package org.akaza.openclinica.service.extract;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Locale;
import java.util.Set;
import org.akaza.openclinica.bean.core.Utils;
import org.akaza.openclinica.bean.odmbeans.AuditLogBean;
import org.akaza.openclinica.bean.odmbeans.AuditLogsBean;
import org.akaza.openclinica.bean.odmbeans.ChildNoteBean;
import org.akaza.openclinica.bean.odmbeans.DiscrepancyNoteBean;
import org.akaza.openclinica.bean.odmbeans.DiscrepancyNotesBean;
import org.akaza.openclinica.bean.odmbeans.ElementRefBean;
import org.akaza.openclinica.bean.odmbeans.OdmClinicalDataBean;
import org.akaza.openclinica.bean.submit.crfdata.ExportFormDataBean;
import org.akaza.openclinica.bean.submit.crfdata.ExportStudyEventDataBean;
import org.akaza.openclinica.bean.submit.crfdata.ExportSubjectDataBean;
import org.akaza.openclinica.bean.submit.crfdata.ImportItemDataBean;
import org.akaza.openclinica.bean.submit.crfdata.ImportItemGroupDataBean;
import org.akaza.openclinica.bean.submit.crfdata.SubjectGroupDataBean;
import org.akaza.openclinica.dao.hibernate.AuditLogEventDao;
import org.akaza.openclinica.dao.hibernate.StudyDao;
import org.akaza.openclinica.dao.hibernate.StudyEventDefinitionDao;
import org.akaza.openclinica.dao.hibernate.StudySubjectDao;
import org.akaza.openclinica.dao.hibernate.StudyUserRoleDao;
import org.akaza.openclinica.dao.hibernate.UserAccountDao;
import org.akaza.openclinica.domain.EventCRFStatus;
import org.akaza.openclinica.domain.Status;
import org.akaza.openclinica.domain.datamap.AuditLogEvent;
import org.akaza.openclinica.domain.datamap.CrfBean;
import org.akaza.openclinica.domain.datamap.DiscrepancyNote;
import org.akaza.openclinica.domain.datamap.DnEventCrfMap;
import org.akaza.openclinica.domain.datamap.DnItemDataMap;
import org.akaza.openclinica.domain.datamap.DnStudyEventMap;
import org.akaza.openclinica.domain.datamap.DnStudySubjectMap;
import org.akaza.openclinica.domain.datamap.DnSubjectMap;
import org.akaza.openclinica.domain.datamap.EventCrf;
import org.akaza.openclinica.domain.datamap.EventDefinitionCrf;
import org.akaza.openclinica.domain.datamap.Item;
import org.akaza.openclinica.domain.datamap.ItemData;
import org.akaza.openclinica.domain.datamap.ItemGroupMetadata;
import org.akaza.openclinica.domain.datamap.Study;
import org.akaza.openclinica.domain.datamap.StudyEvent;
import org.akaza.openclinica.domain.datamap.StudyEventDefinition;
import org.akaza.openclinica.domain.datamap.StudySubject;
import org.akaza.openclinica.domain.datamap.StudyUserRole;
import org.akaza.openclinica.domain.datamap.SubjectEventStatus;
import org.akaza.openclinica.domain.datamap.SubjectGroupMap;
import org.akaza.openclinica.domain.datamap.VersioningMap;
import org.akaza.openclinica.domain.user.UserAccount;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Generate CDISC-ODM clinical data without data set.
*
* @author jnyayapathi
*
*/
public class GenerateClinicalDataServiceImpl implements GenerateClinicalDataService {
protected final static Logger LOGGER = LoggerFactory
.getLogger("org.akaza.openclinica.service.extract.GenerateClinicalDataServiceImpl");
protected final static String DELIMITER = ",";
private final static String GROUPOID_ORDINAL_DELIM = ":";
private final static String INDICATE_ALL="*";
private final static String OPEN_ORDINAL_DELIMITER = "[";
private final static String CLOSE_ORDINAL_DELIMITER = "]";
private static final Object STATUS = "Status";
private static final Object STUDY_EVENT = "study_event";
private static final Object SUBJECT_GROUP_MAP = "subject_group_map";
private static boolean isActiveRoleAtSite = true;
private StudyDao studyDao;
private StudySubjectDao studySubjectDao;
private StudyEventDefinitionDao studyEventDefDao;
private boolean collectDns=true;
private boolean collectAudits=true;
private AuditLogEventDao auditEventDAO;
private Locale locale;
private UserAccountDao userAccountDao;
private StudyUserRoleDao studyUserRoleDao;
public AuditLogEventDao getAuditEventDAO() {
return auditEventDAO;
}
public void setAuditEventDAO(AuditLogEventDao auditEventDAO) {
