Looking for the origin of this error message:
Processing: +([^_]).flv
date: +([^_]).flv: No such file or directory
I started getting this at some point in the last few months (can't say when as I wasn't logging my cron output. I know, I know!).
When I originally wrote this, it worked ok for at least two months. I'm wondering if there was an sh update that broke it?
The script runs via crontab and gets all .flv files in the current directory without an underscore and processes each one. It then checks the modified date for files that have been created in the last 24 hours and runs the yamdi meta tag injector for .flv files.
It seems like it's not recognizing the pattern as a pattern and looking for it as an actual file to me. If I run this script from an ssh shell it works ok, it's only when running via cron that it gives this error.
shopt -s extglob
now=$(date +"%s")
for f in +([^_]).flv; do
echo "Processing: $f"
age=$(date -r "$f" +"%s")
calc=$(((now-age) / 60 / 60))
if(( calc < 24 )); then
echo "$f age=$calc"
yamdi -i "$f" -o "$f".seek
rm "$f"
cp "$f".seek "$f"
touch -d #$age "$f"
fi
done
This is most likely a problem of the wrong shell being used; make sure your script's first line represents the right shell:
#!/bin/bash
for bash, or whatever shell you wrote this for. You might want to check your environment variables that cron may set (that's a very common problem -- one assumes everything is set up correctly, but the environment that cron offers to scripts it executes is different).
Related
I've got case: there's WordPress project where I'm supposed to create a script for updating plugins and commit source changes to the separated branch. While doing this I had run into a strange issue.
Input variable:
akimset,4.0.3
all-in-one-wp-migration,6.71
What I wanted to do was iterating over each line of this variable
while read -r line; do
echo $line
done <<< "$variable"
and this piece of code worked perfectly fine, but when I have added docker-compose logic everything started to act weirdly
while read -r line; do
docker-compose run backend echo $line
done <<< "$variable"
now only one line was executed and after this script exited with 0 and stopped iterating. I have found workaround with:
echo $variable > file.tmp
for line in $(cat file.tmp); do
docker-compose run backend echo $line
done
and that works perfectly fine and it iterates each line. Now my question is: why? ZSH and shell scripting could be a bit misterious and running in edge-cases like this one isn't anything new for me, but I'm wondering why succesfully executed script broke input stream.
The problem with this
while read -r line; do
docker-compose run backend echo $line
done <<< "$variable"
is that docker allocate pseudo-TTY. After the first execution of docker-compose run (first loop) it access to the terminal using up the next lines as input.
You have to pass -T parameter to 'docker-compose run' command in order to avoid docker allocating pseudo-TTY. Then, a working code is:
while read -r line; do
docker-compose run -T backend echo $line
done < $(variable)
Update
The above solution is for docker version 18 and docker-compose version 1.17. For newer version the parameter -T is not working but you can try:
-d instead of -T to run container in background mode BUT no you will not see stdout in terminal.
If you have docker-compose v1.25.0, in your docker-compose.yml add the parameter stdin_open: false to the service.
I was able to solve the same problem by using a different loop :
for line in $(cat $variable)
do
docker-compose run backend echo $line
done
I ran into a nearly identical problem about a year ago, though the shell was bash (the command/problem was also slightly different, but it applied to your issue). I ended up writing the script in zsh.
I'm not certain what's going on, but it's not actually the exit code (you can confirm by running the following):
variable=$'akimset,4.0.3\nall-in-one-wp-migration,6.71'
while read line; do docker-compose run backend print "$line"; print "$?"; done <<<($variable)
... which yielded ...
(akimset,4.0.3
0
(I'm not at all sure where the ( came from and perhaps solving that would answer why this problem happens)
Working Script
for line in "${(f)variable}"; do
docker-compose run backend echo "$line"
done
The (f) flag tells zsh to split on newlines; the "${(f)variable" is in quotes so that any blank lines aren't lost. If you're going to include escap sequences that you want to not be converted to the corresponding values (something that I often need when reading file contents from a variable), make the flags (fV)
My problem is that I have a cluster-server with Torque PBS and want to use it to run a sequence-comparison with the program rapsearch.
The normal RapSearch command is:
./rapsearch -q protein.fasta -d database -o output -e 0.001 -v 10 -x t -z 32
Now I want to run it with 2 nodes on the cluster-server.
I've tried with: echo "./rapsearch -q protein.fasta -d database -o output -e 0.001 -v 10 -x t -z 32" | qsub -l nodes=2 but nothing happened.
Do you have any suggestions? Where I'm wrong? Help please.
Standard output (and error output) files are placed in your home directory by default; take a look. You are looking for a file named STDIN.e[numbers], it will contain the error message.
