Example usage for org.dom4j DocumentHelper createDocument

Introduction

In this page you can find the example usage for org.dom4j DocumentHelper createDocument.

Prototype

public static Document createDocument() 

Source Link

Usage

From source file:gestionecassa.backends.XmlDataBackend.java

License:Open Source License

@Override
public void saveListOfOrders(String id, Collection<Order> list) throws IOException {

    String fileName = xmlDataPath + id + ".xml";

    Document document = DocumentHelper.createDocument();
    Element root = document.addElement("orders");

    for (Order order : list) {
        addOrderToElement(root, order);/*from   ww  w .j  av  a  2 s .com*/
    }

    // for debug purposes
    OutputFormat format = OutputFormat.createPrettyPrint();

    // lets write to a file
    XMLWriter writer = new XMLWriter(new FileWriter(fileName), format);
    //XMLWriter writer = new XMLWriter(new FileWriter(fileName));
    writer.write(document);
    writer.close();
}

---

From source file:gestionecassa.XmlPreferencesHandler.java

License:Open Source License

/**
 * Saves options to a file given by the option type
 * @param preferences /*from  w w  w . ja  va2 s.  c  om*/
 * @throws IOException
 */
public void savePrefs(DataType preferences) throws IOException {

    Document document = DocumentHelper.createDocument();
    Element root = document.addElement("config");
    root.addAttribute("version", preferences.getVersion());
    root.addAttribute("application", preferences.getApplication());

    for (Field field : preferences.getClass().getFields()) {
        try {
            root.addElement(field.getName()).addText(field.get(preferences) + "");
        } catch (IllegalArgumentException ex) {
            logger.warn("campo sbagliato", ex);
        } catch (IllegalAccessException ex) {
            logger.warn("campo sbagliato", ex);
        }
    }

    // lets write to a file
    OutputFormat format = OutputFormat.createPrettyPrint();
    XMLWriter writer = new XMLWriter(new FileWriter(preferences.getFileName()), format);
    writer.write(document);
    writer.close();
}

---

From source file:gov.nih.nci.caintegrator.application.report.LevelOfExpressionIHCReport.java

License:BSD License

/**
 * @param finding//w  w w. jav  a2 s  .c om
 * @param filterMapParams
 * @return Document
 */
public static Document getReportXML(Finding finding, Map filterMapParams) {

    Document document = DocumentHelper.createDocument();

    Element report = document.addElement("Report");
    Element cell = null;
    Element data = null;
    Element dataRow = null;
    //ADD BASIC ATTRIBUTED
    report.addAttribute("reportType", "levelExpression");
    report.addAttribute("groupBy", "none");
    String queryName = finding.getTaskId();
    report.addAttribute("queryName", queryName);
    report.addAttribute("sessionId", "the session id");

    StringBuffer sb = new StringBuffer();

    /* *************************************************************************************************
     * 
     * PROCESS QUERY DETAILS
     * 
     * *************************************************************************************************             * 
     */
    LevelOfExpressionIHCFindingCriteria criteria = (LevelOfExpressionIHCFindingCriteria) finding.getQueryDTO();
    ArrayList<String> queryDetails = new ArrayList();
    if (criteria != null) {
        String tmp = "";
        ArrayList<String> tmpCollection = new ArrayList<String>();
        tmp = criteria.getQueryName() != null ? criteria.getQueryName() : "";
        queryDetails.add("Query Name: " + tmp);
        tmp = "";
        if (criteria.getProteinBiomarkerCrit() != null
                && criteria.getProteinBiomarkerCrit().getProteinNameCollection() != null
                && !criteria.getProteinBiomarkerCrit().getProteinNameCollection().isEmpty()) {
            Set<String> biomarkers = criteria.getProteinBiomarkerCrit().getProteinNameCollection();
            tmpCollection = new ArrayList<String>(biomarkers);
            for (String bm : tmpCollection) {
                if (bm != tmpCollection.get(0)) {
                    tmp += ", " + bm;
                } else {
                    tmp += bm;
                }
            }

        }
        queryDetails.add("Biomarker(s): " + tmp);
        tmpCollection.clear();
        tmp = "";
        if (criteria.getSpecimenCriteria() != null
                && criteria.getSpecimenCriteria().getTimeCourseCollection() != null
                && !criteria.getSpecimenCriteria().getTimeCourseCollection().isEmpty()) {
            Set<String> timepoints = criteria.getSpecimenCriteria().getTimeCourseCollection();
            tmpCollection = new ArrayList<String>(timepoints);
            TimepointStringComparator ts = new TimepointStringComparator();
            Collections.sort(tmpCollection, ts);
            for (String tc : tmpCollection) {
                if (tc != tmpCollection.get(0)) {
                    tmp += ", " + tc;
                } else {
                    tmp += tc;
                }
            }
        }
        queryDetails.add("Timepoint(s): " + tmp);
        tmpCollection.clear();
        tmp = "";
        if (criteria.getStainIntensityCollection() != null
                && !criteria.getStainIntensityCollection().isEmpty()) {
            Set<String> intensity = (Set<String>) criteria.getStainIntensityCollection();
            tmpCollection = new ArrayList<String>(intensity);
            for (String in : tmpCollection) {
                if (in != tmpCollection.get(0)) {
                    tmp += ", " + in;
                } else {
                    tmp += in;
                }
            }

        }
        queryDetails.add("Intensity: " + tmp);
        tmpCollection.clear();
        tmp = "";
        tmp = criteria.getPercentPositiveRangeMin() != null ? criteria.getPercentPositiveRangeMin().toString()
                : "";
        queryDetails.add("% Positive Min: " + tmp);
        tmp = "";
        tmp = criteria.getPercentPositiveRangeMax() != null ? criteria.getPercentPositiveRangeMax().toString()
                : "";
        queryDetails.add("% Positive Max: " + tmp);
        tmp = "";
        if (criteria.getStainLocalizationCollection() != null
                && !criteria.getStainLocalizationCollection().isEmpty()) {
            Set<String> locale = (Set<String>) criteria.getStainLocalizationCollection();
            tmpCollection = new ArrayList<String>(locale);
            for (String lc : tmpCollection) {
                if (lc != tmpCollection.get(0)) {
                    tmp += ", " + lc;
                } else {
                    tmp += lc;
                }
            }

        }
        queryDetails.add("Localization: " + tmp);
        tmpCollection.clear();
        tmp = "";
    }

    String qd = "";
    for (String q : queryDetails) {
        qd += q + " ||| ";
    }

    /* **************************************************************************************************************
     * 
     * BUILD REPORT AS XML
     * 
     * **************************************************************************************************************
     */

    //GET FINDINGS, CAST TO APPROPRIATE FINDINGS AND ADD TO ARRAYLIST (RESULTS)
    ArrayList dFindings = new ArrayList(finding.getDomainFindings());
    ArrayList<LevelOfExpressionIHCFinding> domainFindings = new ArrayList<LevelOfExpressionIHCFinding>(
            dFindings);
    ArrayList<LevelOfExpressionIHCFindingReportBean> results = new ArrayList<LevelOfExpressionIHCFindingReportBean>();
    for (LevelOfExpressionIHCFinding loef : domainFindings) {
        LevelOfExpressionIHCFindingReportBean reportBean = new LevelOfExpressionIHCFindingReportBean(loef);
        results.add(reportBean);
    }

    if (!results.isEmpty()) {

        //SORT THE ARRAYLIST(RESULTS) BY PATIENT DID
        PatientComparator p = new PatientComparator();
        Collections.sort(results, p);

        //CREATE A HASHMAP SORTED BY PATIENT DID AS THE KEY AND THE ARRAYLIST OF REPORTBEANS AS THE VALUE                

        Map<String, ArrayList<LevelOfExpressionIHCFindingReportBean>> reportBeanMap = new HashMap<String, ArrayList<LevelOfExpressionIHCFindingReportBean>>();
        int j = results.size();
        for (int i = 0; i < results.size(); i++) {
            boolean found = false;
            Set<String> keys = reportBeanMap.keySet();
            int key = keys.size();
            if (!keys.isEmpty()) {
                for (String k : keys) {
                    String s = results.get(i).getSpecimenIdentifier() + "_" + results.get(i).getBiomarkerName();
                    if (s.equals(k)) {
                        found = true;
                        reportBeanMap.get(k).add(results.get(i));
                        break;
                    }
                }
                if (!found) {
                    reportBeanMap.put(
                            results.get(i).getSpecimenIdentifier() + "_" + results.get(i).getBiomarkerName(),
                            new ArrayList<LevelOfExpressionIHCFindingReportBean>());
                    reportBeanMap.get(
                            results.get(i).getSpecimenIdentifier() + "_" + results.get(i).getBiomarkerName())
                            .add(results.get(i));
                }
            } else {
                reportBeanMap.put(
                        results.get(i).getSpecimenIdentifier() + "_" + results.get(i).getBiomarkerName(),
                        new ArrayList<LevelOfExpressionIHCFindingReportBean>());
                reportBeanMap
                        .get(results.get(i).getSpecimenIdentifier() + "_" + results.get(i).getBiomarkerName())
                        .add(results.get(i));
            }
            //                   

        }

        //IF THE USER SELECTED TIMEPOINTS FOR WHICH THAT PATIENT DID DID NOT HAVE DATA, CREATE NULL BEANS SO AS TO RENDER A READABLE REPORT
        Set<String> b = reportBeanMap.keySet();
        for (String g : b) {
            while (reportBeanMap.get(g)
                    .size() < (reportBeanMap.get(g).get(0).getTimepointHeaders(criteria).size())) {
                reportBeanMap.get(g)
                        .add(new LevelOfExpressionIHCFindingReportBean(new LevelOfExpressionIHCFinding()));
            }
        }

        //ADD QUERY DETAILS      
        Element details = report.addElement("Query_details");
        cell = details.addElement("Data");
        cell.addText(qd);
        cell = null;

        //ADD HEADERS THAT ARE TIMEPOINT-INDEPENDENT (PATIENT AND BIOMARKER)
        Element headerRow = report.addElement("Row").addAttribute("name", "headerRow");
        ArrayList<String> ntpHeaders = results.get(0).getNonTimepointHeaders();
        for (String ntpHeader : ntpHeaders) {
            cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                    .addAttribute("group", "ntpHeader");
            data = cell.addElement("Data").addAttribute("type", "header").addText(ntpHeader);
            data = null;
            cell = null;
        }

        //ADD HEADERS THAT ARE TIMEPOINT DEPENDENT
        ArrayList<String> headers = results.get(0).getHeaders();
        for (String header : headers) {
            cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                    .addAttribute("group", "header");
            data = cell.addElement("Data").addAttribute("type", "header").addText(header);
            data = null;
            cell = null;
        }

        //ADD TIMEPOINT SUBHEADERS
        ArrayList<String> tpHeaders = results.get(0).getTimepointHeaders(criteria);
        //ArrayList<String> localizations = results.get(0).getTimepointHeaders(criteria);

        TimepointStringComparator ts = new TimepointStringComparator();
        Collections.sort(tpHeaders, ts);
        Element tpHeaderRow = report.addElement("Row").addAttribute("name", "tpHeaderRow");
        // for(String tpHeader : tpHeaders){  
        for (int i = 0; i < tpHeaders.size(); i++) {
            cell = tpHeaderRow.addElement("Cell").addAttribute("type", "header")
                    .addAttribute("class", "firstTP").addAttribute("group", "tpHeader");
            data = cell.addElement("Data").addAttribute("type", "header").addText(tpHeaders.get(i));
            data = null;
            cell = null;
        }

        Set<String> keys = reportBeanMap.keySet();

        // ADD DATA ROWS           
        for (String key : keys) {

            String tp = reportBeanMap.get(key).get(0).getTimepoint();
            Collection<String> localizationCollection = criteria.getStainLocalizationCollection();
            Collection<String> intensityCollection = criteria.getStainIntensityCollection();

