001 /*
002 * BashApplication.java
003 *
004 * Created on July 10, 2003, 11:22 AM
005 *
006 * This file is part of the STAR Scheduler.
007 * Copyright (c) 2002-2006 STAR Collaboration - Brookhaven National Laboratory
008 *
009 * STAR Scheduler is free software; you can redistribute it and/or modify
010 * it under the terms of the GNU General Public License as published by
011 * the Free Software Foundation; either version 2 of the License, or
012 * (at your option) any later version.
013 *
014 * STAR Scheduler is distributed in the hope that it will be useful,
015 * but WITHOUT ANY WARRANTY; without even the implied warranty of
016 * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
017 * GNU General Public License for more details.
018 *
019 * You should have received a copy of the GNU General Public License
020 * along with STAR Scheduler; if not, write to the Free Software
021 * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA
022 */
023 package gov.bnl.star.offline.scheduler.Dispatchers.xgrid;
024
025 import gov.bnl.star.offline.scheduler.*;
026 import gov.bnl.star.offline.scheduler.request.Request;
027 import gov.bnl.star.offline.scheduler.catalog.PhysicalFile;
028 //import gov.bnl.star.offline.scheduler.util.FileListToolkit;
029 //import gov.bnl.star.offline.scheduler.util.FilesystemToolkit;
030 //import gov.bnl.star.offline.scheduler.util.VariablesToolkit;
031 //import gov.bnl.star.offline.scheduler.util.ConfigToolkit;
032 import gov.bnl.star.offline.scheduler.util.*;
033
034
035 import gov.bnl.star.offline.scheduler.util.sandbox.*;
036
037 import java.io.File;
038 import java.io.FileOutputStream;
039 import java.io.PrintStream;
040
041 import java.util.*;
042 import java.util.logging.Level;
043 import java.util.logging.Logger;
044
045
046 /**
047 * Application module for csh.
048 * <p/>
049 * This module defines the interface of a csh task, and prepare the task
050 * information in the following environment variables:
051 * <p/>
052 * $JOBID - the unique job id given by the scheduler<br>
053 * $FILESLIST - the file name of a text file containing the file list assigned to
054 * the job<br>
055 * $INPUTFILECOUNT - the number of files assigned to the job<br>
056 * $INPUTFILExx - the input files associated to the job<br>
057 * <p/>
058 *
059 * @author Gabriele Carcassi, Jerome Lauret, Levente Hajdu
060 * @version 1.0 2002/12/26
061 */
062 public class BashApplication implements java.io.Serializable {
063 static private Logger log = Logger.getLogger(BashApplication.class.getName());
064 private Request request;
065 private Job job;
066 private String scratchDir = "Not_defined_in_config_file";
067 private String submissionCommand;
068 private Map variables;
069 private boolean variablesSet = false;
070
071 /**
072 * Holds value of property recurseCopy.
073 */
074 private boolean recurseCopy = false;
075
076 /**
077 * Holds the value for the property of EnvVariableLimit
078 */
079 private int EnvVariableLimit;
080 private boolean EnvVariableLimitNotReached = true; //Set false if in "any" job the EnvVariableLimit was reached
081
082 /**
083 * Holds value of property copyScript.
084 */
085 private String copyScript;
086
087 /**
088 * Holds value of property storageScript.
089 */
090 private String storageScript;
091
092 /**
093 * Holds value of property registerScript.
094 */
095 private String registerScript;
096
097 /**
098 * Creates a new instance of CSHApplication
099 */
100 public BashApplication() {
101 }
102
103 /** Returns the CSH application module. In the future, the application should
104 * be taken directly from the component library. This method is provided
105 * for compatibility with the old framework.
106 * @return the CSH application module
107 */
108 // public static CSHApplication getInstance() {
109 // // System.out.println("getting copy for ComponentLibrary");
110 // //called aboat 11 times/dispach
111 // return (CSHApplication) ComponentLibrary.getInstance().getComponent("CSHApplication");
112 // }
113
114
115
116 /**
117 * Prepares the task, by creating the script.
