Merge pull request #27 from pepkit/dev

Release 0.2

.gitignore

@@ -0,0 +1,4 @@
+.Rproj.user
+.Rhistory
+.RData
+.Ruserdata

DESCRIPTION

@@ -1,7 +1,7 @@
 Package: pepr
 Type: Package
 Title: Reading Portable Encapsulated Projects
-Version: 0.1
+Version: 0.2
 Date: 2017-08-09
 Authors@R: c(person("Nathan", "Sheffield", email = "[email protected]",
     role = c("aut", "cre")),person("Michal","Stolarczyk",email="[email protected]",role=c("ctb")))

NEWS.md

@@ -1,6 +1,10 @@
-# pepr 0.1
+# pepr 0.2 - 2019-04-17
 
-## 2019-02-01
+## Changed
+
+* keys in the config file: `sample_annotation` to `sample_table`, `sample_subannotation` to `subsample_table`. Backwards compatibility is preserved.
+
+# pepr 0.1 - 2019-02-01
 
 ## Added
 
@@ -16,11 +20,7 @@
 * fixed the problem with paths expansions in sample subannotaitons case
 
 
-# pepr 0.0.4
-
-## 2018-11-14
-
-## Added
+# pepr 0.0.4 - 2018-11-14
 
 ## Changed
 
@@ -30,25 +30,16 @@
 * fix `expandPath()` function, add error when environment variable not found
 
 
-# pepr 0.0.3
-
-## 2018-09-12
+# pepr 0.0.3 - 2018-09-12
 
 ## Added
 
 * add `derived_columns` functionality
 * add `implied_columns` functionality
 * add `subannotation` functionality
 
-## Changed
-
-# pepr 0.0.2 
-
-## 2018-09-06
+#  pepr 0.0.2 - 2018-09-06
 
 ## Added
 
-* first release, includes basic [PEP](https://pepkit.github.io/) reading functions
-
-## Changed
-
+* first release, includes basic [PEP](https://pepkit.github.io/) reading functions

R/loadConfig.R

@@ -33,7 +33,7 @@
   # This used to be all metadata columns; now it's just: results_subdir
   mdn = names(cfg$metadata)
 
-  cfg$metadata = .makeMetadataSectionAbsolute(cfg, parent = dirname(filename))
+  cfg$metadata = .makeMetadataSectionAbsolute(cfg, parent=dirname(filename))
   # make data_sources section absolute
   if(!is.null(cfg$data_sources)) 
     cfg$data_sources = lapply(cfg$data_sources, .expandPath)
@@ -57,7 +57,7 @@
   return(cfg)
 }
 
-.updateSubconfig = function(cfg, sp = NULL) {
+.updateSubconfig = function(cfg, sp=NULL) {
   if (!is.null(sp)) {
     if (is.null(cfg$subprojects[[sp]])) {
       warning("Subproject not found: ", sp)
@@ -70,8 +70,6 @@
   return(cfg)
 }
 
-
-
 .listSubprojects = function(cfg, style="message") {
   # this function can be used in object show method, where cat is preferred 
   # or for user information when the Project is created, where message
@@ -87,8 +85,7 @@
 
   if (length(names(cfg$subprojects)) > 0) {
     # If there are any show a cat and return if needed
-    printFun("  subprojects: ", paste0(names(cfg$subprojects), 
-                                  collapse = ","))
+    printFun("  subprojects: ", paste0(names(cfg$subprojects), collapse=","))
     invisible(names(cfg$subprojects))
   } else{
     # Otherwise return NULL for testing purposes

R/models.R

@@ -231,7 +231,7 @@ setMethod(
 #' projectConfig = system.file(
 #' "extdata",
 #' "example_peps-master",
-#' "example_subannotation1",
+#' "example_subtable1",
 #' "project_config.yaml",
 #' package = "pepr"
 #' )
@@ -253,8 +253,8 @@ setMethod(
   definition = function(.Object, sampleName, subsampleName) {
     if (is.null(.Object@samples$subsample_name))
       stop(
-        "There is no subsample_name attribute in the subannotation
-        table, therefore this method cannot be called."
+        "There is no subsample_name attribute in the subannotation", 
+        " table, therefore this method cannot be called."
       )
     sampleNames = unlist(.Object@samples$sample_name)
     rowNumber = which(sampleNames == sampleName)
@@ -336,18 +336,14 @@ setGeneric("activateSubproject", function(.Object, sp)
 
