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Two more instances in GLI's Gatherer.java were using Java's Process instead of going through SafeProcess?. I had a note in the tickets about this, but it was obscured by being an item in my todo list that was ticked off, because I hadn't originally intended to change these 2 instances to use SafeProcess?, because SafeProcess? didn't have a cancel feature back then. With the recent addition of the cancel feature, the changes became straightforward. Both remaining instances in Gatherer have been changed to use SafeProcess? and it's tested on Linux. Updated the SafeProcess? README.

Line 
1First drafts of this document
2ak19, 30 May 2017
3
4=========================================
5    SAFEPROCESS.JAVA README
6=========================================
7
8GS Java developers should use SafeProcess.java in place of directly using Java's Process class, unless any issues are discovered with SafeProcess.java hereafter.
9
10
11A tailored version of SafeProcess is found both in GLI and GS3's Java src code:
12- gli/src/org/greenstone/gatherer/util/SafeProcess.java
13- greenstone3/src/java/org/greenstone/util/SafeProcess.java
14
15
16This document contains the following sections
17    A. WHY WE SHOULD GO THROUGH SAFEPROCESS INSTEAD OF USING JAVA'S PROCESS DIRECTLY
18    B. MODEL OF SAFEPROCESS THREADS AND INTERRUPT BEHAVIOUR
19    C. USAGE: DEBUGGING
20    D. USAGE: INSTANTIATION & DEFAULT RUNPROCESS VARIANTS
21    E. INTERNAL IMPLEMENTATION DETAILS - USEFUL IF CUSTOMISING SAFEPROCESS' BEHAVIOUR OR CALLING CANCEL ON SAFEPROCESS
22    F. USAGE: CUSTOMISING
23    G. USAGE: CANCELLING
24    H. USAGE: IMPLEMENTING HOOKS AROUND CANCELLING OR PROCESS' END
25    I. USEFUL STATIC METHODS AND STATIC INNER CLASSES
26    J. OTHER USEFUL INSTANCE METHODS
27    K. LINKS AND NOTES ON PROCESSES, PROCESS STREAMS, INTERRUPTING AND DESTROYING PROCESSES
28    L. USEFUL SYNCHRONISATION NOTES AND SUGGESTED READING ON THREADS AND THREAD SAFETY
29    M. TICKETS, COMMITS, TAGS
30    N. GLI vs GS3 CODE's SAFEPROCESS.JAVA - THE DIFFERENCES
31    O. FUTURE WORK, IMPROVEMENTS
32
33_______________________________________________________________________________
34A. WHY WE SHOULD GO THROUGH SAFEPROCESS INSTEAD OF USING JAVA'S PROCESS DIRECTLY
35_______________________________________________________________________________
36
37It's easy to misuse Java's Process class, and this can result in unexpected behaviour and random errors that are hard to track down. Further, the older GLI and GS3 Java src code used to use Java's Process class in different and inconsistent ways, some worse than others. Going through one class, SafeProcess, provides consistency. So if it's buggy, you can fix it in one place.
38
39SafeProcess handles the internal Process' iostreams (input, output and error) properly using separate worker Threads, following http://www.javaworld.com/article/2071275/core-java/when-runtime-exec---won-t.html?page=2.
40
41SafeProcess handles this itself so that the code that uses SafeProcess doesn't need to deal with it, unless customising the processing of the Process' iostreams.
42
43
44
45_________________________________________________________
46B. MODEL OF SAFEPROCESS THREADS AND INTERRUPT BEHAVIOUR
47_________________________________________________________
48
49This section is especially IMPORTANT TO READ IF you're thinking of customising SafeProcess' handling of the internal Process' iostreams, since each of them are always handled in their own distinct worker threads, and you need to remember to deal with ThreadSafety issues.
50
51The primary process Thread:
52The main process internal to a SafeProcess instance is run in whatever thread the SafeProcess instance's runProcess() (or runBasicProcess()) methods are called.
53The SafeProcess instance internally keeps track of this thread, so that any cancel operation can send the InterruptedException to this primary thread.
54
55SafeProcess does NOT inherit from Thread, it is therefore not a Thread. It just runs its internal process in whatever Thread called SafeProcess's runProcess/runBasicProcess methods.
56
57A SafeProcess thread may further launch 0 or 3 additional worker threads, depending on whether runBasicProcess() or a runProcess() variant was called.
58
59In total, using SafeProcess involves
60- 1 thread (the primary thread) when runBasicProcess() is called
61- or 4 threads (the primary thread + 3 worker threads) when any variant of runBasicProcess() is called. If a variant of runProcess() was called, then 3 additional worker threads are spawned by SafeProcess. One for each iostream of the Process: inputstream, outputstream and errorstream. Note that the SafeProcess class will read from the internal Process' outputStream and ErrorStream, and can send/write a string to the Process' inputstream.
62
63
64            SafeProcess thread
65                |
66                |
67        ________________|_______________________________
68        |       |       |       |
69        |       |       |       |
70        |       |       |       |
71    Worker Thread     SafeProcess     Worker Thread   Worker Thread
72    for Process'        Thread     for Process'    for Process'
73    InputStream    (primary)       OutputStream    ErrorStream
74
75
76__________________________________________________
77C. USAGE: DEBUGGING
78__________________________________________________
79
80There's a lot of info that a SafeProcess instance will log during its execution and termination phases, including Exceptions but also very basic things, such as the command that the SafeProcess instance is running and other messages.
81
82Exceptions are always logged, but debugging related messages can be turned off or on. By default, it's turned off. You can turn it on by adjusting the static SafeProcess.DEBUG = 1 and recompiling.
83
84For GS3, the log output uses log4j.
85For GLI, it goes to System.err at present. But if you want it to go to GLI's DebugStream, uncomment the relevant lines in the 3 variants of the static log() functions in SafeProcess.java. Then recompile.
86
87If you're using SafeProcess yourself and wish to log debug statements that are related to how well you're using SafeProcess, you can call one of the static SafeProcess.log() functions yourself. Remember to set the static SafeProcess.DEBUG = 1.
88
89
90There are 4 variants of the log() function:
91
92    - public static void log(String msg)
93    logs the message if debugging is on, DEBUG = 1
94
95    - public static void log(Exception e)
96    logs the stacktrace for the exception, regardless of if debugging is on
97
98    - public static void log(String msg, Exception e)
99    logs the message and logs the stacktrace for the exception, regardless of if debugging is on
100
101    - public static void log(String msg, Exception e, boolean printStackTrace)
102    if debugging is on or if the printStackTrace parameter is true, both the message and the stacktrace for the exception are logged.
103    if debugging is off and the printStackTrace parameter is false, nothing is logged. Call this variant if an exception is expected and you only want to log it in debugging mode. An example of an expected exception are some InterruptedExceptions that may occur over the course of SafeProcess
104
105_______________________________________________________
106D. USAGE: INSTANTIATION & DEFAULT RUNPROCESS VARIANTS
107_______________________________________________________
108
109Usage of the SafeProcess class generally follows the following sequence:
110
1111. instantiate a SafeProcess object using one of the constructors
112    - public SafeProcess(String[] cmd_args)
113    - public SafeProcess(String cmdStr)
114    - public SafeProcess(String[] cmd_args, String[] envparams, File launchDir)
115    Either or both of envparams and launchdir can be null.
116
117
1182. optionally configure your SafeProcess instance.
119Use an appropriate setter method to set some additional fields:
120
121    - public void setInputString(String sendStr)
122    Call this if you wish to write any string to the process' inputstream
123
124    - public void setSplitStdOutputNewLines(boolean split)
125    - public void setSplitStdErrorNewLines(boolean split)
126    Pass in true to either of the above methods if you want to preserve individual lines in the content retrieved from the internal Process' stderr and stdoutput.
127    By default, lines are not split, so you get a String of one single line for the entire output from the Process' stdoutput, and a String of one single line from the Process' stderr output.
