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

Example 31 with StudySubjectBean

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

the class RuleRunner method prepareEmailContents.

HashMap<String, String> prepareEmailContents(RuleSetBean ruleSet, RuleSetRuleBean ruleSetRule, StudyBean currentStudy, RuleActionBean ruleAction) {
    // get the Study Event
    StudyEventBean studyEvent = (StudyEventBean) getStudyEventDao().findByPK(Integer.valueOf(getExpressionService().getStudyEventDefenitionOrdninalCurated(ruleSet.getTarget().getValue())));
    // get the Study Subject
    StudySubjectBean studySubject = (StudySubjectBean) getStudySubjectDao().findByPK(studyEvent.getStudySubjectId());
    // get Study/Site Associated with Subject
    StudyBean theStudy = (StudyBean) getStudyDao().findByPK(studySubject.getStudyId());
    String theStudyName, theSiteName = "";
    if (theStudy.getParentStudyId() > 0) {
        StudyBean theParentStudy = (StudyBean) getStudyDao().findByPK(theStudy.getParentStudyId());
        theStudyName = theParentStudy.getName() + " / " + theParentStudy.getIdentifier();
        theSiteName = theStudy.getName() + " / " + theStudy.getIdentifier();
    } else {
        theStudyName = theStudy.getName() + " / " + theStudy.getIdentifier();
    }
    // get the eventCrf & subsequently the CRF Version
    //EventCRFBean eventCrf = (EventCRFBean) getEventCrfDao().findAllByStudyEvent(studyEvent).get(0);
    EventCRFBean eventCrf = (EventCRFBean) getEventCrfDao().findAllByStudyEventAndCrfOrCrfVersionOid(studyEvent, getExpressionService().getCrfOid(ruleSet.getTarget().getValue())).get(0);
    CRFVersionBean crfVersion = (CRFVersionBean) getCrfVersionDao().findByPK(eventCrf.getCRFVersionId());
    CRFBean crf = (CRFBean) getCrfDao().findByPK(crfVersion.getCrfId());
    String studyEventDefinitionName = getExpressionService().getStudyEventDefinitionFromExpression(ruleSet.getTarget().getValue(), currentStudy).getName();
    studyEventDefinitionName += " [" + studyEvent.getSampleOrdinal() + "]";
    String itemGroupName = getExpressionService().getItemGroupNameAndOrdinal(ruleSet.getTarget().getValue());
    ItemGroupBean itemGroupBean = getExpressionService().getItemGroupExpression(ruleSet.getTarget().getValue());
    ItemBean itemBean = getExpressionService().getItemExpression(ruleSet.getTarget().getValue(), itemGroupBean);
    String itemName = itemBean.getName();
    SectionBean section = (SectionBean) getSectionDAO().findByPK(getItemFormMetadataDAO().findByItemIdAndCRFVersionId(itemBean.getId(), crfVersion.getId()).getSectionId());
    StringBuffer sb = new StringBuffer();
    ResourceBundle respage = ResourceBundleProvider.getPageMessagesBundle();
    sb.append(respage.getString("email_header_1"));
    sb.append(" " + contextPath + " ");
    sb.append(respage.getString("email_header_2"));
    sb.append(" '" + currentStudy.getName() + "' ");
    sb.append(respage.getString("email_header_3"));
    sb.append(" \n\n ");
    sb.append(respage.getString("email_body_1") + " " + theStudyName + " \n ");
    sb.append(respage.getString("email_body_1_a") + " " + theSiteName + " \n ");
    sb.append(respage.getString("email_body_2") + " " + studySubject.getName() + " \n ");
    sb.append(respage.getString("email_body_3") + " " + studyEventDefinitionName + " \n ");
    sb.append(respage.getString("email_body_4") + " " + crf.getName() + " " + crfVersion.getName() + " \n ");
    sb.append(respage.getString("email_body_5") + " " + section.getTitle() + " \n ");
    sb.append(respage.getString("email_body_6") + " " + itemGroupName + " \n ");
    sb.append(respage.getString("email_body_7") + " " + itemName + " \n ");
    sb.append(respage.getString("email_body_8") + " " + ruleAction.getCuratedMessage() + " \n ");
    sb.append(" \n\n ");
    sb.append(respage.getString("email_body_9"));
    sb.append(" " + contextPath + " ");
    sb.append(respage.getString("email_body_10"));
    sb.append(" \n");
    requestURLMinusServletPath = requestURLMinusServletPath == null ? "" : requestURLMinusServletPath;
    sb.append(requestURLMinusServletPath + "/ViewSectionDataEntry?ecId=" + eventCrf.getId() + "&sectionId=" + section.getId() + "&tabId=" + section.getOrdinal());
    // &eventId="+ studyEvent.getId());
    sb.append("\n\n");
    sb.append(respage.getString("email_footer"));
    String subject = contextPath + " - [" + currentStudy.getName() + "] ";
    String ruleSummary = ruleAction.getSummary() != null ? ruleAction.getSummary() : "";
    String message = ruleSummary.length() < 20 ? ruleSummary : ruleSummary.substring(0, 20) + " ... ";
    subject += message;
    HashMap<String, String> emailContents = new HashMap<String, String>();
    emailContents.put("body", sb.toString());
    emailContents.put("subject", subject);
    return emailContents;
}

