Make script that reads argument from command line - bash

I am running quantum chemical calculations by providing the command molcas -f file.input. I now have need for putting the molcas -f into a script that also tails the last 100 lines of the generated file.log, for me to quickly confirm that everything finished the way it's supposed to. So I want to run the script run.sh:
#!/bin/bash
molcas -f [here read the file.input from command line]
tail -100 [here read the file.log]
The question is how I can make the script read the argument I give, and then find on its own the output file (which has the same filename, but with a different extension).
Follow-up
Say I have a bunch of numbered files file-1, file-2, ..., file-n. I would save time if I instead of running
./run.sh file-1.input file-1.log
I run
./run.sh n n
or
./run.sh n.input n.log
assuming that the actual filename and placement of the number n is given in the script. Can that be done?

With this code:
#!/bin/bash
molcas -f "$1"
tail -100 "$2"
You will need to execute the script run.sh as follows:
./run.sh file.input file.log

to be hornest I have/had no clue over molcas, so I jumed to this side to get basic understandings.
The syntax shoould look like this ...
#!/bin/bash
# waiting for input
read -p "Enter a filename (sample.txt): " FILE
# checking for existing file
if [ -e "$FILE" ]; then
read -p "Enter a command for moculas: " CMD
else
echo "Sorry, \"${FILE}\" was not found. Exit prgramm."
exit 1
fi
# I am not sure how this command works.
# maybe you have to edit this line by your self.
molcas $FILE -f "$CMD"
# checking for programm-errors
ERRNO=$?
if [ "$ERRNO" != "" ] && [ "$ERRNO" -gt 0 ]; then
echo "Molcas returned an error. Number: ${ERRNO}"
exit 1
fi
# cuts off the fileending (For example: sample.txt gets sample)
FILENAME="${FILE%.*}"
# checking other files
ERRFILE="${FILENAME}.err"
tail -n 100 $ERRFILE
LOGFILE="${FILENAME}.log"
tail -n 100 $LOGFILE
exit 0
I would have posted more, but its not clear what to do with this data.
Hope this helps a bit.

Related

Collecting Cron Tab entries across servers/users

Struggling with this for a couple of days. Trying to create a space delimited list of $host $useraccount $crontab entries.
I've tried a couple of different ways. Each ending in a different level of disaster, The closest I've come is this, someone point out the obvious thing I'm missing.
#!/usr/bin/bash
#Global Crontab Inventory for Scripts
#
outputfile="/localpath/cronoutput.txt"
LPARLIST=/pathto/LPAR.txt
while read LPAR;
do
ping -c 1 $LPAR > /dev/null
if [ $? -eq 0 ]; then
for user in $(ssh -n $LPAR /opt/freeware/bin/ls /var/spool/cron/crontabs);
do
while read line;
do
echo "$LPAR $user $line"
done <"$(ssh -n "$LPAR" /opt/freeware/bin/tail -n +29 /var/spool/cron/crontabs/$user)"
done
fi
done <$LPARLIST
It seems to be complaining about trying to execute the output of the tail as a command.
./crons.sh: line 11: (Several pages of cropped cron entries): File name too long
./crons.sh: line 11: : No such file or directory
./crons.sh: line 11: #
This is working for me.
#!/bin/bash
#Global Crontab Inventory for Scripts
#
outputfile="/localpath/cronoutput.txt"
LPARLIST=LPAR.txt
cat $LPARLIST |
while read LPAR;
do
ping -c 1 $LPAR > /dev/null
if [ $? -eq 0 ]; then
for user in $(ssh -n root#$LPAR ls /var/spool/cron/crontabs);
do
ssh -n "root#$LPAR" tail -n +29 /var/spool/cron/crontabs/$user |
while read line;
do
echo "$LPAR $user $line"
done
done
fi
done
I prefer cat xxx | while ... instead of redirecting input as you did. In theory it should be the same. I did not spot anything specifically wrong and I did not really change anything -- just rearranged what you had.
The advantage of the cat xxx | while ... technique is you can insert commands between the cat and the while. In this case, I would not do the tail -n +29 because you are guessing the first 29 lines are junk but that might not be true. Rather I would just do a cat of the file and then egrep out the lines that start with a hash #. Again, .... yes, the cat is redundant but who really cares. It is more general and easier to add and delete things.
I don't have the /opt packages installed and I would not depend upon them unless absolutely necessary. You are increasing dependencies. So I just used the local "ls" and "tail". I also added an explicit root# but you don't need that. It just simplified my testing.
Perhaps the ls is overflowing. Try this one:
#!/bin/bash
#Global Crontab Inventory for Scripts
#
outputfile="/localpath/cronoutput.txt"
LPARLIST=LPAR.txt
cat $LPARLIST |
while read LPAR;
do
ping -c 1 $LPAR > /dev/null
if [ $? -eq 0 ]; then
ssh -n root#$LPAR ls /var/spool/cron/crontabs |
while read user
do
ssh -n "root#$LPAR" tail -n +29 /var/spool/cron/crontabs/$user |
while read line;
do
echo "$LPAR $user $line"
done
done
fi
done
Hope this helps...

