changes related to subsamble table functionality; fix #33

R/loadConfig.R

@@ -159,7 +159,7 @@
   return(path)
 }
 
-#' Format a string like python's format function
+#' Format a string like python's format method
 #'
 #' Given a string with environment variables (encoded like \code{${VAR}} or \code{$VAR}), and
 #' other variables (encoded like \code{{VAR}}) this function will substitute
@@ -189,11 +189,6 @@
   argsLengths = lapply(argsUnlisted, length)
   if (any(argsLengths > 1)) {
     pluralID = which(argsLengths > 1)
-    # Remove the previously interpolated, 
-    # thus plural elements from another round of interpolation
-    if (any(names(pluralID) %in% exclude)) {
-      pluralID = pluralID[-which(names(pluralID) %in% exclude)]
-    }
      attrCount = sapply(argsUnlisted, length)[pluralID]
      nrows = unique(attrCount)
      if(length(nrows) > 1) {

R/models.R

@@ -403,8 +403,8 @@ setMethod(
       }
       regex = cfg$data_sources[[sampDataSource]]
       if (!is.null(regex)) {
-        a = .strformat(regex, as.list(samp), exclude, parentDir)
-        samp[[column]] = list(system(sprintf("echo %s",a), intern = TRUE))
+        formatted = .strformat(regex, as.list(samp), exclude, parentDir)
+        samp[[column]] = .matchesAndRegexes(formatted)
       }
       listOfSamples[[iSamp]] = samp
     }
@@ -416,6 +416,7 @@ setMethod(
   .Object
 }
 
+
 .implyAttributes = function(.Object) {
   if (is.null(.Object@config$implied_attributes)) {
     # Backwards compatibility

R/utils.R

@@ -159,6 +159,7 @@ fetchSamples = function(samples, attr=NULL, func=NULL, action="include") {
 #' A designated place for any config transformations/sanity checks, like keys deprecation handling
 #'
 #' @param cfg config or a section of one to sanitize
+#'
 #' @return sanitized config
 #' @export
 .sanitizeConfig = function(cfg) {
@@ -170,4 +171,21 @@ fetchSamples = function(samples, attr=NULL, func=NULL, action="include") {
     }
   }
   return(cfg)
-}
+}
+
+#' Create a list of matched files in the system and unmatched regular expessions
+#'
+#' @param rgx string to expand in the system
+#'
+#' @return a list of all the elements after possible expansion
+.matchesAndRegexes = function(rgx) {
+  res = c()
+  for(i in rgx){
+    matched = Sys.glob(i)
+    if(length(matched) < 1) {
+      matched = i
+    }
+    res = c(res, matched)
+  }
+  return(list(res))
+}

tests/testthat/test_utils.R

@@ -153,10 +153,18 @@ test_that(".expandPath work with both curly braced and non-curly braced
                  .expandPath("${HOME}/my/path/string.txt"))
 })
 
-test_that(".strformat works",{
-    expect_null(.strformat("~/{VAR1}{VAR2}_file", list(VAR1=c("hi","a"), VAR2="hello"), exclude = "VAR1"))
-    expect_is(.strformat("~/{VAR1}{VAR2}_file", list(VAR1="hi", VAR2="hello"), exclude = "test"),"character")
-    expect_is(.strformat("~/{VAR1}{VAR2}_file", list(VAR1="hi", VAR2="hello")),"character")
+test_that(".strformat returns an object of correct class", {
+    expect_is(.strformat("~/{VAR1}{VAR2}_file", list(VAR1="var1a", VAR2="var2a")), "character")
+})
+
+test_that(".strformat works with multiple values", {
+    expect_equal(length(.strformat("{VAR1}_{VAR2}", list(VAR1=c("var1a", "var1b"), VAR2="var2a"))), 2)
+    expect_equal(length(.strformat("{VAR1}_{VAR2}", list(VAR1=c("var1a", "var1b"), VAR2=c("var2a", "var2b")))), 2)
+    expect_equal(length(.strformat("{VAR1}_{VAR2}", list(VAR1=c("var1a", "var1b"), VAR2="var2a"))), 2)
+})
+
+test_that(".strformat fails when multiple multi-replacemenets of different lengths are used", {
+    expect_error(.strformat("{VAR1}_{VAR2}", list(VAR1=c("var1a", "var1b"), VAR2=c("var2a", "var2b","var2c"))))
 })
 
 test_that(".printNestedList produces an output", {