128   
129
130    - public void setExceptionHandler(SafeProcess.ExceptionHandler exception_handler)
131    Use this to register a SafeProcess ExceptionHandler whose gotException() method will get called for each exception encountered during the *primary* thread's execution: the thread that runs the Process. If you wish to handle exceptions that could happen when reading from the Process' outputStream/errorStream, you will need to do that separately. See the section CUSTOMISING. By default, exceptions when reading from Process' output and errorStreams are logged.
132   
133    - public void setMainHandler(SafeProcess.MainProcessHandler handler)
134    To set a handler that will handle the primary (SafeProcess) thread, your handler will need to implement the hooks that will get called during the internal Process' life cycle, such as before and after process.destroy() is called upon a cancel operation.
135
136
1373. call one of the following runProcess() variants on your SafeProcess instance:
138
139    a. public int runBasicProcess()
140
141This variant will not handle the Process' iostreams at all, so it won't launch any worker threads. It merely runs the internal process in the thread from which it is called (the primary thread) and waits until it's done.
142Use this variant if you know that the external process you wish SafeProcess to run will NOT be expecting any input nor be producing any output (in stdout or stderror).
143
144NOTE: Do not call runBasicProcess() if you merely wish to ignore the process' iostreams. Because, in Java 6 and earlier, this can block indefinitely if any of the Process' iostreams contain anything or expect anything. If you wish to ignore a process' iostreams, or if you're not sure if they may need handling, call the zero-argument runProcess() variant described below.
145
146    b. public int runProcess()
147
148This zero argument variant will handle all the Process' iostreams in the DEFAULT manner.
149
150- If you wanted to send something to the Process' inputstream, you ought to have configured this by calling setInputString(sendStr) before calling runProcess(). The DEFAULT behaviour is for sendStr to be written to the internal Process' inputstream as soon as the process runs (happens in its own thread).
151
152- once runProcess() finishes, you can inspect what had come out of the Process' output and error streams by calling, see point 4 below.
153The DEFAULT behaviour of SafeProcess' processing of the stdout and stderr streams is for both streams to be read one line at a time until they have nothing left. Note that both streams are always dealt with in their separate worker threads.
154
155Resources are safely allocated at the end of the worker threads dealing with each of the internal Process' iostream, regardless of whether the Process is allowed to terminate naturally or whether SafeProcess is instructed to prematurely terminate it.
156
157    c. public int runProcess(SafeProcess.LineByLineHandler outLineByLineHandler, SafeProcess.LineByLineHandler errLineByLineHandler)
158Use this variant if you want to do anything specific when each line comes in from the internal Process' stderr and stdout streams. Passing in null for either parameter will return to the default behaviour for that stream.
159You'll want to read further details in the section on CUSTOMISING.
160
161    d. public int runProcess(CustomProcessHandler procInHandler, CustomProcessHandler procOutHandler, CustomProcessHandler procErrHandler)
162Use this variant if you want to completely override the way the internal Process' iostreams are handled. Passing in null for any of the parameters will return to the default behaviour for that stream. You'll want to read further details in the section on CUSTOMISING.
163
164
165All the runProcess() variants do a Process.waitFor(). This means all runProcess() variants block the primary thread, which is the thread in which they're executing, until the internal Process has completed.
166
167If you want to completely override the default behaviour of any of SafeProcess' iostream related worker threads (such as if you want to read a char at a time from the stderr stream and do something, instead of the default behaviour of reading a line at a time from it), then call this method.
168
169You need to pass in an *instance* of SafeProcess.CustomProcessHandler for *each* of the 3 iostreams, since they're running in separate threads and so can't share the same instance.
170
171You can pass in null for any of these, if you want the default SafeProcess handling to apply for that stream's worker thread. For any iostream's default handling that you want to override, however, you'd extend SafeProcess.CustomProcessHandler.
172
173You would need to take care of ThreadSafety yourself if you're extending a SafeProcess.CustomProcessHandler. You can maintain concurrency by using synchronization, for instance. See the section USEFUL SYNCHRONISATION NOTES.
174
175For EXAMPLES OF USE, see GS3's GS2PerlConstructor.java and GLI's DownloadJob.java.
176
177
178Further NOTES:
179All of the variants of the runProcess methods return the internal Process' exit value *after* the internal Process has completed. The exit value will be -1 if the process was prematurely terminated such as by a cancel operation, which would have interrupted the primary and subsidiary threads.
180
181Running a process blocks the primary thread until complete. So all the runProcess variants above *block*. (Unless and until an external thread calls the cancelRunningProcess() method on a reference to the SafeProcess instance, discussed in the section on CANCELLING).
182
183
1844. if necessary, once the process has *terminated*,
185
186- you can read whatever came out from the Process' stderr or stdout by calling whichever is required of:
187public String getStdOutput()
188public String getStdError()
189 
190If you want to do anything special when handling any of the Process' iostreams, see the CUSTOMISING section.
191
192- You can also inspect the exit value of running the process by calling
193public int getExitValue()
194
195The exit value will be -1 if the process was prematurely terminated such as by a cancel operation, which would have interrupted the primary and subsidiary threads.
196The exit value will also be -1 if you call getExitValue() before setting off the SafeProcess via any of the runProcess() variants.
197
198_____________________________________________________________________________________________________________________
199E. INTERNAL IMPLEMENTATION DETAILS - USEFUL IF CUSTOMISING SAFEPROCESS' BEHAVIOUR OR CALLING CANCEL ON SAFEPROCESS
200_____________________________________________________________________________________________________________________
201
202This section is for understanding how SafeProcess runs a Java Process internally. These methods are not public and their details are hidden away in the code.
203
204Calling any of the runProcess() variants does the following internally:
205
2061. calls method doRuntimeExec()
207
208    based on how you configured your SafeProcess instance, this method instantiates and returns a Process object by calling Runtime.exec().
209    A possible improvement may be to consider using the ProcessBuilder class for creating a Process object.
210
2112. calls method waitForStreams()
212
213    Called by all but the runBasicProcess() variant, since the runBasicProcess() variant does not do anything with the Process' iostreams and therefore doesn't use worker threads .
214    This method first starts off all the worker threads, to handle each input or output stream of the Process.
215    Then, it calls waitFor() on the Process object. This is the first of 2 calls that block the primary thread (the Thread the Safeprocess runs its Process object in) until finished.
216
217    One of two things happen,
218    - either the internal Process is allowed to terminate naturally, reaching the end.
219    - Or the Process is interrupted by a cancel action, which will result in an InterruptedException. When an InterruptedException is caught, each of the worker threads is interrupted. The worker threads check for the interrupt flag during any loop, so that they may exit their loop early. If an InterruptException happened, the exitValue after the Process' waitFor() call remains at -1 and the SafeProcess instance sets its boolean forciblyTerminateProcess flag to true, to indicate that it may have to call Process.destroy() and ensure any subprocesses are terminated.
220   
221    Regardless of whether the Process naturally terminates or is prematurely terminated by an InterruptedException upn a cancel,
222    - all the resources such as streams are closed.
223    - the join() method is called on all worker threads. As per the Java API, callin join() on a Thread "Waits for this thread to die." This means the primary thread now waits for the worker threads to all come to a halt. So the section where join() is called on each worker thread also blocks the primary thread until the joins are complete.
224
225Since both the Process.waitFor() phase and the join() phase block the primary thread until finished, an InterruptedException could theoretically have occurred during either phase. However, we don't want an InterruptedException occurring during the join() phase, as an interrupt at this point will break us out of the join (going into an exception handler for the Interruption, prematurely ending the join()) and thus the worker threads would have been prevented from neatly cleaning up after themselves. To prevent InterruptedExceptions from occurring during any of the join() calls on the worker threads, the join() calls are embedded in a section that is marked as not interruptible. Once the join calls are finished, the code in the waitForStreans() method becomes interruptible again and a notify() is sent to anyone that was waiting for the thread to become interruptible. (Technically, the remainder of the code, the rest of the primary thread, does not respond to InterruptedExceptions hereafter, as there are no more waiting/blocking calls after the join()s are over.)
