Examples with CRFVersionBean org.akaza.openclinica.bean.submit.CRFVersionBean used on opensource projects

Example 56 with CRFVersionBean

use of org.akaza.openclinica.bean.submit.CRFVersionBean in project OpenClinica by OpenClinica.

the class ExtractBean method addStudyEventData.

// addStudySubjectData
/*
     * public void addStudySubjectData(Integer studySubjectId, String
     * studySubjectLabel, Date dateOfBirth, String gender, Integer
     * subjectStatusId, Boolean dobCollected, String uniqueIdentifier, String
     * subjectSecondaryLabel) { if (!subjectsAdded.containsKey(studySubjectId))
     * { StudySubjectBean sub = new StudySubjectBean();
     * sub.setId(studySubjectId.intValue()); sub.setLabel(studySubjectLabel);
     *
     * sub.setDateOfBirth(dateOfBirth); if (gender != null && gender.length() >
     * 0) { sub.setGender(gender.charAt(0)); } else { sub.setGender(' '); }
     * sub.setStatus(Status.get(subjectStatusId.intValue())); //
     * sub.setSecondaryLabel(secondaryID);//????
     * sub.setUniqueIdentifier(uniqueIdentifier);
     * sub.setSecondaryLabel(subjectSecondaryLabel); //
     * sub.setEnrollmentDate(enrollmentDate); // TODO need to find enrollment
     * date, later, tbh subjects.add(sub); subjectsAdded.put(studySubjectId,
     * Boolean.TRUE); } }
     */
/**
     * @vbc 08/06/2008 NEW EXTRACT DATA IMPLEMENTATION Combines the two HashMaps
     *      into eventData entries - the data is already filtered for null
     *      values
     */
public void addStudyEventData() {
    /**
         * The two ArrayList are synchronized because they are extracted with
         * "ORDER BY aitem_data_id"
         */
    boolean isfnd = false;
    // initialize
    eventData = new HashMap();
    for (int ik = 0; ik < aBASE_ITEMDATAID.size(); ik++) {
        // get the item_group side
        extractDataset_ITEMGROUPSIDE objgrp = (extractDataset_ITEMGROUPSIDE) hBASE_ITEMGROUPSIDE.get(ik);
        extractDataset_EVENTSIDE objev = (extractDataset_EVENTSIDE) hBASE_EVENTSIDE.get(ik);
        // sanity check - assume both are not null
        Integer itemdataid = (Integer) aBASE_ITEMDATAID.get(ik);
        Integer itemdataid_objgrp = objgrp.itemDataId;
        Integer itemdataid_objev = objev.itemDataId;
        if (itemdataid_objgrp.intValue() == itemdataid.intValue() && itemdataid_objev.intValue() == itemdataid.intValue()) {
            // OK - add entries to the dataEvent
            // initialize
            StudyEventBean event = new StudyEventBean();
            EventCRFBean eventCRF = new EventCRFBean();
            //
            // studyEventDefinitionName
            event.setName(objev.studyEventDefinitionName);
            // studyEventStart
            event.setDateStarted(objev.studyEventDateStart);
            // studyEventEnd
            event.setDateEnded(objev.studyEventDateEnd);
            // studyEventLocation
            event.setLocation(objev.studyEventLoacation);
            // sampleOrdinal
            event.setSampleOrdinal(objev.sampleOrdinal.intValue());
            // .
            // intValue
            // ()
            // studyEventDefinitionId
            event.setStudyEventDefinitionId(objev.studyEvenetDefinitionId.intValue());
            // .
            // intValue
            // (
            // )
            // studySubjectId
            event.setStudySubjectId(objev.studySubjectId.intValue());
            // .
            // intValue
            // ()
            // se
            event.setStartTimeFlag(objev.studyEventStartTimeFlag.booleanValue());
            // .
            // getStartTimeFlag
            // (
            // )
            // se