118 */
119 public void prepareJob() {
120 try {
121
122 PrintStream inputFileList = new PrintStream(new FileOutputStream(new File(getInputFileListName())));
123 createInputFileList(inputFileList);
124 } catch (Exception e) {
125 log.log(Level.SEVERE, "Couldn't create the file list", e);
126 throw new RuntimeException("Couldn't create the file list " + getInputFileListName() + ": " + e.getMessage());
127 }
128
129 try {
130 PrintStream cshScript = new PrintStream(new FileOutputStream(new File(getCSHScriptName())));
131 createCSHScript(cshScript);
132 makeScriptFileExecutable(getCSHScriptName());
133
134 cshScript.close(); //close the CSH stream, or else the job will not run
135
136
137 } catch (Exception e) {
138 log.log(Level.SEVERE, "Couldn't create the script", e);
139 throw new RuntimeException("Couldn't create the script " + getCSHScriptName() + ": " + e.getMessage());
140 }
141 }
142
143 /**
144 * Returns the command line to execute the task set by <CODE>setJob</CODE>.
145 *
146 * @return Command line to execute the task
147 */
148 public String getCommandLine() {
149 return getCSHScriptName();
150 }
151
152 //Hold the chmod string from the config file
153 private String makeExecutableCommand;
154
155 /**
156 * Returns the chmod command from the config file
157 */
158 public String getMakeExecutableCommand() {
159 return makeExecutableCommand;
160 }
161
162 public void setMakeExecutableCommand(String makeExecutableCommand) {
163 this.makeExecutableCommand = makeExecutableCommand;
164 }
165
166
167 /** Calls chmod to make the script executable. **/
168 private void makeScriptFileExecutable(String fileName) {
169 // Hack to make the Unit tests work on windows.
170 // chmod doesn't exist on Windows (if you don't have cygwin)
171 if (System.getProperty("os.name").startsWith("Win")) return;
172
173 try {
174 // TODO: chmod should be a variable. This routine
175 // itself should be OS-flavor independent.
176
177 String chmod = getMakeExecutableCommand() + fileName;
178 //String chmod = "/bin/chmod +x " + fileName;
179
180 log.info("Executing \"" + chmod + "\"");
181
182 java.lang.Process shell = Runtime.getRuntime().exec(chmod);
183 shell.waitFor();
184 } catch (Exception e) {
185 log.log(Level.SEVERE, "Couldn't make the script executable", e);
186 throw new RuntimeException("Couldn't make the script " + fileName +
187 " executable", e);
188 }
189 }
190
191 /**
192 * Sets the task the application will have to prepare.
193 *
194 * @param request the request that originated the task
195 * @param job the job to be executed
196 */
197 public void setJob(Request request, Job job) {
198 this.request = request;
199 this.job = job;
200 scratchDir = null;
201 submissionCommand = null;
202 variables = null;
203 variablesSet = false;
204
205
206 this.scratchDir = ConfigToolkit.findProgram("$SCRATCH", job);
207
208 // if (job.getQueueObj().getBatchSystem().getSite().getProgramLocations() == null)
209 // System.out.println("\nCan't find \"ProgramLocations\" block in " + job.getQueueObj().getBatchSystem().getSite().getSiteName() + "(Site) -->" + job.getQueueObj().getBatchSystem().getName() + "(BatchSystem) block in config file $SCRATCH could not be set !. Please contact your SUMS systems administrator to modify the config file.");
210 // else {
211 // if (job.getQueueObj().getBatchSystem().getSite().getProgramLocations().containsKey("$SCRATCH"))
212 // this.scratchDir = (String) job.getQueueObj().getBatchSystem().getSite().getProgramLocations().get("$SCRATCH");
213 // else
214 // System.out.println("\nThe \"$SCRATCH\" value could not be found in the ProgramLocations map of site=\"" + job.getQueueObj().getBatchSystem().getSite().getSiteName() + "\". Please contact your SUMS systems administrator to modify the config file.");
215 // }
216
217
218
219 }
220
221 /** Sets the scratch directory for the temporary output files of the job.
222 * @param scratchDir the temporary output directory
223 */
224 /*
225 public void setScratchDir(String scratchDir) {
226 this.scratchDir = scratchDir;
227 } */
228
229 /**
230 * Sets the submittion command used to submit the job. This will be included in the
231 * script for resubmission.
232 *
233 * @param submissionCommand the command line to submit the job to the batch system
234 */
235 public void setSubmissionCommand(String submissionCommand) {
236 this.submissionCommand = submissionCommand;
237 }
238
239 /**
240 * Generates the csh script to be submitted through LSF.
