I have a function to check a file against multiple long strings seperated by pipes. I want to put each string in the script on a new line so it's more readable. I've tried adding backslashes to the end of each line but they're just caught within the grep statement.
my_function () {
sudo zcat my_file.gz |
egrep -c 'my_long_string_1 |
my_long_string_2 |
my_long_string_3'
}
This does output a result, however, it's incorrect.
Use egrep like this on multiple lines:
my_function () {
sudo zcat my_file.gz |
egrep -c "my_long_string_1|\
my_long_string_2|\
my_long_string_3"
}
Make sure there is no space before or after backslash and there is no space on new lines before each pattern of egrep.
Related
I'm trying to search for a specific string in a file. The string includes a tilde- I am trying to isolate the line that contains the string "~ ca_cert".
This is my script:
#!/bin/bash
LIST=("~ ca_cert" "backup_window")
FILE=./test
for x in "${LIST[#]}"; do
grep $x $FILE
done
When I run it, it returns other lines that contain tildes. For example, in a file that contains the following, it return all of the lines, when my intention is for it to only return the bottom line that contains ~ ca_cert:
./test:./terraform.tfplan: ~ update in-place
./test:./terraform.tfplan: ~ resource "aws_db_instance" "rds_instance" {
./test:./terraform.tfplan: ~ ca_cert_identifier = "rds-ca-2019" -> "rds-ca-2015"
Problem is not quoting pattern i.e. $x in your grep command. That basically runs your command as grep '~' ca_cert ./test and finds all the lines matching ~ with an error.
However you don't really need to run a loop here. Just use grep -f with process substitution:
grep -Ff <(printf '%s\n' "${LIST[#]}") ./test
./terraform.tfplan: ~ ca_cert_identifier = "rds-ca-2019" -> "rds-ca-2015"
I'm trying to create a bash script that converts a bunch of pdfs into text in order to extract some information but the shell gives me this error:
./AutoBib.sh: line 8: syntax error near unexpected token `pdftotext'
./AutoBib.sh: line 8: ` pdftotext $1 temp.txt'
Here there is an example of my function:
function doi{
pdftotext $1 temp.txt
cat temp.txt | grep doi: | cut -d: -f 2 | head -n 1 >> dois.txt
rm -rf temp.txt
}
doi $PDF
Where the variable PDF is taken in input. Before adding the function it worked, I used to write in my script:
pdftotext $PDF tempo.txt
From Bash manual:
The braces are reserved words, so they must be separated from the list
by blanks or other shell metacharacters.
function ... is an outdated syntax for defining Bash functions. Use this instead:
doi() {
...
}
Since () are meta characters, you don't need a space in this case (though spaces make your code prettier):
doi(){
...
}
Extending this a little, remember that we need a whitespace (space, tab, or newline) after { and before `}' in command grouping, like this:
{ command1; command2; ... }
You need a space after the name of your function and before the {:
function doi {
^
I want to return all files that have the strings: "main(" as well as "foo".
This is like using a multi pattern OR grep but with AND instead.
The best I've come up with is:
grep -rl . -e "main("|while read fname; do grep -rl "$fname" -e "foo"; done
It does the job, but ideally I wouldn't have to write bash script.
E.g.
text1.txt:
int main()
{
stuff....
}
foo
grep command would return text1.txt since it contains the strings 'main(' and 'foo'
Just use awk to match both patterns and print filenames:
awk 'FNR == 1 { m = f = 0 } # reset flags at start of each file
/main\(/ { ++m } /foo/ { ++f } # set flags when patterns match
m && f { print FILENAME; nextfile }' **/*
nextfile is a GNU extension which skips to the next file, rather than the next line. With globstar enabled, ** expands recursively. In an interactive bash shell, it is enabled by default, but in a script you can enable it yourself using shopt -s globstar.
With non-GNU awk, you can use another flag to skip lines and avoid printing the filename multiple times:
awk 'FNR == 1 { m = f = p = 0 } # reset flags at start of each file
p { next } # skip lines once this filename has been printed
/main\(/ { ++m } /foo/ { ++f }
m && f { print FILENAME; ++p }' **/*
Try
grep -rlZ 'main(' | xargs -0 grep -l 'foo'
-Z, --null
Output a zero byte (the ASCII NUL character) instead of the character that normally follows a file
name. For example, grep -lZ outputs a zero byte after each file name instead of the usual newline.