this.auditEventDAO = auditEventDAO;
}
public boolean isCollectDns() {
return collectDns;
}
public void setCollectDns(boolean collectDns) {
this.collectDns = collectDns;
}
public boolean isCollectAudits() {
return collectAudits;
}
public void setCollectAudits(boolean collectAudits) {
this.collectAudits = collectAudits;
}
public StudyEventDefinitionDao getStudyEventDefDao() {
return studyEventDefDao;
}
public void setStudyEventDefDao(StudyEventDefinitionDao studyEventDefDao) {
this.studyEventDefDao = studyEventDefDao;
}
public StudySubjectDao getStudySubjectDao() {
return studySubjectDao;
}
public void setStudySubjectDao(StudySubjectDao studySubjectDao) {
this.studySubjectDao = studySubjectDao;
}
public GenerateClinicalDataServiceImpl() {
}
public GenerateClinicalDataServiceImpl(String StudyOID) {
}
public LinkedHashMap<String,OdmClinicalDataBean> getClinicalData(String studyOID) {
LinkedHashMap<String, OdmClinicalDataBean> hm = new LinkedHashMap<String,OdmClinicalDataBean>();
Study study = new Study();
study.setOc_oid(studyOID);
study = getStudyDao().findByColumnName(studyOID, "oc_oid");
List<StudySubject>studySubjs = study.getStudySubjects();
if(study.getStudies().size()<1)
{
hm.put(studyOID, constructClinicalData(study,studySubjs));
}
//return odmClinicalDataBean;
else{
hm.put(studyOID,constructClinicalData(study,studySubjs));//at study level
for(Study s:study.getStudies()){//all the sites
hm.put(s.getOc_oid(),constructClinicalData(s, s.getStudySubjects()));
}
}
return hm;
// return constructClinicalData(study, studySubjs);
}
private List<StudySubject> listStudySubjects(String studySubjectOID){
ArrayList<StudySubject>studySubjs = new ArrayList<StudySubject>();
StudySubject studySubj = getStudySubjectDao().findByColumnName(
studySubjectOID, "ocOid");
studySubjs.add(studySubj);
return studySubjs;
}
public OdmClinicalDataBean getClinicalData(String studyOID, String studySubjectOID) {
Study study = getStudyDao().findByColumnName(studyOID, "oc_oid");
return constructClinicalData(study,listStudySubjects(studySubjectOID));
}
public StudyDao getStudyDao() {
return studyDao;
}
public void setStudyDao(StudyDao studyDao) {
this.studyDao = studyDao;
}
private OdmClinicalDataBean constructClinicalData(Study study, List<StudySubject> studySubjs) {
return constructClinicalDataStudy(studySubjs, study,null, null);
}
private OdmClinicalDataBean constructClinicalDataStudy(List<StudySubject> studySubjs, Study study,List<StudyEvent>studyEvents,String formVersionOID) {
OdmClinicalDataBean odmClinicalDataBean = new OdmClinicalDataBean();
ExportSubjectDataBean expSubjectBean;
List<ExportSubjectDataBean> exportSubjDataBeanList = new ArrayList<ExportSubjectDataBean>();
for(StudySubject studySubj:studySubjs)
{
studyEvents = (ArrayList<StudyEvent>)getStudySubjectDao().fetchListSEs(studySubj.getOcOid());
if(studyEvents!=null)
{
expSubjectBean = setExportSubjectDataBean(studySubj, study,studyEvents,formVersionOID);
exportSubjDataBeanList.add(expSubjectBean);
odmClinicalDataBean.setExportSubjectData(exportSubjDataBeanList);
odmClinicalDataBean.setStudyOID(study.getOc_oid());
}
}
return odmClinicalDataBean;
// return null;
}
@SuppressWarnings("unchecked")
private ExportSubjectDataBean setExportSubjectDataBean(
StudySubject studySubj, Study study,List<StudyEvent> studyEvents,String formVersionOID) {
ExportSubjectDataBean exportSubjectDataBean = new ExportSubjectDataBean();
if(subjectBelongsToStudy(study,studySubj)){
// exportSubjectDataBean.setAuditLogs(studySubj.getA)
if(studySubj.getSubject()
.getDateOfBirth()!=null)
exportSubjectDataBean.setDateOfBirth(studySubj.getSubject()
.getDateOfBirth() + "");
exportSubjectDataBean.setSubjectGender(studySubj.getSubject().getGender()+"");
for(SubjectGroupMap subjGrpMap: studySubj.getSubjectGroupMaps()){
SubjectGroupDataBean subjGrpDataBean = new SubjectGroupDataBean();
subjGrpDataBean.setStudyGroupClassId("SGC_"+subjGrpMap.getStudyGroupClass().getStudyGroupClassId());
subjGrpDataBean.setStudyGroupClassName(subjGrpMap.getStudyGroup().getStudyGroupClass().getName());