bash call script with variable

What I want to achieve is the following :
I want the subtitles for my TV Show downloaded automatically.
The script "getSubtitle.sh" is ran as soon as the show is downloaded, but it can happen that no subtitle are released yet.
So what I am doing to counter this :
Creating a file each time "getSubtitle.sh" is ran. It contain the location of the script with its arguments, for example :
/Users/theo/logSubtitle/getSubtitle.sh "The Walking Dead - 5x10 - Them.mp4" "The.Walking.Dead.S05E10.480p.HDTV.H264.mp4" "/Volumes/Window HD/Série/The Walking Dead"
If a subtitle has been found, this file will contain only this line, if no subtitle has been found, this file will have 2 lines (the first one being "no subtitle downloaded", and the second one being the path to the script as explained above)
Now, once I get this, I'm planning to run a cron everyday that will do the following :
Remove all file that have only 1 line (Subtitle found), and execute the script again for the remaining file. Here is the full script :
cd ~/logSubtitle/waiting/
for f in *
do nbligne=$(wc -l $f | cut -c 8)
if [ "$nbligne" = "1" ]
then
rm $f
else
command=$(sed -n "2 p" $f)
sh $command 3>&1 1>&2 2>&3 | grep down > $f ; echo $command >> $f
fi
done
This is unfortunately not working, I have the feeling that the script is not called.
When I replace $command by the line in the text file, it is working.
I am sure that $command match the line because of the "echo $command >> $f" at the end of my script.
So I really don't get what I am missing here, any ideas ?
Thanks.
I'm not sure what you're trying to achieve with the cut -c 8 part in wc -l $f | cut -c 8. cut -c 8 will select the 8th character of the output of wc -l.
A suggestion: to check whether your file contains 1 or two lines (and since you'll need the content of the second line, if any, anyway), use mapfile. This will slurp the file in an array, one line per field. You can use the option -n 2 to read at most 2 lines. This will be much more efficient, safe and nice than your solution:
mapfile -t -n 2 ary < file
Then:
if ((${#ary[#]}==1)); then
printf 'File contains one line only: %s\n' "${ary[0]}"
elif ((${#ary[#]==2)); then
printf 'File contains (at least) two lines:\n'
printf ' %s\n' "${ary[#]}"
else
printf >&2 'Error, no lines found in file\n'
fi
Another suggestion: use more quotes!
With this, a better way to write your script:
#!/bin/bash
dir=$HOME/logSubtitle/waiting/
shopt -s nullglob
for f in "$dir"/*; do
mapfile -t -n 2 ary < "$f"
if ((${#ary[#]}==1)); then
rm -- "$f" || printf >&2 "Error, can't remove file %s\n" "$f"
elif ((${#ary[#]}==2)); then
{ sh -c "${ary[1]}" 3>&1 1>&2 2>&3 | grep down; echo "${ary[1]}"; } > "$f"
else
printf >&2 'Error, file %s contains no lines\n' "$f"
fi
done
After the done keyword you can even add the redirection 2>> logfile to a log file if you wish. Make sure the cron job is run with your user: check crontab -l and, if needed, edit it with crontab -e.
Use eval instead of sh. The reason it works with eval and not sh is due to the number of passes to evaluate variables. sh will treat the sed command as its command to execute while eval will evaluate the sed command first and then execute the result.
Briefly explained.

