I am trying to generate a file using cat in bash where inside the bash, i already ran a script, that i saved into a variable then will be used inside the cat. To ran the script and save the output to a variable, I used the following:
declare RESULT=$(./script.pl 5 5 5)
Next, I show an excerpt of the cat file where the variable RESULT is being used.
cat> input.in<<EOF
bla bla
echo $RESULT
EOF
What I obtain after running the bash, is the correct output of the variable RESULT. However, there is a word echo in the beginning of the file (as shown below). This is problematic because I am trying to automate a code, and adding the word echo ruins the code.
echo K_POINTS crystal
64
0.00000000 0.00000000 0.00000000 1.562500e-02
0.00000000 0.00000000 0.25000000 1.562500e-02
0.00000000 0.00000000 0.50000000 1.562500e-02
Can you tell me please what is the problem? Thanks a lot!
Here documents don't run the contents as commands, they just expand values like $RESULT.
cat> input.in<<EOF
bla bla
$RESULT
EOF
If you wanted to actually get the output of a command, you can use $(mycommand myarg) but obviously this is pointless for echo
Maybe I'm not reading this correctly (apologies if so), but it looks like you are expecting the heredoc to be run as a script. It is not. It is just created and cat'ed to input.in, and the string 'echo' is included in that output.
Try removing the string 'echo' from the heredoc (I assume that your perl output starts with the token K_POINTS).
i.e.:
declare RESULT=$(./script.pl 5 5 5)
cat> input.in<<EOF
bla bla
$RESULT
EOF
Related
Can someone fix this for me.
It should copy a version log file to backup after moving to a repo directory
Then it automatically appends line given as input to the log file with some formatting.
That's it.
Assume existence of log file and test directory.
#!/bin/bash
cd ~/Git/test
cp versionlog.MD .versionlog.MD.old
LOGDATE="$(date --utc +%m-%d-%Y)"
read -p "MSG > " VHMSG |
VHENTRY="- **${LOGDATE}** | ${VHMSG}"
cat ${VHENTRY} >> versionlog.MD
shell output
virufac#box:~/Git/test$ ~/.logvh.sh
MSG > testing script
EOF
EOL]
EOL
e
E
CTRL + C to get out of stuck in reading lines of input
virufac#box:~/Git/test$ cat versionlog.MD
directly outputs the markdown
# Version Log
## version 0.0.1 established 01-22-2020
*Working Towards Working Mission 1 Demo in 0.1 *
- **01-22-2020** | discovered faker.Faker and deprecated old namelessgen
EOF
EOL]
EOL
e
E
I finally got it to save the damned input lines to the file instead of just echoing the command I wanted to enter on the screen and not executing it. But... why isn't it adding the lines built from the VHENTRY variable... and why doesn't it stop reading after one line sometimes and this time not. You could see I was trying to do something to tell it to stop reading the input.
After some realizing a thing I had done in the script was by accident... I tried to fix it and saw that the | at the end of the read command was seemingly the only reason the script did any of what it did save to the file in the first place.
I would have done this in python3 if I had know this script wouldn't be the simplest thing I had ever done. Now I just have to know how you do it after all the time spent on it so that I can remember never to think a shell script will save time again.
Use printf to write a string to a file. cat tries to read from a file named in the argument list. And when the argument is - it means to read from standard input until EOF. So your script is hanging because it's waiting for you to type all the input.
Don't put quotes around the path when it starts with ~, as the quotes make it a literal instead of expanding to the home directory.
Get rid of | at the end of the read line. read doesn't write anything to stdout, so there's nothing to pipe to the following command.
There isn't really any need for the VHENTRY variable, you can do that formatting in the printf argument.
#!/bin/bash
cd ~/Git/test
cp versionlog.MD .versionlog.MD.old
LOGDATE="$(date --utc +%m-%d-%Y)"
read -p "MSG > " VHMSG
printf -- '- **%s** | %s\n' "${LOGDATE}" "$VHMSG" >> versionlog.MD
I saw the line data=$(cat) in a bash script (just declaring an empty variable) and am mystified as to what that could possibly do.
I read the man pages, but it doesn't have an example or explanation of this. Does this capture stdin or something? Any documentation on this?
EDIT: Specifically how the heck does doing data=$(cat) allow for it to run this hook script?