subjGrpDataBean.setStudyGroupName(subjGrpMap.getStudyGroup().getName());
exportSubjectDataBean.getSubjectGroupData().add(subjGrpDataBean);
}
exportSubjectDataBean.setStudySubjectId(
studySubj.getLabel());
if(studySubj.getSubject().getUniqueIdentifier()!=null)exportSubjectDataBean.setUniqueIdentifier(studySubj.getSubject().getUniqueIdentifier());
exportSubjectDataBean.setSecondaryId(studySubj.getSecondaryLabel());
exportSubjectDataBean.setStatus(studySubj.getStatus().toString());
if(isCollectAudits())
exportSubjectDataBean.setAuditLogs(fetchAuditLogs(studySubj.getStudySubjectId(),"study_subject", studySubj.getOcOid(), null));
AuditLogsBean subjectGroupMapLogs = fetchAuditLogs(studySubj.getStudySubjectId(),"subject_group_map", studySubj.getOcOid(), null);
AuditLogsBean subjectLogs = fetchAuditLogs(studySubj.getSubject().getSubjectId(),"subject", studySubj.getOcOid(), null);
exportSubjectDataBean.getAuditLogs().getAuditLogs().addAll(subjectGroupMapLogs.getAuditLogs());
exportSubjectDataBean.getAuditLogs().getAuditLogs().addAll(subjectLogs.getAuditLogs());
Collections.sort(exportSubjectDataBean.getAuditLogs().getAuditLogs());
if(isCollectDns())
exportSubjectDataBean.setDiscrepancyNotes(fetchDiscrepancyNotes(studySubj));
exportSubjectDataBean
.setExportStudyEventData(setExportStudyEventDataBean(studySubj,studyEvents,formVersionOID));
exportSubjectDataBean.setSubjectOID(studySubj.getOcOid());
exportSubjectDataBean.setEnrollmentDate(studySubj.getEnrollmentDate()+"");
}
return exportSubjectDataBean;
}
private boolean subjectBelongsToStudy(Study study, StudySubject studySubj) {
boolean subjectBelongs = false;
if(studySubj.getStudy().getOc_oid().equals(study.getOc_oid())){
subjectBelongs = true;
}
else{
if(studySubj.getStudy().getStudy().getOc_oid().equals(study.getOc_oid()))
subjectBelongs=true;
}
return subjectBelongs;
}
private ArrayList<ExportStudyEventDataBean> setExportStudyEventDataBean(
StudySubject ss,List<StudyEvent>sEvents,String formVersionOID) {
ArrayList<ExportStudyEventDataBean> al = new ArrayList<ExportStudyEventDataBean>();
SimpleDateFormat sdf = new SimpleDateFormat("yyyy-MM-dd");
for (StudyEvent se : sEvents) {
if(se!=null){
ExportStudyEventDataBean expSEBean = new ExportStudyEventDataBean();
expSEBean.setLocation(se.getLocation());
if(se.getDateEnd()!=null)
if(se.getEndTimeFlag())
expSEBean.setEndDate(se.getDateEnd() + "");
else
{
String temp = sdf.format(se.getDateEnd());
expSEBean.setEndDate(temp);
}
if(se.getStartTimeFlag())
expSEBean.setStartDate(se.getDateStart() + "");
else
{
String temp = sdf.format(se.getDateStart());
expSEBean.setStartDate(temp);
}
expSEBean.setStudyEventOID(se.getStudyEventDefinition().getOc_oid());
expSEBean.setStudyEventRepeatKey(se.getSampleOrdinal().toString());
if(se.getStudySubject().getSubject().getDateOfBirth()!=null && se.getDateStart()!=null)
expSEBean.setAgeAtEvent(Utils.getAge(se.getStudySubject().getSubject().getDateOfBirth(), se.getDateStart()));
expSEBean.setStatus(fetchStudyEventStatus(se.getSubjectEventStatusId()));
if(collectAudits)
expSEBean.setAuditLogs(fetchAuditLogs(se.getStudyEventId(),"study_event",se.getStudyEventDefinition().getOc_oid(), null));
if(collectDns)
expSEBean.setDiscrepancyNotes(fetchDiscrepancyNotes(se));
expSEBean.setExportFormData(getFormDataForClinicalStudy(ss,se,formVersionOID));
expSEBean.setStudyEventDefinition(se.getStudyEventDefinition());
al.add(expSEBean);
}
}
return al;
}
private ArrayList<ExportFormDataBean> getFormDataForClinicalStudy(
StudySubject ss, StudyEvent se,String formVersionOID) {
List<ExportFormDataBean> formDataBean = new ArrayList<ExportFormDataBean>();
boolean formCheck = true;
if(formVersionOID!=null)formCheck = false;
boolean hiddenCrfCheckPassed=true;
List<CrfBean> hiddenCrfs= new ArrayList<CrfBean>();
for (EventCrf ecrf : se.getEventCrfs()) {
List<EventDefinitionCrf> edcs = se.getStudyEventDefinition().getEventDefinitionCrfs();
hiddenCrfCheckPassed=true;
int siteId=0;
int parentStudyId = 0;
Study study = ss.getStudy();
if (study.getStudy()!=null && isActiveRoleAtSite){
//it is site subject