            event.setEndTimeFlag(objev.studyEventEndTimeFlag.booleanValue());
            // .
            // getEndTimeFlag
            // (
            // )
            // below needs to be added, tbh
            // TODO - @vbc - validate this
            // se
            event.setStatus(Status.get(objev.studyEventStatusId.intValue()));
            // .
            // getStatus
            // (
            // )
            // se
            event.setSubjectEventStatus(SubjectEventStatus.get(objev.studyEventSubjectEventStatusId.intValue()));
            // .
            // getSubjectEventStatus
            // (
            // )
            // @vbc 08/06/2008 NEW EXTRACT DATA IMPLEMENTATION
            // the stage is set on setStatus - skip it
            // event.setStage(se.getStage());
            // se.getId()
            event.setId(objev.studyEventId.intValue());
            // end tbh, 03/08
            // completionStatusId
            eventCRF.setCompletionStatusId(objgrp.eventCrfCompletionStatusId);
            // .
            // intValue
            // (
            // )
            // interviewerName
            eventCRF.setInterviewerName(objgrp.interviewerName);
            // dateCompleted
            eventCRF.setDateCompleted(objgrp.eventCrfDateCompleted);
            // dateValidateCompleted
            eventCRF.setDateValidateCompleted(objgrp.eventCrfDateValidateCompleted);
            eventCRF.setStatus(Status.get(objgrp.eventCrfStatusId));
            // eventCRF.setCreatedDate();//same as interviewed date? NO
            // dateInterviewedv
            eventCRF.setDateInterviewed(objgrp.dateInterviewed);
            // eventCRF.setStatus(status); //this is the one that we want,
            // tbh
            CRFVersionBean crfVersion = new CRFVersionBean();
            // crfVersionName
            crfVersion.setName(objgrp.crfVersionName);
            // crfVersionStatusId
            crfVersion.setStatus(Status.get(objgrp.crfVersionStatusId.intValue()));
            // crfVersionStatusId
            crfVersion.setStatusId(objgrp.crfVersionStatusId.intValue());
            // .
            // intValue
            // (
            // )
            eventCRF.setCrfVersion(crfVersion);
            ArrayList events = new ArrayList();
            events.add(eventCRF);
            // logger.info("///adding an event CRF..."
            // + eventCRF.getInterviewerName());
            // hmm, one to one relationship?
            event.setEventCRFs(events);
            // guard clause to see if it's in there already?
            // not rly, the above is only used in auditlogging
            // could fit in crf and crf version ids here, though
            // FIXME def not one to one relationship, tbh, 03.08
            String key = getStudyEventDataKey(/* studySubjectId.intValue() */
            objev.studySubjectId.intValue(), /* studyEventDefinitionId.intValue() */
            objev.studyEvenetDefinitionId.intValue(), /* sampleOrdinal.intValue()) */
            objev.sampleOrdinal.intValue());
            if (eventData == null) {
                eventData = new HashMap();
            }
            StudyEventBean checkEvent = (StudyEventBean) eventData.get(key);
            if (checkEvent == null) {
                eventData.put(key, event);
            // logger.info("###just CREATED key: " + key + " event: " +
            // event.getName() + " int.name: " +
            // eventCRF.getInterviewerName());
            } else {
            // OK - already saved
            }
        } else {
            isfnd = true;
        }
    //
    }
    // for
    // before return quick count
    logger.debug("Number of entries in the eventData is:" + eventData.size());
}

