Converting CSV to JSON in bash

Question

Trying to convert a CSV file into a JSON

Here is two sample lines :

-21.3214077;55.4851413;Ruizia cordata
-21.3213078;55.4849803;Cossinia pinnata

I would like to get something like :

"occurrences": [
                 {
                "position": [-21.3214077, 55.4851413],
                "taxo": {
                    "espece": "Ruizia cordata"
                 },
                 ...
             }]

Here is my script :

    echo '"occurences": [ '

cat se.csv | while read -r line
  do
      IFS=';' read -r -a array <<< $line;
      echo -n -e '{ "position": [' ${array[0]}
      echo -n -e ',' ${array[1]} ']'
      echo -e ', "taxo": {"espece":"' ${array[2]} '"'
done
echo "]";

I get really strange results :

   "occurences": [ 
 ""position": [ -21.3214077, 55.4851413 ], "taxo": {"espece":" Ruizia cordata
 ""position": [ -21.3213078, 55.4849803 ], "taxo": {"espece":" Cossinia pinnata

What is wrong with my code ?

Is there a reason you aren't using jq, or otherwise JSON-aware tooling? Generating JSON (or other structured-data serializations) with string concatenation is... error-prone at best. — Charles Duffy
– Charles Duffy, Commented Jun 27, 2017 at 12:52
Other than that, there are a lot of bad practices here. You're leaving out a bunch of essential quoting, such that if one of your values contained a whitespace-surrounded * it would be replaced with a list of filenames. You're using -e unnecessarily, so that if your JSON data contained a \n sequence (which, in JSON, should be represented as exactly those characters) it would be replaced with a literal newline; and by virtue of -e your code won't work correctly on shells with a POSIX: standard echo. — Charles Duffy
– Charles Duffy, Commented Jun 27, 2017 at 12:54
re: the missing quoting, by the way -- consider making a habit of running your code through shellcheck.net. — Charles Duffy
– Charles Duffy, Commented Jun 27, 2017 at 13:14

dess · Accepted Answer · 2021-10-28 23:12:33Z

113

Here's a python one-liner/script that'll do the trick:

cat my.csv | python -c 'import csv, json, sys; print(json.dumps([dict(r) for r in csv.DictReader(sys.stdin)]))'

edited Oct 28, 2021 at 23:12

dess

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answered Dec 2, 2020 at 0:57

jstaab

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12 Comments

btk Over a year ago

This should be the accepted solution -- it does the trick for any and all payloads. The jq version is a one-off and requires painstakingly matching the schema

Abraham Labkovsky Over a year ago

I love this idea. I modified slightly to write to file...

cat in.csv | python -c 'import csv, json, sys; f = open("out.json", "x"); f.write(json.dumps([dict(r) for r in csv.DictReader(sys.stdin)])); f.close()'

K14 Over a year ago

to write it to a file just add | > filename.json at the end. Like this:

cat my.csv | python -c 'import csv, json, sys; print(json.dumps([dict(r) for r in csv.DictReader(sys.stdin)]))' | > my.json

btk Over a year ago

@tink imo it's way easier to add headers to the .csv file than futz around with a complicated jq query

cherryblossom Over a year ago

I don't think the dict is needed and you could just do list(csv.DictReader(sys.stdin)) instead.

|

peak · Accepted Answer · 2018-11-23 09:08:44Z

44

The right tool for this job is jq.

jq -Rsn '
  {"occurrences":
    [inputs
     | . / "\n"
     | (.[] | select(length > 0) | . / ";") as $input
     | {"position": [$input[0], $input[1]], "taxo": {"espece": $input[2]}}]}
' <se.csv

emits, given your input:

{
  "occurences": [
    {
      "position": [
        "-21.3214077",
        "55.4851413"
      ],
      "taxo": {
        "espece": "Ruizia cordata"
      }
    },
    {
      "position": [
        "-21.3213078",
        "55.4849803"
      ],
      "taxo": {
        "espece": "Cossinia pinnata"
      }
    }
  ]
}

By the way, a less-buggy version of your original script might look like:

#!/usr/bin/env bash

items=( )
while IFS=';' read -r lat long pos _; do
  printf -v item '{ "position": [%s, %s], "taxo": {"espece": "%s"}}' "$lat" "$long" "$pos"
  items+=( "$item" )
done <se.csv

IFS=','
printf '{"occurrences": [%s]}\n' "${items[*]}"

Note:

There's absolutely no point using cat to pipe into a loop (and good reasons not to); thus, we're using a redirection (<) to open the file directly as the loop's stdin.
read can be passed a list of destination variables; there's thus no need to read into an array (or first to read into a string, and then to generate a heresting and to read from that into an array). The _ at the end ensures that extra columns are discarded (by putting them into the dummy variable named _) rather than appended to pos.
"${array[*]}" generates a string by concatenating elements of array with the character in IFS; we can thus use this to ensure that commas are present in the output only when they're needed.
printf is used in preference to echo, as advised in the APPLICATION USAGE section of the specification for echo itself.
This is still inherently buggy since it's generating JSON via string concatenation. Don't use it.

edited Nov 23, 2018 at 9:08

peak

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answered Jun 27, 2017 at 13:07

Charles Duffy

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4 Comments

HydrUra Over a year ago

Thx, didn't know jq. But I cannot figure it out how to input my CSV. What's $s at the end of your line ?

