I have a tool (written in C) that takes in output file parameter to which the tool writes some output string.
tool -o output-file-name
I would like to invoke the tool from a shell script and have the output string assigned to a variable.
I tried:
var=$(tool -o a.txt 1>/dev/null;cat a.txt && rm a.txt)
The above works, but I would like a more elegant solution.
P.S: I am far from a scripting guru.
You can start the tool without the option -o
tool
or like William Pursell wrote with /dev/stdout as file
tool -o /dev/stdout
or in short form
tool -o -
I'm assuming not possible to change to code to support output to stdout. Probably, because the code is sending additional information (logging) to stdout.
You can use IO redirection or process substitution to eliminate the need to save/recall the data from the file. The construct '>(cat)' argument tell bash the generate a pipe, between 'tool' and 'cat' (which will simply print the file).
# PREFERRED
# IO Redirection, using extra fd (#3).
var=$(./f.sh -o /dev/fd/3 3>&1 1>/dev/null)
# Use process substitution, use extra 'cat' process.
var=$(tool -o >(cat) >/dev/null)
1st solution more efficient (no extra cat running ...). 2nd solution is slightly more compact.
Since you're on linux, you can use tool -o /dev/stdout
Related
I searched online but I didn't find anything that could answer my question.
I'm using a java tool in Ubuntu Linux, calling it with bash command; this tool has two paths for two different input files:
java -Xmx8G -jar picard.jar FastqToSam \
FASTQ=6484_snippet_1.fastq \ #first read file of pair
FASTQ2=6484_snippet_2.fastq \ #second read file of pair
[...]
What I'd like to do is for example, instead of specify the path of a single FASTQ, specify the path of two different files.
So instead of having cat file1 file2 > File and using File as input of FASTQ, I'd like that this operation would be executed on the fly and create the File on the fly, without saving it on the file system (that would be what happens with the command cat file1 file2 > File).
I hope that I've been clear in explaining my question, in case just ask me and I'll try to explain better.
Most well-written shell commands which accept a file name argument also usually accept a list of file name arguments. Like cat file or cat file1 file2 etc.
If the program you are trying to use doesn't support this, and cannot easily be fixed, perhaps your OS or shell makes /dev/stdin available as a pseudo-file.
cat file1 file2 | java -mumble -crash -burn FASTQ=/dev/stdin
Some shells also have process substitutions, which (typically) look to the calling program like a single file containing whatever the process substitution produces on standard output.
java -mumble -crash -burn FASTQ=<(cat file1 file2) FASTQ2=<(cat file3 file4)
If neither of these work, a simple shell script which uses temporary files and deletes them when it's done is a tried and true solution.
#!/bin/sh
: ${4?Need four file name arguments, will process them pairwise}
t=$(mktemp -d -t fastqtwoness.XXXXXXX) || exit
trap 'rm -rf $t' EXIT HUP INT TERM # remove in case of failure or when done
cat "$1" "$2" >$t/1.fastq
cat "$3" "$4" >$t/2.fastq
exec java -mumble -crash -burn FASTQ=$t/1.fastq FASTQ2=$t/2.fastq
I am looking to write a simple script to perform a SSH command on many hosts simultaneously, and which hosts exactly are generated from another script. The problem is that when I run the script using sometihng like sed it doesn't work properly.
It should run like sshall.sh {anything here} and it will run the {anything here} part on all the nodes in the list.
sshall.sh
#!/bin/bash
NODES=`listNodes | grep "node-[0-9*]" -o`
echo "Connecting to all nodes and running: ${#:1}"
for i in $NODES
do
:
echo "$i : Begin"
echo "----------------------------------------"
ssh -q -o "StrictHostKeyChecking no" $i "${#:1}"
echo "----------------------------------------"
echo "$i : Complete";
echo ""
done
When it is run with something like whoami it works but when I run:
[root#myhost bin]# sshall.sh sed -i '/^somebeginning/ s/$/,appendme/' /etc/myconfig.conf
Connecting to all nodes and running: sed -i /^somebeginning/ s/$/,appendme/ /etc/myconfig.conf
node-1 : Begin
----------------------------------------
sed: -e expression #1, char 18: missing command
----------------------------------------
node-1 : Complete
node-2 : Begin
----------------------------------------
sed: -e expression #1, char 18: missing command
----------------------------------------
node-2 : Complete
…
Notice that the quotes disappear on the sed command when sent to the remote client.
