git-svn-id: http://svn.research-infrastructures.eu/public/d4science/gcube/trunk/data-analysis/nlphub@164578 82a268e6-3cf1-43bd-a215-b396298e98cf
This commit is contained in:
Erik Perrone
parent
75a08add56
commit
73ca1ce2eb
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@ -62,8 +62,10 @@ public class NLPMapper extends HttpServlet {
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}
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private void doWork(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
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token = Constants.getToken(request, devMode);
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response.setContentType("application/json");
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response.setCharacterEncoding("utf-8");
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token = Constants.getToken(request, devMode);
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String documentLink = request.getParameter("plink"); // link to text file (workspace)
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String toBeMap = request.getParameter("tobemap");
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System.out.println("tobemap: " + toBeMap);
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@ -74,12 +76,21 @@ public class NLPMapper extends HttpServlet {
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tokens = new String[1];
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tokens[0] = toBeMap;
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}
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System.out.println("token nr. : " + tokens.length);
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String annotations = request.getParameter("annotations");
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String language = request.getParameter("lang");
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PrintWriter writer = response.getWriter();
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try {
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String text = getDocument(documentLink);
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text = text.replaceAll("\n", "\\\\n");;
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text = text.replaceAll("\r", "\\\\r");
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text = text.replaceAll("\t", "\\\\t");
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text = text.replaceAll("\"", "\\\\\"");
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// byte[] b = text.getBytes();
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// System.out.println(Constants.hexDump(b));
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String out = "{";
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out += "\"text\":\"" + text + "\",";
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out += "\"annotations\":\"" + annotations + "\",";
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@ -154,4 +165,6 @@ public class NLPMapper extends HttpServlet {
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String link = ws.getPublicLink(fileName, token);
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return link;
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}
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}
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@ -8,6 +8,7 @@ import java.io.InputStream;
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import java.io.InputStreamReader;
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import java.io.OutputStream;
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import java.io.PrintWriter;
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import java.io.UnsupportedEncodingException;
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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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@ -78,7 +79,6 @@ public class NLPUploader extends HttpServlet {
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private void handleFreeText(HttpServletRequest request, HttpServletResponse response)
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throws ServletException, IOException {
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String freeText = request.getParameter("freetext");
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System.out.println(freeText);
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byte[] content = freeText.getBytes("UTF-8");
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String fileName = generateFileName();
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PrintWriter writer = response.getWriter();
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@ -111,7 +111,7 @@ public class NLPUploader extends HttpServlet {
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byte[] bufferedContent;
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try {
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InputStream fileContent = filePart.getInputStream();
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int offset = 0, len = 100, byteRead = 0;
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int offset = 0, len = 256, byteRead = 0;
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byte[] readBuffer = new byte[len];
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while (byteRead > -1) {
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byteRead = fileContent.read(readBuffer, 0, len);
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@ -157,141 +157,19 @@ public class NLPUploader extends HttpServlet {
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return null;
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}
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// private String getPublicLink(String fileName, String token) throws NlpHubException {
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// try {
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// String link = "";
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// String user = authorizationService().get(token).getClientInfo().getId();
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// String wsRoot = "/Home/" + user + "/Workspace/";
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// String webapp = "https://workspace-repository.d4science.org/home-library-webapp";
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// String uri = webapp + "/rest/GetPublicLink?absPath=" + URLEncoder.encode(wsRoot + fileName, "UTF-8")
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// + "&shortUrl=false";
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// URL url = new URL(uri);
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//
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// // System.out.println(uri);
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//
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// HttpURLConnection connection = (HttpURLConnection) url.openConnection();
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// connection.setRequestProperty(Constants.TOKEN_PARAMETER, token);
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// connection.setDoInput(true);
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// connection.setDoOutput(true);
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// connection.setUseCaches(false);
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// connection.setRequestMethod("GET");
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//
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// BufferedReader r = new BufferedReader(new InputStreamReader(connection.getInputStream()));
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//
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// StringBuffer response = new StringBuffer();
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// String inputLine;
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// while ((inputLine = r.readLine()) != null) {
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// response.append(inputLine);
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// }
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//
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// String xmlOut = response.toString();
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// // System.out.println("xmlOut: " + xmlOut);