This option makes the output unambiguous, even in the presence of file names containing unusual
characters like newlines. This option can be used with commands like find -print0, perl -0, sort -z,
and xargs -0 to process arbitrary file names, even those that contain newline characters.
The first grep would print all filenames containing main( separated by NUL character. xargs would then pass the files to second grep command which would print files containing foo
If the files are small enough and do not contain NUL character,
grep -rlz 'main(.*foo\|foo.*main('
where -z would use NUL as line separator, effectively slurping whole file
For every time the pattern shows up (In this example the case of a 2 digit number) I want to pass that pattern to a script and replace that pattern with the output of a script.
I'm using sed an example of what it should look like would be
echo 'siedi87sik65owk55dkd' | sed 's/[0-9][0-9]/.\/script.sh/g'
Right now this returns
siedi./script.shsik./script.showk./script.shdkd
But I would like it to return
siedi!!!87!!!sik!!!65!!!owk!!!55!!!dkd
This is what is in ./script.sh
#!/bin/bash
echo "!!!$1!!!"
It has to be replaced with the output. In this example I know I could just use a normal sed substitution but I don't want that as an answer.
sed is for simple substitutions on individual lines, that is all. Anything else, even if it can be done, requires arcane language constructs that became obsolete in the mid-1970s when awk was invented and are used today purely for the mental exercise. Your problem is not a simple substitution so you shouldn't try to use sed to solve it.
You're going to want something like:
awk '{
head = ""
tail = $0
while ( match(tail,/[0-9]{2}/) ) {
tgt = substr(tail,RSTART,RLENGTH)
cmd = "./script.sh " tgt
if ( (cmd | getline line) > 0) {
tgt = line
}
close(cmd)
head = head substr(tail,1,RSTART-1) tgt
tail = substr(tail,RSTART+RLENGTH)
}
print head tail
}'
e.g. using an echo in place of your script.sh command:
$ echo 'siedi87sik65owk55dkd' |
awk '{
head = ""
tail = $0
while ( match(tail,/[0-9]{2}/) ) {
tgt = substr(tail,RSTART,RLENGTH)
cmd = "echo !!!" tgt "!!!"
if ( (cmd | getline line) > 0) {
tgt = line
}
close(cmd)
head = head substr(tail,1,RSTART-1) tgt
tail = substr(tail,RSTART+RLENGTH)
}
print head tail
}'
siedi!!!87!!!sik!!!65!!!owk!!!55!!!dkd
Ed's awk solution is obviously the way to go here.
For fun, I tried to come up with a sed solution, and here is (a convoluted GNU sed) one that takes the pattern and the script to be run as parameters; the input is either read from standard input (i.e., you can pipe to it) or from a file supplied as the third argument.
For your example, we'd have infile with contents
siedi87sik65owk55dkd
siedi11sik22owk33dkd
(two lines to demonstrate how this works for multiple lines), then script with contents
#!/bin/bash
echo "!!!${1}!!!"
and finally the solution script itself, so. Usage is
./so pattern script [input]
where pattern is an extended regular expression as understood by GNU sed (with the -r option), script is the name of the command you want to run for each match, and the optional input is the name of the input file if input is not standard input.
For your example, this would be
./so '[[:digit:]]{2}' script infile
or, as a filter,
cat infile | ./so '[[:digit:]]{2}' script
with output
siedi!!!87!!!sik!!!65!!!owk!!!55!!!dkd
siedi!!!11!!!sik!!!22!!!owk!!!33!!!dkd
This is what so looks like:
#!/bin/bash
pat=$1 # The pattern to match
script=$2 # The command to run for each pattern
infile=${3:-/dev/stdin} # Read from standard input if not supplied
# Use sed and have $pattern and $script expand to the supplied parameters
sed -r "
:build_loop # Label to loop back to
h # Copy pattern space to hold space
s/.*($pat).*/.\/\"$script\" \1/ # (1) Extract last match and prepare command
# Replace pattern space with output of command
e
G # (2) Append hold space to pattern space
s/(.*)$pat(.*)/\1~~~\2/ # (3) Replace last match of pattern with ~~~
/\n[^\n]*$pat[^\n]*$/b build_loop # Loop if string contains match
:fill_loop # Label for second loop
s/(.*\n)(.*)\n([^\n]*)~~~([^\n]*)$/\1\3\2\4/ # (4) Replace last ~~~
t fill_loop # Loop if there was a replacement
s/(.*)\n(.*)~~~(.*)$/\2\1\3/ # (5) Final ~~~ replacement
" < "$infile"
The sed command works with two loops. The first one copies the pattern space to the hold space, then removes everything but the last match from the pattern space and prepares the command to be run. After the substitution with (1) in its comment, the pattern space looks like this:
./script 55
The e command (a GNU extension) then replaces the pattern space with the output of this command. After this, G appends the hold space to the pattern space (2). The pattern space now looks like this:
!!!55!!!