How do I go about fixing my bash command?
Is there a better way of achieving this?
Substitute an eval-safe quoted version of your command into a heredoc:
#!/bin/bash
# ^^^^- not /bin/sh; printf %q is an extension
# Put your command into a single string, with each argument quoted to be eval-safe
printf -v cmd_q '%q ' "$#"
while IFS= read -r hostname; do
# run bash -s remotely, with that string passed on stdin
ssh -q -o 'StrictHostKeyChecking no' "$hostname" "bash -s" <<EOF
$cmd_q
EOF
done < <(listNodes | grep -o -e "node-[0-9*]")
Why this works reliably (and other approaches don't):
printf %q knows how to quote contents to be eval'd by that same shell (so spaces, wildcards, various local quoting methods, etc. will always be supported).
Arguments given to ssh are not passed to the remote command individually!
Instead, they're concatenated into a string passed to sh -c.
However: The output of printf %q is not portable to all POSIX-derived shells! It's guaranteed to be compatible with the same shell locally in use -- ksh will always parse output from printf '%q' in ksh, bash will parse output from printf '%q' in bash, etc; thus, you can't safely pass this string on the remote argument vector, because it's /bin/sh -- not bash -- running there. (If you know your remote /bin/sh is provided by bash, then you can run ssh "$hostname" "$cmd_q" safely, but only under this condition).
bash -s reads the script to run from stdin, meaning that passing your command there -- not on the argument vector -- ensures that it'll be parsed into arguments by the same shell that escaped it to be shell-safe.
You want to pass the entire command -- with all of its arguments, spaces, and quotation marks -- to ssh so it can pass it unchanged to the remote shell for parsing.
One way to do that is to put it all inside single quotation marks. But then you'll also need to make sure the single quotation marks within your command are preserved in the arguments, so the remote shell builds the correct arguments for sed.
sshall.sh 'sed -i '"'"'/^somebeginning/ s/$/,appendme/'"'"' /etc/myconfig.conf'
It looks redundant, but '"'"' is a common Bourne trick to get a single quotation mark into a single-quoted string. The first quote ends single-quoting temporarily, the double-quote-single-quote-double-quote construct appends a single quotation mark, and then the single quotation mark resumes your single-quoted section. So to speak.
Another trick that can be helpful for troubleshooting is to add the -v flag do your ssh flags, which will spit out lots of text, but most importantly it will show you exactly what string it's passing to the remote shell for parsing and execution.
--
All of this is fairly fragile around spaces in your arguments, which you'll need to avoid, since you're relying on shell parsing on the opposite end.
Thinking outside the box: instead of dealing with all the quoting issues and the word-splitting in the wrong places, you could attempt to a) construct the script locally (maybe use a here-document?), b) scp the script to the remote end, then c) invoke it there. This easily allows more complex command sequences, with all the power of shell control constructs etc. Debugging (checking proper quoting) would be a breeze by simply looking at the generated script.
I recommend reading the command(s) from the standard input rather than from the command line arguments:
cmd.sh
#!/bin/bash -
# Load server_list with user#host "words" here.
cmd=$(</dev/stdin)
for h in ${server_list[*]}; do
ssh "$h" "$cmd"
done
Usage:
./cmd.sh <<'CMD'
sed -i '/^somebeginning/ s/$/,appendme/' /path/to/file1
# other commands
# here...
CMD
Alternatively, run ./cmd.sh, type the command(s), then press Ctrl-D.
I find the latter variant the most convenient, as you don't even need for here documents, no need for extra escaping. Just invoke your script, type the commands, and press the shortcut. What could be easier?
Explanations
The problem with your approach is that the quotes are stripped from the arguments by the shell. For example, the argument '/^somebeginning/ s/$/,appendme/' will be interpreted as /^somebeginning/ s/$/,appendme/ string (without the single quotes), which is an invalid argument for sed.
