cran release

CRAN-RELEASE

@@ -0,0 +1,2 @@
+This package was submitted to CRAN on 2019-11-03.
+Once it is accepted, delete this file and tag the release (commit e1ceb51848).

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: jsonify
 Type: Package
-Title: Convert between 'R' Objects and Javascript Object Notation (JSON)
+Title: Convert Between 'R' Objects and Javascript Object Notation (JSON)
 Version: 1.0.0
-Date: 2019-02-11
+Date: 2019-11-03
 Authors@R: c(
     person("David", "Cooley", ,"[email protected]", role = c("aut", "cre")),
     person("Chris", "Muir", role = "ctb")

cran-comments.md

@@ -1,8 +1,7 @@
 ## Cran submission updates
 
-* Updates v0.2.0 to v0.2.1
-* updated date field
-* one bug fix and one new method
+* Updates v0.2.1 to v1.0.0
+* added from_json() method
 
 ## R CMD check results
 

inst/include/jsonify/from_json/simplify/simplify.hpp

@@ -653,7 +653,7 @@ namespace from_json {
         }
 
         if( tp == -1 && i > 0 ) {
-          // can't simplify because new column names"
+          // can't simplify because new column names
           return out;
         }
 

inst/include/jsonify/to_json/writers/complex.hpp

@@ -188,18 +188,8 @@ namespace complex {
           const char *h = column_names[ df_col ];
           writer.String( h );
           SEXP this_vec = df[ h ];
+          write_value( writer, this_vec, unbox, digits, numeric_dates, factors_as_string, by, -1, in_data_frame );
 
-          // switch( TYPEOF( this_vec ) ) {
-          // case VECSXP: {
-            write_value( writer, this_vec, unbox, digits, numeric_dates, factors_as_string, by, -1, in_data_frame );
-          //   break;
-          // }
-          // default: {
-          //   Rcpp::Rcout << "by column default" << std::endl;
-          //   // if it's a matrix, or another data.frame??
-          //   switch_vector( writer, this_vec, unbox, digits, numeric_dates, factors_as_string );
-          // }
-          // }
         }
         writer.EndObject();
 
@@ -321,7 +311,7 @@ namespace complex {
               const char *s = list_names[ i ];
               writer.String( s );
             }
-            // setting in_data_frame to false becaseu we're no longer at the data.frame top-level
+            // setting in_data_frame to false because we're no longer at the data.frame top-level
             write_value( writer, recursive_list, unbox, digits, numeric_dates, factors_as_string, by, -1, false ); 
           }
 

src/read_json.cpp

@@ -11,14 +11,21 @@
 rapidjson::Document buffer_string( const char* file, const char* mode, int buffer_size = 1024 ) {
 
   FILE* fp = fopen(file, mode );
-  char readBuffer[ buffer_size ];
+
+
+  //char readBuffer[ buffer_size ];
+  // ISO C++ forbids variable length array ‘readBuffer’ [-Wvla]
+  // https://stackoverflow.com/a/11379442/5977215
+  char *readBuffer = new char[ buffer_size ];
 
   rapidjson::FileReadStream is(fp, readBuffer, sizeof( readBuffer ) );
 
+
   rapidjson::Document d;
   d.ParseStream( is );
   fclose(fp);
 
+  delete[] readBuffer;
   return d;
 }
 

tests/benchmarks.R

@@ -175,6 +175,26 @@ microbenchmark(
 # jsonlite 1.433624 1.486971 1.631894 1.537450 1.563000 2.138424     5
 #  jsonify 1.510242 1.528668 1.920362 1.531584 1.877338 3.153977     5
 
+url <- 'https://github.com/SymbolixAU/data/blob/master/geojson/SA1_2016_VIC.json?raw=true'
+
+js <- readLines(url)
+
+microbenchmark(
+  jsonify = {
+    jfy <- jsonify::from_json( js )
+  },
+  jsonlite = {
+    jlt <- jsonlite::fromJSON( js )
+  },
+  times = 5
+)
+
+# Unit: seconds
+#      expr      min        lq      mean    median        uq       max neval
+#  jsonify  4.14308  4.248493  4.589085  4.298684  5.016845  5.238324     5
+# jsonlite 38.72263 40.025316 40.089307 40.373840 40.646151 40.678591     5
+
+
 ## Filling NAs
 rm(list=ls()); gc()
 set.seed(20191012)

tests/testthat/test-from_json.R

@@ -403,12 +403,7 @@ test_that("round trips work", {
   x <- list(x = 1, y = letters)
   expect_identical( f1(x), x )
   expect_identical( f2(x), x )
-
-  # # TODO
-  # x <- list(1L, "cats", 3L, NA)
-  # expect_identical( f1(x), x )
-  # expect_identical( f2(x), x )
-
+
   x <- data.frame(
     "col1" = c(1, 2),
     "col2" = c(1L, 2L),
@@ -418,7 +413,11 @@ test_that("round trips work", {
   )
   expect_identical( f1(x), x )
 
