draft data loading script

data-raw/reloadCuratedMbioDatasets.R

@@ -1,7 +1,41 @@
 ## each directory in data-raw should represent a curated dataset
+## the name of the directory will become the name of the dataset
 ## it should have subdirectories like `assayData`, `sampleMetadata` and `ontology`
 ## the convenience function here should be called on each directory
 ## the convenience function should build an MbioDataset object
 ## then it should call use_data and overwrite the old object
 
-#usethis::use_data(DATASET, overwrite = TRUE)
+
+buildMbioDatasetFromDataDir <- function(dataDir) {
+    dataSet <- MicrobiomeDB::MbioDataset(
+	    as.list(list.files(paste(dataDir, "assayData", sep = "/"), full.names = TRUE)),
+	    as.list(list.files(paste(dataDir, "sampleMetadata", sep = "/"), full.names = TRUE)),
+	    list.files(paste(dataDir, "ontology", sep = "/"), full.names = TRUE)
+    )
+
+    assign(basename(dataDir), dataSet, envir = as.environment(1)) ## this is the global env
+
+    return(invisible(dataSet))
+}
+
+path <- function(x) {
+    baseDir <- system.file("data", package = "microbiomeData", mustWork = TRUE)
+
+    file.path(file.path(baseDir, x),'.rda',fsep='')
+}
+
+custom_use_data <- function(x) {
+    paths <-path(x)
+
+    mapply(save, list = x, file = paths, MoreArgs = list(envir = as.environment(1), 
+        compress = 'xz', version = 3, ascii = FALSE))
+
+    invisible()
+}
+
+baseDataDir <- system.file("data-raw", package = "microbiomeData", mustWork = TRUE)
+studyDirectories <- list.files(baseDataDir, full.names = TRUE)
+studyDirectories <- studyDirectories[!grepl(".R", studyDirectories, fixed = TRUE)] 
+
+lapply(studyDirectories, buildMbioDatasetFromDataDir)
+custom_use_data(basename(studyDirectories))