How to change parameter in a file, only if the file exists and the parameter is not already set?

#!/bin/bash
# See if registry is set to expire updates
filename=hostnames
> test.log
PARAMETER=Updates
FILE=/etc/.properties
CODE=sudo if [ ! -f $FILE] && grep $PARAMETER $FILE; then echo "File found, parameter not found."
#CODE=grep $PARAMETER $FILE || sudo tee -a /etc/.properties <<< $PARAMETER
while read -r -a line
do
hostname=${line//\"}
echo $hostname":" >> test.log
#ssh -n -t -t $hostname "$CODE" >> test.log
echo $CODE;
done < "$filename"
exit
I want to set "Updates 30" in /etc/.properties on about 50 servers if:
The file exists (not all servers have the software installed)
The parameter "Updates" is not already set in the file (e.g. in case of multiple runs)
I am a little puzzled so far how, because I am not sure if this can be done in 1 line of bash code. The rest of the script works fine.
Ok, here's what i think would be a solution for you. Like explained in this article http://www.unix.com/shell-programming-scripting/181221-bash-script-execute-command-remote-servers-using-ssh.html
invoke the script which contains the commands that you want to be executed at the remote server
Code script 1:
while read -r -a line
do
ssh ${line} "bash -s" < script2
done < "$filename"
To replace a line in a text file, you can use sed (http://www.cyberciti.biz/faq/unix-linux-replace-string-words-in-many-files/)
Code script 2:
PARAMETER=Updates
FILE=/etc/.properties
NEWPARAMETER=Updates ###(What you want to write there)
if [ ! -f $FILE] && grep $PARAMETER $FILE; then exit
sed -i 's/$PARAMETER/$NEWPARAMETER/g' $FILE
So, I'm not certain this covers all your use case, I hope this helps you out if there is anything feel free to ask!

how to check for file with wildcards existance in while loop in shell script

I'm writing a bash shell script where I want to implement a sleep sequence as long as a file exists. Now, in the simplest case this is something like:
while [ -f fileName ]
do
echo "waiting"
sleep 1
done
Now, in my situation the first issue is the following: I want to use wildcards in the fileName. This can be resolved by something like:
fileName="$path/$prefix*$suffix"
while [ -f $fileName ]
do
echo "waiting"
sleep 1
done
However, this fails if more than one file matching the fileName
./testWait.sh: line 11: [: /home/nrc11/egsnrc/BEAM_TB_jaws/130318110457_s.lock: binary operator expected
how do I resolve this?
Here is the (semi) specific example:
#!/bin/bash -u
timeStamp="130318110457"
echo "prefix of files: $timeStamp"
beamDir=$(awk '{ print $0 }' $timeStamp/$timeStamp.beamDir)
file="$EGS_HOME$beamDir/$timeStamp*.lock"
echo $file
while [ -f $file ]
do
echo "waiting"
sleep 1
done
You can use grep on the expanded wildcard to verify that it returns something else than an asterisk after the time stamp:
while echo $file | grep "^$EGS_HOME$beamDir/$timeStamp"'[^*]' ; do
echo "Waiting..."
sleep 1
done
I am very user about this, I trying doing this long back, I used some thing called inotify, a package in linux, try it out, it actually makes your life more easier.