            String localization = reportBeanMap.get(key).get(0).getStainLocalization();
            String intensity = reportBeanMap.get(key).get(0).getStainIntensity();

            if (tpHeaders.contains(tp) && (localizationCollection == null
                    || (localizationCollection != null && localizationCollection.contains(localization)))
                    && (intensityCollection == null
                            || (intensityCollection != null && intensityCollection.contains(intensity)))) {

                dataRow = report.addElement("Row").addAttribute("name", "dataRow");
                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "sample")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "selectable")
                        .addText(reportBeanMap.get(key).get(0).getPatientDID());
                data = null;
                cell = null;
                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "header")
                        .addText(reportBeanMap.get(key).get(0).getBiomarkerName());
                data = null;
                cell = null;

                //GRAB EACH REPORT BEAN IN EACH ARRAYLIST AND MATCH UP TO THE APPROPRIATE TIMEPOINT AS A MAP WITH THE TIMEPOINT AS KEY AND REPORTBEAN THE VALUE
                ArrayList<LevelOfExpressionIHCFindingReportBean> myList = reportBeanMap.get(key);
                Map<String, LevelOfExpressionIHCFindingReportBean> myMap = new HashMap<String, LevelOfExpressionIHCFindingReportBean>();
                ArrayList<LevelOfExpressionIHCFindingReportBean> mySortedMap = new ArrayList<LevelOfExpressionIHCFindingReportBean>();

                for (LevelOfExpressionIHCFindingReportBean ggg : myList) {
                    for (int i = 0; i < tpHeaders.size(); i++) {
                        if (ggg.getTimepoint().equalsIgnoreCase(tpHeaders.get(i))) {
                            myMap.put(tpHeaders.get(i), ggg);
                            break;
                        } else if (ggg.getTimepoint().equals("--")) {
                            if (!myMap.containsKey(tpHeaders.get(i))) {
                                myMap.put(tpHeaders.get(i), ggg);
                                break;
                            }
                        }
                    }
                }

                //SORT MAP BY TIMEPOINT SO THAT THE REPORT BEAN DATA CAN EASILY BE DISPLAYED UNDER THE APPROPRIATE TIEMPOINT
                for (int i = 0; i < tpHeaders.size(); i++) {
                    for (String k : myMap.keySet()) {
                        if (k.equalsIgnoreCase(tpHeaders.get(i))) {
                            mySortedMap.add(myMap.get(k));
                        }
                    }
                }

                //ITERATE OVER THE MAP FOR EACH DATA FIELD WITH ITS CORRESPONDING TIMEPOINT AND BUILD DATA ROWS
                for (LevelOfExpressionIHCFindingReportBean reportBean : mySortedMap) {

                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getPercentPositive());
                    data = null;
                    cell = null;
                }
                for (LevelOfExpressionIHCFindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getStainIntensity());
                    data = null;
                    cell = null;

                }
                for (LevelOfExpressionIHCFindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getStainLocalization());
                    data = null;
                    cell = null;

                }
                for (LevelOfExpressionIHCFindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getInvasivePresentation());
                    data = null;
                    cell = null;

                }
                for (LevelOfExpressionIHCFindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getOverallExpression());
                    data = null;
                    cell = null;

                }
            }
        }

    }

    else {
        //TODO: handle this error
        sb.append("<br><Br>Level of Expression is empty<br>");
    }

    return document;
}

---

From source file:gov.nih.nci.caintegrator.application.report.LossOfExpressionIHCReport.java

License:BSD License

public static Document getReportXML(Finding finding, Map filterMapParams) {

    Document document = DocumentHelper.createDocument();

    Element report = document.addElement("Report");
    Element cell = null;// w  ww .j  a va  2 s. co  m
    Element data = null;
    Element dataRow = null;
    //ADD BASIC ATTRIBUTED
    report.addAttribute("reportType", "IHC Loss Of Expression");
    report.addAttribute("groupBy", "none");
    String queryName = finding.getTaskId();
    report.addAttribute("queryName", queryName);
    report.addAttribute("sessionId", "the session id");

    StringBuffer sb = new StringBuffer();

    /* *************************************************************************************************
     * 
     * PROCESS QUERY DETAILS
     * 
     * *************************************************************************************************             * 
     */
    LossOfExpressionIHCFindingCriteria criteria = (LossOfExpressionIHCFindingCriteria) finding.getQueryDTO();
    ArrayList<String> queryDetails = new ArrayList();
    if (criteria != null) {
        String tmp = "";
        ArrayList<String> tmpCollection = new ArrayList<String>();
        tmp = criteria.getQueryName() != null ? criteria.getQueryName() : "";
        queryDetails.add("Query Name: " + tmp);
        tmp = "";
        if (criteria.getProteinBiomarkerCrit() != null
                && criteria.getProteinBiomarkerCrit().getProteinNameCollection() != null
                && !criteria.getProteinBiomarkerCrit().getProteinNameCollection().isEmpty()) {
            Set<String> biomarkers = criteria.getProteinBiomarkerCrit().getProteinNameCollection();
            tmpCollection = new ArrayList<String>(biomarkers);
            for (String bm : tmpCollection) {
                if (bm != tmpCollection.get(0)) {
                    tmp += ", " + bm;
                } else {
                    tmp += bm;
                }
            }

        }
        queryDetails.add("Biomarker(s): " + tmp);
        tmpCollection.clear();
        tmp = "";
        if (criteria.getSpecimenCriteria() != null
                && criteria.getSpecimenCriteria().getTimeCourseCollection() != null
                && !criteria.getSpecimenCriteria().getTimeCourseCollection().isEmpty()) {
            Set<String> timepoints = criteria.getSpecimenCriteria().getTimeCourseCollection();
            tmpCollection = new ArrayList<String>(timepoints);
            TimepointStringComparator ts = new TimepointStringComparator();
            Collections.sort(tmpCollection, ts);
            for (String tc : tmpCollection) {
                if (tc != tmpCollection.get(0)) {
                    tmp += ", " + tc;
                } else {
                    tmp += tc;
                }
            }
        }
        queryDetails.add("Timepoint(s): " + tmp);
        tmpCollection.clear();
        tmp = "";
        if (criteria.getBenignSumOperator() != null && criteria.getBenignSum() != null) {
            tmp = criteria.getBenignSumOperator() + " " + criteria.getBenignSum().toString();
        }
        queryDetails.add("Benign Sum: " + tmp);
        tmp = "";
        if (criteria.getInvasiveSumOperator() != null && criteria.getInvasiveSum() != null) {
            tmp = criteria.getInvasiveSumOperator() + " " + criteria.getInvasiveSum().toString();
        }
        queryDetails.add("Invasive Sum: " + tmp);
        tmp = "";
        if (criteria.getResultCodeCollection() != null && !criteria.getResultCodeCollection().isEmpty()) {
            Set<String> resultCodes = (Set<String>) criteria.getResultCodeCollection();
            tmpCollection = new ArrayList<String>(resultCodes);
            for (String rc : tmpCollection) {
                if (rc != tmpCollection.get(0)) {
                    tmp += ", " + rc;
                } else {
                    tmp += rc;
                }
            }

        }
        queryDetails.add("Loss Result: " + tmp);
        tmpCollection.clear();
        tmp = "";
    }

    String qd = "";
    for (String q : queryDetails) {
        qd += q + " ||| ";
    }

    /* **************************************************************************************************************
     * 
     * BUILD REPORT AS XML
     * 
     * **************************************************************************************************************
     */

    //GET FINDINGS, CAST TO APPROPRIATE FINDINGS AND ADD TO ARRAYLIST (RESULTS)
    ArrayList dFindings = new ArrayList(finding.getDomainFindings());
    ArrayList<LossOfExpressionIHCFinding> domainFindings = new ArrayList<LossOfExpressionIHCFinding>(dFindings);
    ArrayList<LossOfExpressionIHCFindingReportBean> results = new ArrayList<LossOfExpressionIHCFindingReportBean>();
    for (LossOfExpressionIHCFinding loef : domainFindings) {
        LossOfExpressionIHCFindingReportBean reportBean = new LossOfExpressionIHCFindingReportBean(loef);
        results.add(reportBean);
    }

    if (!results.isEmpty()) {

        //SORT THE ARRAYLIST(RESULTS) BY PATIENT DID
        PatientComparator p = new PatientComparator();
        Collections.sort(results, p);

        //CREATE A HASHMAP SORTED BY PATIENT DID AS THE KEY AND THE ARRAYLIST OF REPORTBEANS AS THE VALUE                

        Map<String, ArrayList<LossOfExpressionIHCFindingReportBean>> reportBeanMap = new HashMap<String, ArrayList<LossOfExpressionIHCFindingReportBean>>();

        for (int i = 0; i < results.size(); i++) {
            boolean found = false;
            Set<String> keys = reportBeanMap.keySet();
            if (!keys.isEmpty()) {
                for (String k : keys) {
                    String s = results.get(i).getSpecimenIdentifier() + "_" + results.get(i).getBiomarkerName();

                    if (s.equals(k)) {
                        found = true;
                        reportBeanMap.get(k).add(results.get(i));
                        break;
                    }
                }
                if (!found) {
                    reportBeanMap.put(
                            results.get(i).getSpecimenIdentifier() + "_" + results.get(i).getBiomarkerName(),
                            new ArrayList<LossOfExpressionIHCFindingReportBean>());
                    reportBeanMap.get(
                            results.get(i).getSpecimenIdentifier() + "_" + results.get(i).getBiomarkerName())
                            .add(results.get(i));

                }
            } else {

                reportBeanMap.put(
                        results.get(i).getSpecimenIdentifier() + "_" + results.get(i).getBiomarkerName(),
                        new ArrayList<LossOfExpressionIHCFindingReportBean>());
                reportBeanMap
                        .get(results.get(i).getSpecimenIdentifier() + "_" + results.get(i).getBiomarkerName())
                        .add(results.get(i));
            }
        }

        //IF THE USER SELECTED TIMEPOINTS FOR WHICH THAT PATIENT DID DID NOT HAVE DATA, CREATE NULL BEANS SO AS TO RENDER A READABLE REPORT
        Set<String> b = reportBeanMap.keySet();
        for (String g : b) {
            while (reportBeanMap.get(g)
                    .size() < (reportBeanMap.get(g).get(0).getTimepointHeaders(criteria).size())) {
                reportBeanMap.get(g)
                        .add(new LossOfExpressionIHCFindingReportBean(new LossOfExpressionIHCFinding()));
            }
        }

        //ADD QUERY DETAILS      
        Element details = report.addElement("Query_details");
        cell = details.addElement("Data");
        cell.addText(qd);
        cell = null;

        //ADD HEADERS THAT ARE TIMEPOINT-INDEPENDENT (PATIENT AND BIOMARKER)
        Element headerRow = report.addElement("Row").addAttribute("name", "headerRow");
        ArrayList<String> ntpHeaders = results.get(0).getNonTimepointHeaders();
        for (String ntpHeader : ntpHeaders) {
            cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                    .addAttribute("group", "ntpHeader");
            data = cell.addElement("Data").addAttribute("type", "header").addText(ntpHeader);
            data = null;
            cell = null;
        }

        //ADD HEADERS THAT ARE TIMEPOINT DEPENDENT
        ArrayList<String> headers = results.get(0).getHeaders();
        for (String header : headers) {
            cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                    .addAttribute("group", "header");
            data = cell.addElement("Data").addAttribute("type", "header").addText(header);
            data = null;
            cell = null;
        }

        //ADD TIMEPOINT SUBHEADERS
        ArrayList<String> tpHeaders = results.get(0).getTimepointHeaders(criteria);
        TimepointStringComparator ts = new TimepointStringComparator();
        Collections.sort(tpHeaders, ts);
        Element tpHeaderRow = report.addElement("Row").addAttribute("name", "tpHeaderRow");
        // for(String tpHeader : tpHeaders){  
        for (int i = 0; i < tpHeaders.size(); i++) {
            cell = tpHeaderRow.addElement("Cell").addAttribute("type", "header")
                    .addAttribute("class", "firstTP").addAttribute("group", "tpHeader");
            data = cell.addElement("Data").addAttribute("type", "header").addText(tpHeaders.get(i));
            data = null;
            cell = null;
        }

        Set<String> keys = reportBeanMap.keySet();
        // ADD DATA ROWS         
        for (String key : keys) {

            String tp = reportBeanMap.get(key).get(0).getTimepoint();
            Integer invasiveSumCrit = criteria.getInvasiveSum();
            String invasiveSumOpCrit = criteria.getInvasiveSumOperator();