siteId = study.getStudyId();
parentStudyId = study.getStudy().getStudyId();
hiddenCrfs = listOfHiddenCrfs(siteId,parentStudyId,edcs,ecrf);
if(hiddenCrfs.contains(ecrf.getCrfVersion().getCrf()))
{
hiddenCrfCheckPassed = false;
}
}
//This logic is to use the same method for both S_OID/SS_OID/*/* and full path
if(hiddenCrfCheckPassed){
if(!formCheck)
{ if(ecrf.getCrfVersion().getOcOid().equals(formVersionOID))
formCheck=true;
else
formCheck=false;
}
if(formCheck){
ExportFormDataBean dataBean = new ExportFormDataBean();
dataBean.setItemGroupData(fetchItemData(ecrf.getCrfVersion()
.getItemGroupMetadatas(), ecrf.getEventCrfId(), ecrf
.getCrfVersion().getVersioningMaps(), ecrf));
dataBean.setFormOID(ecrf.getCrfVersion().getOcOid());
if(ecrf.getDateInterviewed()!=null)
dataBean.setInterviewDate(ecrf.getDateInterviewed() + "");
if(ecrf.getInterviewerName()!=null)
dataBean.setInterviewerName(ecrf.getInterviewerName());
//dataBean.setStatus(EventCRFStatus.getByCode(Integer.valueOf(ecrf.getStatus().getCode())).getI18nDescription(getLocale()));
dataBean.setStatus(fetchEventCRFStatus(ecrf));
if(ecrf.getCrfVersion().getName()!=null)
dataBean.setCrfVersion(ecrf.getCrfVersion().getName());
if(collectAudits)
dataBean.setAuditLogs(fetchAuditLogs(ecrf.getEventCrfId(),"event_crf", ecrf.getCrfVersion().getOcOid(), null));
if(collectDns)
dataBean.setDiscrepancyNotes(fetchDiscrepancyNotes(ecrf));
formDataBean.add(dataBean);
if(formVersionOID!=null)formCheck=false;
}
}
}
return (ArrayList<ExportFormDataBean>) formDataBean;
}
private List<CrfBean> listOfHiddenCrfs(Integer siteId, Integer parentStudyId, List<EventDefinitionCrf> edcs, EventCrf ecrf) {
boolean found = false;
int crfId = ecrf.getCrfVersion().getCrf().getCrfId();
List<CrfBean> hiddenCrfs = new ArrayList<CrfBean>();
LOGGER.info("The study subject is at the site/study " + siteId);
for (EventDefinitionCrf eventDefCrf : edcs) {
if (eventDefCrf.getCrf().getCrfId() == crfId && eventDefCrf.getStudy().getStudyId() == siteId) {
found = true;
if (eventDefCrf.getHideCrf()) {
hiddenCrfs.add(eventDefCrf.getCrf());
}
}
}
if (!found) {
for (EventDefinitionCrf eventDefCrf : edcs) {
if (eventDefCrf.getCrf().getCrfId() == crfId && eventDefCrf.getStudy().getStudyId() == parentStudyId && eventDefCrf.getHideCrf()) {
hiddenCrfs.add(eventDefCrf.getCrf());
}
}
}
return hiddenCrfs;
}
// This logic is taken from eventCRFBean.
private String fetchEventCRFStatus(EventCrf ecrf) {
String stage = null;
Status status = Status.getByCode(ecrf.getStatusId());
if (ecrf.getEventCrfId()<=0 || status.getCode()<=0) {
stage =EventCRFStatus.UNCOMPLETED.getI18nDescription(getLocale());
}
if (status.equals(Status.AVAILABLE)) {
stage = EventCRFStatus.INITIAL_DATA_ENTRY.getI18nDescription(getLocale());
}
if (status.equals(Status.PENDING)) {
if (ecrf.getValidatorId()!= 0) {
stage = EventCRFStatus.DOUBLE_DATA_ENTRY.getI18nDescription(getLocale());
} else {
stage = EventCRFStatus.INITIAL_DATA_ENTRY_COMPLETE.getI18nDescription(getLocale());
}
}
if (status.equals(Status.UNAVAILABLE)) {
stage = EventCRFStatus.DOUBLE_DATA_ENTRY_COMPLETE.getI18nDescription(getLocale());
}
if (status.equals(Status.LOCKED)) {
stage = EventCRFStatus.LOCKED.getI18nDescription(getLocale());
}
if (status.equals(Status.DELETED)) {
stage = EventCRFStatus.INVALID.getI18nDescription(getLocale());
}
if (status.equals(Status.AUTO_DELETED)) {
stage = EventCRFStatus.INVALID.getI18nDescription(getLocale());
}
return stage;
}
private ArrayList<ImportItemGroupDataBean> fetchItemData(
Set<ItemGroupMetadata> set, int eventCrfId, List<VersioningMap> vms, EventCrf eventCrf) {
String groupOID, itemOID;
String itemValue = null;
String itemDataValue;
HashMap<String, ArrayList<String>> oidMap = new HashMap<String, ArrayList<String>>();
HashMap<String, List<ItemData>> oidDNAuditMap = new HashMap<String, List<ItemData>>();
List<ItemData> itds = eventCrf.getItemDatas();
// For each metadata get the group, and then get list of all items in
// that group.so we can a data structure of groupOID and list of
// itemOIDs with corresponding values will be created.
