212 lines
7.5 KiB
Java
212 lines
7.5 KiB
Java
package org.gcube.data.analysis.nlphub.nlp;
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import java.io.BufferedReader;
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import java.io.ByteArrayInputStream;
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import java.io.InputStreamReader;
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import java.net.HttpURLConnection;
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import java.net.URL;
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import java.net.URLEncoder;
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import java.nio.charset.StandardCharsets;
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import java.util.ArrayList;
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import javax.xml.parsers.DocumentBuilderFactory;
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import org.gcube.data.analysis.nlphub.is.DMDiscover;
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import org.gcube.data.analysis.nlphub.legacy.AsyncHttpRequest;
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import org.gcube.data.analysis.nlphub.shared.Constants;
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import org.slf4j.Logger;
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import org.slf4j.LoggerFactory;
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import org.w3c.dom.Document;
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import org.w3c.dom.Node;
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import org.w3c.dom.NodeList;
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import org.xml.sax.InputSource;
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public class NlpAsyncNerRunner extends AsyncHttpRequest {
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private static final Logger logger = LoggerFactory.getLogger(NlpAsyncNerRunner.class);
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public static final String WPS_EXECUTE_URL = "?request=Execute&service=WPS&Version=1.0.0";
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public static final String WPS_DESCRIBE_PROCESS_URL = "?request=DescribeProcess&service=WPS&Version=1.0.0";
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// private String identifier, token, httpMethod, annotations, publicLink,
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// dataMiner;
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private String identifier;
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private RunnerCommander commander;
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public NlpAsyncNerRunner(String dataMiner, String identifier, String token, String publicLink, String annotations,
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String language, RunnerCommander commander) throws Exception {
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super();
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this.commander = commander;
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this.identifier = identifier;
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String httpMethod = "GET";
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if (dataMiner == null || dataMiner.isEmpty()) {
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try {
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DMDiscover discoverDataMinerService = new DMDiscover();
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dataMiner = discoverDataMinerService.retrieveServiceUrl(token);
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} catch (Exception e) {
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logger.error("Error retrieving DataMiner service:" + e.getMessage(), e);
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throw new Exception("Error retrieving DataMiner service:" + e.getMessage());
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}
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}
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// else
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// this.dataMiner = "http://" + dataMiner;
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logger.debug("NlpAsyncNerRunner: Create Excution Request");
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logger.debug("NlpAsyncNerRunner: [identifier=" + identifier + ", httpMethod=" + httpMethod + ", annotations="
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+ annotations + ", publicLink=" + publicLink + ", dataminer=" + dataMiner + "]");
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ArrayList<NlpParameter> params = buildParameterString(dataMiner, identifier, publicLink, annotations, token);
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StringBuilder serviceUrl = new StringBuilder();
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serviceUrl.append(dataMiner);
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serviceUrl.append(WPS_EXECUTE_URL);
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serviceUrl.append("&lang=en-US&Identifier=");
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serviceUrl.append(identifier);
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serviceUrl.append("&");
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serviceUrl.append(setParams(params));
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serviceUrl.append("&gcube-token=" + token);
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logger.debug("NlpAsyncNerRunner: [serviceUrl=" + serviceUrl + ", method=" + httpMethod + "]");
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super.setBaseUrl(serviceUrl.toString());
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super.setMethod(httpMethod);
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}
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/*
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* public NlpAsyncNerRunner(String baseUrl, String method) { super(baseUrl,
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* method, null); }
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*/
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/*
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* public String getIdentifier() { return identifier; }
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*
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*
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* public String getToken() { return token; }
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*
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* public String getHttpMethod() { return httpMethod; }
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*/
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private String setParams(ArrayList<NlpParameter> parameters) {
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logger.debug("Set Params");
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String url = "DataInputs=";
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for (NlpParameter p : parameters) {
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try {
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url += p.getName() + "=" + URLEncoder.encode((String) p.getValue(), "UTF-8") + ";";
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} catch (Exception ex) {
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logger.error(ex.getLocalizedMessage());
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}
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}
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return url;
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}
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private ArrayList<NlpParameter> buildParameterString(String dataMiner, String identifier, String publicLink,
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String annotations, String token) {
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ArrayList<NlpParameter> parameters = new ArrayList<>();
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HttpURLConnection connection = null;
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BufferedReader r = null;
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try {
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StringBuilder serviceUrl = new StringBuilder();
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serviceUrl.append(dataMiner);
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serviceUrl.append(WPS_DESCRIBE_PROCESS_URL);
