
ResourceBundleProvider.updateLocale(locale);
respage = ResourceBundleProvider.getPageMessagesBundle(locale);
this.ds = ds;
}
/*
* purpose: look up EventCRFBeans by the following: Study Subject, Study Event, CRF Version, using the
* findByEventSubjectVersion method in EventCRFDAO. May return more than one, hmm.
*/
public List<EventCRFBean> fetchEventCRFBeans(ODMContainer odmContainer, UserAccountBean ub) {
ArrayList<EventCRFBean> eventCRFBeans = new ArrayList<EventCRFBean>();
ArrayList<Integer> eventCRFBeanIds = new ArrayList<Integer>();
EventCRFDAO eventCrfDAO = new EventCRFDAO(ds);
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
StudyDAO studyDAO = new StudyDAO(ds);
StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
UpsertOnBean upsert = odmContainer.getCrfDataPostImportContainer().getUpsertOn();
// If Upsert bean is not present, create one with default settings
if (upsert == null)
upsert = new UpsertOnBean();
String studyOID = odmContainer.getCrfDataPostImportContainer().getStudyOID();
StudyBean studyBean = studyDAO.findByOid(studyOID);
ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
String sampleOrdinal = studyEventDataBean.getStudyEventRepeatKey() == null ? "1" : studyEventDataBean.getStudyEventRepeatKey();
StudyEventDefinitionBean studyEventDefinitionBean = studyEventDefinitionDAO.findByOidAndStudy(studyEventDataBean.getStudyEventOID(),
studyBean.getId(), studyBean.getParentStudyId());
logger.info("find all by def and subject " + studyEventDefinitionBean.getName() + " study subject " + studySubjectBean.getName());
StudyEventBean studyEventBean = (StudyEventBean) studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectBean.getId(),
studyEventDefinitionBean.getId(), Integer.parseInt(sampleOrdinal));
// @pgawade 16-March-2011 Do not allow the data import
// if event status is one of the - stopped, signed,
// locked
if (studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.LOCKED)
|| studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SIGNED)
|| studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.STOPPED)) {
return null;
}
for (FormDataBean formDataBean : formDataBeans) {
CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formDataBean.getFormOID());
for (CRFVersionBean crfVersionBean : crfVersionBeans) {
ArrayList<EventCRFBean> eventCrfBeans = eventCrfDAO.findByEventSubjectVersion(studyEventBean, studySubjectBean, crfVersionBean);
// what if we have begun with creating a study
// event, but haven't entered data yet? this would
// have us with a study event, but no corresponding
// event crf, yet.
if (eventCrfBeans.isEmpty()) {
logger.debug(" found no event crfs from Study Event id " + studyEventBean.getId() + ", location " + studyEventBean.getLocation());
// spell out criteria and create a bean if
// necessary, avoiding false-positives
if ((studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SCHEDULED)
|| studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.DATA_ENTRY_STARTED) || studyEventBean
.getSubjectEventStatus().equals(SubjectEventStatus.COMPLETED)) && upsert.isNotStarted()) {
EventCRFBean newEventCrfBean = new EventCRFBean();
newEventCrfBean.setStudyEventId(studyEventBean.getId());
newEventCrfBean.setStudySubjectId(studySubjectBean.getId());
newEventCrfBean.setCRFVersionId(crfVersionBean.getId());
newEventCrfBean.setDateInterviewed(new Date());
newEventCrfBean.setOwner(ub);
newEventCrfBean.setInterviewerName(ub.getName());
newEventCrfBean.setCompletionStatusId(1);// place
// filler
newEventCrfBean.setStatus(Status.AVAILABLE);
newEventCrfBean.setStage(DataEntryStage.INITIAL_DATA_ENTRY);
// these will be updated later in the
// workflow
newEventCrfBean = (EventCRFBean) eventCrfDAO.create(newEventCrfBean);
// eventCrfBeans.add(newEventCrfBean);
logger.debug(" created and added new event crf");
if (!eventCRFBeanIds.contains(newEventCrfBean.getId())) {
eventCRFBeans.add(newEventCrfBean);
eventCRFBeanIds.add(newEventCrfBean.getId());
}
}
}
// below to prevent duplicates
for (EventCRFBean ecb : eventCrfBeans) {
Integer ecbId = new Integer(ecb.getId());
if ((upsert.isDataEntryStarted() && ecb.getStage().equals(DataEntryStage.INITIAL_DATA_ENTRY))
|| (upsert.isDataEntryComplete() && ecb.getStage().equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE)))
if (!eventCRFBeanIds.contains(ecbId)) {
eventCRFBeans.add(ecb);
eventCRFBeanIds.add(ecbId);
}
}
}
}
}
}
// if it's null, throw an error, since they should be existing beans for
// iteration one
return eventCRFBeans;
}
/*
* purpose: returns false if any of the forms/EventCRFs fail the UpsertOnBean rules.