241 *
242 * @param out the stream on which to print the script
243 */
244 private void createCSHScript(PrintStream out) {
245 // Sets the shell that will interpret the script
246
247 ////////////test area////////////////
248 Map config = (Map) ComponentLibrary.getInstance().getComponent("registerScript");
249
250 out.println("#!/bin/csh");
251 //out.println("#!/bin/sh");
252
253 out.println("# -------------------------------------- ");
254 out.println("# Script generated at " + new Date() +
255 " by the STAR scheduler and submitted with");
256 out.println("# " + submissionCommand);
257 out.println("# -------------------------------------- ");
258
259 out.println("\n" + getInitializationScript());
260
261 Map env = getEnvironmentVariables();
262 Iterator variables = env.keySet().iterator();
263 Iterator FilesNameVariable = env.keySet().iterator();
264
265 // Sets all the environment variable.
266 out.println();
267 out.println("# Preparing environment variables");
268
269 String varName, varValue;
270
271
272 int counter = 0;
273 String padding = "";
274 while (variables.hasNext()) { //First pass prints all the environment variables that do not start with "INPUTFILE"
275 varName = (String) variables.next();
276 varValue = (String) env.get(varName);
277 if ((!varName.startsWith("INPUTFILE")) || (varName.matches("INPUTFILECOUNT"))) {
278 out.println(padding + "setenv " + varName + " " + varValue);
279 }
280 }
281
282 while (FilesNameVariable.hasNext()) { //Second pass prints all the environment variables that start with "INPUTFILE"
283 varName = (String) FilesNameVariable.next();
284 varValue = (String) env.get(varName);
285 if (varName.startsWith("INPUTFILE") && (!varName.matches("INPUTFILECOUNT"))) {
286 if (counter == EnvVariableLimit) {
287 out.println("#");
288 out.println("# Note: The configuration requested a limitation of the");
289 out.println("# number of INPUTFILE(n) environemnt variables at " + EnvVariableLimit);
290 out.println("# The rest of the variables will be commented.");
291 out.println("#");
292 padding = "# ";
293
294 if(EnvVariableLimitNotReached){ //Print the warning to the user only one time then flip EnvVariableLimitNotReached to false
295 System.out.println("\n\n***************************************");
296 System.out.println("The configuration requested a limitation of the number of INPUTFILE(n) environment variables at " + EnvVariableLimit + ", the rest will be commented out.\n");
297 System.out.println("***************************************\n");
298 EnvVariableLimitNotReached = false;
299 }
300 }
301 counter++;
302 out.println(padding + "setenv " + varName + " " + varValue);
303 }
304 }
305
306 /* MLM
307 // Creates the scratch directory
308 out.println();
309 out.println("# Creating the scratch directory, return failure status");
310 out.println("mkdir -p $SCRATCH");
311 out.println("set STS=$status");
312 out.println("if (! -d $SCRATCH) then");
313 out.println(" echo \"Scheduler:: Failed to create $SCRATCH on $HOST\"");
314 out.println(" exit $STS");
315 out.println("endif");
316 */
317
318
319 if(request.getSandbox() != null){
320 out.println();
321 out.println(importPakages());
322 }
323
324
325 out.println();
326 out.println("#Note: The default directory in which jobs start has be fix to $SCRATCH");
327 out.println("cd $SCRATCH"); //Note: This line sets the startup directory to $SCRATCH. It resolves the problem of different batch systems starting in different directories.
328
329
330 out.println("echo \"--------------------------------\"");
331 out.println("echo \'" + gov.bnl.star.offline.scheduler.SchedulerCommandLine.getProgramName() + " we are starting in $SCRATCH :\' `/bin/pwd`");
332 out.println("echo \"--------------------------------\"");
333 out.println("/bin/ls -l");
334
335 // soft linking to home dir removed for now because sandbox will replace this command
336 //out.println("ln -s " + FilesystemToolkit.getCurrentDirectory() + "/* ."); //Note: This line sets the startup directory to $SCRATCH. It resolves the problem of different batch systems starting in different directories.
