Merge pull request #23 from MesquiteProject/development

v3.11 pull request development into master

Source/mesquite/zephyr/IQTreeRunnerCIPRes/IQTreeRunnerCIPRes.java

@@ -365,7 +365,7 @@ public Class getDutyClass() {
 	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.
 	 * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/
 	public int getVersionOfFirstRelease(){
-		return -100;  
+		return -3100;  
 	}
 
 	public String getName() {

Source/mesquite/zephyr/IQTreeRunnerSSH/IQTreeRunnerSSH.java

@@ -58,6 +58,10 @@ public Class getExternalProcessRunnerClass(){
 		return SSHRunner.class;
 	}
 
+	/*.................................................................................................................*/
+	public void reportNewTreeAvailable(){
+		log("[New tree acquired]");
+ 	}
 
 	/*.................................................................................................................*/
 	public  String queryOptionsDialogTitle() {
@@ -69,7 +73,7 @@ public  String queryOptionsDialogTitle() {
 	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.
 	 * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/
 	public int getVersionOfFirstRelease(){
-		return -2500;  
+		return -3000;  
 	}
 
 	public String getName() {

Source/mesquite/zephyr/LocalScriptRunner/LocalScriptRunner.java

@@ -22,6 +22,7 @@
 import mesquite.zephyr.lib.*;
 
 public class LocalScriptRunner extends ScriptRunner implements ActionListener, ItemListener, OutputFileProcessor, ShellScriptWatcher {
+
 	ExternalProcessManager externalRunner;
 	ShellScriptRunner scriptRunner;
 
@@ -36,7 +37,6 @@ public class LocalScriptRunner extends ScriptRunner implements ActionListener, I
 
 	StringBuffer extraPreferences;
 	boolean deleteAnalysisDirectory = false;
-	boolean leaveAnalysisDirectoryIntact = false;
 
 	/*.================================================================..*/
 	public boolean startJob(String arguments, Object condition, boolean hiredByName) {

Source/mesquite/zephyr/PAUPLikelihoodRunnerSSH/PAUPLikelihoodRunnerSSH.java

@@ -34,6 +34,10 @@ public String getExternalProcessRunnerModuleName(){
 	public Class getExternalProcessRunnerClass(){
 		return SSHRunner.class;
 	}
+	/*.................................................................................................................*/
+	public void reportNewTreeAvailable(){
+		log("[New tree acquired]");
+ 	}
 
 	/*.................................................................................................................*/
 

Source/mesquite/zephyr/RAxMLRunnerSSH/RAxMLRunnerSSH.java

@@ -44,6 +44,12 @@ public Class getExternalProcessRunnerClass(){
 	public String getTestedProgramVersions(){
 		return "8.2.10";
 	}
+
+	/*.................................................................................................................*/
+	public void reportNewTreeAvailable(){
+		log("[New tree acquired]");
+ 	}
+
 
 	public String getLogText() {
 		String log= externalProcRunner.getStdOut();
@@ -95,7 +101,7 @@ public String[] modifyOutputPaths(String[] outputFilePaths){
 	 * then the number refers to the Mesquite version.  This should be used only by modules part of the core release of Mesquite.
 	 * If a NEGATIVE integer, then the number refers to the local version of the package, e.g. a third party package*/
 	public int getVersionOfFirstRelease(){
-		return -2500;  
+		return -3000;  
 	}
 
 	public String getName() {

Source/mesquite/zephyr/SSHRunner/SSHRunner.java

@@ -82,12 +82,6 @@ public void setForgetPassword(boolean forgetPassword){
 	}
 
 
-	public String getMessageIfUserAbortRequested () {
-		return "Do you wish to stop the analysis conducted via SSH?  No intermediate trees will be saved if you do.";
-	}
-	public String getMessageIfCloseFileRequested () {  
-		return "If Mesquite closes this file, it will not stop the run on the server.  To stop the run on the server, press the \"Stop\" link in the analysis window before closing.";  
-	}
 