*/
public boolean eventCRFStatusesValid(ODMContainer odmContainer, UserAccountBean ub) {
ArrayList<EventCRFBean> eventCRFBeans = new ArrayList<EventCRFBean>();
ArrayList<Integer> eventCRFBeanIds = new ArrayList<Integer>();
EventCRFDAO eventCrfDAO = new EventCRFDAO(ds);
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
StudyDAO studyDAO = new StudyDAO(ds);
StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
UpsertOnBean upsert = odmContainer.getCrfDataPostImportContainer().getUpsertOn();
// If Upsert bean is not present, create one with default settings
if (upsert == null)
upsert = new UpsertOnBean();
String studyOID = odmContainer.getCrfDataPostImportContainer().getStudyOID();
StudyBean studyBean = studyDAO.findByOid(studyOID);
ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
String sampleOrdinal = studyEventDataBean.getStudyEventRepeatKey() == null ? "1" : studyEventDataBean.getStudyEventRepeatKey();
StudyEventDefinitionBean studyEventDefinitionBean = studyEventDefinitionDAO.findByOidAndStudy(studyEventDataBean.getStudyEventOID(),
studyBean.getId(), studyBean.getParentStudyId());
logger.info("find all by def and subject " + studyEventDefinitionBean.getName() + " study subject " + studySubjectBean.getName());
StudyEventBean studyEventBean = (StudyEventBean) studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectBean.getId(),
studyEventDefinitionBean.getId(), Integer.parseInt(sampleOrdinal));
// @pgawade 16-March-2011 Do not allow the data import
// if event status is one of the - stopped, signed,
// locked
if (studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.LOCKED)
|| studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SIGNED)
|| studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.STOPPED)) {
return true;
}
for (FormDataBean formDataBean : formDataBeans) {
CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formDataBean.getFormOID());
for (CRFVersionBean crfVersionBean : crfVersionBeans) {
ArrayList<EventCRFBean> eventCrfBeans = eventCrfDAO.findByEventSubjectVersion(studyEventBean, studySubjectBean, crfVersionBean);
// what if we have begun with creating a study
// event, but haven't entered data yet? this would
// have us with a study event, but no corresponding
// event crf, yet.
if (eventCrfBeans.isEmpty()) {
logger.debug(" found no event crfs from Study Event id " + studyEventBean.getId() + ", location " + studyEventBean.getLocation());
if ((studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.SCHEDULED)
|| studyEventBean.getSubjectEventStatus().equals(SubjectEventStatus.DATA_ENTRY_STARTED) || studyEventBean
.getSubjectEventStatus().equals(SubjectEventStatus.COMPLETED))) {
if (!upsert.isNotStarted())
return false;
}
}
// below to prevent duplicates
for (EventCRFBean ecb : eventCrfBeans) {
Integer ecbId = new Integer(ecb.getId());
if (!(ecb.getStage().equals(DataEntryStage.INITIAL_DATA_ENTRY) && upsert.isDataEntryStarted())
&& !(ecb.getStage().equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) && upsert.isDataEntryComplete()))
return false;
}
}
}
}
}
return true;
}
/*
* purpose: Build a map of EventCRFs and the statuses they should have post-import. Assumes EventCRFs have been
* created for "Not Started" forms.
*/
public HashMap<Integer, String> fetchEventCRFStatuses(ODMContainer odmContainer) {
HashMap<Integer, String> eventCRFStatuses = new HashMap<Integer, String>();
EventCRFDAO eventCrfDAO = new EventCRFDAO(ds);
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
StudyDAO studyDAO = new StudyDAO(ds);
StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
String studyOID = odmContainer.getCrfDataPostImportContainer().getStudyOID();
StudyBean studyBean = studyDAO.findByOid(studyOID);
ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
String sampleOrdinal = studyEventDataBean.getStudyEventRepeatKey() == null ? "1" : studyEventDataBean.getStudyEventRepeatKey();
StudyEventDefinitionBean studyEventDefinitionBean = studyEventDefinitionDAO.findByOidAndStudy(studyEventDataBean.getStudyEventOID(),
studyBean.getId(), studyBean.getParentStudyId());
logger.info("find all by def and subject " + studyEventDefinitionBean.getName() + " study subject " + studySubjectBean.getName());
StudyEventBean studyEventBean = (StudyEventBean) studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectBean.getId(),
studyEventDefinitionBean.getId(), Integer.parseInt(sampleOrdinal));
for (FormDataBean formDataBean : formDataBeans) {
CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formDataBean.getFormOID());
for (CRFVersionBean crfVersionBean : crfVersionBeans) {
ArrayList<EventCRFBean> eventCrfBeans = eventCrfDAO.findByEventSubjectVersion(studyEventBean, studySubjectBean, crfVersionBean);
for (EventCRFBean ecb : eventCrfBeans) {
Integer ecbId = new Integer(ecb.getId());
if (!eventCRFStatuses.keySet().contains(ecbId) && formDataBean.getEventCRFStatus() != null) {
eventCRFStatuses.put(ecb.getId(), formDataBean.getEventCRFStatus());
}
}
}
}
}
}
return eventCRFStatuses;
}
public SummaryStatsBean generateSummaryStatsBean(ODMContainer odmContainer, List<DisplayItemBeanWrapper> wrappers, ImportCRFInfoContainer importCrfInfo) {
int countSubjects = 0;
int countEventCRFs = 0;
int discNotesGenerated = 0;
for (DisplayItemBeanWrapper wr : wrappers) {
HashMap validations = wr.getValidationErrors();
discNotesGenerated += validations.size();
}
ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
countSubjects += subjectDataBeans.size();
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
// this would be the place to add more stats
for (FormDataBean formDataBean : formDataBeans) {
countEventCRFs += 1;
}
}
}
SummaryStatsBean ssBean = new SummaryStatsBean();
ssBean.setDiscNoteCount(discNotesGenerated);
ssBean.setEventCrfCount(countEventCRFs);
ssBean.setStudySubjectCount(countSubjects);
ssBean.setSkippedCrfCount(importCrfInfo.getCountSkippedEventCrfs());
return ssBean;
}
public List<DisplayItemBeanWrapper> lookupValidationErrors(HttpServletRequest request, ODMContainer odmContainer, UserAccountBean ub,
HashMap<String, String> totalValidationErrors, HashMap<String, String> hardValidationErrors, ArrayList<Integer> permittedEventCRFIds)
throws OpenClinicaException {
DisplayItemBeanWrapper displayItemBeanWrapper = null;
HashMap validationErrors = new HashMap();
List<DisplayItemBeanWrapper> wrappers = new ArrayList<DisplayItemBeanWrapper>();
ImportHelper importHelper = new ImportHelper();
FormDiscrepancyNotes discNotes = new FormDiscrepancyNotes();
DiscrepancyValidator discValidator = new DiscrepancyValidator(request, discNotes);
// create a second Validator, this one for hard edit checks
HashMap<String, String> hardValidator = new HashMap<String, String>();
StudyEventDAO studyEventDAO = new StudyEventDAO(ds);
StudyDAO studyDAO = new StudyDAO(ds);
StudyBean studyBean = studyDAO.findByOid(odmContainer.getCrfDataPostImportContainer().getStudyOID());
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
StudyEventDefinitionDAO sedDao = new StudyEventDefinitionDAO(ds);
int maxOrdinal = 1;
HashMap<String, ItemDataBean> blankCheck = new HashMap<String, ItemDataBean>();
// << TBH #5548, checking for blank item datas
String hardValidatorErrorMsgs = "";
ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
int totalEventCRFCount = 0;
int totalItemDataBeanCount = 0;
// int totalValidationErrors = 0;
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
ArrayList<DisplayItemBean> displayItemBeans = new ArrayList<DisplayItemBean>();
logger.debug("iterating through subject data beans: found " + subjectDataBean.getSubjectOID());
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
totalEventCRFCount += studyEventDataBeans.size();
// ArrayList<Integer> eventCRFBeanIds = new ArrayList<Integer>();
// to stop repeats...?
StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(subjectDataBean.getSubjectOID(), studyBean.getId());
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
// resetting max ordinal here, to try and stop 'multiple item creation'
// 5975, tbh 10/2010
maxOrdinal = 1;
// << 5975, tbh 2010
int parentStudyId = studyBean.getParentStudyId();
StudyEventDefinitionBean sedBean = sedDao.findByOidAndStudy(studyEventDataBean.getStudyEventOID(), studyBean.getId(), parentStudyId);
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
logger.debug("iterating through study event data beans: found " + studyEventDataBean.getStudyEventOID());
int ordinal = 1;
try {
ordinal = new Integer(studyEventDataBean.getStudyEventRepeatKey()).intValue();
} catch (Exception e) {
// trying to catch NPEs, because tags can be without the
// repeat key
}
StudyEventBean studyEvent = (StudyEventBean) studyEventDAO.findByStudySubjectIdAndDefinitionIdAndOrdinal(studySubjectBean.getId(),
sedBean.getId(), ordinal);
displayItemBeans = new ArrayList<DisplayItemBean>();
// INIT here instead, tbh 08/2008
for (FormDataBean formDataBean : formDataBeans) {
maxOrdinal = 1;// JN:Moving maxOrdinal here, so max ordinal is there per form rather than per study
// eventData bean
displayItemBeanWrapper = null;
// displayItemBeans = new ArrayList<DisplayItemBean>();
// list initialized in only one place above, tbh 08/2008
CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
EventCRFDAO eventCRFDAO = new EventCRFDAO(ds);
ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formDataBean.getFormOID());
ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
// >>> tbh 05/22/2010
if ((crfVersionBeans == null) || (crfVersionBeans.size() == 0)) {
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_crf_version_oid_did_not_generate"));
Object[] arguments = { formDataBean.getFormOID() };
throw new OpenClinicaException(mf.format(arguments), "");
}
CRFVersionBean crfVersion = crfVersionBeans.get(0);
// if you have a mispelled form oid you get an error here
// need to error out gracefully and post an error
logger.debug("iterating through form beans: found " + crfVersion.getOid());
// may be the point where we cut off item groups etc and
// instead work on sections
EventCRFBean eventCRFBean = eventCRFDAO.findByEventCrfVersion(studyEvent, crfVersion);
// >>tbh, 09/2008
// logger.debug("found event crf bean: using study event " + studyEvent.getId() +
// " crf version name: " + crfVersion.getOid());
// >>
EventDefinitionCRFDAO eventDefinitionCRFDAO = new EventDefinitionCRFDAO(ds);
EventDefinitionCRFBean eventDefinitionCRF = eventDefinitionCRFDAO.findByStudyEventIdAndCRFVersionId(studyBean, studyEvent.getId(),
crfVersion.getId());
if (eventCRFBean != null) {
if (permittedEventCRFIds.contains(new Integer(eventCRFBean.getId()))) {
// if and only if it's in the correct status do we need
// to generate the beans
// <<tbh, 09/2008
// also need to create a group name checker here for
// correctness, tbh
for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
ArrayList<ItemBean> blankCheckItems = new ArrayList<ItemBean>();
// << TBH reset of the blank checks
ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
logger.debug("iterating through group beans: " + itemGroupDataBean.getItemGroupOID());
// put a checker in here
ItemGroupDAO itemGroupDAO = new ItemGroupDAO(ds);
ItemGroupBean testBean = itemGroupDAO.findByOid(itemGroupDataBean.getItemGroupOID());
if (testBean == null) {
// TODO i18n of message
// logger.debug("hit the exception for item groups! " +
// itemGroupDataBean.getItemGroupOID());
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("your_item_group_oid_for_form_oid"));
Object[] arguments = { itemGroupDataBean.getItemGroupOID(), formDataBean.getFormOID() };
throw new OpenClinicaException(mf.format(arguments), "");
// throw new OpenClinicaException("message
// here", "");
// your_item_group_oid_for_form_oid
}
totalItemDataBeanCount += itemDataBeans.size();
for (ImportItemDataBean importItemDataBean : itemDataBeans) {
logger.debug(" iterating through item data beans: " + importItemDataBean.getItemOID());
ItemDAO itemDAO = new ItemDAO(ds);
ItemFormMetadataDAO itemFormMetadataDAO = new ItemFormMetadataDAO(ds);
// ItemDataDAO itemDataDAO = new ItemDataDAO(ds);
List<ItemBean> itemBeans = itemDAO.findByOid(importItemDataBean.getItemOID());
if (!itemBeans.isEmpty()) {
ItemBean itemBean = itemBeans.get(0);
logger.debug(" found " + itemBean.getName());
// throw a
// null
// pointer?