for (ItemData itemData : itds) {
List<ItemGroupMetadata> igmetadatas = itemData.getItem().getItemGroupMetadatas();
for (ItemGroupMetadata igGrpMetadata : igmetadatas) {
groupOID = igGrpMetadata.getItemGroup().getOcOid();
if (!oidMap.containsKey(groupOID)) {
String groupOIDOrdnl = groupOID;
ArrayList<String> itemsValues = new ArrayList<String>();
ArrayList<ItemData> itemDatas = new ArrayList<ItemData>();
List<ItemGroupMetadata> allItemsInAGroup = igGrpMetadata
.getItemGroup().getItemGroupMetadatas();
for (ItemGroupMetadata itemGrpMetada : allItemsInAGroup) {
itemOID = itemGrpMetada.getItem().getOcOid();
itemsValues = new ArrayList<String>();
/* List<ItemData> itds = itemGrpMetada.getItem()
.getItemDatas();*/
// look for the key
// of same group and ordinal and add this item to
// that hashmap
itemsValues = new ArrayList<String>();
itemDataValue = fetchItemDataValue(itemData,
itemData.getItem());
itemDatas = new ArrayList<ItemData>();
itemValue = itemOID + DELIMITER + itemDataValue;
itemsValues.add(itemValue);
groupOIDOrdnl = groupOID + GROUPOID_ORDINAL_DELIM
+ itemData.getOrdinal();
if (itemData.getItem().getOcOid() == itemOID) {
if (oidMap.containsKey(groupOIDOrdnl)) {
ArrayList<String> itemgrps = oidMap
.get(groupOIDOrdnl);
List<ItemData>itemDataTemps = oidDNAuditMap.get(groupOIDOrdnl);
if (!itemgrps.contains(itemValue)) {
itemgrps.add(itemValue);
oidMap.remove(groupOIDOrdnl);
itemDataTemps.add(itemData);
oidDNAuditMap.remove(groupOIDOrdnl);
}
oidMap.put(groupOIDOrdnl, itemgrps);
oidDNAuditMap.put(groupOIDOrdnl, itemDataTemps);
} else {
oidMap.put(groupOIDOrdnl, itemsValues);
itemDatas.add(itemData);
oidDNAuditMap.put(groupOIDOrdnl, itemDatas);
}
}
}
}
}
}
return populateImportItemGrpBean(oidMap,oidDNAuditMap);
}
private String fetchItemDataValue(ItemData itemData, Item item) {
String idValue = itemData.getValue();
return idValue;
}
private ArrayList<ImportItemGroupDataBean> populateImportItemGrpBean(
HashMap<String, ArrayList<String>> oidMap, HashMap<String, List<ItemData>> oidDNAuditMap) {
Set<String> keysGrpOIDs = oidMap.keySet();
ArrayList<ImportItemGroupDataBean> iigDataBean = new ArrayList<ImportItemGroupDataBean>();
ImportItemGroupDataBean importItemGrpDataBean = new ImportItemGroupDataBean();
for (String grpOID : keysGrpOIDs) {
ArrayList<String> vals = oidMap.get(grpOID);
importItemGrpDataBean = new ImportItemGroupDataBean();
int groupIdx = grpOID.indexOf(GROUPOID_ORDINAL_DELIM);
if (groupIdx != -1) {
importItemGrpDataBean.setItemGroupOID(grpOID.substring(0,
groupIdx));
importItemGrpDataBean.setItemGroupRepeatKey(grpOID.substring(
groupIdx + 1, grpOID.length()));
ArrayList<ImportItemDataBean> iiDList = new ArrayList<ImportItemDataBean>();
for (String value : vals) {
ImportItemDataBean iiDataBean = new ImportItemDataBean();
int index = value.indexOf(DELIMITER);
if (!value.trim().equalsIgnoreCase(DELIMITER)) {
iiDataBean.setItemOID(value.substring(0, index));
iiDataBean.setValue(value.substring(index + 1,
value.length()));
if(isCollectAudits()||isCollectDns()){
iiDataBean = fetchItemDataAuditValue(oidDNAuditMap.get(grpOID),iiDataBean);
}
// if(isCollectDns())
// iiDataBean.setDiscrepancyNotes(fetchDiscrepancyNotes(oidDNAuditMap.get(grpOID)));
iiDList.add(iiDataBean);
}
}
importItemGrpDataBean.setItemData(iiDList);
iigDataBean.add(importItemGrpDataBean);
}
}
return iigDataBean;
}
private ImportItemDataBean fetchItemDataAuditValue(List<ItemData> list,
ImportItemDataBean iiDataBean) {
for(ItemData id:list){
if(id.getItem().getOcOid().equals(iiDataBean.getItemOID())){
if(isCollectAudits())
iiDataBean.setAuditLogs(fetchAuditLogs(id.getItemDataId(),"item_data", iiDataBean.getItemOID(), null));
if(isCollectDns())
iiDataBean.setDiscrepancyNotes(fetchDiscrepancyNotes(id));
return iiDataBean;
}
}
return iiDataBean;
}
private DiscrepancyNotesBean fetchDiscrepancyNotes(ItemData itemData) {
List<DnItemDataMap> dnItemDataMaps = itemData.getDnItemDataMaps();
DiscrepancyNotesBean dnNotesBean = new DiscrepancyNotesBean() ;
dnNotesBean.setEntityID(itemData.getItem().getOcOid());
if(isCollectDns())
{
DiscrepancyNoteBean dnNoteBean = new DiscrepancyNoteBean();
ArrayList<DiscrepancyNoteBean> dnNotes = new ArrayList<DiscrepancyNoteBean>();
boolean addDN = true;
for(DnItemDataMap dnItemDataMap:dnItemDataMaps){
DiscrepancyNote dn = dnItemDataMap.getDiscrepancyNote();
addDN=true;
fillDNObject(dnNoteBean, dnNotes, addDN, dn, null);
}
dnNotesBean.setDiscrepancyNotes(dnNotes);
}
return dnNotesBean;
}
private DiscrepancyNotesBean fetchDiscrepancyNotes(EventCrf eventCrf) {
LOGGER.info("Fetching the discrepancy notes..");
List<DnEventCrfMap> dnEventCrfMaps = eventCrf.getDnEventCrfMaps();
