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ndjson : Wicked-fast Streaming JSON (‘ndjson’) Reader

Rcpp/C++11 wrapper for https://github.com/nlohmann/json

The goal is to create a completely “flat” data.frame-like structure from ndjson records in plain text ndjson files or gzip’d ndjson files.

Installation guidance for Linux/BSD-ish systems

CRAN has binaries for Windows and macOS. To build this on UNIX-like systems, you need at least g++4.9 or clang++. This is a forced requirement by the ndjson library.

The least painful way to do this is to install gcc >= 4.9 (and you should install ccache while you’re at it) and mmodfiy ~/.R/Makevars thusly:

# Use whatever version of (g++ >=4.9 or clang++) that you downloaded
VER=-4.9
CC=ccache gcc$(VER)
CXX=ccache g++$(VER)
SHLIB_CXXLD=g++$(VER)
FC=ccache gfortran
F77=ccache gfortran

Why `ndjson` + Examples

An example of such files are the output from Rapid7 internet-wide scans, such as their HTTPS study. A gzip’d extract of 100,000 of one of those scans weighs in abt about 171MB. The records sometimes contain heavily nested JSON elements depending on how comprehensive the certificate data and other fields were. A typical record will look like this:

{
  "vhost": "teamchat.buzzpoints.com",
  "host": "52.87.143.83",
  "certsubject": {
    "CN": "teamchat.buzzpoints.com"
  },
  "ip": "52.87.143.83",
  "data": "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",
  "port": "443"
}

A system.time(df <- stream_in("https-extract.json.gz")) results in:

   user  system elapsed 
 14.822   0.224  15.189

on a 13" MacBook Pro and produces:

Classes ‘tbl_dt’, ‘tbl’, ‘data.table’ and 'data.frame': 100000 obs. of  36 variables:
 $ certsubject.CN                 : chr  "*.tio.ch" "*.starwoodhotels.com" "a.ssl.fastly.net" "a.ssl.fastly.net" ...
 $ data                           : chr  "SFRUUC8xLjEgNDAzIEZvcmJpZGRlbg0KU2VydmVyOiBjbG91ZGZsYXJlLW5naW54DQpEYXRlOiBNb24sIDIyIEF1ZyAyMDE2IDE3OjE2OjE2IEdNVA0KQ29udGVudC1"| __truncated__ "SFRUUC8xLjAgNDAwIEJhZCBSZXF1ZXN0DQpTZXJ2ZXI6IEFrYW1haUdIb3N0DQpNaW1lLVZlcnNpb246IDEuMA0KQ29udGVudC1UeXBlOiB0ZXh0L2h0bWwNCkNvbnR"| __truncated__ "SFRUUC8xLjEgNTAwIERvbWFpbiBOb3QgRm91bmQNClNlcnZlcjogVmFybmlzaA0KUmV0cnktQWZ0ZXI6IDANCmNvbnRlbnQtdHlwZTogdGV4dC9odG1sDQpDYWNoZS1"| __truncated__ "SFRUUC8xLjEgNTAwIERvbWFpbiBOb3QgRm91bmQNClNlcnZlcjogVmFybmlzaA0KUmV0cnktQWZ0ZXI6IDANCmNvbnRlbnQtdHlwZTogdGV4dC9odG1sDQpDYWNoZS1"| __truncated__ ...
 $ host                           : chr  "104.20.28.6" "104.80.186.186" "151.101.255.54" "151.101.158.15" ...
 $ ip                             : chr  "104.20.28.6" "104.80.186.186" "151.101.255.54" "151.101.158.15" ...
 $ port                           : chr  "443" "443" "443" "443" ...
 $ vhost                          : chr  "104.20.28.6" "104.80.186.186" "a.ssl.fastly.net" "a.ssl.fastly.net" ...
 $ certsubject.C                  : chr  NA "US" "US" "US" ...
 $ certsubject.L                  : chr  NA "Stamford" "San Francisco" "San Francisco" ...
 $ certsubject.O                  : chr  NA "STARWOOD HOTELS AND RESORTS WORLDWIDE, INC." "Fastly, Inc." "Fastly, Inc." ...
 $ certsubject.OU                 : chr  NA "IT Solutions" NA NA ...
 $ certsubject.ST                 : chr  NA "Connecticut" "California" "California" ...
 $ certsubject.emailAddress       : chr  NA NA NA NA ...
 $ certsubject.UNDEF              : chr  NA NA NA NA ...
 $ certsubject.businessCategory   : chr  NA NA NA NA ...
 $ certsubject.postalCode         : chr  NA NA NA NA ...
 $ certsubject.serialNumber       : chr  NA NA NA NA ...
 $ certsubject.street             : chr  NA NA NA NA ...
 $ certsubject.SN                 : chr  NA NA NA NA ...
 $ certsubject.unstructuredName   : chr  NA NA NA NA ...
 $ certsubject.ITU-T              : chr  NA NA NA NA ...
 $ certsubject.GN                 : chr  NA NA NA NA ...
 $ certsubject.description        : chr  NA NA NA NA ...
 $ certsubject.subjectAltName     : chr  NA NA NA NA ...
 $ certsubject.name               : chr  NA NA NA NA ...
 $ certsubject.DC                 : chr  NA NA NA NA ...
 $ certsubject.postOfficeBox      : chr  NA NA NA NA ...
 $ certsubject.dnQualifier        : chr  NA NA NA NA ...
 $ certsubject.generationQualifier: chr  NA NA NA NA ...
 $ certsubject.initials           : chr  NA NA NA NA ...
 $ certsubject.pseudonym          : chr  NA NA NA NA ...
 $ certsubject.title              : chr  NA NA NA NA ...
 $ certsubject                    : int  NA NA NA NA NA NA NA NA NA NA ...
 $ certsubject.unstructuredAddress: chr  NA NA NA NA ...
 $ certsubject.UID                : chr  NA NA NA NA ...
 $ certsubject.mail               : chr  NA NA NA NA ...
 $ certsubject.Mail               : chr  NA NA NA NA ...
 - attr(*, ".internal.selfref")=<externalptr>