 setMethod(
   f = "activateSubproject",
-  signature = signature(.Object = "Project", sp = "character"),
+  signature = signature(.Object="Project", sp="character"),
   definition = function(.Object, sp) {
     .Object@config = .updateSubconfig(.Object@config, sp)
-
     # Ensure that metadata paths are absolute and return the config.
     # This used to be all metadata columns; now it's just: results_subdir
     mdn = names(.Object@config$metadata)
-
     .Object@config$metadata =
-      .makeMetadataSectionAbsolute(.Object@config,
-                                   parent = dirname(.Object@file))
-
+      .makeMetadataSectionAbsolute(.Object@config, parent=dirname(.Object@file))
     .Object = .loadSampleAnnotation(.Object)
     .Object = .loadSampleSubannotation(.Object)
     .Object = .applyConstantAttributes(.Object)
@@ -468,24 +464,46 @@ setMethod(
   } else {
     sampleReadFunc = utils::read.table
   }
-  sampleAnnotationPath = .Object@config$metadata$sample_annotation
-  if (.safeFileExists(sampleAnnotationPath)) {
+  if(is.null(.Object@config$metadata$sample_table)){
+    if(!is.null(.Object@config$metadata$sample_annotation)){
+      .Object@config$metadata$sample_table = 
+        .Object@config$metadata$sample_annotation
+      warning("'sample_annotation' key in the 'metadata' section of the config "
+              ,"is deprecated. Use 'sample_table' instead.")
+    } else{
+        if(!is.null(.Object@config$subprojects)){
+          # if there are any subprojects, just warn and return empty data.table,
+          # maybe there's a 'sample_table' specified in the subproject
+          warning("No 'sample_table' key in the 'metadata' section of the " 
+                  ,"config")
+          .Object@samples = data.table::data.table()
+          return(.Object)
+        } else{
+          stop("No 'sample_table' key in the 'metadata' section of the config")
+        }
+    }
+  }
+  sampleAnnotationPath = .Object@config$metadata$sample_table
+  if(.safeFileExists(sampleAnnotationPath)){
     samples = sampleReadFunc(sampleAnnotationPath)
   } else{
-    if(!is.null(.Object@config$subprojects)){
-    warning("No sample annotation file: ", sampleAnnotationPath)
-    samples = data.table::data.table()
-    }else{
-      stop("No sample annotation file: ", sampleAnnotationPath)
-    }
+    stop("The sample annotation sheet does not exist: ", sampleAnnotationPath)
   }
   .Object@samples = samples
   return(.Object)
 }
 
-.loadSampleSubannotation = function(.Object) {
+.loadSampleSubannotation = function(.Object){
   # Extracting needed slots
-  sampleSubannotationPath = .Object@config$metadata$sample_subannotation
+  if(is.null(.Object@config$metadata$subsample_table)){
+    if(!is.null(.Object@config$metadata$sample_subannotation)){
+      .Object@config$metadata$subsample_table = 
+        .Object@config$metadata$sample_subannotation
+      warning("'sample_subannotation' key in the 'metadata' section of the"
+              ,"config is deprecated. Use 'subsample_table' instead.")
+    }
+  }
+  sampleSubannotationPath = .Object@config$metadata$subsample_table
   samples = .Object@samples
   samples = .listifyDF(samples)
   #Reading sample subannonataion table, just like in annotation table
@@ -522,6 +540,9 @@ setMethod(
       # The column exists
       whichColSamples = which(names(samples) == colName)
       whichRowSamples = which(samples$sample_name == iName)
+      if(length(whichRowSamples) < 1){
+        stop("No samples named '", iName, "'")
+      }
       # Inserting element(s) into the list
       colList[[whichRowSamples]] = subTable[[colName]]
       # Inserting the list as a column in the data.frame

R/utils.R

@@ -1,8 +1,8 @@
 
 #' Create an absolute path from a primary target and a parent candidate.
 #
-#' @param perhapsRelative: Path to primary target directory.
-#' @param  parent a path to parent folder to use if target isn't absolute.
+#' @param perhapsRelative Path to primary target directory.
+#' @param parent a path to parent folder to use if target isn't absolute.
 #
 #' @return	Target itself if already absolute, else target nested within parent.
 .makeAbsPath = function(perhapsRelative, parent) {
@@ -88,7 +88,7 @@
 #' fetchSamples(s,attr = "sample_name", func=function(x){ grep("pig_",x) },action="include")
 #' @export
 fetchSamples = function(samples, attr=NULL, func=NULL, action="include"){
-  if(!is(samples, "data.table"))
+  if(!methods::is(samples, "data.table"))
     stop("'samples' argument has to be a data.table object, got: '",
          class(samples),"'")
   if(!action %in% c("include","exclude"))
@@ -114,7 +114,7 @@ fetchSamples = function(samples, attr=NULL, func=NULL, action="include"){
       }
     }
   }
-  if(length(rowIdx) < 1 || (!is(rowIdx,"integer")))
+  if(length(rowIdx) < 1 || (!methods::is(rowIdx,"integer")))
     stop("your function returned invalid indices: '", rowIdx,"'")
   # use action arg
   if(action=="include") return(samples[rowIdx, ])

inst/extdata/example_peps-master/.gitignore

@@ -89,4 +89,7 @@ target/
 
 
 # Rcaches
-RCache/*
+RCache/*
+
+# macOS
+*.DS_Store