Example 57 with CRFVersionBean

use of org.akaza.openclinica.bean.submit.CRFVersionBean in project OpenClinica by OpenClinica.

the class ExtractBean method getSEDCRFStatus.

// private String getSEDCRFName(int sedInd, int crfInd) {
// syncCRFIndex(sedInd, crfInd);
// return currentCRF.getName();
// }
// private String getSEDCRFVersionName(int h, int sedInd, int crfInd) {
// syncCRFIndex(sedInd, crfInd);
//
// StudyEventBean seb = getEvent(h, sedInd, crfInd);
//
// String returnMe = "";
// //ArrayList versions = currentCRF.getVersions();//returns zero results
// EventCRFBean eventCRF = null;
// if (seb.getEventCRFs().size() > 0) {
// logger.info("found getEventCRFs.size " + seb.getEventCRFs().size());
// for (int t = 0; t < seb.getEventCRFs().size(); t++) {
// eventCRF = (EventCRFBean) seb.getEventCRFs().get(t);
// returnMe = eventCRF.getCrfVersion().getName();
// //logger.info("found versions.size "+versions.size());
// //for (int s = 0; s < versions.size(); s++) {
// // CRFVersionBean version = (CRFVersionBean)versions.get(s);
// // if (version.getId()==eventCRF.getCRFVersionId()) {
// // returnMe = version.getName();
// //break;
// // }
// //}
// }
//
// }
// logger.info("returning the following for crf version name: " + returnMe);
// return returnMe;
// }
private String getSEDCRFStatus(int h, int sedInd, int crfInd) {
    // BADS Flag
    syncCRFIndex(sedInd, crfInd);
    StudyEventBean seb = getEvent(h, sedInd, crfInd);
    Status ecStatus = Status.AVAILABLE;
    EventCRFBean eventCRF = null;
    if (seb.getEventCRFs().size() > 0) {
        eventCRF = (EventCRFBean) seb.getEventCRFs().get(0);
    }
    String crfVersionStatus = "";
    SubjectEventStatus status = SubjectEventStatus.NOT_SCHEDULED;
    CRFVersionBean crfv = new CRFVersionBean();
    crfv.setStatus(Status.AVAILABLE);
    // modified stage so that crfVersionStatus could be the same as what it
    // shows in subject matrix - as required.
    DataEntryStage stage = DataEntryStage.INVALID;
    try {
        stage = eventCRF.getStage();
        ecStatus = eventCRF.getStatus();
        // SubjectEventStatus.get(
        status = seb.getSubjectEventStatus();
        // eventCRF
        // .getCompletionStatusId());
        crfv = eventCRF.getCrfVersion();
    } catch (NullPointerException e) {
        logger.info("exception hit, status set to not scheduled");
    }
    // currentCRF.getStatus().getName();
    //
    logger.info("event crf stage: " + stage.getName() + ", event crf status: " + ecStatus.getName() + ", STATUS: " + status.getName() + " crf version: " + crfv.getStatus().getName() + " data entry stage: " + stage.getName());
    if (stage.equals(DataEntryStage.INVALID) || ecStatus.equals(Status.INVALID)) {
        stage = DataEntryStage.UNCOMPLETED;
    }
    crfVersionStatus = stage.getName();
    if (status.equals(SubjectEventStatus.LOCKED) || status.equals(SubjectEventStatus.SKIPPED) || status.equals(SubjectEventStatus.STOPPED)) {
        crfVersionStatus = DataEntryStage.LOCKED.getName();
    } else if (status.equals(SubjectEventStatus.INVALID)) {
        crfVersionStatus = DataEntryStage.LOCKED.getName();
    } else if (!currentCRF.getStatus().equals(Status.AVAILABLE)) {
        crfVersionStatus = DataEntryStage.LOCKED.getName();
    } else if (!crfv.getStatus().equals(Status.AVAILABLE)) {
        crfVersionStatus = DataEntryStage.LOCKED.getName();
    }
    logger.info("returning: " + crfVersionStatus);
    return crfVersionStatus;
}

Example 58 with CRFVersionBean

use of org.akaza.openclinica.bean.submit.CRFVersionBean in project OpenClinica by OpenClinica.

the class OdmExtractDAO method setDataWithOCAttributes.