226
227Marking the join() phase as an uninterruptible section of code helps when the cancelRunProcess() is called on the SafeProcess instance by a separate thread, such as a GUI thread with a cancel button that triggered the call to cancelRunProcess(). The cancelRunProcess() method only interrupts the primary SafeProcess thread if it is in an interruptible section of code. If the primary thread is uninterruptible when cancelRunProcess() was called, then the method either
228- returns immediately if called by a GUI thread (EventDispatchThread),
229- or if cancelRunProcess(boolean forceWaitUntilInterruptible) is called with forceWaitUntilInterruptible, even if the caller is the EventDispatchThread, it will wait until the primary thread is interruptible before it returns from the cancelRunProcess() method. The wait() call blocks until notify()ed that the primary thread has become interruptible again.
230
231The cancelRunningProcess() method, which is called by a Thread external to the primary SafeProcess thread, therefore only causes an InterruptedException on the primary SafeProcess thread. It never sends an interruption during or after the primary thread is in an uninterruptible section, since only the waitFor() phase is ever to be interrupted, as waitFor() is the only phase when the external process is actually running, while the subsequent phases are already in closing down naturally and only need to do cleanup thereafter. If cancelRunningProcess() is called when the primary thread is in the uninterruptible phase after waitFor(), the cancelRunningProcess() method returns straight away or can be told to wait until the uninterupptible phase is done. Either way, it won't cause an interrupt any more, as the process is already naturally closing down.
232
233
2343. If and only if SafeProcess was cancelled, so that its Process is to be prematurely terminated, does SafeProcess call destroyProcess(). (It is not called on natural termination.) destroyProcess() ensures both the external process that is run, denoted by the Process object, and also any subprocesses that are launched by the external process are all terminated.
235
236- On Linux (only tested on Ubuntu), it was found that the simple sequence of events from interrupting the worker threads to the join()s called on them (which closed off al resources used by the worker threads) was sufficient to cleanly end the Process and any subprocesses.
237
238- On Windows, it needs to call Process.destroy() to terminate the Process and further needs to obtain the childids of any subprocesses this launched and terminate them recursively in a Windows-specific manner by calling the Windows specific kill command on each process id.
239The method "public static long getProcessID(Process p)" uses the newly included Java Native Access library to obtain the processID of any Process. Then the childpids of any process denoted by pid are obtained with the command:
240
241    "wmic process where (parentprocessid=<pid>) get processid"
242
243Having the pids of all processes to be terminated, one of "wmic process <pid> delete", "taskkill /f /t /PID <pid>" or "tskill pid" commands is invoked, whichever is available, to recursively and forcibly terminate any process and its subprocesses, by their pid. The taskkill command works like kill -9 (kill -KILL) rather than like kill -TERM.
244
245The wmic prompt-like tool, which has been present since Windows XP, not only recongises the command to delete a process by pid, but it also has commands to get the childids of a process denoted by pid, and vice-versa (to find the parent pid if you know a childpid). Much more is possible with wmic. The tskill command has also been available for a long time, taskkill is newer and may have appeared with Windows Vista or later.
246
247- On Mac, pressing cancel when building a collection in GLI launches the perl processes full-import.pl followed by full-buildcol.pl. The buildcol phase terminates even without a process.destroy() being necessary, which is as on Linux. However, for full-import.pl, process.destroy() firstly is necessary: as always, process.destroy() is able to destroy the Process that was launched (full-import.pl), but not any subprocesses that this launched in turn (such as import.pl). So on Mac, during destroyProcess(), an operating system command is issued to terminate the process and its subprocesses. See the NOTE at the end of the section.
248
249On Linux, SafeProcess() does not issue operating system commands to terminate the internal Process upon cancel, since on Linux both a process and its subprocesses seem to come to an end on their own in such a case. Nevertheless, SafeProcess now also includes code to send an OS level command to terminate a process with its subprocesses on Linux too. The way SafeProcess works on premature termination, with interrupts and closing of resources, doesn't yet require an OS level command. However, there's now a variant of destroyProcess() which takes a boolean parameter which, if false, will force an OS level command to be issued on Linux too if an entire process group (process and subprocesses) is to be destroyed.
250
251On Mac, the command is "pkill -TERM -P <pid>". This is to kill a process and subprocesses. It was tested successfully on Mac Snow Leopard.
252
253However, on Linux, this command only terminates the top level process, while any subprocesses are left running. On Linux, the OS level command to terminate the entire process group is "kill -TERM -<pid>", which has been tested successfully on Ubuntu. Note the hyphen in front of the <pid>, which treats the pid as a process group id, and terminates the entire process tree. (In contrast, the more common "kill -TERM <pid>" only terminates the top level process on Mac and Linux, leaving subprocesses running).
254
255For more information, see https://stackoverflow.com/questions/8533377/why-child-process-still-alive-after-parent-process-was-killed-in-linux
256
257NOTE:
258This note documents weird behaviour on Mac, which has not been explained yet, but which the above operating system commands to terminate the process group successfully taken care of anyway.
259
260When running the full-import.pl and full-buildcol.pl in sequence from the command line on a Mac, the regular "kill -TERM <pid> signal" only terminates the top level process and not subprocesses. To kill the entire process group, the OS specific command for killing a process (mentioned above) must be issued instead.
261When full-import.pl is run from GLI, both process.destroy() and the regular "kill -TERM <pid> signal" are able to successfully terminate the top level process, but not subprocesses. In this, sending the TERM signal results in behaviour similar to the situation with running full-import.pl from the command line.
262
263However, when full-buildcol.pl is run from GLI on a Mac the behaviour is inconsistent with the command line and with running full-import.pl from GLI. When full-buildcol.pl is run from GLI, the Process and subprocesses all terminate tidily on their own when cancel is pressed, not requiring either process.destroy() or the OS command to terminate even the top level process ID, nor requiring the command to terminate the process group either. This behaviour is similar to how both full-import.pl and full-buildcol.pl scripts come to a clean close upon cancel on Linux. In such cases, sending a TERM signal to the process (group) id returns an exitvalue of 1. This exitvalue can mean that the kill signal didn't work, but in these cases, it specifically indicates that the process was already terminated before the TERM signal was even sent to kill the process.
264
265A specific detail of the process of killing a process group on Linux and Mac is that a TERM signal is sent first. If the return value was 0, a signal was successfully sent. If it is 1 it failed in some way, including the possibility that process was already terminated. If neither of these, then it's assumed the return value indicates the termination signal was unsuccessful, and a KILL signal is sent next.
266
267Preliminary investigation of the weird behaviour on Mac has revealed the following:
268a. Sending a Ctrl-C is different in two ways from sending a kill -TERM signal.
269- Ctrl-C is "kill -2" or "kill -INT", whereas "kill -TERM" is the same as "kill -15" (and "kill -KILL" is "kill -9", which doesn't allow the killed process to do cleanup first).
270- Ctrl-C kills the foreground process of the progress group targeted by the Ctrl-C (or the process group indicated by pid). In contrast, kill -TERM or kill -KILL terminate the process with the given pid, which is likely to be a background process if any subprocesses were launched by it.
271
272b. Pressing Ctrl-C when full-import.pl is running may give the impression of having terminated the entire process group if you happen to issue the Ctrl-C at a point when full-import.pl hasn't launched any subprocesses. The parent process is killed, and therefore can't launch further subprocesses, so it looks like hte entire process tree was successfully terminated. However, if you issue Ctrl-C when a subprocess is running, that subprocess (the foreground process) is all that's terminated, while background processes are still running and can continue to launch subprocesses.
273
274Sending a regular kill -TERM or kill -KILL signal to the parent process of a process group will kill the parent process (but not the process group, unless you explicitly issued the command to terminate an entire process group). Killing the parent process will prevent future subprocesses from being launched by the parent process, but child processes remain runnning.