Charles Duffy Over a year ago

Oh -- that was reading from a string, not a file. Sorry 'bout that, left it in from testing.

Charles Duffy Over a year ago

actually, I edited that out a while ago -- could you refresh to be sure you're seeing the current version of the answer?

Greg Over a year ago

that is some beautiful stuff, thanks... i like the use of inputs there.

Raman · Accepted Answer · 2019-08-20 05:33:23Z

25

The accepted answer uses jq to parse the input. This works but jq doesn't handle escapes i.e. input from a CSV produced from Excel or similar tools is quoted like this:

foo,"bar,baz",gaz

will result in the incorrect output, as jq will see 4 fields, not 3.

One option is to use tab-separated values instead of comma (as long as your input data doesn't contain tabs!), along with the accepted answer.

Another option is to combine your tools, and use the best tool for each part: a CSV parser for reading the input and turning it into JSON, and jq for transforming the JSON into the target format.

The python-based csvkit will intelligently parse the CSV, and comes with a tool csvjson which will do a much better job of turning the CSV into JSON. This can then be piped through jq to convert the flat JSON output by csvkit into the target form.

With the data provided by the OP, for the desired output, this as as simple as:

csvjson --no-header-row  |
  jq '.[] | {occurrences: [{ position: [.a, .b], taxo: {espece: .c}}]}'

Note that csvjson automatically detects ; as the delimiter, and without a header row in the input, assigns the json keys as a, b, and c.

The same also applies to writing to CSV files -- csvkit can read a JSON array or new-line delimited JSON, and intelligently output a CSV via in2csv.

edited Aug 20, 2019 at 5:33

answered May 31, 2019 at 20:55

Raman

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2 Comments

Tobias J Over a year ago

Perfect, thanks! I knew there had to be a better way than parsing CSV with jq!

Marcos Roberto Silva Over a year ago

In my opinion csvjson is the best approach for this since it also can infer the data types, and not treat numbers as string, avoiding to add double quotes in it.

richardkmiller · Accepted Answer · 2020-12-16 20:21:57Z

17

John Kerl's Miller tool has this built-in:

mlr --c2j --jlistwrap cat INPUT.csv > OUTPUT.json

answered Dec 16, 2020 at 20:21

richardkmiller

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1 Comment

Nirmalya Over a year ago

I love 'jq' but this is really nice, at least for converting a column-header carrying CSV to JSON. @richardkmiller

Tsuneo Yoshioka · Accepted Answer · 2022-06-29 09:42:17Z

6

Here is the Ruby one-liner solution:

ruby -r json -r csv -e 'puts CSV.parse(STDIN, headers:true).map(&:to_h).to_json' < INPUT.csv

answered Jun 29, 2022 at 9:42

Tsuneo Yoshioka

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Comments

Ondra Žižka · Accepted Answer · 2018-09-27 00:18:15Z

5

Here is an article on the subject: https://infiniteundo.com/post/99336704013/convert-csv-to-json-with-jq

It also uses JQ, but a bit different approach using split() and map().

jq --slurp --raw-input \
   'split("\n") | .[1:] | map(split(";")) |
      map({
         "position": [.[0], .[1]],
         "taxo": {
             "espece": .[2]
          }
      })' \
  input.csv > output.json

It doesn't handle separator escaping, though.

edited Sep 27, 2018 at 0:18

answered Aug 30, 2018 at 14:32

Ondra Žižka

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6 Comments

Charles Duffy Over a year ago

This is a good general approach! Perhaps you might edit to work with the OP's data structure? (Or would a 3rd-party edit doing so be welcome?)

Ondra Žižka Over a year ago

@CharlesDuffy, I gave it a shot, but not tested - feel free to fix/improve.

Charles Duffy Over a year ago

Needed some minor tweaks -- changing from ',' to ';' as the separator, changing ".[3]" to .[2]; and --raw-output wasn't serving any purpose (it's ignored when output isn't a string).

Charles Duffy Over a year ago

Also, the .[1:] (skipping the first line) is only appropriate if input has a header; that was true in the blog post, but I'm not sure it's true here.

