Example usage for org.dom4j Node selectSingleNode

List of usage examples for org.dom4j Node selectSingleNode

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Introduction

In this page you can find the example usage for org.dom4j Node selectSingleNode.

Prototype

Node selectSingleNode(String xpathExpression);

Source Link

Document

selectSingleNode evaluates an XPath expression and returns the result as a single Node instance.

Usage

From source file:org.kuali.ext.mm.utility.JpaToOjbMetadata.java

License:Educational Community License

public static void main(String[] args) throws Exception {
    String filename = args[0];//www .j  a  va 2s.  c om

    try {
        SAXReader saxReader = new SAXReader();
        Document document = saxReader.read(filename);

        List<Node> boList = document.selectNodes("//bo");

        for (Node bo : boList) {
            //             String boName = bo.selectSingleNode("@name").getStringValue();
            String className = bo.selectSingleNode("@class").getStringValue();

            Class<? extends PersistableBusinessObject> boClass = (Class<? extends PersistableBusinessObject>) Class
                    .forName(className);
            //              PropertyDescriptor[] props = PropertyUtils.getPropertyDescriptors( boClass );

            StringBuffer sb = new StringBuffer(1000);
            Table tableAnnotation = boClass.getAnnotation(Table.class);

            sb.append("   <class-descriptor class=\"").append(boClass.getName()).append("\" table=\"");
            sb.append(tableAnnotation.name()).append("\">\r\n");

            getClassFields(boClass, sb, null);
            getReferences(boClass, sb);
            sb.append("   </class-descriptor>\r\n");

            System.out.println(sb.toString());

            //            FileWriter outputfile = null;
            //              try
            //              {
            //                 outputfile = new FileWriter(getOutputFilePath(className) + "ojb-" + boName + ".xml");
            //                 outputfile.write(sb.toString());
            //                 System.out.println("Created: " + getOutputFilePath(className) + "ojb-" + boName + ".xml");
            //              }
            //              catch(IOException e)
            //              {
            //                 System.err.println("Error writing bean data to file.");
            //              }
            //              finally {
            //                 outputfile.close();
            //              }
        }
    } catch (DocumentException e) {
        System.err.println("Error parsing xml document.");
    } catch (ClassNotFoundException e) {
        e.printStackTrace();
    }