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//
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// String begin = "<string>";
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// String end = "</string>";
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// int b = xmlOut.indexOf(begin);
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// int e = xmlOut.indexOf(end);
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//
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// if (xmlOut.contains("Exception") || (e < 0) || (b < 0)) {
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// String message = "Invalid link: " + URLEncoder.encode(xmlOut, "UTF-8");
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// logger.error(message);
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// throw new NlpHubException(message, null);
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// }
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//
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// link = xmlOut.substring(b + begin.length(), e);
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// return link;
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//
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// } catch (Exception e) {
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// logger.error(e.getLocalizedMessage());
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// throw new NlpHubException(e.getLocalizedMessage(), e);
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// }
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// }
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//
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// private void deleteFile(String fileName, String token) throws NlpHubException {
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// try {
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// String user = authorizationService().get(token).getClientInfo().getId();
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// String wsRoot = "/Home/" + user + "/Workspace/";
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// String webapp = "https://workspace-repository.d4science.org/home-library-webapp";
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// String uri = webapp + "/rest/Delete?absPath=" + URLEncoder.encode(wsRoot + fileName, "UTF-8");
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// URL url = new URL(uri);
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//
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// // System.out.println(uri);
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//
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// HttpURLConnection connection = (HttpURLConnection) url.openConnection();
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// connection.setRequestProperty(Constants.TOKEN_PARAMETER, token);
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// connection.setDoInput(true);
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// connection.setDoOutput(true);
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// connection.setUseCaches(false);
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// connection.setRequestMethod("GET");
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//
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// BufferedReader r = new BufferedReader(new InputStreamReader(connection.getInputStream()));
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//
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// StringBuffer response = new StringBuffer();
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// String inputLine;
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// while ((inputLine = r.readLine()) != null) {
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// response.append(inputLine);
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// }
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//
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// String xmlOut = response.toString();
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// // System.out.println(xmlOut);
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// } catch (Exception e) {
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// logger.error(e.getLocalizedMessage());
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// throw new NlpHubException(e.getLocalizedMessage(), e);
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// }
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// }
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//
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// private boolean uploadFile(byte[] in, String name, String description, String token) throws NlpHubException {
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// OutputStream output = null;
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// try {
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// String user = authorizationService().get(token).getClientInfo().getId();
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// String wsRoot = "/Home/" + user + "/Workspace/";
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// String webapp = "https://workspace-repository.d4science.org/home-library-webapp";
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// String uri = webapp + "/rest/Upload?name=" + URLEncoder.encode(name, "UTF-8") + "&description="
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// + URLEncoder.encode(description, "UTF-8") + "&parentPath=" + URLEncoder.encode(wsRoot, "UTF-8");
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// URL url = new URL(uri);
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//
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// // System.out.println(uri);
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//
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// HttpURLConnection connection = (HttpURLConnection) url.openConnection();
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// connection.setRequestProperty(Constants.TOKEN_PARAMETER, token);
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// connection.setDoInput(true);
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// connection.setDoOutput(true);
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// connection.setUseCaches(false);
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// connection.setRequestProperty(Constants.CONTENT_TYPE, Constants.MIME_TEXT);
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// connection.setRequestMethod("POST");
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// output = connection.getOutputStream();
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// output.write(in);
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//
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// BufferedReader r = new BufferedReader(new InputStreamReader(connection.getInputStream()));
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//
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// StringBuffer response = new StringBuffer();
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// String inputLine;
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// while ((inputLine = r.readLine()) != null) {
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// response.append(inputLine);
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// }
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//
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// String xmlOut = response.toString();
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// // System.out.println(xmlOut);
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// if (xmlOut.contains("Exception"))
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// return false;
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// return true;
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//
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// } catch (Exception e) {
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// logger.error(e.getLocalizedMessage());
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// throw new NlpHubException(e.getLocalizedMessage(), e);
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// } finally {
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// // output stream must be closed anyway...
