Substitute variable in sed inside Makefile - bash

I've been throught all possible answers in SO but still I cannot make my script work.
I have a query script in SPARQL with a line that needs to substitute the mark %contributor% by a variable between "<>"
?link dcterms:contributor %contributor%
Into
?link dcterms:contributor <http://newurl>
If I execute the code in the shell, the substitution is done properly and I see my query with the %contributor% tag successfully substituted. But when executed inside a Makefile, even with the double $$ dollar to allow the expansion of variables I don't manage to get it done.
for l in `cat sref.csv`; do \
QUERY=$$(cat queries/table_knowledge.rq | sed "s#%contributor%#<$$l>#g") ; \
echo $$QUERY ; \
done
Also like this it does not work:
QUERY=$$(cat queries/table_knowledge.rq | sed 's/%contributor%/<$(l)>/g') ; \
or
QUERY=$$(cat queries/table_knowledge.rq | sed 's/%contributor%/<${l}>/g') ; \

Use double quotes so that sed would expand variables.
Use a separator different than / since the replacement contains /
QUERY=$(cat queries/table_knowledge.rq | sed "s|%contributor%|<${l}>|g") ;
Test:
$ test="http://test.com"
$ echo "?link dcterms:contributor %contributor%" > source.file
$ x=$(cat source.file|sed "s|%contributor%|<${test}>|g")
$ echo $x
?link dcterms:contributor <http://test.com>

Related

Double quotes containing variable not working in sed [duplicate]

