Examples with StudyGroupClassBean org.akaza.openclinica.bean.managestudy.StudyGroupClassBean used on opensource projects

Example 26 with StudyGroupClassBean

use of org.akaza.openclinica.bean.managestudy.StudyGroupClassBean in project OpenClinica by OpenClinica.

the class ExtractBean method computeReportData.

public void computeReportData(ReportBean answer) {
    answer.nextCell("Subject Event Item Values (Item-CRF-Ordinal)");
    answer.nextRow();
    // ///////////////////
    // //
    // COLUMNS //
    // //
    // ///////////////////
    answer.nextCell("SubjID");
    answer.nextCell("ProtocolID");
    // then CRF info
    if (dataset.isShowSubjectDob()) {
        if (study.getStudyParameterConfig().getCollectDob().equals("2")) {
            answer.nextCell("YOB");
        } else if (study.getStudyParameterConfig().getCollectDob().equals("1")) {
            answer.nextCell("DOB");
        }
    }
    if (dataset.isShowSubjectGender()) {
        answer.nextCell("Gender");
    }
    // TODO add additional labels here
    if (dataset.isShowSubjectStatus()) {
        answer.nextCell("SubjectStatus");
        eventDescriptions.put("SubjectStatus", "Subject Status");
    }
    // TODO set datainfo-settable code here, tbh
    if (dataset.isShowSubjectUniqueIdentifier() && "1".equals(showUniqueId)) {
        answer.nextCell("UniqueID");
        eventDescriptions.put("UniqueID", "Unique ID");
    }
    if (dataset.isShowSubjectSecondaryId()) {
        answer.nextCell("SecondaryID");
        eventDescriptions.put("SecondaryID", "SecondaryID");
    }
    // subject group info here, tbh
    if (dataset.isShowSubjectGroupInformation()) {
        // logger.info("got this far in subject group columns...");
        for (int y = 0; y < studyGroupClasses.size(); y++) {
            // logger.info("found a study group class here: "+y);
            StudyGroupClassBean studyGroupClassBean = (StudyGroupClassBean) studyGroupClasses.get(y);
            answer.nextCell(studyGroupClassBean.getName());
            // logger.info("found the name:
            // "+studyGroupClassBean.getName());
            // YW 10-31-2007, for SPSS, eventHeader probably doesn't match
            // the final header which will be validated
            eventDescriptions.put(studyGroupClassBean.getName(), studyGroupClassBean.getName());
        }
    }
    // ////////////////////
    // sed column labels
    int numSEDs = getNumSEDs();
    for (int i = 1; i <= numSEDs; i++) {
        int numSamples = getSEDNumSamples(i);
        for (int j = 1; j <= numSamples; j++) {
            if (dataset.isShowEventLocation()) {
                String location = getColumnLabel(i, j, "Location", numSamples);
                String description = getColumnDescription(i, j, "Location For ", currentDef.getName(), numSamples);
                answer.nextCell(location);
                eventHeaders.add(location);
                eventDescriptions.put(location, description);
            }
            if (dataset.isShowEventStart()) {
                String start = getColumnLabel(i, j, "StartDate", numSamples);
                String description = getColumnDescription(i, j, "Start Date For ", currentDef.getName(), numSamples);
                answer.nextCell(start);
                eventHeaders.add(start);
                eventDescriptions.put(start, description);
            }
            if (dataset.isShowEventEnd()) {
                String end = getColumnLabel(i, j, "EndDate", numSamples);
                String description = getColumnDescription(i, j, "End Date For ", currentDef.getName(), numSamples);
                answer.nextCell(end);
                eventHeaders.add(end);
                eventDescriptions.put(end, description);
            }
            if (dataset.isShowEventStatus()) {
                String eventStatus = getColumnLabel(i, j, "SubjectEventStatus", numSamples);
                String description = getColumnDescription(i, j, "Event Status For ", currentDef.getName(), numSamples);
                answer.nextCell(eventStatus);
                eventHeaders.add(eventStatus);
                eventDescriptions.put(eventStatus, description);
            }
            if (dataset.isShowSubjectAgeAtEvent() && ("1".equals(study.getStudyParameterConfig().getCollectDob()) || "2".equals(study.getStudyParameterConfig().getCollectDob()))) {
                String subjectAgeAtEvent = getColumnLabel(i, j, "AgeAtEvent", numSamples);
                String description = getColumnDescription(i, j, "Age At Event for ", currentDef.getName(), numSamples);
                answer.nextCell(subjectAgeAtEvent);
                eventHeaders.add(subjectAgeAtEvent);