protected void setDataWithOCAttributes(StudyBean study, DatasetBean dataset, OdmClinicalDataBean data, String odmVersion, Iterator iter, HashMap<Integer, String> oidPoses, String odmType) {
    String subprev = "";
    HashMap<String, Integer> sepos = new HashMap<String, Integer>();
    String seprev = "";
    String formprev = "";
    HashMap<String, Integer> igpos = new HashMap<String, Integer>();
    String igprev = "";
    String oidPos = "";
    StudyBean parentStudy = study.getParentStudyId() > 0 ? (StudyBean) new StudyDAO(this.ds).findByPK(study.getParentStudyId()) : study;
    setStudyParemeterConfig(parentStudy);
    HashSet<Integer> sgcIdSet = new HashSet<Integer>();
    HashMap<String, String> subOidPoses = new HashMap<String, String>();
    HashMap<String, String> evnOidPoses = new HashMap<String, String>();
    String studySubjectOids = "";
    String sedOids = "";
    String ecIds = "";
    while (iter.hasNext()) {
        HashMap row = (HashMap) iter.next();
        String studySubjectLabel = (String) row.get("study_subject_oid");
        // String label = (String) row.get("label");
        Integer sgcId = (Integer) row.get("sgc_id");
        String sgcName = (String) row.get("sgc_name");
        String sgName = (String) row.get("sg_name");
        String sedOID = (String) row.get("definition_oid");
        Boolean studyEventRepeating = (Boolean) row.get("definition_repeating");
        Integer sampleOrdinal = (Integer) row.get("sample_ordinal");
        Date startDate = (Date) row.get("date_start");
        String cvOID = (String) row.get("crf_version_oid");
        // ecId should
        Integer ecId = (Integer) row.get("event_crf_id");
        // be unique;
        Date dob = (Date) row.get("date_of_birth");
        CRFVersionBean cvBean = cvdao.findByOid(cvOID);
        CRFBean cBean = (CRFBean) crfdao.findByPK(cvBean.getCrfId());
        String key = studySubjectLabel;
        ExportSubjectDataBean sub = new ExportSubjectDataBean();
        if (subprev.equals(studySubjectLabel)) {
            int p = data.getExportSubjectData().size() - 1;
            sub = data.getExportSubjectData().get(p);
            // ------ add openclinica subject_group
            if (sgcId > 0) {
                int presize = sgcIdSet.size();
                sgcIdSet.add(sgcId);
                if (sgcIdSet.size() > presize) {
                    sgcIdSet.add(sgcId);
                    SubjectGroupDataBean sgd = new SubjectGroupDataBean();
                    sgd.setStudyGroupClassId("SGC_" + sgcId);
                    sgd.setStudyGroupClassName(sgcName);
                    sgd.setStudyGroupName(sgName);
                    sub.getSubjectGroupData().add(sgd);
                }
            }
        // ------ finish adding openclinica subject_group
        } else {
            subprev = studySubjectLabel;
            studySubjectOids += "'" + studySubjectLabel + "', ";
            sub.setSubjectOID(studySubjectLabel);
            // ----- add openclinica subject attributes
            sub.setStudySubjectId((String) row.get("label"));
            if (dataset.isShowSubjectUniqueIdentifier()) {
                sub.setUniqueIdentifier((String) row.get("unique_identifier"));
            }
            if (dataset.isShowSubjectSecondaryId()) {
                sub.setSecondaryId((String) row.get("secondary_label"));
            }
            if (dob != null) {
                if (dataset.isShowSubjectDob()) {
                    if (parentStudy.getStudyParameterConfig().getCollectDob().equals("2")) {
                        Calendar cal = Calendar.getInstance();
                        cal.setTime(dob);
                        int year = cal.get(Calendar.YEAR);
                        if (year > 0) {
                            sub.setYearOfBirth(year);
                        }
                    } else {
                        sub.setDateOfBirth(new SimpleDateFormat("yyyy-MM-dd").format(dob));
                    }
                }
            }
            if (dataset.isShowSubjectGender()) {
                sub.setSubjectGender((String) row.get("gender"));
            }
            if (dataset.isShowSubjectStatus()) {
                sub.setStatus(Status.get((Integer) row.get("status_id")).getName());
            }
            // ------ add openclinica subject_group
            if (sgcId > 0) {
                sgcIdSet.clear();
                sgcIdSet.add(sgcId);
                SubjectGroupDataBean sgd = new SubjectGroupDataBean();
                sgd.setStudyGroupClassId("SGC_" + sgcId);
                sgd.setStudyGroupClassName(sgcName);
                sgd.setStudyGroupName(sgName);
                sub.getSubjectGroupData().add(sgd);
            }
            // ------ finish adding openclinica subject_group
            data.getExportSubjectData().add(sub);
            seprev = "";
            formprev = "";
            igprev = "";
        }
        oidPos = data.getExportSubjectData().size() - 1 + "";
        subOidPoses.put(studySubjectLabel, oidPos);
        ExportStudyEventDataBean se = new ExportStudyEventDataBean();
        // key += sedOID + sampleOrdinal;
        key += sedOID;
        if (!seprev.equals(key) || !sepos.containsKey(key + sampleOrdinal)) {
            sepos.put(key + sampleOrdinal, sub.getExportStudyEventData().size());
            seprev = key;
            sedOids += "'" + sedOID + "', ";