In my bash script I have an external (received from user) string, which I should use in sed pattern.
REPLACE="<funny characters here>"
sed "s/KEYWORD/$REPLACE/g"
How can I escape the $REPLACE string so it would be safely accepted by sed as a literal replacement?
NOTE: The KEYWORD is a dumb substring with no matches etc. It is not supplied by user.
Warning: This does not consider newlines. For a more in-depth answer, see this SO-question instead. (Thanks, Ed Morton & Niklas Peter)
Note that escaping everything is a bad idea. Sed needs many characters to be escaped to get their special meaning. For example, if you escape a digit in the replacement string, it will turn in to a backreference.
As Ben Blank said, there are only three characters that need to be escaped in the replacement string (escapes themselves, forward slash for end of statement and & for replace all):
ESCAPED_REPLACE=$(printf '%s\n' "$REPLACE" | sed -e 's/[\/&]/\\&/g')
# Now you can use ESCAPED_REPLACE in the original sed statement
sed "s/KEYWORD/$ESCAPED_REPLACE/g"
If you ever need to escape the KEYWORD string, the following is the one you need:
sed -e 's/[]\/$*.^[]/\\&/g'
And can be used by:
KEYWORD="The Keyword You Need";
ESCAPED_KEYWORD=$(printf '%s\n' "$KEYWORD" | sed -e 's/[]\/$*.^[]/\\&/g');
# Now you can use it inside the original sed statement to replace text
sed "s/$ESCAPED_KEYWORD/$ESCAPED_REPLACE/g"
Remember, if you use a character other than / as delimiter, you need replace the slash in the expressions above wih the character you are using. See PeterJCLaw's comment for explanation.
Edited: Due to some corner cases previously not accounted for, the commands above have changed several times. Check the edit history for details.
The sed command allows you to use other characters instead of / as separator:
sed 's#"http://www\.fubar\.com"#URL_FUBAR#g'
The double quotes are not a problem.
The only three literal characters which are treated specially in the replace clause are / (to close the clause), \ (to escape characters, backreference, &c.), and & (to include the match in the replacement). Therefore, all you need to do is escape those three characters:
sed "s/KEYWORD/$(echo $REPLACE | sed -e 's/\\/\\\\/g; s/\//\\\//g; s/&/\\\&/g')/g"
Example:
$ export REPLACE="'\"|\\/><&!"
$ echo fooKEYWORDbar | sed "s/KEYWORD/$(echo $REPLACE | sed -e 's/\\/\\\\/g; s/\//\\\//g; s/&/\\\&/g')/g"
foo'"|\/><&!bar
Based on Pianosaurus's regular expressions, I made a bash function that escapes both keyword and replacement.
function sedeasy {
sed -i "s/$(echo $1 | sed -e 's/\([[\/.*]\|\]\)/\\&/g')/$(echo $2 | sed -e 's/[\/&]/\\&/g')/g" $3
}
Here's how you use it:
sedeasy "include /etc/nginx/conf.d/*" "include /apps/*/conf/nginx.conf" /etc/nginx/nginx.conf
It's a bit late to respond... but there IS a much simpler way to do this. Just change the delimiter (i.e., the character that separates fields). So, instead of s/foo/bar/ you write s|bar|foo.
And, here's the easy way to do this:
sed 's|/\*!50017 DEFINER=`snafu`#`localhost`\*/||g'
The resulting output is devoid of that nasty DEFINER clause.
It turns out you're asking the wrong question. I also asked the wrong question. The reason it's wrong is the beginning of the first sentence: "In my bash script...".
I had the same question & made the same mistake. If you're using bash, you don't need to use sed to do string replacements (and it's much cleaner to use the replace feature built into bash).
Instead of something like, for example:
function escape-all-funny-characters() { UNKNOWN_CODE_THAT_ANSWERS_THE_QUESTION_YOU_ASKED; }
INPUT='some long string with KEYWORD that need replacing KEYWORD.'
A="$(escape-all-funny-characters 'KEYWORD')"
B="$(escape-all-funny-characters '<funny characters here>')"
OUTPUT="$(sed "s/$A/$B/g" <<<"$INPUT")"
you can use bash features exclusively:
INPUT='some long string with KEYWORD that need replacing KEYWORD.'
A='KEYWORD'
B='<funny characters here>'
OUTPUT="${INPUT//"$A"/"$B"}"
Use awk - it is cleaner:
$ awk -v R='//addr:\\file' '{ sub("THIS", R, $0); print $0 }' <<< "http://file:\_THIS_/path/to/a/file\\is\\\a\\ nightmare"
http://file:\_//addr:\file_/path/to/a/file\\is\\\a\\ nightmare
Here is an example of an AWK I used a while ago. It is an AWK that prints new AWKS. AWK and SED being similar it may be a good template.
ls | awk '{ print "awk " "'"'"'" " {print $1,$2,$3} " "'"'"'" " " $1 ".old_ext > " $1 ".new_ext" }' > for_the_birds
