parallel: --pipe can now only read from STDIN.

doc/release_new_version

@@ -209,12 +209,12 @@ New in this release:
   http://www.keylength.com/en/4/ the signing key was changed from
   1024D/ID:FFFFFFF1 to 9888R/ID:88888888.
 
-* Job ad asking for GNU Parallel expertise
-  http://seattle.craigslist.org/est/sof/4006079352.html
-
 * Agalma: an automated phylogenomics workflow
   http://arxiv.org/pdf/1307.6432
 
+* Job ad asking for GNU Parallel expertise
+  http://seattle.craigslist.org/est/sof/4006079352.html
+
 * Transient Beowulf Clustering with GNU Parallel and SSHfs
   http://www.reddit.com/r/linux/comments/1ka8mn/transient_beowulf_clustering_with_gnu_parallel/
 
@@ -233,15 +233,21 @@ New in this release:
 * Using GNU Parallel to roll-your-own Map Reduce!
   http://www.rankfocus.com/?p=1
 
-* TimeMachineっぽいバックアップスクリプト
-  http://rio.tc/2013/07/timemachine-1.html
-
 * Using GNU Parallel with Amazon
   media.amazonwebservices.com/AWS_Amazon_EMR_Best_Practices.pdf
 
 * Some useful comments on GNU Parallel
   https://news.ycombinator.com/item?id=6209767
 
+* Using GNU Parallel to count reads mapping to genes for multiple BAMs
+  http://drduanehassane.com/blog/sequencing-resources
+
+* TimeMachineっぽいバックアップスクリプト
+  http://rio.tc/2013/07/timemachine-1.html
+
+* GNU ParallelでAndroid NDKの全バージョンを一括ダウンロード
+  http://qiita.com/mazgi/items/b10bf0ff3da2045d19ab
+
 * Bug fixes and man page updates.
 
 

src/parallel

@@ -68,7 +68,7 @@ if(@ARGV) {
 
 my @fhlist;
 @fhlist = map { open_or_exit($_) } @opt::a;
-if(not @fhlist) {
+if(not @fhlist and not $opt::pipe) {
     @fhlist = (*STDIN);
 }
 if($opt::skip_first_line) {
@@ -280,7 +280,7 @@ if($Global::semaphore) {
 $SIG{TERM} = \&start_no_new_jobs;
 start_more_jobs();
 if($opt::pipe) {
-    spreadstdin(@fhlist);
+    spreadstdin();
 }
 ::debug("Start draining\n");
 drain_job_queue();
@@ -301,7 +301,6 @@ sub __PIPE_MODE__ {}
 sub spreadstdin {
     # read a record
     # Spawn a job and print the record to it.
-    my @fhlist = @_; # Filehandles to read from (Defaults to STDIN)
     my $buf = "";
     my $header = "";
     if($opt::header) {
@@ -343,7 +342,7 @@ sub spreadstdin {
     my $chunk_number = 1;
     my $one_time_through;
     my $blocksize = $opt::blocksize;
-    for my $in (@fhlist) {
+    my $in = *STDIN;
 	piperead: while(1) {
 	    my $anything_written = 0;
 	    if(not read($in,substr($buf,length $buf,0),$blocksize)) {
@@ -426,7 +425,6 @@ sub spreadstdin {
 		::warning("A full record was not matched in a block. Increasing to --blocksize ".$blocksize."\n");
 	    }
 	} 
-    }
     # If there is anything left in the buffer write it
     substr($buf,0,0) = "";
     write_record_to_pipe($chunk_number++,\$header,\$buf,$recstart,$recend,length $buf);
@@ -731,7 +729,7 @@ sub get_options_from_array {
 sub parse_options {
     # Returns: N/A
     # Defaults:
-    $Global::version = 20130817;
+    $Global::version = 20130819;
     $Global::progname = 'parallel';
     $Global::infinity = 2**31;
     $Global::debug = 0;
@@ -1220,8 +1218,8 @@ sub read_args_from_command_line {
 		}
 	    }
 
-		if($group eq $Global::arg_file_sep
+	    if($group eq $Global::arg_file_sep
-		    or ($opt::internal_pipe_means_argfiles and $opt::pipe)
+	       or ($opt::internal_pipe_means_argfiles and $opt::pipe)
 		) {
 		# Group of file names on the command line.
 		# Append args into -a
@@ -1506,7 +1504,7 @@ sub start_another_job {
 		    return 0;
 		}
 	    } while ($job->is_already_in_joblog());
-	    debug("Command to run on '".$job->sshlogin()."': '".$job->replaced()."'\n");
+	    debug("Command to run on '".$job->sshlogin()->string()."': '".$job->replaced()."'\n");
             if($job->start()) {
                 $Global::running{$job->pid()} = $job;
 		if($opt::pipe) {
@@ -2847,8 +2845,8 @@ sub processes_available_by_system_limit {
         not $more_filehandles and last;
         $max_system_proc_reached and last;
 	my $before_getting_arg = time;
-        if($Global::semaphore) {
+        if($Global::semaphore or $opt::pipe) {
-	    # Skip
+	    # Skip: No need to get args
         } elsif(defined $opt::retries and $count_jobs_already_read) {
             # For retries we may need to run all jobs on this sshlogin
             # so include the already read jobs for this sshlogin
@@ -4677,10 +4675,15 @@ sub new {
     if($sum == 0) {
 	if($command eq "") {
 	    $command = $Global::replace{'{}'};
-	} else {
+	} elsif($opt::pipe) {
+	    # With --pipe you can have ::: or not
+	    if(@opt::a) {
+		$command .=" ".$Global::replace{'{}'};
+	    }
+        } else {
 	    # Add {} to the command if there are no {...}'s
 	    $command .=" ".$Global::replace{'{}'};
-        }
+	}
 	($sum,$len->{'no_args'},$len->{'context'},$len->{'contextgroups'},
 	 %replacecount) = number_of_replacements($command,$context_replace);
     }
@@ -4730,11 +4733,15 @@ sub populate {
     # max line length is reached
     # Returns: N/A
     my $self = shift;
-    if($opt::pipe) {
+#    if($opt::pipe) {
-	# --pipe => Do no read any args
+#	# --pipe => Do no read any args
-	$self->push([Arg->new("")]);
+#	$self->push([Arg->new("")]);
-	return;
+#	return;
-    }
+#    }
+#    if($opt::roundrobin) {
+#	$self->push([Arg->new("")]);
+#	return;
+#    }
     my $next_arg;
     while (not $self->{'arg_queue'}->empty()) {
 	$next_arg = $self->{'arg_queue'}->get();
@@ -5096,6 +5103,8 @@ sub replace_placeholders {
     my $context_replace = $self->{'context_replace'};
     my $replaced;
 
+#    print ::my_dump($self);
+
     if($self->{'context_replace'}) {
 	$replaced = $self->context_replace_placeholders($target,$quote);
     } else {
@@ -5105,6 +5114,11 @@ sub replace_placeholders {
 }
 
 sub context_replace_placeholders {
+    # Replace foo{}bar with fooargbar 
+    # Input:
+    #   target = foo{}bar
+    #   quote = should this be quoted?
+    # Returns: $target
     my $self = shift;
     my $target = shift;
     my $quote = shift;
@@ -5143,6 +5157,10 @@ sub context_replace_placeholders {
     while($tt =~ s/(\S*(?:$rep_str_regexp|$rep_str_pos_regexp|$rep_seq_regexp)\S*)/\0/o) {
 	$word{$1} ||= 1;
     }
+    if(not %word) {
+	# The line did no contain any replacementstrings => return unchanged
+	return $target;	
+    }
     # For each word: Generate the replacement string for that word.
     for my $origword (keys %word) {
 	my @pos_replacements=();
@@ -5778,7 +5796,7 @@ sub read_arg_from_fh {
 sub expand_combinations {
     # Input:
     #   ([xmin,xmax], [ymin,ymax], ...)
-    # Returns ([x,y,...],[x,y,...])
+    # Returns: ([x,y,...],[x,y,...])
     # where xmin <= x <= xmax and ymin <= y <= ymax
     my $minmax_ref = shift;
     my $xmin = $$minmax_ref[0];

src/parallel.texi

@@ -59,8 +59,6 @@ after the list of options. That will give you an idea of what GNU
 @strong{parallel} is capable of.
 
 You can also watch the intro video for a quick introduction:
-http://tinyogg.com/watch/TORaR/ http://tinyogg.com/watch/hfxKj/ and
-http://tinyogg.com/watch/YQuXd/ or
 http://www.youtube.com/playlist?list=PL284C9FF2488BC6D1
 
 @chapter OPTIONS

testsuite/tests-to-run/parallel-local21.sh

@@ -5,7 +5,7 @@ seq 4 5 >/tmp/in45
 
 echo "### Test basic --shebang-wrap"
 cat <<EOF > /tmp/basic--shebang-wrap
-#!/usr/local/bin/parallel --shebang-wrap /usr/bin/perl
+#!/usr/local/bin/parallel --shebang-wrap -k /usr/bin/perl
 
 print "Shebang from perl with args @ARGV\n";
 EOF
@@ -13,11 +13,11 @@ EOF
 chmod 755 /tmp/basic--shebang-wrap
 /tmp/basic--shebang-wrap arg1 arg2
 echo "### Test basic --shebang-wrap Same as"
-parallel /usr/bin/perl /tmp/basic--shebang-wrap ::: arg1 arg2
+parallel -k /usr/bin/perl /tmp/basic--shebang-wrap ::: arg1 arg2
 echo "### Test basic --shebang-wrap stdin"
 (echo arg1; echo arg2) | /tmp/basic--shebang-wrap
 echo "### Test basic --shebang-wrap Same as"
-(echo arg1; echo arg2) | parallel /usr/bin/perl /tmp/basic--shebang-wrap
+(echo arg1; echo arg2) | parallel -k /usr/bin/perl /tmp/basic--shebang-wrap
 rm /tmp/basic--shebang-wrap
 
 
@@ -47,12 +47,6 @@ print "Shebang from perl with args @ARGV\n";
 EOF
 
 chmod 755 /tmp/pipe--shebang-wrap
-echo Suboptimal
-/tmp/pipe--shebang-wrap :::: /tmp/in12 /tmp/in45
-echo Optimal
-/tmp/pipe--shebang-wrap /tmp/in12 /tmp/in45
-echo "### Test --shebang-wrap --pipe with parser options Same as"
-parallel -k --pipe /usr/bin/perl\ -p /tmp/pipe--shebang-wrap :::: /tmp/in12 /tmp/in45
 echo "### Test --shebang-wrap --pipe with parser options stdin"
 cat /tmp/in12 /tmp/in45 | /tmp/pipe--shebang-wrap
 echo "### Test --shebang-wrap --pipe with parser options Same as"

testsuite/tests-to-run/parallel-local6.sh

@@ -1,13 +1,18 @@
 #!/bin/bash
 
-echo '### Test --joblog with exitval and Test --joblog with signal'
+echo '### Test --joblog with exitval and Test --joblog with signal -- timing dependent'
-parallel --joblog /tmp/parallel_joblog_exitval 'sleep {} && echo sleep was not killed=BAD' ::: 100 2>/dev/null &
+rm /tmp/parallel_sleep
-parallel --joblog /tmp/parallel_joblog_signal 'sleep {}' ::: 100 2>/dev/null &
+#parallel --joblog /tmp/parallel_joblog_signal 'echo foo >/tmp/parallel_sleep; sleep {}' ::: 30 2>/dev/null &
+parallel --joblog /tmp/parallel_joblog_signal 'sleep {}' ::: 30 2>/dev/null &
+parallel --joblog /tmp/parallel_joblog_exitval 'echo foo >/tmp/parallel_sleep; sleep {} && echo sleep was not killed=BAD' ::: 30 2>/dev/null &
+while [ ! -e /tmp/parallel_sleep ] ; do
+  sleep 1
+done
 sleep 1
 killall -6 sleep
-sleep 2
+wait
-grep -q 134 /tmp/parallel_joblog_exitval && echo exitval OK
+grep -q 134 /tmp/parallel_joblog_exitval && echo exitval=128+6 OK
 grep -q '[^0-9]6[^0-9]' /tmp/parallel_joblog_signal && echo signal OK
 
-rm /tmp/parallel_joblog_exitval /tmp/parallel_joblog_signal
+#rm /tmp/parallel_joblog_exitval /tmp/parallel_joblog_signal
 

testsuite/tests-to-run/test60.sh

@@ -43,8 +43,4 @@ echo '### Test --wd .';
   ssh $SSHLOGIN2 mkdir -p mydir; 
   mkdir -p $HOME/mydir; cd $HOME/mydir; 
   parallel --workdir . -S $SSHLOGIN2 ::: pwd
-
-echo '### bug #35544: --pipe would read from :::: (-a)'; 
-  parallel -j1 --pipe echo foo\;cat ::: a b c :::: <(seq 3) <(seq 4 6)
-
 EOF

testsuite/wanted-results/parallel-local21

@@ -47,33 +47,6 @@ Shebang from perl with args
 Shebang from perl with args 
 5
 ### Test --shebang-wrap --pipe with parser options
-Suboptimal
-Shebang from perl with args 
-1
-Shebang from perl with args 
-2
-Shebang from perl with args 
-4
-Shebang from perl with args 
-5
-Optimal
-Shebang from perl with args 
-1
-Shebang from perl with args 
-2
-Shebang from perl with args 
-4
-Shebang from perl with args 
-5
-### Test --shebang-wrap --pipe with parser options Same as
-Shebang from perl with args 
-1
-Shebang from perl with args 
-2
-Shebang from perl with args 
-4
-Shebang from perl with args 
-5
 ### Test --shebang-wrap --pipe with parser options stdin
 Shebang from perl with args 
 1

testsuite/wanted-results/parallel-local4

@@ -91,7 +91,7 @@ echo '### bug #39360: --joblog does not work with --pipe'
 ### bug #39360: --joblog does not work with --pipe
   seq 100 | parallel --joblog - --pipe wc | tr '0-9' 'X'
 Seq	Host	Starttime	Runtime	Send	Receive	Exitval	Signal	Command
-X	:	XXXXXXXXXX.XXX	X.XXX	X	X	X	X	wc 
+X	:	XXXXXXXXXX.XXX	X.XXX	X	X	X	X	wc
     XXX     XXX     XXX
 echo '### bug #39572: --tty and --joblog do not work'
 ### bug #39572: --tty and --joblog do not work

testsuite/wanted-results/parallel-local6

@@ -1,3 +1,3 @@
-### Test --joblog with exitval and Test --joblog with signal
+### Test --joblog with exitval and Test --joblog with signal -- timing dependent
-exitval OK
+exitval=128+6 OK
 signal OK

testsuite/wanted-results/test60

@@ -70,16 +70,3 @@ redhat9.tange.dk
 /home/parallel/mydir
 ### Test --wd .
 /home/parallel/mydir
-### bug #35544: --pipe would read from :::: (-a)
-foo
-a
-b
-c
-foo
-1
-2
-3
-foo
-4
-5
-6