I have several .json files similar to this.
{
"AcquisitionNumber": 1,
"TotalReadoutTime": 0.035,
"IntendedFor": "func/sub-02_task-rest_run-01_bold.nii.gz"
}
I want to change the sub number in the "IntendedFor" line using a bash variable, looping over different subs.For example if sub is 03:
sub=03
echo $sub
03
How can I change the value of sub-02 to sub-03 using this bash variable?
Use jq:
jq --arg sub "$sub" '.IntendedFor |= sub("(?<=sub-)[^_]+"; $sub)' file
Note that your jq binary must be compiled with regex support in order to use sub function.
And, you can implement inline editing using a for loop and temporary files:
sub=03
for jsonfile in *.json; do
tempfile=$(mktemp -u)
jq --arg sub "$sub" '.IntendedFor|=sub("(?<=sub-)[^_]+";$sub)' "$jsonfile" > "$tempfile"
mv "$tempfile" "$jsonfile"
done
With jq and bash:
value=$(jq -r '.IntendedFor' file)
new_value="${value/sub-02/sub-03}"
jq --arg new "$new_value" '.IntendedFor |= $new' file
Output:
{
"AcquisitionNumber": 1,
"TotalReadoutTime": 0.035,
"IntendedFor": "func/sub-03_task-rest_run-01_bold.nii.gz"
}
--arg option to pass shell variables to jq
Using sponge (part of moreutils):
for f in *.json; do
jq --arg sub "$sub" '.IntendedFor |= sub("/sub-[^_]+";"/sub-"+$sub)' "$f" | sponge "$f"
done
In any case, a simple regex suffices.
See:
There are better ways of doing this, but there is a bash-solution:
#!/bin/bash
fromstring="sub-02"
tostring="sub-03"
while read line; do
case "$line" in
(*IntendedFor*) echo $(line/$fromstring/$tostring) ;;
(*) echo $line ;;
esac
done < JSONfile
cat is a UUOc` (Unnecessary Use Of cat). Unless you are concatenating files, if you find yourself doing cat somethingelse, then it is probably a UUOc. Here using redirection, e.g. while read line; do ... done <jsonfile is the proper way of feeding the while loop. I suspect the ding comes from the fact that parsing json or xml in bash is simply unwise, there is zero format validation. That is why we have tools like jq and xmlstartlet.
cat from the answer, which makes it work completely in bash, without external programs.
${variable//pattern/replacement}, see stackoverflow.com/q/13043344/3208553
jq