Merge pull request #13 from pepkit/dev

v0.0.4

.gitignore

@@ -1,3 +1,4 @@
 .Rproj.user
 .Rhistory
 .RData
+.DS_Store

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BiocProject
 Title: Bioconductor Management with Portable Encapsulated Project (PEP) Objects
-Version: 0.0.3
+Version: 0.0.4
 Authors@R: c(person("Michal", "Stolarczyk", email = "[email protected]",role = c("aut", "cre")), 
 	person("Nathan", "Sheffield", email = "[email protected]",role = c("aut")))
 Description: A Bioconductor-oriented project management class. It wraps the

NEWS.md

@@ -1,3 +1,13 @@
+# BiocProject 0.0.4
+
+## Unreleased
+
+## Changed
+
+* better custom data loading function error/warning communication
+* all exceptions are caught with `BiocProject` constructor
+* fix `.updateSubconfig(.Object@config, sp) : Subproject not found:` warning in `toProject` method
+
 # BiocProject 0.0.3
 
 ## 2018-12-21

R/methods.R

@@ -116,7 +116,7 @@ setMethod(
 #' @param .Object an object of \code{\link{BiocProject-class}}
 #' @param subproject a character with the name of the subproject
 #' that should be activated during the converstion 
-#' to the \code{\link[pepr]{Project-class}} object
+#' to the \code{\link[pepr]{Project-class}} object (optional)
 #'
 #' @return an object of \code{\link[pepr]{Project-class}} object
 #' 
@@ -134,7 +134,7 @@ setMethod(
 #' toProject(bp)
 #'
 #' @export
-setGeneric("toProject", function(.Object,subproject=character())
+setGeneric("toProject", function(.Object,subproject=NULL)
   standardGeneric("toProject"))
 
 #' @export
@@ -147,9 +147,9 @@ setMethod(
 )
 
 
-#' Extract data from \code{\link[pepr]{Project-class}} objects
+#' Extract data from \code{\link{BiocProject-class}} objects
 #'
-#' This method extracts the data from \code{\link[pepr]{Project-class}} objects
+#' This method extracts the data from \code{\link{BiocProject-class}} objects
 #'
 #' @param .Object an object of \code{\link{BiocProject-class}}
 #'

R/utils.R

@@ -1,36 +1,48 @@
 # internal function used for wrapping the user-supplied function meessages 
 # in a box
-.wrapFunMessages = function(str, type) {
-  str = trimws(str, which = "both")
-  n = options("width")[[1]]
-  header = paste0(" Your function ", type, "(s) ")
-  nH = floor(nchar(header) / 2)
-  nFill = floor(n / 2)
-  message(rep("-", nFill - nH), header, rep("-", nFill - nH))
-  message("\n", str, "\n")
-  message(rep("-", n))
+.wrapFunMessages = function(messages, type) {
+          n = options("width")[[1]]
+          header = ifelse(
+                    length(messages) > 1,
+                    paste0(" Your function ", type, "s (", length(messages), ") "),
+                    paste0(" Your function ", type, " ")
+          )
+          nH = floor(nchar(header) / 2)
+          nFill = floor(n / 2)
+          message("\n",rep("-", nFill - nH), header, rep("-", nFill - nH))
+          i = 1
+          for (i in seq_along(messages)) {
+                    m = trimws(messages[i], which="both")
+                    message("\n", type, " ", i , ": ", m, "\n")
+          }
+          message(rep("-", n), "\n")
 }
+
 # internal function that wraps the external function execution
 # in tryCatch to indicate problems with the external function execution
-.callBiocFun = function(f, a) {
-  readData = tryCatch({
-    do.call(f, a)
-  }, warning = function(w) {
-    warning(
-      "There are warnings associated with your function execution."
-    )
-    .wrapFunMessages(w$message,"warning")
-    message("No data was read. Creating an empty BiocProject object...")
-    return(w$message)
-  }, error = function(e) {
-    warning(
-      "There are errors associated with your function execution."
-    )
-    .wrapFunMessages(e$message,"error")
-    message("No data was read. Creating an empty BiocProject object...")
-    return(e$message)
-  })
-  return(readData)
+.callBiocFun <- function(func, arguments) 
+{ 
+          .warnings = c()
+          frameNumber <- sys.nframe()
+          wHandler <- function(w){ 
+                    # warning handler 
+                    assign(".warnings", append(.warnings,w$message), 
+                           envir = sys.frame(frameNumber))
+                    invokeRestart("muffleWarning") 
+          }
+          eHandler <- function(e){
+                    # error handler 
+                    .wrapFunMessages(e$message,"error")
+                    message("No data was read. Creating an empty BiocProject object...")
+                    message("The error message was saved in the .Data slot.")
+                    e$message
+          } 
+          res = withCallingHandlers(tryCatch(do.call(func, arguments), error = eHandler),warning = wHandler)
+          if(length(.warnings) > 0){
+                    warning("There were warnings associated with your function execution.")
+                    .wrapFunMessages(.warnings,"warning")
+          }
+          return(res)
 }
 