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// if (output != null)
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// try {
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// output.close();
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// } catch (IOException e) {
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// logger.error(e.getLocalizedMessage());
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// }
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// }
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// }
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private String generateFileName() {
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long now = System.currentTimeMillis();
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return "auto-nlp-" + now;
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}
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private byte[] escapeForJson(byte[] content) throws UnsupportedEncodingException {
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String text = new String(content, "UTF-8");
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text = text.replaceAll("\n", "\\\n");
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text = text.replaceAll("\r", "\\\r");
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text = text.replaceAll("\t", "\\\t");
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text = text.replaceAll("\"", "\\\"");
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//text = text.replaceAll("\\", "\\\\");
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System.out.println("*** text\n" + text);
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return text.getBytes("UTF-8");
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}
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}
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@ -16,5 +16,23 @@ public class Constants {
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}
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return token;
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}
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public static String hexDump(byte[] bytes) {
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char[] hexArray = "0123456789ABCDEF".toCharArray();
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char[] hexChars = new char[bytes.length * 3];
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for (int j = 0; j < bytes.length; j++) {
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hexChars[3*j] = hexArray[bytes[j] / 16];
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hexChars[3*j+1] = hexArray[bytes[j] % 16];
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hexChars[3*j+2] = ' ';
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}
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return new String(hexChars);
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}
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/*
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public static void main(String[] args) {
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String text = "I am here in\nPisa.";
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System.out.println(text);
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System.out.println(hexDump(text.getBytes()));
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text = text.replaceAll("\n", "\\\\n");
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System.out.println(hexDump(text.getBytes()));
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}*/
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}
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@ -266,6 +266,10 @@ select {
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}
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}
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#result-text-div {
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overflow-y: auto;
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}
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/*
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input[type="checkbox"]:not(:checked){
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position: unset !important;
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@ -30,6 +30,7 @@
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var savedAnnotations = "";
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var jsonContent = null;
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var named = null;
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var resultText = "";
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// ------------------------------------------------------------------------------------------------------
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// Starting point: get the csv file with algorithm parameters and set the page with valid algs info.
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@ -43,12 +44,6 @@
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contentType : "text/plain; charset=utf-8",
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success : function(data, stato) {
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$("#ner-result-container").hide();
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// --------------------