275
276The Java method Process.destroy(), used by GLI until the recent modifications to ensure the entire process group is terminated, behaves more like kill -TERM/kill -KILL than Ctrl-C: the actuall parent Process launched with Runtime.exec() is killed, but not subprocesses. This means that Ctrl-C is not a proper test of GLI's behaviour.
277
278Future investigation into the weird behaviour, if this ever needs to be explained, can proceed from the above. At present. issuing operating system commands to kill an entire process tree seem to work sufficiently in all cases tested, despite the weird distinctive behaviour of full-buildcol.pl on a Mac when run from GLI.
279
280__________________________________________________
281F. USAGE: CUSTOMISING
282__________________________________________________
283
284This section deals with if you want to provide customise behaviour for any of the worker threads that deal with the internal Process object's iostreams, or if you want to do some extra work at any major milestone in the outer SafeProcess instance's life cycle.
285
286
287CUSTOMISING THE BEHAVIOUR OF THE WORKER THREADS THAT HANDLE THE INTERNAL PROCESS' IOSTREAMS:
288
289Always bear in mind that each of the streams is handled in its own separate worker thread!
290So you'll need to take care of ThreadSafety yourself, if you're implementing a SafeProcess.LineByLineHandler or SafeProcess.CustomProcessHandler. You can maintain concurrency by using synchronization, for instance. See the section USEFUL SYNCHRONISATION NOTES.
291
292Customising the worker threads can be done in one of two ways:
293- you extend SafeProcess.LineByLineHandler (for the Process' stderr/stdout streams you're interested in) and then call the matching runProcess() method
294- if you want to do something drastically different, you extend SafeProcess.CustomProcessHandler (for any of the internal Process' iostreams you're interested in) and then call the matching runProcess() method
295
296    a. public int runProcess(SafeProcess.LineByLineHandler outLineByLineHandler, SafeProcess.LineByLineHandler errLineByLineHandler)
297
298If you want to deal with EACH LINE coming out of the internal Process' stdout and/or stderr streams yourself, implement SafeProcess.LineByLineHandler. You may want a different implementation if you want to deal with the Process' stdout and stderr streams differently, or the same implementation if you want to deal with them identically. Either way, you need a *separate* SafeProcess.LineByLineHandler instance for each of these two streams, since they're running in separate threads. Pass the distinct instances in to the runProcess method as parameters.
299
300You can pass null for either parameter, in which case the default behaviour for that iostream takes place, as described for the zero-argument runProcess() variant.
301
302
303Writing your own SafeProcess.LineByLineHandler:
304- extend SafeProcess.LineByLineHandler. You can make it a static inner class where you need it.
305- make the constructor call the super constructor, passing in one of SafeProcess.STDERR|STDOUT|STDIN, to indicate the specific iostream for any instantiated instance.
306- For debugging, in order to identify what stream (stderr or stdout) you're working with, you can print the thread's name by calling the CustomProcessHandler's method
307    public String getThreadNamePrefix()
308- Provide an implementation for the LineByLineHandler methods
309    public void gotLine(String line)
310    public void gotException(Exception e);
311
312Whenever the worker thread gets a line from that outputstream (stderr or stdout) of the internal process, it will call that stream's associated gotLine(line) implemention.
313Whenever the worker thread encounters an exception during the processing of that outputstream (stderr or stdout), it will call that stream's associated gotException(exception) implemention.
314
315Remember, you can use the same implementation (LineByLineHandler subclass) for both stderr and stdout outputstreams, but you must use different *instances* of the class for each stream!
316
317For EXAMPLES OF USE, see GLI's GShell.java.
318
319
320    b. public int runProcess(CustomProcessHandler procInHandler, CustomProcessHandler procOutHandler, CustomProcessHandler procErrHandler)
321
322If you want to completely override the default behaviour of any of SafeProcess' iostream related worker threads (such as if you want to read a char at a time from the stderr stream and do something, instead of the default behaviour of reading a line at a time from it), then call this method.
323
324You need to pass in an *instance* of SafeProcess.CustomProcessHandler for *each* of the 3 iostreams, since they're running in separate threads and so can't share the same instance.
325
326You can pass in null for any of these, if you want the default SafeProcess handling to apply for that stream's worker thread. For any iostream's default handling that you want to override, however, you'd implement SafeProcess.CustomProcessHandler.
327
328
329Writing your own SafeProcess.CustomProcessHandler:
330- extend SafeProcess.CustomProcessHandler. You can make it a static inner class where you need it.
331- make the constructor call the super constructor, passing in one of SafeProcess.STDERR|STDOUT|STDIN, to indicate the specific iostream for any instantiated instance.
332- implement the following method of CustomProcessHandler
333    public abstract void run(Closeable stream);
334
335Start by first casting the stream to InputStream, if the CustomProcessHandler is to read from the internal Process' stderr or stdout streams,
336else cast to Outputstream if CustomProcessHandler is to write to the internal Process' stdin stream.
337- Since you're implementing the "run()" method of the worker Thread for that iostream, you will write the code to handle any exceptions yourself
338- For debugging, in order to identify what stream you're working with, you can print the thread's name by calling the CustomProcessHandler's method
339    public String getThreadNamePrefix()
340
341Remember, you can use the same implementation (CustomProcessHandler subclass) for each of the internal process' iostreams, but you must use different *instances* of the class for each stream!
342
343For EXAMPLES OF USE, see GS3's GS2PerlConstructor.java and GLI's DownloadJob.java.
344
345
346ADDING CUSTOM HANDLERS TO HOOK INTO KEY MOMENTS OF THE EXECUTION OF THE PRIMARY THREAD:
347
348Remember that the primary thread is the thread in which the internal Process is executed in, which is whatever Thread the runProcess() method is called on your SafeProcess instance.
349
350If you just want to handle exceptions that may occur at any stage during the execution of the primary thread
351- provide an implementation of SafeProcess.ExceptionHandler:
352    public static interface ExceptionHandler {
353
354        public void gotException(Exception e);
355    }
356- configure your SafeProcess instance by calling setExceptionHandler(SafeProcess.ExceptionHandler eh) on it *before* calling a runProcess() method on that instance.
357- For EXAMPLES OF USE, see GLI's GShell.java.
358
359If, during the execution of the primary thread, you want to do some complex things during a cancel operation, such as or before and after a process is destroyed, then
360- implement SafeProcess.MainProcessHandler. See the Interface definition below. For further details, refer to the sections "CANCELLING" and "IMPLEMENTING HOOKS AROUND CANCELLING OR PROCESS' END".
361- configure your SafeProcess instance by calling setMainHandler(MainProcessHandler mph) on it *before* calling a runProcess() method on that instance.
362- For EXAMPLES OF USE, see GLI's DownloadJob.java.
363
364    public static interface MainProcessHandler {
365
366        /**
367         * Called before the streamgobbler join()s.
368         * If not overriding, the default implementation should be:
369         * public boolean beforeWaitingForStreamsToEnd(boolean forciblyTerminating) { return forciblyTerminating; }
370         * When overriding:
371         * @param forciblyTerminating is true if currently it's been decided that the process needs to be
372         * forcibly terminated. Return false if you don't want it to be. For a basic implementation,
373         * return the parameter.
374         * @return true if the process is still running and therefore still needs to be destroyed, or if
375         * you can't determine whether it's still running or not. Process.destroy() will then be called.
376         * @return false if the process has already naturally terminated by this stage. Process.destroy()
377         * won't be called, and neither will the before- and after- processDestroy methods of this class.
378        */
379        public boolean beforeWaitingForStreamsToEnd(boolean forciblyTerminating);
380
381        /**
382         * Called after the streamgobbler join()s have finished.
383         * If not overriding, the default implementation should be:
384         * public boolean afterStreamsEnded(boolean forciblyTerminating) { return forciblyTerminating; }
385         * When overriding:
386         * @param forciblyTerminating is true if currently it's been decided that the process needs to be
387         * forcibly terminated. Return false if you don't want it to be. For a basic implementation,
388         * return the parameter (usual case).