337
338
339 // Adds the command to be executed
340 out.println();
341 out.println("###################################################");
342 //out.println("/bin/csh -s ___EOD"+job.getJobID()+"__");
343 out.println("# User command BEGIN ----------------------------->");
344
345 //Let the RDLApplicationResolver try to resolve the test, if it can not use the back up
346 //if(request.getCommand() != null)
347
348
349 if (job.getQueueObj() != null && request.getCommand() == null) {
350 if (job.getQueueObj().getRDLApplicationResolver() != null)
351 out.println(job.getQueueObj().getRDLApplicationResolver().resolve(request.getApplication(), request.getTask()));
352 else
353 out.println(request.getCommand());
354 } else
355 out.println(request.getCommand());
356
357
358 out.println("# <------------------------------User command BEGIN");
359 //out.println("___EOD"+job.getJobID()+"__");
360 out.println("###################################################");
361
362 // Copy output files
363 out.println();
364 out.println("# Copy output files (if any where specified)");
365 out.print(generateScriptFragment(request.getOutputList()));
366
367 /* MLM
368 // Delete the scratch directory
369 out.println();
370 out.println("# Delete the scratch directory");
371 out.println("/bin/rm -fr $SCRATCH");
372 */
373 }
374
375 String generateScriptFragment(List outputList) {
376 StringBuffer buffer = new StringBuffer();
377
378 String scriptsString = " ";
379 for (int nOutput = 0; nOutput < outputList.size(); nOutput++) {
380 OutputFile output = (OutputFile) outputList.get(nOutput);
381 if (output.getActionList().size() != 0) {
382 for (int nOutputAction = 0; nOutputAction < output.getActionList().size(); nOutputAction++) {
383 String script = ((OutputAction) output.getActionList().get(nOutputAction)).getScriptName();
384 if (scriptsString.indexOf(script) == -1)
385 scriptsString = scriptsString.concat(script + " ");
386 }
387 }
388 }
389
390 //TODO think about how this can be moved to the config file
391
392 //copy output actions sripts to the local site
393 /*
394 if (scriptsString.length() != 1) {
395 //This only should be used for pdsf, but its hard coded for testing now
396 buffer.append("setenv X509_CERT_DIR /auto/pkg/globus-common/certificates \n");
397 buffer.append("module use /usr/local/pkg/HRM/pkg/modules/rh8 \n");
398 buffer.append("module load hrm/1.2.8a \n");
399 buffer.append("module load globus/2.4.3 orbacus \n");
400 buffer.append("module load rrs \n");
401 buffer.append("module load gcc/2.95.3-thread \n");
402 buffer.append("foreach file (" + scriptsString + ")\n" +
403 " globus-url-copy -p 25 gsiftp://" + ConfigToolkit.getToolkit().myLocalFileGateKeeper().getName() + getHelperScripts() + "$file file:$SCRATCH/$file \n" +
404 " chmod +x $file\n" +
405 "end \n");
406 } */
407
408
409 for (int nOutput = 0; nOutput < outputList.size(); nOutput++) {
410
411 OutputFile output = (OutputFile) outputList.get(nOutput);
412 if (output.getActionList().size() != 0) {
413
414 //buffer.append("setenv OUTPUTFILE").append(nOutput).append(" file:/$SCRATCH/").append(output.getFromScratch()).append("\n");
415
416
417 for (int nOutputAction = 0; nOutputAction < output.getActionList().size(); nOutputAction++) {
418
419
420 // if (output.getActionList().get(nOutputAction) instanceof OutputCopyAction) {
421 // buffer.append(generateScriptFragment(nOutput, (OutputCopyAction) output.getActionList().get(nOutputAction)));
422 // } else if (output.getActionList().get(nOutputAction) instanceof OutputRegisterAction) {
423 // buffer.append(generateScriptFragment(nOutput, (OutputRegisterAction) output.getActionList().get(nOutputAction)));
424 // } else {
425 // log.severe("Unsupported OutputAction time found: " + output.getActionList().get(nOutputAction).getClass().getName());
426 // throw new RuntimeException("Unsupported OutputAction time found");
427 // }
428
429 OutputAction outputAction = (OutputAction) output.getActionList().get(nOutputAction);
430 buffer.append(outputAction.makeScriptString(output.getFromScratch(), ConfigToolkit.getToolkit().myLocalFileGateKeeper().getName()));
431
432 //System.out.println(" " + outputAction.getScriptName());
433 //outputAction.getScriptName();
434
435 }
436 } else {
437
438 //This code copys files back from FromScratch at the uers request //the path has should be added
439 //String gridCopy = "globus-url-copy file://$SCRATCH/".concat(output.getFromScratch()).concat(" ").concat("gsiftp://").concat(getGatekeepr()).concat("/").concat(output.getToURL().getPath()).concat("\n");
440 String gridCopy = FillCopyCommand(getGridCopyCommand(), output.getFromScratch(), output.getToURL().getPath(), true) + "\n";
441 String cpCopy = FillCopyCommand(getCopyCommand(), output.getFromScratch(), output.getToURL().getPath(), false) + "\n";
442 if (recurseCopy) cpCopy = FillCopyCommand(getRecursiveCopyCommand(), output.getFromScratch(), output.getToURL().getPath(), false) + "\n";
443
444
445
446
447 /* This code was replaced with the code below. With the configuration file reshape, the type of queue (local/grid) can be determined by looking at the user�s local site and the queues local site.