DiscrepancyNotesBean dnNotesBean = new DiscrepancyNotesBean() ;
dnNotesBean.setEntityID(eventCrf.getCrfVersion().getOcOid());
DiscrepancyNoteBean dnNoteBean = new DiscrepancyNoteBean();
ArrayList<DiscrepancyNoteBean> dnNotes = new ArrayList<DiscrepancyNoteBean>();
boolean addDN = true;
for(DnEventCrfMap dnItemDataMap:dnEventCrfMaps){
DiscrepancyNote dn = dnItemDataMap.getDiscrepancyNote();
addDN=true;
fillDNObject(dnNoteBean, dnNotes, addDN, dn, dnItemDataMap.getDnEventCrfMapId().getColumnName());
}
dnNotesBean.setDiscrepancyNotes(dnNotes);
return dnNotesBean;
}
private DiscrepancyNotesBean fetchDiscrepancyNotes(StudySubject studySubj) {
List<DnStudySubjectMap> dnMaps = studySubj.getDnStudySubjectMaps();
DiscrepancyNotesBean dnNotesBean = new DiscrepancyNotesBean() ;
dnNotesBean.setEntityID(studySubj.getOcOid());
DiscrepancyNoteBean dnNoteBean = new DiscrepancyNoteBean();
DiscrepancyNoteBean dnSubjBean = new DiscrepancyNoteBean();
ArrayList<DiscrepancyNoteBean> dnNotes = new ArrayList<DiscrepancyNoteBean>();
boolean addDN = true;
for(DnStudySubjectMap dnMap:dnMaps){
DiscrepancyNote dn = dnMap.getDiscrepancyNote();
addDN=true;
fillDNObject(dnNoteBean, dnNotes, addDN, dn, dnMap.getDnStudySubjectMapId().getColumnName());
}
dnNotesBean.setDiscrepancyNotes(dnNotes);
List<DnSubjectMap> dnSubjMaps = studySubj.getSubject().getDnSubjectMaps();
ArrayList<DiscrepancyNoteBean> dnSubjs = new ArrayList<DiscrepancyNoteBean>();
for(DnSubjectMap dnMap:dnSubjMaps){
DiscrepancyNote dn = dnMap.getDiscrepancyNote();
addDN=true;
fillDNObject(dnSubjBean, dnSubjs, addDN, dn, dnMap.getDnSubjectMapId().getColumnName());
}
for(DiscrepancyNoteBean dnSubjMap:dnSubjs)
dnNotesBean.getDiscrepancyNotes().add(dnSubjMap);
return dnNotesBean;
}
private DiscrepancyNotesBean fetchDiscrepancyNotes(StudyEvent studyEvent) {
List<DnStudyEventMap> dnMaps = studyEvent.getDnStudyEventMaps();
DiscrepancyNotesBean dnNotesBean = new DiscrepancyNotesBean() ;
dnNotesBean.setEntityID(studyEvent.getStudyEventDefinition().getOc_oid());
DiscrepancyNoteBean dnNoteBean = new DiscrepancyNoteBean();
ArrayList<DiscrepancyNoteBean> dnNotes = new ArrayList<DiscrepancyNoteBean>();
boolean addDN = true;
for(DnStudyEventMap dnMap:dnMaps){
DiscrepancyNote dn = dnMap.getDiscrepancyNote();
addDN=true;
fillDNObject(dnNoteBean, dnNotes, addDN, dn, dnMap.getDnStudyEventMapId().getColumnName());
}
dnNotesBean.setDiscrepancyNotes(dnNotes);
return dnNotesBean;
}
private void fillDNObject(DiscrepancyNoteBean dnNoteBean,
ArrayList<DiscrepancyNoteBean> dnNotes, boolean addDN,
DiscrepancyNote dn, String columnName) {
if(dn.getParentDiscrepancyNote()!=null){
}
else{
dnNoteBean = new DiscrepancyNoteBean();
dnNoteBean.setStatus(dn.getResolutionStatus().getName());
dnNoteBean.setNoteType(dn.getEntityType());
dnNoteBean.setOid("DN_"+dn.getDiscrepancyNoteId());
dnNoteBean.setNoteType(dn.getDiscrepancyNoteType().getName());
dnNoteBean.setDateUpdated(dn.getDateCreated());
dnNoteBean.setEntityName(columnName);
for(DiscrepancyNote childDN:dn.getChildDiscrepancyNotes()){
ChildNoteBean childNoteBean = new ChildNoteBean();
childNoteBean.setOid("CDN_"+childDN.getDiscrepancyNoteId());
ElementRefBean userRef = new ElementRefBean();
childNoteBean.setDescription(childDN.getDescription());
childNoteBean.setStatus(childDN.getResolutionStatus().getName());
childNoteBean.setDetailedNote(childDN.getDetailedNotes());
childNoteBean.setDateCreated(childDN.getDateCreated());
if(childDN.getUserAccountByOwnerId()!=null)
{
childNoteBean.setOwnerUserName(childDN.getUserAccountByOwnerId().getUserName());
childNoteBean.setOwnerFirstName(childDN.getUserAccountByOwnerId().getFirstName());
childNoteBean.setOwnerLastName(childDN.getUserAccountByOwnerId().getLastName());
}
if(childDN.getUserAccount()!=null)
{
userRef.setElementDefOID("USR_"+childDN.getUserAccount().getUserId());
userRef.setUserName(childDN.getUserAccount().getUserName());
userRef.setFullName(childDN.getUserAccount().getFirstName()+" "+childDN.getUserAccount().getLastName());
}
else
{
userRef.setElementDefOID("");
userRef.setUserName("");
userRef.setFullName("");
}
childNoteBean.setUserRef(userRef);
dnNoteBean.getChildNotes().add(childNoteBean);
}
dnNoteBean.setNumberOfChildNotes(dnNoteBean.getChildNotes().size());
if(!dnNotes.contains(dnNoteBean))
{
dnNotes.add(dnNoteBean);
}
}
}
private AuditLogsBean fetchAuditLogs(int entityID,
String itemDataAuditTable, String entityValue, String anotherAuditLog) {
AuditLogsBean auditLogsBean = new AuditLogsBean();
if(isCollectAudits()){
AuditLogEvent auditLog = new AuditLogEvent();
auditLog.setEntityId(new Integer(entityID));