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// the following 2 lines are only for develop
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//$("#ner-result-container").show();
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//$("#ner-ui").hide();
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// --------------------
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var lineTokens = manageCsvData(data);
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getAlgorithms(lineTokens);
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buildAnnotationsAndLanguages();
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@ -58,27 +53,29 @@
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$("#back-ner-ui-button").click(function() {
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$("#ner-result-container").hide();
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$("#ner-ui").show();
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$("#input-textarea").val("");
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publicLink = null;
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jsonContent = null;
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});
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// the following line is only for develop
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/*
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var devData = "{\"link\":\"http://data.d4science.org/Wm5XY1p0TlFIM3NXZnZ1SkhLRlRMK3l6N05jVFhiSXFHbWJQNStIS0N6Yz0\",\"output\":"
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+ "{\"text\":\"yes, we can do it tomorrow in the evening.\",\"annotations\":\"Date,Sentence\",\"language\":\"English\",\"result\":"
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+ "[{\"algorithm\":\"ENGLISH_NAMED_ENTITY_RECOGNIZER\",\"entities\":[{\"Date\":[{\"indices\":[18,26],\"ruleFinal\":\"DateOnlyFinal\",\"kind\":\"date\",\"rule\":\"GazDateWords\"}]},{\"Sentence\":[{\"indices\":[0,42]}]}]}]}}";
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var devData = "{\"link\":\"http://data.d4science.org/Wm5XY1p0TlFIM3NXZnZ1SkhLRlRMK3l6N05jVFhiSXFHbWJQNStIS0N6Yz0\",\"output\":"
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+ "{\"text\":\"yes, we can do it tomorrow in the evening.\",\"annotations\":\"Date,Sentence\",\"language\":\"English\",\"result\":"
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+ "[{\"algorithm\":\"ENGLISH_NAMED_ENTITY_RECOGNIZER\",\"entities\":[{\"Date\":[{\"indices\":[18,26],\"ruleFinal\":\"DateOnlyFinal\",\"kind\":\"date\",\"rule\":\"GazDateWords\"}]},{\"Sentence\":[{\"indices\":[0,42]}]}]}]}}";
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devData = "{\"link\":\"http://data.d4science.org/dXZ5L3RrRjYyTWNXZnZ1SkhLRlRMeXZzd1prOVFqWDFHbWJQNStIS0N6Yz0\",\"output\":"
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+ "{\"text\":\"In the 1970s, Iraq under Baath Party dictator Brigadier General Ahmad Hassan al-Bakr had grown close to the Soviet Union, "
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+ "with which it signed a treaty of friendship in 1972 and from which it began importing arms. In 1973, al-Bakr supported the Syrians in their war with Israel.\","
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+ "\"annotations\":\"Date,Person\",\"language\":\"English\",\"result\": [{\"algorithm\":\"ENGLISH_NAMED_ENTITY_RECOGNIZER\",\"entities\":[{\"Date\":[{\"indices\":[3,12],"
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+ "\"ruleFinal\":\"DateOnlyFinal\",\"kind\":\"date\",\"rule\":\"YearSpan1\"},{\"indices\":[169,173],\"ruleFinal\":\"DateOnlyFinal\",\"kind\":\"date\",\"rule\":\"YearContext1\"},"
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+ "{\"indices\":[217,221],\"ruleFinal\":\"YearOnlyFinal\",\"kind\":\"date\",\"rule\":\"TempYear2\"}]},{\"Person\":[{\"indices\":[46,76],\"firstName\":\"Ahmad\",\"ruleFinal\":\""
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+ "PersonFinal\",\"gender\":\"unknown\",\"surname\":\"Hassan\",\"kind\":\"personName\",\"rule\":\"PersonTitleGenderUnknown\",\"title\":\"Brigadier\"},{\"indices\":[77,84],\"firstName\":"
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+ "\"al\",\"ruleFinal\":\"PersonFinal\",\"gender\":\"male\",\"surname\":\"Bakr\",\"kind\":\"fullName\",\"rule\":\"PersonFull\"},{\"indices\":[223,230],\"firstName\":\"al\",\"ruleFinal\":\"PersonFinal\",\"gender\":\"male\",\"surname\":\"Bakr\",\"kind\":\"fullName\",\"rule\":\"PersonFull\"}]}]}]}}";
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showResult(devData);
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devData = "{\"link\":\"http://data.d4science.org/dXZ5L3RrRjYyTWNXZnZ1SkhLRlRMeXZzd1prOVFqWDFHbWJQNStIS0N6Yz0\",\"output\":"
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+ "{\"text\":\"In the 1970s, Iraq under Baath Party dictator Brigadier General Ahmad Hassan al-Bakr had grown close to the Soviet Union, "
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+ "with which it signed a treaty of friendship in 1972 and from which it began importing arms. In 1973, al-Bakr supported the Syrians in their war with Israel.\","
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+ "\"annotations\":\"Date,Person\",\"language\":\"English\",\"result\": [{\"algorithm\":\"ENGLISH_NAMED_ENTITY_RECOGNIZER\",\"entities\":[{\"Date\":[{\"indices\":[3,12],"