            String invasiveSum = reportBeanMap.get(key).get(0).getInvasiveSum();
            String invasiveSumOp = reportBeanMap.get(key).get(0).getInvasiveSumOperator();

            int j = 0;

            if (invasiveSumCrit != null && invasiveSumOpCrit != null) {
                j = new Integer(invasiveSum).compareTo(invasiveSumCrit);
            }

            Integer benignSumCrit = criteria.getBenignSum();
            String benignSumOpCrit = criteria.getBenignSumOperator();

            String benignSum = reportBeanMap.get(key).get(0).getBenignSum();
            String benignSumOp = reportBeanMap.get(key).get(0).getBenignSumOperator();

            int h = 0;

            if (benignSumCrit != null && benignSumOpCrit != null) {
                h = new Integer(benignSum).compareTo(benignSumCrit);
            }

            Collection<String> resultCodeCollection = criteria.getResultCodeCollection();
            String resultCode = reportBeanMap.get(key).get(0).getLossResult();

            // filter time points, invasice sum, benign sum, and result code to match what were in the search criteria

            if (tpHeaders.contains(tp)
                    && (resultCodeCollection == null
                            || (resultCodeCollection != null && resultCodeCollection.contains(resultCode)))
                    && ((invasiveSumCrit == null && invasiveSumOpCrit == null)
                            || (invasiveSumCrit != null
                                    && (invasiveSumOpCrit != null && invasiveSumOpCrit.equals("="))
                                    && invasiveSumCrit.toString().equals(invasiveSum))
                            || (invasiveSumCrit != null
                                    && (invasiveSumOpCrit != null && invasiveSumOpCrit.equals(">=")) && j >= 0)
                            || (invasiveSumCrit != null
                                    && (invasiveSumOpCrit != null && invasiveSumOpCrit.equals("<=")) && j <= 0))
                    && ((benignSumCrit == null && benignSumOpCrit == null)
                            || (benignSumCrit != null
                                    && (benignSumOpCrit != null && benignSumOpCrit.equals("="))
                                    && benignSumCrit.toString().equals(benignSum))
                            || (benignSumCrit != null
                                    && (benignSumOpCrit != null && benignSumOpCrit.equals(">=")) && h >= 0)
                            || (benignSumCrit != null
                                    && (benignSumOpCrit != null && benignSumOpCrit.equals("<=")) && h <= 0))) {

                dataRow = report.addElement("Row").addAttribute("name", "dataRow");
                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "sample")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "selectable")
                        .addText(reportBeanMap.get(key).get(0).getPatientDID());
                data = null;
                cell = null;
                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "header")
                        .addText(reportBeanMap.get(key).get(0).getBiomarkerName());
                data = null;
                cell = null;

                //GRAB EACH REPORT BEAN IN EACH ARRAYLIST AND MATCH UP TO THE APPROPRIATE TIMEPOINT AS A MAP WITH THE TIMEPOINT AS KEY AND REPORTBEAN THE VALUE
                ArrayList<LossOfExpressionIHCFindingReportBean> myList = reportBeanMap.get(key);
                Map<String, LossOfExpressionIHCFindingReportBean> myMap = new HashMap<String, LossOfExpressionIHCFindingReportBean>();
                ArrayList<LossOfExpressionIHCFindingReportBean> mySortedMap = new ArrayList<LossOfExpressionIHCFindingReportBean>();

                for (LossOfExpressionIHCFindingReportBean ggg : myList) {
                    for (int i = 0; i < tpHeaders.size(); i++) {
                        if (ggg.getTimepoint().equalsIgnoreCase(tpHeaders.get(i))) {
                            myMap.put(tpHeaders.get(i), ggg);
                            break;
                        } else if (ggg.getTimepoint().equals("--")) {
                            if (!myMap.containsKey(tpHeaders.get(i))) {
                                myMap.put(tpHeaders.get(i), ggg);
                                break;
                            }
                        }
                    }
                }

                //SORT MAP BY TIMEPOINT SO THAT THE REPORT BEAN DATA CAN EASILY BE DISPLAYED UNDER THE APPROPRIATE TIEMPOINT
                for (int i = 0; i < tpHeaders.size(); i++) {
                    for (String k : myMap.keySet()) {
                        if (k.equalsIgnoreCase(tpHeaders.get(i))) {
                            mySortedMap.add(myMap.get(k));
                        }
                    }
                }

                //ITERATE OVER THE MAP FOR EACH DATA FIELD WITH ITS CORRESPONDING TIMEPOINT AND BUILD DATA ROWS
                for (LossOfExpressionIHCFindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getBenignPresentValue());
                    data = null;
                    cell = null;
                }

                if (invasiveSumOp.equals("--")) {

                    for (LossOfExpressionIHCFindingReportBean reportBean : mySortedMap) {
                        cell = dataRow.addElement("Cell").addAttribute("type", "data")
                                .addAttribute("class", "data").addAttribute("group", "data");
                        data = cell.addElement("Data").addAttribute("type", "header")
                                .addText(reportBean.getInvasiveSum());
                        data = null;
                        cell = null;

                    }
                }

                for (LossOfExpressionIHCFindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getBenignSum());
                    data = null;
                    cell = null;

                }
                for (LossOfExpressionIHCFindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getInvasiveBenignDiff());
                    data = null;
                    cell = null;

                }
                for (LossOfExpressionIHCFindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getComments());
                    data = null;
                    cell = null;

                }
                for (LossOfExpressionIHCFindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getLossResult());
                    data = null;
                    cell = null;

                }
            }
        }
    }

    else {
        //TODO: handle this error
        sb.append("<br><Br>Loss of Expression is empty<br>");
    }

    return document;
}

---

From source file:gov.nih.nci.caintegrator.application.report.P53Report.java

License:BSD License

/**
  * @param finding//from   ww  w. j  av  a2s  . c  o  m
  * @param filterMapParams
  * @return Document
  */
public static Document getReportXML(Finding finding, Map filterMapParams) {

    Document document = DocumentHelper.createDocument();

    Element report = document.addElement("Report");
    Element cell = null;
    Element data = null;
    Element dataRow = null;
    //ADD BASIC ATTRIBUTED
    report.addAttribute("reportType", "p53Mutation");
    report.addAttribute("groupBy", "none");
    String queryName = finding.getTaskId();
    report.addAttribute("queryName", queryName);
    report.addAttribute("sessionId", "the session id");

    StringBuffer sb = new StringBuffer();

    /* *************************************************************************************************
     * 
     * PROCESS QUERY DETAILS
     * 
     * *************************************************************************************************             * 
     */
    P53FindingCriteria criteria = (P53FindingCriteria) finding.getQueryDTO();
    ArrayList<String> queryDetails = new ArrayList();
    if (criteria != null) {
        String tmp = "";
        ArrayList<String> tmpCollection = new ArrayList<String>();
        tmp = criteria.getQueryName() != null ? criteria.getQueryName() : "";
        queryDetails.add("Query Name: " + tmp);
        tmp = "";

        if (criteria.getSpecimenCriteria() != null
                && criteria.getSpecimenCriteria().getTimeCourseCollection() != null
                && !criteria.getSpecimenCriteria().getTimeCourseCollection().isEmpty()) {
            Set<String> timepoints = criteria.getSpecimenCriteria().getTimeCourseCollection();
            tmpCollection = new ArrayList<String>(timepoints);
            TimepointStringComparator ts = new TimepointStringComparator();
            Collections.sort(tmpCollection, ts);
            for (String tc : tmpCollection) {
                if (tc != tmpCollection.get(0)) {
                    tmp += ", " + tc;
                } else {
                    tmp += tc;
                }
            }
        }
        queryDetails.add("Timepoint(s): " + tmp);
        tmpCollection.clear();
        tmp = "";
        if (criteria.getMutationStatusCollection() != null
                && !criteria.getMutationStatusCollection().isEmpty()) {
            Set<String> mutationStatus = (Set<String>) criteria.getMutationStatusCollection();
            tmpCollection = new ArrayList<String>(mutationStatus);
            for (String in : tmpCollection) {
                if (in != tmpCollection.get(0)) {
                    tmp += ", " + in;
                } else {
                    tmp += in;
                }
            }

        }
        queryDetails.add("Mutation Status: " + tmp);
        tmpCollection.clear();
        tmp = "";

        if (criteria.getMutationTypeCollection() != null && !criteria.getMutationTypeCollection().isEmpty()) {
            Set<String> mutationType = (Set<String>) criteria.getMutationTypeCollection();
            tmpCollection = new ArrayList<String>(mutationType);
            for (String lc : tmpCollection) {
                if (lc != tmpCollection.get(0)) {
                    tmp += ", " + lc;
                } else {
                    tmp += lc;
                }
            }

        }
        queryDetails.add("Mutation Type: " + tmp);
        tmpCollection.clear();
        tmp = "";
    }

    String qd = "";
    for (String q : queryDetails) {
        qd += q + " ||| ";
    }

    /* **************************************************************************************************************
     * 
     * BUILD REPORT AS XML
     * 
     * **************************************************************************************************************
     */

    //GET FINDINGS, CAST TO APPROPRIATE FINDINGS AND ADD TO ARRAYLIST (RESULTS)
    ArrayList dFindings = new ArrayList(finding.getDomainFindings());
    ArrayList<P53MutationFinding> domainFindings = new ArrayList<P53MutationFinding>(dFindings);
    ArrayList<P53FindingReportBean> results = new ArrayList<P53FindingReportBean>();
    for (P53MutationFinding p53f : domainFindings) {
        P53FindingReportBean reportBean = new P53FindingReportBean(p53f);
        results.add(reportBean);
    }

    if (!results.isEmpty()) {

        //SORT THE ARRAYLIST(RESULTS) BY PATIENT DID

        PatientComparator p = new PatientComparator();
        Collections.sort(results, p);

        //CREATE A HASHMAP SORTED BY PATIENT DID AS THE KEY AND THE ARRAYLIST OF REPORTBEANS AS THE VALUE                

        //  Map<String,ArrayList<P53FindingReportBean>> reportBeanMap = new HashMap<String,ArrayList<P53FindingReportBean>>();
        Map<String, ArrayList<P53FindingReportBean>> reportBeanMap = new HashMap<String, ArrayList<P53FindingReportBean>>();

        int j = results.size();
        for (int i = 0; i < results.size(); i++) {
            boolean found = false;
            Set<String> keys = reportBeanMap.keySet();
            int key = keys.size();
            if (!keys.isEmpty()) {
                for (String k : keys) {
                    String s = results.get(i).getSpecimenIdentifier();
                    if (s.equals(k)) {
                        found = true;
                        reportBeanMap.get(k).add(results.get(i));
                        break;
                    }
                }
                if (!found) {
                    reportBeanMap.put(results.get(i).getSpecimenIdentifier(),
                            new ArrayList<P53FindingReportBean>());
                    reportBeanMap.get(results.get(i).getSpecimenIdentifier()).add(results.get(i));
                }
            } else {
                reportBeanMap.put(results.get(i).getSpecimenIdentifier(),
                        new ArrayList<P53FindingReportBean>());
                reportBeanMap.get(results.get(i).getSpecimenIdentifier()).add(results.get(i));
            }
            //                   

        }

        //IF THE USER SELECTED TIMEPOINTS FOR WHICH THAT PATIENT DID DID NOT HAVE DATA, CREATE NULL BEANS SO AS TO RENDER A READABLE REPORT
        Set<String> b = reportBeanMap.keySet();
        for (String g : b) {
            while (reportBeanMap.get(g)
                    .size() < (reportBeanMap.get(g).get(0).getTimepointHeaders(criteria).size())) {
                reportBeanMap.get(g).add(new P53FindingReportBean(new P53MutationFinding()));
            }
        }

        //ADD QUERY DETAILS      
        Element details = report.addElement("Query_details");
        cell = details.addElement("Data");
        cell.addText(qd);
        cell = null;

        //ADD HEADERS THAT ARE TIMEPOINT-INDEPENDENT (PATIENT)
        Element headerRow = report.addElement("Row").addAttribute("name", "headerRow");
        ArrayList<String> ntpHeaders = results.get(0).getNonTimepointHeaders();
        for (String ntpHeader : ntpHeaders) {

