hrbrmstr
/
ndjson
1
0
Fork 0
Code Issues Pull Requests Releases Wiki Activity
You can not select more than 25 topics Topics must start with a letter or number, can include dashes ('-') and can be up to 35 characters long.
25 Commits
1 Branch
2 Tags
503 KiB
 
 
Tree: ba349b07b1
Branches Tags
${ item.name }
Create tag ${ searchTerm }
Create branch ${ searchTerm }
from 'ba349b07b1'
${ noResults }
Bob Rudis ba349b07b1
travis uses gcc 4.8; seeing if this fixes the travis error 		8 years ago
R `flatten()` 8 years ago
inst/extdata gz ndjson 8 years ago
man `flatten()` 8 years ago
src flatten 8 years ago
tests tests 8 years ago
.Rbuildignore Title Case 8 years ago
.gitignore initial commit 8 years ago
.travis.yml travis uses gcc 4.8; seeing if this fixes the travis error 8 years ago
CONDUCT.md conduct / gitlab url 8 years ago
DESCRIPTION `flatten()` 8 years ago
NAMESPACE `flatten()` 8 years ago
NEWS.md `flatten()` 8 years ago
README.Rmd Travis 8 years ago
README.md `flatten()` 8 years ago
cran-comments.md NEWS 8 years ago
ndjson.Rproj initial commit 8 years ago

README.md

CRAN\_Status\_Badge downloads

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.

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: 5
## $ url     <chr> "http://httpbin.org/stream/100", "http://httpbin.org/stream/100", "http://httpbin.org/stream/100", ...
## $ headers <data.frame> c("httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", ...
## $ args    <data.frame> 
## $ 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, 23, 24, 25, 26, 2...
## $ origin  <chr> "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22...

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

## Observations: 100
## Variables: 5
## $ url     <chr> "http://httpbin.org/stream/100", "http://httpbin.org/stream/100", "http://httpbin.org/stream/100", ...
## $ headers <data.frame> c("httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", "httpbin.org", ...
## $ args    <data.frame> 
## $ 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, 23, 24, 25, 26, 2...
## $ origin  <chr> "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22", "50.252.233.22...

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 2.560371 2.729220 2.851222 2.798205 2.881642  4.105664   100  a 
##  jsonlite 8.266456 8.629907 9.007069 8.857477 9.036219 11.338596   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 2.679325 2.786938 2.873180 2.831197 2.894630 4.451697   100  a 
##  jsonlite 7.772496 8.102557 8.377006 8.235461 8.418297 9.926089   100   b

Test Results

library(ndjson)
library(testthat)

date()

## [1] "Wed Sep 14 15:47:10 2016"

test_dir("tests/")

## testthat results ========================================================================================================
## OK: 4 SKIPPED: 0 FAILED: 0
## 
## DONE ===================================================================================================================
## Your tests are geometric!

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.