448 if(output.getToURL().toString().toLowerCase().startsWith("gsiftp:")){
449 buffer.append(gridCopy);
450 }
451 //else if the user starts his request with file: then use cp
452 else if(output.getToURL().toString().toLowerCase().startsWith("file:")){
453 buffer.append(cpCopy);
454 }
455 // else if the jobs is sent to a queue that has Implementation = "grid" than use globus-url-copy
456 else if (((Queue) job.getQueueObj()).getImplementation().startsWith("grid")){
457 buffer.append(gridCopy);
458 }
459 else{ //just use cp if all else fails
460 buffer.append(cpCopy);
461 }
462 */
463
464
465 if (ConfigToolkit.getToolkit().isLocalQueue(job.getQueueObj())) {
466 buffer.append(cpCopy);
467 } else {
468 buffer.append(gridCopy);
469 }
470
471
472 }
473 }
474 return buffer.toString();
475 }
476
477
478 /** deprecated **/
479 String generateScriptFragment(int nOutput, OutputCopyAction action) {
480 /*
481 StringBuffer fragment = new StringBuffer();
482 if (action.getFileRef() != null) {
483 if (action.getStorageService() != null) {
484 fragment.append("setenv OUTPUTFILE").append(nOutput).append('_').
485 append(action.getFileRef()).append(" `").append(getStorageScript()).
486 append(" \"").append(action.getStorageService()).append("\" `").
487 append(action.getURI().getPath()).append("\n");
488
489 } else {
490 fragment.append("setenv OUTPUTFILE").append(nOutput).append('_').
491 append(action.getFileRef()).append(" ").
492 append(action.getURI()).append("\n");
493 }
494 fragment.append(getCopyScript()).append(" $OUTPUTFILE").append(nOutput).
495 append(" $OUTPUTFILE").append(nOutput).append('_').append(action.getFileRef()).
496 append("\n");
497 } else {
498 fragment.append(getCopyScript()).append(" $OUTPUTFILE").append(nOutput);
499 if (action.getStorageService() != null) {
500 fragment.append(" `").append(getStorageScript()).append(" \"").append(action.getStorageService()).append("\" `").append(action.getURI().getPath()).append("\n");
501 } else {
502 fragment.append(" ").append(action.getURI()).append("\n");
503 }
504 }
505 return fragment.toString();
506 */ return " ";
507 }
508
509 /** deprecated **/
510 String generateScriptFragment(int nOutput, OutputRegisterAction action) {
511 /*
512 StringBuffer fragment = new StringBuffer();
513 fragment.append(getRegisterScript()).append(" $OUTPUTFILE").append(nOutput);
514 if (action.getFileRef() != null) {
515 fragment.append('_'). append(action.getFileRef());
516 }
517 int queryStart = action.getURI().getSchemeSpecificPart().indexOf('?');
518 queryStart++;
519 fragment.append(" '").append(action.getURI().getSchemeSpecificPart().substring(queryStart)).append("'\n");
520 return fragment.toString();
521 */ return " ";
522 }
523
524 /**
525 * Generates the input file list. It consists of full path names, one line for each
526 * one.
527 *
528 * @param out the stream on which to print the file list
529 */
530 private void createInputFileList(PrintStream out) {
531 //printJobInputList(job.getInput());
532
533 variables = new TreeMap();
534
535 if ("paths".equals(request.getFileListType())) {
536 FileListToolkit.createPathsFileList(out, job.getInput(), variables);
537 } else if ("rootd".equals(request.getFileListType())) {
538 FileListToolkit.createLocalRemoteFileList(out, job.getInput(), variables, false);
539 } else if ("xrootd".equals(request.getFileListType())) {
540 FileListToolkit.createLocalRemoteFileList(out, job.getInput(), variables, true);
541 }
542 }
543 private void printJobInputList(List jobList){
544 System.out.println("-----------------------------------------------");
545 for (int i = 0; i < jobList.size(); i++) {
546 PhysicalFile physicalFile = (PhysicalFile) jobList.get(i);
547 System.out.println("File n."+i+ "is:"+physicalFile.getStorage()+"::"+physicalFile.getPath()+"::"+physicalFile.getFilename());
548 System.out.println("\n");
549 }
550 System.out.println("------------------------------------------------\n");
551 }
552
553 /**
554 * Returns the path and name for the csh script.