#!/bin/bash
# Runs all executable pre-commit-* hooks and exits after,
# if any of them was not successful.
#
# Based on
# http://osdir.com/ml/git/2009-01/msg00308.html
data=$(cat)
exitcodes=()
hookname=`basename $0`
# Run each hook, passing through STDIN and storing the exit code.
# We don't want to bail at the first failure, as the user might
# then bypass the hooks without knowing about additional issues.
for hook in $GIT_DIR/hooks/$hookname-*; do
test -x "$hook" || continue
echo "$data" | "$hook"
exitcodes+=($?)
done
https://github.com/henrik/dotfiles/blob/master/git_template/hooks/pre-commit
cat will catenate its input to its output.
In the context of the variable capture you posted, the effect is to assign the statement's (or containing script's) standard input to the variable.
The command substitution $(command) will return the command's output; the assignment will assign the substituted string to the variable; and in the absence of a file name argument, cat will read and print standard input.
The Git hook script you found this in captures the commit data from standard input so that it can be repeatedly piped to each hook script separately. You only get one copy of standard input, so if you need it multiple times, you need to capture it somehow. (I would use a temporary file, and quote all file name variables properly; but keeping the data in a variable is certainly okay, especially if you only expect fairly small amounts of input.)
Doing:
t#t:~# temp=$(cat)
hello how
are you?
t#t:~# echo $temp
hello how are you?
(A single Controld on the line by itself following "are you?" terminates the input.)
As manual says
cat - concatenate files and print on the standard output
Also
cat Copy standard input to standard output.
here, cat will concatenate your STDIN into a single string and assign it to variable temp.
Say your bash script script.sh is:
#!/bin/bash
data=$(cat)
Then, the following commands will store the string STR in the variable data:
echo STR | bash script.sh
bash script.sh < <(echo STR)
bash script.sh <<< STR
My problem is that the result is jumbled. Consider this script:
#!/bin/bash
INPUT="filelist.txt"
i=0;
while read label
do
i=$[$i+1]
echo "HELLO${label}WORLD"
done <<< $'1\n2\n3\n4'
i=0;
while read label
do
i=$[$i+1]
echo "HELLO${label}WORLD"
done < "$INPUT"
filelist.txt
5
8
15
67
...
The first loop, with the immediate input (through something I believe is called a herestring (the <<< operator) gives the expected output
HELLO1WORLD
HELLO2WORLD
HELLO3WORLD
HELLO4WORLD
The second loop, which reads from the file, gives the following jumbled output:
WORLD5
WORLD8
WORLD15
WORLD67
I've tried echo $label: This works as expected in both cases, but the concatenation fails in the second case as described. Further, the exact same code works on my Win 7, git-bash environment. This issue is on OSX 10.7 Lion.
How to concatenate strings in bash |
Bash variables concatenation |
concat string in a shell script
Well, just as I was about to hit post, the solution hit me. Sharing here so someone else can find it - it took me 3 hours to debug this (despite being on SO for almost all that time) so I see value in addressing this specific (common) use case.
The problem is that filelist.txt was created in Windows. This means it has CRLF line endings, while OSX (like other Unix-like environments) expects LF only line endings. (See more here: Difference between CR LF, LF and CR line break types?)
I used the answer here to convert the file before consumption. Using sed I managed to replace only the final line's carriage return, so I stuck to known guns and went for the perl approach. Final script is below:
#!/bin/bash
INPUTFILE="filelist.txt"
INPUT=$(perl -pe 's/\r\n|\n|\r/\n/g' "$INPUTFILE")
i=0;
while read label
do
i=$[$i+1]
echo "HELLO${label}WORLD"
done <<< $'INPUT'
Question has been asked in a different form at Bash: Concatenating strings fails when read from certain files
I'm trying to extract a substring from an Oracle error message so I can email it off to an administrator using awk, this part of the code is trying to find where the important bit I want to extract.
starts here's what I have....
(The table name is incorrect to generate the error)
validate_iwpcount(){
DB_RETURN_VALUE=`sqlplus -s $DB_CRED <<END
SELECT count(COLUMN)
FROM INCORRECT_TABLE NAME;
exit
END`
a="$DB_RETURN_VALUE"
b="ERROR at line"
awk -v a="$a" -v b="$b" 'BEGIN{print index(a,b)}'
echo $DB_RETURN_VALUE
}
Strange thing is no matter how big that $DB_RETURN_VALUE is the return value from awk is always 28. Im assuming that somewhere in this error message there's something linux either thinks is a implcit delimiter of somesort and its messing with the count or something stranger. This works fine with regular strings as opposed to what oracle gives me.
Could anybody shine a light on this?