}

From source file:org.light.portlets.youtube.YouTubePortlet.java

License:Apache License

public void processAction(ActionRequest request, ActionResponse response)
        throws PortletException, java.io.IOException {
    String action = request.getParameter("action");
    if ("search".equals(action)) {
        String tag = request.getParameter("tag");
        if (tag != null && tag.trim().length() > 0) {
            String url = "http://www.youtube.com/api2_rest?method=youtube.videos.list_by_tag&dev_id=4adPqGmch9M&tag="
                    + tag;/*from  w w  w .j  a v a 2s.  com*/
            HttpServletRequest httpServletRequest = (HttpServletRequest) request
                    .getAttribute("httpServletRequest");
            try {
                URL youTubeUrl = new URL(url);
                URLConnection con = youTubeUrl.openConnection();
                InputStream in = con.getInputStream();
                //                  StringBuffer buffer = new  StringBuffer();
                //                   int i;
                //                  while ((i = in.read()) != -1){
                //                        buffer.append((char) i);
                //                  }
                //                  String text = buffer.toString();               
                //                  Document document = DocumentHelper.parseText(text);
                Document document = new SAXReader().read(in);
                List list1 = document.selectNodes("//ut_response/video_list/video");
                List<VideoBean> videos = new ArrayList<VideoBean>();
                for (Iterator iter = list1.iterator(); iter.hasNext();) {
                    Node node = (Node) iter.next();
                    String author = node.selectSingleNode("author").getStringValue();
                    String id = node.selectSingleNode("id").getStringValue();
                    String title = node.selectSingleNode("title").getStringValue();
                    String desc = node.selectSingleNode("description").getStringValue();
                    String picUrl = node.selectSingleNode("thumbnail_url").getStringValue();
                    String videoUrl = node.selectSingleNode("url").getStringValue();
                    String seconds = node.selectSingleNode("length_seconds").getStringValue();
                    String ratingAvg = node.selectSingleNode("rating_avg").getStringValue();
                    String ratingCount = node.selectSingleNode("rating_count").getStringValue();
                    String viewCount = node.selectSingleNode("view_count").getStringValue();
                    String commentCount = node.selectSingleNode("comment_count").getStringValue();
                    String tags = node.selectSingleNode("tags").getStringValue();
                    VideoBean video = new VideoBean(author, id, title, desc, picUrl, videoUrl, seconds,
                            ratingAvg, ratingCount, viewCount, commentCount, tags);
                    videos.add(video);
                }
                request.getPortletSession().setAttribute("youTubes", videos, PortletSession.APPLICATION_SCOPE);
            } catch (Exception e) {
            }
        } else {
            request.getPortletSession().setAttribute("youTubes", null, PortletSession.APPLICATION_SCOPE);
        }
    }
    if ("author".equals(action)) {
        String searchAuthor = request.getParameter("author");
        String url = "http://www.youtube.com/api2_rest?method=youtube.videos.list_by_user&dev_id=4adPqGmch9M&user="
                + searchAuthor;
        HttpServletRequest httpServletRequest = (HttpServletRequest) request.getAttribute("httpServletRequest");
        try {
            URL youTubeUrl = new URL(url);
            URLConnection con = youTubeUrl.openConnection();
            InputStream in = con.getInputStream();
            Document document = new SAXReader().read(in);
            List list1 = document.selectNodes("//ut_response/video_list/video");
            List<VideoBean> videos = new ArrayList<VideoBean>();
            for (Iterator iter = list1.iterator(); iter.hasNext();) {
                Node node = (Node) iter.next();
                String author = node.selectSingleNode("author").getStringValue();
                String id = node.selectSingleNode("id").getStringValue();
                String title = node.selectSingleNode("title").getStringValue();
                String desc = node.selectSingleNode("description").getStringValue();
                String picUrl = node.selectSingleNode("thumbnail_url").getStringValue();
                String videoUrl = node.selectSingleNode("url").getStringValue();
                String seconds = node.selectSingleNode("length_seconds").getStringValue();
                String ratingAvg = node.selectSingleNode("rating_avg").getStringValue();
                String ratingCount = node.selectSingleNode("rating_count").getStringValue();
                String viewCount = node.selectSingleNode("view_count").getStringValue();
                String commentCount = node.selectSingleNode("comment_count").getStringValue();
                String tags = node.selectSingleNode("tags").getStringValue();
                VideoBean video = new VideoBean(author, id, title, desc, picUrl, videoUrl, seconds, ratingAvg,
                        ratingCount, viewCount, commentCount, tags);
                videos.add(video);
            }
            request.getPortletSession().setAttribute("youTubes", videos, PortletSession.APPLICATION_SCOPE);
        } catch (Exception e) {
        }
    }
    if ("featured".equals(action)) {
        String url = "http://www.youtube.com/api2_rest?method=youtube.videos.list_featured&dev_id=4adPqGmch9M";
        HttpServletRequest httpServletRequest = (HttpServletRequest) request.getAttribute("httpServletRequest");
        try {
            URL youTubeUrl = new URL(url);
            URLConnection con = youTubeUrl.openConnection();
            InputStream in = con.getInputStream();
            Document document = new SAXReader().read(in);
            List list1 = document.selectNodes("//ut_response/video_list/video");
            List<VideoBean> videos = new ArrayList<VideoBean>();
            for (Iterator iter = list1.iterator(); iter.hasNext();) {
                Node node = (Node) iter.next();
                String author = node.selectSingleNode("author").getStringValue();
                String id = node.selectSingleNode("id").getStringValue();
                String title = node.selectSingleNode("title").getStringValue();
                String desc = node.selectSingleNode("description").getStringValue();
                String picUrl = node.selectSingleNode("thumbnail_url").getStringValue();
                String videoUrl = node.selectSingleNode("url").getStringValue();
                String seconds = node.selectSingleNode("length_seconds").getStringValue();
                String ratingAvg = node.selectSingleNode("rating_avg").getStringValue();
                String ratingCount = node.selectSingleNode("rating_count").getStringValue();
                String viewCount = node.selectSingleNode("view_count").getStringValue();
                String commentCount = node.selectSingleNode("comment_count").getStringValue();
                String tags = node.selectSingleNode("tags").getStringValue();
                VideoBean video = new VideoBean(author, id, title, desc, picUrl, videoUrl, seconds, ratingAvg,
                        ratingCount, viewCount, commentCount, tags);
                videos.add(video);
            }
            request.getPortletSession().setAttribute("youTubes", videos, PortletSession.APPLICATION_SCOPE);
        } catch (Exception e) {
        }
    }
    if ("clear".equals(action)) {
        request.getPortletSession().setAttribute("youTubes", null, PortletSession.APPLICATION_SCOPE);
    }
}