Of course, you can escape the command with the built-in printf as suggested in other answer here. But the command becomes not very readable after escaping. For example
printf %q 'sed -i /^somebeginning/ s/$/,appendme/ /home/ruslan/tmp/file1.txt'
produces
sed\ -i\ /\^somebeginning/\ s/\$/\,appendme/\ /home/ruslan/tmp/file1.txt
which is not very readable, and will look ugly, if you print it to the screen in order to show the progress.
That's why I prefer to read from the standard input and leave the command intact. My script prints the command strings to the screen, and I see them just in the form I have written them.
Note, the for .. in loop iterates $IFS-separated "words", and is generally not preferred way to traverse an array. It is generally better to invoke read -r in a while loop with adjusted $IFS. I have used the for loop for simplicity, as the question is really about invoking the ssh command.
Logging into multiple systems over SSH and using the same (or variations on the same) command is the basic use case behind ansible. The system is not without significant flaws, but for simple use cases is pretty great. If you want a more solid solution without too much faffing about with escaping and looping over hosts, take a look.
Ansible has a 'raw' module which doesn't even require any dependencies on the target hosts, and you might find that a very simple way to achieve this sort of functionality in a way that frees you from the considerations of looping over hosts, handling errors, marshalling the commands, etc and lets you focus on what you're actually trying to achieve.
In terminal, sometimes I would like to display the standard output and also save it as a backup. but if I use redirection ( > &> etc), it does not display the output in the terminal anymore.
I think I can do for example ls > localbackup.txt | cat localbackup.txt. But it just doesn't feel right. Is there any shortcut to achieve this?
Thank you!
tee is the command you are looking for:
ls | tee localbackup.txt
In addition to using tee to duplicate the output (and it's worth mentioning that tee is able to append to the file instead of overwriting it, by using tee -a, so that you can run several commands in sequence and retain all of the output), you can also use tail -f to "follow" the output file from a parallel process (e.g. a separate terminal):
command1 >localbackup.txt # create output file
command2 >>localbackup.txt # append to output
and from a separate terminal, at the same time:
tail -f localbackup.txt # this will keep outputting as text is appended to the file
In bash, calling foo would display any output from that command on the stdout.
Calling foo > output would redirect any output from that command to the file specified (in this case 'output').
Is there a way to redirect output to a file and have it display on stdout?
The command you want is named tee:
foo | tee output.file
For example, if you only care about stdout:
ls -a | tee output.file
If you want to include stderr, do:
program [arguments...] 2>&1 | tee outfile
2>&1 redirects channel 2 (stderr/standard error) into channel 1 (stdout/standard output), such that both is written as stdout. It is also directed to the given output file as of the tee command.
Furthermore, if you want to append to the log file, use tee -a as:
program [arguments...] 2>&1 | tee -a outfile
$ program [arguments...] 2>&1 | tee outfile
2>&1 dumps the stderr and stdout streams.
tee outfile takes the stream it gets and writes it to the screen and to the file "outfile".
This is probably what most people are looking for. The likely situation is some program or script is working hard for a long time and producing a lot of output. The user wants to check it periodically for progress, but also wants the output written to a file.
The problem (especially when mixing stdout and stderr streams) is that there is reliance on the streams being flushed by the program. If, for example, all the writes to stdout are not flushed, but all the writes to stderr are flushed, then they'll end up out of chronological order in the output file and on the screen.
It's also bad if the program only outputs 1 or 2 lines every few minutes to report progress. In such a case, if the output was not flushed by the program, the user wouldn't even see any output on the screen for hours, because none of it would get pushed through the pipe for hours.
Update: The program unbuffer, part of the expect package, will solve the buffering problem. This will cause stdout and stderr to write to the screen and file immediately and keep them in sync when being combined and redirected to tee. E.g.:
$ unbuffer program [arguments...] 2>&1 | tee outfile
Another way that works for me is,
<command> |& tee <outputFile>
as shown in gnu bash manual
Example:
ls |& tee files.txt
If ‘|&’ is used, command1’s standard error, in addition to its standard output, is connected to command2’s standard input through the pipe; it is shorthand for 2>&1 |. This implicit redirection of the standard error to the standard output is performed after any redirections specified by the command.