Ondra Žižka Over a year ago

@CharlesDuffy, how would you parse the headers and then made the map automatically? Imagine you have different CSV files with different columns and want the JSON object keys derived from the header. Does jq have some kind of variables? Or perhaps an extra call to `jq ... .[:1] to fill a Bash array, somehow?

|

Cyril Chaboisseau · Accepted Answer · 2022-09-10 10:19:12Z

3

Here is another way using Miller (mlr)

mlr --implicit-csv-header --icsv --fs ';' --ojson label position,taxo,espece example.csv

which will produce the following

[
{
  "position": -21.3214077,
  "taxo": 55.4851413,
  "espece": "Ruizia cordata"
},
{
  "position": -21.3213078,
  "taxo": 55.4849803,
  "espece": "Cossinia pinnata"
}
]

or if you use --ojsonl (JSON line) instead of plain JSON will generate the following

{"position": -21.3214077, "taxo": 55.4851413, "espece": "Ruizia cordata"}
{"position": -21.3213078, "taxo": 55.4849803, "espece": "Cossinia pinnata"}

answered Sep 10, 2022 at 10:19

Cyril Chaboisseau

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Comments

peak · Accepted Answer · 2018-11-24 03:01:58Z

In general, if your jq has the inputs built-in filter (available since jq 1.5), then it is better to use it rather than the -s command-line option.

Here in any case is a solution using inputs. This solution is also variable-free.

{"occurrences":
  [inputs
   | select(length > 0)
   | . / ";"
   | {"position": [.[0], .[1]], 
      "taxo": {"espece": .[2]}} ]}

SSV, CSV, and all that

The above of course assumes that the file has semicolon-separated fields in each line, and that there are none of the complications associated with CSV files.

If the input has fields that are strictly delimited by a single character, then jq should have no problems handling it. Otherwise, it might be best to use a tool that can reliably convert to the TSV (tab-separated value) format, which jq can handle directly.

Ondra Žižka · Accepted Answer · 2018-10-25 02:24:27Z

1

Because the jq solution does not handle CSV escaping, column names at the first line, commented-out lines and other common CSV "features", I have extended the CSV Cruncher tool to allow reading CSV and writing it as JSON. It's not exactly "Bash", but neither is jq :)

It's primarily a CSV-as-SQL processing app, so it's not completely trivial, but here is the trick:

./crunch -in myfile.csv -out output.csv --json -sql 'SELECT * FROM myfile'

It also allows output as JSON object per line or proper JSON array. See the documentation.

It's in beta quality, so all feedback or pull requests are welcome.

answered Oct 25, 2018 at 2:24

Ondra Žižka

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Comments

Jeff Mercado · Accepted Answer · 2019-06-01 08:45:39Z

If you want to go crazy, you can write a parser using jq. Here's my implementation which can be thought of as the inverse of the @csv filter. Throw this into your .jq file.

def do_if(pred; update):
    if pred then update else . end;
def _parse_delimited($_delim; $_quot; $_nl; $_skip):
    [($_delim, $_quot, $_nl, $_skip)|explode[]] as [$delim, $quot, $nl, $skip] |
    [0,1,2,3,4,5] as [$s_start,$s_next_value,$s_read_value,$s_read_quoted,$s_escape,$s_final] |
    def _append($arr; $value):
        $arr + [$value];
    def _do_start($c):
        if $c == $nl then
            [$s_start, null, null, _append(.[3]; [""])]
        elif $c == $delim then
            [$s_next_value, null, [""], .[3]]
        elif $c == $quot then
            [$s_read_quoted, [], [], .[3]]
        else
            [$s_read_value, [$c], [], .[3]]
        end;
    def _do_next_value($c):
        if $c == $nl then
            [$s_start, null, null, _append(.[3]; _append(.[2]; ""))]
        elif $c == $delim then
            [$s_next_value, null, _append(.[2]; ""), .[3]]
        elif $c == $quot then
            [$s_read_quoted, [], .[2], .[3]]
        else
            [$s_read_value, [$c], .[2], .[3]]
        end;
    def _do_read_value($c):
        if $c == $nl then
            [$s_start, null, null, _append(.[3]; _append(.[2]; .[1]|implode))]
        elif $c == $delim then
            [$s_next_value, null, _append(.[2]; .[1]|implode), .[3]]
        else
            [$s_read_value, _append(.[1]; $c), .[2], .[3]]
        end;
    def _do_read_quoted($c):
        if $c == $quot then
            [$s_escape, .[1], .[2], .[3]]
        else
            [$s_read_quoted, _append(.[1]; $c), .[2], .[3]]
        end;
    def _do_escape($c):
        if $c == $nl then
            [$s_start, null, null, _append(.[3]; _append(.[2]; .[1]|implode))]
        elif $c == $delim then
            [$s_next_value, null, _append(.[2]; .[1]|implode), .[3]]
        else
            [$s_read_quoted, _append(.[1]; $c), .[2], .[3]]
        end;
    def _do_final($c):
        .;
    def _do_finalize:
        if .[0] == $s_start then
            [$s_final, null, null, .[3]]
        elif .[0] == $s_next_value then
            [$s_final, null, null, _append(.[3]; [""])]
        elif .[0] == $s_read_value then
            [$s_final, null, null, _append(.[3]; _append(.[2]; .[1]|implode))]
        elif .[0] == $s_read_quoted then
            [$s_final, null, null, _append(.[3]; _append(.[2]; .[1]|implode))]
        elif .[0] == $s_escape then
            [$s_final, null, null, _append(.[3]; _append(.[2]; .[1]|implode))]
        else # .[0] == $s_final
            .
        end;
    reduce explode[] as $c (
        [$s_start,null,null,[]];
        do_if($c != $skip;
            if .[0] == $s_start then
                _do_start($c)
            elif .[0] == $s_next_value then
                _do_next_value($c)
            elif .[0] == $s_read_value then
                _do_read_value($c)
            elif .[0] == $s_read_quoted then
                _do_read_quoted($c)
            elif .[0] == $s_escape then
                _do_escape($c)
            else # .[0] == $s_final
                _do_final($c)
            end
        )
    )
    | _do_finalize[3][];
def parse_delimited($delim; $quot; $nl; $skip):
    _parse_delimited($delim; $quot; $nl; $skip);
def parse_delimited($delim; $quot; $nl):
    parse_delimited($delim; $quot; $nl; "\r");
def parse_delimited($delim; $quot):
    parse_delimited($delim; $quot; "\n");
def parse_delimited($delim):
    parse_delimited($delim; "\"");
def parse_csv:
    parse_delimited(",");