// hopefully
// not if
// its been
// checked...
DisplayItemBean displayItemBean = new DisplayItemBean();
displayItemBean.setItem(itemBean);
ArrayList<ItemFormMetadataBean> metadataBeans = itemFormMetadataDAO.findAllByItemId(itemBean.getId());
logger.debug(" found metadata item beans: " + metadataBeans.size());
// groupOrdinal = the ordinal in item
// groups,
// for repeating items
int groupOrdinal = 1;
if (itemGroupDataBean.getItemGroupRepeatKey() != null) {
try {
groupOrdinal = new Integer(itemGroupDataBean.getItemGroupRepeatKey()).intValue();
if (groupOrdinal > maxOrdinal) {
maxOrdinal = groupOrdinal;
}
} catch (Exception e) {
// do nothing here currently, we are
// looking for a number format
// exception
// from the above.
logger.debug("found npe for group ordinals, line 344!");
}
}
ItemDataBean itemDataBean = createItemDataBean(itemBean, eventCRFBean, importItemDataBean.getValue(), ub, groupOrdinal);
blankCheckItems.add(itemBean);
String newKey = groupOrdinal + "_" + itemGroupDataBean.getItemGroupOID() + "_" + itemBean.getOid() + "_"
+ subjectDataBean.getSubjectOID();
blankCheck.put(newKey, itemDataBean);
logger.info("adding " + newKey + " to blank checks");
if (!metadataBeans.isEmpty()) {
ItemFormMetadataBean metadataBean = metadataBeans.get(0);
// also
// possible
// nullpointer
displayItemBean.setData(itemDataBean);
displayItemBean.setMetadata(metadataBean);
// set event def crf?
displayItemBean.setEventDefinitionCRF(eventDefinitionCRF);
String eventCRFRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
// if you do indeed leave off this in the XML it will pass but return 'null'
// tbh
attachValidator(displayItemBean, importHelper, discValidator, hardValidator, request, eventCRFRepeatKey,
studySubjectBean.getOid());
displayItemBeans.add(displayItemBean);
} else {
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("no_metadata_could_be_found"));
Object[] arguments = { importItemDataBean.getItemOID() };
throw new OpenClinicaException(mf.format(arguments), "");
// respage.getString("No Metadata could
// be
// found for your item key " +
// importItemDataBean.getItemOID(), "");
}
} else {
// report the error there
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("no_item_could_be_found"));
Object[] arguments = { importItemDataBean.getItemOID() };
throw new OpenClinicaException(mf.format(arguments), "");
// throw new OpenClinicaException("No Item
// could
// be found with the key " +
// importItemDataBean.getItemOID(), "");
}
}// end item data beans
logger.debug(".. found blank check: " + blankCheck.toString());
// logger.debug(".. and found blank check items: " + blankCheckItems.toString());
// >> TBH #5548 did we create any repeated blank spots? If so, fill them in with an Item
// Data Bean
// JN: this max Ordinal can cause problems as it assumes the latest values, and when
// there
// is an entry with nongroup towards the
// end. Refer: MANTIS 6113
for (int i = 1; i <= maxOrdinal; i++) {
for (ItemBean itemBean : blankCheckItems) {
String newKey = i + "_" + itemGroupDataBean.getItemGroupOID() + "_" + itemBean.getOid() + "_"
+ subjectDataBean.getSubjectOID();
if (blankCheck.get(newKey) == null) {
// if it already exists, Do Not Add It.
ItemDataBean itemDataCheck = getItemDataDao().findByItemIdAndEventCRFIdAndOrdinal(itemBean.getId(),
eventCRFBean.getId(), i);
logger.debug("found item data bean id: " + itemDataCheck.getId() + " for ordinal " + i);
if (itemDataCheck.getId() == 0) {
ItemDataBean blank = createItemDataBean(itemBean, eventCRFBean, "", ub, i);
DisplayItemBean displayItemBean = new DisplayItemBean();
displayItemBean.setItem(itemBean);
displayItemBean.setData(blank);
// displayItemBean.setMetadata(metadataBean);
// set event def crf?
displayItemBean.setEventDefinitionCRF(eventDefinitionCRF);
String eventCRFRepeatKey = studyEventDataBean.getStudyEventRepeatKey();
// if you do indeed leave off this in the XML it will pass but return
// 'null'
// tbh
displayItemBeans.add(displayItemBean);
logger.debug("... adding display item bean");
}
}
logger.debug("found a blank at " + i + ", adding " + blankCheckItems.size() + " blank items");
}
}
// << tbh #5548
blankCheckItems = new ArrayList<ItemBean>();
}// end item group data beans
}// matches if on permittedCRFIDs
CRFDAO crfDAO = new CRFDAO(ds);
CRFBean crfBean = crfDAO.findByVersionId(crfVersion.getCrfId());
// seems like an extravagance, but is not contained in crf
// version or event crf bean
validationErrors = discValidator.validate();
// totalValidationErrors += validationErrors.size();
// totalValidationErrors.
