Reading JSON file from R

Question

I try reading a JSON file from R using rjson but keep getting errors. I validated the JSON file using various online validators. Here is the content of the JSON file:

{
   "scenarios": [
      {
         "files": {
            "type1": "/home/blah/Desktop/temp/scen_0.type1",
            "type2": "/home/blah/Desktop/temp/scen_0.type2"
         },
         "ID": "scen_0",
         "arr": [],
         "TypeToElementStatsFilename": {
            "type1": "/home/blah/Desktop/temp/scen_0.type1.elements",
            "type2": "/home/blah/Desktop/temp/scen_0.type2.elements"
         }
      }
   ],
   "randomSeed": "39327314969888",
   "zone": {
      "length": 1000000,
      "start": 1
   },
   "instanceFilename": "/home/blah/bloo/data/XY112.zip",
   "txtFilename": "/home/blah/bloo/data/XY112.txt",
   "nSimulations": 2,
   "TypeTodbFilename": {
      "type1": "/home/blah/bloo/data/map.type1.oneAmb.XY112.out"
   },
   "arr": {
      "seg11": {
         "length": 1000,
         "start": 147000
      },
      "seg12": {
         "length": 1000,
         "start": 153000
      },
      "seg5": {
         "length": 1000,
         "start": 145000
      },
      "seg6": {
         "length": 1000,
         "start": 146000
      },
      "seg1": {
         "length": 100,
         "start": 20000
      }
   },
   "outPath": "/home/blah/Desktop/temp",
   "instanceID": "XY112",
   "arrIds": [
      "seg5",
      "seg6",
      "seg1",
      "seg11",
      "seg12"
   ],
   "truth": {
      "files": {
         "type1": "/home/blah/Desktop/temp/truth.type1",
         "type2": "/home/blah/Desktop/temp/truth.type2"
      },
      "ID": "truth",
      "TypeToElementStatsFilename": {
         "type1": "/home/blah/Desktop/temp/truth.type1.elements",
         "type2": "/home/blah/Desktop/temp/truth.type2.elements"
      }
   }
}

And the error:

> json_file <- "~/json"
> json_data <- fromJSON(paste(readLines(json_file), collapse=""))
Error in fromJSON(paste(readLines(json_file), collapse = "")) :
  unexpected character: :

It would help if you tell us what version of rjson. Is this still an open issue as of 2013? — smci
– smci, Commented Apr 17, 2013 at 7:38

Jonathan Dobbie · Accepted Answer · 2010-08-06 08:04:18Z

6

RJSON freaks out about empty arrays.

fromJSON( '{ "arr": [ ] }')

Error in fromJSON("{ \"arr\": [ ] }") : unexpected character: :

answered Aug 6, 2010 at 8:04

Jonathan Dobbie

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1 Comment

David B Over a year ago

+1 thanks. apparently it fails not only on empty arrays, but also on empty objects. I'll send an email to the maintainer, since I think these are valid in JSON.

Greg · Accepted Answer · 2010-08-06 17:26:40Z

2

You can try the fromJSON function in the RJSONIO package hosted at http://www.omegahat.org. It seems to read the file fine.

answered Aug 6, 2010 at 17:26

Greg

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Comments

Vagabond · Accepted Answer · 2015-03-26 10:14:24Z

There's a fix for this.

Create a new function to replace the existing getURL function used in RCurl and you should have your solution.

myGetURL <- function(...) {
    rcurlEnv <- getNamespace("RCurl")
    mapUnicodeEscapes <- get("mapUnicodeEscapes", rcurlEnv)
    unlockBinding("mapUnicodeEscapes", rcurlEnv)
    assign("mapUnicodeEscapes", function(str) str, rcurlEnv)
    on.exit({
        assign("mapUnicodeEscapes", mapUnicodeEscapes, rcurlEnv)
        lockBinding("mapUnicodeEscapes", rcurlEnv)
    }, add = TRUE)
    return(getURL(...))
}

Test:

> json <- myGetURL("http://abicky.net/hatena/rcurl/a.json")
> cat(json, fill = TRUE)
{"a":"\\\"\u0030\\\""}
> fromJSON(json)
$a
[1] "\\\"0\\\""

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