For your data, you would want to change the delimiter to semicolons.

$ cat se.csv
-21.3214077;55.4851413;Ruizia cordata
-21.3213078;55.4849803;Cossinia pinnata
$ jq -R 'parse_delimited(";")' se.csv
[
  "-21.3214077",
  "55.4851413",
  "Ruizia cordata"
]
[
  "-21.3213078",
  "55.4849803",
  "Cossinia pinnata"
]

This will work fine for most inputs to parse a line at a time, but if your data has literal newlines, you will want to read the entire file as a string.

$ cat input.csv
Year,Make,Model,Description,Price
1997,Ford,E350,"ac, abs, moon",3000.00
1999,Chevy,"Venture ""Extended Edition""","",4900.00
1999,Chevy,"Venture ""Extended Edition, Very Large""",,5000.00
1996,Jeep,Grand Cherokee,"MUST SELL!
air, moon roof, loaded",4799.00
$ jq -Rs 'parse_csv' input.csv
[
  "Year",
  "Make",
  "Model",
  "Description",
  "Price"
]
[
  "1997",
  "Ford",
  "E350",
  "ac, abs, moon",
  "3000.00"
]
[
  "1999",
  "Chevy",
  "Venture \"Extended Edition\"",
  "",
  "4900.00"
]
[
  "1999",
  "Chevy",
  "Venture \"Extended Edition, Very Large\"",
  "",
  "5000.00"
]
[
  "1996",
  "Jeep",
  "Grand Cherokee",
  "MUST SELL!\nair, moon roof, loaded",
  "4799.00"
]

The bug is on _do_finalize, in the case where the last character is a delimiter. In that case, instead of saving .[2], it discards it. Replacing it with something like delimiter on _do_next_value fixes it.

Johannes Kasimir · Accepted Answer · 2021-09-08 19:25:05Z

1

A version of Jstaabs answer that avoids storing the whole dictionary structure in memory before printing, in case the CSV file is large.

import csv, json, sys

for r in csv.DictReader(sys.stdin):
    print(dict(r))

Note this outputs JSON lines format and not exactly JSON.

Here's a version which outputs a proper JSON array, at the expense of being longer.

import csv, json, sys

sys.stdout.write('[')

first = True
for r in csv.DictReader(sys.stdin):
    if not first:
        sys.stdout.write(',')
    first = False
    json.dump(dict(r), sys.stdout)

sys.stdout.write(']')

edited Sep 8, 2021 at 19:25

answered Sep 8, 2021 at 11:16

Johannes Kasimir

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Comments

Richard · Accepted Answer · 2022-09-02 18:25:51Z

0

For anyone looking for a php one-liner solution:

php -r 'echo json_encode(array_map(''str_getcsv'', file(''file.csv'')));'

If you need to specify a different delimiter:

php -r 'echo json_encode(array_map(fn($line) => str_getcsv($line, '';''), file(''file.csv'')));'

You might also use some flags when using json_decode:

https://www.php.net/manual/pt_BR/function.json-encode.php

answered Sep 2, 2022 at 18:25

Richard

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