Test if a command outputs an empty string

How can I test if a command outputs an empty string?
Previously, the question asked how to check whether there are files in a directory. The following code achieves that, but see rsp's answer for a better solution.
Empty output
Commands don’t return values – they output them. You can capture this output by using command substitution; e.g. $(ls -A). You can test for a non-empty string in Bash like this:
if [[ $(ls -A) ]]; then
echo "there are files"
else
echo "no files found"
fi
Note that I've used -A rather than -a, since it omits the symbolic current (.) and parent (..) directory entries.
Note: As pointed out in the comments, command substitution doesn't capture trailing newlines. Therefore, if the command outputs only newlines, the substitution will capture nothing and the test will return false. While very unlikely, this is possible in the above example, since a single newline is a valid filename! More information in this answer.
Exit code
If you want to check that the command completed successfully, you can inspect $?, which contains the exit code of the last command (zero for success, non-zero for failure). For example:
files=$(ls -A)
if [[ $? != 0 ]]; then
echo "Command failed."
elif [[ $files ]]; then
echo "Files found."
else
echo "No files found."
fi
More info here.
TL;DR
if [[ $(ls -A | head -c1 | wc -c) -ne 0 ]]; then ...; fi
Thanks to netj
for a suggestion to improve my original:if [[ $(ls -A | wc -c) -ne 0 ]]; then ...; fi
This is an old question but I see at least two things that need some improvement or at least some clarification.
First problem
First problem I see is that most of the examples provided here simply don't work. They use the ls -al and ls -Al commands - both of which output non-empty strings in empty directories. Those examples always report that there are files even when there are none.
For that reason you should use just ls -A - Why would anyone want to use the -l switch which means "use a long listing format" when all you want is test if there is any output or not, anyway?
So most of the answers here are simply incorrect.
Second problem
The second problem is that while some answers work fine (those that don't use ls -al or ls -Al but ls -A instead) they all do something like this:
run a command
buffer its entire output in RAM
convert the output into a huge single-line string
compare that string to an empty string
What I would suggest doing instead would be:
run a command
count the characters in its output without storing them
or even better - count the number of maximally 1 character using head -c1(thanks to netj for posting this idea in the comments below)
compare that number with zero
So for example, instead of:
if [[ $(ls -A) ]]
I would use:
if [[ $(ls -A | wc -c) -ne 0 ]]
# or:
if [[ $(ls -A | head -c1 | wc -c) -ne 0 ]]
Instead of:
if [ -z "$(ls -lA)" ]
I would use:
if [ $(ls -lA | wc -c) -eq 0 ]
# or:
if [ $(ls -lA | head -c1 | wc -c) -eq 0 ]
and so on.
For small outputs it may not be a problem but for larger outputs the difference may be significant:
$ time [ -z "$(seq 1 10000000)" ]
real 0m2.703s
user 0m2.485s
sys 0m0.347s
Compare it with:
$ time [ $(seq 1 10000000 | wc -c) -eq 0 ]
real 0m0.128s
user 0m0.081s
sys 0m0.105s
And even better:
$ time [ $(seq 1 10000000 | head -c1 | wc -c) -eq 0 ]
real 0m0.004s
user 0m0.000s
sys 0m0.007s
Full example
Updated example from the answer by Will Vousden:
if [[ $(ls -A | wc -c) -ne 0 ]]; then
echo "there are files"
else
echo "no files found"
fi
Updated again after suggestions by netj:
if [[ $(ls -A | head -c1 | wc -c) -ne 0 ]]; then
echo "there are files"
else
echo "no files found"
fi
Additional update by jakeonfire:
grep will exit with a failure if there is no match. We can take advantage of this to simplify the syntax slightly:
if ls -A | head -c1 | grep -E '.'; then
echo "there are files"
fi
if ! ls -A | head -c1 | grep -E '.'; then
echo "no files found"
fi
Discarding whitespace
If the command that you're testing could output some whitespace that you want to treat as an empty string, then instead of:
| wc -c
you could use:
| tr -d ' \n\r\t ' | wc -c
or with head -c1:
| tr -d ' \n\r\t ' | head -c1 | wc -c
or something like that.
Summary
First, use a command that works.
Second, avoid unnecessary storing in RAM and processing of potentially huge data.
The answer didn't specify that the output is always small so a possibility of large output needs to be considered as well.
if [ -z "$(ls -lA)" ]; then
echo "no files found"
else
echo "There are files"
fi
This will run the command and check whether the returned output (string) has a zero length.
You might want to check the 'test' manual pages for other flags.
Use the "" around the argument that is being checked, otherwise empty results will result in a syntax error as there is no second argument (to check) given!
Note: that ls -la always returns . and .. so using that will not work, see ls manual pages. Furthermore, while this might seem convenient and easy, I suppose it will break easily. Writing a small script/application that returns 0 or 1 depending on the result is much more reliable!
