I tried to run a Tcl script that creates a geometry file from an input file (where the geometry is defined). The script can be run simply as script.tcl inputfile.
When I run it (on both Mac and Linux) using either wish or tclsh command, I get this error:
can't read "startreg(1)": no such variable
while executing
"if { $startreg($i)==0 && $stopreg($i)==0 } {
# All are material 1, change nothing
} else {
for {set iz $startz($i)} {$iz<=$stopz($i)} {incr i..."
invoked from within
"if [string compare $descrip regions]==0 {
# Get the mednum, start and stop regions
seek $fileid $startpos start
while { [eof $fileid] != 1 } {
..."
(procedure "read_inputfile" line 214)
invoked from within
"read_inputfile "
invoked from within
"if [file exists $inputfile]==1 {
read_inputfile
} else {
puts "The file $inputfile doesn't exist!"
exit
}"
(file "~/EGS_Windows/preview3d.tcl" line 580)
Any help/suggestion would be highly appreciated!
TA
You apparently have never initialized that variable.
% array set startreg {}
% puts $startreg(1)
can't read "startreg(1)": no such element in array
% unset startreg
% puts $startreg(1)
can't read "startreg(1)": no such variable
Is startreg a global variable, and you forgot to global startreg in a proc?
I notice another error in the stacktrace
if [string compare $descrip regions]==0 {
You surely want braces around the condition, so that the test is performed when you expect it to be performed:
if {[string compare $descrip regions]==0} {
This applies to all if expressions, and all expressions in general. See this wiki page: http://wiki.tcl.tk/10225
In this case, if {$descrip eq "regions"} is more clear.
Related
i have process that generates a value. I want to forward this value into an value output channel. but i can not seem to get it working in one "go" - i'll always have to generate a file to the output and then define a new channel from the first:
process calculate{
input:
file div from json_ch.collect()
path "metadata.csv" from meta_ch
output:
file "dir/file.txt" into inter_ch
script:
"""
echo ${div} > alljsons.txt
mkdir dir
python3 $baseDir/scripts/calculate.py alljsons.txt metadata.csv dir/
"""
}
ch = inter_ch.map{file(it).text}
ch.view()
how do I fix this?
thanks!
best, t.
If your script performs a non-trivial calculation, writing the result to a file like you've done is absolutely fine - there's nothing really wrong with this approach. However, since the 'inter_ch' channel already emits files (or paths), you could simple use:
ch = inter_ch.map { it.text }
It's not entirely clear what the objective is here. If the desire is to reduce the number of channels created, consider instead switching to the new DSL 2. This won't let you avoid writing your calculated result to a file, but it might mean you can avoid an intermediary channel, potentially.
On the other hand, if your Python script actually does something rather trivial and can be refactored away, it might be possible to assign a (global) variable (below the script: keyword) such that it can be referenced in your output declaration, like the line x = ... in the example below:
Valid output
values
are value literals, input value identifiers, variables accessible in
the process scope and value expressions. For example:
process foo {
input:
file fasta from 'dummy'
output:
val x into var_channel
val 'BB11' into str_channel
val "${fasta.baseName}.out" into exp_channel
script:
x = fasta.name
"""
cat $x > file
"""
}
Other than that, your options are limited. You might have considered using the env output qualifier, but this just adds some syntactic-sugar to your shell script at runtime, such that an output file is still created:
Contents of test.nf:
process test {
output:
env myval into out_ch
script:
'''
myval=$(calc.py)
'''
}
out_ch.view()
Contents of bin/calc.py (chmod +x):
#!/usr/bin/env python
print('foobarbaz')
Run with:
$ nextflow run test.nf
N E X T F L O W ~ version 21.04.3
Launching `test.nf` [magical_bassi] - revision: ba61633d9d
executor > local (1)
[bf/48815a] process > test [100%] 1 of 1 ✔
foobarbaz
$ cat work/bf/48815aeefecdac110ef464928f0471/.command.sh
#!/bin/bash -ue
myval=$(calc.py)
# capture process environment
set +u
echo myval=$myval > .command.env
I am beginning to think my search skills are lacking.
I trying to find any articles on how with Groovy, to open an interactive process, read its output and then write to the process depending on the output text. All I can find is how printing, reading and writing with files. Nothing about how to Write to a interactive process.
The process is asking for a password
Write the password to process
Something like this if possible:
def process = "some-command.sh".execute()
process.in.eachLine { line ->
if (line.contains("enter password")) {
process.out.write("myPassword")
}
}
This here works reading from the process output:
def process = "some-command.sh".execute()
process.in.eachLine { line ->
println line
}
Though it stops when the process is asking for input. It does not print out the line with the question.
Edit: Found out why it did not print the line with the ask password. It was not a new line. The question was a simple print (not println). How do I read when there is not yet a new line?
I have been told expect can be used, but I am looking for a solution which does not require a dependency.