Example 32 with StudySubjectBean

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

the class RuleSetBulkRuleRunner method populateForRuleSetBasedView.

private List<RuleSetBasedViewContainer> populateForRuleSetBasedView(List<RuleSetBasedViewContainer> theList, RuleSetBean ruleSet, RuleBean rule, String akey, RuleActionBean ruleAction) {
    StudyEventBean studyEvent = (StudyEventBean) getStudyEventDao().findByPK(Integer.valueOf(getExpressionService().getStudyEventDefenitionOrdninalCurated(ruleSet.getTarget().getValue())));
    // for (String akey : actionsToBeExecuted.keySet()) {
    // for (RuleActionBean ruleAction : actionsToBeExecuted.get(akey)) {
    RuleSetBasedViewContainer container = new RuleSetBasedViewContainer(rule.getName(), rule.getOid(), rule.getExpression().getValue(), akey, ruleAction.getActionType().toString(), ruleAction.getSummary());
    if (!theList.contains(container)) {
        theList.add(container);
    }
    StudySubjectBean studySubject = (StudySubjectBean) getStudySubjectDao().findByPK(studyEvent.getStudySubjectId());
    theList.get(theList.indexOf(container)).addSubject(studySubject.getLabel());
    // }
    return theList;
}

Example 33 with StudySubjectBean

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

the class DiscrepancyNoteUtil method filterDiscNotesBySubject.

/**
     * Filter a List of DiscrepancyNoteBeans by subject id.
     *
     * @param allDiscNotes
     *            A List of DiscrepancyNoteBeans prior to filtering.
     * @param subjectId
     *            An int subject id.
     * @param dataSource
     *            A DataSource object used by DAO methods.
     * @return The filtered List of DiscrepancyNoteBeans.
     */
public List<DiscrepancyNoteBean> filterDiscNotesBySubject(List<DiscrepancyNoteBean> allDiscNotes, int subjectId, DataSource dataSource) {
    // Do not filter this List if the subjectId < 1
    if (!(subjectId >= 1)) {
        return allDiscNotes;
    }
    StudySubjectDAO studySubjDAO = new StudySubjectDAO(dataSource);
    StudySubjectBean studySubjBean = new StudySubjectBean();
    studySubjBean = (StudySubjectBean) studySubjDAO.findByPK(subjectId);
    List<DiscrepancyNoteBean> newDiscNotes = new ArrayList<DiscrepancyNoteBean>();
    for (DiscrepancyNoteBean dnBean : allDiscNotes) {
        if (dnBean.getSubjectName().equalsIgnoreCase(studySubjBean.getLabel())) {
            newDiscNotes.add(dnBean);
        }
    }
    return newDiscNotes;
}

Example 34 with StudySubjectBean

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

the class RandomizeService method getStudySubjectAttrValue.

