// Path: core/src/main/java/org/mskcc/cbio/oncokb/util/FileUtils.java
// public class FileUtils {
//     private FileUtils() {
//         throw new AssertionError();
//     }
// 
//     /**
//      * read local files and return content
//      * @param pathToFile
//      * @return
//      * @throws IOException
//      */
//     public static String readLocal(String pathToFile) throws IOException {
//         return readStream(new FileInputStream(pathToFile));
//     }
// 
//     /**
//      * return remote files and return content
//      * @param urlToFile
//      * @return
//      * @throws IOException
//      */
//     public static String readRemote(String urlToFile) throws IOException {
//         URL url = new URL(urlToFile);
//         return readStream(url.openStream());
//     }
// 
//     public static String readMSKPortal(String urlToFile) throws IOException {
//         URL myURL = new URL(urlToFile);
//         HttpURLConnection myURLConnection = (HttpURLConnection)myURL.openConnection();
//         myURLConnection.setRequestProperty ("Authorization", "Bearer " + PropertiesUtils.getProperties("cbioportal.token"));
//         myURLConnection.setRequestMethod("GET");
//         return readStream(myURLConnection.getInputStream());
//     }
// 
//     public static String readPublicOncoKBRemote(String urlToFile) throws IOException {
//         URL myURL = new URL(urlToFile);
//         HttpURLConnection myURLConnection = (HttpURLConnection)myURL.openConnection();
//         myURLConnection.setRequestProperty ("Authorization", "Bearer " + PropertiesUtils.getProperties("public_oncokb.token"));
//         myURLConnection.setRequestMethod("GET");
//         return readStream(myURLConnection.getInputStream());
//     }
// 
//     /**
//      * read a stream and return content
//      * @param is
//      * @return
//      * @throws IOException
//      */
//     public static String readStream(InputStream is) throws IOException {
//         List<String> lines = readTrimedLinesStream(is);
//         return StringUtils.join(lines, "\n");
//     }
// 
//     public static List<String> readTrimedLinesStream(InputStream is) throws IOException {
//         return readLinesStream(is, true);
//     }
// 
//     /**
//      * read a stream and return lines
//      * @param is
//      * @return
//      * @throws IOException
//      */
//     public static List<String> readLinesStream(InputStream is, boolean trim) throws IOException {
//         BufferedReader in = new BufferedReader(new InputStreamReader(is, "UTF-8"));
// 
//         List<String> lines = new ArrayList<String>();
//         String line;
//         while ((line = in.readLine()) != null) {
//             if (trim) {
//                 line = line.trim();
//             }
//             if (!line.isEmpty())
//                 lines.add(line);
//         }
//         in.close();
// 
//         return lines;
//     }
// 
//     public static String getFileName(FileName fileName, FileExtension fileExtension) {
//         return fileName.getName() + fileExtension.getExtension();
//     }
// }


import org.mskcc.cbio.oncokb.model.Gene;
import org.mskcc.cbio.oncokb.util.ApplicationContextSingleton;
import org.mskcc.cbio.oncokb.util.FileUtils;
import org.mskcc.cbio.oncokb.util.GeneUtils;
import java.io.IOException;
import java.util.List;
package org.mskcc.cbio.oncokb.importer;


public class ChangeHugoSymbol {
    private ChangeHugoSymbol() {
        throw new AssertionError();
    }

    private static final String CHANGE_HUGO_FILE = "/data/change-hugo-symbol.txt";

    public static void main(String[] args) throws IOException {

// Path: core/src/main/java/org/mskcc/cbio/oncokb/util/FileUtils.java
// public class FileUtils {
//     private FileUtils() {
//         throw new AssertionError();
//     }
// 
//     /**
//      * read local files and return content
//      * @param pathToFile
//      * @return
//      * @throws IOException
//      */
//     public static String readLocal(String pathToFile) throws IOException {
//         return readStream(new FileInputStream(pathToFile));
//     }
// 
//     /**
//      * return remote files and return content
//      * @param urlToFile
//      * @return
//      * @throws IOException
//      */
//     public static String readRemote(String urlToFile) throws IOException {
//         URL url = new URL(urlToFile);
//         return readStream(url.openStream());
//     }
// 
//     public static String readMSKPortal(String urlToFile) throws IOException {
//         URL myURL = new URL(urlToFile);
//         HttpURLConnection myURLConnection = (HttpURLConnection)myURL.openConnection();
//         myURLConnection.setRequestProperty ("Authorization", "Bearer " + PropertiesUtils.getProperties("cbioportal.token"));
//         myURLConnection.setRequestMethod("GET");
//         return readStream(myURLConnection.getInputStream());
//     }
// 
//     public static String readPublicOncoKBRemote(String urlToFile) throws IOException {
//         URL myURL = new URL(urlToFile);
//         HttpURLConnection myURLConnection = (HttpURLConnection)myURL.openConnection();
//         myURLConnection.setRequestProperty ("Authorization", "Bearer " + PropertiesUtils.getProperties("public_oncokb.token"));
//         myURLConnection.setRequestMethod("GET");
//         return readStream(myURLConnection.getInputStream());
//     }
// 
//     /**
//      * read a stream and return content
//      * @param is
//      * @return
//      * @throws IOException
//      */
//     public static String readStream(InputStream is) throws IOException {
//         List<String> lines = readTrimedLinesStream(is);
//         return StringUtils.join(lines, "\n");
//     }
// 
//     public static List<String> readTrimedLinesStream(InputStream is) throws IOException {
//         return readLinesStream(is, true);
//     }
// 
//     /**
//      * read a stream and return lines
//      * @param is
//      * @return
//      * @throws IOException
//      */
//     public static List<String> readLinesStream(InputStream is, boolean trim) throws IOException {
//         BufferedReader in = new BufferedReader(new InputStreamReader(is, "UTF-8"));
// 
//         List<String> lines = new ArrayList<String>();
//         String line;
//         while ((line = in.readLine()) != null) {
//             if (trim) {
//                 line = line.trim();
//             }
//             if (!line.isEmpty())
//                 lines.add(line);
//         }
//         in.close();
// 
//         return lines;
//     }
// 
//     public static String getFileName(FileName fileName, FileExtension fileExtension) {
//         return fileName.getName() + fileExtension.getExtension();
//     }
// }


// Path: core/src/main/java/org/mskcc/cbio/oncokb/importer/ChangeHugoSymbol.java
import org.mskcc.cbio.oncokb.model.Gene;
import org.mskcc.cbio.oncokb.util.ApplicationContextSingleton;
import org.mskcc.cbio.oncokb.util.FileUtils;
import org.mskcc.cbio.oncokb.util.GeneUtils;
import java.io.IOException;
import java.util.List;

package org.mskcc.cbio.oncokb.importer;


public class ChangeHugoSymbol {
    private ChangeHugoSymbol() {
        throw new AssertionError();
    }

    private static final String CHANGE_HUGO_FILE = "/data/change-hugo-symbol.txt";

    public static void main(String[] args) throws IOException {

        List<String> lines = FileUtils.readTrimedLinesStream(