389         * @return true if the process is still running and therefore still needs to be destroyed, or if
390         * can't determine whether it's still running or not. Process.destroy() will then be called.
391         * @return false if the process has already naturally terminated by this stage. Process.destroy()
392         * won't be called, and neither will the before- and after- processDestroy methods of this class.
393        */
394        public boolean afterStreamsEnded(boolean forciblyTerminating);
395
396        /**
397         * called after join()s and before process.destroy()/destroyProcess(Process), iff forciblyTerminating
398         */
399        public void beforeProcessDestroy();
400 
401        /**
402         * Called after process.destroy()/destroyProcess(Process), iff forciblyTerminating
403         */
404        public void afterProcessDestroy();
405
406        /**
407         * Always called after process ended: whether it got destroyed or not
408         */
409        public void doneCleanup(boolean wasForciblyTerminated);
410    }
411
412__________________________________________________
413G. USAGE: CANCELLING
414__________________________________________________
415
416SafeProcess provides a way to cancel an internal Process that is run by SafeProcess, and which will ensure that the internal process and worker threads all safely terminate and tidily clean up after themselves.
417
418As explained, SafeProcess internally accomplishes this by sending an InterruptedException on the primary thread that's running the internal Process. An InterruptedException is sent only when SafeProcess is in an "interruptible" phase, as no interruption is necessary at any other time such as cleanup.
419
420Only a thread *external* to the SafeProcess' primary thread, such as a GUI thread, can call cancelRunningProcess() on a reference to the SafeProcess instance. Two variants are available:
421
422- boolean cancelRunningProcess()
423- boolean cancelRunningProcess(boolean forceWaitUntilInterruptible)
424
425The boolean value returned is true if an interrupt had to be sent, or false if one didn't need to be sent. An interrupt does not need to be sent if
426    - the process was never yet run by the time cancel was called or
427    - the internal Process has already naturally terminated and the SafeProcess has moved on to some stage of the cleanup phase by the time cancel was called.
428
429If you want to inspect the return value, a good variable name is sentInterrupt. For example,
430    boolean sentInterrupt = mySafeProc.cancelRunningProcess();
431
432
433Programming pattern:
434A graphical interface may have a Cancel button associated with an actionPerformed() method, which will be run from a GUI/EventDispatchThread when the user presses cancel. Either directly or indirectly, actionPerfomed() during a cancel action needs to lead to one of the cancelRunningProcess() method variants being called on the SafeProcess instance.
435
436The variant you choose depends on whether the thread that invokes cancel on the SafeProcess is an EventDispatchThread (a GUI thread), or else, whether you are willing to wait until SafeProcess is interruptible. If you're calling the cancel method from a GUI thread or otherwise don't care to wait, call the zero-argument variant. Otherwise, you can call the single argument version and pass in true for forceWaitUntilInterruptible.
437
438
439Usage:
440- Usually, there is no need to bother waiting for the uninterruptible phase to finish, so you can call the zero-argument version of cancelRunningProcess(), and continue as before.
441
442- If you're calling from a GUI thread and want to disable your cancel button during the uninterruptible phase, however short this may be, in order to give proper feedback to the user, then you can implement the hooks of the SafeProcess.MainHandler interface as explained in the next section.
443
444- Call the cancelRunningProcess(forceWaitUntilInterruptible=true) variant if you're not calling from a GUI thread and you want to wait until SafeProcess becomes interruptible again (if you happened to have invoked the cancel method during an uninterruptible phase).
445
446
447Further details:
448Calling cancelRunningProcess(forceWaitUntilInterruptible=true) forces the method to only return when the SafeProcess has internally become "interruptible". There is a very brief phase at the start of a SafeProcess' cleanup period that blocks until the worker threads have cleanly terminated. This phase should not be interrupted (as would have happened upon an InterruptedException being sent just then), as the uninterruptible phase happens after the internal process has finished and the process is properly terminating.
449
450If the cancel method happened to be called during this "blocking" phase and if this phase were to theoretically take long and if cancelRunningProcess() were not to return immediately if the calling thread is a GUI thread, then your graphical interface, or at least the cancel button, would have been unresponsive until the cancelRunningProcess() method finally returned. But this uninterruptible phase is short, and it always terminates, so calling cancelRunningProcess() is sufficient. And it always returns immediately if the caller is a GUI thread. The zero-argument variant of cancelRunningProecss() internally calls cancelRunningProcess(forceWaitUntilInterruptible=false) and causes the method to return immediately: either cancelRunningProcess was called when SafeProcess was interruptible and it sends an InterruptedException to the primary thread and returns, or cancelRunningProcess got called when SafeProcess was in an uninterruptible phase. And if the caller was a GUI thread (or if forceWaitUntilInterruptible was set to false), the cancelRunningProcess() method would also return immediately.
451
452
453For EXAMPLES OF USE, see GLI's GShell.java and DownloadJob.java.
454
455_________________________________________________________________
456H. USAGE: IMPLEMENTING HOOKS AROUND CANCELLING OR PROCESS' END
457_________________________________________________________________
458
459- Implement the SafeProcess.MainProcessHandler Interface, see the decription below and the section CUSTOMISING.
460- Write the hooks you want.
461- If you don't really intend to override beforeWaitingForStreamsToEnd(boolean forciblyTerminating) or afterStreamsEnded(boolean forciblyTerminating), then return the boolean parameter forciblyTerminating.
462- For EXAMPLES OF USE, see GLI's DownloadJob.java.
463
464
465The SafeProcess.MainProcessHandler provides hooks into various key stages of the SafeProcess instance's life cycle. Specifically, the clean up and termination stages of its life cycle. Currently, all stages that you can write hooks for come after the internal process has come to an end either naturally or prematurely.
466
467
468If your code needs to do some special processes during any of these stages, override them.
469
470The stages are:
471
472    1. boolean beforeWaitingForStreamsToEnd(boolean forciblyTerminating)
473
474    Called after Process.waitFor() (when the internal Process has naturally or prematurely ended) and before the worker threads are join()ed (when the cleanup phase has begun, which always occurs, regardless of whether the Process had ended naturally or was cancelled). The parameter forciblyTerminating is true if the Process had been cancelled during an interruptible phase, or if an unexpected exception had occurred. In both cases, the internal Process object may need to be destroy()ed. But if the Process had only been cancelled during an uninterruptible phase, it means it had already naturally terminated and has started cleaning up. In such cases, the internal Process object does not need to be destroy()ed and forciblyTerminating will be false.
475
476    If not overriding, return the parameter. If overriding, even if the parameter is true, you may determine the process has come to a natural end after all. In that case, the process need not be destroyed, so you'd return false. For an example, see GLI's DownloadJob.java.
477
478    If you want to disable your cancel button temporarily while the join() is taking place, this is the method to do it.
479
480
481    2. boolean afterStreamsEnded(boolean forciblyTerminating)
482
483    Called after the worker threads are join()ed, which is the start of the clean up phase. This method is also always called and the parameter indicates whether it's so far been determined that the process needs to be destroyed or not. If not overriding, return the parameter.
484
485    If you want to re-enable your cancel button since the join() have by now taken place, this is the method to do so.
486
487
488    3. void beforeProcessDestroy()
489    4. void afterProcessDestroy()
490
491    These two methods are only called if destroy() needed to be called on the internal Process object (if the Process did not come to a natural end for any reason, including being cancelled during an interruptible phase or if an unexpected exception occurred).
492
493
494    5. void doneCleanup(boolean wasForciblyTerminated)
495
496    This method is always called at the very end of the SafeProcess' lifecycle, regardless of whether the internal Process naturally terminated or needed to be destroyed as happens upon premature termination. If the process needed to be destroyed, then the parameter wasForciblyTerminated would be true.