private String getStudySubjectAttrValue(String expr, EventCRFBean eventCrfBean, RuleSetBean ruleSet) {
    String value = "";
    StudySubjectDAO<String, ArrayList> ssdao = new StudySubjectDAO<>(ds);
    SubjectDAO subdao = new SubjectDAO(ds);
    StudyGroupClassDAO sgcdao = new StudyGroupClassDAO(ds);
    StudyGroupDAO sgdao = new StudyGroupDAO(ds);
    StudyDAO<String, ArrayList> sdao = new StudyDAO<>(ds);
    StudySubjectBean ssBean = (StudySubjectBean) ssdao.findByPK(eventCrfBean.getStudySubjectId());
    SubjectBean subjectBean = (SubjectBean) subdao.findByPK(ssBean.getSubjectId());
    String prefix = "STUDYGROUPCLASSLIST";
    String param = expr.split("\\.", -1)[1].trim();
    if (param.equalsIgnoreCase("BIRTHDATE")) {
        value = subjectBean.getDateOfBirth().toString();
    } else if (param.equalsIgnoreCase("SEX")) {
        if (String.valueOf(subjectBean.getGender()).equals("m"))
            value = "Male";
        else
            value = "Female";
    // value =String.valueOf(ssBean.getGender());
    } else if (param.startsWith(prefix)) {
        String gcName = param.substring(21, param.indexOf("\"]"));
        StudyGroupBean sgBean = sgdao.findSubjectStudyGroup(ssBean.getId(), gcName);
        if (sgBean != null)
            value = sgBean.getName();
    }
    return value;
}

Example 35 with StudySubjectBean

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

the class OdmFileCreation method createODMFile.

