My so.txt contains below line:
PRE 2022-03-16/
Date is = 2022-03-16
awsdate= cut -c 5-14 so.txt
sysdates=`date +%Y-%m-%d`
echo $sysdates
if [[ "$awsdate" == "$sysdates" ]] ;
then
echo "dates are matching"
else
echo "dates are not matching"
fi
Output:
2022-03-16
2022-03-16
dates are not matching
With above script I am trying to compare dates in Linux. Although the dates are same I am still getting dates are not matching. Why is this?
Probably a quoting error. Use quotes and command substitution properly. This works:
so.txt:
PRE 2022-03-16/
test.sh:
Note: shellcheck test.sh comes up clean now.
#!/bin/bash
awsdate="$(cut -c 5-14 so.txt)"
sysdates="$(date +%Y-%m-%d)"
echo "$sysdates"
if [[ "$awsdate" == "$sysdates" ]]; then
echo "dates are matching"
else
echo "dates are not matching"
fi
Cmd and output:
$ ./test.sh
2022-03-16
dates are matching
Run shellcheck on your original script and see what it says for errors.
Here is what I see:
Bad test.sh:
#!/bin/bash
awsdate= cut -c 5-14 so.txt
sysdates=`date +%Y-%m-%d`
echo $sysdates
if [[ "$awsdate" == "$sysdates" ]] ;
then
echo "dates are matching"
else
echo "dates are not matching"
fi
Run shellcheck on it. I am using shellcheck --version of version: 0.8.0. These are all of your errors and problems:
$ shellcheck test.sh
In test.sh line 1:
awsdate= cut -c 5-14 so.txt
^-- SC2148 (error): Tips depend on target shell and yours is unknown. Add a shebang or a 'shell' directive.
^-- SC1007 (warning): Remove space after = if trying to assign a value (for empty string, use var='' ... ).
In test.sh line 2:
sysdates=`date +%Y-%m-%d`
^--------------^ SC2006 (style): Use $(...) notation instead of legacy backticks `...`.
Did you mean:
sysdates=$(date +%Y-%m-%d)
In test.sh line 3:
echo $sysdates
^-------^ SC2086 (info): Double quote to prevent globbing and word splitting.
Did you mean:
echo "$sysdates"
In test.sh line 4:
if [[ "$awsdate" == "$sysdates" ]] ;
^------^ SC2154 (warning): awsdate is referenced but not assigned.
For more information:
https://www.shellcheck.net/wiki/SC2148 -- Tips depend on target shell and y...
https://www.shellcheck.net/wiki/SC1007 -- Remove space after = if trying to...
https://www.shellcheck.net/wiki/SC2154 -- awsdate is referenced but not ass...
References:
my notes on shellcheck: https://github.com/ElectricRCAircraftGuy/eRCaGuy_hello_world/tree/master/bash#shellcheck
Related
I have tried all the solutions available on stack overflow, but when I use if condition with with it always results true.
I need to find a line in the file and see if it doesn't exit then insert the line in that file, but it always results that the line already exists.
Here is my script
isInFile=$(grep -q '^export' /etc/bashrc)
if [[ $isInFile == 0 ]];
then
echo "line is not present";
echo "export PROMPT_COMMAND='RETRN_VAL=\$?;logger -p local6.debug \"\$(whoami) [\$\$]: \$(history 1 | sed \"s/^[ ]*[0-9]\+[ ]*//\" )\"'" >> /etc/bashrc;
source /etc/bashrc;
else
echo "line is in the file";
fi
It always says that
line is in the file
The if statement branches based on the exit status of the command it's given. [[ is just one command you can use, it's not mandatory syntax. At an interactive prompt, enter help if
Do this:
if grep -q '^export' /etc/bashrc
then
# exit status of grep is zero: the pattern DOES MATCH the file
echo "line is in the file";
else
# exit status of grep is non-zero: the pattern DOES NOT MATCH the file
echo "line is not present";
echo "export PROMPT_COMMAND='RETRN_VAL=\$?;logger -p local6.debug \"\$(whoami) [\$\$]: \$(history 1 | sed \"s/^[ ]*[0-9]\+[ ]*//\" )\"'" >> /etc/bashrc;
source /etc/bashrc;
fi
I see 2 issues in your code:
if [[ $isInFile == 0 ]]; --If condition should not terminate with ;. Remove that.
The expression you are checking is always an empty string. Try echo $isInFile. What you are checking is output of the command, not its return value. Instead, you should remove -q from your grep expression and check if the output is empty or not.