            // on the report page, should not display labtrak id
            if (!ntpHeader.equalsIgnoreCase("LabTrak ID")) {
                cell = headerRow.addElement("Cell").addAttribute("type", "header")
                        .addAttribute("class", "header").addAttribute("group", "ntpHeader");
                data = cell.addElement("Data").addAttribute("type", "header").addText(ntpHeader);
                data = null;
                cell = null;
            }
        }

        //ADD HEADERS THAT ARE TIMEPOINT DEPENDENT
        ArrayList<String> headers = results.get(0).getHeaders();
        for (String header : headers) {

            cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                    .addAttribute("group", "header");
            data = cell.addElement("Data").addAttribute("type", "header").addText(header);
            data = null;
            cell = null;
        }

        //ADD TIMEPOINT SUBHEADERS
        ArrayList<String> tpHeaders = results.get(0).getTimepointHeaders(criteria);

        TimepointStringComparator ts = new TimepointStringComparator();
        Collections.sort(tpHeaders, ts);
        Element tpHeaderRow = report.addElement("Row").addAttribute("name", "tpHeaderRow");

        // this is leave the first space empty

        cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                .addAttribute("group", "ntpHeader");
        data = cell.addElement("Data").addAttribute("type", "header").addText("");
        System.out.println(")))" + data.toString());
        data = null;
        cell = null;

        for (int i = 0; i < tpHeaders.size(); i++) {

            cell = tpHeaderRow.addElement("Cell").addAttribute("type", "header")
                    .addAttribute("class", "firstTP").addAttribute("group", "tpHeader");
            data = cell.addElement("Data").addAttribute("type", "header").addText(tpHeaders.get(i));
            data = null;
            cell = null;
        }

        Set<String> keys = reportBeanMap.keySet();

        // ADD DATA ROWS           
        for (String key : keys) {

            String tp = reportBeanMap.get(key).get(0).getTimepoint();
            Collection<String> mutationStatusCollection = criteria.getMutationStatusCollection();
            Collection<String> mutationTypeCollection = criteria.getMutationTypeCollection();

            String mutationStatus = reportBeanMap.get(key).get(0).getMutationStatus();
            String mutationType = reportBeanMap.get(key).get(0).getMutationType();

            if (tpHeaders.contains(tp) && (mutationStatusCollection == null
                    || (mutationStatusCollection != null && mutationStatusCollection.contains(mutationStatus)))
                    && (mutationTypeCollection == null || (mutationTypeCollection != null
                            && mutationTypeCollection.contains(mutationType)))) {

                dataRow = report.addElement("Row").addAttribute("name", "dataRow");
                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "sample")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "selectable")
                        .addText(reportBeanMap.get(key).get(0).getPatientDID());
                data = null;
                cell = null;

                //GRAB EACH REPORT BEAN IN EACH ARRAYLIST AND MATCH UP TO THE APPROPRIATE TIMEPOINT AS A MAP WITH THE TIMEPOINT AS KEY AND REPORTBEAN THE VALUE
                ArrayList<P53FindingReportBean> myList = reportBeanMap.get(key);
                Map<String, P53FindingReportBean> myMap = new HashMap<String, P53FindingReportBean>();
                ArrayList<P53FindingReportBean> mySortedMap = new ArrayList<P53FindingReportBean>();

                for (P53FindingReportBean ggg : myList) {
                    for (int i = 0; i < tpHeaders.size(); i++) {
                        if (ggg.getTimepoint().equalsIgnoreCase(tpHeaders.get(i))) {
                            myMap.put(tpHeaders.get(i), ggg);
                            break;
                        } else if (ggg.getTimepoint().equals("--")) {
                            if (!myMap.containsKey(tpHeaders.get(i))) {
                                myMap.put(tpHeaders.get(i), ggg);
                                break;
                            }
                        }
                    }
                }

                //SORT MAP BY TIMEPOINT SO THAT THE REPORT BEAN DATA CAN EASILY BE DISPLAYED UNDER THE APPROPRIATE TIEMPOINT
                for (int i = 0; i < tpHeaders.size(); i++) {
                    for (String k : myMap.keySet()) {
                        if (k.equalsIgnoreCase(tpHeaders.get(i))) {
                            mySortedMap.add(myMap.get(k));
                        }
                    }
                }

                //ITERATE OVER THE MAP FOR EACH DATA FIELD WITH ITS CORRESPONDING TIMEPOINT AND BUILD DATA ROWS
                for (P53FindingReportBean reportBean : mySortedMap) {

                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getMutationStatus());
                    data = null;
                    cell = null;
                }
                for (P53FindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getMutationType());
                    data = null;
                    cell = null;

                }
                for (P53FindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getExonOrIntronLocation());
                    data = null;
                    cell = null;

                }
                for (P53FindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getBaseChange());
                    data = null;
                    cell = null;

                }
                for (P53FindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getCodonAminoacidChange());
                    data = null;
                    cell = null;

                }
                for (P53FindingReportBean reportBean : mySortedMap) {
                    cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                            .addAttribute("group", "data");
                    data = cell.addElement("Data").addAttribute("type", "header")
                            .addText(reportBean.getProteinStructuralDomain());
                    data = null;
                    cell = null;

                }
            }
        }

    }

    else {
        //TODO: handle this error
        sb.append("<br><Br>Level of Expression is empty<br>");
    }

    return document;
}

---

From source file:gov.nih.nci.ispy.web.reports.quick.QuickClinicalReport.java

License:BSD License

public static StringBuffer quickSampleReport(String sessionId, String taskId) {

    BusinessTierCache cacheManager = ApplicationFactory.getBusinessTierCache();
    ISPYClinicalFinding clinicalFinding = (ISPYClinicalFinding) cacheManager
            .getObjectFromSessionCache(sessionId, taskId);
    StringBuffer html = new StringBuffer();
    List<PatientData> patientsData = clinicalFinding.getPatientData();
    if (!patientsData.isEmpty()) {
        ImagingFileBasedQueryService iqs = (ImagingFileBasedQueryService) ImagingFileBasedQueryService
                .getInstance();/* ww w.ja  va 2  s  .  co m*/
        Document document = DocumentHelper.createDocument();
        Element table = document.addElement("table").addAttribute("id", "reportTable").addAttribute("class",
                "report");
        Element tr = null;
        Element td = null;
        tr = table.addElement("tr").addAttribute("class", "header");

        //                String longHeaders = "ISPY_ID, NCIA_IMAGE, INST_ID, AGE, AGECAT, RACE_ID, SSTAT, SURVDTD, CHEMOCAT, CHEMO, TAM, HERCEPTIN, DOSEDENSEANTHRA, DOSEDENSETAXANE, MENOSTATUS, SENTINELNODESAMPLE, SENTINELNODERESULT, HIST_TYPE_INV_OS, HISTOLOGICGRADEOS, ER_TS, PGR_TS, ERPOS, PGRPOS, HER2COMMUNITYPOS, HER2COMMUNITYMETHOD, SURGERYLUMPECTOMY, SURGERYMASTECTOMY, HISTOLOGICTYPEPS, INITLUMP_FUPMAST, SURGERY, REASON_NO_SURG, RTTHERAPY, RTBREAST, RTBOOST, RTAXILLA, RTSNODE, RTIMAMNODE, RTCHESTW, RTOTHER, TSIZECLINICAL, NSIZECLINICAL, STAGETE, STAGENE, STAGEME, CLINICALSTAGE, CLINRESPT1_T2, CLINRESPT1_T3, CLINRESPT1_T4, Morphologic pattern at T1, LES_T1, LES_T2, LES_T3, LES_T4, LD_T1, LD_T2, LD_T3, LD_T4, MRI % change T1_T2, MRI % change T1_T3, MRI % change T1_T4," +
        //                "MRI % change T2_T3, MRI % change T2_T4, MRI % change T3_T4, DCISONLYPS, PTUMOR1SZCM_MICRO_1, HISTOLOGICGRADEPS, NUMPOSNODESPS, NODESEXAMINEDPS, PATHOLOGYSTAGEPS,InSituHistoPS, InvDzHistoPS, InvDzMultiFoc, InvDzCellularity, SurgMargins, yT, yN, yM, RCBIndex, localProgTimeD (days), distProgTimeD (days)";

        // 04-17-2010, delete following columns: HISTOLOGICTYPEPS, LES_T1, LES_T2, LES_T3, LES_T4, LD_T1, LD_T2, LD_T3, LD_T4,
        String longHeaders = "ISPY_ID, NCIA_IMAGE, INST_ID, AGE, AGECAT, RACE_ID, SSTAT, SURVDTD, CHEMOCAT, CHEMO, TAM, HERCEPTIN, DOSEDENSEANTHRA, DOSEDENSETAXANE, MENOSTATUS, SENTINELNODESAMPLE, SENTINELNODERESULT, HIST_TYPE_INV_OS, HISTOLOGICGRADEOS, ER_TS, PGR_TS, ERPOS, PGRPOS, HER2COMMUNITYPOS, HER2COMMUNITYMETHOD, SURGERYLUMPECTOMY, SURGERYMASTECTOMY, INITLUMP_FUPMAST, SURGERY, REASON_NO_SURG, RTTHERAPY, RTBREAST, RTBOOST, RTAXILLA, RTSNODE, RTIMAMNODE, RTCHESTW, RTOTHER, TSIZECLINICAL, NSIZECLINICAL, STAGETE, STAGENE, STAGEME, CLINICALSTAGE, CLINRESPT1_T2, CLINRESPT1_T3, CLINRESPT1_T4, Morphologic pattern at T1, MRI % change T1_T2, MRI % change T1_T3, MRI % change T1_T4,"
                + "MRI % change T2_T3, MRI % change T2_T4, MRI % change T3_T4, DCISONLYPS, PTUMOR1SZCM_MICRO_1, HISTOLOGICGRADEPS, NUMPOSNODESPS, NODESEXAMINEDPS, PATHOLOGYSTAGEPS,InSituHistoPS, InvDzHistoPS, InvDzMultiFoc, InvDzCellularity, SurgMargins, yT, yN, yM, RCBIndex, localProgTimeD (days), distProgTimeD (days)";

        String[] heads = StringUtils.split(longHeaders, ",");
        for (String h : heads) {
            td = tr.addElement("td").addAttribute("class", "header").addText(h.trim());
        }
        for (PatientData pd : patientsData) {
            tr = table.addElement("tr").addAttribute("class", "data");
            String tmp = "";
            String dv = "-";
            if (pd == null) {
                for (int i = 0; i < heads.length - 2; i++) {
                    td = tr.addElement("td").addAttribute("class", "header").addText(dv);
                }
            } else if (pd != null) {
                tmp = pd.getISPY_ID() != null ? pd.getISPY_ID() : dv;
                td = tr.addElement("td").addText(tmp).addAttribute("name", "patient")
                        .addAttribute("class", "patient").addAttribute("id", tmp).addElement("input")
                        .addAttribute("type", "checkbox").addAttribute("name", "checkable")
                        .addAttribute("class", "saveElement").addAttribute("value", pd.getISPY_ID());

                if (iqs.hasImagingData(pd.getISPY_ID())) {
                    String link = iqs.buildImagingLink(pd);
                    try {
                        String encodedLink = URLEncoder.encode(link, "UTF-8");
                        td = tr.addElement("td").addElement("a")
                                .addAttribute("onclick", "javascript:window.open('" + link
                                        + "','new','toolbar=yes,width=800,height=600,location=yes,status=yes,menubar=yes,scrollbars=yes,resizable=yes');")
                                .addElement("img").addAttribute("src", "images/nciaLink.png");
                    } catch (UnsupportedEncodingException e) {
                        // TODO Auto-generated catch block
                        e.printStackTrace();
                    }