siedi87sik65owk55dkd
The substitution at (3) replaces the last match with a string hopefully not equal to the pattern and we get
!!!55!!!
siedi87sik65owk~~~dkd
The loop repeats if the last line of the pattern space still has a match for the pattern. After three loops, the pattern space looks like this:
!!!87!!!
!!!65!!!
!!!55!!!
siedi~~~sik~~~owk~~~dkd
The second loop now replaces the last ~~~ with the second to last line of the pattern space with substitution (4). The command uses lots of "not a newline" ([^\n]) to make sure we're not pulling the wrong replacement for ~~~.
Because of the way command (4) is written, the loop ends with one last substitution to go, so before command (5), we have this pattern space:
!!!87!!!
siedi~~~sik!!!65!!!owk!!!55!!!dkd
Command (5) is a simpler version of command (4), and after it, the output is as desired.
This seems to be fairly robust and can deal with spaces in the name of the script to be run as long as it's properly quoted when calling:
./so '[[:digit:]]{2}' 'my script' infile
This would fail if
The input file contains ~~~ (solvable by replacing all occurrences at the start, putting them back at the end)
The output of script contains ~~~
The pattern contains ~~~
i.e., the solution very much depends on ~~~ being unique.
Because nobody asked: so as a one-liner.
#!/bin/bash
sed -re ":b;h;s/.*($1).*/.\/\"$2\" \1/;e" -e "G;s/(.*)$1(.*)/\1~~~\2/;/\n[^\n]*$1[^\n]*$/bb;:f;s/(.*\n)(.*)\n([^\n]*)~~~([^\n]*)$/\1\3\2\4/;tf;s/(.*)\n(.*)~~~(.*)$/\2\1\3/" < "${3:-/dev/stdin}"
Still works!
A conceptually simpler multi-utility solution:
Using GNU utilities:
echo 'siedi87sik65owk55dkd' |
sed 's|[0-9]\{2\}|$(./script.sh &)|g' |
xargs -d'\n' -I% sh -c 'echo '\"%\"
Using BSD utilities (also works with GNU utilities):
echo 'siedi87sik65owk55dkd' |
sed 's|[0-9]\{2\}|$(./script.sh &)|g' | tr '\n' '\0' |
xargs -0 -I% sh -c 'echo '\"%\"
The idea is to use sed to translate the tokens of interest lexically into a string containing shell command substitutions that invoke the target script with the token, and then pass the result to the shell for evaluation.
Note:
Any embedded " and $ characters in the input must be \-escaped.
xargs -d'\n' (GNU) and tr '\n' '\0' / xargs -0 (BSD) are only needed to correctly preserve whitespace in the input - if that is not needed, the following POSIX-compliant solution will do:
echo 'siedi87sik65owk55dkd' |
sed 's|[0-9]\{2\}|$(./script.sh &)|g' | tr '\n' '\0' |
xargs -I% sh -c 'printf "%s\n" '\"%\"
How to I concatenate stdin to a string, like this?
echo "input" | COMMAND "string"
and get
inputstring
A bit hacky, but this might be the shortest way to do what you asked in the question (use a pipe to accept stdout from echo "input" as stdin to another process / command:
echo "input" | awk '{print $1"string"}'
Output:
inputstring
What task are you exactly trying to accomplish? More context can get you more direction on a better solution.