auditLog.setAuditTable(itemDataAuditTable);
auditLogsBean.setEntityID(entityValue);
ArrayList<AuditLogEvent> auditLogEvent = (getAuditEventDAO().findByParam(auditLog, anotherAuditLog));
auditLogsBean= fetchODMAuditBean(auditLogEvent,auditLogsBean);
}
return auditLogsBean;
}
private AuditLogsBean fetchODMAuditBean(ArrayList<AuditLogEvent> auditLogEvents,AuditLogsBean auditLogsBean ) {
for(AuditLogEvent auditLogEvent:auditLogEvents){
AuditLogBean auditBean = new AuditLogBean();
auditBean.setOid("AL_"+auditLogEvent.getAuditId());
auditBean.setDatetimeStamp(auditLogEvent.getAuditDate());
if(auditLogEvent.getEntityName()!=null && auditLogEvent.getEntityName().equals(STATUS))
{
/* if(auditLogEvent.getAuditTable().equals(EVENT_CRF)){
auditBean.setNewValue(EventCRFStatus.getByCode(Integer.valueOf(auditLogEvent.getNewValue())).getDescription());
auditBean.setOldValue(EventCRFStatus.getByCode(Integer.valueOf(auditLogEvent.getOldValue())).getDescription());
}
else */
if(auditLogEvent.getAuditTable().equals(STUDY_EVENT)){
auditBean.setNewValue(fetchStudyEventStatus(Integer.valueOf(auditLogEvent.getNewValue())));
auditBean.setOldValue(fetchStudyEventStatus(Integer.valueOf(auditLogEvent.getOldValue())));
}else if (auditLogEvent.getAuditTable().equals(SUBJECT_GROUP_MAP)){
auditBean.setNewValue(auditLogEvent.getNewValue());
auditBean.setOldValue(auditLogEvent.getOldValue());
}
else{
auditBean.setNewValue(Status.getByCode(Integer.valueOf(auditLogEvent.getNewValue())).getI18nDescription(getLocale()));
auditBean.setOldValue(Status.getByCode(Integer.valueOf(auditLogEvent.getOldValue())).getI18nDescription(getLocale()));
}
}
else{
auditBean.setNewValue(auditLogEvent.getNewValue()==null?"":auditLogEvent.getNewValue());
auditBean.setOldValue(auditLogEvent.getOldValue()==null?"":auditLogEvent.getOldValue());
}
auditBean.setReasonForChange(auditLogEvent.getReasonForChange()==null?"":auditLogEvent.getReasonForChange());
String auditEventTypeName = auditLogEvent.getAuditLogEventType().getName();
auditEventTypeName = auditEventTypeName.replace(' ', '_');
auditEventTypeName = auditEventTypeName.substring(0, 1).toLowerCase() + auditEventTypeName.substring(1);
auditLogEvent.getAuditLogEventType().setName(auditEventTypeName);
auditBean.setType(auditLogEvent.getAuditLogEventType().getI18nName(locale));
auditBean.setValueType(auditLogEvent.getEntityName()==null?"":auditLogEvent.getEntityName());
if(auditLogEvent.getUserAccount()!=null && auditLogEvent.getUserAccount().getUserId()!=0)
{
auditBean.setUserId("USR_"+auditLogEvent.getUserAccount().getUserId());
auditBean.setUserName(auditLogEvent.getUserAccount().getUserName());
auditBean.setName(auditLogEvent.getUserAccount().getFirstName()+" "+auditLogEvent.getUserAccount().getLastName());
}
else
{
auditBean.setUserId("");
auditBean.setUserName("");
auditBean.setName("");
}
auditLogsBean.getAuditLogs().add(auditBean);
}
return auditLogsBean;
}
private String fetchStudyEventStatus(Integer valueOf) {
return SubjectEventStatus.getByCode(valueOf).getI18nDescription(getLocale());
}
/**
* This is a generic method where the control enters first. Regardless what URL is being used. Depending upon the combination of URL parameters, further course is determined.
*/
@Override
public LinkedHashMap<String, OdmClinicalDataBean> getClinicalData(String studyOID, String studySubjectOID,
String studyEventOID, String formVersionOID,Boolean collectDNs,Boolean collectAudit, Locale locale, int userId) {
setLocale(locale);
setCollectDns(collectDNs);
setCollectAudits(collectAudit);
LinkedHashMap<String,OdmClinicalDataBean> clinicalDataHash = new LinkedHashMap<String, OdmClinicalDataBean>();
UserAccount userAccount = getUserAccountDao().findByColumnName(userId,"userId");
LOGGER.debug("Entering the URL with "+studyOID+":"+studySubjectOID+":"+studyEventOID+":"+formVersionOID+":DNS:"+collectDNs+":Audits:"+collectAudit);
LOGGER.info("Determining the generic paramters...");
Study study = getStudyDao().findByOcOID(studyOID);
int parentStudyId =0;
int studyId = study.getStudyId();
if (study.getStudy()!=null){
isActiveRoleAtSite=true;
parentStudyId = study.getStudy().getStudyId();
}else{
parentStudyId= studyId;
isActiveRoleAtSite=false;
}
ArrayList <StudyUserRole> surlist = getStudyUserRoleDao().findAllUserRolesByUserAccount(userAccount, studyId, parentStudyId);
if (surlist==null || surlist.size()==0){
// Does not have permission to view study or site info / return null
return null;
}
// This piece of code identifies if the study subject is assigned to study level or site level. If the study subject assigned to site is pulled from study level this will get the site OID correctly displayed.