public HashMap<String, Integer> createODMFile(String odmVersion, long sysTimeBegin, String generalFileDir, DatasetBean datasetBean, StudyBean currentStudy, String generalFileDirCopy, ExtractBean eb, Integer currentStudyId, Integer parentStudyId, String studySubjectNumber, boolean zipped, boolean saveToDB, boolean deleteOld, String odmType, UserAccountBean userBean) {
    Integer ssNumber = getStudySubjectNumber(studySubjectNumber);
    MetaDataCollector mdc = new MetaDataCollector(dataSource, datasetBean, currentStudy, ruleSetRuleDao);
    AdminDataCollector adc = new AdminDataCollector(dataSource, datasetBean, currentStudy);
    ClinicalDataCollector cdc = new ClinicalDataCollector(dataSource, datasetBean, currentStudy);
    MetaDataCollector.setTextLength(200);
    if (deleteOld) {
        File file = new File(generalFileDir);
        if (file.isDirectory()) {
            files = file.listFiles();
            oldFiles = Arrays.asList(files);
        }
    }
    if (odmVersion != null) {
        // by default odmVersion is 1.2
        if ("1.3".equals(odmVersion)) {
            ODMBean odmb = new ODMBean();
            odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 ODM1-3-0.xsd");
            ArrayList<String> xmlnsList = new ArrayList<String>();
            xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
            odmb.setXmlnsList(xmlnsList);
            odmb.setODMVersion("1.3");
            mdc.setODMBean(odmb);
            adc.setOdmbean(odmb);
            cdc.setODMBean(odmb);
        } else if ("oc1.2".equals(odmVersion)) {
            ODMBean odmb = new ODMBean();
            // odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.2 OpenClinica-ODM1-2-1.xsd");
            odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.2 OpenClinica-ODM1-2-1-OC1.xsd");
            ArrayList<String> xmlnsList = new ArrayList<String>();
            xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.2\"");
            // xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/openclinica_odm/v1.2\"");
            xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/odm_ext_v121/v3.1\"");
            xmlnsList.add("xmlns:OpenClinicaRules=\"http://www.openclinica.org/ns/rules/v3.1\"");
            odmb.setXmlnsList(xmlnsList);
            odmb.setODMVersion("oc1.2");
            mdc.setODMBean(odmb);
            adc.setOdmbean(odmb);
            cdc.setODMBean(odmb);
        } else if ("oc1.3".equals(odmVersion)) {
            ODMBean odmb = mdc.getODMBean();
            // odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0.xsd");
            // odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0-OC1.xsd");
            odmb.setSchemaLocation("http://www.cdisc.org/ns/odm/v1.3 OpenClinica-ODM1-3-0-OC3-0.xsd");
            ArrayList<String> xmlnsList = new ArrayList<String>();
            xmlnsList.add("xmlns=\"http://www.cdisc.org/ns/odm/v1.3\"");
            // xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/openclinica_odm/v1.3\"");
            xmlnsList.add("xmlns:OpenClinica=\"http://www.openclinica.org/ns/odm_ext_v130/v3.1\"");
            xmlnsList.add("xmlns:OpenClinicaRules=\"http://www.openclinica.org/ns/rules/v3.1\"");
            odmb.setXmlnsList(xmlnsList);
            odmb.setODMVersion("oc1.3");
            odmb.setOdmType(odmType);
            mdc.setODMBean(odmb);
            adc.setOdmbean(odmb);
            cdc.setODMBean(odmb);
        }
    }
    //////////////////////////////////////////
    ////////// MetaData Extraction //////////
    mdc.collectFileData();
    MetaDataReportBean metaReport = new MetaDataReportBean(mdc.getOdmStudyMap(), coreResources);
    metaReport.setODMVersion(odmVersion);
    metaReport.setOdmBean(mdc.getODMBean());
    metaReport.createChunkedOdmXml(Boolean.TRUE);
    long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
    String ODMXMLFileName = mdc.getODMBean().getFileOID() + ".xml";
    int fId = createFileK(ODMXMLFileName, generalFileDir, metaReport.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
    if (!"".equals(generalFileDirCopy)) {
        int fId2 = createFileK(ODMXMLFileName, generalFileDirCopy, metaReport.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
    }
    //////////////////////////////////////////
    ////////// AdminData Extraction //////////
    adc.collectFileData();
    AdminDataReportBean adminReport = new AdminDataReportBean(adc.getOdmAdminDataMap());
    adminReport.setODMVersion(odmVersion);
    adminReport.setOdmBean(mdc.getODMBean());
    adminReport.createChunkedOdmXml(Boolean.TRUE);
    sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
    fId = createFileK(ODMXMLFileName, generalFileDir, adminReport.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
    if (!"".equals(generalFileDirCopy)) {
        int fId2 = createFileK(ODMXMLFileName, generalFileDirCopy, adminReport.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
    }
    //////////////////////////////////////////
    ////////// ClinicalData Extraction ///////
    DatasetDAO dsdao = new DatasetDAO(dataSource);
    String sql = eb.getDataset().getSQLStatement();