1.bat
#echo off
echo gogogo
set /P V=input me:
echo V=%V%
this script waits for input just after :
gogogo
input me:
this means that eachLine not triggered for input me because no new line after it
however the previous line gogogo could be caught
and following script works for gogogo but does not work for input me
groovy
def process = "1.bat".execute()
process.in.eachLine { line ->
if (line.contains("gogogo")) {
process.out.write("myPassword\n".getBytes("UTF-8"))
process.out.flush()
}
}
groovy2
probably this could be optimized.. following script works without new line:
def process = "1.bat".execute()
def pout = new ByteArrayOutputStream()
def perr = new ByteArrayOutputStream()
process.consumeProcessOutput(pout, perr) //starts listening threads and returns immediately
while(process.isAlive()){
Thread.sleep(1234)
if(pout.toString("UTF-8").endsWith("input me:")){
process.out.write("myPassword\n".getBytes("UTF-8"))
process.out.flush()
}
}
I have input data of type
abc 12d
uy 76d
ce 12a
with the lines being separated by \n and the values by \t.
The data comes from a shell command:
brlist = 'mycommand'.execute().text
Then I want to get this into a map:
brmap = brlist.split("\n").collectEntries {
tkns = it.tokenize("\t")
[ (tkns[0]): tkns[1] ]
}
I also tried
brmap = brlist.split("\n").collectEntries {
it.tokenize("\t").with { [ (it[0]): it[1] ] }
}
Both ways gave the same result, which is a map with a single entry:
brmap.toString()
# prints "[abc:12d]"
Why does only the first line of the input data end up being in the map?
Your code works, which means the input String brlist isn't what you say it is...
Are you sure that's what you have? Try printing brlist, and then it inside collectEntries
As an aside, this does the same thing as your code:
brlist.split('\n')*.split('\t')*.toList().collectEntries()
Or you could try (incase it's spaces not tabs, this will expect both)
brlist.split('\n')*.split(/\s+/)*.toList().collectEntries()
This code works
// I use 4 spaces as tab.
def text = 'sh abc.sh'.execute().text.replaceAll(" " * 4, "\t")
brmap = text.split("\n").collectEntries {
tkns = it.tokenize("\t")
[(tkns[0]) : tkns[1]]
}
assert[abc:"12d", uy:"76d", ce:"12a"] == brmap
abc.sh
#!/bin/sh
echo "abc 12d"
echo "uy 76d"
echo "ce 12a
Also, I think your groovy code is correct. maybe your mycommand has some problem.
Ok, thanks for the hints, it is a bug in Jenkins: https://issues.jenkins-ci.org/browse/JENKINS-26481.
And it has been mentioned here before: Groovy .each only iterates one time
So running into an issue with my code here not sure what exactly i'm doing wrong i pass it the two arguments it searches for the file but its always going to does not exist.
i pass this to the file
perl restore.cgi users_old_52715.tar.gz Ace_Walker
its not finding the file it exist i assure you.
#!/usr/bin/perl
use Archive::Tar;
my $tarPath = $ARGV[0];
my $playerfile = $ARGV[1].".ini";
my $tar = Archive::Tar->new($tarPath);
if ($tar->contains_file($playerfile)) {
$tar->read($tarPath);
$tar->extract_file($playerfile, './' );
print "Successfully restored $playerfile to production enviroment\n";
exit 0;
}else{
print $playefile." does not exist in this archive!\n";
exit 0;
}
Just writing Scott Hunter's comment as an answer:
Try using an absolute path instead of a relative one.
if( $tar->extract_file($playerfile, './'.$playerfile )){
print "Successfully restored $playerfile to production enviroment\n";
}
exit 0;
man Archive::Tar :
$tar->extract_file( $file, [$extract_path] )
Write an entry, whose name is equivalent to the file name provided to disk. Optionally takes a second parameter, which is the full native path (including filename) the entry will be written to.
My first question is:
Is this possible to do this, since now I have a perl script which reads Html file and extract data to display on another html file.
If the answer for the question above is Yes, my second question would be:
How to do this?
Sorry to ask frankly as this, but since I'm so new for perl, and I have to take this task, so I'm here for some useful advice or suggestion to guide me through this task. Appreciate your help in advance.