if(!studySubjectOID.equals(INDICATE_ALL))
{
StudySubjectDao ssdao =getStudySubjectDao();
StudySubject ss = (StudySubject) getStudySubjectDao().findByColumnName(
studySubjectOID, "ocOid");
studyOID = ss.getStudy().getOc_oid();
}
if(studyEventOID.equals(INDICATE_ALL) && formVersionOID.equals(INDICATE_ALL)&&!studySubjectOID.equals(INDICATE_ALL) && !studyOID.equals(INDICATE_ALL))
{
LOGGER.info("Adding all the study events,formevents as it is a *");
LOGGER.info("study subject is not all and so is study");
clinicalDataHash.put(studyOID, getClinicalData(studyOID, studySubjectOID));
return clinicalDataHash;
}
else if(studyEventOID.equals(INDICATE_ALL) && formVersionOID.equals(INDICATE_ALL)&& studySubjectOID.equals(INDICATE_ALL) && !studyOID.equals(INDICATE_ALL))
{
LOGGER.info("At the study level.. study event,study subject and forms are *");
return getClinicalData(studyOID);
}
else if(!studyEventOID.equals(INDICATE_ALL)&&!studySubjectOID.equals(INDICATE_ALL) && !studyOID.equals(INDICATE_ALL) && formVersionOID.equals(INDICATE_ALL))
{
LOGGER.info("Obtaining the form version specific");
clinicalDataHash.put(studyOID, getClinicalDatas(studyOID,studySubjectOID,studyEventOID,null));
return clinicalDataHash;
}
else if(!studyEventOID.equals(INDICATE_ALL)&&!studySubjectOID.equals(INDICATE_ALL) && !studyOID.equals(INDICATE_ALL) && !formVersionOID.equals(INDICATE_ALL))
{
clinicalDataHash.put(studyOID, getClinicalDatas(studyOID,studySubjectOID,studyEventOID,formVersionOID));
return clinicalDataHash;
}
return null;
}
private void setLocale(Locale locale) {
this.locale=locale;
}
private Locale getLocale(){
return locale;
}
private OdmClinicalDataBean getClinicalDatas(String studyOID,
String studySubjectOID, String studyEventOID,String formVersionOID) {
int seOrdinal = 0;
String temp = studyEventOID;
List<StudyEvent>studyEvents = new ArrayList<StudyEvent>();
StudyEventDefinition sed = null ;
Study study = getStudyDao().findByColumnName(studyOID, "oc_oid");
List<StudySubject> ss = listStudySubjects(studySubjectOID);
int idx = studyEventOID.indexOf(OPEN_ORDINAL_DELIMITER);
LOGGER.info("study event oridinal is.."+idx);
if(idx>0)
{
studyEventOID= studyEventOID.substring(0,idx);
seOrdinal = new Integer(temp.substring(idx+1, temp.indexOf(CLOSE_ORDINAL_DELIMITER))).intValue();
}
sed = getStudyEventDefDao().findByColumnName(studyEventOID, "oc_oid");
LOGGER.info("study event ordinal.."+seOrdinal);
if(seOrdinal>0)
{
studyEvents = fetchSE(seOrdinal,sed.getStudyEvents(),studySubjectOID);
}
else
{
studyEvents = fetchSE(sed.getStudyEvents(),studySubjectOID);
}
return constructClinicalDataStudy(ss,study,studyEvents,formVersionOID) ;
}
private List<StudyEvent> fetchSE(int seOrdinal, List<StudyEvent> studyEvents,String ssOID) {
List<StudyEvent> sEs = new ArrayList<StudyEvent>();
LOGGER.debug("fetching all the study events");
for(StudyEvent se:studyEvents){
if(se.getSampleOrdinal()==seOrdinal &&se.getStudySubject().getOcOid().equals(ssOID))
{
sEs.add(se);
}
}
return sEs;
}
private List<StudyEvent> fetchSE( List<StudyEvent> studyEvents,String ssOID) {
List<StudyEvent> sEs = new ArrayList<StudyEvent>();
for(StudyEvent se:studyEvents){
if(se.getStudySubject().getOcOid().equals(ssOID))
{
sEs.add(se);
}
}
return sEs;
}
public UserAccountDao getUserAccountDao() {
return userAccountDao;
}
public void setUserAccountDao(UserAccountDao userAccountDao) {
this.userAccountDao = userAccountDao;
}
public StudyUserRoleDao getStudyUserRoleDao() {
return studyUserRoleDao;
}
public void setStudyUserRoleDao(StudyUserRoleDao studyUserRoleDao) {
this.studyUserRoleDao = studyUserRoleDao;
}
}