From 4e8d11053dfe8934b41713fda81e972c67de6fbe Mon Sep 17 00:00:00 2001
From: Danielle Callan <dcallan@upenn.edu>
Date: Thu, 7 Mar 2024 15:39:52 -0500
Subject: [PATCH] get tests passing again

---
 R/methods.R                            | 12 ++++++++++--
 tests/testthat/test-GetComputeResult.R |  8 +-------
 2 files changed, 11 insertions(+), 9 deletions(-)

diff --git a/R/methods.R b/R/methods.R
index 7f79313..da0da6b 100644
--- a/R/methods.R
+++ b/R/methods.R
@@ -1,3 +1,6 @@
+## TODO should import and reexport a bunch of functions and data from the data and computes package
+## TODO should think some about how to organize these methods and the others into files etc.
+
 #' Get Microbiome Dataset Compute Result
 #' 
 #' Get the compute result from a Microbiome Dataset in a particular format.
@@ -47,11 +50,16 @@ setMethod("getComputeResult", "DifferentialAbundanceResult", function(object, fo
     return(data.table::setDT(object@statistics))
 })
 
+#' @importFrom microbiomeData getSampleMetadata
+#' @importFrom microbiomeData getSampleMetadataIdColumns
 mergeComputeResultAndMetadata <- function(computeResult, dataset, metadataVariables) {
     dt <- getComputeResult(computeResult, "data.table")
-    metadata <- getSampleMetadata(dataset, metadataVariables)
+    metadata <- microbiomeData::getSampleMetadata(dataset, includeIds = TRUE, metadataVariables = metadataVariables)
 
-    metadataIdColumns <- getSampleMetadataIdColumnNames(dataset)
+    metadataIdColumns <- microbiomeData::getSampleMetadataIdColumns(dataset)
+    print(metadataIdColumns)
+    print(head(names(dt)))
+    print(head(names(metadata)))
     dt <- merge(dt, metadata, by = metadataIdColumns, all.x = TRUE)
 
     return(dt)
diff --git a/tests/testthat/test-GetComputeResult.R b/tests/testthat/test-GetComputeResult.R
index 833d24b..9edf762 100644
--- a/tests/testthat/test-GetComputeResult.R
+++ b/tests/testthat/test-GetComputeResult.R
@@ -1,11 +1,5 @@
 test_that("we can get compute results in different formats", {
-    dataFile1 <- '../../inst/extdata/DiabImmune/DiabImmune_entity_16SRRNAV4Assay.txt'
-    metadataFile1 <- '../../inst/extdata/DiabImmune/DiabImmune_ParticipantRepeatedMeasure.txt'
-    dataFile2 <- '../../inst/extdata/DiabImmune/DiabImmune_MetagenomicSequencingAssay.txt'
-    metadataFile2 <- '../../inst/extdata/DiabImmune/DiabImmune_Participant.txt'
-    metadataFile3 <- '../../inst/extdata/DiabImmune/DiabImmune_Sample.txt'
-    ontologyFile <- '../../inst/extdata/DiabImmune/DiabImmune_OntologyMetadata.txt'
-    mbioDataset <- MbioDataset(list(dataFile1, dataFile2), list(metadataFile1, metadataFile2, metadataFile3), ontologyFile)
+    mbioDataset <- microbiomeData::DiabImmune
     genus <- getCollection(mbioDataset, "16S Genus", continuousMetadataOnly = TRUE)
 
     # make sure metadata dont contain IRIs