From source file:org.metaeffekt.core.inventory.processor.MavenCentralVersionProcessor.java

License:Apache License

private void updateLatestVersion(CloseableHttpClient client, HttpGet request, Artifact artifact,
        final LRUMap queryCache) throws URISyntaxException, IOException, HttpException, DocumentException {

    String artifactId = artifact.getId();
    int index = artifactId.indexOf("-" + artifact.getVersion());
    if (index != -1) {
        artifactId = artifactId.substring(0, index);
    }//w  w  w.j a va  2 s .  c  om
    if (StringUtils.hasText(artifact.getGroupId())) {
        String[] groupIds = artifact.getGroupId().split("\\|");
        String latestVersions = null;
        for (int i = 0; i < groupIds.length; i++) {
            String replacedUri = URI_PATTERN_ARTIFACT_RESOLVE.replaceAll("\\$\\{artifactId\\}",
                    artifactId.replace(" ", "-"));
            replacedUri = replacedUri.replaceAll("\\$\\{groupId\\}", groupIds[i].replace(" ", ""));

            LOG.info("Querying: {}", replacedUri);
            String latestVersion = (String) queryCache.get(replacedUri);
            String latestVersionMethod1 = null;
            if (latestVersion == null) {
                request.setURI(new URI(replacedUri));
                CloseableHttpResponse response = client.execute(request);
                try {
                    if (response.getStatusLine().getStatusCode() == HttpStatus.SC_OK) {
                        SAXReader reader = new SAXReader();
                        Document document = reader.read(response.getEntity().getContent());
                        Node node;
                        LinkedHashMap<String, String> map = new LinkedHashMap<String, String>();
                        List<String> timestamps = new ArrayList<String>();
                        @SuppressWarnings("unchecked")
                        List<Node> docNodes = document.selectNodes("//response/result/doc");
                        if (docNodes != null) {
                            for (Object result : docNodes) {
                                Node resultNode = (Node) result;
                                node = resultNode.selectSingleNode("str[@name='v']");
                                String version = node.getText();
                                node = resultNode.selectSingleNode("long[@name='timestamp']");
                                String timestamp = node.getText();

                                // the timestamp alone may have duplicated
                                // therefore we append the version
                                timestamp = timestamp + version;

                                map.put(timestamp, version);
                                timestamps.add(timestamp);
                            }
                            if (!timestamps.isEmpty()) {
                                Collections.sort(timestamps);
                                latestVersionMethod1 = map.get(timestamps.get(timestamps.size() - 1));
                            }
                        }
                    }
                } finally {
                    response.close();
                }

                // method2
                String replacedUri2 = URI_PATTERN_ARTIFACT_RESOLVE_METHOD2.replaceAll("\\$\\{artifactId\\}",
                        artifactId.replace(" ", "-"));
                replacedUri2 = replacedUri2.replaceAll("\\$\\{groupId\\}", groupIds[i].replace(" ", ""));
                request.setURI(new URI(replacedUri2));
                response = client.execute(request);
                String latestVersionMethod2 = null;
                try {
                    if (response.getStatusLine().getStatusCode() == HttpStatus.SC_OK) {
                        SAXReader reader = new SAXReader();
                        Document document = reader.read(response.getEntity().getContent());
                        int numEntries = Integer
                                .parseInt(document.selectSingleNode("//response/result").valueOf("@numFound"));