// totalValidationErrors.addAll(validationErrors);
for (Object errorKey : validationErrors.keySet()) {
// logger.debug(errorKey.toString() + " -- " + validationErrors.get(errorKey));
// JN: to avoid duplicate errors
if (!totalValidationErrors.containsKey(errorKey.toString()))
totalValidationErrors.put(errorKey.toString(), validationErrors.get(errorKey).toString());
// assuming that this will be put back in to the core
// method's hashmap, updating statically, tbh 06/2008
logger.debug("+++ adding " + errorKey.toString());
}
logger.debug("-- hard validation checks: --");
for (Object errorKey : hardValidator.keySet()) {
logger.debug(errorKey.toString() + " -- " + hardValidator.get(errorKey));
hardValidationErrors.put(errorKey.toString(), hardValidator.get(errorKey));
// updating here 'statically' tbh 06/2008
hardValidatorErrorMsgs += hardValidator.get(errorKey) + "<br/><br/>";
}
String studyEventId = studyEvent.getId() + "";
String crfVersionId = crfVersion.getId() + "";
logger.debug("creation of wrapper: original count of display item beans " + displayItemBeans.size() + ", count of item data beans "
+ totalItemDataBeanCount + " count of validation errors " + validationErrors.size() + " count of study subjects "
+ subjectDataBeans.size() + " count of event crfs " + totalEventCRFCount + " count of hard error checks "
+ hardValidator.size());
// possibly create the import summary here
logger.debug("creation of wrapper: max ordinal found " + maxOrdinal);
// check if we need to overwrite
DataEntryStage dataEntryStage = eventCRFBean.getStage();
Status eventCRFStatus = eventCRFBean.getStatus();
boolean overwrite = false;
// tbh >>
// //JN: Commenting out the following 2 lines, coz the prompt should come in the cases on
if (// eventCRFStatus.equals(Status.UNAVAILABLE) ||
dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY_COMPLETE) || dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY_COMPLETE)
|| dataEntryStage.equals(DataEntryStage.INITIAL_DATA_ENTRY) || dataEntryStage.equals(DataEntryStage.DOUBLE_DATA_ENTRY)) {
overwrite = true;
}
// << tbh, adding extra statuses to prevent appending, 06/2009
// SummaryStatsBean ssBean = new SummaryStatsBean();
// ssBean.setDiscNoteCount(totalValidationErrors);
// ssBean.setEventCrfCount(totalEventCRFCount);
// ssBean.setStudySubjectCount(subjectDataBeans.size());
// // add other stats here, tbh
// not working here, need to do it in a different method,
// tbh
// summary stats added tbh 05/2008
// JN: Changed from validationErrors to totalValidationErrors to create discrepancy notes for
// all
// the
displayItemBeanWrapper = new DisplayItemBeanWrapper(displayItemBeans, true, overwrite, validationErrors, studyEventId, crfVersionId,
studyEventDataBean.getStudyEventOID(), studySubjectBean.getLabel(), eventCRFBean.getCreatedDate(), crfBean.getName(),
crfVersion.getName(), studySubjectBean.getOid(), studyEventDataBean.getStudyEventRepeatKey());
// JN: Commenting out the following code, since we shouldn't re-initialize at this point, as
// validationErrors would get overwritten and the
// older errors will be overriden. Moving it after the form.
// Removing the comments for now, since it seems to be creating duplicate Discrepancy Notes.
validationErrors = new HashMap();
discValidator = new DiscrepancyValidator(request, discNotes);
// reset to allow for new errors...
}
}// after forms
// validationErrors = new HashMap();
// discValidator = new DiscrepancyValidator(request, discNotes);
if (displayItemBeanWrapper != null && displayItemBeans.size() > 0)
wrappers.add(displayItemBeanWrapper);
}// after study events
// remove repeats here? remove them below by only forwarding the
// first
// each wrapper represents an Event CRF and a Form, but we don't
// have all events for all forms
// need to not add a wrapper for every event + form combination,
// but instead for every event + form combination which is present
// look at the hack below and see what happens
}// after study subjects
// throw the OC exception here at the end, if hard edit checks are not
// empty
// we statically update the hash map here, so it should not have to be
// thrown, tbh 06/2008
if (!hardValidator.isEmpty()) {
// throw new OpenClinicaException(hardValidatorErrorMsgs, "");
}
return wrappers;
}
private ItemDataBean createItemDataBean(ItemBean itemBean, EventCRFBean eventCrfBean, String value, UserAccountBean ub, int ordinal) {
ItemDataBean itemDataBean = new ItemDataBean();
itemDataBean.setItemId(itemBean.getId());
itemDataBean.setEventCRFId(eventCrfBean.getId());
itemDataBean.setCreatedDate(new Date());
itemDataBean.setOrdinal(ordinal);
itemDataBean.setOwner(ub);
itemDataBean.setStatus(Status.UNAVAILABLE);
itemDataBean.setValue(value);
return itemDataBean;
}
private void attachValidator(DisplayItemBean displayItemBean, ImportHelper importHelper, DiscrepancyValidator v, HashMap<String, String> hardv,
javax.servlet.http.HttpServletRequest request, String eventCRFRepeatKey, String studySubjectOID) throws OpenClinicaException {
org.akaza.openclinica.bean.core.ResponseType rt = displayItemBean.getMetadata().getResponseSet().getResponseType();
String itemOid = displayItemBean.getItem().getOid() + "_" + eventCRFRepeatKey + "_" + displayItemBean.getData().getOrdinal() + "_" + studySubjectOID;
// note the above, generating an ordinal on top of the OID to view
// errors. adding event crf repeat key here, tbh
// need to add a per-subject differentator, what if its a diff subject
// with the same item, repeat key and ordinal???