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+ "\"ruleFinal\":\"DateOnlyFinal\",\"kind\":\"date\",\"rule\":\"YearSpan1\"},{\"indices\":[169,173],\"ruleFinal\":\"DateOnlyFinal\",\"kind\":\"date\",\"rule\":\"YearContext1\"},"
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+ "{\"indices\":[217,221],\"ruleFinal\":\"YearOnlyFinal\",\"kind\":\"date\",\"rule\":\"TempYear2\"}]},{\"Person\":[{\"indices\":[46,76],\"firstName\":\"Ahmad\",\"ruleFinal\":\""
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+ "PersonFinal\",\"gender\":\"unknown\",\"surname\":\"Hassan\",\"kind\":\"personName\",\"rule\":\"PersonTitleGenderUnknown\",\"title\":\"Brigadier\"},{\"indices\":[77,84],\"firstName\":"
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+ "\"al\",\"ruleFinal\":\"PersonFinal\",\"gender\":\"male\",\"surname\":\"Bakr\",\"kind\":\"fullName\",\"rule\":\"PersonFull\"},{\"indices\":[223,230],\"firstName\":\"al\",\"ruleFinal\":\"PersonFinal\",\"gender\":\"male\",\"surname\":\"Bakr\",\"kind\":\"fullName\",\"rule\":\"PersonFull\"}]}]}]}}";
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showResult(devData);
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*/
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// --------------------------------------
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$("#execute-button").css("background-color", pageGray);
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$("#upload-button")
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@ -126,6 +123,7 @@
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onSelect : function(files) {
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showProgress();
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textAreaEnable(false);
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$("#input-textarea").val("");
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},
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onSuccess : function(files, data, xhr) {
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hideProgress();
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@ -155,7 +153,7 @@
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});
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},
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error : function(richiesta, stato, errori) {
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alert("Unexpected Error");
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alert("Unexpected Error. Status: " + richiesta.status);
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}
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});
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@ -298,7 +296,8 @@
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},
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error : function(richiesta, stato,
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errori) {
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alert("Unexpected Error");
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alert("Unexpected Error. Status: "
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+ richiesta.status);
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hideProgress();
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textAreaEnable(true);
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$("#file-info").empty();
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@ -370,7 +369,7 @@
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error : function(richiesta, stato, errori) {
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hideProgress();
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textAreaEnable(true);
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alert("Unexpected Error");
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alert("Unexpected Error. Status: " + richiesta.status);
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resetExecuteButton();
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}
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});
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@ -404,7 +403,7 @@
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$("#reset-upload").hide();
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savedAnnotations = "";
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publicLink = null;
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alert("Unexpected Error");
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alert("Unexpected Error. Status: " + richiesta.status);
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}
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});
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}
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@ -413,7 +412,11 @@
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$("#ner-ui").hide();
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$("#ner-result-container").show();
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jsonContent = JSON.parse(purgeJson(data));
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jsonContent = data;
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//jsonContent = JSON.parse(purgeJson(data));
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//resultText = jsonToText(jsonContent.output.text);
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resultText = jsonContent.output.text;
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$("#result-header").empty();
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$("#result-params-div").empty();