For more information, refer redirection
You can primarily use Zoredache solution, but If you don't want to overwrite the output file you should write tee with -a option as follow :
ls -lR / | tee -a output.file
Something to add ...
The package unbuffer has support issues with some packages under fedora and redhat unix releases.
Setting aside the troubles
Following worked for me
bash myscript.sh 2>&1 | tee output.log
Thank you ScDF & matthew your inputs saved me lot of time..
Using tail -f output should work.
In my case I had the Java process with output logs. The simplest solution to display output logs and redirect them into the file(named logfile here) was:
my_java_process_run_script.sh |& tee logfile
Result was Java process running with output logs displaying and
putting them into the file with name logfile
You can do that for your entire script by using something like that at the beginning of your script :
#!/usr/bin/env bash
test x$1 = x$'\x00' && shift || { set -o pipefail ; ( exec 2>&1 ; $0 $'\x00' "$#" ) | tee mylogfile ; exit $? ; }
# do whaetever you want
This redirect both stderr and stdout outputs to the file called mylogfile and let everything goes to stdout at the same time.
It is used some stupid tricks :
use exec without command to setup redirections,
use tee to duplicates outputs,
restart the script with the wanted redirections,
use a special first parameter (a simple NUL character specified by the $'string' special bash notation) to specify that the script is restarted (no equivalent parameter may be used by your original work),
try to preserve the original exit status when restarting the script using the pipefail option.
Ugly but useful for me in certain situations.
Bonus answer since this use-case brought me here:
In the case where you need to do this as some other user
echo "some output" | sudo -u some_user tee /some/path/some_file
Note that the echo will happen as you and the file write will happen as "some_user" what will NOT work is if you were to run the echo as "some_user" and redirect the output with >> "some_file" because the file redirect will happen as you.
Hint: tee also supports append with the -a flag, if you need to replace a line in a file as another user you could execute sed as the desired user.
< command > |& tee filename # this will create a file "filename" with command status as a content, If a file already exists it will remove existed content and writes the command status.
< command > | tee >> filename # this will append status to the file but it doesn't print the command status on standard_output (screen).
I want to print something by using "echo" on screen and append that echoed data to a file
echo "hi there, Have to print this on screen and append to a file"
tee is perfect for this, but this will also do the job
ls -lr / > output | cat output
I'm looking for a little shell script that will take anything piped into it, and dump it to a file.. for email debugging purposes. Any ideas?
The unix command tee does this.
man tee
cat > FILENAME
You're not alone in needing something similar... in fact, someone wanted that functionality decades ago and developed tee :-)
Of course, you can redirect stdout directly to a file in any shell using the > character:
echo "hello, world!" > the-file.txt
The standard unix tool tee can do this. It copies input to output, while also logging it to a file.
Use Procmail. Procmail is your friend. Procmail is made for this sort of thing.
Use <<command>> | tee <<file>> for piping a command <<command>> into a file <<file>>.
This will also show the output.
If you want to analyze it in the script:
while /bin/true; do
read LINE
echo $LINE > $OUTPUT
done
But you can simply use cat. If cat gets something on the stdin, it will echo it to the stdout, so you'll have to pipe it to cat >$OUTPUT. These will do the same. The second works for binary data also.
If you want a shell script, try this:
#!/bin/sh
exec cat >/path/to/file
If exim or sendmail is what's writing into the pipe, then procmail is a good answer because it'll give you file locking/serialization and you can put it all in the same file.
If you just want to write into a file, then
- tee > /tmp/log.$$
or
- cat > /tmp/log.$$
might be good enough.
Huh? I guess, I don't get the question?
Can't you just end your pipe into a >> ~file
For example
echo "Foobar" >> /home/mo/dumpfile
will append Foobar to the dumpfile (and create dumpfile if necessary). No need for a shell script... Is that what you were looking for?
if you don't care about outputting the result
cat - > filename
or
cat > filename