Here's a part of the code, since the whole chunk is quite long:
$date=localtime();
($TWDAY, $TMTH, $TD1D, $TSE, $TYY) = split(/\s+/, $date);
$TSE =~ s/\://g;
$STAMP=_."$TD1D$TMTH$TYY";
#ServerInfo=();
#--------------------------------------------------------------------------- -------------------------------
# Read Directory
#----------------------------------------------------------------------------------------------------------
$myDir=getcwd;
#----------------------------------------------------------------------------------------------------------
# INITIALIZE HTML FORMAT
#----------------------------------------------------------------------------------------------------------
&HTML_FORMAT;
#----------------------------------------------------------------------------------------------------------
# REPORT
#----------------------------------------------------------------------------------------------------------
if (! -d "$myDir/report") { mkdir("$myDir/report");};
$REPORTFILE="$myDir/report/checkpack".".htm";
open OUT,">$REPORTFILE" or die "\nCannot open out file $REPORTFILE\n\n";
print OUT "$Tag_Header";
#----------------------------------------------------------------------------------------------------------
sub numSort {
if ($b < $a) { return -1; }
elsif ($a == $b) { return 0;}
elsif ($b > $a) { return 1; }
}
#ArrayDir = sort numSort #DirArray;
#while (<#ArrayDir>) {
#OutputDir=grep { -f and -T } glob "$myDir/*.htm $myDir/*.html";
#}
#----------------------------------------------------------------------------------------------------------
#ReadLine3=();
$xyxycnt=0;
foreach $InputFile (#OutputDir) { #---- MAIN
$filename=(split /\//, $InputFile) [-1]; print "-"x80 ; print "\nFilename\t:$filename\n";
open IN, "<$InputFile" or die "Cannot open Input file $InputFile\n";
#MyData=();
$DataCnt=0;
#MyLine=();
$MyLineCnt=0;
while (<IN>) {
$LINE=$_;
chomp($LINE);
$LINE=~s/\<br\>/XYXY/ig;
$LINE=~s/\<\/td\>/ \nXYZXYZ\n/ig;
$LINE=~s/\<dirname\>/xxxdirnameyyy/ig;
$LINE=linetrim3($LINE);
$LINE=linetrim($LINE);
$LINE=~s/XYXY/\<br\>/ig;
$LINE=~s/xxxdirnameyyy/< dirname >/ig;
$LINE=~s/^\s+//ig;
print OUT2 "$LINE\n";
if (defined($LINE)) { $MyData[$DataCnt]="$LINE"; $DataCnt++ ; }
}
close IN;
foreach $ReadFile (#MyData) { #--- Mydata
$MyLineCnt++;
$MyLine[$MyLineCnt]="";
#### FILENAME
$ServerInfo[0]="$filename";
#### IP ADDRESS
if ($ReadFile =~ /Host\/Device Name\:/) {
#print "$ReadFile\n"
($Hostname)=(split /\:|\s+/, $ReadFile)[3]; print "$Hostname\n";
&myServerInfo("$Hostname","1");
}
if ($ReadFile =~ /IP Address\(es\)/) {#ListIP=(); $SwIP=1; $CntIP=0 ; };
#### OPERATING SYSTEM & VERSION
if ($ReadFile =~ /Operating System\:/) {
$SwIP=0;
$OS= (split /\:|\s+/, $ReadFile)[3]; &myServerInfo("$OS","3") ; print "$OS\n";
$OSVer= (split /\:|\s+/, $ReadFile)[-2]; &myServerInfo("$OSVer","4") ; print "$OSVer\n";
};
#### GET IP VALUE
if ($SwIP==1) {
$ReadFile=(split /\:/,$ReadFile) [2];
$ReadFile=~s/[a-z|A-Z]|\(|\)|\// /ig; print "$ReadFile\n";
if ($CntIP==0) {
#$ListIP[$CntIP]=(split /\s+/,$ReadFile) [1];
#ListIP="$ReadFile";
} elsif ($CntIP==1) { print "\n\t\t $ReadFile\n" ; $ListIP[$CntIP]="\n$ReadFile";
} else { print "\t\t $ReadFile\n" ; $ListIP[$CntIP]="\n$ReadFile"; };
$CntIP++;
}
I'm afraid if you don't understand what is going on in this program and you also don't understand how to approach a task like this at all, Stack Overflow might not be the right place to get help.
Let me try to show you the approach I would take with this. I'm assuming there is more code.
First, write down a list of everything you know:
What is the input format of the existing file
Where does the existing file come from now
What is the output format of the existing file
Where does the generated output file go afterwards
What does the new file look like
Where does the new file come from
Use perltidy to indent the inherited code so you can read it better. The default options should be enough.
Read the code, take notes about what pieces do what, add comments
Write a unit test for the desired output format. You can use Test::More. Another useful testing module here is Test::File.
Refactor the part that generated the output format to work with a certain data structure. Use your tests to make sure you don't break it.
Write code to parse the new file into the data structure from the point above. Now you can plug that in and get the expected output.
Refactor the part that takes the old input file from the existing file location to be a function, so you can later switch it for the new one.
Write code to get the new file from the new file location.
Document what you did so the next guy is not in the same situation. Remember that could be you in half a year.
Also add use strict and use warnings while you refactor to catch errors more easily. If stuff breaks because of that, make it work before you continue. Those pragmas tell you what's wrong. The most common one you will encounter is Global symbol "$foo" requires explicit package name. That means you need to put my in front of the first assignment, or declare the variable before.
If you have specific questions, ask them as a new question with a short example. Read how to ask to make sure you will get help on those.
Good luck!
After seing your comment I am thinking you want a different input and a different output. In that case, disregard this, throw away the old code and start from scratch. If you don't know enough Perl, get a book like Curtis Poe's Beginning Perl if you already know programming. If not, check out Learning Perl by Randal L. Schwartz.