                        if (numEntries == 1) {
                            Node node = document
                                    .selectSingleNode("//response/result/doc/str[@name='latestVersion']");
                            if (node != null) {
                                latestVersionMethod2 = node.getText();
                            }
                        }
                    }
                } finally {
                    response.close();
                }

                if (latestVersionMethod1 != null) {
                    latestVersion = latestVersionMethod1;

                    if (!latestVersionMethod1.equals(latestVersionMethod2)) {
                        latestVersion = latestVersion + "|" + latestVersionMethod2;
                    }
                } else {
                    latestVersion = latestVersionMethod2;
                }

                if (latestVersion == null) {
                    latestVersion = "n.a.";
                }
                if (latestVersions == null) {
                    latestVersions = latestVersion;
                } else {
                    latestVersions += "|" + latestVersion;
                }
                queryCache.put(replacedUri, latestVersions);
            } else {
                latestVersions = latestVersion;
            }
        }
        LOG.info("Latest version: {}", latestVersions);
        artifact.setLatestAvailableVersion(latestVersions);
    }
}

From source file:org.mskcc.cbio.oncokb.quest.VariantAnnotationXMLV2.java

/**
 * This is a hacky way to run VEP. We should switch to web service once that is ready.
 *//*w w w  .  ja  va2 s .c  om*/
private static void runVcf2Maf(String inputXml, Map<Alteration, String> mapAlterationXml, String diagnosis)
        throws IOException, DocumentException, InterruptedException {
    File tmpFile = File.createTempFile("temp-oncokb-input-", ".xml");
    tmpFile.deleteOnExit();
    String inputPath = tmpFile.getAbsolutePath();
    String outputPath = inputPath.substring(0, inputPath.length() - 3) + "oncokb.xml";

    FileWriter writer = new FileWriter(tmpFile);
    writer.append(inputXml);
    writer.close();

    String vepMafXmlPl = System.getenv("VEP_MAF_XML_PL");
    if (null == vepMafXmlPl) {
        throw new IOException("VEP_MAF_XML_PL was not defined");
    }

    Process proc = Runtime.getRuntime().exec(new String[] { "perl", vepMafXmlPl, inputPath });
    proc.waitFor();

    InputStream stderr = proc.getErrorStream();
    InputStreamReader isr = new InputStreamReader(stderr);
    BufferedReader br = new BufferedReader(isr);
    String line = null;
    System.out.println("<ERROR>");
    while ((line = br.readLine()) != null)
        System.out.println(line);
    System.out.println("</ERROR>");
    int exitVal = proc.waitFor();
    System.out.println("Process exitValue: " + exitVal);

    SAXReader reader = new SAXReader();
    Document document = reader.read(outputPath);

    List<Node> variantNodes = document.selectNodes("//document/sample/test/variant");
    for (Node node : variantNodes) {
        String alterationXml = "<variant_type>small_nucleotide_variant</variant_type>\n"
                + node.selectSingleNode("genomic_locus").asXML() + node.selectSingleNode("allele").asXML();

        String geneSymbol = node.selectSingleNode("allele/transcript/hgnc_symbol").getText();
        GeneBo geneBo = ApplicationContextSingleton.getGeneBo();
        Gene gene = geneBo.findGeneByHugoSymbol(geneSymbol);

        String proteinChange = node.selectSingleNode("allele/transcript/hgvs_p_short").getText();

        Alteration alteration = new Alteration();
        alteration.setAlterationType(AlterationType.MUTATION);
        alteration.setGene(gene);
        alteration.setName(proteinChange);

        AlterationUtils.annotateAlteration(alteration, proteinChange);

        mapAlterationXml.put(alteration, alterationXml);
    }

}

From source file:org.mskcc.cbio.oncokb.quest.VariantAnnotationXMLV2.java

private static void handleCNA(Node cnaNode, Map<Alteration, String> mapAlterationXml, String diagnosis) {
    Gene gene = parseGene(cnaNode, "gene");
    if (gene == null) {
        return;//from   w w w .  j  av a 2s. c o  m
    }

    String type = cnaNode.selectSingleNode("type").getText();

    Alteration alteration = new Alteration();
    alteration.setGene(gene);
    alteration.setAlteration(type);
    alteration.setAlterationType(AlterationType.MUTATION); // TODO: this needs to be fixed