            se.setStudyEventOID(sedOID);
            // ----- add openclinica study event attributes
            if (startDate != null && dataset.isShowSubjectAgeAtEvent() && dob != null) {
                se.setAgeAtEvent(Utils.getAge(dob, startDate));
            }
            if (dataset.isShowEventLocation()) {
                se.setLocation((String) row.get("se_location"));
            }
            if (dataset.isShowEventStart() && startDate != null) {
                if ((Boolean) row.get("start_time_flag") == Boolean.TRUE) {
                    se.setStartDate(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss").format(startDate));
                } else {
                    se.setStartDate(new SimpleDateFormat("yyyy-MM-dd").format(startDate));
                }
            }
            Date endDate = (Date) row.get("date_end");
            if (dataset.isShowEventEnd() && endDate != null) {
                if ((Boolean) row.get("end_time_flag") == Boolean.TRUE) {
                    se.setEndDate(new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss").format(endDate));
                } else {
                    se.setEndDate(new SimpleDateFormat("yyyy-MM-dd").format(endDate));
                }
            }
            if (dataset.isShowEventStatus()) {
                se.setStatus(SubjectEventStatus.get((Integer) row.get("event_status_id")).getName());
            }
            // ----- finish adding study event attributes
            se.setStudyEventRepeatKey(studyEventRepeating ? sampleOrdinal + "" : "-1");
            sub.getExportStudyEventData().add(se);
            formprev = "";
            igprev = "";
        } else {
            se = sub.getExportStudyEventData().get(sepos.get(key + sampleOrdinal));
        }
        oidPos += "---" + (sub.getExportStudyEventData().size() - 1);
        evnOidPoses.put(key, oidPos);
        ExportFormDataBean form = new ExportFormDataBean();
        key += cvOID;
        if (formprev.equals(key)) {
            form = se.getExportFormData().get(se.getExportFormData().size() - 1);
        } else {
            formprev = key;
            ecIds += "'" + ecId + "', ";
            form.setFormOID(cBean.getOid());
            // ----- add openclinica crf attributes
            if (dataset.isShowCRFversion()) {
                form.setCrfVersion((String) row.get("crf_version"));
            }
            if (dataset.isShowCRFstatus()) {
                form.setStatus(this.getCrfVersionStatus(se.getStatus(), (Integer) row.get("cv_status_id"), (Integer) row.get("ec_status_id"), (Integer) row.get("validator_id")));
            }
            if (dataset.isShowCRFinterviewerName()) {
                form.setInterviewerName((String) row.get("interviewer_name"));
            }
            if (dataset.isShowCRFinterviewerDate()) {
                try {
                    form.setInterviewDate(new SimpleDateFormat("yyyy-MM-dd").format((Date) row.get("date_interviewed")));
                } catch (NullPointerException npe) {
                    logger.debug("caught NPE for interviewDate");
                // Comment it out for: 11592. For this exaction function, interviewDate should be kept as the
                // same as in database.
                // form.setInterviewDate(new SimpleDateFormat("yyyy-MM-dd").format(new Date()));
                }
            }
            // ----- finish adding crf attributes
            se.getExportFormData().add(form);
            igprev = "";
        }
        oidPos += "---" + (se.getExportFormData().size() - 1);
        // ecId should be distinct
        oidPoses.put(ecId, oidPos);
        oidPos = "";
    }
    studySubjectOids = studySubjectOids.length() > 0 ? studySubjectOids.substring(0, studySubjectOids.length() - 2).trim() : studySubjectOids;
    sedOids = sedOids.length() > 0 ? sedOids.substring(0, sedOids.length() - 2).trim() : sedOids;
    ecIds = ecIds.length() > 0 ? ecIds.substring(0, ecIds.length() - 2).trim() : ecIds;
    if (odmType != null && odmType.equalsIgnoreCase("clinical_data")) {
        logger.debug("No Audit logs or discrepancy Notes");
    } else {
        if (studySubjectOids.length() > 0) {
            this.setOCSubjectDataAuditLogs(parentStudy, data, studySubjectOids, subOidPoses);
            this.setOCEventDataAuditLogs(parentStudy, data, studySubjectOids, evnOidPoses);
            if (ecIds.length() > 0) {
                this.setOCFormDataAuditLogs(parentStudy, data, studySubjectOids, ecIds, oidPoses);
            } else {
                logger.debug("OdmExtractDAO.setOCFormDataAuditLogs wasn't called because of empty ecIds");
            }
            this.setOCSubjectDataDNs(data, studySubjectOids, subOidPoses);
            if (sedOids.length() > 0) {
                this.setOCEventDataDNs(data, sedOids, studySubjectOids, evnOidPoses);
            } else {
                logger.info("OdmExtractDAO.setOCEventDataDNs wasn't called because of empty sedOids");
            }
        } else {
            logger.debug("OdmExtractDAO methods(setOCSubjectDataAuditLogs,setOCEventDataAuditLogs,setOCFormDataAuditLogs," + "setOCSubjectDataDNs,setOCEventDataDNs) weren't called because of empty studySubjectOids");
        }
        if (ecIds.length() > 0) {
            this.setOCFormDataDNs(data, ecIds, oidPoses);
        } else {
            logger.debug("OdmExtractDAO.setOCFormDataDNs wasn't called because of empty ecIds");
        }
    }
}

