overhaul deserialize.cpp for extremely flexible queries, generalize decompression

[knapply]

addresses #43

Life got busy and I underestimated how tricky the more flexible queries would get.

Still WIP, but on track.

[knapply]

@eddelbuettel I (finally) got back to this.

I think the only point of concern you might have is regarding the parameters.

Originally, we had error_ok= and on_error=.

After approaching this a dozen different ways, I landed on separating parsing errors (where the JSON is simply invalid) and query errors (where a query doesn't return anything, but there's nothing wrong with the JSON itself).

With that an mind, I split them into parse_error_ok=/on_parse_error= and query_error_ok=/on_query_error=. So this would be a breaking change in that regard as error_ok=/on_error= are gone.

Other than that, there's some cool query functionality and we can handle .gz, .bz2, and .xz compressed files.

I'd like to reinforce the tests and re-walk through (and yes, hit the ChangeLog and such), but almost there.

[eddelbuettel]

I think we're not at a stage we have to worry about breaking params. We are still evolving quite a bit.

Will try to take a look later or tomorrow but still have another burning issue to take care of myself. No rush. And still really lovely to see you chipping away at it and building something awesome.

[knapply]

Naturally, I forgot NEWS/ChangeLog..... will fix ASAP

[knapply]

I'm working on the ChangeLog and decided I need some better notes myself (which uncovered some refinements that I'm now fixing).

These are the "big-picture" ideas:

library(RcppSimdJson)

Better Queries

We can still pass a single query= that’s applied to each json= element.

json_to_query <- c(json1 = '["a",{"b":{"c": [[1,2,3],[4,5,6]]}}]',
                   json2 = '["a",{"b":{"c": [[7,8,9],[10,11,12]],"d":[[13,14,15,16],[17,18,19,20]]}}]')
#                                                                 ^^^ json1 doesn't have "d"

fparse(json_to_query, query = "1/b/c")

## $json1
##      [,1] [,2] [,3]
## [1,]    1    2    3
## [2,]    4    5    6
## 
## $json2
##      [,1] [,2] [,3]
## [1,]    7    8    9
## [2,]   10   11   12

But now we can also pass multiple “flat” queries (a named or unnamed character vector). Each element of query= is applied to all elements of json=.

This is the preferred method if each json= has roughly the same schema and we want to extract the same data from each of them.

fparse(json_to_query, query = c(query1 = "1/b/c",
                                query2 = "1/b/c/0",
                                query3 = "1/b/c/1"))

## $json1
## $json1$query1
##      [,1] [,2] [,3]
## [1,]    1    2    3
## [2,]    4    5    6
## 
## $json1$query2
## [1] 1 2 3
## 
## $json1$query3
## [1] 4 5 6
## 
## 
## $json2
## $json2$query1
##      [,1] [,2] [,3]
## [1,]    7    8    9
## [2,]   10   11   12
## 
## $json2$query2
## [1] 7 8 9
## 
## $json2$query3
## [1] 10 11 12

When we want to extract different data from each json=, such as when the schemata aren’t related, we can also specify a “nested” query. This is a list of character vectors that are applied in a zip-like fashion.

fparse(json_to_query,
       query = list(queries1 = c(c1 = "1/b/c/0",
                                 c2 = "1/b/c/1"),
                    queries2 = c(d1 = "1/b/d/0",
                                 d2 = "1/b/d/1")))

## $queries1
## $queries1$c1
## [1] 1 2 3
## 
## $queries1$c2
## [1] 4 5 6
## 
## 
## $queries2
## $queries2$d1
## [1] 13 14 15 16
## 
## $queries2$d2
## [1] 17 18 19 20

Compressed Files

We now handle .gz, .bz2, and .xz files that are decompressed to a raw vector (via memDecompress()).

.read_compress_write_load <- function(file_path, temp_dir) {
    types <- c("gzip", "bzip2", "xz")
    exts <- c("gz",    "bz2",   "xz")

    init <- readBin(file_path, n = file.size(file_path), what = "raw")

    mapply(function(type, ext) {
        target_path <- paste0(temp_dir, "/", basename(file_path), ".", ext)
        writeBin(memCompress(init, type = type), target_path)
        RcppSimdJson::fload(target_path)
    }, types, exts, SIMPLIFY = FALSE)
}

my_temp_dir <- sprintf("%s/rcppsimdjson-compressed-files", tempdir())
dir.create(my_temp_dir)
all_files <- dir(
    system.file("jsonexamples", package = "RcppSimdJson"),
    recursive = TRUE,
    pattern = "\\.json$",
    full.names = TRUE
)
names(all_files) <- basename(all_files)
res <- t(sapply(all_files, .read_compress_write_load, my_temp_dir))
unlink(my_temp_dir)

stopifnot(all(apply(
    res, 1L, 
    function(.x) identical(.x[[1]], .x[[2]]) && 
        identical(.x[[1]], .x[[3]])
)))