Following code should work:
isInFile=$(grep '^export' /etc/bashrc)
if [ -z "$isInFile" ]
then
echo "line is not present";
echo "export PROMPT_COMMAND='RETRN_VAL=\$?;logger -p local6.debug \"\$(whoami) [\$\$]: \$(history 1 | sed \"s/^[ ]*[0-9]\+[ ]*//\" )\"'" >> /etc/bashrc;
source /etc/bashrc;
else
echo "line is in the file";
fi
-z check for emptiness of variable.
I want to check if a file contains a specific string or not in bash. I used this script, but it doesn't work:
if [[ 'grep 'SomeString' $File' ]];then
# Some Actions
fi
What's wrong in my code?
if grep -q SomeString "$File"; then
Some Actions # SomeString was found
fi
You don't need [[ ]] here. Just run the command directly. Add -q option when you don't need the string displayed when it was found.
The grep command returns 0 or 1 in the exit code depending on
the result of search. 0 if something was found; 1 otherwise.
$ echo hello | grep hi ; echo $?
1
$ echo hello | grep he ; echo $?
hello
0
$ echo hello | grep -q he ; echo $?
0
You can specify commands as an condition of if. If the command returns 0 in its exitcode that means that the condition is true; otherwise false.
$ if /bin/true; then echo that is true; fi
that is true
$ if /bin/false; then echo that is true; fi
$
As you can see you run here the programs directly. No additional [] or [[]].
In case if you want to check whether file does not contain a specific string, you can do it as follows.
if ! grep -q SomeString "$File"; then
Some Actions # SomeString was not found
fi
In addition to other answers, which told you how to do what you wanted, I try to explain what was wrong (which is what you wanted.
In Bash, if is to be followed with a command. If the exit code of this command is equal to 0, then the then part is executed, else the else part if any is executed.
You can do that with any command as explained in other answers: if /bin/true; then ...; fi
[[ is an internal bash command dedicated to some tests, like file existence, variable comparisons. Similarly [ is an external command (it is located typically in /usr/bin/[) that performs roughly the same tests but needs ] as a final argument, which is why ] must be padded with a space on the left, which is not the case with ]].
Here you needn't [[ nor [.
Another thing is the way you quote things. In bash, there is only one case where pairs of quotes do nest, it is "$(command "argument")". But in 'grep 'SomeString' $File' you have only one word, because 'grep ' is a quoted unit, which is concatenated with SomeString and then again concatenated with ' $File'. The variable $File is not even replaced with its value because of the use of single quotes. The proper way to do that is grep 'SomeString' "$File".
Shortest (correct) version:
grep -q "something" file; [ $? -eq 0 ] && echo "yes" || echo "no"
can be also written as
grep -q "something" file; test $? -eq 0 && echo "yes" || echo "no"
but you dont need to explicitly test it in this case, so the same with:
grep -q "something" file && echo "yes" || echo "no"
##To check for a particular string in a file
cd PATH_TO_YOUR_DIRECTORY #Changing directory to your working directory
File=YOUR_FILENAME
if grep -q STRING_YOU_ARE_CHECKING_FOR "$File"; ##note the space after the string you are searching for
then
echo "Hooray!!It's available"
else
echo "Oops!!Not available"
fi
grep -q [PATTERN] [FILE] && echo $?
The exit status is 0 (true) if the pattern was found; otherwise blankstring.
if grep -q [string] [filename]
then
[whatever action]
fi
Example
if grep -q 'my cat is in a tree' /tmp/cat.txt
then
mkdir cat
fi
In case you want to checkif the string matches the whole line and if it is a fixed string, You can do it this way
grep -Fxq [String] [filePath]
example
searchString="Hello World"
file="./test.log"
if grep -Fxq "$searchString" $file
then
echo "String found in $file"
else
echo "String not found in $file"
fi
From the man file:
-F, --fixed-strings
Interpret PATTERN as a list of fixed strings, separated by newlines, any of
which is to be matched.
(-F is specified by POSIX.)
-x, --line-regexp
Select only those matches that exactly match the whole line. (-x is specified by
POSIX.)
-q, --quiet, --silent
Quiet; do not write anything to standard output. Exit immediately with zero
status if any match is
found, even if an error was detected. Also see the -s or --no-messages
option. (-q is specified by
POSIX.)