    StringBuilder sb = new StringBuilder();
    sb.append("<variant_type>copy_number_alteration</variant_type>\n");
    sb.append(cnaNode.asXML()).append("\n");
    sb.append(VariantAnnotationXML.annotate(alteration, diagnosis));

    mapAlterationXml.put(alteration, sb.toString());
}

From source file:org.mskcc.cbio.oncokb.quest.VariantAnnotationXMLV2.java

private static Gene parseGene(Node node, String genePath) {
    GeneBo geneBo = ApplicationContextSingleton.getGeneBo();
    Gene gene = null;/*from w  ww . ja  v a 2s  .  c  o m*/
    Node entrezGeneIdNode = node.selectSingleNode(genePath + "/entrez_gene_id");
    Node hugoSymbolNode = node.selectSingleNode(genePath + "/hgnc_symbol");
    if (entrezGeneIdNode != null) {
        int entrezId = Integer.parseInt(entrezGeneIdNode.getText());
        gene = geneBo.findGeneByEntrezGeneId(entrezId);
    }

    if (gene == null && hugoSymbolNode != null) {
        String symbol = hugoSymbolNode.getText();
        gene = geneBo.findGeneByHugoSymbol(symbol);
    }

    if (gene == null) {
        // a gene not in system
        gene = new Gene();
        gene.setEntrezGeneId(Integer.parseInt(entrezGeneIdNode.getText()));
        gene.setHugoSymbol(hugoSymbolNode.getText());
    }

    return gene;
}

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

static void importData(File xmlFile, int cancerStudyId) throws Exception {
    MySQLbulkLoader.bulkLoadOn();/*w w  w . j ava 2 s.c o m*/

    // add unknow attriutes -- this 
    for (ClinicalAttribute ca : getClinicalAttributes()) {
        if (DaoClinicalAttribute.getDatum(ca.getAttrId()) == null) {
            DaoClinicalAttribute.addDatum(ca);
        }
    }

    SAXReader reader = new SAXReader();
    Document document = reader.read(xmlFile);

    List<Node> patientNodes = document.selectNodes("//Patients/Patient");

    long clinicalEventId = DaoClinicalEvent.getLargestClinicalEventId();
    CancerStudy cancerStudy = DaoCancerStudy.getCancerStudyByInternalId(cancerStudyId);

    Map<String, String> mapSu2cSampleIdSampleId = getMapSu2cSampleIdSampleId(cancerStudyId);

    for (Node patientNode : patientNodes) {
        String patientId = patientNode.selectSingleNode("PtProtocolStudyId").getText();
        Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudyId, patientId);
        if (patient == null) {
            continue;
        }

        System.out.println("Importing " + patientId);

        // processing clinical data
        // patient clinical data
        List<ClinicalData> patientClinicalData = parsePatientClinicalData(patientNode, patientId,
                cancerStudyId);
        for (ClinicalData cd : patientClinicalData) {
            if (DaoClinicalData.getDatum(cancerStudy.getCancerStudyStableId(), cd.getStableId(),
                    cd.getAttrId()) == null) {
                DaoClinicalData.addPatientDatum(patient.getInternalId(), cd.getAttrId(), cd.getAttrVal());
            }
        }
        // sample clinical data
        List<ClinicalData> sampleClinicalData = parseClinicalDataFromSpecimen(patientNode, cancerStudyId,
                mapSu2cSampleIdSampleId);
        for (ClinicalData cd : sampleClinicalData) {
            if (DaoClinicalData.getDatum(cancerStudy.getCancerStudyStableId(), cd.getStableId(),
                    cd.getAttrId()) == null) {
                Sample sample = DaoSample.getSampleByCancerStudyAndSampleId(cancerStudyId, cd.getStableId());
                DaoClinicalData.addSampleDatum(sample.getInternalId(), cd.getAttrId(), cd.getAttrVal());
            }
        }

