wip: fixing MbioDataset constructor and methods

microbiomeDB · Feb 13, 2024 · cec9738 · cec9738
1 parent 04f8238
commit cec9738
Show file tree

Hide file tree

Showing 4 changed files with 11 additions and 11 deletions.
diff --git a/R/class-MbioDataset.R b/R/class-MbioDataset.R
@@ -112,7 +112,7 @@ check_mbio_dataset <- function(object) {
     # check that at least some ancestorIdColumns are shared between collections and sampleMetadata
     sampleMetadataAncestorIds <- object@metadata@ancestorIdColumns
     if (!!length(sampleMetadataAncestorIds)) {
-        if (!all(lapply(object@collections, function(x) any(x@ancestorIdColumns %in% sampleMetadataAncestorIds)))) {
+        if (!all(sapply(object@collections, function(x) any(x@ancestorIdColumns %in% sampleMetadataAncestorIds)))) {
             msg <- "at least one ancestorIdColumn must be shared between collections and sampleMetadata"
             errors <- c(errors, msg)
         }

diff --git a/R/constructors-MbioDataset.R b/R/constructors-MbioDataset.R
@@ -228,7 +228,7 @@ sampleMetadataBuilder <- function(dataSource) {
     sampleMetadata <- new("SampleMetadata",
         data=dt,
         recordIdColumn = recordIdColumn,
-        ancestorIdColumns = findAncestorIdColumns
+        ancestorIdColumns = ancestorIdColumns
     )
 
     return(sampleMetadata)

diff --git a/R/methods-MbioDataset.R b/R/methods-MbioDataset.R
@@ -48,10 +48,10 @@ setMethod("getCollection", "MbioDataset", function(object, collectionName = char
     }
 
     abundanceData <- microbiomeComputations::AbundanceData(
-        data = object@collections[[collectionName]][[1]]@data, 
-        sampleMetadata = sampleMetadataBuilder(object@metadata), 
-        recordIdColumn = object@collections[[collectionName]][[1]]@recordIdColumn,
-        ancestorIdColumns = object@collections[[collectionName]][[1]]@ancestorIdColumns
+        data = object@collections[collectionName][[1]]@data, 
+        sampleMetadata = object@metadata, 
+        recordIdColumn = object@collections[collectionName][[1]]@recordIdColumn,
+        ancestorIdColumns = object@collections[collectionName][[1]]@ancestorIdColumns
     )
 
     return(abundanceData)
@@ -94,6 +94,6 @@ setMethod("getComputeResult", "CorrelationResult", function(object, format = c("
 #' @importFrom microbiomeComputations DifferentialAbundanceResult
 #' @export
 setMethod("getComputeResult", "DifferentialAbundanceResult", function(object, format = c("data.table")) {
-    format <- veupathUtils::matchArg(format)
+    format <- veupathUtils::matchArg(format) 
     return(object@statistics)
 })
diff --git a/tests/testthat/test-MbioDataset.R b/tests/testthat/test-MbioDataset.R
@@ -60,10 +60,10 @@ test_that("we can update collection names and get collections", {
     expect_equal(getCollectionNames(testDataset)[[1]], "My Collection")
 
     testCollection <- getCollection(testDataset, "My Collection")
-    expect_s4_class(testCollection, "Collection")
-    expect_equal(testCollection@name, "My Collection")
-    expect_equal(testCollection@data, data.frame(entity.id = 1, entity.collection_x = 1, entity.collection_y = 2))
+    expect_s4_class(testCollection, "AbundanceData")
+    expect_equal(testCollection@data, data.frame(entity.id = 1, entity.collection_x = 1, entity.collection_y = 2, ancestor.y = 1))
     expect_equal(testCollection@recordIdColumn, "entity.id")
+    expect_equal(testCollection@ancestorIdColumns, "ancestor.y")
 })
 
 test_that("we can get compute results in different formats", {
@@ -74,7 +74,7 @@ test_that("we can get compute results in different formats", {
     metadataFile3 <- '../../inst/extdata/DiabImmune/DiabImmune_Sample.txt'
     mbioDataset <- MbioDataset(list(dataFile1, dataFile2), list(metadataFile1, metadataFile2, metadataFile3))
 
-    correlationOutput <- microbiomeComputations::correlation(getCollection(mbioDataset, "16S Genus"))
+    correlationOutput <- microbiomeComputations::correlation(getCollection(mbioDataset, "16S EUPATH_0009256")) ## Genus
     correlationDT <- getComputeResult(correlationOutput, "data.table")
 
     expect_equal(inherits(correlationDT, "data.table"), TRUE)