CrashRevovery.java

package gov.lanl.application.TPTD.applet;

import gov.lanl.application.treeDecorator.applet.communication.TreeDecoratorCommunication;
import gov.lanl.application.treeDecorator.dataStructures.DecoratorTable;
import gov.lanl.application.treeDecorator.enumeration.DecorationEnumHelper;
import gov.lanl.application.treePruner.applet.TreePrunerCommunication;
import gov.lanl.application.treePruner.applet.TreePrunerCommunicationNames;
import gov.lanl.application.treePruner.custom.data.WorkingSet;

import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStreamReader;
import java.net.HttpURLConnection;
import java.net.MalformedURLException;
import java.net.URL;
import java.util.ArrayList;

import org.json.JSONArray;
import org.json.JSONException;
import org.json.JSONObject;
import org.json.JSONTokener;



public class CrashRevovery {
	ArrayList<String> crashRecoveryAccessions = new ArrayList<String>();
	WorkingSet ws = new WorkingSet();
	URL savedAccURL;
	String TPgetURL = AppletParams.URLprefix + "/id/"+AppletParams.filename;
	public void treePrunerCrashRecoveryInit() {
		String TPgetJSON = "";
		JSONObject crashRecoveryJO;
		JSONArray recoveredAccessions = null;
		// String savedAcc = "file:////Users/kmohan/Desktop/2.txt";
		if(AppletParams.isTreePrunerForBHB()){
			TreePrunerCommunication.lockWSComm();
		}
		if (AppletParams.savedAccFlag.equals("true")) {
			// wait till all the nodes have been successfully painted on the
			// applet. After 2 secs hoping that all tree branches would have
			// successfully painted by then
			// we will call the crash recovery and repaint the tree(see below).
			// START
			long wait, time;
			wait = System.currentTimeMillis();
			while (true) {
				time = System.currentTimeMillis() - wait;
				if (time >= 2000) // 2 seconds wait
					break;
			}
			// wait till all the nodes have been successfully painted on the
			// applet. After 2 secs hoping that all tree branches would have
			// successfully painted by then
			// we will call the crash recovery and repaint the tree (see below).
			// END
			System.out.println("TPGetURL");
			System.out.println(TPgetURL);
			try {
				savedAccURL = new URL(TPgetURL);
				HttpURLConnection crashRecConn = (HttpURLConnection) savedAccURL.openConnection();
				crashRecConn.setRequestMethod("GET");
				BufferedReader rd;
				crashRecConn.setDoInput (true);
		        rd = new BufferedReader(new InputStreamReader(crashRecConn.getInputStream()));
		        String line;
		        while ((line = rd.readLine()) != null) {
		        	TPgetJSON += line; 
		        }
		        rd.close();
		        crashRecConn.disconnect();
		        
		        if(!TPgetJSON.equals("")){
		        	JSONTokener jt = new JSONTokener(TPgetJSON);
		        	crashRecoveryJO = new JSONObject(jt);
		        	System.out.println("IncomingJSONString");
		        	System.out.println(crashRecoveryJO.toString(2));
		        	JSONObject innerJO = crashRecoveryJO.getJSONObject(TreePrunerCommunicationNames.PRUNER.getName());
		        	recoveredAccessions = innerJO.getJSONArray(TreePrunerCommunicationNames.SEQ_ACC_TO_REMOVE.getName());
		        	for (int i = 0; i < recoveredAccessions.length(); i++) {
		    			crashRecoveryAccessions.add(recoveredAccessions.getString(i));
		    		}
		        }
		        else {
		        	throw new IOException();
		        }
			} catch (MalformedURLException e1) {
				e1.printStackTrace();
			} catch (IOException e) {
				System.err.println("Unable to read from file of saved accession");
				e.printStackTrace();
			} catch (JSONException e) {
				System.err.println("JSON Exception has occured");
				e.printStackTrace();
			}
			ws.crashRecovery(crashRecoveryAccessions);
			TreePrunerCommunication.lastAction = TreePrunerCommunicationNames.SAVE.getName();
			ws.copyAccToRememberAcc();
			ws.clear("removeActive");
			// Repaint the tree. START
			SubTreePanel.refreshAllWindows();
			// atvappletframe.getATVpanel().getATVtreePanel().repaint();
			// Repaint the tree. END
		} // end of if(saved_session_before.equals("true")){
	} // end of crashRecoveryInit
	
	public void treeDecoratorCrashRecoveryInit(){
		if (AppletParams.savedAccFlag.equals("true")) {
			// wait till all the nodes have been successfully painted on the
			// applet. After 2 secs hoping that all tree branches would have
			// successfully painted by then
			// we will call the crash recovery and repaint the tree(see below).
			// START
			long wait, time;
			wait = System.currentTimeMillis();
			while (true) {
				time = System.currentTimeMillis() - wait;
				if (time >= 2000) // 2 seconds wait
					break;
			}
			// wait till all the nodes have been successfully painted on the
			// applet. After 2 secs hoping that all tree branches would have
			// successfully painted by then
			// we will call the crash recovery and repaint the tree (see below).
			// END
			AutoSave.resetAutoSave();
			TreeDecoratorCommunication.getSavedDecorationsComm();
			DecoratorTable.copyStuffToSavedStuff();
			DecorationEnumHelper.populateBranchColorNodes();
			DecoratorTable.updateLegend();
			//refresh all windows
			SubTreePanel.refreshAllWindows();
			//	print(DecoratorTable.decoratorTable);
		}
	}
}