555 *
556 * @return the csh script path and name
557 */
558 public String getCSHScriptName() {
559
560 //return FilesystemToolkit.getCurrentDirectory() + "/sched" + job.getJobID() + ".csh";
561 return FilesystemToolkit.getCurrentDirectory() + "/" + getCSHScriptFileName();
562
563 }
564
565
566 /**
567 * Returns the name for the csh script (without the path).
568 *
569 * @return the csh script name (without the path)
570 */
571 public String getCSHScriptFileName() {
572 /*
573 The path is being dropped because different drivers for mounting the PanFS path are reporting the path differently. Instated we will put �cd $path� before the command we execute.
574 Example:
575 /pdirect/star+institutions/data05/scratch/lbhajdu/p-w
576 /star/data05/scratch/lbhajdu/
577 */
578 return this.getJobName() + "sched" + job.getJobID() + ".csh";
579 }
580
581
582 /**
583 * Returns the name for the input file list file.
584 *
585 * @return the input file list name
586 */
587 public String getInputFileListName() {
588 //return FilesystemToolkit.getCurrentDirectory() + "/" + this.getJobName() + "sched" + job.getJobID() + ".list";
589 return "sched" + job.getJobID() + ".list";
590 }
591
592
593 private Map getEnvironmentVariables() {
594
595 if (variables == null) variables = new TreeMap(); //This can still be null if there is no filelist
596 if(variables.containsKey("JOBID")) return variables; //if added one time do not add then again
597
598 variables.put("JOBID", job.getJobID());
599
600 variables.put("REQUESTID", job.getRequestID());
601 variables.put("PROCESSID", job.getProcessID());
602
603 // FIXME: scratch dir should be passed in a nicer way
604 variables.put("SCRATCH", scratchDir);
605
606 variables.put("FILELIST", getInputFileListName());
607
608 List inputList = job.getInput();
609 variables.put("INPUTFILECOUNT", Integer.toString(inputList.size()));
610
611 //This is now done in FileListToolkit
612 // for (int nFile = 0; nFile < inputList.size(); nFile++) {
613 // PhysicalFile file = (PhysicalFile) inputList.get(nFile);
614 // variables.put("INPUTFILE" + nFile, file.getPath() + "/" + file.getFilename());
615 // }
616
617
618 //If there is only one input file per csh make an Environment Variable called FILEBASENAME
619 if (inputList.size() == 1) {
620 PhysicalFile file = (PhysicalFile) inputList.get(0);
621 if (!(file.getFilename().indexOf(".") == -1))
622 variables.put("FILEBASENAME", file.getFilename().substring(0, file.getFilename().indexOf(".")));
623 else
624 variables.put("FILEBASENAME", file.getFilename());
625 } else { //All other times FILEBASENAME will be set to this value
626 //variables.put("FILEBASENAME", "FILEBASENAME.NOT.INITIALIZED." + job.getJobID());
627 variables.put("FILEBASENAME", "\"\""); //Blank is better because people may use the variable FILEBASENAME. (JL, LH)
628 }
629
630
631 String APP = ConfigToolkit.findProgram("$APP", job); //ComponentLibrary.getInstance().getProgramLocation(job.getQueueObj().getBatchSystem().getSite(), "$APP");
632 if(APP != null){
633 APP = APP.trim();
634 if(APP.trim() != "") variables.put("APP", APP);
635 }
636
637 String DATA = ConfigToolkit.findProgram("$DATA", job); //ComponentLibrary.getInstance().getProgramLocation(job.getQueueObj().getBatchSystem().getSite(), "$DATA");
638 if(DATA != null){
639 DATA = DATA.trim();
640 if(DATA.trim().length() > 0) variables.put("DATA", DATA);
641 }
642
643 return variables;
644 }
645
646 /**
647 * Returns the file for standard input redirection.
648 *
649 * @return stdin file
650 */
651 public String getStdin() {
652 if (job.getStdin() != null) {
653 return VariablesToolkit.substituteVariables(job.getStdin().getPath(), this.getEnvironmentVariables());
654 //CSHApplication.getInstance().getEnvironmentVariables());
655 }
656
657 return null;
658 }
659
660 /**
661 * Returns the file for standard output redirection.