All of the certificate sub-field data elents have been expanded and we have a highly performant tbl_dt to work with now either in dplyr syntax or data.table heiroglyphic syntax. Just go see what you have to do in jsonlite to get a similar output (and how long it will take).

pryr::object_size(df) for that shows it’s consuming 394 MB, which means we can read in many more extracts comfortably on a reasonably configured system and most (if not all) of it on a well-configured AWS box.

However, if you do end up trying to work with that scan data, it’s highly recommended that you use jq to filter out the fields or records you want into a more compact ndjson file.

The following functions are implemented:

stream_in: Stream in ndjson from a file (handles .gz files)
validate: Validate JSON records in an ndjson file (handles .gz files)
flatten: Flatten a character vector of individual JSON lines

There are no current plans for a stream_out() function since jsonlite::stream_out() does a great job tossing data.frame-like structures out to an ndjson file.

Installation

devtools::install_git("https://gitlab.com/hrbrmstr/ndjson.git")

Usage

library(ndjson)
library(microbenchmark)

# current verison
packageVersion("ndjson")

## [1] '0.3.0.0'

flatten('{"top":{"next":{"final":1,"end":true},"another":"yes"},"more":"no"}')

## Source: local data table [1 x 4]
## 
## # tbl_dt [1 × 4]
##    more top.another top.next.end top.next.final
##   <chr>       <chr>        <lgl>          <dbl>
## 1    no         yes         TRUE              1

f <- system.file("extdata", "test.json", package="ndjson")
gzf <- system.file("extdata", "testgz.json.gz", package="ndjson")

dplyr::glimpse(ndjson::stream_in(f))

## Observations: 100
## Variables: 8
## $ args                    <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,...
## $ headers.Accept          <chr> "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*",...
## $ headers.Accept-Encoding <chr> "identity", "identity", "identity", "identity", "identity", "identity", "identity",...
## $ headers.Host            <chr> "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin...
## $ headers.User-Agent      <chr> "Wget/1.18 (darwin15.5.0)", "Wget/1.18 (darwin15.5.0)", "Wget/1.18 (darwin15.5.0)",...
## $ id                      <dbl> 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 2...
## $ origin                  <chr> "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22"...
## $ url                     <chr> "http://httpbin.org/stream/100", "http://httpbin.org/stream/100", "http://httpbin.o...

