I am writing multiple lines in a variable to a file as part of my build step in groovy jenkins.
def output = GetProfiles()
String[] rev = output.toString().split("\n");
for(int i=0;i<rev.length;i++) {
String cred = rev[i]
bat "#echo off && echo $cred >> \"$tmpDir\\credentials\""
}
GetProfiles returns multiple lines of data and the above code works. However, it takes alot of time as it writes to the file line by line.
Is there a better approach to writing the entire set of lines in the variable to a file in one go? I tried encasing the echo command in () but that doesn't work.
bat "#echo off && (echo $output) > \"$tmpDir\\credentials\""
def output = GetProfiles().toString()
writeFile( file: "$tmpDir/credentials", text: output )
Related
Code snippet:
my $node = shift;
my $runCmd = "cmviewcl -v -f line -p ".$package_name." | awk -F \"[:|=]\" \'(\$1 == \"script_log_file\") { print \$2 }\'";
my $logfile = $output[0];
chomp $logfile;
#DC1_list = utils::getDC1Host($hash_ref);
#DC2_list = utils::getDC2Host($hash_ref);
foreach $node1 (#DC1_list) {
$runCmd = "cmexec $node1 echo \"\" > ".$logfile;
Please let me know the what's this line means:
$runCmd = "cmexec $node1 echo \"\" > ".$logfile;
it was written before as:
$runCmd = "cmexec $node1 rm -rf ".$logfile;
which probably means remove the file in logfile variable forced recursive, but later changed to the above. so
what's it's doing?
Remove a file is different than an empty file.
The first option keep the file but override the content with "" (2x double quote), the second one remove the file.
Maybe your application need the file exist, because of this you cannot remove it.
If you have really copied this line verbatim, it is pretty nonsense.
Let's assume that the variables mentioned here have the folllowing values:
runCmd has value FOO
node1 has value BAR
logfile has value BAZ
After parameter expansion and making the quoting a bit more legible, this leaves you with a line equivalent to
FOO = 'cmexec BAR echo "" >' .BAZ
This means that a command named FOO is invoked. It must either be an executable file in the PATH, or a function. This command gets three parameters:
First parameter : a lonely equal sign
Second parameter: The string cmexec BAR echo "" >
Third paramete : the string .BAZ
I don't believe that anybody would seriously write such a command; my guess is that you made a typo, or error when doing a copy&paste of this command.
I have a nextflow script that creates a variable from a text file, and I need to pass the value of that variable to a command line order (which is a bioconda package). Those two processes happen inside the "script" part. I have tried to call the variable using the '$' symbol without any results, I think because using that symbol in the script part of a nextflow script is for calling variables defined in the input part.
To make myself clearer, here is a code sample of what I'm trying to achieve:
params.gz_file = '/path/to/file.gz'
params.fa_file = '/path/to/file.fa'
params.output_dir = '/path/to/outdir'
input_file = file(params.gz_file)
fasta_file = file(params.fa_file)
process foo {
//publishDir "${params.output_dir}", mode: 'copy',
input:
path file from input_file
path fasta from fasta_file
output:
file ("*.html")
script:
"""
echo 123 > number.txt
parameter=`cat number.txt`
create_report $file $fasta --flanking $parameter
"""
}
By doig this the error I recieve is:
Error executing process > 'foo'
Caused by:
Unknown variable 'parameter' -- Make sure it is not misspelt and defined somewhere in the script before using it
Is there any way to call the variable parameter inside the script without Nextflow interpreting it as an input file? Thanks in advance!
The documentation re the script block is useful here:
Since Nextflow uses the same Bash syntax for variable substitutions in
strings, you need to manage them carefully depending on if you want to
evaluate a variable in the Nextflow context - or - in the Bash
environment execution.
One solution is to escape your shell (Bash) variables by prefixing them with a back-slash (\) character, like in the following example:
process foo {
script:
"""
echo 123 > number.txt
parameter="\$(cat number.txt)"
echo "\${parameter}"
"""
}
Another solution is to instead use a shell block, where dollar ($) variables are managed by your shell (Bash interpreter), while exclamation mark (!) variables are handled by Nextflow. For example:
process bar {
echo true
input:
val greeting from 'Hello', 'Hola', 'Bonjour'
shell:
'''
echo 123 > number.txt
parameter="$(cat number.txt)"
echo "!{greeting} parameter ${parameter}"
'''
}
declare "parameter" in the top 'params' section.
params.parameter="1234"
(..)
script:
"""
(...)
create_report $file $fasta --flanking ${params.parameter}
(...)
"""
(...)
and call "nextflow run" with "--parameter 87678"
I am trying to execute set of commands from jenkinsfile.
The problem is, when I try to assign the value of stdout to a variable it is not working.
I tried different combinations of double quotes and single quotes, but so far no luck.
Here I executed the script with latest version of jenkinsfile as well as old version. Putting shell commands inside """ """ is not allowing to create new variable and giving error like client_name command does not exist.