662 *
663 * @return stdout file
664 */
665 public String getStdout() {
666 if (job.getStdout() != null) {
667 if (job.getStdout() == Request.discard) {
668 return "/dev/null";
669 }
670
671 return VariablesToolkit.substituteVariables(job.getStdout().getPath(), this.getEnvironmentVariables());
672 // CSHApplication.getInstance().getEnvironmentVariables());
673 }
674
675 return null;
676 }
677
678 /**
679 * Returns the file for standard error redirection.
680 *
681 * @return stderr file
682 */
683 public String getStderr() {
684 if (job.getStderr() != null) {
685 if (job.getStderr() == Request.discard) {
686 return "/dev/null";
687 }
688
689 return VariablesToolkit.substituteVariables(job.getStderr().getPath(), this.getEnvironmentVariables());
690 //CSHApplication.getInstance().getEnvironmentVariables());
691 }
692
693 return null;
694 }
695
696 /**
697 * Returns the job name to be assigned to the batch system.
698 *
699 * @return the job name to be used by the batch system
700 */
701 public String getJobName() {
702 return request.getName();
703 }
704
705 /**
706 * Getter for property recurseCopy.
707 *
708 * @return Value of property recurseCopy.
709 */
710 public boolean isRecurseCopy() {
711 return this.recurseCopy;
712 }
713
714 /**
715 * Setter for property recurseCopy.
716 *
717 * @param recurseCopy New value of property recurseCopy.
718 */
719 public void setRecurseCopy(boolean recurseCopy) {
720 this.recurseCopy = recurseCopy;
721 }
722
723
724 /**
725 * Getter for property EnvVariableLimit.
726 *
727 * @return Value of property EnvVariableLimit.
728 */
729 public int getEnvVariableLimit() {
730 return this.EnvVariableLimit;
731 }
732
733 /**
734 * Setter for property EnvVariableLimit.
735 *
736 * @param EnvVariableLimit New value of property EnvVariableLimit.
737 */
738 public void setEnvVariableLimit(int EnvVariableLimit) {
739 this.EnvVariableLimit = EnvVariableLimit;
740 }
741
742
743 /**
744 * Getter for property copyScript.
745 *
746 * @return Value of property copyScript.
747 */
748 public String getCopyScript() {
749 return this.copyScript;
750 }
751
752 /**
753 * Setter for property copyScript.
754 *
755 * @param copyScript New value of property copyScript.
756 */
757 public void setCopyScript(String copyScript) {
758 this.copyScript = copyScript;
759 }
760
761 /**
762 * Getter for property storageScript.
763 *
764 * @return Value of property storageScript.
765 */
766 public String getStorageScript() {
767 return this.storageScript;
768 }
769
770 /**
771 * Setter for property storageScript.
772 *
773 * @param storageScript New value of property storageScript.
774 */
775 public void setStorageScript(String storageScript) {
776 this.storageScript = storageScript;
777 }
778
779 /**
780 * Getter for property registerScript.
781 *
782 * @return Value of property registerScript.
783 */
784 public String getRegisterScript() {
785 return this.registerScript;
786 }
787
788 /**
789 * Setter for property registerScript.
790 *
791 * @param registerScript New value of property registerScript.
792 */
793 public void setRegisterScript(String registerScript) {
794 this.registerScript = registerScript;
795 }
796
797
798 private String gridCopyCommand = "(gridCopyCommand not set in config file file!)";
799
800 /**
801 * sets the command for copying files back, when the user asks for <output fromScratch="/path/x" toURL="gsiftp:/path/x"/>
802 * use (fromScratch) for source and (toURL) for destination.
803 * Example: globus-url-copy file://$SCRATCH/(fromScratch) gsiftp://stragrid04.star.bnl.gov/(toURL)
804 */
805 public void setGridCopyCommand(String gridCopyCommand) {
806 this.gridCopyCommand = gridCopyCommand;
807 }
808
809 public String getGridCopyCommand() {
810 return gridCopyCommand;
811 }
812
813 private String CopyCommand = "(CopyCommand not set in config file file!)";
814
815 /**
816 * sets the command for copying files back, when the user asks for <output fromScratch=x toURL="file:/path/"/>
817 * use (fromScratch) for source and (toURL) for destination.