                eventDescriptions.put(subjectAgeAtEvent, description);
            }
        }
    }
    // item-crf-ordinal column labels
    for (int i = 1; i <= numSEDs; i++) {
        int numSamples = getSEDNumSamples(i);
        // int numSEDCRFs = getSEDNumCRFs(i);
        for (int j = 1; j <= numSamples; j++) {
            int numSEDCRFs = getSEDNumCRFs(i);
            if (dataset.isShowCRFcompletionDate()) {
                // logger.info();
                String crfCompletionDate = getColumnLabel(i, j, "CompletionDate", numSamples);
                // FIXME
                String description = getColumnDescription(i, j, "Completion Date for ", currentDef.getName(), numSamples);
                // is
                // this
                // correct?
                answer.nextCell(crfCompletionDate);
                eventHeaders.add(crfCompletionDate);
                eventDescriptions.put(crfCompletionDate, description);
            }
            if (dataset.isShowCRFinterviewerDate()) {
                String interviewerDate = getColumnLabel(i, j, "InterviewDate", numSamples);
                // FIXME
                String description = getColumnDescription(i, j, "Interviewed Date for ", currentDef.getName(), numSamples);
                // is
                // this
                // correct?
                answer.nextCell(interviewerDate);
                eventHeaders.add(interviewerDate);
                eventDescriptions.put(interviewerDate, description);
            }
            if (dataset.isShowCRFinterviewerName()) {
                String interviewerName = getColumnLabel(i, j, "InterviewerName", numSamples);
                // FIXME
                String description = getColumnDescription(i, j, "Interviewer Name for ", currentDef.getName(), numSamples);
                // is
                // this
                // correct?
                answer.nextCell(interviewerName);
                eventHeaders.add(interviewerName);
                eventDescriptions.put(interviewerName, description);
            }
            if (dataset.isShowCRFstatus()) {
                // numSamples
                String crfStatus = getColumnLabel(i, j, "CRFVersionStatus", numSamples);
                // ?
                // ?
                // ?
                // FIXME
                String description = getColumnDescription(i, j, "Event CRF Status for ", currentDef.getName(), numSamples);
                // is
                // this
                // correct?
                answer.nextCell(crfStatus);
                eventHeaders.add(crfStatus);
                eventDescriptions.put(crfStatus, description);
            }
            if (dataset.isShowCRFversion()) {
                String crfCompletionDate = getColumnLabel(i, j, "VersionName", numSamples);
                // FIXME
                String description = getColumnDescription(i, j, "CRF Version Name for ", currentDef.getName(), numSamples);
                // is
                // this
                // correct?
                answer.nextCell(crfCompletionDate);
                eventHeaders.add(crfCompletionDate);
                eventDescriptions.put(crfCompletionDate, description);
            }
        }
    }
    for (int i = 1; i <= numSEDs; i++) {
        int numSamples = getSEDNumSamples(i);
        for (int j = 1; j <= numSamples; j++) {
            int numSEDCRFs = getSEDNumCRFs(i);
            for (int k = 1; k <= numSEDCRFs; k++) {
                // add CRF level descriptions here, tbh
                int numItems = getNumItems(i, k);
                for (int l = 1; l <= numItems; l++) {
                    // for (int m = 0; m <= maxItemDataBeanOrdinal; m++) {
                    for (Iterator iter = groupNames.entrySet().iterator(); iter.hasNext(); ) {
                        java.util.Map.Entry groupEntry = (java.util.Map.Entry) iter.next();
                        String groupName = (String) groupEntry.getKey();
                        logger.info("*** Found a row in groupNames: key " + groupName);
                        // groupName, it will not be added to item title
                        if (inKeys(i, j, k, l, groupName)) {
                            Integer groupCount = (Integer) groupEntry.getValue();
                            for (int m = 1; m <= groupCount.intValue(); m++) {
                                answer.nextCell(getColumnItemLabel(i, j, k, l, numSamples, m, groupName));
                                DisplayItemHeaderBean dih = new DisplayItemHeaderBean();
                                dih.setItemHeaderName(getColumnItemLabel(i, j, k, l, numSamples, m, groupName));
                                // ItemBean item = new ItemBean();