String nodeLabel = env.PrimaryNode ? env.PrimaryNode : "slave1"
echo "Running on node [${nodeLabel}]"
node("${nodeLabel}"){
sh "p4 print -q -o config.yml //c/test/gradle/hk/config.yml"
def config = readYaml file: 'devops-config.yml'
def out = sh (script:"client_name=${config.BasicVars.p4_client}; " +
'echo "client name: $client_name"' +
" cmd_output = p4 clients -e $client_name" +
' echo "out variable: $cmd_output"',returnStdout: true)
}
I want to assign the stdout from the command p4 clients -e $client_name to variable cmd_output.
But when I execute the code the error that is thrown is:
NoSuchPropertyException: client_name is not defined at line cmd_output = p4 clients -e $client_name
What am I missing here?
Your problem here is that all the $ are interpreted by jenkins when the string is in double quotes. So the first 2 times there's no problem since the first variable comes from jenkins and the second time it's a single quote string.
The the third variable is in a double quote string, therefore jenkins tries to replace the variable with its value but it can't find it since it's generated only when the shell script is executed.
The solution is to escape the $ in $client_name (or define client_name in an environment block).
I rewrote the block:
String nodeLabel = env.PrimaryNode ? env.PrimaryNode : "slave1"
echo "Running on node [${nodeLabel}]"
node("${nodeLabel}"){
sh "p4 print -q -o config.yml //c/test/gradle/hk/config.yml"
def config = readYaml file: 'devops-config.yml'
def out = sh (script: """
client_name=${config.BasicVars.p4_client}
echo "client name: \$client_name"
cmd_output = p4 clients -e \$client_name
echo "out variable: \$cmd_output"
""", returnStdout: true)
}
In Windows Command Line I normally write empty line in a file with
echo; >> file
However, what I have now is a variable
$param1%
If I want echo to write it in the file I have to do
echo %param1% >> file
HERE IS WHERE THE PROBLEM START :
If I'd like an empty like I'd make
set param1=;
However since the ; is not in contact with the echo word the command is
echo ; >> file
which write the ; in the file...
I need the variable to sometime contains text, and sometime nothing. How can I do it?
if "%param1%"=="" echo;>>file else echo %param1%>>file
If a param1 variable does not exist (the same as set "param1="), then %param1% results to:
In a .bat script: %param1% results to an empty string (a string of zero length);
In a CLI window: %param1% results to the %param1% string.
In a .bat script use (note no spaces surrounding %param1%)
>> file (echo;%param1%)
In a CLI window use
>>file (if not defined param1 (echo;) else echo;%param1%)
Note proper using of parentheses in if-else! For instance, check interesting result of next command:
if ""=="" echo;"THEN branch">>file else echo;"ELSE branch">>file
Output:
==>if ""=="" echo;"THEN branch">>file else echo;"ELSE branch">>file
==>type file
"THEN branch" else echo;"ELSE branch"
I am currently running this script in Windows 7.
So, I have a program that is meant to color-code output from another command (mkmk) and tally up varying numbers of errors and other notable stats, etc. So right now, it starts as a batch file which
Turns off echo
Sets some color values to variables
Calls the mkmk command and the awk script together
The awk script then parses line by line, and calls a function which then calls an exe that performs the Colorizing. Works like follows:
/: error/ {
CntError++ ;
TraError[CntError] = $0;
colorf(cErrorDcb,$0) ;
next
}
function colorf(fg, str ) {
if ( Couleur < 1 )
{
printf("%s\n",str);
}
else
{
if ( System == "UNIX" )
{
printf("%s%s%s%s\n",fg,bg,str,NORMAL);
}
else
{
system("Colorize.exe /c:" fg " \"" str "\"");
printf("\n");
}
}
}
So, everything works, EXCEPT that every time system("Colorize.exe") is called (a lot), the command is outputted in the terminal and clutters up the output. It doesn't appear to be affected by the #echo off command in my batch file since it is called inside the awk script. Is there anyway to hide only these system commands but keep the rest of my awk output?
I have no idea what the magical Windows incantations are to control what displays on the terminal but in general instead of calling system() and letting the command it calls produce it's own output that's getting mixed in with the awk output, use getline to read the result of the call to populate a variable and then print that from awk. Something like this:
/: error/ {
TraError[++CntError] = $0
print colorf(cErrorDcb,$0)
next
}
function colorf(fg, str, cmd, line, colorStr) {
if ( Couleur < 1 ) {
colorStr = str
}
else if ( System == "UNIX" ) {
colorStr = fg bg str NORMAL
}
else {
cmd = "Colorize.exe /c:" fg " \"" str "\""
colorStr = ( (cmd | getline line) > 0 ? line : str )
close(cmd)
}
return colorStr
}
I got rid of all of the useless semi-colons too.
Best advice - get cygwin!