                } else {
                    td = tr.addElement("td").addText(dv);
                }

                tmp = pd.getInst_ID() != null ? pd.getInst_ID() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getPatientAge() != null ? pd.getPatientAge().toString() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getAgeCategory() != null ? pd.getAgeCategory().toString() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getRace() != null ? pd.getRace().toString() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getSSTAT() != null ? pd.getSSTAT() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getSURVDTD() != null ? pd.getSURVDTD() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getChemoCat() != null ? pd.getChemoCat() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getChemo() != null ? pd.getChemo() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getTAM() != null ? pd.getTAM() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getHerceptin() != null ? pd.getHerceptin() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getDosedenseanthra() != null ? pd.getDosedenseanthra() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getDosedensetaxane() != null ? pd.getDosedensetaxane() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getMenoStatus() != null ? pd.getMenoStatus() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getSentinelNodeSample() != null ? pd.getSentinelNodeSample() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getSentinelNodeResult() != null ? pd.getSentinelNodeResult() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getHistTypeOfInvasiveTumor() != null ? pd.getHistTypeOfInvasiveTumor() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getHistologicGradeOS() != null ? pd.getHistologicGradeOS() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getER_TS() != null ? pd.getER_TS() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getPGR_TS() != null ? pd.getPGR_TS() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getERpos() != null ? pd.getERpos() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getPgRpos() != null ? pd.getPgRpos() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getHER2CommunityPOS() != null ? pd.getHER2CommunityPOS() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getHER2CommunityMethod() != null ? pd.getHER2CommunityMethod() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getSurgeryLumpectomy() != null ? pd.getSurgeryLumpectomy() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getSurgeryMastectomy() != null ? pd.getSurgeryMastectomy() : dv;
                td = tr.addElement("td").addText(tmp);

                //04-17-2010, delete HISTOLOGICTYPEPS
                //                        tmp = pd.getHistTypePS()!=null  ? pd.getHistTypePS() : dv;
                //                        td = tr.addElement("td").addText(tmp);

                tmp = pd.getINITLUMP_FUPMAST() != null ? pd.getINITLUMP_FUPMAST() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getSurgery() != null ? pd.getSurgery() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getReasonNoSurg() != null ? pd.getReasonNoSurg() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getRTTherapy() != null ? pd.getRTTherapy() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getRTBreast() != null ? pd.getRTBreast() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getRTBOOST() != null ? pd.getRTBOOST() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getRTAXILLA() != null ? pd.getRTAXILLA() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getRTSNODE() != null ? pd.getRTSNODE() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getRTIMAMNODE() != null ? pd.getRTIMAMNODE() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getRTChestW() != null ? pd.getRTChestW() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getRTOTHER() != null ? pd.getRTOTHER() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getTSizeClinical() != null ? pd.getTSizeClinical() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getNSizeClinical() != null ? pd.getNSizeClinical() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getStageTE() != null ? pd.getStageTE() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getStageNE() != null ? pd.getStageNE() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getSTAGEME() != null ? pd.getSTAGEME() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getClinicalStageStr() != null ? pd.getClinicalStageStr() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getClinRespT1_T2() != null ? pd.getClinRespT1_T2() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getClinRespT1_T3() != null ? pd.getClinRespT1_T3() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getClinRespT1_T4() != null ? pd.getClinRespT1_T4() : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getMorphology() != null ? pd.getMorphology().toString() : dv;
                td = tr.addElement("td").addText(tmp);

                // 04-17-2010, delete LES_T1, LES_T2, LES_T3, LES_T4, LD_T1, LD_T2, LD_T3, LD_T4
                //                        tmp = pd.getLES_T1()!=null  ? pd.getLES_T1() : dv;
                //                        td = tr.addElement("td").addText(tmp);
                //                        
                //                        tmp = pd.getLES_T2()!=null  ? pd.getLES_T2() : dv;
                //                        td = tr.addElement("td").addText(tmp);
                //                        
                //                        tmp = pd.getLES_T3()!=null  ? pd.getLES_T3() : dv;
                //                        td = tr.addElement("td").addText(tmp);
                //                        
                //                        tmp = pd.getLES_T4()!=null  ? pd.getLES_T4() : dv;
                //                        td = tr.addElement("td").addText(tmp);
                //                        
                //                        tmp = pd.getLdT1()!=null  ? Double.toString(pd.getLdT1()) : dv;
                //                        td = tr.addElement("td").addText(tmp);
                //                        
                //                        tmp = pd.getLdT2()!=null  ? Double.toString(pd.getLdT2()) : dv;
                //                        td = tr.addElement("td").addText(tmp);
                //                        
                //                        tmp = pd.getLdT3()!=null  ? Double.toString(pd.getLdT3()) : dv;
                //                        td = tr.addElement("td").addText(tmp);
                //                        
                //                        tmp = pd.getLdT4()!=null  ? Double.toString(pd.getLdT4()) : dv;
                //                        td = tr.addElement("td").addText(tmp);

                tmp = pd.getMriPctChangeT1_T2() != null ? String.valueOf(pd.getMriPctChangeT1_T2()) : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getMriPctChangeT1_T3() != null ? String.valueOf(pd.getMriPctChangeT1_T3()) : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getMriPctChangeT1_T4() != null ? String.valueOf(pd.getMriPctChangeT1_T4()) : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getMriPctChangeT2_T3() != null ? Double.toString(pd.getMriPctChangeT2_T3()) : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getMriPctChangeT2_T4() != null ? Double.toString(pd.getMriPctChangeT2_T4()) : dv;
                td = tr.addElement("td").addText(tmp);

                tmp = pd.getMriPctChangeT3_T4() != null ? Double.toString(pd.getMriPctChangeT3_T4()) : dv;
                td = tr.addElement("td").addText(tmp);

                // dispaly path data

                // change dcisonly to dcisonlyps

                tmp = pd.getDCISOnlyPS() != null ? pd.getDCISOnlyPS() : dv;
                td = tr.addElement("td").addText(tmp);

                // Ptumor1szcm_micro_1
                tmp = pd.getPtumor1szcm_micro_1() != null ? pd.getPtumor1szcm_micro_1().toString() : dv;
                td = tr.addElement("td").addText(tmp);

                // HistologicGradePS

                tmp = pd.getHistologicGradePS() != null ? pd.getHistologicGradePS() : dv;
                td = tr.addElement("td").addText(tmp);

                //NumPosNodes
                tmp = pd.getNumPosNodesPS() != null ? pd.getNumPosNodesPS() : dv;
                td = tr.addElement("td").addText(tmp);

                //NodesExamined
                tmp = pd.getNodesExaminedPS() != null ? pd.getNodesExaminedPS() : dv;
                td = tr.addElement("td").addText(tmp);

                // PathologyStage
                tmp = pd.getPathologyStagePS() != null ? pd.getPathologyStagePS() : dv;
                td = tr.addElement("td").addText(tmp);

                // InSituHisto
                tmp = pd.getInSituHistoPS() != null ? pd.getInSituHistoPS() : dv;
                td = tr.addElement("td").addText(tmp);

                // invDzHisto
                tmp = pd.getInvDzHistoPS() != null ? pd.getInvDzHistoPS() : dv;
                td = tr.addElement("td").addText(tmp);

                //invDzMultiFoc

                tmp = pd.getInvDzMultiFoc() != null ? pd.getInvDzMultiFoc() : dv;
                td = tr.addElement("td").addText(tmp);

                //invDzCellularity

                tmp = pd.getInvDzCellularity() != null ? pd.getInvDzCellularity() : dv;
                td = tr.addElement("td").addText(tmp);

                //surgMargins

                tmp = pd.getSurgMargins() != null ? pd.getSurgMargins() : dv;
                td = tr.addElement("td").addText(tmp);

                //yT

                tmp = pd.getYT() != null ? pd.getYT() : dv;
                td = tr.addElement("td").addText(tmp);

                //yN

                tmp = pd.getYN() != null ? pd.getYN() : dv;
                td = tr.addElement("td").addText(tmp);

                //yM

                tmp = pd.getYM() != null ? pd.getYM() : dv;
                td = tr.addElement("td").addText(tmp);

                // rcb index
                tmp = pd.getRcbIndexSize() != null ? pd.getRcbIndexSize() : dv;
                td = tr.addElement("td").addText(tmp);

                //localProgTimeD:days

                tmp = (pd.getLocalProgTimeD() != null && pd.getLocalProgTimeD().toString().indexOf("-") == -1)
                        ? pd.getLocalProgTimeD().toString()
                        : dv;
                td = tr.addElement("td").addText(tmp);

                //distProgTimeD:days

                tmp = pd.getDistProgTimeD() != null ? pd.getDistProgTimeD().toString() : dv;
                td = tr.addElement("td").addText(tmp);

            }
        }
        html.append(document.asXML());
    } else {
        html.append("No Data for selected clinical parameters");
    }
    return html;
}

---

From source file:gov.nih.nci.ispy.web.reports.quick.QuickClinicalReport.java

License:BSD License

public static StringBuffer quickSampleReport(List<String> sampleIds, String sessionId, String taskId) {
    Set set = new HashSet();
    set.addAll(sampleIds);//from   w w w.  j a  v a2  s . c  om

    if (set.size() < sampleIds.size()) {
        sampleIds.clear();
        sampleIds.addAll(set);
    }

    String dv = "-";
    StringBuffer html = new StringBuffer();
    Document document = DocumentHelper.createDocument();

    if (sampleIds != null) {

        try {

            IdMapperFileBasedService idMapper = IdMapperFileBasedService.getInstance();
            ImagingFileBasedQueryService iqs = (ImagingFileBasedQueryService) ImagingFileBasedQueryService
                    .getInstance();

            //List<RegistrantInfo> registrants = 
            List<SampleInfo> samples = idMapper.getSampleInfoForLabtrackIds(sampleIds);
            //List<ClinicalData> clinicalDataList = new ArrayList<ClinicalData>();
            ClinicalDataService cqs = ClinicalDataServiceFactory.getInstance();

            List<PatientData> pdList = new ArrayList<PatientData>();

            if (samples.isEmpty()) {
                html.append("No Data");
                return html;
            }

            //WHEN switching to the new PatientData method of getting data
            //remove the for loop below

            /*
            for (SampleInfo si : samples) {
              clinicalDataList.add(cqs.getClinicalDataForPatientDID(si.getISPYId(), si.getTimepoint()));
            }
            */

            if (sampleIds != null) {
                int count = 0;

                Element table = document.addElement("table").addAttribute("id", "reportTable")
                        .addAttribute("class", "report");
                Element tr = null;
                Element td = null;
                tr = table.addElement("tr").addAttribute("class", "header");

                //String longHeaders = "ISPY_ID, LabTrak ID, NCIA_IMAGE, INST_ID, AGE, AGECAT, RACE_ID, SSTAT, SURVDTD, CHEMOCAT, CHEMO, TAM, HERCEPTIN, MENOSTATUS, SENTINELNODESAMPLE, SENTINELNODERESULT, HIST_TYPE_INV_OS, HISTOLOGICGRADEOS, ER_TS, PGR_TS, HER2COMMUNITYPOS, HER2COMMUNITYMETHOD, SURGERYLUMPECTOMY, SURGERYMASTECTOMY, HISTOLOGICTYPEPS, INITLUMP_FUPMAST, SURGERY, DCISONLYPS, PTUMOR1SZCM_MICRO, HISTOLOGICGRADEPS, NUMPOSNODESPS, NODESEXAMINEDPS, PATHOLOGYSTAGEPS, REASON_NO_SURG, RTTHERAPY, RTBREAST, RTBOOST, RTAXILLA, RTSNODE, RTIMAMNODE, RTCHESTW, RTOTHER, TSIZECLINICAL, NSIZECLINICAL, STAGETE, STAGENE, STAGEME, CLINICALSTAGE, CLINRESPT1_T2, CLINRESPT1_T3, CLINRESPT1_T4, Morphologic pattern at T1, LES_T1, LES_T2, LES_T3, LES_T4, LD_T1, LD_T2, LD_T3, LD_T4, MRI % change T1_T2, MRI % change T1_T3, MRI % change T1_T4," +
                //"MRI % change T2_T3, MRI % change T2_T4, MRI % change T3_T4";