                                dih.setItem(currentItem);
                                itemNames.add(dih);
                            }
                        }
                    }
                }
            }
        }
    }
    answer.nextRow();
    // ////////////////
    for (int h = 1; h <= getNumSubjects(); h++) {
        DisplayItemDataBean didb = new DisplayItemDataBean();
        String label = getSubjectStudyLabel(h);
        answer.nextCell(label);
        didb.setSubjectName(label);
        String protocolId = getParentProtocolId();
        answer.nextCell(protocolId);
        didb.setStudyLabel(protocolId);
        // subject column data
        if (dataset.isShowSubjectDob()) {
            if (study.getStudyParameterConfig().getCollectDob().equals("2")) {
                String yob = getSubjectYearOfBirth(h);
                answer.nextCell(yob);
                didb.setSubjectDob(yob);
            } else if (study.getStudyParameterConfig().getCollectDob().equals("1")) {
                String dob = getSubjectDateOfBirth(h);
                answer.nextCell(dob);
                didb.setSubjectDob(dob);
            }
        }
        if (dataset.isShowSubjectGender()) {
            String gender = getSubjectGender(h);
            answer.nextCell(gender);
            didb.setSubjectGender(gender);
        }
        // TODO column headers above, column values here, tbh
        if (dataset.isShowSubjectStatus()) {
            String status = getSubjectStatusName(h);
            answer.nextCell(status);
            didb.setSubjectStatus(status);
        }
        if (dataset.isShowSubjectUniqueIdentifier() && "1".equals(showUniqueId)) {
            String uniqueName = getSubjectUniqueIdentifier(h);
            answer.nextCell(uniqueName);
            didb.setSubjectUniqueId(uniqueName);
        }
        if (dataset.isShowSubjectSecondaryId()) {
            String secondaryId = getSubjectSecondaryId(h);
            answer.nextCell(secondaryId);
            didb.setSubjectSecondaryId(secondaryId);
        }
        if (dataset.isShowSubjectGroupInformation()) {
            ArrayList studyGroupList = new ArrayList();
            // studyGroupMap =
            studyGroupList = getStudyGroupMap(h);
            // "+studyGroupMap.toString());
            for (int y = 0; y < studyGroupClasses.size(); y++) {
                StudyGroupClassBean sgcBean = (StudyGroupClassBean) studyGroupClasses.get(y);
                // if the subject is in the group...
                // logger.info("iterating through keys:
                // "+sgcBean.getId());
                Iterator iter = studyGroupList.iterator();
                /*
                     * case 0 - no groups assigned - should just have a blank
                     * here
                     */
                if (!iter.hasNext()) {
                    answer.nextCell("");
                    didb.setGroupName(Integer.valueOf(sgcBean.getId()), "");
                }
                /*
                     * case 1 - one or more groups assigned - runs through the
                     * maps and assigns them in rows
                     */
                while (iter.hasNext()) {
                    studyGroupMap = (HashMap) iter.next();
                    if (studyGroupMap.containsKey(Integer.valueOf(sgcBean.getId()))) {
                        StudyGroupBean groupBean = (StudyGroupBean) studyGroupMap.get(Integer.valueOf(sgcBean.getId()));
                        // logger.info("found a group name in a group
                        // class: "+groupBean.getName());
                        answer.nextCell(groupBean.getName());
                        didb.setGroupName(Integer.valueOf(sgcBean.getId()), groupBean.getName());
                        break;
                    // didb.setGroupName(groupBean.getName());
                    // otherwise we don't enter anything...
                    } else {
                        answer.nextCell("");
                        didb.setGroupName(Integer.valueOf(sgcBean.getId()), "");
                    }
                // end if
                }
            // end while
            }
        // end for
        }
        // sed column values
        for (int i = 1; i <= numSEDs; i++) {
            int numSamples = getSEDNumSamples(i);
            // add event-specific attributes here, tbh
            for (int j = 1; j <= numSamples; j++) {
                if (dataset.isShowEventLocation()) {
                    String location = getEventLocation(h, i, j);
                    answer.nextCell(location);
                    didb.getEventValues().add(location);
                }
                if (dataset.isShowEventStart()) {