However, I see that you're using ./rapsearch but are not really being explicit about what directory you're in. Your problem is therefore probably a matter of changing directory into the directory that you submitted from. When your terminal is in the directory of the rapsearch executable, try echo "cd \$PBS_O_WORKDIR && ./rapsearch [arguments]" | qsub [arguments] to submit your job to the cluster.
Other tips:
You could add rapsearch to your path if you use it often. Then you can use it like a regular command anywhere. It's a matter of adding the line export PATH=/full/path/to/rapsearch/bin:$PATH to your .bashrc file.
Create a submission script for use with qsub. Here is a good example.
I am learning the shell language. I have creating a shell script whose function is to login into the DB and run a .sql file. Following are the contents of the script -
#!/bin/bash
set -x
echo "Login to postgres user for autoqa_rpt_production"
$DB_PATH -U $POSTGRESS_USER $Auto_rpt_production$TARGET_DB -p $TARGET_PORT
echo "Running SQL Dump - auto_qa_db_sync"
\\i auto_qa_db_sync.sql
After running the above script, I get the following error
./autoqa_script.sh: 39: ./autoqa_script.sh: /i: not found
Following one article, I tried reversing the slash but it didn't worked.
I don't understand why this is happening. Because when I try manually running the sql file, it works properly. Can anyone help?
#!/bin/bash
set -x
echo "Login to postgres user for autoqa_rpt_production and run script"
$DB_PATH -U $POSTGRESS_USER $Auto_rpt_production$TARGET_DB -p $TARGET_PORT -f auto_qa_db_sync.sql
The lines you put in a shell script are (moreless, let's say so for now) equivalent to what you would put right to the Bash prompt (the one ending with '$' or '#' if you're a root). When you execute a script (a list of commands), one command will be run after the previous terminates.
What you wanted to do is to run the client and issue a "\i ./autoqa_script.sh" comand in it.
What you did was to run the client, and after the client terminated, issue that command in Bash.
You should read about Bash pipelines - these are the way to run programs and input text inside them. Following your original idea to solving the problem, you'd write something like:
echo '\i auto_qa_db_sync.sql' | $DB_PATH -U $POSTGRESS_USER $Auto_rpt_production$TARGET_DB -p $TARGET_PORT
Hope that helps to understand.
While trying to write a script, I found an interesting issue with cat today. If I do the following at the command line, everything works properly:
var=$(ssh user#server "cat /directory/myfile.sh")
echo $var > ~/newfile.sh
This works and I have a script file with all the proper formatting and can run it. However, if I do the EXACT same thing in a script:
#!/bin/sh
var=$(ssh user#server "cat /directory/myfile.sh")
echo $var > ~/newfile.sh
The file is mangled with carriage returns and weird formatting.
Does anyone know why this is happening? My goal is to ultimately cat a script from a server and run it locally on my machine.
EDIT
I now know that this is happening because of my invoking #!/bin/sh in my shell script. The command line works because I'm using zsh and it is preserving the formatting.
Is there a way to cat back the results regardless of the shell?
As you seem to have figured out, word splitting is off by default on zsh, but on in sh, bash, etc. You can prevent word splitting in all shells by quoting the variable:
echo "$var" > ~/newfile.sh
Note that echo appends a newline to its output by default, which you can suppress (on most echo implementations and builtins) with -n.
I've got:
$ rsync -azv zope#myserver:/smb/Data/*/*/* ~/rsynced_samples/
And I want it to run forever, syncing any new file as soon as it appears on myserver:
(specifying a poll interval, such as 4 seconds would be an ok comprise)
Instead of rsync you can use inotifywait which use kernel specific file changes triggers.
This script (inotify.sh) can you give an idea:
#!/bin/bash
directory=$1
inotifywait -q -m --format '%f' -e modify -e move -e create -e delete ${directory} | while read line
do
echo "doing something with: $line";
# for example:
# cp $line to <somewhere>
You can invoke this script specifying the "monitor" directory, in this way
./inotify.sh ~/Desktop/
The $line variable contains the full file path.
If you want to limit to only newly created files you can use on the flag "-e create"
Use cron to set up a check based on your time interval (say, every minute, perhaps?) . This link should help: http://www.cyberciti.biz/faq/how-do-i-add-jobs-to-cron-under-linux-or-unix-oses/
Note that a cron tab is set up on your machine side, not in your bash script
also useful: http://benr75.com/pages/using_crontab_mac_os_x_unix_linux
and here is a code example:
1) crontab -e // this opens up your current crontab or creates one if it does not exist
2) enter: * * * * * file.sh >> log.txt // this would pipe the output of your file to a log file and run it every minute.
hope that helps