-
+
+  x <- list(1L, "cats", 3L, NA)
+  f2 <- function( x ) from_json( to_json( x, unbox = TRUE ), simplify = FALSE )
+  expect_identical( f2(x), x )
+
 })
 
 

tests/testthat/test-from_json_simplify.R

@@ -36,26 +36,6 @@ test_that("R Lists simplified to vectors",{
 
 test_that("simplify types",{
 
-  ## tests function only works for arrays
-
-  ## mapping
-  # 0 - null
-  # 1 - false
-  # 2 - true
-  # 3 - object
-  # 4 - array
-  # 5 - string
-  # 6 - number 
-  #   - 8 - int
-  #   - 9 - double
-
-  ## Simplification rules (oposite of 'to_json')
-  ## 1. array -> vector
-  ## 2. array of arrays (of arrays of arrays ... ) 
-  ##  - each array is a vector (as per 1.)
-  ##  - each vector becomes a list element
-  ##  - 
-
   x <- 1:4
   js <- to_json( x )
   #js
@@ -137,20 +117,14 @@ test_that("arrays of arrays of same length go to matrix",{
   x <- from_json( js )
   expect_equal(x, matrix(1:6, ncol = 2, byrow = T ) )
 
-  # x <- from_json( js, by = "col" )
-  # expect_equal(x, matrix(1:6, ncol = 2, byrow = F ) )
-
-
 })
 
 test_that("array of arrays of different lenghts go to list",{
 
   js <- '[[1,2],[1,2,3]]'
   x <- from_json( js )
   expect_equal( x, list(1:2, 1:3))
-
-  ## TODO
-  ## - 
+
   js <- '[[5,[6,7]]]'
   x <- from_json( js )
   expect_equal( x, list( list( 5, 6:7 )  ) ) 
@@ -159,9 +133,6 @@ test_that("array of arrays of different lenghts go to list",{
   x <- from_json( js )
   expect_equal( x, list( list( 5, c("6","a") )  ) )
 
-  ## compare with 
-  # jsonlite::fromJSON( js )
-
   js <- '[[1,2],[3,4],[5,[6,7]]]'
   x <- from_json( js )
   expect_equal( x, list( c(1,2), c(3,4), list(5, 6:7) ) )
@@ -178,5 +149,3 @@ test_that("array of various types converted to matrices",{
   expect_equal(x, matrix(c(1.1,2,3,4), ncol = 2, byrow = T ) )
 })
 
-
-

vignettes/jsonify.Rmd

@@ -2,9 +2,17 @@
 title: "jsonify"
 author: "David Cooley"
 date: "`r Sys.Date()`"
-output: rmarkdown::html_vignette
+output: 
+    html_document:
+        toc: true
+        toc_float: true
+        number_sections: false
+        theme: flatly
+header-includes: 
+    - \usepackage{tikz}
+    - \usetikzlibrary{arrows}
 vignette: >
-  %\VignetteIndexEntry{Vignette Title}
+  %\VignetteIndexEntry{Jsonify}
   %\VignetteEngine{knitr::rmarkdown}
   %\VignetteEncoding{UTF-8}
 ---
@@ -18,6 +26,8 @@ knitr::opts_chunk$set(
 library(jsonify)
 ```
 
+# To JSON
+
 There are two types of R objects we need to handle when converting to JSON, simple and complex.
 
 1. Simple - scalars, vectors, matrices
@@ -144,4 +154,50 @@ pretty_json( df )
 
 ```
 
+# From JSON
+
+Use `from_json()` to convert from JSON to an R object. 
+
+
+```{r}
+## scalar / vector
+js <- '[1,2,3]'
+from_json( js )
+
+## matrix
+js <- '[[1,2],[3,4],[5,6]]'
+from_json( js )
+
+## data.frame
+js <- '[{"x":1,"y":"a"},{"x":2,"y":"b"}]'
+from_json( js )
+```
+
+## Simplifying and NAs
+
+By default `from_json()` will try and simplify 
+
+- arrays to vectors
+- arrays of arrays to matrices
+- array of objects with consistent key-value pairs to data.frames
+
+If an array contains objects with different keys, for example `'[{"x":1},{"y":2}]'`, `from_json()` will not simplify this to a data.frame, because it would have to assume and insert `NA`s in rows where data is missing. 
+
+```{r}
+js <- '[{"x":1},{"y":2}]'
+from_json( js )
+```
+
+You can override this default and use `fill_na = TRUE` to force it to a data.frame with `NA`s in place of missing values
+
+```{r}
+js <- '[{"x":1},{"y":2}]'
+from_json( js, fill_na = TRUE )
+```
+
+
+
+
+
+