It looks excessive, but somehow that combination of quotes works to keep the ' printed as literals. Then if I remember correctly the vaiables are just surrounded with quotes like this: "$1". Try it, let me know how it works with SED.
These are the escape codes that I've found:
* = \x2a
( = \x28
) = \x29
" = \x22
/ = \x2f
\ = \x5c
' = \x27
? = \x3f
% = \x25
^ = \x5e
sed is typically a mess, especially the difference between gnu-sed and bsd-sed
might just be easier to place some sort of sentinel at the sed side, then a quick pipe over to awk, which is far more flexible in accepting any ERE regex, escaped hex, or escaped octals.
e.g. OFS in awk is the true replacement ::
date | sed -E 's/[0-9]+/\xC1\xC0/g' |
mawk NF=NF FS='\xC1\xC0' OFS='\360\237\244\241'
1 Tue Aug 🤡 🤡:🤡:🤡 EDT 🤡
(tested and confirmed working on both BSD-sed and GNU-sed - the emoji isn't a typo that's what those 4 bytes map to in UTF-8 )
There are dozens of answers out there... If you don't mind using a bash function schema, below is a good answer. The objective below was to allow using sed with practically any parameter as a KEYWORD (F_PS_TARGET) or as a REPLACE (F_PS_REPLACE). We tested it in many scenarios and it seems to be pretty safe. The implementation below supports tabs, line breaks and sigle quotes for both KEYWORD and replace REPLACE.
NOTES: The idea here is to use sed to escape entries for another sed command.
CODE
F_REVERSE_STRING_R=""
f_reverse_string() {
: 'Do a string reverse.
To undo just use a reversed string as STRING_INPUT.
Args:
STRING_INPUT (str): String input.
Returns:
F_REVERSE_STRING_R (str): The modified string.
'
local STRING_INPUT=$1
F_REVERSE_STRING_R=$(echo "x${STRING_INPUT}x" | tac | rev)
F_REVERSE_STRING_R=${F_REVERSE_STRING_R%?}
F_REVERSE_STRING_R=${F_REVERSE_STRING_R#?}
}
# [Ref(s).: https://stackoverflow.com/a/2705678/3223785 ]
F_POWER_SED_ECP_R=""
f_power_sed_ecp() {
: 'Escape strings for the "sed" command.
Escaped characters will be processed as is (e.g. /n, /t ...).
Args:
F_PSE_VAL_TO_ECP (str): Value to be escaped.
F_PSE_ECP_TYPE (int): 0 - For the TARGET value; 1 - For the REPLACE value.
Returns:
F_POWER_SED_ECP_R (str): Escaped value.
'
local F_PSE_VAL_TO_ECP=$1
local F_PSE_ECP_TYPE=$2
# NOTE: Operational characters of "sed" will be escaped, as well as single quotes.
# By Questor
if [ ${F_PSE_ECP_TYPE} -eq 0 ] ; then
# NOTE: For the TARGET value. By Questor
F_POWER_SED_ECP_R=$(echo "x${F_PSE_VAL_TO_ECP}x" | sed 's/[]\/$*.^[]/\\&/g' | sed "s/'/\\\x27/g" | sed ':a;N;$!ba;s/\n/\\n/g')
else
# NOTE: For the REPLACE value. By Questor
F_POWER_SED_ECP_R=$(echo "x${F_PSE_VAL_TO_ECP}x" | sed 's/[\/&]/\\&/g' | sed "s/'/\\\x27/g" | sed ':a;N;$!ba;s/\n/\\n/g')
fi
F_POWER_SED_ECP_R=${F_POWER_SED_ECP_R%?}
F_POWER_SED_ECP_R=${F_POWER_SED_ECP_R#?}
}
# [Ref(s).: https://stackoverflow.com/a/24134488/3223785 ,
# https://stackoverflow.com/a/21740695/3223785 ,
# https://unix.stackexchange.com/a/655558/61742 ,
# https://stackoverflow.com/a/11461628/3223785 ,
# https://stackoverflow.com/a/45151986/3223785 ,
# https://linuxaria.com/pills/tac-and-rev-to-see-files-in-reverse-order ,
# https://unix.stackexchange.com/a/631355/61742 ]
F_POWER_SED_R=""
f_power_sed() {
: 'Facilitate the use of the "sed" command. Replaces in files and strings.
Args:
F_PS_TARGET (str): Value to be replaced by the value of F_PS_REPLACE.
F_PS_REPLACE (str): Value that will replace F_PS_TARGET.
F_PS_FILE (Optional[str]): File in which the replacement will be made.
F_PS_SOURCE (Optional[str]): String to be manipulated in case "F_PS_FILE" was
not informed.
F_PS_NTH_OCCUR (Optional[int]): [1~n] - Replace the nth match; [n~-1] - Replace
the last nth match; 0 - Replace every match; Default 1.
Returns:
F_POWER_SED_R (str): Return the result if "F_PS_FILE" is not informed.
'
local F_PS_TARGET=$1
local F_PS_REPLACE=$2
local F_PS_FILE=$3
local F_PS_SOURCE=$4
local F_PS_NTH_OCCUR=$5
if [ -z "$F_PS_NTH_OCCUR" ] ; then
F_PS_NTH_OCCUR=1
fi
local F_PS_REVERSE_MODE=0
if [ ${F_PS_NTH_OCCUR} -lt -1 ] ; then
F_PS_REVERSE_MODE=1
f_reverse_string "$F_PS_TARGET"
F_PS_TARGET="$F_REVERSE_STRING_R"
f_reverse_string "$F_PS_REPLACE"
F_PS_REPLACE="$F_REVERSE_STRING_R"
f_reverse_string "$F_PS_SOURCE"
F_PS_SOURCE="$F_REVERSE_STRING_R"
F_PS_NTH_OCCUR=$((-F_PS_NTH_OCCUR))
fi
f_power_sed_ecp "$F_PS_TARGET" 0
F_PS_TARGET=$F_POWER_SED_ECP_R
f_power_sed_ecp "$F_PS_REPLACE" 1
F_PS_REPLACE=$F_POWER_SED_ECP_R