Try this:
if [[ $(grep "SomeString" $File) ]] ; then
echo "Found"
else
echo "Not Found"
fi
I done this, seems to work fine
if grep $SearchTerm $FileToSearch; then
echo "$SearchTerm found OK"
else
echo "$SearchTerm not found"
fi
grep -q "something" file
[[ !? -eq 0 ]] && echo "yes" || echo "no"
I want to check if some variable is starting with some string (A-) and ending with digit in shell script.
My script (test.sh):
#!/bin/bash
VAR=A-1
if [[ $VAR =~ A-*[0-9 ] ]]; then
echo "yes"
else
echo "no"
fi
The error I get after running sh test.sh:
test.sh: 5: test.sh: [[: not found
I tried to change the concession to:
if [ $VAR =~ A-*[0-9 ] ]; then
and got this error: test.sh: 5: [: A-1: unexpected operator
The variables should always be quoted:
VAR="A-1"
The issue in your code is with the space in the square brackets: [...] which you've defined in the regex: [0-9 ].
There shouldn't be any space within it.
The correct code to check if some variable is starting with A- and ending with digit should be :
#!/bin/bash
VAR="A-1"
if [[ "$VAR" =~ ^A-.*[0-9]$ ]]; then
echo "yes"
else
echo "no"
fi
Please note the double quotes around the variable VAR.
As per the OP's comments, it looks like sh is being used instead bash , as the regex matching operator : =~ doesn't work in sh and is bash specific.
Updated code using sh:
#!/bin/sh
VAR="A-1"
if echo "$VAR"| grep -Eq "^A-.*[0-9]$"
then
echo "Yes"
else
echo "no"
fi
The regex to match a string which starts with A- and ends with a digit
should be: ^A-.*[0-9]$ or more strictly ^A-.*[[:digit:]]$.
Then please modify your scpipt as:
#!/bin/bash
VAR="A-1"
if [[ $VAR =~ ^A-.*[0-9]$ ]]; then
echo "yes"
else
echo "no"
fi
Then invoke it with bash test.sh, not with sh test.sh.
sh test.sh does not use bash to run the script, it uses sh, which, depending on the system, may not have the same capabilities as bash.
You can use:
bash test.sh
Or:
chmod a+rx test.sh # one time only
./test.sh # your script is set to use /bin/bash in the #! line.
Try something like : ${VAR:${#VAR}-1:1}
Cf. https://www.cyberciti.biz/tips/bash-shell-parameter-substitution-2.html
[[ "${VAR:${#VAR}-1:1}" =~ [0-9] ]] && echo yes
i stumbled in a confusing way of conditionally returning value based on variable. I would like to check if process is successful then echo "process success", but if it's failed, i want to check specific error message then return the error message,
ERRMSG="$(cd /nonexist 2>&1)"
if [ $? -ne 0 ]
then
if [ -z "$ERRMSG|grep -o 'No such file or directory'|head -1" ]
then
echo "empty" >> $FQLOGNAME
else
echo $ERRMSG|grep -o 'No such file or directory'|head -1 >> $FQLOGNAME
fi
else
echo "success" >> $FQLOGNAME
fi
Please advice,
Thanks
You don't need to use grep to check if a string contains a substring. The built-in pattern matching in Bash is sufficient. This code should do something close to what you want:
if ERRMSG=$(cd /nonexist 2>&1) ; then
echo 'process success'
elif [[ $ERRMSG == *'No such file or directory'* ]] ; then
echo 'No such file or directory'
else
echo 'empty'
fi >> "$FQLOGNAME"
See the Conditional Constructs section of the Bash Reference Manual for details of the pattern matching capabilities of [[...]].
I've retained the ERRMSG and FQLOGNAME variables, but note that it's best to avoid ALL_UPPERCASE variable names. There is a danger that they will clash with environment variables or Bash builtin variables. See Correct Bash and shell script variable capitalization.
To find error messages defined by a pattern in multi-line error messages, and only print the first one, you can use regular expression matching (=~) in [[...]]. To provide a concrete example, this code assumes that error messages consist of 'ERROR' followed by one or more spaces followed by a decimal number:
# Example function for testing
function dostuff
{
printf 'Output line A\n'
printf 'Encountered ERROR 29\n' >&2
printf 'Output line B\n'
printf 'Encountered ERROR 105\n' >&2
printf 'Output line C\n'
return 1
}
# Regular expression matching an error string
readonly error_rx='ERROR +[0-9]+'
if ERRMSG=$(dostuff 2>&1) ; then
echo 'process success'
elif [[ $ERRMSG =~ $error_rx ]] ; then
printf '%s\n' "${BASH_REMATCH[0]}"
else
echo 'empty'
fi >> "$FQLOGNAME"
It appends 'ERROR 29' to the log file.