if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXT) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.TEXTAREA)) {
ItemFormMetadataBean ifm = displayItemBean.getMetadata();
String widthDecimal = ifm.getWidthDecimal();
// what if it's a date? parse if out so that we go from iso 8601 to
// mm/dd/yyyy
if (displayItemBean.getItem().getDataType().equals(ItemDataType.DATE)) {
// pass it if it is blank, tbh
if (!"".equals(displayItemBean.getData().getValue())) {
String dateValue = displayItemBean.getData().getValue();
SimpleDateFormat sdf_sqldate = new SimpleDateFormat("yyyy-MM-dd");
try {
Date originalDate = sdf_sqldate.parse(dateValue);
String replacementValue = new SimpleDateFormat("MM/dd/yyyy").format(originalDate);
displayItemBean.getData().setValue(dateValue);
} catch (ParseException pe1) {
// next version; fail if it does not pass iso 8601
MessageFormat mf = new MessageFormat("");
mf.applyPattern(respage.getString("you_have_a_date_value_which_is_not"));
Object[] arguments = { displayItemBean.getItem().getOid() };
hardv.put(itemOid, mf.format(arguments));
}
}
} else if (displayItemBean.getItem().getDataType().equals(ItemDataType.ST)) {
int width = Validator.parseWidth(widthDecimal);
if (width > 0 && displayItemBean.getData().getValue().length() > width) {
hardv.put(itemOid, "This value exceeds required width=" + width);
}
}
// what if it's a number? should be only numbers
else if (displayItemBean.getItem().getDataType().equals(ItemDataType.INTEGER)) {
try {
Integer testInt = new Integer(displayItemBean.getData().getValue());
int width = Validator.parseWidth(widthDecimal);
if (width > 0 && displayItemBean.getData().getValue().length() > width) {
hardv.put(itemOid, "This value exceeds required width=" + width);
}
// now, didn't check decimal for testInt.
} catch (Exception e) {// should be a sub class
// pass if blank, tbh 07/2010
if (!"".equals(displayItemBean.getData().getValue())) {
hardv.put(itemOid, "This value is not an integer.");
}
}
}
// what if it's a float? should be only numbers
else if (displayItemBean.getItem().getDataType().equals(ItemDataType.REAL)) {
try {
Float testFloat = new Float(displayItemBean.getData().getValue());
int width = Validator.parseWidth(widthDecimal);
if (width > 0 && displayItemBean.getData().getValue().length() > width) {
hardv.put(itemOid, "This value exceeds required width=" + width);
}
int decimal = Validator.parseDecimal(widthDecimal);
if (decimal > 0 && BigDecimal.valueOf(new Double(displayItemBean.getData().getValue()).doubleValue()).scale() > decimal) {
hardv.put(itemOid, "This value exceeds required decimal=" + decimal);
}
} catch (Exception ee) {
// pass if blank, tbh
if (!"".equals(displayItemBean.getData().getValue())) {
hardv.put(itemOid, "This value is not a real number.");
}
}
}
// what if it's a phone number? how often does that happen?
request.setAttribute(itemOid, displayItemBean.getData().getValue());
displayItemBean = importHelper.validateDisplayItemBeanText(v, displayItemBean, itemOid);
// errors = v.validate();
} else if (rt.equals(ResponseType.CALCULATION) || rt.equals(ResponseType.GROUP_CALCULATION)) {
if (displayItemBean.getItem().getDataType().equals(ItemDataType.REAL)) {
ItemFormMetadataBean ifm = displayItemBean.getMetadata();
String widthDecimal = ifm.getWidthDecimal();
int decimal = Validator.parseDecimal(widthDecimal);
if (decimal > 0) {
try {
Double d = new Double(displayItemBean.getData().getValue());
if (BigDecimal.valueOf(d).scale() > decimal) {
hardv.put(itemOid, "This value exceeds required decimal=" + decimal);
}
} catch (Exception e) {
if (!"".equals(displayItemBean.getData().getValue())) {
hardv.put(itemOid, "This value is not a real number.");
}
}
}
}
}
// JN commenting out the following as we dont need hard edits for these cases, they need to be soft stops and DN
// should be filed REF MANTIS 6271
else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.RADIO) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECT)) {
// logger.info(itemOid + "is a RADIO or
// a SELECT ");
// adding a new hard edit check here; response_option mismatch
String theValue = matchValueWithOptions(displayItemBean, displayItemBean.getData().getValue(), displayItemBean.getMetadata().getResponseSet()
.getOptions());
request.setAttribute(itemOid, theValue);
logger.debug(" found the value for radio/single: " + theValue);
if (theValue == null && displayItemBean.getData().getValue() != null && !displayItemBean.getData().getValue().isEmpty()) {
// fail it here
logger.debug("-- theValue was NULL, the real value was " + displayItemBean.getData().getValue());
hardv.put(itemOid, "This is not in the correct response set.");
// throw new OpenClinicaException("One of your items did not
// have the correct response set. Please review Item OID "
// + displayItemBean.getItem().getOid() + " repeat key " +
// displayItemBean.getData().getOrdinal(), "");
}
displayItemBean = importHelper.validateDisplayItemBeanSingleCV(v, displayItemBean, itemOid);
// errors = v.validate();
} else if (rt.equals(org.akaza.openclinica.bean.core.ResponseType.CHECKBOX) || rt.equals(org.akaza.openclinica.bean.core.ResponseType.SELECTMULTI)) {
// logger.info(itemOid + "is a CHECKBOX
// or a SELECTMULTI ");
String theValue = matchValueWithManyOptions(displayItemBean, displayItemBean.getData().getValue(), displayItemBean.getMetadata().getResponseSet()
.getOptions());
request.setAttribute(itemOid, theValue);