497
498
499___________________________________________________
500I. USEFUL STATIC METHODS AND STATIC INNER CLASSES
501___________________________________________________
502
503public static boolean isAvailable(String programName)
504    - Runs the `which` cmd over the program and returns true or false
505    - `which` is included in winbin for Windows, and is part of unix systems
506
507static public boolean processRunning(Process process)
508    - returns true if the internal Process is currently running and hasn't come to an end. That is, this method returns true if Process.waitFor() is still blocking
509    - If the SafeProcess is in its cleanup/termination phase, then this method will return false, even though SafeProcess is still doing stuff.
510    - If you want to know when SafeProcess has finished in its entirety, call the instance method processRunning() on the SafeProcess object.
511
512public static long getProcessID(Process p)
513    - uses java native access (JNA, version 4.1.0 from 2013). The JNA jar files have been included into gli's lib and GS3's lib.
514    - For more details, see gli/lib/README.txt, section "B. THE jna.jar and jna-platform.jar FILES"
515
516public static void destroyProcess(Process p)
517    - will terminate any subprocesses launched by the Process p
518    - uses java native access to get processid
519    - uses OS system calls to terminate the Process and any subprocesses
520
521public static boolean closeProcess(Process prcs)
522    - will attempt to close your Process iostreams and destroy() the Process object at the end.
523
524public static boolean closeResource(Closeable resourceHandle)
525    - will attempt to cleanly close your resource (file/stream handle), logging on Exception
526
527public static boolean closeSocket(Socket resourceHandle)
528    - will attempt to cleanly close your Socket, logging on Exception.
529    - From Java 7 onwards, calling closeResource() would suffice on Sockets too. But in Java 6, Sockets didn't yet implement Closeable, so this method is to ensure backwards compatibility.
530
531public static class OutputStreamGobbler extends Thread
532    - A class that can write to a Process' inputstream from its own Thread.
533
534public static class InputStreamGobbler extends Thread
535    - Class that can read from a Process' output or error stream in its own Thread.
536    - A separate instance should be created for each stream, so that each stream has its own Thread.
537
538
539
540Package access: static methods to prematurely terminate any process denoted by processID and any subprocesses it may have launched
541
542static void killWinProcessWithID(long processID)
543
544static boolean killUnixProcessWithID(long processID)
545    - for Mac/Linux
546
547
548__________________________________________________
549J. OTHER USEFUL INSTANCE METHODS
550__________________________________________________
551
552public synchronized boolean processRunning()
553    - returns true if the SafeProcess instance has started its internal Process or is still cleaning up on its termination
554
555public boolean cancelRunningProcess()
556public boolean cancelRunningProcess(boolean forceWaitUntilInterruptible)
557    - cancel the SafeProcess instance
558    - untimately synchronized, so threadsafe
559    - returns true if the process were still running so that an interrupt needed to be sent to terminate it, returns false if sending an interrupt was unnecessary because the process had already entered the start of its termination phase when cancel was called. Will also return false if the process was never run by the time cancel was called.
560    - usually you want to call the zero-argument version
561    - See the section CANCELLING for further details
562
563_________________________________________________________________________________________________
564K. LINKS AND NOTES ON PROCESSES, PROCESS STREAMS, INTERRUPTING AND DESTROYING PROCESSES
565_________________________________________________________________________________________________
566
567Processes and streams
568
569- http://www.javaworld.com/article/2071275/core-java/when-runtime-exec---won-t.html?page=2
570explains why SafeProcess.java is implemented with worker threads to handle a Process' iostreams.
571- http://steveliles.github.io/invoking_processes_from_java.html
572- http://mark.koli.ch/leaky-pipes-remember-to-close-your-streams-when-using-javas-runtimegetruntimeexec
573
574
575Interrupting a Process:
576
577- http://stackoverflow.com/questions/2126997/who-is-calling-the-java-thread-interrupt-method-if-im-not
578- http://stackoverflow.com/questions/13623445/future-cancel-method-is-not-working?noredirect=1&lq=1
579- http://stackoverflow.com/questions/3976344/handling-interruptedexception-in-java
580- http://stackoverflow.com/questions/4906799/why-invoke-thread-currentthread-interrupt-when-catch-any-interruptexception
581- http://stackoverflow.com/questions/4906799/why-invoke-thread-currentthread-interrupt-when-catch-any-interruptexception
582- https://praveer09.github.io/technology/2015/12/06/understanding-thread-interruption-in-java/
583
584
585Destroying a process and subprocesses on various OS:
586
587- Need process id, pid, for which Java Native Access libraries (jar files) are required.
588http://stackoverflow.com/questions/4750470/how-to-get-pid-of-process-ive-just-started-within-java-program
589- To find the processID of the process launched by SafeProcess, need to use Java Native Access (JNA) jars, available jna.jar and jna-platform.jar.
590    http://stackoverflow.com/questions/4750470/how-to-get-pid-of-process-ive-just-started-within-java-program
591    http://stackoverflow.com/questions/35842/how-can-a-java-program-get-its-own-process-id
592    http://www.golesny.de/p/code/javagetpid
593    https://github.com/java-native-access/jna/blob/master/www/GettingStarted.md
594    We're using JNA v 4.1.0, downloaded from https://mvnrepository.com/artifact/net.java.dev.jna/jna
595
596WINDOWS NOTES:
597- Can't artificially send Ctrl-C: stackoverflow.com/questions/1835885/send-ctrl-c-to-process-open-by-java
598
599 On Windows, p.destroy() terminates process p that Java launched,
600 but does not terminate any processes that p may have launched. Presumably since they didn't form a proper process tree.
601    https://social.msdn.microsoft.com/Forums/windowsdesktop/en-US/e3cb7532-87f6-4ae3-9d80-a3afc8b9d437/how-to-kill-a-process-tree-in-cc-on-windows-platform?forum=vclanguage
602    https://msdn.microsoft.com/en-us/library/windows/desktop/ms684161(v=vs.85).aspx
603
604 Searching for: "forcibly terminate external process launched by Java on Windows"   
605 Not possible: stackoverflow.com/questions/1835885/send-ctrl-c-to-process-open-by-java
606 But can use taskkill or tskill or wmic commands to terminate a process by processID
607 stackoverflow.com/questions/912889/how-to-send-interrupt-key-sequence-to-a-java-process
608 Taskkill command can kill by Image Name, such as all running perl, e.g. taskkill /f /im perl.exe
609 But what if we kill perl instances not launched by GS?
610    /f Specifies to forcefully terminate the process(es). We need this flag switched on to kill childprocesses.
611    /t Terminates the specified process and any child processes which were started by it.
612            /t didn't work to terminate subprocesses. Maybe since the process wasn't launched as
613            a properly constructed processtree.
614    /im is the image name (the name of the program), see Image Name column in Win Task Manager.
615   
616 We don't want to kill all perl running processes.
617 Another option is to use wmic, available since Windows XP, to kill a process based on its command
618 which we sort of know (SafeProcess.command) and which can be seen in TaskManager under the
619 "Command Line" column of the Processes tab.
620    https://superuser.com/questions/52159/kill-a-process-with-a-specific-command-line-from-command-line
621 The following works kill any Command Line that matches -site localsite lucene-jdbm-demo
622    C:>wmic PATH win32_process Where "CommandLine like '%-site%localsite%%lucene-jdbm-demo%'" Call Terminate
623 "WMIC Wildcard Search using 'like' and %"
624    https://codeslammer.wordpress.com/2009/02/21/wmic-wildcard-search-using-like-and/
625 However, we're not even guaranteed that every perl command GS launches will contain the collection name
626 Nor do we want to kill all perl processes that GS launches with bin\windows\perl\bin\perl, though this works:
627    wmic PATH win32_process Where "CommandLine like '%bin%windows%perl%bin%perl%'" Call Terminate
628 The above could kill GS perl processes we don't intend to terminate, as they're not spawned by the particular
629 Process we're trying to terminate from the root down.
630   
631 Solution: We can use taskkill or the longstanding tskill or wmic to kill a process by ID. Since we can
632 kill an external process that SafeProcess launched OK, and only have trouble killing any child processes
633 it launched, we need to know the pids of the child processes.
634 
635 We can use Windows' wmic to discover the childpids of a process whose id we know.
636 And we can use JNA to get the process ID of the external process that SafeProcess launched.
637 
638 See links further above on how to find the processID of the process launched by SafeProcess on various OS,
639 and where to find the JNA jars needed for this.
640 
641 WMIC can show us a list of parent process id and process id of running processes, and then we can
642 kill those child processes with a specific process id.
643    https://superuser.com/questions/851692/track-which-program-launches-a-certain-process
644    http://stackoverflow.com/questions/7486717/finding-parent-process-id-on-windows
645 WMIC can get us the pids of all childprocesses launched by parent process denoted by parent pid.
646 And vice versa:
647    if you know the parent pid and want to know all the pids of the child processes spawned:
648        wmic process where (parentprocessid=596) get processid
649    if you know a child process id and want to know the parent's id:
650        wmic process where (processid=180) get parentprocessid
651 
652 The above is the current solution.
653 
654 Linux ps equivalent on Windows is "tasklist", see
655    http://stackoverflow.com/questions/4750470/how-to-get-pid-of-process-ive-just-started-within-java-program
656
657
658MAC/UNIX NOTES:
659- Kill signals, their names and numerical equivalents: http://www.faqs.org/qa/qa-831.html
660- Killing a processtree (a process group) on Unix:
661https://stackoverflow.com/questions/8533377/why-child-process-still-alive-after-parent-process-was-killed-in-linux
662Works on Linux but not Mac: kill -TERM -pid
663Works on Mac but not Linux: pkill -TERM -P pid did work
664- https://stackoverflow.com/questions/28332888/return-value-of-kill
665    "kill returns an exit code of 0 (true) if the process still existed it and was killed.
666    kill returns an exit code of 1 (false) if the kill failed, probably because the process was no longer running."
667- https://superuser.com/questions/343031/sigterm-with-a-keyboard-shortcut
668Ctrl-C sends a SIGNINT, not SIGTERM or SIGKILL. And on Ctrl-C, "the signal is sent to the foreground *process group*."
669- https://linux.die.net/man/1/kill (manual)
670- https://unix.stackexchange.com/questions/117227/why-pidof-and-pgrep-are-behaving-differently
671- https://unix.stackexchange.com/questions/67635/elegantly-get-list-of-children-processes
672- https://stackoverflow.com/questions/994033/mac-os-x-quickest-way-to-kill-quit-an-entire-process-tree-from-within-a-cocoa-a
673- https://unix.stackexchange.com/questions/132224/is-it-possible-to-get-process-group-id-from-proc
674- https://unix.stackexchange.com/questions/99112/default-exit-code-when-process-is-terminated
675
676_______________________________________________________________________________________
677L. USEFUL SYNCHRONISATION NOTES AND SUGGESTED READING ON THREADS AND THREAD SAFETY
678_______________________________________________________________________________________
679
680Things worth reading on Concurrency and Thread safety:
681
682- Deitel and Deitel's newer editions of their Java books have updated their chapter on Concurrency.
683- http://docs.oracle.com/javase/tutorial/uiswing/concurrency/
684series of Java articles on concurrency again.
685- https://docs.oracle.com/javase/tutorial/essential/concurrency/atomicvars.html
686On "primitive" like variables that provide instrinsic locks.
687
688
689Notes on synchronization:
690
691- You can declare methods are synchronized. For example,
692    public synchronized void doStuff()
693This implicitly synchronizes on the *instance* of the class on which this method is called.
694
695- Within any methods, you can synchronize on specific objects to just lock on them. You have a synchronized code block within which you can manipulate the object.
696
697Keep synchronized blocks and methods as short as you can.
698There are some subtle issues related to using synchronized methods, as explained below, that can result in deadlocks.
699
700
701More reading:
702
703- http://stackoverflow.com/questions/574240/is-there-an-advantage-to-use-a-synchronized-method-instead-of-a-synchronized-blo
704
705       "Not only do synchronized methods not lock the whole class, but they don't lock the whole instance either. Unsynchronized methods in the class may still proceed on the instance."
706       "Only the syncronized methods are locked. If there are fields you use within synced methods that are accessed by unsynced methods, you can run into race conditions."
707       
708       "synchronizing on "this" is considered in some circles to be an anti-pattern. The unintended consequence is that outside of the class someone can lock on an object reference that is equal to "this" and prevent other threads from passing the barriers within the class potentially creating a deadlock situation. Creating a "private final Object = new Object();" variable purely for locking purposes is the often used solution. Here's another question relating directly to this issue.
709
710- http://stackoverflow.com/questions/442564/avoid-synchronizedthis-in-java?lq=1"
711
712       "A private lock is a defensive mechanism, which is never a bad idea.
713
714       Also, as you alluded to, private locks can control granularity. One set of operations on an object might be totally unrelated to another but synchronized(this) will mutually exclude access to all of them."
715
716
717- http://stackoverflow.com/questions/8393883/is-synchronized-keyword-exception-safe
718     "In any scoped thread-safe block, the moment you get out of it, the thread-safety is gone."
719     "In case of an exception the lock will be released."
720
721- http://stackoverflow.com/questions/8259479/should-i-synchronize-listener-notifications-or-not
722     "Use a CopyOnWriteArrayList for your listener arrays."
723     "If you use the CopyOnWriteArrayList, then you don't have to synchronize when iterating."
724     "CopyOnWriteArrayList is thread-safe, so there is no need to synchronize."
725
726     "Use a ConcurrentLinkedQueue<Listener> ... for this kind of problems: adding, removing and iterating simultaneously on a collection.
727     A precision : this solution prevents a listener from being called from the very moment it is deregistered."
728     "It means that you start iterating, an element is added, it will be called, another is removed, it won't, all this in the same iteration cycle.
729     It's the best of both world: ensuring synchronization, while being fine grained on who gets called and who's not."
730
731Examples of using CopyOnWriteArrayList: in GLI's shell/GShell.java and GS3's gsdl3/build/CollectionConstructor.java
732
733- http://stackoverflow.com/questions/8260205/when-a-listener-is-removed-is-it-okay-that-the-event-be-called-on-that-listener
734
735- http://stackoverflow.com/questions/2282166/java-synchronizing-on-primitives
736     
737     1. You can't lock on a primitive and
738     2. Don't lock on a Long unless you're careful how you construct them. Long values created by autoboxing or Long.valueOf() in a certain range are guaranteed to be the same across the JVM which means other threads could be locking on the same exact Long object and giving you cross-talk. This can be a subtle concurrency bug (similar to locking on intern'ed strings).
739
740     Cross-talk:
741     "In electronics, crosstalk is any phenomenon by which a signal transmitted on one circuit or channel of a transmission system creates an undesired effect in another circuit or channel. Crosstalk is usually caused by undesired capacitive, inductive, or conductive coupling from one circuit, part of a circuit, or channel, to another."
742
743
744__________________________________________________
745M. TICKETS, COMMITS, TAGS
746__________________________________________________
747
748The following was already documented in ticket http://trac.greenstone.org/ticket/895
749
750    Other Java classes of GLI and GS3 src code were shifted from using Java's Process class directly to using our new SafeProcess class.