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serviceUrl.append("&lang=en-US&Identifier=");
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serviceUrl.append(identifier);
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logger.debug("DescribeProcess Requested: " + serviceUrl);
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serviceUrl.append("&gcube-token=");
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serviceUrl.append(token);
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URL url = new URL(serviceUrl.toString());
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connection = (HttpURLConnection) url.openConnection();
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connection.setRequestMethod("GET");
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connection.setDoInput(true);
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connection.setDoOutput(false);
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connection.setUseCaches(false);
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r = new BufferedReader(new InputStreamReader(connection.getInputStream()));
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Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new InputSource(r));
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doc.getDocumentElement().normalize();
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NodeList nListInput = doc.getElementsByTagName("Input");
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for (int i = 0; i < nListInput.getLength(); i++) {
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Node nodeInput = nListInput.item(i);
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NlpParameter nlpParam = new NlpParameter();
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NodeList inputChildren = nodeInput.getChildNodes();
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// try to find the name and the type of the input parameter
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for (int j = 0; j < inputChildren.getLength(); j++) {
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Node node = inputChildren.item(j);
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// for the moment we limit the type at 'file' and
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// 'annotations'
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if (node.getNodeName().equals("ows:Identifier")) {
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nlpParam.setName(node.getTextContent());
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} else if (node.getNodeName().equals("ows:Title")) {
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nlpParam.setDescription(node.getTextContent());
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} else if (node.getNodeName().equals("ows:Abstract")) {
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String text = node.getTextContent().toLowerCase();
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if ((text.indexOf("file") >= 0) || (text.indexOf("text") >= 0)) {
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nlpParam.setObjectType(NlpParameter.INPUT_FILE);
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nlpParam.setValue(publicLink);
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} else if ((text.indexOf("annotation") >= 0) || (text.indexOf("list") >= 0)) {
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nlpParam.setObjectType(NlpParameter.INPUT_ANNOTATIONS);
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nlpParam.setValue(annotations.replaceAll(",", "|"));
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}
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}
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}
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parameters.add(nlpParam);
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}
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} catch (Exception e) {
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logger.error("NlpAsyncNerRunner buildParameterString: " + e.getLocalizedMessage(), e);
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} finally {
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try {
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if (r != null)
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r.close();
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if (connection != null)
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connection.disconnect();
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} catch (Exception e) {
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logger.error(e.getLocalizedMessage(), e);
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}
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}
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return parameters;
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}
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public long getElapsedTime() {
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return elapsedTime;
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}
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@Override
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public void asyncHttpRequestCallback() {
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elapsedTime = System.currentTimeMillis() - elapsedTime;
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logger.debug("ID: " + identifier.substring(identifier.lastIndexOf(".") + 1) + " elapsed time: " + elapsedTime);
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String result = super.getResult();
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String theLink = "";
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try {
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BufferedReader r = new BufferedReader(
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new InputStreamReader(new ByteArrayInputStream(result.getBytes(StandardCharsets.UTF_8))));
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Document doc = DocumentBuilderFactory.newInstance().newDocumentBuilder().parse(new InputSource(r));
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doc.getDocumentElement().normalize();
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NodeList nListResult = doc.getElementsByTagName("ogr:Result");
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for (int i = 0, found = 0; (i < nListResult.getLength()) && (found == 0); i++) {
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Node nodeResult = nListResult.item(i);
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NodeList list = nodeResult.getChildNodes();
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String res = "";
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for (int j = 0; j < list.getLength(); j++) {
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Node node = list.item(j);
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if (node.getNodeName().equals("d4science:Data")) {
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res = node.getTextContent();
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} else if (node.getNodeName().equals("d4science:MimeType")) {
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if (node.getTextContent().equals("application/d4science")) {
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found = 1;
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}
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}
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}
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if (found > 0) {
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theLink = res;
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}
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}
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commander.updateResultList(identifier.substring(identifier.lastIndexOf(".") + 1) + ":::" + theLink);
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} catch (Exception e) {
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commander.updateResultList(
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identifier.substring(identifier.lastIndexOf(".") + 1) + ":::" + Constants.ERROR_ID);
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logger.error(e.getLocalizedMessage(), e);
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}
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}
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}
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