Reopen #34 (#39)

set all active binding names to snake case
ropensci · Jun 25, 2021 · 63bc7b3 · 63bc7b3
1 parent 7c99d76
commit 63bc7b3
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Showing 4 changed files with 19 additions and 11 deletions.
diff --git a/R/DataSpaceStudy.R b/R/DataSpaceStudy.R
@@ -194,6 +194,13 @@ DataSpaceStudy <- R6Class(
           ...
         )
 
+        ## set variable names that are returned as camel case with slash to snake case
+        setnames(
+          dataset,
+          names(dataset),
+          tolower(gsub("/[A-z]+", "", gsub("^([A-z]+)([A-Z])", "\\1_\\2", names(dataset))))
+        )
+
         # convert to data.table
         setDT(dataset)
       } else {
@@ -229,8 +236,8 @@ DataSpaceStudy <- R6Class(
         # update 'n'
         private$.availableNIDatasets[name == datasetName, n := nrow(dataset)]
 
-        # change "subject_id" to "ParticipantId" to be consistent with other datasets
-        setnames(dataset, c("subject_id", "prot"), c("ParticipantId", "study_prot"), skip_absent = TRUE)
+        # change "subject_id" to "participant_id" to be consistent with other datasets
+        setnames(dataset, c("subject_id", "prot"), c("participant_id", "study_prot"), skip_absent = TRUE)
       }
 
       # merge extra information
@@ -243,11 +250,11 @@ DataSpaceStudy <- R6Class(
           if (!identical(datasetName, "Demographics")) {
             dem <- self$getDataset("Demographics")
 
-            subj <- ifelse(private$.study == "", "Subject", "Participant")
-            cols <- c(paste0(subj, "Visit/Visit"), "study_prot")
+            subj <- ifelse(private$.study == "", "subject", "participant")
+            cols <- c(paste0(subj, "_visit"), "study_prot")
             dem <- dem[, -cols, with = FALSE]
 
-            key <- paste0(subj, "Id")
+            key <- paste0(subj, "_id")
             setkeyv(dem, key)
             setkeyv(dataset, key)
 

diff --git a/README.md b/README.md
@@ -217,7 +217,7 @@ NAb <- cvd408$getDataset("NAb")
 dim(NAb)
 #> [1] 540  33
 colnames(NAb)
-#>  [1] "ParticipantId"          "ParticipantVisit/Visit" "visit_day"             
+#>  [1] "participant_id"         "participant_visit"      "visit_day"             
 #>  [4] "assay_identifier"       "summary_level"          "specimen_type"         
 #>  [7] "antigen"                "antigen_type"           "virus"                 
 #> [10] "virus_type"             "virus_insert_name"      "clade"                 

diff --git a/tests/testthat/helper.R b/tests/testthat/helper.R
@@ -1,2 +1,3 @@
+## Set STAGING to TRUE in .Renviron to run tests against staging server.
 assign("onStaging", identical(tolower(Sys.getenv("STAGING")), "true"))
 assign("baseUrl", ifelse(onStaging, "https://dataspace-staging.cavd.org", "https://dataspace.cavd.org"))
diff --git a/tests/testthat/test-study.R b/tests/testthat/test-study.R
@@ -35,8 +35,8 @@ test_study <- function(study, datasets, niDatasets = c(), groupId = NULL, groupL
   }
 
   test_that("can connect to studies", {
-    expect_is(cavd, "DataSpaceStudy")
-    expect_is(cavd, "R6")
+    expect_is(cavd, "DataSpaceStudy", info=cavd[1])
+    expect_is(cavd, "R6", info=cavd[1])
   })
 
   if ("DataSpaceStudy" %in% class(cavd)) {
@@ -200,15 +200,15 @@ test_study <- function(study, datasets, niDatasets = c(), groupId = NULL, groupL
       test_that("`getDataset`", {
         for (datasetName in cavd$availableDatasets$name) {
           dataset <- try(cavd$getDataset(datasetName), silent = TRUE)
-          expect_is(dataset, "data.table", info = datasetName)
+          expect_is(dataset, "data.table", info = paste(datasetName, study, groupId))
           expect_gt(nrow(dataset), 0)
         }
       })
 
       test_that("`getDataset` (label)", {
         for (datasetLabel in cavd$availableDatasets$label) {
           dataset <- try(cavd$getDataset(datasetLabel), silent = TRUE)
-          expect_is(dataset, "data.table", info = datasetLabel)
+          expect_is(dataset, "data.table", info = paste(datasetLabel, study, groupId))
           expect_gt(nrow(dataset), 0)
         }
       })
@@ -217,7 +217,7 @@ test_study <- function(study, datasets, niDatasets = c(), groupId = NULL, groupL
         for (i in seq_len(nrow(cavd$availableDatasets))) {
           datasetName <- cavd$availableDatasets$name[i]
           dataset <- try(cavd$getDataset(datasetName), silent = TRUE)
-          expect_is(dataset, "data.table", info = datasetName)
+          expect_is(dataset, "data.table", info = paste(datasetName, study, groupId))
 
           if (cavd$availableDatasets$integrated[i]) {
             datasetN <- cavd$availableDatasets$n[i]