818 * Example: /bin/cp $SCRATCH/(fromScratch) (toURL)
819 */
820 public void setCopyCommand(String CopyCommand) {
821 this.CopyCommand = CopyCommand;
822 }
823
824 public String getCopyCommand() {
825 return CopyCommand;
826 }
827
828 private String recursiveCopyCommand = "(recursiveCopyCommand not set in config file file!)";
829
830 /**
831 * sets the command for copying files back, when the user asks for <output fromScratch=x toURL="file:/path/"/>
832 * use (fromScratch) for source and (toURL) for destination.
833 * Example: /bin/cp -r $SCRATCH/(fromScratch) (toURL)
834 */
835 public void setRecursiveCopyCommand(String recursiveCopyCommand) {
836 this.recursiveCopyCommand = recursiveCopyCommand;
837 }
838
839 public String getRecursiveCopyCommand() {
840 return recursiveCopyCommand;
841 }
842
843 /**
844 * replaces the (fromScratch) and the (toURL) in the copy command with the true path
845 */
846 public String FillCopyCommand(String command, String fromScratch, String toURL, boolean isGrid) {
847
848 if (!isGrid) {
849 if (fromScratch.matches("^\\Q./\\E.*"))
850 fromScratch = fromScratch.replaceAll("(^\\Q.\\E)(.*)", "`pwd`$2");
851 else
852 fromScratch = "$SCRATCH/".concat(fromScratch);
853 }
854
855 StringBuffer buffer = new StringBuffer();
856 buffer.append(command);
857 while (buffer.indexOf("(fromScratch)") != -1) {
858 buffer.replace(buffer.indexOf("(fromScratch)"), (buffer.indexOf("(fromScratch)") + "(fromScratch)".length()), fromScratch);
859 }
860
861 while (buffer.indexOf("(toURL)") != -1) {
862 buffer.replace(buffer.indexOf("(toURL)"), (buffer.indexOf("(toURL)") + "(toURL)".length()), toURL);
863 }
864
865
866 while (buffer.indexOf("(copyBackGateKeeper)") != -1) {
867 //ConfigToolkit.getToolkit().myLocalFileGateKeeper().getName();
868 buffer.replace(buffer.indexOf("(copyBackGateKeeper)"), (buffer.indexOf("(copyBackGateKeeper)") + "(copyBackGateKeeper)".length()), ConfigToolkit.getToolkit().myLocalFileGateKeeper().getName());
869 }
870
871 //This did not working, it would fail with "Illegal group reference" when fromScratch or toURL had a '$' in it.
872 //return command.replaceAll("\\(fromScratch\\)", fromScratch).replaceAll("\\(toURL\\)", toURL);
873
874 return buffer.toString();
875
876 }
877
878
879 private String helperScripts = "[helper_script_path_not_set]";
880
881 public String getHelperScripts() {
882 return helperScripts;
883 }
884
885 public void setHelperScripts(String helperScripts) {
886 this.helperScripts = helperScripts;
887 }
888
889 private String initializationScript = "";
890 public String getInitializationScript(){return this.initializationScript; }
891 public void setInitializationScript(String initializationScript){this.initializationScript = initializationScript; }
892
893
894 public String importPakages(){
895 String importPakagesText = "\n#import pakages \n";
896
897 Sandbox sandbox = request.getSandbox();
898
899 //Add warnings about special sandbox grid requirements here:
900 if(! ConfigToolkit.getToolkit().isLocalQueue(job.getQueueObj())){
901
902 if(sandbox.getClass().getName().matches(".*ZipSandbox$")){
903 if (! getEnvironmentVariables().containsKey("DATA")){
904 String Warning = "Warning: Scheduler has no configuration information for $DATA at site " + job.getAccessPoint().getSite().getSiteName() + ". If $DATA is not set in the environment of the worker node the sandbox will fail. For more information please contact your scheduler administrator.";
905 System.out.println("\n\n" + Warning + "\n");
906 log.log(Level.SEVERE, Warning);
907 }
908 }
909 }
910
911
912
913 importPakagesText = importPakagesText.concat(sandbox.InitializationCommands());
914
915 List packages = sandbox.getPackages();
916
917 for(int i = 0; i != packages.size(); i++){
918 SandboxPackage sandboxPackage = (SandboxPackage) packages.get(i);
919
920 if(! sandbox.PackageExists(sandboxPackage)){ //This to see if the package dose not exist
921 //make the package
922 sandbox.MakePackage(sandboxPackage, request);
923 }
924
925 importPakagesText = importPakagesText.concat(sandbox.installCommand(sandboxPackage, job));
926 }
927
928 return importPakagesText;
929 }
930
931 }