751
752    GLI src code classes that were changed:
753    /Scratch/ak19/gs3-svn-15Nov2016/gli>fgrep -rl "Process" src
754
755    + src/org/greenstone/gatherer/util/SafeProcess.java
756    + src/org/greenstone/gatherer/gui/FormatConversionDialog.java
757    + src/org/greenstone/gatherer/gui/DownloadPane.java
758    + src/org/greenstone/gatherer/util/GS3ServerThread.java
759    + 4 src/org/greenstone/gatherer/Gatherer.java [All 4 instances that used Process now go through SafeProcess instead]
760    + 1 src/org/greenstone/gatherer/download/ServerInfoDialog.java
761    + 2 src/org/greenstone/gatherer/greenstone/Classifiers.java
762    + 2 src/org/greenstone/gatherer/greenstone/Plugins.java
763    + 1 src/org/greenstone/gatherer/collection/ScriptOptions.java
764    + !! src/org/greenstone/gatherer/util/ExternalProgram.java && file/FileAssociationManager.java
765
766    After updating GS3 src code to using SafeProcess, returned to GLI:
767    - VERY HARD:
768     + 1 src/org/greenstone/gatherer/shell/GShell.java
769    - VERY, VERY HARD:
770     + 2 src/org/greenstone/gatherer/download/DownloadJob.java
771
772
773    GS3 src code classes that were changed:
774    > fgrep -r "Process" . | grep -v ".svn" | grep -v "~" | less
775
776    + 2 ./java/org/greenstone/admin/guiext/Command.java
777    X ./java/org/greenstone/gsdl3/util/Processing.java
778    + MANY OCCURRENCES ./java/org/greenstone/gsdl3/service/MapRetrieve.java
779    + Uses Processing 2 times: ./java/org/greenstone/gsdl3/util/GDBMWrapper.java
780    + ./java/org/greenstone/util/BrowserLauncher.java
781    + ./java/org/greenstone/util/RunTarget.java
782
783    In the GLI and GS3 src files modified to use SafeProcess above, only the modifications to GS3's Command.java, MapRetrieve.java and GDMBWrapper.java are untested. All others have been tested, at least on Linux. Many have also been tested on Windows.
784
785    Tested GLI's collection building (uses GShell.java's modifications) and DownloadJob.java on all 3 OS. Both have a Cancel button that should cancel any processes and subprocesses launched. Before the modifications, subprocesses would still be running on Windows and during (full-)import on the Mac when cancel was pressed. But now have added code to SafeProcess to issue OS specific system calls to terminate the process and its subprocesses successfully on Windows and Mac too.
786
787    Also tested GS3 user comments and the online GS3's doc editor's meta editing followed by rebuilding. All worked successfully on Linux, Windows and Mac with the modifications to use SafeProcess.
788
789    The modifications to GLI started with GS3ServerThread.java and other *easily* changed classes in
790    - http://trac.greenstone.org/changeset/31582 (beginning of GLI modification)
791    - until http://trac.greenstone.org/changeset/31665 (GS3 src code modification).
792
793    The version of GS3 and GLI Java code before the GS3 src was modified is at
794    - http://trac.greenstone.org/browser/main/tags/GS3-src-SafeProcess
795
796    Next, GLI's GShell.java and any associated files were modified along with SafeProcess, to support cancelling.
797
798    Then, around 22 May, GLI's DownloadJob.java and any associated class files were modified along with SafeProcess to ensure subprocesses were safely terminated on Windows when the download action was cancelled OR when building (GShell.java) was cancelled. The Mac modifications to SafeProcess to ensure subprocesses were terminated was finished on 26 May 2017.
799
800    The tagged version of the GS3 and GLI Java code for when all the changes related to using SafeProcess were made to GS3 and GLI code is at
801    - http://trac.greenstone.org/browser/main/tags/UsingSafeProcess
802
803_________________________________________________________
804N. GLI vs GS3 CODE's SAFEPROCESS.JAVA - THE DIFFERENCES
805_________________________________________________________
806
807- package name
808    GLI: package org.greenstone.gatherer.util;
809    GS3: package org.greenstone.util;
810- imports:
811    GLI: import org.greenstone.gatherer.DebugStream;
812- GS3 uses Misc.java and GLI uses Utility.java for determining the OS and the appropriate newline character representation for the OS.
813- GS3 uses its Logger object for logging messages, GLI uses System.err (Debugstream code is presently commented out).
814
815
816    $ diff gli/src/org/greenstone/gatherer/util/SafeProcess.java src/java/org/greenstone/util/SafeProcess.java
817    -----------------------------------------------------------------------------------------------------------
818    1c1
819    < package org.greenstone.gatherer.util;
820    ---
821    > package org.greenstone.util;
822    27c27
823    < import org.greenstone.gatherer.DebugStream;
824    ---
825    > //import org.greenstone.gatherer.DebugStream;
826    56c56
827    <     ///static Logger logger = Logger.getLogger(org.greenstone.util.SafeProcess.class.getName());
828    ---
829    >     static Logger logger = Logger.getLogger(org.greenstone.util.SafeProcess.class.getName());
830    153a154
831    >
832    816c817
833    <   if(Utility.isMac()) {
834    ---
835    >   if(Misc.isMac()) {
836    880c881
837    <     if(Utility.isWindows()) {
838    ---
839    >     if(Misc.isWindows()) {
840    909c910
841    <   if(!Utility.isMac() && canSkipExtraWorkIfLinux) {
842    ---
843    >   if(!Misc.isMac() && canSkipExtraWorkIfLinux) {
844    1284c1285
845    <           outputstr.append(Utility.NEWLINE); // "\n" is system dependent (Win must be "\r\n")
846    ---
847    >           outputstr.append(Misc.NEWLINE); // "\n" is system dependent (Win must be "\r\n")
848    1381c1382
849    <       /*if(Utility.isWindows()) {
850    ---
851    >       /*if(Misc.isWindows()) {
852    1416c1417
853    <   //logger.info(msg);
854    ---
855    >   logger.info(msg);
856    1418c1419
857    <   System.err.println(msg);
858    ---
859    >   //System.err.println(msg);
860    1424c1425
861    <   //logger.error(msg, e);
862    ---
863    >   logger.error(msg, e);
864    1426,1427c1427,1428
865    <   System.err.println(msg);
866    <   e.printStackTrace();
867    ---
868    >   //System.err.println(msg);
869    >   //e.printStackTrace();
870    1434c1435
871    <   //logger.error(e);
872    ---
873    >   logger.error(e);
874    1436c1437
875    <   e.printStackTrace();
876    ---
877    >   //e.printStackTrace();
878
879    -----------------------------------------------------------------------------------------------------------
880
881
882__________________________________________________
883O. FUTURE WORK, IMPROVEMENTS
884__________________________________________________
885
886- On Windows, Perl could launch processes as proper ProcessTrees: http://search.cpan.org/~gsar/libwin32-0.191/
887Then killing the root process will kill child processes naturally, and we won't need to call OS commands to terminate a process.
888- Need to find a Mac (or Unix) equivalent way creating Process Tree in Perl too.
889
890Eventually, instead of running a windows/mac or even linux command to kill the process ourselves, investigate if it is useful to change over to use
891    https://github.com/flapdoodle-oss/de.flapdoodle.embed.process/blob/master/src/main/java/de/flapdoodle/embed/process/runtime/Processes.java
892- mentioned by http://stackoverflow.com/questions/4750470/how-to-get-pid-of-process-ive-just-started-within-java-program
893- works with Apache license, http://www.apache.org/licenses/LICENSE-2.0
894- This is a Java class that uses JNA to terminate processes. It also has the getProcessID() method.
895- However, does it kill subprocesses? (The OS specific commands presently issued in SafeProcess.destroyProcess() ensure subprocesses are killed.)
896
897
898Currently, SafeProcess does Java things the way that older Java versions recognise and accept, not only for backwards compatibility with earlier versions of Java, but in order to minimise the number of drastic changes from porting the existing Greenstone GLI and GS3 code to using SafeProcess.
899
900- In future, think of changing the method doRuntimeExec() over to using ProcessBuilder, instead of Runtime.exec(). ProcessBuilder seems to have been introduced from Java 5.
901https://docs.oracle.com/javase/7/docs/api/java/lang/ProcessBuilder.html
902See also https://zeroturnaround.com/rebellabs/how-to-deal-with-subprocesses-in-java/
903which suggests using Apache Common Exec to launch processes and says what will be forthcoming in Java 9
904
905- Instead of creating and running Threads the usual way, should we use features of newer Java versions like the Concurrency API and Executor which uses Threadpools, and let Executor handle these details? Improvements would be with multicore systems
906https://stackoverflow.com/questions/3330430/does-java-have-support-for-multicore-processors-parallel-processing
907
908
909
910
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