local F_PS_SED_RPL=""
if [ ${F_PS_NTH_OCCUR} -eq -1 ] ; then
# NOTE: We kept this option because it performs better when we only need to replace
# the last occurrence. By Questor
# [Ref(s).: https://linuxhint.com/use-sed-replace-last-occurrence/ ,
# https://unix.stackexchange.com/a/713866/61742 ]
F_PS_SED_RPL="'s/\(.*\)$F_PS_TARGET/\1$F_PS_REPLACE/'"
elif [ ${F_PS_NTH_OCCUR} -gt 0 ] ; then
# [Ref(s).: https://unix.stackexchange.com/a/587924/61742 ]
F_PS_SED_RPL="'s/$F_PS_TARGET/$F_PS_REPLACE/$F_PS_NTH_OCCUR'"
elif [ ${F_PS_NTH_OCCUR} -eq 0 ] ; then
F_PS_SED_RPL="'s/$F_PS_TARGET/$F_PS_REPLACE/g'"
fi
# NOTE: As the "sed" commands below always process literal values for the "F_PS_TARGET"
# so we use the "-z" flag in case it has multiple lines. By Quaestor
# [Ref(s).: https://unix.stackexchange.com/a/525524/61742 ]
if [ -z "$F_PS_FILE" ] ; then
F_POWER_SED_R=$(echo "x${F_PS_SOURCE}x" | eval "sed -z $F_PS_SED_RPL")
F_POWER_SED_R=${F_POWER_SED_R%?}
F_POWER_SED_R=${F_POWER_SED_R#?}
if [ ${F_PS_REVERSE_MODE} -eq 1 ] ; then
f_reverse_string "$F_POWER_SED_R"
F_POWER_SED_R="$F_REVERSE_STRING_R"
fi
else
if [ ${F_PS_REVERSE_MODE} -eq 0 ] ; then
eval "sed -i -z $F_PS_SED_RPL \"$F_PS_FILE\""
else
tac "$F_PS_FILE" | rev | eval "sed -z $F_PS_SED_RPL" | tac | rev > "$F_PS_FILE"
fi
fi
}
MODEL
f_power_sed "F_PS_TARGET" "F_PS_REPLACE" "" "F_PS_SOURCE"
echo "$F_POWER_SED_R"
EXAMPLE
f_power_sed "{ gsub(/,[ ]+|$/,\"\0\"); print }' ./ and eliminate" "[ ]+|$/,\"\0\"" "" "Great answer (+1). If you change your awk to awk '{ gsub(/,[ ]+|$/,\"\0\"); print }' ./ and eliminate that concatenation of the final \", \" then you don't have to go through the gymnastics on eliminating the final record. So: readarray -td '' a < <(awk '{ gsub(/,[ ]+/,\"\0\"); print; }' <<<\"$string\") on Bash that supports readarray. Note your method is Bash 4.4+ I think because of the -d in readar"
echo "$F_POWER_SED_R"
IF YOU JUST WANT TO ESCAPE THE PARAMETERS TO THE SED COMMAND
MODEL
# "TARGET" value.
f_power_sed_ecp "F_PSE_VAL_TO_ECP" 0
echo "$F_POWER_SED_ECP_R"
# "REPLACE" value.
f_power_sed_ecp "F_PSE_VAL_TO_ECP" 1
echo "$F_POWER_SED_ECP_R"
IMPORTANT: If the strings for KEYWORD and/or replace REPLACE contain tabs or line breaks you will need to use the "-z" flag in your "sed" command. More details here.
EXAMPLE
f_power_sed_ecp "{ gsub(/,[ ]+|$/,\"\0\"); print }' ./ and eliminate" 0
echo "$F_POWER_SED_ECP_R"
f_power_sed_ecp "[ ]+|$/,\"\0\"" 1
echo "$F_POWER_SED_ECP_R"
NOTE: The f_power_sed_ecp and f_power_sed functions above was made available completely free as part of this project ez_i - Create shell script installers easily!.
Standard recommendation here: use perl :)
echo KEYWORD > /tmp/test
REPLACE="<funny characters here>"
perl -pi.bck -e "s/KEYWORD/${REPLACE}/g" /tmp/test
cat /tmp/test
don't forget all the pleasure that occur with the shell limitation around " and '
so (in ksh)
Var=">New version of \"content' here <"
printf "%s" "${Var}" | sed "s/[&\/\\\\*\\"']/\\&/g' | read -r EscVar
echo "Here is your \"text\" to change" | sed "s/text/${EscVar}/g"
If the case happens to be that you are generating a random password to pass to sed replace pattern, then you choose to be careful about which set of characters in the random string. If you choose a password made by encoding a value as base64, then there is is only character that is both possible in base64 and is also a special character in sed replace pattern. That character is "/", and is easily removed from the password you are generating:
# password 32 characters log, minus any copies of the "/" character.
pass=`openssl rand -base64 32 | sed -e 's/\///g'`;
If you are just looking to replace Variable value in sed command then just remove
Example:
sed -i 's/dev-/dev-$ENV/g' test to sed -i s/dev-/dev-$ENV/g test
I have an improvement over the sedeasy function, which WILL break with special characters like tab.
function sedeasy_improved {
sed -i "s/$(
echo "$1" | sed -e 's/\([[\/.*]\|\]\)/\\&/g'
| sed -e 's:\t:\\t:g'
)/$(
echo "$2" | sed -e 's/[\/&]/\\&/g'
| sed -e 's:\t:\\t:g'
)/g" "$3"
}
So, whats different? $1 and $2 wrapped in quotes to avoid shell expansions and preserve tabs or double spaces.
Additional piping | sed -e 's:\t:\\t:g' (I like : as token) which transforms a tab in \t.
An easier way to do this is simply building the string before hand and using it as a parameter for sed
rpstring="s/KEYWORD/$REPLACE/g"
sed -i $rpstring test.txt