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@ -422,26 +425,26 @@
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$("#result-header")
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.append(
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"<p>You can download the result file from <a href='" + jsonContent.link +"'>here</a></p>");
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$("#result-text-div").append("<p>" + jsonContent.output.text + "</p>");
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var localText = resultText;
|
||||
localText = resultText.replace(/\n/g, "<br>");
|
||||
$("#result-text-div").empty();
|
||||
$("#result-text-div").append("<p>" + localText + "</p>");
|
||||
|
||||
showAnnotationList(jsonContent.output.annotations);
|
||||
}
|
||||
|
||||
showAnnotationList = function(list) {
|
||||
/*var colors = [ "ef2c23", "9c62de", "61de6c", "de61d2", "dec062",
|
||||
"23efde", "232bde" ];*/
|
||||
|
||||
var colors = [];
|
||||
var colors = [];
|
||||
var annotations = list.split(",");
|
||||
for(var i=0; i<annotations.length; i++) {
|
||||
for (var i = 0; i < annotations.length; i++) {
|
||||
colors[colors.length] = randomRGB();
|
||||
}
|
||||
|
||||
|
||||
$("#result-params-div")
|
||||
.append("<form id='colored-annotations'></form>");
|
||||
for (var i = 0; i < annotations.length; i++) {
|
||||
var cb = "<input type='radio' name='foo' named='" + annotations[i] + "' value='" + colors[i] + "' id='color-" + i + "' class='filled-in'>";
|
||||
cb += "<label for='color-" + i + "'><span style='color:#" + colors[i] + "'>"
|
||||
cb += "<label for='color-" + i + "'><span style='font-weight:bold; color:#" + colors[i] + "'>"
|
||||
+ annotations[i] + "</span></label><br>";
|
||||
$("#colored-annotations").append(cb);
|
||||
}
|
||||
|
|
@ -452,29 +455,57 @@
|
|||
});
|
||||
}
|
||||
|
||||
countSubstringOccurrencies = function(string, substring) {
|
||||
var occurrencies = 0;
|
||||
var index = 0;
|
||||
var s = string;
|
||||
while(index >= 0) {
|
||||
index = s.indexOf(substring);
|
||||
if(index >= 0) {
|
||||
occurrencies++;
|
||||
s = s.substring(index + 1);
|
||||
}
|
||||
}
|
||||
return occurrencies;
|
||||
}
|
||||
|
||||
rewriteText = function(annotation, color) {
|
||||
$("#result-text-div").empty();
|
||||
console.log(annotation + " " + color);
|
||||
var complement = "#" + (0xFFFFFF - eval("0x" + color.substring(1))).toString(16);
|
||||
complement = "#FAFAFA";
|
||||
var complement = "#"
|
||||
+ (0xFFFFFF - eval("0x" + color.substring(1))).toString(16);
|
||||
complement = "#F0F0F0";
|
||||
var indices = getIndices(annotation);
|
||||
var indexedText = "";
|
||||
|
||||
if (indices.length == 0)
|
||||
if (indices.length == 0) {
|
||||
indexedText = resultText;
|
||||
indexedText = indexedText.replace(/\n/g, "<br>");
|
||||
$("#result-text-div").append("<p>" + indexedText + "</p>");
|
||||
return;
|
||||
}
|
||||
|
||||
var t = 0;
|
||||
var offset = 0;
|
||||
for (var i = 0; i < indices.length; i++) {
|
||||
var index = indices[i];
|
||||
var start = index[0];
|
||||
var end = index[1];
|
||||
indexedText += jsonContent.output.text.substring(t, start);
|
||||
indexedText += resultText.substring(t, start);
|
||||
offset += countSubstringOccurrencies(resultText.substring(t, start), "\n");
|
||||
offset += countSubstringOccurrencies(resultText.substring(t, start), "\r");
|
||||
offset += countSubstringOccurrencies(resultText.substring(t, start), "\t");
|
||||
start += offset;
|
||||
end += offset;
|
||||
var colored = "<span style='color:" + color + "; background:" + complement + "; font-weight:bold;'>"
|
||||
+ jsonContent.output.text.substring(start, end) + "</span>";
|
||||
+ resultText.substring(start, end) + "</span>";
|
||||
indexedText += colored;
|
||||
t = end;
|
||||
}
|
||||
if (t < jsonContent.output.text.length)
|
||||
indexedText += jsonContent.output.text.substring(t);
|
||||
$("#result-text-div").empty();
|
||||
if (t < resultText.length)
|
||||
indexedText += resultText.substring(t);
|
||||
|
||||
indexedText = indexedText.replace(/\n/g, "<br>");
|
||||
$("#result-text-div").append("<p>" + indexedText + "</p>");
|
||||
}
|
||||
|
||||
|
|
@ -587,16 +618,36 @@
|
|||
}
|
||||
|
||||
purgeJson = function(json) {
|
||||
return json.replace("\n", "");
|
||||
console.log("purgeJson:before: " + json.length);
|
||||
var purged = json.replace(/\n/g, "\\\\n").replace(/\r/g, "\\\\r")
|
||||
.replace(/\t/g, "\\\\t");
|
||||
console.log("purgeJson:after : " + purged.length);
|
||||
return purged;
|
||||
}
|
||||
|
||||
jsonToText = function(json) {
|
||||
console.log("jsonToText:before: " + json.length);
|
||||
var purged = json.replace(/\\n/g, "");
|
||||
console.log("jsonToText:after : " + purged.length);
|
||||
return purged;
|
||||
//return json.replace(/\\n/g, "\n");
|
||||
}
|
||||
|
||||
randomRGB = function() {
|
||||
var letters = '0123456789ABCDEF';
|
||||
var color = '';
|
||||
for (var i = 0; i < 6; i++) {
|
||||
color += letters[Math.floor(Math.random() * 16)];
|
||||
}
|
||||
return color;
|
||||
var color = '';
|
||||
var couple = '';
|
||||
for(var i=0; i < 3; i++) {
|
||||
do {
|
||||
couple = '';
|
||||
for(j=0; j<2; j++) {
|
||||
couple += letters[Math.floor(Math.random() * 16)];
|
||||
}
|
||||
} while((255 - parseInt("0x" + couple)) < 48)
|
||||
color += couple;
|
||||
}
|
||||
|
||||
return color;
|
||||
}
|
||||
</script>
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue