Hi I am new to tcl and I am trying to run a command in a for loop, while this command does what it needs to do, but, it throws an exception, which causes the loop to break. So, I need to ignore any error that is produced by this command and still try the command each time in my for loop.
for loop {
#do some stuff
$chassis exportPacketTrace $new_name -compress false 1 2 both #try this but ignore its error and continue
#do some stuff
}
Please help me with a good solution for this problem
if {[catch {$chassis exportPacketTrace $new_name -compress false 1 2 both} issue]} {
puts "There is a failure and it is ignored"
puts "Reason for failure : $issue"
}
Reference : catch
Related
I am trying to have a process that is launched only if a combination of conditions is met, but when checking if a channel has a path to a file, it always returns it as empty. Probably I am doing something wrong, in that case please correct my code. I tried to follow some of the suggestions in this issue but no success.
Consider the following minimal example:
process one {
output:
file("test.txt") into _chProcessTwo
script:
"""
echo "Hello world" > "test.txt"
"""
}
// making a copy so I check first if something in the channel or not
// avoids raising exception of MultipleInputChannel
_chProcessTwo.into{
_chProcessTwoView;
_chProcessTwoCheck;
_chProcessTwoUse
}
//print contents of channel
println "Channel contents: " + _chProcessTwoView.toList().view()
process two {
input:
file(myInput) from _chProcessTwoUse
when:
(!_chProcessTwoCheck.toList().isEmpty())
script:
def test = _chProcessTwoUse.toList().isEmpty() ? "I'm empty" : "I'm NOT empty"
println "The outcome is: " + test
}
I want to have process two run if and only if there is a file in the _chProcessTwo channel.
If I run the above code I obtain:
marius#dev:~/pipeline$ ./bin/nextflow run test.nf
N E X T F L O W ~ version 19.09.0-edge
Launching `test.nf` [infallible_gutenberg] - revision: 9f57464dc1
[c8/bf38f5] process > one [100%] 1 of 1 ✔
[- ] process > two -
[/home/marius/pipeline/work/c8/bf38f595d759686a497bb4a49e9778/test.txt]
where the last line are actually the contents of _chProcessTwoView
If I remove the when directive from the second process I get:
marius#mg-dev:~/pipeline$ ./bin/nextflow run test.nf
N E X T F L O W ~ version 19.09.0-edge
Launching `test.nf` [modest_descartes] - revision: 5b2bbfea6a
[57/1b7b97] process > one [100%] 1 of 1 ✔
[a9/e4b82d] process > two [100%] 1 of 1 ✔
[/home/marius/pipeline/work/57/1b7b979933ca9e936a3c0bb640c37e/test.txt]
with the contents of the second worker .command.log file being: The outcome is: I'm empty
I tried also without toList()
What am I doing wrong? Thank you in advance
Update: a workaround would be to check _chProcessTwoUse.view() != "" but that is pretty dirty
Update 2 as required by #Steve, I've updated the code to reflect a bit more the actual conditions i have in my own pipeline:
def runProcessOne = true
process one {
when:
runProcessOne
output:
file("inputProcessTwo.txt") into _chProcessTwo optional true
file("inputProcessThree.txt") into _chProcessThree optional true
script:
// this would replace the probability that output is not created
def outputSomething = false
"""
if ${outputSomething}; then
echo "Hello world" > "inputProcessTwo.txt"
echo "Goodbye world" > "inputProcessThree.txt"
else
echo "Sorry. Process one did not write to file."
fi
"""
}
// making a copy so I check first if something in the channel or not
// avoids raising exception of MultipleInputChannel
_chProcessTwo.into{
_chProcessTwoView;
_chProcessTwoCheck;
_chProcessTwoUse
}
//print contents of channel
println "Channel contents: " + _chProcessTwoView.view()
println _chProcessTwoView.view() ? "Me empty" : "NOT empty"
process two {
input:
file(myInput) from _chProcessTwoUse
when:
(runProcessOne)
script:
"""
echo "The outcome is: ${myInput}"
"""
}
process three {
input:
file(defaultInput) from _chUpstreamProcesses
file(inputFromProcessTwo) from _chProcessThree
script:
def extra_parameters = _chProcessThree.isEmpty() ? "" : "--extra-input " + inputFromProcessTwo
"""
echo "Hooray! We got: ${extra_parameters}"
"""
}
As #Steve mentioned, I should not even check if a channel is empty, NextFlow should know better to not initiate the process. But I think in this construct I will have to.
Marius
I think part of the problem here is that process 'one' creates only optional outputs. This makes dealing with the optional inputs in process 'three' a bit tricky. I would try to reconcile this if possible. If this can't be reconciled, then you'll need to deal with the optional inputs in process 'three'. To do this, you'll basically need to create a dummy file, pass it into the channel using the ifEmpty operator, then use the name of the dummy file to check whether or not to prepend the argument's prefix. It's a bit of a hack, but it works pretty well.
The first step is to actually create the dummy file. I like shareable pipelines, so I would just create this in your baseDir, perhaps under a folder called 'assets':
mkdir assets
touch assets/NO_FILE
Then pass in your dummy file if your '_chProcessThree' channel is empty:
params.dummy_file = "${baseDir}/assets/NO_FILE"
dummy_file = file(params.dummy_file)
process three {
input:
file(defaultInput) from _chUpstreamProcesses
file(optfile) from _chProcessThree.ifEmpty(dummy_file)
script:
def extra_parameters = optfile.name != 'NO_FILE' ? "--extra-input ${optfile}" : ''
"""
echo "Hooray! We got: ${extra_parameters}"
"""
}
Also, these lines are problematic:
//print contents of channel
println "Channel contents: " + _chProcessTwoView.view()
println _chProcessTwoView.view() ? "Me empty" : "NOT empty"
Calling view() will emit all values from the channel to stdout. You can ignore whatever value it returns. Unless you enable DSL2, the channel will then be empty. I think what you're looking for here is a closure:
_chProcessTwoView.view { "Found: $it" }
Be sure to append -ansi-log false to your nextflow run command so the output doesn't get clobbered. HTH.
In my Perl 6 script, I want to do a (preferably non-blocking) check of standard input to see if data is available. If this is the case, then I want to process it, otherwise I want to do other stuff.
Example (consumer.p6):
#!/usr/bin/perl6
use v6.b;
use fatal;
sub MAIN() returns UInt:D {
while !$*IN.eof {
if some_fancy_check_for_STDIN() { #TODO: this needs to be done.
for $*IN.lines -> $line {
say "Process '$line'";
}
}
say "Do something Else.";
}
say "I'm done.";
return 0;
}
As a STDIN-Generator I wrote another Perl6 script (producer.p6):
#!/usr/bin/perl6
use v6.b;
use fatal;
sub MAIN() returns UInt:D {
$*OUT.say("aaaa aaa");
sleep-until now+2;
$*OUT.say("nbbasdf");
sleep-until now+2;
$*OUT.say("xxxxx");
sleep-until now+2;
return 0;
}
If consumer.p6 works as expected, it should produce the following output, if called via ./producer.p6 | ./consumer.p6:
Process 'aaaa aaa'
Do something Else.
Process 'nbbasdf'
Do something Else.
Process 'xxxxx'
Do something Else.
I'm done.
But actually, it produces the following output (if the if condition is commented out):
Process 'aaaa aaa'
Process 'nbbasdf'
Process 'xxxxx'
Do something Else.
I'm done.
You are using an old version of Perl 6, as v6.b is from before the official release of the language.
So some of what I have below may need a newer version to work.
Also why are you using sleep-until now+2 instead of sleep 2?
One way to do this is to turn the .lines into a Channel, then you can use .poll.
#!/usr/bin/env perl6
use v6.c;
sub MAIN () {
# convert it into a Channel so we can poll it
my $lines = $*IN.Supply.lines.Channel;
my $running = True;
$lines.closed.then: {$running = False}
while $running {
with $lines.poll() -> $line {
say "Process '$line'";
}
say "Do something Else.";
sleep ½;
}
say "I'm done.";
}
Note that the code above blocks at the my $lines = … line currently; so it doesn't start doing something until the first line comes in. To get around that you could do the following
my $lines = supply {
# unblock the $*IN.Supply.lines call
whenever start $*IN.Supply {
whenever .lines { .emit }
}
}.Channel;
I know I ask a lot of questions and I know there is a lot on here about this exactly what I am trying to do but I have not been able to get it to work in my script nor figure out why it does not let me do this. I am trying to run several commands using exec in the background and the tests can range anywhere between 5 and 45 minutes (longer if they have to cue for a license). It takes forever to run them back to back so I was wondering what I need to do to make my script wait for them to finish before moving on the the next section of script.
while {$cnt <= $len} {
# Begin count for running tests
set testvar [lindex $f $cnt]
if {[file exists $path0/$testvar] == 1} {
cd $testvar
} else {
exec mkdir $testvar
cd $testvar
exec create_symobic_link_here
}
# Set up test environment
exec -ignorestderr make clean
exec -ignorestderr make depends
puts "Running $testvar"
set runtest [eval exec -ignorestderr bsub -I -q lin_i make $testvar SEED=1 VPDDUMP=on |tail -n 1 >> $path0/runtestfile &]
cd ../
incr cnt
}
I know there is nothing here to make the script wait for the process to finish but I have tried many different things any this is the only way I can get it to run everything. It just doesn't wait.
One way is to modify your tests to create a "finished" file. This file should be created whether the test completes correctly or fails.
Modify the startup loop to remove this file before starting the test:
catch { file delete $path0/$testvar/finished }
Then create a second loop:
while { true } {
after 60000
set cnt 1 ; # ?
set result 0
while { $cnt <= $len } {
set testvar [lindex $f $cnt]
if { [file exists $path0/$testvar/finished] } {
incr result
}
incr cnt
}
if { $result == $len } {
break
}
}
This loop as written will never exit if any one test doesn't create the 'finished' file. So I would add in an additional stop condition (no more than one hour) to exit the loop.
Another way would be to save the process ids of the background processes in a list and then the second loop would check each process id to see if it is still running. This method would not require any modifications to the test, but is a little harder to implement (not too hard on unix/mac, harder on windows).
Edit: loop using process id check:
To use process ids, the main loop needs to be modified to save the process ids of the background jobs:
Before the main loop starts, clear the process id list:
set pidlist {}
In the main loop, save the process ids from the exec command (In tcl, [exec ... &] returns the background process id):
lappend pidlist $runtest ; # goes after the exec bsub...
A procedure to check for the existence of a process (for unix/mac). Tcl/Tk does not have any process control commands, so the unix 'kill' command is used. 'kill -0' on unix only checks for process existence, and does not affect the execution of the process.
# return 0 if the process does not exist, 1 if it does
proc checkpid { ppid } {
set pexists [catch {exec kill -0 $ppid}]
return [expr {1-$pexists}]
}
And the second loop to check to see if the tests are done becomes:
set tottime 0
while { true } {
after 60000
incr tottime 1 ; # in minutes
set result 0
foreach {pid} $pidlist {
if { ! [checkpid $pid] } {
incr result
}
}
if { $result == $len } {
break
}
if { $tottime > 120 } {
puts "Total test time exceeded."
break ; # or exit
}
}
If a test process gets hung and never exits, this loop will never exit, so a second stop condition on total time is used.
#!/usr/bin/tclsh
proc test {} {
aaa
}
test
When I run this script I get error message:
invalid command name "aaa"
while executing
"aaa"
(procedure "test" line 2)
invoked from within
"test"
(file "./a.tcl" line 7)
If I run test command in catch I get only first line of error message.
#!/usr/bin/tclsh
proc test {} {
aaa
}
catch test msg
puts $msg
This prints:
invalid command name "aaa"
Is it possible to get full error message (file, line, procedure) in catch command? My program has many files and by getting just one line of error message it is difficult to find from where is it.
The short answer is to look at the value of errorInfo which will contain the stack trace.
The more complete answer is to look at the catch and the return manual pages and make use of the -optionsVarName parameter to the catch statement to collect the more detailed information provided. The return manual page gives some information on using this. But a rough example from an interactive session:
% proc a {} { catch {funky} err detail; return $detail }
% a
-code 1 -level 0 -errorstack {INNER {invokeStk1 funky} CALL a} -errorcode NONE -errorinfo {invalid command name "funky"
while executing
"funky"} -errorline 1
%
The detail variable is a dictionary, so use dict get $detail -errorinfo to get that particular item.
I am attempting to set up a small test environment (homelab) using CentOS 6.6, Rancid 3.1, Looking Glass, and some Cisco Switches/Routers, with httpd acting as the handler. I have picked up a little perl by means of this endeavor, but python (more 2 than 3) is my background. Right now, everything on the rancid side of things works without issue: bin/clogin successfully logs into all of the equipment in the router.db file, and logging of the configs is working as expected. All switches/routers to be accessed are available and online, verified by ssh connection to devices as well as using bin/clogin.