// logger.debug(" found the value for checkbx/multi: " + theValue);
if (theValue == null && displayItemBean.getData().getValue() != null && !displayItemBean.getData().getValue().isEmpty()) {
// fail it here? found an 0,1 in the place of a NULL
// logger.debug("-- theValue was NULL, the real value was " + displayItemBean.getData().getValue());
hardv.put(itemOid, "This is not in the correct response set.");
}
displayItemBean = importHelper.validateDisplayItemBeanMultipleCV(v, displayItemBean, itemOid);
// errors = v.validate();
}
}
private String matchValueWithOptions(DisplayItemBean displayItemBean, String value, List options) {
String returnedValue = null;
if (!options.isEmpty()) {
for (Object responseOption : options) {
ResponseOptionBean responseOptionBean = (ResponseOptionBean) responseOption;
if (responseOptionBean.getValue().equals(value)) {
// if (((ResponseOptionBean)
// responseOption).getText().equals(value)) {
displayItemBean.getData().setValue(((ResponseOptionBean) responseOption).getValue());
return ((ResponseOptionBean) responseOption).getValue();
}
}
}
return returnedValue;
}
/*
* difference from the above is only a 'contains' in the place of an 'equals'. and a few other switches...also need
* to keep in mind that there are non-null values that need to be taken into account
*/
private String matchValueWithManyOptions(DisplayItemBean displayItemBean, String value, List options) {
String returnedValue = null;
// boolean checkComplete = true;
String entireOptions = "";
String[] simValues = value.split(",");
String simValue = value.replace(",", "");
// also remove all spaces, so they will fit up with the entire set
// of options
simValue = simValue.replace(" ", "");
boolean checkComplete = true;
if (!options.isEmpty()) {
for (Object responseOption : options) {
ResponseOptionBean responseOptionBean = (ResponseOptionBean) responseOption;
// logger.debug("testing response option bean get value: " + responseOptionBean.getValue());
// entireOptions += responseOptionBean.getValue() + "{0,1}|";//
// once, or not at all
entireOptions += responseOptionBean.getValue();
// trying smth new, tbh 01/2009
// logger.debug("checking on this string: " +
// entireOptions + " versus this value " + simValue);
// checkComplete = Pattern.matches(entireOptions, simValue); //
// switch values, tbh
// if (!checkComplete) {
// return returnedValue;
// }
}
// remove spaces, since they are causing problems:
entireOptions = entireOptions.replace(" ", "");
// following may be superfluous, tbh
ArrayList nullValues = displayItemBean.getEventDefinitionCRF().getNullValuesList();
for (Object nullValue : nullValues) {
NullValue nullValueTerm = (NullValue) nullValue;
entireOptions += nullValueTerm.getName();
// logger.debug("found and added " + nullValueTerm.getName());
}
for (String sim : simValues) {
sim = sim.replace(" ", "");
// logger.debug("checking on this string: " + entireOptions + " versus this value " + sim);
checkComplete = entireOptions.contains(sim);// Pattern.matches(
// entireOptions,
// sim);
if (!checkComplete) {
return returnedValue;
}
}
}
return value;
}
/*
* meant to answer the following questions 3.a. is that study subject in that study? 3.b. is that study event def in
* that study? 3.c. is that site in that study? 3.d. is that crf version in that study event def? 3.e. are those
* item groups in that crf version? 3.f. are those items in that item group?
*/
public List<String> validateStudyMetadata(ODMContainer odmContainer, int currentStudyId) {
List<String> errors = new ArrayList<String>();
MessageFormat mf = new MessageFormat("");
// throw new OpenClinicaException(mf.format(arguments), "");
try {
StudyDAO studyDAO = new StudyDAO(ds);
String studyOid = odmContainer.getCrfDataPostImportContainer().getStudyOID();
StudyBean studyBean = studyDAO.findByOid(studyOid);
if (studyBean == null) {
mf.applyPattern(respage.getString("your_study_oid_does_not_reference_an_existing"));
Object[] arguments = { studyOid };
errors.add(mf.format(arguments));
// errors.add("Your Study OID " + studyOid + " does not
// reference an existing Study or Site in the database. Please
// check it and try again.");
// throw an error here because getting the ID would be difficult
// otherwise
logger.debug("unknown study OID");
throw new OpenClinicaException("Unknown Study OID", "");
} else if (studyBean.getId() != currentStudyId) {
mf.applyPattern(respage.getString("your_current_study_is_not_the_same_as"));
Object[] arguments = { studyBean.getName() };
//
// errors.add("Your current study is not the same as the Study "
// + studyBean.getName()
// + ", for which you are trying to enter data. Please log out
// of your current study and into the study for which the data
// is keyed.");
errors.add(mf.format(arguments));
}
ArrayList<SubjectDataBean> subjectDataBeans = odmContainer.getCrfDataPostImportContainer().getSubjectData();
StudySubjectDAO studySubjectDAO = new StudySubjectDAO(ds);
StudyEventDefinitionDAO studyEventDefinitionDAO = new StudyEventDefinitionDAO(ds);
CRFVersionDAO crfVersionDAO = new CRFVersionDAO(ds);
ItemGroupDAO itemGroupDAO = new ItemGroupDAO(ds);
ItemDAO itemDAO = new ItemDAO(ds);
if (subjectDataBeans != null) {// need to do this so as not to
// throw the exception below and
// report all available errors, tbh
for (SubjectDataBean subjectDataBean : subjectDataBeans) {
String oid = subjectDataBean.getSubjectOID();