res

##                                       gzip          bzip2         xz           
## apache_builds.json                    List,15       List,15       List,15      
## github_events.json                    List,8        List,8        List,8       
## instruments.json                      List,9        List,9        List,9       
## mesh.json                             List,8        List,8        List,8       
## numbers.json                          Numeric,10001 Numeric,10001 Numeric,10001
## random.json                           List,4        List,4        List,4       
## adversarial.json                      List,1        List,1        List,1       
## demo.json                             List,1        List,1        List,1       
## flatadversarial.json                  List,2        List,2        List,2       
## che-1.geo.json                        List,2        List,2        List,2       
## che-2.geo.json                        List,2        List,2        List,2       
## che-3.geo.json                        List,2        List,2        List,2       
## google_maps_api_compact_response.json List,4        List,4        List,4       
## google_maps_api_response.json         List,4        List,4        List,4       
## twitter_api_compact_response.json     List,16       List,16       List,16      
## twitter_api_response.json             List,25       List,25       List,25      
## repeat.json                           List,4        List,4        List,4       
## smalldemo.json                        List,8        List,8        List,8       
## truenull.json                         Logical,2000  Logical,2000  Logical,2000 
## twitter_timeline.json                 List,21       List,21       List,21      
## twitter.json                          List,2        List,2        List,2       
## twitterescaped.json                   List,2        List,2        List,2       
## update-center.json                    List,6        List,6        List,6

Smarter URL Handling

With compressed files supported, we can better leverage the compressed_download= parameter.

Additionally, remote JSON files are now downloaded simultaneously if (getOption("download.file.method", default = "auto") == "libcurl").

json_urls <- c(
    "https://raw.githubusercontent.com/eddelbuettel/rcppsimdjson/master/inst/jsonexamples/small/smalldemo.json",
    "https://raw.githubusercontent.com/eddelbuettel/rcppsimdjson/master/inst/jsonexamples/small/demo.json"
)

my_temp_dir <- sprintf("%s/rcppsimdjson-downloads", tempdir())
dir.create(my_temp_dir)

fload(json_urls,
      query = list(c(width = "Thumbnail/Width", 
                     height = "Thumbnail/Height"),
                   c(width = "Image/Thumbnail/Width", 
                     height = "Image/Thumbnail/Height")),
      temp_dir = my_temp_dir,
      keep_temp_files = TRUE,
      compressed_download = TRUE)

## $smalldemo.json
## $smalldemo.json$width
## [1] 100
## 
## $smalldemo.json$height
## [1] 125
## 
## 
## $demo.json
## $demo.json$width
## [1] 100
## 
## $demo.json$height
## [1] 125

list.files(my_temp_dir)

## [1] "demo52a53d7b405d.json.gz"      "smalldemo52a53feccca8.json.gz"

Lurking Windows Trap Fixed

Windows was mangling non-ASCII UTF-8.

The issue/fix are essentially the same as https://github.com/SymbolixAU/jsonify/pull/57 and it’s now tested (rather, a test is present) that uses a mix of 1-4 byte characters.

extended_unicode <- '"լ ⿕  ٷ 豈 ٸ 㐀 ٹ 丂 Ɗ 一 á ٵ ̝ ѵ ̇ ˥ ɳ Ѡ · վ  й ף ޑ  ц Ґ  ӎ Љ ß ϧ ͎ ƽ ޜ է ϖ y Î վ Ο Ӊ ٻ ʡ ө ȭ ˅ ޠ ɧ ɻ ث ́ ܇ ܧ ɽ Ո 戸 Ð 坮 ٳ 䔢 찅 곂 묨 ß ᇂ ƻ 䏐 ܄ 㿕 ս ّ 昩 僫 똠 Ɯ ٰ É"'
fparse(extended_unicode)

## [1] "լ ⿕  ٷ 豈 ٸ 㐀 ٹ 丂 Ɗ 一 á ٵ ̝ ѵ ̇ ˥ ɳ Ѡ · վ  й ף ޑ  ц Ґ  ӎ Љ ß ϧ ͎ ƽ ޜ է ϖ y Î վ Ο Ӊ ٻ ʡ ө ȭ ˅ ޠ ɧ ɻ ث ́ ܇ ܧ ɽ Ո 戸 Ð 坮 ٳ 䔢 찅 곂 묨 ß ᇂ ƻ 䏐 ܄ 㿕 ս ّ 昩 僫 똠 Ɯ ٰ É"

fparse(charToRaw(extended_unicode))

## [1] "լ ⿕  ٷ 豈 ٸ 㐀 ٹ 丂 Ɗ 一 á ٵ ̝ ѵ ̇ ˥ ɳ Ѡ · վ  й ף ޑ  ц Ґ  ӎ Љ ß ϧ ͎ ƽ ޜ է ϖ y Î վ Ο Ӊ ٻ ʡ ө ȭ ˅ ޠ ɧ ɻ ث ́ ܇ ܧ ɽ Ո 戸 Ð 坮 ٳ 䔢 찅 곂 묨 ß ᇂ ƻ 䏐 ܄ 㿕 ս ّ 昩 僫 똠 Ɯ ٰ É"