Right now, I have placed the lg.cgi and lgform.cgi files into var/www/cgi-bin/ which allows the forms to be run as cgi scripts. I had to modify the files to split on ';' instead of ':' due to the change in the .db file in Rancid 3.1:#record = split('\:', $_); was replaced with: #record = split('\;', $_); etc. Once that change was made, I was able to load the lgform.cgi with the proper router.db parsing. At this point, it seemed like everything should be good to go. When I attempt to ping from one of those devices out to 8.8.8.8, the file correctly redirects to lg.cgi, and the page loads, but with
main is unavailable. Try again later.
as the error, where 'main' is the router hostname. Using this output, I was able to find the function responsible for this output. Here it is before I added anything:
sub DoRsh
{
my ($router, $mfg, $cmd, $arg) = #_;
my($ctime) = time();
my($val);
my($lckobj) = LockFile::Simple->make(-delay => $lock_int,
-max => $max_lock_wait, -hold => $max_lock_hold);
if ($pingcmd =~ /\d$/) {
`$pingcmd $router`;
} else {
`$pingcmd $router 56 1`;
}
if ($?) {
print "$router is unreachable. Try again later.\n";
return(-1);
}
if ($LG_SINGLE) {
if (! $lckobj->lock("$cache_dir/$router")) {
print "$router is busy. Try again later.\n";
return(-1);
}
}
$val = &DoCmd($router, $mfg, $cmd, $arg);
if ($LG_SINGLE) {
$lckobj->unlock("$cache_dir/$router");
}
return($val);
}
In order to dig in a little deeper, I peppered that function with several print statements. Here is the modified function, followed by the output from the loaded lg.cgi page:
sub DoRsh
{
my ($router, $mfg, $cmd, $arg) = #_;
my($ctime) = time();
my($val);
my($lckobj) = LockFile::Simple->make(-delay => $lock_int,
-max => $max_lock_wait, -hold => $max_lock_hold);
if ($pingcmd =~ /\d$/) {
`$pingcmd $router`;
} else {
`$pingcmd $router 56 1`;
}
print "About to test the ($?) branch.\n";
print "Also who is the remote_user?:' $remote_user'\n";
print "What about the ENV{REMOTE_USER} '$ENV{REMOTE_USER}'\n";
print "Here is the ENV{HOME}: '$ENV{HOME}'\n";
if ($?) {
print "$lckobj is the lock object.\n";
print "#_ something else to look at.\n";
print "$? whatever this is suppose to be....\n";
print "Some variables:\n";
print "$mfg is the mfg.\n";
print "$cmd was the command passed in with $arg as the argument.\n";
print "$pingcmd $router\n";
print "$cloginrc - Is the cloginrc pointing correctly?\n";
print "$LG_SINGLE the next value to be tested.\n";
print "$router is unreachable. Try again later.\n";
return(-1);
}
if ($LG_SINGLE) {
if (! $lckobj->lock("$cache_dir/$router")) {
print "$router is busy. Try again later.\n";
return(-1);
}
}
$val = &DoCmd($router, $mfg, $cmd, $arg);
if ($LG_SINGLE) {
$lckobj->unlock("$cache_dir/$router");
}
return($val);
}
OUTPUT:
About to test the (512) branch.
Also who is the remote_user?:' '
What about the ENV{REMOTE_USER} ''
Here is the ENV{HOME}: '.'
LockFile::Simple=HASH(0x1a13650) is the lock object.
main cisco ping 8.8.8.8 something else to look at.
512 whatever this is suppose to be....
Some variables:
cisco is the mfg.
ping was the command passed in with 8.8.8.8 as the argument.
/bin/ping -c 1 main
./.cloginrc - Is the cloginrc pointing correctly?
1 the next value to be tested.
main is unreachable. Try again later.
I can provide the code for when DoRsh is called, if necessary, but it looks mostly like this:&DoRsh($router, $mfg, $cmd, $arg);.
From what I can tell the '$?' special variable (or at least according to
this reference it is a special var) is returning the 512 value, which is causing that fork to test true. The problem is I don't know what that 512 means, nor where it is coming from. Using the ref site's description ("The status returned by the last pipe close, backtick (``) command, or system operator.") and the formation of the conditional tree above, I can see that it is some error of some kind, but I don't know how else to proceed with this inspection. I'm wondering if maybe it is in response to some permission issue, since the remote_user variable is null, when I didn't expect it to be. Any guidance anyone may be able to provide would be helpful. Furthermore, if there is any information that I may have skipped over, that I didn't think to include, or that may prove helpful, please ask, and I will provide to the best of my ability
May be you put in something like
my $pingret=$pingcmd ...;
print 'Ping result was:'.$pingret;
And check the returned strings?