    String st_sed_in = dsdao.parseSQLDataset(sql, true, true);
    String st_itemid_in = dsdao.parseSQLDataset(sql, false, true);
    int datasetItemStatusId = eb.getDataset().getDatasetItemStatus().getId();
    String ecStatusConstraint = dsdao.getECStatusConstraint(datasetItemStatusId);
    String itStatusConstraint = dsdao.getItemDataStatusConstraint(datasetItemStatusId);
    Iterator<OdmStudyBase> it = cdc.getStudyBaseMap().values().iterator();
    while (it.hasNext()) {
        JobTerminationMonitor.check();
        OdmStudyBase u = it.next();
        ArrayList newRows = dsdao.selectStudySubjects(u.getStudy().getId(), 0, st_sed_in, st_itemid_in, dsdao.genDatabaseDateConstraint(eb), ecStatusConstraint, itStatusConstraint);
        ///////////////
        int fromIndex = 0;
        boolean firstIteration = true;
        while (fromIndex < newRows.size()) {
            JobTerminationMonitor.check();
            int toIndex = fromIndex + ssNumber < newRows.size() ? fromIndex + ssNumber : newRows.size() - 1;
            List x = newRows.subList(fromIndex, toIndex + 1);
            fromIndex = toIndex + 1;
            String studySubjectIds = "";
            for (int i = 0; i < x.size(); i++) {
                StudySubjectBean sub = new StudySubjectBean();
                sub = (StudySubjectBean) x.get(i);
                studySubjectIds += "," + sub.getId();
            }
            // for
            studySubjectIds = studySubjectIds.replaceFirst(",", "");
            ClinicalDataUnit cdata = new ClinicalDataUnit(dataSource, datasetBean, cdc.getOdmbean(), u.getStudy(), cdc.getCategory(), studySubjectIds);
            cdata.setCategory(cdc.getCategory());
            cdata.collectOdmClinicalData();
            FullReportBean report = new FullReportBean();
            report.setClinicalData(cdata.getOdmClinicalData());
            report.setOdmStudyMap(mdc.getOdmStudyMap());
            report.setODMVersion(odmVersion);
            // report.setOdmStudy(mdc.getOdmStudy());
            report.setOdmBean(mdc.getODMBean());
            if (firstIteration && fromIndex >= newRows.size()) {
                report.createChunkedOdmXml(Boolean.TRUE, true, true);
                firstIteration = false;
            } else if (firstIteration) {
                report.createChunkedOdmXml(Boolean.TRUE, true, false);
                firstIteration = false;
            } else if (fromIndex >= newRows.size()) {
                report.createChunkedOdmXml(Boolean.TRUE, false, true);
            } else {
                report.createChunkedOdmXml(Boolean.TRUE, false, false);
            }
            fId = createFileK(ODMXMLFileName, generalFileDir, report.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
            if (!"".equals(generalFileDirCopy)) {
                int fId2 = createFileK(ODMXMLFileName, generalFileDirCopy, report.getXmlOutput().toString(), datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
            }
        }
    }
    sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
    fId = createFileK(ODMXMLFileName, generalFileDir, "</ODM>", datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, saveToDB, zipped, deleteOld, userBean);
    if (!"".equals(generalFileDirCopy)) {
        int fId2 = createFileK(ODMXMLFileName, generalFileDirCopy, "</ODM>", datasetBean, sysTimeEnd, ExportFormatBean.XMLFILE, false, zipped, deleteOld, userBean);
    }
    //////////////////////////////////////////
    ////////// pre pagination extraction /////
    /*
         * mdc.collectFileData();
         * adc.collectOdmAdminDataMap();
         * cdc.collectOdmClinicalDataMap();
         * FullReportBean report = new FullReportBean();
         * report.setClinicalDataMap(cdc.getOdmClinicalDataMap());
         * report.setAdminDataMap(adc.getOdmAdminDataMap());
         * report.setOdmStudyMap(mdc.getOdmStudyMap());
         * report.setOdmBean(mdc.getODMBean());
         * report.setODMVersion(odmVersion);
         * report.createOdmXml(Boolean.TRUE);
         * long sysTimeEnd = System.currentTimeMillis() - sysTimeBegin;
         * String ODMXMLFileName = mdc.getODMBean().getFileOID() + ".xml";
         * int fId = this.createFile(ODMXMLFileName, generalFileDir, report.getXmlOutput().toString(), datasetBean,
         * sysTimeEnd, ExportFormatBean.XMLFILE, true);
         * if (!"".equals(generalFileDirCopy)) {
         * int fId2 = this.createFile(ODMXMLFileName, generalFileDirCopy, report.getXmlOutput().toString(), datasetBean,
         * sysTimeEnd, ExportFormatBean.XMLFILE, false);
         * }
         */
    HashMap answerMap = new HashMap<String, Integer>();
    // JN: Zipped in the next stage as thats where the ODM file is named and copied over in default categories.
    // if(zipped)
    // { try {
    // zipFile(ODMXMLFileName,generalFileDir);
    //
    // } catch (IOException e) {
    // // TODO Auto-generated catch block
    // logger.error(e.getMessage());
    // e.printStackTrace();
    // }
    //
    // } // return ODMXMLFileName;
    answerMap.put(ODMXMLFileName, new Integer(fId));
    return answerMap;
}