/** monitors the run. */ public boolean monitorAndCleanUpShell() { lastModified = null; boolean stillGoing = true; if (outputFilePaths != null) { lastModified = new long[outputFilePaths.length]; LongArray.deassignArray(lastModified); } if (!StringUtil.blank( runningFilePath)) // is file at runningFilePath; watch for its disappearance while (MesquiteFile.fileExists(runningFilePath) && stillGoing) { processOutputFiles(); try { Thread.sleep(sleepTime); } catch (InterruptedException e) { MesquiteMessage.notifyProgrammer( "InterruptedException in shell script executed by " + name); return false; } stillGoing = watcher == null || watcher.continueShellProcess(proc); } if (outputFileProcessor != null) outputFileProcessor.processCompletedOutputFiles(outputFilePaths); return true; }
/** * executes a shell script at "scriptPath". If runningFilePath is not blank and not null, then * Mesquite will create a file there that will serve as a flag to Mesquite that the script is * running. */ public boolean executeInShell() { proc = null; try { ShellScriptUtil.setScriptFileToBeExecutable(scriptPath); if (!StringUtil.blank(runningFilePath)) { if (StringUtil.blank(runningFileMessage)) MesquiteFile.putFileContents(runningFilePath, "Script running...", true); else MesquiteFile.putFileContents(runningFilePath, runningFileMessage, true); if (appendRemoveCommand && MesquiteFile.fileExists(runningFilePath)) MesquiteFile.appendFileContents( scriptPath, StringUtil.lineEnding() + ShellScriptUtil.getRemoveCommand(runningFilePath), true); // append remove command to guarantee that the runningFile is deleted // +StringUtil.lineEnding()+ShellScriptUtil.getExitCommand() } proc = ShellScriptUtil.executeScript(scriptPath, visibleTerminal); } catch (IOException e) { MesquiteMessage.warnProgrammer("IOException in shell script executed by " + name); return false; } return true; }
public void runFilesAvailable(int fileNum) { String[] logFileNames = getLogFileNames(); if ((progIndicator != null && progIndicator.isAborted()) || logFileNames == null) return; String[] outputFilePaths = new String[logFileNames.length]; outputFilePaths[fileNum] = externalProcRunner.getOutputFilePath(logFileNames[fileNum]); String filePath = outputFilePaths[fileNum]; if (fileNum == 0 && outputFilePaths.length > 0 && !StringUtil.blank(outputFilePaths[0]) && !bootstrapOrJackknife()) { // tree file if (ownerModule instanceof NewTreeProcessor) { String treeFilePath = filePath; if (taxa != null) { TaxaSelectionSet outgroupSet = (TaxaSelectionSet) taxa.getSpecsSet(outgroupTaxSetString, TaxaSelectionSet.class); ((NewTreeProcessor) ownerModule).newTreeAvailable(treeFilePath, outgroupSet); } else ((NewTreeProcessor) ownerModule).newTreeAvailable(treeFilePath, null); } } else if (fileNum == 1 && outputFilePaths.length > 1 && !StringUtil.blank(outputFilePaths[1]) && !bootstrapOrJackknife()) { // log file if (MesquiteFile.fileExists(filePath)) { String s = MesquiteFile.getFileLastContents(filePath); if (!StringUtil.blank(s)) if (progIndicator != null) { parser.setString(s); String rep = parser.getFirstToken(); // generation number logln(""); if (MesquiteInteger.isNumber(rep)) { int numReps = MesquiteInteger.fromString(rep) + 1; progIndicator.setText( "Replicate: " + numReps); // + ", ln L = " + parser.getNextToken()); if (bootstrapOrJackknife()) { logln("Replicate " + numReps + " of " + bootstrapreps); } logln("Replicate " + numReps + " of " + totalNumHits); progIndicator.spin(); double timePerRep = 0; if (MesquiteInteger.isCombinable(numReps) && numReps > 0) { timePerRep = timer.timeSinceVeryStartInSeconds() / numReps; // this is time per rep } int timeLeft = 0; if (bootstrapOrJackknife()) { timeLeft = (int) ((bootstrapreps - numReps) * timePerRep); } else { String token = parser.getNextToken(); // algorithm token = parser.getNextToken(); // Tree token = parser.getNextToken(); // Score String best = parser.getNextToken(); // Best logln(" Score " + token + "; best found so far " + best); timeLeft = (int) ((totalNumHits - numReps) * timePerRep); } logln( " Running time so far " + StringUtil.secondsToHHMMSS((int) timer.timeSinceVeryStartInSeconds()) + ", approximate time remaining " + StringUtil.secondsToHHMMSS(timeLeft)); } } count++; } else if (MesquiteTrunk.debugMode) logln("*** File does not exist (" + filePath + ") ***"); } }