 	public  boolean canCalculateTimeRemaining(int repsCompleted){
 		if (communicator!=null)
@@ -184,6 +178,12 @@ public Object doCommand(String commandName, String arguments, CommandChecker che
 		if (checker.compare(this.getClass(), "Sets the sshServerProfile", "[file path]", commandName, "setServerProfileName")) {
 			String sshServerProfileName = parser.getFirstToken(arguments);
 			sshServerProfile = sshServerProfileManager.getSSHServerProfile(sshServerProfileName);
+			if (sshServerProfile==null) {
+				logln("***********************************");
+				logln(" WARNING  ");
+				logln("SSH Server Profile \"" + sshServerProfileName + "\" could not be found");
+				logln("***********************************");
+			}
 			return sshServerProfile;
 		} else if (checker.compare(this.getClass(), "Revives the communicator", "[file path]", commandName, "reviveCommunicator")) {
 			logln("Reviving SSH Communicator");
@@ -500,6 +500,7 @@ private boolean prepareCommunicator(boolean hasBeenReconnected, String userName)
 		communicator.setHasBeenReconnected(hasBeenReconnected);
 		if (sshServerProfile!=null) {
 			communicator.setSSHServerProfile(sshServerProfile);
+			communicator.setPollInterval(sshServerProfile.getPollingInterval());
 			if (!sshServerProfile.getName().equals(communicator.getSshServerProfileName())) // we've changed to a different 
 					communicator.forgetPassword();
 			//else
@@ -536,8 +537,10 @@ public boolean startExecution(){  //do we assume these are disconnectable?
 		if (communicator.checkUsernamePassword(false)) {
 			if (communicator.createRemoteWorkingDirectory()) {
 				communicator.transferFilesToServer(inputFilePaths, inputFileNames);
+				communicator.setFilesToNotDownload(inputFileNames);
 				if (MesquiteFile.fileExists(localScriptFilePath)) {
 					communicator.transferFileToServer(localScriptFilePath, scriptFileName);
+					communicator.addToFilesToNotDownload(scriptFileName);
 					communicator.setRemoteFileToExecutable(scriptFileName);
 				}
 				successfulStart = true;
@@ -549,6 +552,7 @@ public boolean startExecution(){  //do we assume these are disconnectable?
 			forgetPassword = false;
 			if (scriptBased) {
 				communicator.addEmptyFileToWorkingDirectory(ShellScriptUtil.runningFileName);
+				communicator.addToFilesToNotDownload(ShellScriptUtil.runningFileName);
 				return communicator.sendCommands(new String[] {getExecuteScriptCommand("./"+scriptFileName, visibleTerminal)},true, true, true);  // this works on Linux or Mac
 				//	return communicator.sendCommands(new String[] {getExecuteScriptCommand(getRemoteScriptPath(), visibleTerminal)},true, true, true);  // this works on Mac
 			}
@@ -568,9 +572,23 @@ public boolean monitorExecution(ProgressIndicator progIndicator){
 	public String checkStatus(){
 		return null;
 	}
+
+	public String getMessageIfUserAbortRequested () {
+		if (scriptBased)
+			return " Mesquite will stop its monitoring of the analysis, but it will not be able to directly stop the other program on the remote server.  To stop the other program, you will need to "
+					+ "log into the remote server and stop the program on it.";
+		return "";
+	}
+	public String getMessageIfCloseFileRequested () { 
+		if (scriptBased)
+			return "If Mesquite closes this file, it will not stop the run on the server.  To stop the other program on the remote server, you will need to "
+			+ "log into the remote server and stop the program on it.";
+		return "";
+	}
+
 	public boolean stopExecution(){
 		if (communicator!=null) {
-			communicator.deleteJob(null);
+			communicator.stopJob(null);
 			communicator.setAborted(true);
 		}
 		return true;