                    String start = getEventStart(h, i, j);
                    answer.nextCell(start);
                    didb.getEventValues().add(start);
                }
                if (dataset.isShowEventEnd()) {
                    String end = getEventEnd(h, i, j);
                    answer.nextCell(end);
                    didb.getEventValues().add(end);
                }
                if (dataset.isShowEventStatus()) {
                    String status = getEventStatus(h, i, j);
                    answer.nextCell(status);
                    didb.getEventValues().add(status);
                }
                if (dataset.isShowSubjectAgeAtEvent() && ("1".equals(study.getStudyParameterConfig().getCollectDob()) || "2".equals(study.getStudyParameterConfig().getCollectDob()))) {
                    String ageAtEvent = currentSubject.getDateOfBirth() != null ? getAgeAtEvent(h, i, j) : "";
                    answer.nextCell(ageAtEvent);
                    didb.getEventValues().add(ageAtEvent);
                }
            }
        }
        // item-crf-ordinal column labels
        for (int i = 1; i <= numSEDs; i++) {
            int numSamples = getSEDNumSamples(i);
            for (int j = 1; j <= numSamples; j++) {
                if (dataset.isShowCRFcompletionDate()) {
                    String completionDate = getCRFCompletionDate(h, i, j);
                    answer.nextCell(completionDate);
                    didb.getEventValues().add(completionDate);
                }
                if (dataset.isShowCRFinterviewerDate()) {
                    String interviewerDate = getCRFInterviewerDate(h, i, j);
                    answer.nextCell(interviewerDate);
                    didb.getEventValues().add(interviewerDate);
                }
                if (dataset.isShowCRFinterviewerName()) {
                    String interviewerName = getCRFInterviewerName(h, i, j);
                    answer.nextCell(interviewerName);
                    didb.getEventValues().add(interviewerName);
                }
                if (dataset.isShowCRFstatus()) {
                    String crfStatus = getSEDCRFStatus(h, i, j);
                    answer.nextCell(crfStatus);
                    didb.getEventValues().add(crfStatus);
                }
                if (dataset.isShowCRFversion()) {
                    String crfVersion = getSEDCRFVersionName(h, i, j);
                    answer.nextCell(crfVersion);
                    didb.getEventValues().add(crfVersion);
                }
            }
        // end j
        }
        for (int i = 1; i <= numSEDs; i++) {
            int numSamples = getSEDNumSamples(i);
            // restart j so that text reports match tbh 03/08
            for (int j = 1; j <= numSamples; j++) {
                int numSEDCRFs = getSEDNumCRFs(i);
                for (int k = 1; k <= numSEDCRFs; k++) {
                    // add CRF-level column data here, tbh
                    int numItems = getNumItems(i, k);
                    for (int l = 1; l <= numItems; l++) {
                        // {
                        for (java.util.Iterator iter = groupNames.entrySet().iterator(); iter.hasNext(); ) {
                            java.util.Map.Entry groupEntry = (java.util.Map.Entry) iter.next();
                            String groupName = (String) groupEntry.getKey();
                            if (inKeys(i, j, k, l, groupName)) {
                                // logger.info("found group name at line
                                // 703: " + groupName);
                                Integer groupCount = (Integer) groupEntry.getValue();
                                // groupCount);
                                for (int m = 1; m <= groupCount.intValue(); m++) {
                                    String data = getDataByIndex(h, i, j, k, l, m, groupName);
                                    // a guard clause here to take care of
                                    // empties...
                                    // if (!data.equals("") ||
                                    // !groupName.equals(UNGROUPED)) {
                                    answer.nextCell(data);
                                    didb.getItemValues().add(data);
                                }
                            }
                        // }
                        // removing guard clause for now, tbh
                        // and the column code above should look about
                        // the same, tbh
                        }
                    }
                }
            }
        }
        rowValues.add(didb);
        answer.nextRow();
    }
}