dplyr::glimpse(ndjson::stream_in(gzf))

## Observations: 100
## Variables: 8
## $ args                    <int> NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA, NA,...
## $ headers.Accept          <chr> "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*",...
## $ headers.Accept-Encoding <chr> "identity", "identity", "identity", "identity", "identity", "identity", "identity",...
## $ headers.Host            <chr> "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin...
## $ headers.User-Agent      <chr> "Wget/1.18 (darwin15.5.0)", "Wget/1.18 (darwin15.5.0)", "Wget/1.18 (darwin15.5.0)",...
## $ id                      <dbl> 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 2...
## $ origin                  <chr> "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22"...
## $ url                     <chr> "http://httpbin.org/stream/100", "http://httpbin.org/stream/100", "http://httpbin.o...

dplyr::glimpse(jsonlite::stream_in(file(f), flatten=TRUE, verbose=FALSE))

## Observations: 100
## Variables: 7
## $ url                     <chr> "http://httpbin.org/stream/100", "http://httpbin.org/stream/100", "http://httpbin.o...
## $ id                      <int> 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 2...
## $ origin                  <chr> "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22"...
## $ headers.Host            <chr> "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin...
## $ headers.Accept-Encoding <chr> "identity", "identity", "identity", "identity", "identity", "identity", "identity",...
## $ headers.Accept          <chr> "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*",...
## $ headers.User-Agent      <chr> "Wget/1.18 (darwin15.5.0)", "Wget/1.18 (darwin15.5.0)", "Wget/1.18 (darwin15.5.0)",...

dplyr::glimpse(jsonlite::stream_in(gzfile(gzf), flatten=TRUE, verbose=FALSE))

## Observations: 100
## Variables: 7
## $ url                     <chr> "http://httpbin.org/stream/100", "http://httpbin.org/stream/100", "http://httpbin.o...
## $ id                      <int> 0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 2...
## $ origin                  <chr> "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22"...
## $ headers.Host            <chr> "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin...
## $ headers.Accept-Encoding <chr> "identity", "identity", "identity", "identity", "identity", "identity", "identity",...
## $ headers.Accept          <chr> "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*", "*/*",...
## $ headers.User-Agent      <chr> "Wget/1.18 (darwin15.5.0)", "Wget/1.18 (darwin15.5.0)", "Wget/1.18 (darwin15.5.0)",...

microbenchmark(
    ndjson={ ndjson::stream_in(f) },
  jsonlite={ jsonlite::stream_in(file(f), flatten=TRUE, verbose=FALSE) }
)

## Unit: milliseconds
##      expr      min       lq     mean   median       uq       max neval cld
##    ndjson 2.694575 2.883204 3.000030 2.956595 3.033864  4.319816   100  a 
##  jsonlite 8.487524 9.011873 9.411114 9.151305 9.334732 12.523081   100   b

microbenchmark(
    ndjson={ ndjson::stream_in(gzf) },
  jsonlite={ jsonlite::stream_in(gzfile(gzf), flatten=TRUE, verbose=FALSE) }
)

## Unit: milliseconds
##      expr      min       lq     mean   median       uq       max neval cld
##    ndjson 2.856464 2.957216 3.030433 3.005832 3.069114  3.436334   100  a 
##  jsonlite 8.302337 8.631042 9.021032 8.795794 9.031557 12.158147   100   b

Test Results

library(ndjson)
library(testthat)

date()

## [1] "Tue Sep 27 11:08:18 2016"

test_dir("tests/")

## testthat results ========================================================================================================
## OK: 4 SKIPPED: 0 FAILED: 0
## 
## DONE ===================================================================================================================

Please note that this project is released with a Contributor Code of Conduct. By participating in this project you agree to abide by its terms.

Installation guidance for Linux/BSD-ish systems

Why ndjson + Examples

Installation

Usage

Test Results

Why `ndjson` + Examples