For those who want an elegant, bash version-independent solution (in fact should work in other modern shells) and those who love to use one-liners for quick tasks. Here we go!
ls | grep . && echo 'files found' || echo 'files not found'
(note as one of the comments mentioned, ls -al and in fact, just -l and -a will all return something, so in my answer I use simple ls
Bash Reference Manual
6.4 Bash Conditional Expressions
-z string
True if the length of string is zero.
-n string
string
True if the length of string is non-zero.
You can use shorthand version:
if [[ $(ls -A) ]]; then
echo "there are files"
else
echo "no files found"
fi
As Jon Lin commented, ls -al will always output (for . and ..). You want ls -Al to avoid these two directories.
You could for example put the output of the command into a shell variable:
v=$(ls -Al)
An older, non-nestable, notation is
v=`ls -Al`
but I prefer the nestable notation $( ... )
The you can test if that variable is non empty
if [ -n "$v" ]; then
echo there are files
else
echo no files
fi
And you could combine both as if [ -n "$(ls -Al)" ]; then
Sometimes, ls may be some shell alias. You might prefer to use $(/bin/ls -Al). See ls(1) and hier(7) and environ(7) and your ~/.bashrc (if your shell is GNU bash; my interactive shell is zsh, defined in /etc/passwd - see passwd(5) and chsh(1)).
I'm guessing you want the output of the ls -al command, so in bash, you'd have something like:
LS=`ls -la`
if [ -n "$LS" ]; then
echo "there are files"
else
echo "no files found"
fi
sometimes "something" may come not to stdout but to the stderr of the testing application, so here is the fix working more universal way:
if [[ $(partprobe ${1} 2>&1 | wc -c) -ne 0 ]]; then
echo "require fixing GPT parititioning"
else
echo "no GPT fix necessary"
fi
Here's a solution for more extreme cases:
if [ `command | head -c1 | wc -c` -gt 0 ]; then ...; fi
This will work
for all Bourne shells;
if the command output is all zeroes;
efficiently regardless of output size;
however,
the command or its subprocesses will be killed once anything is output.
All the answers given so far deal with commands that terminate and output a non-empty string.
Most are broken in the following senses:
They don't deal properly with commands outputting only newlines;
starting from Bash≥4.4 most will spam standard error if the command output null bytes (as they use command substitution);
most will slurp the full output stream, so will wait until the command terminates before answering. Some commands never terminate (try, e.g., yes).
So to fix all these issues, and to answer the following question efficiently,
How can I test if a command outputs an empty string?
you can use:
if read -n1 -d '' < <(command_here); then
echo "Command outputs something"
else
echo "Command doesn't output anything"
fi
You may also add some timeout so as to test whether a command outputs a non-empty string within a given time, using read's -t option. E.g., for a 2.5 seconds timeout:
if read -t2.5 -n1 -d '' < <(command_here); then
echo "Command outputs something"
else
echo "Command doesn't output anything"
fi
Remark. If you think you need to determine whether a command outputs a non-empty string, you very likely have an XY problem.
Here's an alternative approach that writes the std-out and std-err of some command a temporary file, and then checks to see if that file is empty. A benefit of this approach is that it captures both outputs, and does not use sub-shells or pipes. These latter aspects are important because they can interfere with trapping bash exit handling (e.g. here)
tmpfile=$(mktemp)
some-command &> "$tmpfile"
if [[ $? != 0 ]]; then
echo "Command failed"
elif [[ -s "$tmpfile" ]]; then
echo "Command generated output"
else
echo "Command has no output"
fi
rm -f "$tmpfile"
Sometimes you want to save the output, if it's non-empty, to pass it to another command. If so, you could use something like
list=`grep -l "MY_DESIRED_STRING" *.log `
if [ $? -eq 0 ]
then
/bin/rm $list
fi
This way, the rm command won't hang if the list is empty.
As mentioned by tripleee in the question comments , use moreutils ifne (if input not empty).
In this case we want ifne -n which negates the test:
ls -A /tmp/empty | ifne -n command-to-run-if-empty-input
The advantage of this over many of the another answers when the output of the initial command is non-empty. ifne will start writing it to STDOUT straight away, rather than buffering the entire output then writing it later, which is important if the initial output is slowly generated or extremely long and would overflow the maximum length of a shell variable.
There are a few utils in moreutils that arguably should be in coreutils -- they're worth checking out if you spend a lot of time living in a shell.
In particular interest to the OP may be dirempty/exists tool which at the time of writing is still under consideration, and has been for some time (it could probably use a bump).

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