change json file by bash script

Not the answer for everyone, but if you already happen to have NodeJs installed in your system, you can use it to easily manipulate JSON.

eg:

#!/usr/bin/env bash
jsonFile=$1;

node > out_${jsonFile} <<EOF
//Read data
var data = require('./${jsonFile}');

//Manipulate data
delete data.key3
data.key4 = 'new value!';

//Output data
console.log(JSON.stringify(data));

EOF

Heck, if you only need to do JSON manipulation and you have node (ie: You don't really need any other bash functionality) you could directly write a script using node as the interpreter:

#! /usr/bin/env node
var data = require('./'+ process.argv[2]);
/*manipulate*/
console.log(JSON.stringify(data));

Building off Lenny's answer, we can use node's -p option, which evaluates the given script and writes the output to stdout.

Using the spread operator for easy modification gives:

node -p "JSON.stringify({...require('./data.json'), key4: 'value4'}, null, 2)" > data.json

to change a file in place, use the sponge command

echo '{ "k": "old value" }' >f.json

cat f.json | jq '.k = $v' --arg v 'new value' | sponge f.json

see also: jq issue Edit files in place #105

alternative to jq: jaq

echo '{ "k": "old value" }' >f.json

jaq -i '.k = $v' --arg v 'new value' f.json

... but jaq has less features than jq

Here's a pure bash example, including the "comma issue".

#!/bin/bash
# This bash script just uses the sed command to 
#   replace/insert a new key at/before/after an 
#   existing key in a json file 
# The comma issue:
# - replace: with/without, as previous entry
# - before: always add
# - after: add before, if there was none
SED_CMD="/tmp/sed_cmd.tmp"
JSFILE1="./data1.json"
JSFILE2="./data2.json"
JSFILE3="./data3.json"
SEARCH_KEY="key3"
# create json input file
echo -e '{\n\t"key1": "value1",\n\t"key2": "value2",\n\t"key3": "value3"\n}' > $JSFILE1
echo -e "input:"
cat $JSFILE1
# duplicate twice
cp $JSFILE1 $JSFILE2 && cp $JSFILE1 $JSFILE3
# find the SEARCH_KEY and store the complete line to SEARCH_LINE 
SEARCH_LINE=`cat data.json | grep $SEARCH_KEY`
echo "SEARCH_LINE=>$SEARCH_LINE<"
# replace SEARCH_LINE
IS_COMMA=`echo $SEARCH_LINE | grep ","`
[ -z "$IS_COMMA" ] && \
    echo "s+$SEARCH_LINE+\t\"keyNew\": \"New\"+g" > $SED_CMD || \
    echo "s+$SEARCH_LINE+\t\"keyNew\": \"New\",+g" > $SED_CMD
sed -i -f $SED_CMD $JSFILE1
echo -e "replace:"
cat $JSFILE1
# insert before SEARCH_LINE
echo "s+$SEARCH_LINE+\t\"keyNew\": \"New\",\n$SEARCH_LINE+g" > $SED_CMD
sed -i -f $SED_CMD $JSFILE2
echo -e "before:"
cat $JSFILE2
# insert after SEARCH_LINE
IS_COMMA=`echo $SEARCH_LINE | grep ","`
[ -z "$IS_COMMA" ] && \
    echo "s+$SEARCH_LINE+$SEARCH_LINE,\n\t\"keyNew\": \"New\"+g" > $SED_CMD || \
    echo "s+$SEARCH_LINE+$SEARCH_LINE\n\t\"keyNew\": \"New\",+g" > $SED_CMD
sed -i -f $SED_CMD $JSFILE3
echo -e "after:"
cat $JSFILE3
exit 0

how can I add and remove a new key (i.e "key4": "value4") by bash script?

Please use a dedicated JSON parser, like xidel.

Add a new attribute:

$ xidel -s "input.json" -e '($json).key4:="value4"'          # Xidel exclusive syntax, dot notation)
$ xidel -s "input.json" -e '$json("key4"):="value4"'         # Xidel exclusive syntax, JSONiq notation)
$ xidel -s "input.json" -e '$json?key4:="value4"'            # Xidel exclusive syntax, XPath 3.1 syntax)
$ xidel -s "input.json" -e '{|$json,{"key4":"value4"}|}'     # JSONiq syntax (deprecated)
$ xidel -s "input.json" -e 'map:put($json,"key4",4)'         # XQuery 3.1 map functions
$ xidel -s "input.json" -e 'map:merge(($json,{"key4":4}))'   # XQuery 3.1 map functions
{
  "key1": "value1",
  "key2": "value2",
  "key3": "value3",
  "key4": "value4"
}

Remove the attribute "key3":

$ xidel -s "input.json" --xmlns:jnlib="http://jsoniq.org/function-library" -e 'jnlib:remove-keys($json,"key3")'   # JSONiq jnlib functions (deprecated)
$ xidel -s "input.json" -e 'map:remove($json,"key3")'   # XQuery 3.1 map functions
{
  "key1": "value1",
  "key2": "value2"
}

Change the attribute "key3" value to "value4":

$ xidel -s "input.json" -e '($json).key3:="value4"'           # Xidel exclusive syntax, dot notation)
$ xidel -s "input.json" -e '$json("key3"):="value4"'          # Xidel exclusive syntax, JSONiq notation)
$ xidel -s "input.json" -e '$json?key3:="value4"'             # Xidel exclusive syntax, XPath 3.1 syntax)
$ xidel -s "input.json" -e 'map:put($json,"key3","value4")'   # XQuery 3.1 map functions
$ xidel -s "input.json" -e 'map:merge(($json,{"key3":"value4"}),{"duplicates":"use-last"})'   # XQuery 3.1 map functions
{
  "key1": "value1",
  "key2": "value2",
  "key3": "value4"
}