        // processing timeline data
        List<ClinicalEvent> clinicalEvents = new ArrayList<ClinicalEvent>();
        long diagnositicDate = parseStatusesAndReturnDiagnosisDate(clinicalEvents, patientNode, patientId,
                cancerStudyId);
        parseClinicalEventsFromSpecimen(clinicalEvents, patientNode, patientId, cancerStudyId);
        parseMedicalTherapies(clinicalEvents, patientNode, patientId, cancerStudyId);
        parseRadiationTherapies(clinicalEvents, patientNode, patientId, cancerStudyId);
        parseBrachyTherapies(clinicalEvents, patientNode, patientId, cancerStudyId);
        parseDiagnostics(clinicalEvents, patientNode, patientId, cancerStudyId);
        parseLabTests(clinicalEvents, patientNode, patientId, cancerStudyId);
        for (ClinicalEvent clinicalEvent : clinicalEvents) {
            clinicalEvent.setClinicalEventId(++clinicalEventId);
            if (clinicalEvent.getStartDate() != null) {
                clinicalEvent.setStartDate(clinicalEvent.getStartDate() - diagnositicDate);
            }
            if (clinicalEvent.getStopDate() != null) {
                clinicalEvent.setStopDate(clinicalEvent.getStopDate() - diagnositicDate);
            }
            DaoClinicalEvent.addClinicalEvent(clinicalEvent);
        }
    }

    MySQLbulkLoader.flushAll();
}

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static List<ClinicalData> parsePatientClinicalData(Node patientNode, String patientId,
        int cancerStudyId) {
    List<ClinicalData> clinicalData = new ArrayList<ClinicalData>();
    //        Node node = patientNode.selectSingleNode("PtProtocolStudyId");
    //        if (node!=null) {
    //            clinicalData.add(new ClinicalData(cancerStudyId, patientId, "PATIENT_ID", node.getText()));
    //        }// w w  w  . j a v a 2  s .c o  m

    Node node = patientNode.selectSingleNode("PtRace");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "RACE", node.getText()));
    }

    node = patientNode.selectSingleNode("PtRegistrationAge");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "AGE", node.getText()));
    }

    node = patientNode.selectSingleNode("Categories/Category/Category");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "PATIENT_CATEGORY", node.getText()));
    }

    node = patientNode.selectSingleNode("ClinicalStages/ClinicalStage/ClinStageT");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "CLIN_T_Stage", node.getText()));
    }

    node = patientNode.selectSingleNode("ClinicalStages/ClinicalStage/ClinStageN");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "CLIN_N_Stage", node.getText()));
    }

    node = patientNode.selectSingleNode("ClinicalStages/ClinicalStage/ClinStageM");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "CLIN_M_Stage", node.getText()));
    }

    node = patientNode.selectSingleNode("Pathologies/Pathology/PathHistology");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "HISTOLOGY", node.getText()));
    }

    node = patientNode.selectSingleNode("Pathologies/Pathology/PathResult");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "PATH_RESULT", node.getText()));
    }

    node = patientNode
            .selectSingleNode("Pathologies/Pathology/PathologyStageGrades/PathologyStageGrade/PathStageT");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "PATH_T_STAGE", node.getText()));
    }

    node = patientNode
            .selectSingleNode("Pathologies/Pathology/PathologyStageGrades/PathologyStageGrade/PathStageN");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "PATH_N_STAGE", node.getText()));
    }

    node = patientNode
            .selectSingleNode("Pathologies/Pathology/PathologyStageGrades/PathologyStageGrade/PathStageM");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "PATH_M_STAGE", node.getText()));
    }

    node = patientNode.selectSingleNode("Pathologies/Pathology/ProstateBiopsyPaths/ProstateBiopsyPath/PathGG1");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "GLEASON_SCORE_1", node.getText()));
    }

    node = patientNode.selectSingleNode("Pathologies/Pathology/ProstateBiopsyPaths/ProstateBiopsyPath/PathGG2");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "GLEASON_SCORE_2", node.getText()));
    }

    node = patientNode.selectSingleNode("Pathologies/Pathology/ProstateBiopsyPaths/ProstateBiopsyPath/PathGGS");
    if (node != null) {
        clinicalData.add(new ClinicalData(cancerStudyId, patientId, "GLEASON_SCORE", node.getText()));
    }

    return clinicalData;
}

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static void parseMedicalTherapies(List<ClinicalEvent> clinicalEvents, Node patientNode,
        String patientId, int cancerStudyId) {
    List<Node> treatmentNodes = patientNode.selectNodes("MedicalTherapies/MedicalTherapy");

    for (Node treatmentNode : treatmentNodes) {
        Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudyId, patientId);
        ClinicalEvent clinicalEvent = new ClinicalEvent();
        clinicalEvent.setPatientId(patient.getInternalId());
        clinicalEvent.setEventType("TREATMENT");
        clinicalEvent.addEventDatum("TREATMENT_TYPE", "Medical Therapy");