                // String longHeaders = "ISPY_ID, LabTrak ID, NCIA_IMAGE, INST_ID, AGE, AGECAT, RACE_ID, SSTAT, SURVDTD, CHEMOCAT, CHEMO, TAM, HERCEPTIN, DOSEDENSEANTHRA, DOSEDENSETAXANE, MENOSTATUS, SENTINELNODESAMPLE, SENTINELNODERESULT, HIST_TYPE_INV_OS, HISTOLOGICGRADEOS, ER_TS, PGR_TS, HER2COMMUNITYPOS, HER2COMMUNITYMETHOD, SURGERYLUMPECTOMY, SURGERYMASTECTOMY, HISTOLOGICTYPEPS, INITLUMP_FUPMAST, SURGERY, DCISONLYPS, PTUMOR1SZCM_MICRO, HISTOLOGICGRADEPS, NUMPOSNODESPS, NODESEXAMINEDPS, PATHOLOGYSTAGEPS, REASON_NO_SURG, RTTHERAPY, RTBREAST, RTBOOST, RTAXILLA, RTSNODE, RTIMAMNODE, RTCHESTW, RTOTHER, TSIZECLINICAL, NSIZECLINICAL, STAGETE, STAGENE, STAGEME, CLINICALSTAGE, CLINRESPT1_T2, CLINRESPT1_T3, CLINRESPT1_T4, Morphologic pattern at T1, LES_T1, LES_T2, LES_T3, LES_T4, LD_T1, LD_T2, LD_T3, LD_T4, MRI % change T1_T2, MRI % change T1_T3, MRI % change T1_T4," +
                // "MRI % change T2_T3, MRI % change T2_T4, MRI % change T3_T4";

                // these are the fields from the new clincial data and pathology data file: 10/22-2007, this method is used when trying to obtain clincial data from hoa reports

                //                    String longHeaders = "ISPY_ID, LabTrak ID, NCIA_IMAGE, INST_ID, AGE, AGECAT, RACE_ID, SSTAT, SURVDTD, CHEMOCAT, CHEMO, TAM, HERCEPTIN, DOSEDENSEANTHRA, DOSEDENSETAXANE, MENOSTATUS, SENTINELNODESAMPLE, SENTINELNODERESULT, HIST_TYPE_INV_OS, HISTOLOGICGRADEOS, ER_TS, PGR_TS, ERPOS, PGRPOS, HER2COMMUNITYPOS, HER2COMMUNITYMETHOD, SURGERYLUMPECTOMY, SURGERYMASTECTOMY, HISTOLOGICTYPEPS, INITLUMP_FUPMAST, SURGERY, REASON_NO_SURG, RTTHERAPY, RTBREAST, RTBOOST, RTAXILLA, RTSNODE, RTIMAMNODE, RTCHESTW, RTOTHER, TSIZECLINICAL, NSIZECLINICAL, STAGETE, STAGENE, STAGEME, CLINICALSTAGE, CLINRESPT1_T2, CLINRESPT1_T3, CLINRESPT1_T4, Morphologic pattern at T1, LES_T1, LES_T2, LES_T3, LES_T4, LD_T1, LD_T2, LD_T3, LD_T4, MRI % change T1_T2, MRI % change T1_T3, MRI % change T1_T4," +
                //                    "MRI % change T2_T3, MRI % change T2_T4, MRI % change T3_T4, DCISONLYPS, PTUMOR1SZCM_MICRO_1, HISTOLOGICGRADEPS, NUMPOSNODESPS, NODESEXAMINEDPS, PATHOLOGYSTAGEPS,InSituHistoPS, InvDzHistoPS, InvDzMultiFoc, InvDzCellularity, SurgMargins, yT, yN, yM, RCBIndex,localProgTimeD (ays),distProgTimeD (days)";

                // 04/17/2010, delete HISTOLOGICTYPEPS, LES_T1, LES_T2, LES_T3, LES_T4, LD_T1, LD_T2, LD_T3, LD_T4,
                String longHeaders = "ISPY_ID, LabTrak ID, NCIA_IMAGE, INST_ID, AGE, AGECAT, RACE_ID, SSTAT, SURVDTD, CHEMOCAT, CHEMO, TAM, HERCEPTIN, DOSEDENSEANTHRA, DOSEDENSETAXANE, MENOSTATUS, SENTINELNODESAMPLE, SENTINELNODERESULT, HIST_TYPE_INV_OS, HISTOLOGICGRADEOS, ER_TS, PGR_TS, ERPOS, PGRPOS, HER2COMMUNITYPOS, HER2COMMUNITYMETHOD, SURGERYLUMPECTOMY, SURGERYMASTECTOMY, INITLUMP_FUPMAST, SURGERY, REASON_NO_SURG, RTTHERAPY, RTBREAST, RTBOOST, RTAXILLA, RTSNODE, RTIMAMNODE, RTCHESTW, RTOTHER, TSIZECLINICAL, NSIZECLINICAL, STAGETE, STAGENE, STAGEME, CLINICALSTAGE, CLINRESPT1_T2, CLINRESPT1_T3, CLINRESPT1_T4, Morphologic pattern at T1, MRI % change T1_T2, MRI % change T1_T3, MRI % change T1_T4,"
                        + "MRI % change T2_T3, MRI % change T2_T4, MRI % change T3_T4, DCISONLYPS, PTUMOR1SZCM_MICRO_1, HISTOLOGICGRADEPS, NUMPOSNODESPS, NODESEXAMINEDPS, PATHOLOGYSTAGEPS,InSituHistoPS, InvDzHistoPS, InvDzMultiFoc, InvDzCellularity, SurgMargins, yT, yN, yM, RCBIndex,localProgTimeD (ays),distProgTimeD (days)";

                String[] heads = StringUtils.split(longHeaders, ",");
                for (String h : heads) {
                    td = tr.addElement("td").addAttribute("class", "header").addText(h.trim());
                }

                for (SampleInfo si : samples) {

                    if (si != null) {

                        //PatientData pd = cqs.getPatientDataForPatientDID(si.getISPYId());
                        Set<String> ispyIds = new HashSet<String>();
                        ispyIds.add(si.getISPYId());
                        ISPYclinicalDataQueryDTO dto = new ISPYclinicalDataQueryDTO();
                        dto.setRestrainingSamples(ispyIds);
                        dto.setReturnAll(false);
                        Set<PatientData> pdSet = cqs.getClinicalData(dto);

                        for (PatientData pd : pdSet) {
                            pdList.add(pd);
                            tr = table.addElement("tr").addAttribute("class", "data");

                            String tmp = "";

                            tmp = si.getISPYId() != null ? si.getISPYId() : dv;
                            td = tr.addElement("td").addText(tmp).addAttribute("name", "patient")
                                    .addAttribute("class", "patient").addAttribute("id", tmp)
                                    .addElement("input").addAttribute("type", "checkbox")
                                    .addAttribute("name", "checkable").addAttribute("class", "saveElement")
                                    .addAttribute("value", pd.getISPY_ID());

                            tmp = si.getLabtrackId() != null ? si.getLabtrackId() : dv;
                            td = tr.addElement("td").addText(tmp);

                            if (pd == null) {
                                for (int i = 0; i < heads.length - 2; i++) {
                                    td = tr.addElement("td").addAttribute("class", "header").addText(dv);
                                }
                            } else if (pd != null) {
                                //                            tmp = pd.getDataExtractDT()!=null  ? pd.getDataExtractDT() : dv;
                                //                            td = tr.addElement("td").addText(tmp);

                                if (iqs.hasImagingData(pd.getISPY_ID())) {
                                    String link = iqs.buildImagingLink(pd);
                                    try {
                                        String encodedLink = URLEncoder.encode(link, "UTF-8");
                                        td = tr.addElement("td").addElement("a")
                                                .addAttribute("onclick", "javascript:window.open('" + link
                                                        + "','new','toolbar=yes,width=800,height=600,location=yes,status=yes,menubar=yes,scrollbars=yes,resizable=yes');")
                                                .addElement("img").addAttribute("src", "images/nciaLink.png");
                                    } catch (UnsupportedEncodingException e) {
                                        // TODO Auto-generated catch block
                                        e.printStackTrace();
                                    }
                                } else {
                                    td = tr.addElement("td").addText(dv);
                                }

                                tmp = pd.getInst_ID() != null ? pd.getInst_ID() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getPatientAge() != null ? pd.getPatientAge().toString() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getAgeCategory() != null ? pd.getAgeCategory().toString() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getRace() != null ? pd.getRace().toString() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getSSTAT() != null ? pd.getSSTAT() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getSURVDTD() != null ? pd.getSURVDTD() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getChemoCat() != null ? pd.getChemoCat() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getChemo() != null ? pd.getChemo() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getTAM() != null ? pd.getTAM() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getHerceptin() != null ? pd.getHerceptin() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getDosedenseanthra() != null ? pd.getDosedenseanthra() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getDosedensetaxane() != null ? pd.getDosedensetaxane() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getMenoStatus() != null ? pd.getMenoStatus() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getSentinelNodeSample() != null ? pd.getSentinelNodeSample() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getSentinelNodeResult() != null ? pd.getSentinelNodeResult() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getHistTypeOfInvasiveTumor() != null ? pd.getHistTypeOfInvasiveTumor()
                                        : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getHistologicGradeOS() != null ? pd.getHistologicGradeOS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getER_TS() != null ? pd.getER_TS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getPGR_TS() != null ? pd.getPGR_TS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getERpos() != null ? pd.getERpos() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getPgRpos() != null ? pd.getPgRpos() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getHER2CommunityPOS() != null ? pd.getHER2CommunityPOS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getHER2CommunityMethod() != null ? pd.getHER2CommunityMethod() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getSurgeryLumpectomy() != null ? pd.getSurgeryLumpectomy() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getSurgeryMastectomy() != null ? pd.getSurgeryMastectomy() : dv;
                                td = tr.addElement("td").addText(tmp);

                                //04-17-2010, delete HISTOLOGICTYPEPS
                                //                                  tmp = pd.getHistTypePS()!=null  ? pd.getHistTypePS() : dv;
                                //                                  td = tr.addElement("td").addText(tmp);

                                tmp = pd.getINITLUMP_FUPMAST() != null ? pd.getINITLUMP_FUPMAST() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getSurgery() != null ? pd.getSurgery() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getReasonNoSurg() != null ? pd.getReasonNoSurg() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getRTTherapy() != null ? pd.getRTTherapy() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getRTBreast() != null ? pd.getRTBreast() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getRTBOOST() != null ? pd.getRTBOOST() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getRTAXILLA() != null ? pd.getRTAXILLA() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getRTSNODE() != null ? pd.getRTSNODE() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getRTIMAMNODE() != null ? pd.getRTIMAMNODE() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getRTChestW() != null ? pd.getRTChestW() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getRTOTHER() != null ? pd.getRTOTHER() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getTSizeClinical() != null ? pd.getTSizeClinical() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getNSizeClinical() != null ? pd.getNSizeClinical() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getStageTE() != null ? pd.getStageTE() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getStageNE() != null ? pd.getStageNE() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getSTAGEME() != null ? pd.getSTAGEME() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getClinicalStageStr() != null ? pd.getClinicalStageStr() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getClinRespT1_T2() != null ? pd.getClinRespT1_T2() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getClinRespT1_T3() != null ? pd.getClinRespT1_T3() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getClinRespT1_T4() != null ? pd.getClinRespT1_T4() : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getMorphology() != null ? pd.getMorphology().toString() : dv;
                                td = tr.addElement("td").addText(tmp);

                                // 04-17-2010, delete LES_T1, LES_T2, LES_T3, LES_T4, LD_T1, LD_T2, LD_T3, LD_T4                                                       
                                //                                  tmp = pd.getLES_T1()!=null  ? pd.getLES_T1() : dv;
                                //                                  td = tr.addElement("td").addText(tmp);
                                //                                  
                                //                                  tmp = pd.getLES_T2()!=null  ? pd.getLES_T2() : dv;
                                //                                  td = tr.addElement("td").addText(tmp);
                                //                                  
                                //                                  tmp = pd.getLES_T3()!=null  ? pd.getLES_T3() : dv;
                                //                                  td = tr.addElement("td").addText(tmp);
                                //                                  
                                //                                  tmp = pd.getLES_T4()!=null  ? pd.getLES_T4() : dv;
                                //                                  td = tr.addElement("td").addText(tmp);
                                //                                  
                                //                                  tmp = pd.getLdT1()!=null  ? Double.toString(pd.getLdT1()) : dv;
                                //                                  td = tr.addElement("td").addText(tmp);
                                //                                  
                                //                                  tmp = pd.getLdT2()!=null  ? Double.toString(pd.getLdT2()) : dv;
                                //                                  td = tr.addElement("td").addText(tmp);
                                //                                  
                                //                                  tmp = pd.getLdT3()!=null  ? Double.toString(pd.getLdT3()) : dv;
                                //                                  td = tr.addElement("td").addText(tmp);
                                //                                  
                                //                                  tmp = pd.getLdT4()!=null  ? Double.toString(pd.getLdT4()) : dv;
                                //                                  td = tr.addElement("td").addText(tmp);