Example 59 with CRFVersionBean

use of org.akaza.openclinica.bean.submit.CRFVersionBean in project OpenClinica by OpenClinica.

the class CRFVersionDAO method findByPK.

public EntityBean findByPK(int ID) {
    CRFVersionBean eb = new CRFVersionBean();
    this.setTypesExpected();
    HashMap variables = new HashMap();
    variables.put(new Integer(1), new Integer(ID));
    String sql = digester.getQuery("findByPK");
    ArrayList alist = this.select(sql, variables);
    Iterator it = alist.iterator();
    if (it.hasNext()) {
        eb = (CRFVersionBean) this.getEntityFromHashMap((HashMap) it.next());
    }
    return eb;
}

Example 60 with CRFVersionBean

use of org.akaza.openclinica.bean.submit.CRFVersionBean in project OpenClinica by OpenClinica.

the class CRFVersionDAO method findByFullName.

public EntityBean findByFullName(String version, String crfName) {
    CRFVersionBean eb = new CRFVersionBean();
    this.setTypesExpected();
    HashMap variables = new HashMap();
    variables.put(new Integer(1), version);
    variables.put(new Integer(2), crfName);
    String sql = digester.getQuery("findByFullName");
    ArrayList alist = this.select(sql, variables);
    Iterator it = alist.iterator();
    if (it.hasNext()) {
        eb = (CRFVersionBean) this.getEntityFromHashMap((HashMap) it.next());
    }
    return eb;
}