        Node node = treatmentNode.selectSingleNode("MedTxDate");
        if (node == null) {
            System.err.println("no date");
            continue;
        }/*from w ww. ja v  a  2s  .com*/
        clinicalEvent.setStartDate(Long.parseLong(node.getText()));

        node = treatmentNode.selectSingleNode("MedTxStopDate");
        if (node != null) {
            clinicalEvent.setStopDate(Long.parseLong(node.getText()));
        }

        node = treatmentNode.selectSingleNode("MedTxType");
        if (node != null) {
            clinicalEvent.addEventDatum("SUBTYPE", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxIndication");
        if (node != null) {
            clinicalEvent.addEventDatum("INDICATION", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxAgent");
        if (node != null) {
            clinicalEvent.addEventDatum("AGENT", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxDose");
        if (node != null) {
            clinicalEvent.addEventDatum("DOSE", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxTotalDose");
        if (node != null) {
            clinicalEvent.addEventDatum("TOTAL_DOSE", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxUnits");
        if (node != null) {
            clinicalEvent.addEventDatum("UNIT", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxSchedule");
        if (node != null) {
            clinicalEvent.addEventDatum("SCHEDULE", node.getText());
        }

        node = treatmentNode.selectSingleNode("MedTxRoute");
        if (node != null) {
            clinicalEvent.addEventDatum("ROUTE", node.getText());
        }

        clinicalEvents.add(clinicalEvent);
    }
}

From source file:org.mskcc.cbio.portal.scripts.ImportCaisesClinicalXML.java

License:Open Source License

private static void parseRadiationTherapies(List<ClinicalEvent> clinicalEvents, Node patientNode,
        String patientId, int cancerStudyId) {
    List<Node> treatmentNodes = patientNode.selectNodes("RadiationTherapies/RadiationTherapy");

    for (Node treatmentNode : treatmentNodes) {
        Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(cancerStudyId, patientId);
        ClinicalEvent clinicalEvent = new ClinicalEvent();
        clinicalEvent.setPatientId(patient.getInternalId());
        clinicalEvent.setEventType("TREATMENT");
        clinicalEvent.addEventDatum("TREATMENT_TYPE", "Radiation Therapy");

        Node node = treatmentNode.selectSingleNode("RadTxDate");
        if (node == null) {
            System.err.println("no date");
            continue;
        }/*w w w.j av a 2s. c  o  m*/
        clinicalEvent.setStartDate(Long.parseLong(node.getText()));

        node = treatmentNode.selectSingleNode("RadTxStopDate");
        if (node != null) {
            clinicalEvent.setStopDate(Long.parseLong(node.getText()));
        }

        node = treatmentNode.selectSingleNode("RadTxType");
        if (node != null) {
            clinicalEvent.addEventDatum("SUBTYPE", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxIndication");
        if (node != null) {
            clinicalEvent.addEventDatum("INDICATION", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxIntent");
        if (node != null) {
            clinicalEvent.addEventDatum("INTENT", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxDosePerFraction");
        if (node != null) {
            clinicalEvent.addEventDatum("DOSE_PER_FRACTION", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxTotalDose");
        if (node != null) {
            clinicalEvent.addEventDatum("TOTAL_DOSE", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxUnits");
        if (node != null) {
            clinicalEvent.addEventDatum("UNIT", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxNumFractions");
        if (node != null) {
            clinicalEvent.addEventDatum("NUM_FRACTIONS", node.getText());
        }

        node = treatmentNode.selectSingleNode("RadTxTarget");
        if (node != null) {
            clinicalEvent.addEventDatum("TARGET", node.getText());
        }

        clinicalEvents.add(clinicalEvent);
    }
}