                                tmp = pd.getMriPctChangeT1_T2() != null
                                        ? String.valueOf(pd.getMriPctChangeT1_T2())
                                        : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getMriPctChangeT1_T3() != null
                                        ? String.valueOf(pd.getMriPctChangeT1_T3())
                                        : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getMriPctChangeT1_T4() != null
                                        ? String.valueOf(pd.getMriPctChangeT1_T4())
                                        : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getMriPctChangeT2_T3() != null
                                        ? Double.toString(pd.getMriPctChangeT2_T3())
                                        : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getMriPctChangeT2_T4() != null
                                        ? Double.toString(pd.getMriPctChangeT2_T4())
                                        : dv;
                                td = tr.addElement("td").addText(tmp);

                                tmp = pd.getMriPctChangeT3_T4() != null
                                        ? Double.toString(pd.getMriPctChangeT3_T4())
                                        : dv;
                                td = tr.addElement("td").addText(tmp);

                                // dispaly path data

                                // dcisonly

                                tmp = pd.getDCISOnlyPS() != null ? pd.getDCISOnlyPS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                // Ptumor1szcm_micro_1
                                tmp = pd.getPtumor1szcm_micro_1() != null
                                        ? pd.getPtumor1szcm_micro_1().toString()
                                        : dv;
                                td = tr.addElement("td").addText(tmp);

                                // HistologicGradePS

                                tmp = pd.getHistologicGradePS() != null ? pd.getHistologicGradePS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                //NumPosNodes
                                tmp = pd.getNumPosNodesPS() != null ? pd.getNumPosNodesPS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                //NodesExamined
                                tmp = pd.getNodesExaminedPS() != null ? pd.getNodesExaminedPS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                // PathologyStage
                                tmp = pd.getPathologyStagePS() != null ? pd.getPathologyStagePS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                // InSituHisto
                                tmp = pd.getInSituHistoPS() != null ? pd.getInSituHistoPS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                // invDzHisto
                                tmp = pd.getInvDzHistoPS() != null ? pd.getInvDzHistoPS() : dv;
                                td = tr.addElement("td").addText(tmp);

                                //invDzMultiFoc

                                tmp = pd.getInvDzMultiFoc() != null ? pd.getInvDzMultiFoc() : dv;
                                td = tr.addElement("td").addText(tmp);

                                //invDzCellularity

                                tmp = pd.getInvDzCellularity() != null ? pd.getInvDzCellularity() : dv;
                                td = tr.addElement("td").addText(tmp);

                                //surgMargins

                                tmp = pd.getSurgMargins() != null ? pd.getSurgMargins() : dv;
                                td = tr.addElement("td").addText(tmp);

                                //yT

                                tmp = pd.getYT() != null ? pd.getYT() : dv;
                                td = tr.addElement("td").addText(tmp);

                                //yN

                                tmp = pd.getYN() != null ? pd.getYN() : dv;
                                td = tr.addElement("td").addText(tmp);

                                //yM

                                tmp = pd.getYM() != null ? pd.getYM() : dv;
                                td = tr.addElement("td").addText(tmp);

                                // rcb index
                                tmp = pd.getRcbIndexSize() != null ? pd.getRcbIndexSize() : dv;
                                td = tr.addElement("td").addText(tmp);

                                // LocalProgTimeD
                                tmp = pd.getLocalProgTimeD() != null ? pd.getLocalProgTimeD().toString() : dv;
                                td = tr.addElement("td").addText(tmp);

                                // DistProgTimeD
                                tmp = pd.getDistProgTimeD() != null ? pd.getDistProgTimeD().toString() : dv;
                                td = tr.addElement("td").addText(tmp);

                            }
                        }

                    }

                }
                if (!pdList.isEmpty()) {
                    ISPYClinicalFinding clinicalFinding = new ISPYClinicalFinding(sessionId, taskId, null,
                            FindingStatus.Running);
                    clinicalFinding.setPatientData(pdList);
                    FindingReportBean frb = new FindingReportBean();
                    frb.setFinding(clinicalFinding);
                    ApplicationFactory.getPresentationTierCache().addPersistableToSessionCache(
                            clinicalFinding.getSessionId(), clinicalFinding.getTaskId(), frb);
                }
            }
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    return html.append(document.asXML());
}

---

From source file:gov.nih.nci.ispy.web.reports.quick.QuickReporterReport.java

License:BSD License

public static StringBuffer quickReporterReport(List<String> reporters, String session, String taskId) {
    StringBuffer html = new StringBuffer();
    Document document = DocumentHelper.createDocument();
    Element table = document.addElement("table").addAttribute("id", "reportTable").addAttribute("class",
            "report");
    Element tr = null;//from ww  w  .j  av a2  s  .  c  om
    Element td = null;

    tr = table.addElement("tr").addAttribute("class", "header");
    td = tr.addElement("td").addAttribute("class", "header").addText("Reporter");
    td = tr.addElement("td").addAttribute("class", "header").addText("Gene Symbol");
    td = tr.addElement("td").addAttribute("class", "header").addText("GenBank AccId");
    td = tr.addElement("td").addAttribute("class", "header").addText("LocusLink");

    if (reporters != null) {
        try {
            GeneExprAnnotationService geService = GeneExprAnnotationServiceFactory.getInstance();

            List<ReporterAnnotation> reporterAnnotations = geService.getAnnotationsListForReporters(reporters);
            for (ReporterAnnotation reporterAnnotation : reporterAnnotations) {
                if (reporterAnnotation != null) {

                    tr = table.addElement("tr").addAttribute("class", "data");

                    //String reporter = reporterAnnotation.getReporter()!=null ? reporterAnnotation.getReporter().getValue().toString() : "N/A";
                    td = tr.addElement("td").addText(reporterAnnotation.getReporterId());
                    //html.append("ReporterID :" +reporterResultset.getReporter().getValue().toString() + "<br/>");
                    Collection<String> geneSymbols = (Collection<String>) reporterAnnotation.getGeneSymbols();
                    String genes = "";
                    if (geneSymbols != null) {
                        genes = StringUtils.join(geneSymbols.toArray(), ",");
                    }
                    if (!genes.equals("")) {
                        td = tr.addElement("td").addText(genes).addAttribute("class", "gene")
                                .addAttribute("name", "gene").addAttribute("id", genes).addElement("input")
                                .addAttribute("type", "checkbox").addAttribute("name", "checkable")
                                .addAttribute("class", "saveElement").addAttribute("value", genes);
                    } else {
                        td = tr.addElement("td").addText(genes).addAttribute("class", "gene")
                                .addAttribute("name", "gene").addAttribute("id", genes);
                    }
                    Collection<String> genBank_AccIDS = (Collection<String>) reporterAnnotation
                            .getGenbankAccessions();
                    String accs = "";
                    if (genBank_AccIDS != null) {
                        accs = StringUtils.join(genBank_AccIDS.toArray(), ",");
                    }

                    td = tr.addElement("td").addText(accs);

                    Collection<String> locusLinkIDs = (Collection<String>) reporterAnnotation.getLocusLinkIds();
                    String ll = "";
                    if (locusLinkIDs != null) {
                        ll = StringUtils.join(locusLinkIDs.toArray(), ",");
                    }

                    td = tr.addElement("td").addText(ll);
                }
            }
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    //return html;
    return html.append(document.asXML());
}

---

From source file:gov.nih.nci.ispy.web.xml.ClassComparisonReport.java

License:BSD License

public static Document getReportXML(Finding finding, Map filterMapParams, boolean allAnnotations) {

    allAnnotations = true; //force this for now ISPY prerelease - RCL 3/2

    DecimalFormat resultFormat = new DecimalFormat("0.0000");
    DecimalFormat sciFormat = new DecimalFormat("0.00E0");
    DecimalFormat tmpsciFormat = new DecimalFormat("###0.0000#####################");

    /*/*  w w  w  .ja  v a  2  s.co m*/
     *  this is for filtering, we will want a p-value filter for CC
     */
    ArrayList filter_string = new ArrayList(); // hashmap of genes | reporters | cytobands
    String filter_type = "show"; // show | hide
    String filter_element = "none"; // none | gene | reporter | cytoband

    if (filterMapParams.containsKey("filter_string") && filterMapParams.get("filter_string") != null)
        filter_string = (ArrayList) filterMapParams.get("filter_string");
    if (filterMapParams.containsKey("filter_type") && filterMapParams.get("filter_type") != null)
        filter_type = (String) filterMapParams.get("filter_type");
    if (filterMapParams.containsKey("filter_element") && filterMapParams.get("filter_element") != null)
        filter_element = (String) filterMapParams.get("filter_element");

    String defaultV = "--";
    String delim = " | ";

    Document document = DocumentHelper.createDocument();

    Element report = document.addElement("Report");
    Element cell = null;
    Element data = null;
    Element dataRow = null;
    //add the atts
    report.addAttribute("reportType", "Class Comparison");
    //fudge these for now
    report.addAttribute("groupBy", "none");
    String queryName = "none";
    queryName = finding.getTaskId();

    //set the queryName to be unique for session/cache access
    report.addAttribute("queryName", queryName);
    report.addAttribute("sessionId", "the session id");
    report.addAttribute("creationTime", "right now");

    StringBuffer sb = new StringBuffer();

    int recordCount = 0;
    int totalSamples = 0;

    //TODO: instance of
    ClassComparisonFinding ccf = (ClassComparisonFinding) finding;

    //process the query details
    ArrayList<String> queryDetails = new ArrayList();
    ClassComparisonQueryDTO ccdto = (ClassComparisonQueryDTO) ccf.getQueryDTO();
    String reporterType = ccdto.getArrayPlatformDE().getValueObject();

    if (ccdto != null) {
        String tmp = "";
        tmp = ccdto.getQueryName() != null ? ccdto.getQueryName() : "";
        queryDetails.add("Query Name: " + tmp);
        tmp = ccdto.getArrayPlatformDE() != null ? ccdto.getArrayPlatformDE().getValue().toString() : "";
        queryDetails.add("Array Platform: " + tmp);

        tmp = "";
        List<ClinicalQueryDTO> grps = ccdto.getComparisonGroups() != null ? ccdto.getComparisonGroups()
                : new ArrayList();
        Collection grs = new ArrayList();
        for (ClinicalQueryDTO cdto : grps) {
            if (cdto.getQueryName() != null)
                grs.add(cdto.getQueryName());
        }

        tmp += StringUtils.join(grs.toArray(), ", ") + " (baseline)";
        queryDetails.add("Groups: " + tmp);
        /*
        noHTMLString = noHTMLString.replaceAll("<", "{");
        noHTMLString = noHTMLString.replaceAll(">", "}");
        noHTMLString = noHTMLString.replaceAll("&nbsp;", " ");
        */
        tmp = ccdto.getExprFoldChangeDE() != null ? ccdto.getExprFoldChangeDE().getValue().toString() : "";
        queryDetails.add("Fold Change: " + tmp);
        //queryDetails.add("Institutions: " + ccdto.getInstitutionDEs());
        tmp = ccdto.getMultiGroupComparisonAdjustmentTypeDE() != null
                ? ccdto.getMultiGroupComparisonAdjustmentTypeDE().getValue().toString()
                : "";
        queryDetails.add("Multi Group: " + tmp);
        tmp = ccdto.getStatisticalSignificanceDE() != null
                ? ccdto.getStatisticalSignificanceDE().getValue().toString()
                : "";
        queryDetails.add("Stat Sig.: " + tmp);
        tmp = ccdto.getStatisticTypeDE() != null ? ccdto.getStatisticTypeDE().getValue().toString() : "";
        queryDetails.add("Stat Type: " + tmp);
    }
    /*
    queryDetails.add("Analysis Result name: " + ccform.getAnalysisResultName());
    queryDetails.add("Array Platform: " + ccform.getArrayPlatform());
    queryDetails.add("Baseline group: " + ccform.getBaselineGroup());
    queryDetails.add("Comparison Groups: " + ccform.getSelectedGroups()[0].toString());
    queryDetails.add("Comparison Adjustment: " + ccform.getComparisonAdjustment());
    //queryDetails.add("Comp. Adj. Coll: " + ccform.getComparisonAdjustmentCollection());
    //queryDetails.add("Existing Groups: " + ccform.getExistingGroups());
    //queryDetails.add("Existing group list: " + ccform.getExistingGroupsList());
    //queryDetails.add("Fold Change: " + ccform.getFoldChange());
    queryDetails.add("Fold Change auto: " + ccform.getFoldChangeAuto());
    //queryDetails.add("Fold change auto list: " + ccform.getFoldChangeAutoList());
    //queryDetails.add("Fold change manual: " + ccform.getFoldChangeManual());
    queryDetails.add("Stastic: " + ccform.getStatistic());
    queryDetails.add("Stastical method: " + ccform.getStatisticalMethod());
    //queryDetails.add("Stastical method coll.: " + ccform.getStatisticalMethodCollection());
    queryDetails.add("Stastical significance: " + ccform.getStatisticalSignificance());
    */
    String qd = "";
    for (String q : queryDetails) {
        qd += q + " ||| ";
    }

    if (ccf != null) {

        Element details = report.addElement("Query_details");
        cell = details.addElement("Data");
        cell.addText(qd);
        cell = null;