Source/mesquite/zephyr/TreeInferenceCoordinator/TreeInferenceCoordinator.java

@@ -89,6 +89,14 @@ TreeInferenceHandler findHandlerByID(int id){
 		return null;
 	}
 	/*.................................................................................................................*/
+	String getExtraLinks(TreeInferenceHandler e) {
+		return e.getExtraLinks();
+	}
+	/*.................................................................................................................*/
+	String getNameForStopLink(TreeInferenceHandler e) {
+		return "Stop";
+	}
+	/*.................................................................................................................*/
 	int whichInferenceInLog = 0;
 	String getStatusHTML(int numLinesPerHandler){
 		String body="";
@@ -102,7 +110,8 @@ String getStatusHTML(int numLinesPerHandler){
 			String logTest = "";
 			for (int i = 0; i<handlers.size(); i++) {
 				TreeInferenceHandler e=(TreeInferenceHandler)handlers.elementAt(i);
-				body +=  " (<a href = \"kill-" + e.getID() + "\">Stop</a>) " + e.getHTMLDescriptionOfStatus(numLinesPerHandler) + "<p><hr size=\"3\" noshade=\"noshade\" />";
+				body +=  " (<a href = \"kill-" + e.getID() + "\">"+getNameForStopLink(e)+"</a>) " + getExtraLinks(e)+ e.getHTMLDescriptionOfStatus(numLinesPerHandler) 
+				+"<p><hr size=\"3\" noshade=\"noshade\" />";
 				if (i==whichInferenceInLog) {
 					extraPanelText.append("Log from " + e.getInferenceName() + "\n===================\n"); 
 					String lt = e.getLogText();
@@ -252,23 +261,37 @@ else if (checker.compare(this.getClass(), "link touched", null, commandName, "li
 				if (handler != null) {
 					int response = 1;
 					logln("User request to stop tree inference");
+					String message = handler.getMessageIfUserAbortRequested();
 					if (handler.canStoreLatestTree()){
-						String message = handler.getMessageIfUserAbortRequested();
 						response = AlertDialog.queryLongMessage(containerOfModule(), "Save tree?", "Save the current tree in the inference?", message, "Save", "Don't Save", "Cancel", 2, "");
 						if (response==0)
 							handler.storeLatestTree();
 						if (response<2) {
 							handler.setUserAborted();
 							handler.stopInference();
 						}
-					} else if (AlertDialog.query(this, "Abort analysis", "Do you want to abort analysis? Preliminary trees will not be saved.", "OK", "Cancel")) {
+					} else if (AlertDialog.query(this, "Abort analysis", "Do you want to abort analysis? Preliminary trees will not be saved. "+message, "OK", "Cancel")) {
 							handler.setUserAborted();
 							handler.stopInference();
 					}
 
+					return null;
+				}
+			} else if (token != null && token.startsWith("extra")){
+				Parser parser = new Parser();
+				parser.setWhitespaceString("-");
+				String idS = token.substring(6, token.length());
+				parser.setString(idS);
+				String command = parser.getFirstToken();
+				String idString = parser.getNextToken();
+				int id = MesquiteInteger.fromString(idString);
+				TreeInferenceHandler handler = findHandlerByID(id);
+				if (handler != null) {
+					handler.dealWithExtraLink(command);
 					return null;
 				}
 			}
+
 		}
 		else
 			return  super.doCommand(commandName, arguments, checker);

Source/mesquite/zephyr/TreeInferenceLiaison/TreeInferenceLiaison.java

@@ -53,6 +53,15 @@ public String getMessageIfCloseFileRequested (){
 			 return inferenceTask.getMessageIfCloseFileRequested();
 		return null;
 	}
+	/*.................................................................................................................*/
+	public String getExtraLinks() {
+		//return "(<a href = \"extra-harvest-" + this.getID() + "\">Harvest Results</a>) ";
+		return "";
+	}
+	/*.................................................................................................................*/
+	public void dealWithExtraLink(String command) {
+		//logln("User request to harvest trees");
+	}
 
 	/*.................................................................................................................*/
 	public String getHTMLDescriptionOfStatus(int numLines){