get toJSON tests passing again

R/methods-KPartiteNetwork.R

@@ -20,7 +20,7 @@ toJSONGeneric <- getGeneric("toJSON", package = "veupathUtils")
 #' @export
 setMethod(toJSONGeneric, "Partitions", function(object, named = c(TRUE, FALSE)) {
     named <- veupathUtils::matchArg(named)
-    tmp <- veupathUtils::S4SimpleListToJSON(object, FALSE)
+    tmp <- veupathUtils::S4SimpleListToJSON(object, TRUE)
 
     if (named) tmp <- paste0('{"partitions":', tmp, "}")
 
@@ -39,7 +39,7 @@ setMethod(toJSONGeneric, "KPartiteNetwork", function(object, named = c(TRUE, FAL
 
     nodes_json <- veupathUtils::toJSON(object@nodes, named = FALSE)
     links_json <- veupathUtils::toJSON(object@links, named = FALSE)
-    partitions_json <- veupathUtils::toJSON(object@partitions, named = TRUE)
+    partitions_json <- veupathUtils::toJSON(object@partitions, named = FALSE)
 
     # TODO this doesnt conform to the api in the data service, bc there we explicitly have a bipartite network and not a kpartite
     # we have `columns1NodeIds` and `columns2NodeIds` instead of `partitions`. i think this is better though.

R/methods-Nodes.R

@@ -97,4 +97,4 @@ setMethod(toJSONGeneric, signature("NodeIdList"), function(object, named = c(TRU
     if (named) tmp <- paste0('{"nodeIds":', tmp, "}")
 
     return(tmp)
-}) 
+})

tests/testthat/test-kpartite-network.R

@@ -122,12 +122,12 @@ test_that("toJSON works for k-partite networks", {
   )
   json <- veupathUtils::toJSON(net)
   jsonList <- jsonlite::fromJSON(json)
-  expect_equal(jsonList$network$data$links$source, c('A','B','C'))
-  expect_equal(jsonList$network$data$links$target, c('B','A','D'))
-  expect_equal(jsonList$network$data$links$weight, c(10,20,30))
-  expect_equal(jsonList$network$data$nodes$id, c('A','B','C','D'))
-  expect_equal(list(jsonList$network$data$partitions[1,],jsonList$network$data$partitions[2,]), list(c('A','C'), c('B','D')))
-  expect_equal(length(jsonList$network$config$variables), 0)
+  expect_equal(jsonList$bipartitenetwork$data$links$source, c('A','B','C'))
+  expect_equal(jsonList$bipartitenetwork$data$links$target, c('B','A','D'))
+  expect_equal(jsonList$bipartitenetwork$data$links$weight, c(10,20,30))
+  expect_equal(jsonList$bipartitenetwork$data$nodes$id, c('A','B','C','D'))
+  expect_equal(jsonList$bipartitenetwork$data$partitions$nodeIds, list(c('A','C'), c('B','D')))
+  expect_equal(length(jsonList$bipartitenetwork$config$variables), 0)
 })
 
 test_that("we can build a KPartiteNetwork from an edgeList data.frame", {