        Element headerRow = report.addElement("Row").addAttribute("name", "headerRow");
        cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                .addAttribute("group", "header");
        data = cell.addElement("Data").addAttribute("type", "header").addText("Reporter");
        data = null;
        cell = null;
        cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                .addAttribute("group", "header");
        data = cell.addElement("Data").addAttribute("type", "header").addText("Group Avg");
        data = null;
        cell = null;
        cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                .addAttribute("group", "header");
        String isAdj = ccf.arePvaluesAdjusted() ? " (Adjusted) " : "";
        data = cell.addElement("Data").addAttribute("type", "header").addText("P-Value" + isAdj);
        data = null;
        cell = null;

        cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                .addAttribute("group", "header");
        data = cell.addElement("Data").addAttribute("type", "header").addText("Fold Change");
        data = null;
        cell = null;

        cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "header")
                .addAttribute("group", "header");
        data = cell.addElement("Data").addAttribute("type", "header").addText("Gene Symbol");
        data = null;
        cell = null;

        //starting annotations...get them only if allAnnotations == true
        if (allAnnotations) {
            cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv")
                    .addAttribute("group", "header");
            data = cell.addElement("Data").addAttribute("type", "header").addText("GenBank Acc");
            data = null;
            cell = null;
            cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv")
                    .addAttribute("group", "header");
            data = cell.addElement("Data").addAttribute("type", "header").addText("Locus link");
            data = null;
            cell = null;
            cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv")
                    .addAttribute("group", "header");
            data = cell.addElement("Data").addAttribute("type", "header").addText("GO Id");
            data = null;
            cell = null;
            cell = headerRow.addElement("Cell").addAttribute("type", "header").addAttribute("class", "csv")
                    .addAttribute("group", "header");
            data = cell.addElement("Data").addAttribute("type", "header").addText("Pathways");
            data = null;
            cell = null;
        }

        /* done with the headerRow and SampleRow Elements, time to add data rows */

        /*
        Map<String,ReporterResultset> reporterResultsetMap = null;
        reporterResultsetMap = ccf.getReporterAnnotationsMap();
        */

        List<ClassComparisonResultEntry> classComparisonResultEntrys = ccf.getResultEntries();
        List<String> reporterIds = new ArrayList<String>();

        for (ClassComparisonResultEntry classComparisonResultEntry : classComparisonResultEntrys) {
            if (classComparisonResultEntry.getReporterId() != null) {
                reporterIds.add(classComparisonResultEntry.getReporterId());
            }
        }

        Map reporterResultsetMap = null;
        try {
            GeneExprAnnotationService geService = GeneExprAnnotationServiceFactory.getInstance();
            reporterResultsetMap = geService.getAnnotationsMapForReporters(reporterIds);
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
        /*
        //new stuff
        AnnotationHandler h = new AnnotationHandler();
        Map reporterResultsetMap = null;
        if(allAnnotations){
           //Map<String, ReporterAnnotations> reporterResultsetMap = null;
           try {
          reporterResultsetMap = h.getAllAnnotationsFor(reporterIds);
           } catch (Exception e) {
          e.printStackTrace();
           }
        }
        else   {
           //Map<String, String> reporterResultsetMap = null;
           try {
          reporterResultsetMap = h.getGeneSymbolsFor(reporterIds);
           } catch (Exception e) {
          // TODO Auto-generated catch block
          e.printStackTrace();
           }
        }
        */

        /*
        //this looks like a failsafe for the old method
        if(reporterResultsetMap == null)   {
         try {
            reporterResultsetMap = GeneExprAnnotationService.getAnnotationsMapForReporters(reporterIds);
         }
         catch(Exception e){}
          }
          */

        for (ClassComparisonResultEntry ccre : ccf.getResultEntries()) {

            dataRow = report.addElement("Row").addAttribute("name", "dataRow");
            cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "reporter")
                    .addAttribute("group", "data");
            data = cell.addElement("Data").addAttribute("type", reporterType).addText(ccre.getReporterId());
            data = null;
            cell = null;
            cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                    .addAttribute("group", "data");
            data = cell.addElement("Data").addAttribute("type", "header")
                    .addText(resultFormat.format(ccre.getMeanGrp1()) + " / "
                            + resultFormat.format(ccre.getMeanBaselineGrp()));
            data = null;
            cell = null;
            cell = dataRow.addElement("Cell").addAttribute("type", "pval").addAttribute("class", "data")
                    .addAttribute("group", "data");
            //String pv = (ccre.getPvalue() == null) ? String.valueOf(ccre.getPvalue()) : "N/A";
            String pv = defaultV;
            BigDecimal bigd;
            try {
                bigd = new BigDecimal(ccre.getPvalue());
                pv = bigd.toPlainString();
            } catch (Exception e) {
                //missing value
            }
            data = cell.addElement("Data").addAttribute("type", "header").addText(pv);
            data = null;
            cell = null;
            cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "data")
                    .addAttribute("group", "data");
            data = cell.addElement("Data").addAttribute("type", "header")
                    .addText(String.valueOf(resultFormat.format(ccre.getFoldChange())));
            data = null;
            cell = null;

            //if only showing genes
            if (!allAnnotations && reporterResultsetMap != null) {
                String reporterId = ccre.getReporterId().toUpperCase().trim();
                String genes = reporterResultsetMap.get(reporterId) != null
                        ? (String) reporterResultsetMap.get(reporterId)
                        : defaultV;
                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "header").addText(genes);
                data = null;
                cell = null;
            } else {
                //get the gene symbols for this reporter
                //ccre.getReporterId()
                String genes = defaultV;

                //start annotations
                String accIds = defaultV;
                String llink = defaultV;
                String go = defaultV;
                String pw = defaultV;

                if (reporterResultsetMap != null) { // && reporterIds != null
                    //int count = 0;
                    String reporterId = ccre.getReporterId().toUpperCase().trim();
                    //ReporterResultset reporterResultset = reporterResultsetMap.get(reporterId);
                    ReporterAnnotation ra = (ReporterAnnotation) reporterResultsetMap.get(reporterId);

                    //Collection<String> geneSymbols = (Collection<String>)reporterResultset.getAssiciatedGeneSymbols();
                    if (ra != null) {
                        List geneSymbols = ra.getGeneSymbols();
                        //if(geneSymbols != null)   
                        //   genes = geneSymbols.toString();

                        if (geneSymbols != null) {
                            genes = StringUtils.join(geneSymbols.toArray(), delim);
                        }

                        Collection<String> genBank_AccIDS = (Collection<String>) ra.getGenbankAccessions();
                        if (genBank_AccIDS != null) {
                            accIds = StringUtils.join(genBank_AccIDS.toArray(), delim);
                        }
                        Collection<String> locusLinkIDs = (Collection<String>) ra.getLocusLinkIds();
                        if (locusLinkIDs != null) {
                            llink = StringUtils.join(locusLinkIDs.toArray(), delim);
                        }
                        Collection<String> goIds = (Collection<String>) ra.getGOIds();
                        if (goIds != null) {
                            go = StringUtils.join(goIds.toArray(), delim);
                        }
                        Collection<String> pathways = (Collection<String>) ra.getPathwayIds();
                        if (pathways != null) {
                            pw = StringUtils.join(pathways.toArray(), delim);
                        }
                    }
                }

                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "gene")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "header").addText(genes);
                data = null;
                cell = null;
                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "header").addText(accIds);
                data = null;
                cell = null;
                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "header").addText(llink);
                data = null;
                cell = null;
                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "header").addText(go);
                data = null;
                cell = null;
                cell = dataRow.addElement("Cell").addAttribute("type", "data").addAttribute("class", "csv")
                        .addAttribute("group", "data");
                data = cell.addElement("Data").addAttribute("type", "header").addText(pw);
                data = null;
                cell = null;

            }
        }
    } else {
        //TODO: handle this error
        sb.append("<br><Br>Class Comparison is empty<br>");
    }

    return document;
}

---

From source file:gov.nih.nci.rembrandt.web.reports.quick.QuickClinicalReport.java

License:BSD License

public static StringBuffer quickSampleReport(List<String> sampleIds) {
    StringBuffer html = new StringBuffer();
    Document document = DocumentHelper.createDocument();
    String dv = "--";

    if (sampleIds != null) {
        Map<String, SampleResultset> sampleResultsetMap;
        try {// w w  w.ja  va  2  s  .c om
            sampleResultsetMap = ClinicalDataValidator.getClinicalAnnotationsMapForSamples(sampleIds);
            if (sampleResultsetMap != null && sampleIds != null) {
                int count = 0;

                Element table = document.addElement("table").addAttribute("id", "reportTable")
                        .addAttribute("class", "report");
                Element tr = null;
                Element td = null;

                tr = table.addElement("tr").addAttribute("class", "header");
                List<String> heads = new ArrayList<String>();
                heads = ClinicalSampleReport.getClinicalHeaderValues();
                for (String h : heads) {
                    td = tr.addElement("td").addAttribute("class", "header").addText(h);
                }

                for (String sampleId : sampleIds) {
                    SampleResultset sampleResultset = sampleResultsetMap.get(sampleId);
                    //lose this
                    if (sampleResultset != null && sampleResultset.getSampleIDDE() != null) {
                        System.out.println(++count + " SampleID :"
                                + sampleResultset.getSampleIDDE().getValue().toString());
                    }
                    //end lose
                    if (sampleResultset != null) {
                        List dataRows = new ArrayList();
                        dataRows = ClinicalSampleReport.getClinicalRowValues(sampleResultset);

                        tr = table.addElement("tr").addAttribute("class", "data");

                        for (int i = 0; i < dataRows.size(); i++) {
                            td = tr.addElement("td").addText(DEUtils.checkNull(dataRows.get(i)));
                        }
                        /*
                        String sid = sampleResultset.getSampleIDDE()!=null && sampleResultset.getSampleIDDE().getValue() != null ?sampleResultset.getSampleIDDE().getValue().toString() : dv;
                        td = tr.addElement("td").addText(sid);
                                
                        String dis = sampleResultset.getDisease() != null && sampleResultset.getDisease().getValue() != null ?sampleResultset.getDisease().getValue().toString() : dv;
                        td = tr.addElement("td").addText(dis);
                                
                        String gen = sampleResultset.getGenderCode() != null && sampleResultset.getGenderCode().getValue() != null ? sampleResultset.getGenderCode().getValue().toString() : dv;
                        td = tr.addElement("td").addText(gen);
                                
                        String age = sampleResultset.getAgeGroup() != null && sampleResultset.getAgeGroup().getValue() != null ? sampleResultset.getAgeGroup().getValue().toString() : dv;
                        td = tr.addElement("td").addText(age);
                                
                        String slength = sampleResultset.getSurvivalLength() != null ? String.valueOf(sampleResultset.getSurvivalLength()) : dv;
                        td = tr.addElement("td").addText(slength);
                        */
                    }

                }
            }
        } catch (Exception e) {
            // TODO Auto-generated catch block
            e.printStackTrace();
        }
    }
    return html.append(document.asXML());
}

---

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