more metadata stuff

IPS-LMU · Nov 2, 2020 · e1c0bc1 · e1c0bc1
1 parent 368782a
commit e1c0bc1
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Showing 2 changed files with 36 additions and 19 deletions.
diff --git a/R/emuR-database.flatfiledata.R b/R/emuR-database.flatfiledata.R
@@ -2,19 +2,24 @@ read_and_join_key_value_tsv <- function(emuDBhandle,
                                         file, 
                                         x, 
                                         bundleName, 
-                                        sessionName){
+                                        sessionName,
+                                        delim = "\t"){
   if(file.exists(file)){
-    key_value_tsv = readr::read_tsv(file, col_types = readr::cols())
+    browser()
+    key_value_tsv = readr::read_delim(file, 
+                                      col_types = readr::cols(),
+                                      delim)
     if(all(names(key_value_tsv) == c("key", "value"))){
       key_value_tsv_pivoted = tidyr::pivot_wider(key_value_tsv, names_from = "key", values_from = "value")
       if(missing(bundleName) && missing(sessionName)){
         res = dplyr::full_join(x, key_value_tsv_pivoted, by = character())
       } else if(missing(bundleName) && !missing(sessionName)) {
         # join by session
-        browser()
         key_value_tsv_pivoted$session = sessionName
         res = dplyr::left_join(x, key_value_tsv_pivoted, by = "session")
-      } 
+      } else if(!missing(bundleName) && !missing(sessionName)){
+        stop("handeling bundle key value pairs not implemented yet!")
+      }
     } else {
       stop(path2tsv, " doesn't only contain the columns 'key' and 'value'. Only these two columns are permitted!")
     }
@@ -38,7 +43,18 @@ read_and_join_long_tsv <- function(emuDBhandle, file, x){
   }
 }
 
-##' Join flat file .tsv data to x 
+##' Join flat file data (UTF-8 .tsv/.csv files) to x 
+##' 
+##' Function to join flat file data that is present within 
+##' the directories of an emuDB to a tibble/data.frame object
+##' usually either produced by \link{query} or \link{get_trackdata}. As
+##' it uses the "session" and "bundle" columns to perform the joins these
+##' have to be present in x. 
+##' 
+##' This function recognizes 2 types flat files files:
+##' \itemize{
+##' \item *_keyValue files
+##' }
 ##' 
 ##' @param emuDBhandle emuDB handle object (see \link{load_emuDB})
 ##' @param sessionPattern A regular expression pattern matching session names to be searched from the database
@@ -53,10 +69,11 @@ read_and_join_long_tsv <- function(emuDBhandle, file, x){
 ##' }
 ##' \code{session}, \code{b}
 ##' @export
-join_tsvs <- function(emuDBhandle, 
-                      x,
-                      sessionPattern = '.*', 
-                      bundlePattern = '.*'){
+join_flatFileData <- function(emuDBhandle, 
+                              x,
+                              sessionPattern = '.*', 
+                              bundlePattern = '.*',
+                              fileExtension = '.tsv'){
 
   # gen. strat. move from bundles to session to emuDB level
   all_bundles = list_bundles(emuDBhandle)
@@ -66,24 +83,24 @@ join_tsvs <- function(emuDBhandle,
   all_bundles = all_bundles[
     grepl(pattern = sessionPattern, x = all_bundles, perl = T) 
     & grepl(pattern = bundlePattern, x = all_bundles, perl = T)
-    ]
+  ]
 
   ##############################
   # handle emuDB level
 
   # get keyValue tsv file on emuDB level
-  path2tsv = file.path(emuDBhandle$basePath, paste0(emuDBhandle$dbName, "_keyValue.", "tsv"))
+  path2tsv = file.path(emuDBhandle$basePath, paste0(emuDBhandle$dbName, "_keyValue", fileExtension))
   x = read_and_join_key_value_tsv(emuDBhandle, file = path2tsv, x = x)
-
+  
   # get long tsv file on emuDB level
-  path2tsv = file.path(emuDBhandle$basePath, paste0(emuDBhandle$dbName, "_long.", "tsv"))
+  path2tsv = file.path(emuDBhandle$basePath, paste0(emuDBhandle$dbName, "_long", fileExtension))
   x = read_and_join_long_tsv(emuDBhandle, file = path2tsv, x)
 
   ##############################
   # handle session level
   for(session_name in unique(all_bundles$session)){
     # get keyValue tsv file on session level
-    path2tsv = file.path(emuDBhandle$basePath, paste0(session_name, session.suffix), paste0(session_name, "_keyValue.", "tsv"))  
+    path2tsv = file.path(emuDBhandle$basePath, paste0(session_name, session.suffix), paste0(session_name, "_keyValue", fileExtension))  
     x = read_and_join_key_value_tsv(emuDBhandle, file = path2tsv, x = x, sessionName = session_name)
   }
 

diff --git a/tests/testthat/test_emuR-database.flatfiledata.R b/tests/testthat/test_emuR-database.flatfiledata.R
@@ -31,7 +31,7 @@ db = load_emuDB(path2db,
                 inMemoryCache = internalVars$testingVars$inMemoryCache, 
                 verbose = F)
 
-test_that("join_tsvs works on emuDB level", {
+test_that("join_flatFileData works on emuDB level", {
 
   # key value emuDB data
   flat_data = tibble::tibble(key = c("location", "institution"), value = c("Muenchen", "IPS"))
@@ -40,7 +40,7 @@ test_that("join_tsvs works on emuDB level", {
 
   sl = query(db, "Phonetic == S")
 
-  sl_joined = join_tsvs(db, sl)
+  sl_joined = join_flatFileData(db, sl)
 
   expect_true(all(c("location", "institution") %in% names(sl_joined)))
 
@@ -56,11 +56,11 @@ test_that("join_tsvs works on emuDB level", {
 
   readr::write_tsv(x = long_data, file = file.path(db$basePath, paste0(db$dbName, "_long.", "tsv")))
 
-  sl_joined = join_tsvs(db, sl)
+  sl_joined = join_flatFileData(db, sl)
   expect_equal(length(which(is.na(sl_joined$eyecolor))), 7)
 })
 
-test_that("join_tsvs works on session level", {
+test_that("join_flatFileData works on session level", {
 
   # key value session data
   flat_data = tibble::tibble(key = c("location", "fudge", "speed"), value = c("Muenchen", "yummy", "fast"))
@@ -69,7 +69,7 @@ test_that("join_tsvs works on session level", {
 
   sl = query(db, "Phonetic == S")
 
-  sl_joined = join_tsvs(db, sl)
+  sl_joined = join_flatFileData(db, sl)
 
   expect_true(all(c("location.x", "location.y") %in% names(sl_joined)))