Example 27 with StudyGroupClassBean

use of org.akaza.openclinica.bean.managestudy.StudyGroupClassBean in project OpenClinica by OpenClinica.

the class StudyGroupClassDAO method findAllByStudy.

@Override
public ArrayList findAllByStudy(StudyBean study) {
    ArrayList answer = new ArrayList();
    this.setTypesExpected();
    this.setTypeExpected(11, TypeNames.STRING);
    this.setTypeExpected(12, TypeNames.STRING);
    HashMap variables = new HashMap();
    variables.put(new Integer(1), new Integer(study.getId()));
    variables.put(new Integer(2), new Integer(study.getId()));
    ArrayList alist = this.select(digester.getQuery("findAllByStudy"), variables);
    Iterator it = alist.iterator();
    while (it.hasNext()) {
        HashMap hm = (HashMap) it.next();
        StudyGroupClassBean group = (StudyGroupClassBean) this.getEntityFromHashMap(hm);
        group.setStudyName((String) hm.get("study_name"));
        logger.info("study Name" + group.getStudyName());
        group.setGroupClassTypeName((String) hm.get("type_name"));
        answer.add(group);
    }
    return answer;
}

Example 28 with StudyGroupClassBean

use of org.akaza.openclinica.bean.managestudy.StudyGroupClassBean in project OpenClinica by OpenClinica.

the class UpdateSubjectGroupClassServlet method processRequest.

@Override
public void processRequest() throws Exception {
    String action = request.getParameter("action");
    FormProcessor fp = new FormProcessor(request);
    int classId = fp.getInt("id");
    if (classId == 0) {
        addPageMessage(respage.getString("please_choose_a_subject_group_class_to_edit"));
        forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
    } else {
        StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(sm.getDataSource());
        StudyGroupDAO sgdao = new StudyGroupDAO(sm.getDataSource());
        if (!fp.isSubmitted()) {
            StudyGroupClassBean sgcb = (StudyGroupClassBean) sgcdao.findByPK(classId);
            ArrayList groups = sgdao.findAllByGroupClass(sgcb);
            request.setAttribute("groupTypes", GroupClassType.toArrayList());
            session.setAttribute("group", sgcb);
            session.setAttribute("studyGroups", groups);
            forwardPage(Page.UPDATE_SUBJECT_GROUP_CLASS);
        } else {
            if (action.equalsIgnoreCase("confirm")) {
                confirmGroup();
            } else if (action.equalsIgnoreCase("submit")) {
                submitGroup();
            } else {
                addPageMessage(respage.getString("no_action_specified"));
                forwardPage(Page.SUBJECT_GROUP_CLASS_LIST_SERVLET);
            }
        }
    }
}

Example 29 with StudyGroupClassBean

use of org.akaza.openclinica.bean.managestudy.StudyGroupClassBean in project OpenClinica by OpenClinica.

the class ListStudySubjectTableFactory method getColumnNamesMap.

private void getColumnNamesMap() {
    ArrayList<String> columnNamesList = new ArrayList<String>();
    columnNamesList.add("studySubject.label");
    columnNamesList.add("studySubject.status");
    columnNamesList.add("enrolledAt");
    columnNamesList.add("studySubject.oid");
    columnNamesList.add("subject.charGender");
    columnNamesList.add("studySubject.secondaryLabel");
    for (StudyGroupClassBean studyGroupClass : getStudyGroupClasses()) {
        columnNamesList.add("sgc_" + studyGroupClass.getId());
    }
    for (StudyEventDefinitionBean studyEventDefinition : getStudyEventDefinitions()) {
        columnNamesList.add("sed_" + studyEventDefinition.getId());
    }
    columnNamesList.add("actions");
    columnNames = columnNamesList.toArray(columnNames);
}

Example 30 with StudyGroupClassBean

use of org.akaza.openclinica.bean.managestudy.StudyGroupClassBean in project OpenClinica by OpenClinica.

the class ListStudySubjectTableFactory method getColumnNames.

private void getColumnNames() {
    ArrayList<String> columnNamesList = new ArrayList<String>();
    columnNamesList.add("label");
    columnNamesList.add("status");
    columnNamesList.add("enrolledAt");
    columnNamesList.add("oid");
    columnNamesList.add("subject.charGender");
    columnNamesList.add("secondaryLabel");
    for (StudyGroupClassBean studyGroupClass : getStudyGroupClasses()) {
        columnNamesList.add("sgc_" + studyGroupClass.getId());
    }
    for (StudyEventDefinitionBean studyEventDefinition : getStudyEventDefinitions()) {
        columnNamesList.add("sed_" + studyEventDefinition.getId());
    }
    columnNamesList.add("actions");
    columnNames = columnNamesList.toArray(columnNames);
}