Many thanks
28 seems to be the right answer for the query you have (slightly amended to avoid an ORA-00936, and with tabs in the script). The message you're echoing includes a file expansion; the raw message is:
FROM IW_PRODUCTzS
*
ERROR at line 2:
ORA-00942: table or view does not exist
The * is expanded when you echo $DB_RETURN_VALUE, so the directory you're executing this from seem to have logs mail_files scripts in it, and they are being shown through expansion of the *. If you run it from different directories the echoed message length will vary, but the length of the actual message from Oracle stays the same - the length is changing (through the expansion) after the SQL*Plus call and after awk has done its thing. You can avoid that expansion with echo "$DB_RETURN_VALUE" instead, though I don't suppose you actually want to see that full message anyway in the end.
The substring from character 28 gives you what you want though:
validate_iwpcount(){
DB_RETURN_VALUE=`sqlplus -s $CENSYS_ORACLE_UID <<END
SELECT count(COLUMN_NAME)
FROM IW_PRODUCTzS;
exit
END`
# To see the original message; note the double-quotes
# echo "$DB_RETURN_VALUE"
a="$DB_RETURN_VALUE"
b="ERROR at line"
p=`awk -v a="$a" -v b="$b" 'BEGIN{print index(a,b)}'`
if [ ${p} -gt 0 ]; then
awk -v a="$a" -v p="$p" 'BEGIN{print substr(a,p)}'
fi
}
validate_iwpcount
... displays just:
ERROR at line 2:
ORA-00942: table or view does not exist
I'm sure that can be simplified, maybe into a single awk call, but I'm not that familiar with it.
I have a test script which has a lot of commands and will generate lots of output, I use set -x or set -v and set -e, so the script would stop when error occurs. However, it's still rather difficult for me to locate which line did the execution stop in order to locate the problem.
Is there a method which can output the line number of the script before each line is executed?
Or output the line number before the command exhibition generated by set -x?
Or any method which can deal with my script line location problem would be a great help.
Thanks.
You mention that you're already using -x. The variable PS4 denotes the value is the prompt printed before the command line is echoed when the -x option is set and defaults to : followed by space.
You can change PS4 to emit the LINENO (The line number in the script or shell function currently executing).
For example, if your script reads:
$ cat script
foo=10
echo ${foo}
echo $((2 + 2))
Executing it thus would print line numbers:
$ PS4='Line ${LINENO}: ' bash -x script
Line 1: foo=10
Line 2: echo 10
10
Line 3: echo 4
4
http://wiki.bash-hackers.org/scripting/debuggingtips gives the ultimate PS4 that would output everything you will possibly need for tracing:
export PS4='+(${BASH_SOURCE}:${LINENO}): ${FUNCNAME[0]:+${FUNCNAME[0]}(): }'
In Bash, $LINENO contains the line number where the script currently executing.
If you need to know the line number where the function was called, try $BASH_LINENO. Note that this variable is an array.
For example:
#!/bin/bash
function log() {
echo "LINENO: ${LINENO}"
echo "BASH_LINENO: ${BASH_LINENO[*]}"
}
function foo() {
log "$#"
}
foo "$#"
See here for details of Bash variables.
PS4 with value $LINENO is what you need,
E.g. Following script (myScript.sh):
#!/bin/bash -xv
PS4='${LINENO}: '
echo "Hello"
echo "World"
Output would be:
./myScript.sh
+echo Hello
3 : Hello
+echo World
4 : World
Workaround for shells without LINENO
In a fairly sophisticated script I wouldn't like to see all line numbers; rather I would like to be in control of the output.
Define a function
echo_line_no () {
grep -n "$1" $0 | sed "s/echo_line_no//"
# grep the line(s) containing input $1 with line numbers
# replace the function name with nothing
} # echo_line_no
Use it with quotes like
echo_line_no "this is a simple comment with a line number"
Output is
16 "this is a simple comment with a line number"
if the number of this line in the source file is 16.
This basically answers the question How to show line number when executing bash script for users of ash or other shells without LINENO.
Anything more to add?
Sure. Why do you need this? How do you work with this? What can you do with this? Is this simple approach really sufficient or useful? Why do you want to tinker with this at all?
Want to know more? Read reflections on debugging
Simple (but powerful) solution: Place echo around the code you think that causes the problem and move the echo line by line until the messages does not appear anymore on screen - because the script has stop because of an error before.
Even more powerful solution: Install bashdb the bash debugger and debug the script line by line
If you're using $LINENO within a function, it will cache the first occurrence. Instead use ${BASH_LINENO[0]}