Write/read recursive structure S4 objects - json

Question

I have a recursive structure of S4 objects , that can be presented ( this is a simple version) by theses 2 classes:
cl2 <-
setClass("cl2",
representation(
id = "numeric",
date="Date"),
prototype = list(
date=Sys.Date(),
id=sample(1:100,1)
)
)
cl1 <-
setClass("cl1",
representation(
date="Date",
cl2 = "cl2"
),
prototype = list(
date=Sys.Date()
)
)
I would like to save/load objects of type cl1. I opt to use json format(suitable for unstructured objects). The problem is with dates. Dates are coerced to numeric? Is there an option/solution to get dates in the right format when I serialize the object? Note that the objects can contains other objects ( recursive structure) so I would like that all dates are in the good format.
cat(RJSONIO::toJSON(cl1(),pretty=TRUE))
{
"date" : 16861,
"cl2" : {
"id" : 90,
"date" : 16861
}
}
A solution can be to replace dates by character. But I will loose the validation mechanism of S4 object and I should implement the date validation for all objects. Thanks in advance for any help.
An expected output should be like :
{
"date" :"2016-03-01",
"cl2" : {
"id" : 76,
"date" : "2016-03-01"
}
}

Answer 1

Reading the documentation of toJSON I found an interesting parameter:
force unclass/skip objects of classes with no defined JSON mapping
So I tried and I think this would match you need as you can simply ignore the class entry:
> s <- jsonlite::toJSON(cl1(),force=TRUE,auto_unbox=TRUE,pretty=TRUE)
> s
{
"date": "2016-03-01",
"cl2": {
"date": "2016-03-01",
"id": 67,
"class": "cl2"
},
"class": "cl1"
}
Drawback: This is still no loadable "as-is" to s4 objects with fromJSON as it will give a named list back, analyzing the list recursively to recreate S4 objects is doable, but you'll have to create the necessary as implementation to turn a named list to your classes, for your example:
setAs('list', 'cl2',
function(from, to) {
new(to, id=from[['id']], date=as.Date(from[['date']]))
})
setAs('list','cl1',
function(from, to) {
new(to,date=as.Date(from[['date']],cl2=as(from[['cl2']],'cl2')))
})
With a dummy input from previous output:
input <- '
{
"date": "2016-03-05",
"cl2": {
"date": "2016-02-01",
"id": 83,
"class": "cl2"
},
"class": "cl1"
}'
This gives:
> as(fromJSON(input),'cl1')
An object of class "cl1"
Slot "date":
[1] "2016-03-05"
Slot "cl2":
An object of class "cl2"
Slot "id":
[1] 67
Slot "date":
[1] "2016-03-01"
I let you adapt this to your real use case, probably using fromJSON(input,FALSE) to get a 'pure' list to coerce with lapply for example if you have multiples instances of your cl1 class in the json input.

Answer 2

One option is to use the jsonlite package to serialize. Indeed jsonlite::tojson respects date and serilze them in well formated form. The problem is jsonlite::toJSON is not defined for S4 objects. My solution is to coerce the object to a list and then seralize it:
## S4 method to coerce any S4 object to a list
setMethod("as.list",signature(x="ANY"),
function(x) {
Map(
function(y) if (isS4(slot(x,y))) as.list(slot(x,y)) else slot(x,y)
,slotNames(class(x)))
})
## coercion
jsonlite::toJSON(as.list(cl1()),pretty=TRUE,auto_unbox=TRUE)
{
"date": "2016-03-01",
"cl2": {
"id": 24,
"date": "2016-03-01"
}
}
udpdate
in as.list I replace lapply by Map to create a named list.

Answer 3

For the recursive reading of S4 classes from JSON you can use a similar approach:
library(RJSONIO)
createParser <- function(className) {
setAs("list", className, function(from, to) {
to <- new(to)
for (n in names(from)) {
if (isS4(slot(to, n))) {
c <- class(slot(to, n))[[1]]
o <- as(from[[n]], c)
slot(to, n) = o
} else {
slot(to, n) = from[[n]]
}
}
to
})
}
Name <- setClass("Name", slots=c("first"="character", "last"="character"))
createParser("Name")
Customer <- setClass("Customer", slots=c("name"="Name", "age"="numeric"))
createParser("Customer")
Case <- setClass("Case", slots=c("customer"="Customer"))
createParser("Case")
c1 <- Case(customer=Customer(name=Name(first="Mika", last="R"), age=100))
j <- RJSONIO::toJSON(c1)
l <- RJSONIO::fromJSON(j, simplify = FALSE)
as(l, "Case")