Unix user created variables

I am going though some growing pains with Unix. My question:
I want to be able to print all my user defined variables in my shell. Let say I do the following in the shell:
$ x=9
$ y="Help"
$ z=-18
$ R="My 4th variable"
How would I go about printing:
x y z R
You should record your variables first at runtime with set, then compare it later to see which variables were added. Example:
#!/bin/bash
set | grep -E '^[^[:space:]]+=' | cut -f 1 -d = | sort > /tmp/previous.txt
a=1234
b=1234
set | grep -E '^[^[:space:]]+=' | cut -f 1 -d = | sort > /tmp/now.txt
comm -13 /tmp/previous.txt /tmp/now.txt
Output:
a
b
PIPESTATUS
Notice that there are still other variables produced by the shell but is not declared by the user. You can filter them with grep -v. It depends on the shell as well.
Add: Grep and cut could simply be just one sed a well: sed -n 's/^\([^[:space:]]\+\)=.*/\1/p'
Type set:
$ set
Apple_PubSub_Socket_Render=/tmp/launch-jiNTOC/Render
BASH=/bin/bash
BASH_ARGC=()
BASH_ARGV=()
BASH_LINENO=()
BASH_SOURCE=()
BASH_VERSINFO=([0]="3" [1]="2" [2]="51" [3]="1" [4]="release" [5]="x86_64-apple-darwin13")
BASH_VERSION='3.2.51(1)-release'
COCOS2DROOT=/Users/andy/Source/cocos2d
COLUMNS=80
DIRSTACK=()
...
(Oh, and BTW, you appear to have your variable syntax incorrect as you assign, say, A but print $A)
If variables are exported then you can use env command in Unix.

replace and delete characters in a shell script

I have a shell script to automate builds of my programm. I need to transform versioning numbers like V4_5_1-RC1 to 4.5.1-RC1. The V should be removed and the _ should be replaced with .. I tried several things, for example with sed:
$NAMEEXT = "V4_5_1-RC1"
$lffNameRSC = ${sed -e "s/V//g" <<< $NAMEEXT}
$lffNameRSC = ${sed -e "s/_/./g" <<< $lffNameRSC}
echo $lffNameRSC
but I'm getting errors.
./makerelease.sh: line 113: ${sed -e "s/V//g" <<< $NAMEEXT}: bad substitution
./makerelease.sh: line 114: ${sed -e "s/_/./g" <<< $lffNameRSC}: bad substitution
there should be no spaces around =
there should be $(..) instead of ${..} to evaluate the command
there should not be $ in variable assignment statement
With
#!/bin/bash
NAMEEXT="V4_5_1-RC1"
lffNameRSC=$(sed -e "s/V//g" <<< $NAMEEXT)
lffNameRSC=$(sed -e "s/_/./g" <<< $lffNameRSC)
echo $lffNameRSC
you will get
4.5.1-RC1
And, by the way, it could be done easier, like
$> echo "V4_5_1-RC1" | sed "s/V//g; s/_/./g"
4.5.1-RC1
Bash parameter expansion can do what you want without any external tools:
NAMEEXT="V4_5_1-RC1"
version=${NAMEEXT#V} # remove the leading V
version=${version//_/.} # replace all _ with .
echo $version # ==> 4.5.1-RC1

