/*
 *
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 *
 *   http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 *
*/
package org.apache.airavata.gsi.ssh.impl;

import com.jcraft.jsch.Channel;
import com.jcraft.jsch.ChannelExec;
import org.apache.airavata.gsi.ssh.api.CommandOutput;

import java.io.ByteArrayOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;

public class StandardOutReader implements CommandOutput {

    String stdOutputString = null;
    ByteArrayOutputStream errorStream = new ByteArrayOutputStream();
    public void onOutput(Channel channel) {
        try {
            StringBuffer pbsOutput = new StringBuffer("");
            InputStream inputStream =  channel.getInputStream();
            byte[] tmp = new byte[1024];
            while (true) {
                while (inputStream.available() > 0) {
                    int i = inputStream.read(tmp, 0, 1024);
                    if (i < 0) break;
                    pbsOutput.append(new String(tmp, 0, i));
                }
                if (channel.isClosed()) {
                    String output = pbsOutput.toString();
                    this.setStdOutputString(output);
                    break;
                }
                try {
                } catch (Exception ignored) {
                }
            }
        } catch (IOException e) {
            e.printStackTrace();
        }

    }


    public void exitCode(int code) {
        System.out.println("Program exit code - " + code);
    }

    public String getStdOutputString() {
        return stdOutputString;
    }

    public void setStdOutputString(String stdOutputString) {
        this.stdOutputString = stdOutputString;
    }

    public String getStdErrorString() {
        return errorStream.toString();
    }

    public OutputStream getStandardError() {
        return errorStream;
    }
}

@@ -917,16 +917,17 @@
 elExec;%0A
+%0A
 import o
@@ -1377,16 +1377,126 @@
 er(%22%22);%0A
+            try %7B%0A%09%09%09%09Thread.sleep(1000);%0A%09%09%09%7D catch (InterruptedException e) %7B%0A%09%09%09%09e.printStackTrace();%0A%09%09%09%7D%0A
         

fix AIRAVATA-1346