For more information about Bash's built-in regular expression matching see mklement0's answer to "How do I use a regex in a shell script?".
Make it simpler and easier:
if ! ERRMSG=$(cd /nonexist 2>&1); then
if <<<"$ERRMSG" grep -q 'No such file or directory'; then
# if the error string contains the message 'No such file or directory'
echo "empty" >> "$FQLOGNAME"
else
printf "Unhandled cd error: %s" "$ERRMSG" >> "$FQLOGNAME"
fi
else
echo "process success" >> "$FQLOGNAME"
fi
if statements checks for the return status of a COMMAND. [ or test is just a command, which return a status. The return status of assignment is the same as command status. What I mean, is that out=$(cmd); if [ "$?" -eq 0 ]; then is the same as if out=$(cmd); then.
Using HERE-strings is a bit better than echo "$string". Echo is not that much portable, better get used to printf "%s" "$string" which is a portable way. However HERE-strings puts additional EOF at the end of the stream, which sometimes breaks while read loops, but for most cases works ok.
Don't if [ -z "$(echo smth | grep ..)" ]; then. You can just check grep return status, just if echo smth | grep ...; then or with HERE-strings if <<<"smth" grep -q ...; then or if grep -q ... file; then. The -q option which has --quiet or --silent alternatives makes grep produce no output.
The quoting is not needed when assigning a variable from a single command substitution. tmp="$(...)" is just the same as tmp=$(...).
then, elif, else statement that I have programmed in a bash script. I know that it works because I can run the same command in the terminal interface and see that it is doing what I want it to do. However when I run it in a script it seems to always jump to the else statement and not detect anything. Can anybody help explain why this is so? Here is my script code:
if [ -e "$1" ]
then
for line in `samtools view -H $1`
do
if [[ "$line" == *NCBI-Build-36\.1* ]]
then
echo "hg18"
break
elif [[ "$line" == *hg19* ]]
then
echo "hg19"
break
else
echo "Reference was not found, manual entry required: "
read ans
echo "$ans"
break
fi
done
else
echo -e "Usage: \e[1;32mreadRef.sh \e[1;36mbamfile.bam"
fi
No matter what file I plug in it always skips to the else and asks me for manual entry.
Here is the command I ran on terminal:
for line in `samtools view -H $bignormal`; do if [[ "$line" == *NCBI-Build-36\.1* ]]; then echo "YES - $line"; else echo "NO - $line"; fi; done
And the output is like this:
NO - #HD
NO - VN:1.0
NO - GO:none
NO - SO:coordinate
NO - #SQ
NO - SN:1
NO - LN:247249719
YES - AS:NCBI-Build-36.1
YES - UR:http://www.bcgsc.ca/downloads/genomes/9606/NCBI-Build-36.1/bwa_ind/genome/
NO - SP:Homo
NO - sapiens
.
.
.
Why is the script not detecting the string I am looking for, but it is in terminal?
EDIT:
I tried what Charles said, this is the output:
:+'[' -e /projects/rcorbettprj2/DLBCL/CNV/RG065/normal/A01440_8_lanes_dupsFlagged.bam ']'
::+samtools view -H /projects/rcorbettprj2/DLBCL/CNV/RG065/normal/A01440_8_lanes_dupsFlagged.bam
:+for line in '`samtools view -H $1`'
:+case "$line" in
:+echo 'Reference was not found, manual entry required: '
Reference was not found, manual entry required:
:+read ans
I think your code has a logic error nobody's spotted yet. I'm not sure, since you haven't told us what the script's supposed to be doing, but it looks to me like what you want is to ask for manual entry only if you don't find a match to either of your patterns anywhere in the output, but what you're actually doing is examining only the first word of output for a match. And from your sample output, the first word is "#HD", which doesn't match either pattern, so the script is doing exactly what I'd expect.
Now, assuming I'm right and that the point is to look for either pattern anywhere in the output, you can actually simplify things a bit. Mainly, you don't need the loop, you can just do a single comparison to look for the pattern in the entire output at once:
#!/bin/bash
if [ -e "$1" ]
then
output="$(samtools view -H "$1")"
if [[ "$output" == *NCBI-Build-36.1* ]]
then
echo "hg18"
elif [[ "$output" == *hg19* ]]
then
echo "hg19"
else
read -p "Reference was not found, manual entry required: " ans
echo "$ans"
fi
done
else
echo -e "Usage: \e[1;32mreadRef.sh \e[1;36mbamfile.bam"
fi