Update - responding to comment:
#NoamRoss
The more idiomatic way of doing what you want is then:
echo 'http://dx.doi.org/'"$(pbpaste)"
The $(...) syntax is called command substitution. In short, it executes the commands enclosed in a new subshell, and substitutes the its stdout output to where the $(...) was invoked in the parent shell. So you would get, in effect:
echo 'http://dx.doi.org/'"rsif.2012.0125"
use cat - to read from stdin, and put it in $() to throw away the trailing newline
echo input | COMMAND "$(cat -)string"
However why don't you drop the pipe and grab the output of the left side in a command substitution:
COMMAND "$(echo input)string"
I'm often using pipes, so this tends to be an easy way to prefix and suffix stdin:
echo -n "my standard in" | cat <(echo -n "prefix... ") - <(echo " ...suffix")
prefix... my standard in ...suffix
There are some ways of accomplish this, i personally think the best is:
echo input | while read line; do echo $line string; done
Another can be by substituting "$" (end of line character) with "string" in a sed command:
echo input | sed "s/$/ string/g"
Why i prefer the former? Because it concatenates a string to stdin instantly, for example with the following command:
(echo input_one ;sleep 5; echo input_two ) | while read line; do echo $line string; done
you get immediatly the first output:
input_one string
and then after 5 seconds you get the other echo:
input_two string
On the other hand using "sed" first it performs all the content of the parenthesis and then it gives it to "sed", so the command
(echo input_one ;sleep 5; echo input_two ) | sed "s/$/ string/g"
will output both the lines
input_one string
input_two string
after 5 seconds.
This can be very useful in cases you are performing calls to functions which takes a long time to complete and want to be continuously updated about the output of the function.
You can do it with sed:
seq 5 | sed '$a\6'
seq 5 | sed '$ s/.*/\0 6/'
In your example:
echo input | sed 's/.*/\0string/'
I know this is a few years late, but you can accomplish this with the xargs -J option:
echo "input" | xargs -J "%" echo "%" "string"
And since it is xargs, you can do this on multiple lines of a file at once. If the file 'names' has three lines, like:
Adam
Bob
Charlie
You could do:
cat names | xargs -n 1 -J "%" echo "I like" "%" "because he is nice"
Also works:
seq -w 0 100 | xargs -I {} echo "string "{}
Will generate strings like:
string 000
string 001
string 002
string 003
string 004
...
The command you posted would take the string "input" use it as COMMAND's stdin stream, which would not produce the results you are looking for unless COMMAND first printed out the contents of its stdin and then printed out its command line arguments.
It seems like what you want to do is more close to command substitution.
http://www.gnu.org/software/bash/manual/html_node/Command-Substitution.html#Command-Substitution
With command substitution you can have a commandline like this:
echo input `COMMAND "string"`
This will first evaluate COMMAND with "string" as input, and then expand the results of that commands execution onto a line, replacing what's between the ‘`’ characters.
cat will be my choice: ls | cat - <(echo new line)
With perl
echo "input" | perl -ne 'print "prefix $_"'
Output:
prefix input
A solution using sd (basically a modern sed; much easier to use IMO):
# replace '$' (end of string marker) with 'Ipsum'
# the `e` flag disables multi-line matching (treats all lines as one)
$ echo "Lorem" | sd --flags e '$' 'Ipsum'
Lorem
Ipsum#no new line here
You might observe that Ipsum appears on a new line, and the output is missing a \n. The reason is echo's output ends in a \n, and you didn't tell sd to add a new \n. sd is technically correct because it's doing exactly what you are asking it to do and nothing else.
However this may not be what you want, so instead you can do this:
# replace '\n$' (new line, immediately followed by end of string) by 'Ipsum\n'
# don't forget to re-add the `\n` that you removed (if you want it)
$ echo "Lorem" | sd --flags e '\n$' 'Ipsum\n'
LoremIpsum
If you have a multi-line string, but you want to append to the end of each individual line:
$ ls
foo bar baz
$ ls | sd '\n' '/file\n'
bar/file
baz/file
foo/file
I want to prepend my sql script with "set" statement before running it.
So I echo the "set" instruction, then pipe it to cat. Command cat takes two parameters : STDIN marked as "-" and my sql file, cat joins both of them to one output. Next I pass the result to mysql command to run it as a script.
echo "set #ZERO_PRODUCTS_DISPLAY='$ZERO_PRODUCTS_DISPLAY';" | cat - sql/test_parameter.sql | mysql
p.s. mysql login and password stored in .my.cnf file