Get string between strings in bash

I want to get the string between <sometag param=' and '>
I tried to use the method from Get any string between 2 string and assign a variable in bash to get the "x":
echo "<sometag param='x'><irrelevant stuff='nonsense'>" | tr "'" _ | sed -n 's/.*<sometag param=_\(.*\)_>.*/\1/p'
The problem (apart from low efficiency because I just cannot manage to escape the apostrophe correctly for sed) is that sed matches the maximum, i.e. the output is:
x_><irrelevant stuff=_nonsense
but the correct output would be the minimum-match, in this example just "x"
Thanks for your help
You are probably looking for something like this:
sed -n "s/.*<sometag param='\([^']*\)'>.*/\1/p"
Test:
echo "<sometag param='x'><irrelevant stuff='nonsense'>" | sed -n "s/.*<sometag param='\([^']*\)'>.*/\1/p"
Results:
x
Explanation:
Instead of a greedy capture, use a non-greedy capture like: [^']* which means match anything except ' any number of times. To make the pattern stick, this is followed by: '>.
You can also use double quotes so that you don't need to escape the single quotes. If you wanted to escape the single quotes, you'd do this:
-
... | sed -n 's/.*<sometag param='\''\([^'\'']*\)'\''>.*/\1/p'
Notice how that the single quotes aren't really escaped. The sed expression is stopped, an escaped single quote is inserted and the sed expression is re-opened. Think of it like a four character escape sequence.
Personally, I'd use GNU grep. It would make for a slightly shorter solution. Run like:
... | grep -oP "(?<=<sometag param=').*?(?='>)"
Test:
echo "<sometag param='x'><irrelevant stuff='nonsense'>" | grep -oP "(?<=<sometag param=').*?(?='>)"
Results:
x
You don't have to assemble regexes in those cases, you can just use ' as the field separator
in="<sometag param='x'><irrelevant stuff='nonsense'>"
IFS="'" read x whatiwant y <<< "$in" # bash
echo "$whatiwant"
awk -F\' '{print $2}' <<< "$in" # awk

Why doesn't this use of sed command work?

I'm have a bash script that I use to manipulate files on a computation cluster.
The files I am trying to manipulate are of the format:
beadSize=6.25
minBoxSize=2.2
lipids=1200
chargedLipids=60
cations=0
HEAD=0
CHEAD=-2
BODY=2
TAIL=3
ION=-1
RHO_BODY=10
RHO_TAIL=14
tol=1e-10
lb=7.1
FTsize=8
ROUNDS=1000000
ftROUNDS=10
wROUNDS=1000
dt=0.01
alpha=1
transSize=0.15
transSizeZ=0.0
ionsTransSize=2.8
ionsTransSizeZ=2.8
rotateSize=0.18
volSize=8
modSize=0.0
forceFactor=2
kappaCV=0
sysSize=26
zSize=300
iVal=1
split=0
randSeed=580
I call a function inside a loop:
for per in $(seq 70 -5 5); do
for seed in {580..583}; do
for c in {"fs","fd","bfs","bfd"}; do
let count=$count+1
startJob $per $seed $c $count
done
done
done
and the lines I use to manipulate:
let n=$1*12
echo $n
cat trm.dat | sed '/memFile*/d' | sed '/rStart*/d' | sed '/test*/d'| sed 's/modSize=[0-9.]*/modSize=0.0/' | sed 's/chachargedLipids=[0-9]*/chargedLipids="$n"/' | grep char #> propFile.dat
for $per=15, for example, I expect $n==180. However when I run the script I see:
180
chargedLipids=120
What am I doing wrong?
Note
I have also tried to use:
sed "s/chachargedLipids=[0-9]*/chargedLipids=$n/"
With the same result.
chacharged != charged, and the final sed is doing nothing. With single quotes, you would expect to see the literal text chargedLipids="$n" in your output if a replacement was being made.

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