StudySubjectBean studySubjectBean = studySubjectDAO.findByOidAndStudy(oid, studyBean.getId());
if (studySubjectBean == null) {
mf.applyPattern(respage.getString("your_subject_oid_does_not_reference"));
Object[] arguments = { oid };
errors.add(mf.format(arguments));
// errors.add("Your Subject OID " + oid + " does not
// reference an existing Subject in the Study.");
logger.debug("logged an error with subject oid " + oid);
}
ArrayList<StudyEventDataBean> studyEventDataBeans = subjectDataBean.getStudyEventData();
if (studyEventDataBeans != null) {
for (StudyEventDataBean studyEventDataBean : studyEventDataBeans) {
String sedOid = studyEventDataBean.getStudyEventOID();
StudyEventDefinitionBean studyEventDefintionBean = studyEventDefinitionDAO.findByOidAndStudy(sedOid, studyBean.getId(),
studyBean.getParentStudyId());
if (studyEventDefintionBean == null) {
mf.applyPattern(respage.getString("your_study_event_oid_for_subject_oid"));
Object[] arguments = { sedOid, oid };
errors.add(mf.format(arguments));
// errors.add("Your Study Event OID " + sedOid +
// " for Subject OID " + oid
// + " does not reference an existing Study
// Event in the Study.");
logger.debug("logged an error with se oid " + sedOid + " and subject oid " + oid);
}
ArrayList<FormDataBean> formDataBeans = studyEventDataBean.getFormData();
if (formDataBeans != null) {
for (FormDataBean formDataBean : formDataBeans) {
String formOid = formDataBean.getFormOID();
ArrayList<CRFVersionBean> crfVersionBeans = crfVersionDAO.findAllByOid(formOid);
// ideally we should look to compare
// versions within
// seds;
// right now just check nulls
if (crfVersionBeans != null && crfVersionBeans.size() > 0) {
for (CRFVersionBean crfVersionBean : crfVersionBeans) {
if (crfVersionBean == null) {
mf.applyPattern(respage.getString("your_crf_version_oid_for_study_event_oid"));
Object[] arguments = { formOid, sedOid };
errors.add(mf.format(arguments));
// errors.add("Your CRF Version
// OID " + formOid + " for Study
// Event OID " + sedOid
// + " does not reference a
// proper CRF Version in that
// Study Event.");
logger.debug("logged an error with form " + formOid + " and se oid " + sedOid);
}
}
} else {
mf.applyPattern(respage.getString("your_crf_version_oid_did_not_generate"));
Object[] arguments = { formOid };
errors.add(mf.format(arguments));
// errors.add("Your CRF Version OID " +
// formOid
// + " did not generate any results in
// the database. Please check it and try
// again.");
}
ArrayList<ImportItemGroupDataBean> itemGroupDataBeans = formDataBean.getItemGroupData();
if (itemGroupDataBeans != null) {
for (ImportItemGroupDataBean itemGroupDataBean : itemGroupDataBeans) {
String itemGroupOID = itemGroupDataBean.getItemGroupOID();
List<ItemGroupBean> itemGroupBeans = itemGroupDAO.findAllByOid(itemGroupOID);
if (itemGroupBeans != null) {
logger.debug("number of item group beans: " + itemGroupBeans.size());
logger.debug("item group oid: " + itemGroupOID);
for (ItemGroupBean itemGroupBean : itemGroupBeans) {
if (itemGroupBean == null) {
mf.applyPattern(respage.getString("your_item_group_oid_for_form_oid"));
Object[] arguments = { itemGroupOID, formOid };
errors.add(mf.format(arguments));
// errors.add("Your Item
// Group OID " +
// itemGroupOID + " for
// Form OID " + formOid
// + " does not
// reference a proper
// Item Group in that
// CRF Version.");
}
}
} else {
mf.applyPattern(respage.getString("the_item_group_oid_did_not"));
Object[] arguments = { itemGroupOID };
errors.add(mf.format(arguments));
// errors.add("The Item Group
// OID " + itemGroupOID
// + " did not generate any
// results in the database,
// please check it and try
// again.");
}
ArrayList<ImportItemDataBean> itemDataBeans = itemGroupDataBean.getItemData();
if (itemDataBeans != null) {
for (ImportItemDataBean itemDataBean : itemDataBeans) {
String itemOID = itemDataBean.getItemOID();
List<ItemBean> itemBeans = itemDAO.findByOid(itemOID);
if (itemBeans != null) {
logger.debug("found itembeans: ");
for (ItemBean itemBean : itemBeans) {
if (itemBean == null) {
mf.applyPattern(respage.getString("your_item_oid_for_item_group_oid"));
Object[] arguments = { itemOID, itemGroupOID };
errors.add(mf.format(arguments));
// errors.add(
// "Your
// Item OID " +
// itemOID + "
// for Item
// Group OID " +
// itemGroupOID
// + " does not
// reference a
// proper Item
// in the Item
// Group.");
} else {
logger.debug("found " + itemBean.getOid() + ", passing");
}
}
}
}
} else {
mf.applyPattern(respage.getString("the_item_group_oid_did_not_contain_item_data"));
Object[] arguments = { itemGroupOID };
errors.add(mf.format(arguments));
// errors.add("The Item Group
// OID " + itemGroupOID
// + " did not contain any Item
// Data in the XML file, please
// check it and try again.");
}
}
} else {
mf.applyPattern(respage.getString("your_study_event_contains_no_form_data"));
Object[] arguments = { sedOid };
errors.add(mf.format(arguments));
// errors.add("Your Study Event " +
// sedOid
// + " contains no Form Data, or the
// Form OIDs are incorrect. Please check
// it and try again.");
}
}
}
}
}
}
}
} catch (OpenClinicaException oce) {
} catch (NullPointerException npe) {
logger.debug("found a nullpointer here");
}
// if errors == null you pass, if not you fail
return errors;
}
private ItemDataDAO getItemDataDao() {
itemDataDao = this.itemDataDao != null ? itemDataDao : new ItemDataDAO(ds);
return itemDataDao;
}
}