 #' Create an absolute path from a primary target and a parent candidate.

inst/extdata/example_peps-master/example_BiocProject_exceptions/project_config.yaml

@@ -0,0 +1,6 @@
+metadata:
+  sample_annotation: sample_annotation.csv
+
+bioconductor:
+  read_fun_name: readBedFilesExceptions
+  read_fun_path: readBedFilesExceptions.R

inst/extdata/example_peps-master/example_BiocProject_exceptions/readBedFilesExceptions.R

@@ -0,0 +1,18 @@
+readBedFilesExceptions = function(project) {
+  warning("first test warning")
+  warning("second test warning")
+  stop("test error")
+  paths = pepr::samples(project)$file_path
+  sampleNames = pepr::samples(project)$sample_name
+  setwd(dirname(project@file))
+  result = lapply(paths, function(x){
+    df = read.table(x)
+    colnames(df) = c('chr', 'start', 'end')
+    gr = GenomicRanges::GRanges(df) 
+  })
+  names(result) = sampleNames
+  return(result)
+
+}
+
+

inst/extdata/example_peps-master/example_BiocProject_exceptions/sample_annotation.csv

@@ -0,0 +1,3 @@
+sample_name,file_path
+laminB1Lads,data/laminB1Lads.bed
+vistaEnhancers,data/vistaEnhancers.bed

update_examples.sh

@@ -5,5 +5,6 @@ mkdir -p inst/extdata/example_peps-master/example_BiocProject
 mkdir -p inst/extdata/example_peps-master/example_BiocProject_remote
 mv example_peps-master/example_BiocProject inst/extdata/example_peps-master
 mv example_peps-master/example_BiocProject_remote inst/extdata/example_peps-master
+mv example_peps-master/example_BiocProject_exceptions inst/extdata/example_peps-master
 rm -rf example_peps-master 
 rm master.zip

vignettes/1getStarted.Rmd

@@ -168,7 +168,7 @@ The function specified can be a data processing function of any complexity, but
 1. the argument must be a [`pepr::Project`](http://code.databio.org/pepr/reference/Project-class.html) object (should use that input to load all the relevant data into `R`),
 1. must return one or more data objects. 
 
-For example, consider the [parseEncodeRegions function](https://raw.githubusercontent.com/pepkit/example_peps/master/example_BiocProject/parseEncodeRegions.R):
+For example, consider the [readBedFiles function](https://github.com/pepkit/example_peps/blob/master/example_BiocProject/readBedFiles.R):
 
 ```{r echo=FALSE, eval=TRUE, comment=""}
 processFunction =  system.file(
@@ -181,11 +181,32 @@ processFunction =  system.file(
 source(processFunction)
 readBedFiles
 ```
+# Data reading function error/warning handling 
 
-# Advanced `BiocProject` features
+The `BiocProject` constructor provides a way to rigorously monitor exceptions related to your data reading function. All the produced warnings and errors are caught, processed and displayed in an organized way:
 
-See this [BiocProject advanced features vignette](./2multipleArguments.html) if you want to:
+```{r}
+configFile = system.file(
+  "extdata",
+  "example_peps-master",
+  "example_BiocProject_exceptions",
+  "project_config.yaml",
+  package = "BiocProject"
+)
 
-* use a anonymous function instead of one defined *a priori*
+bpExceptions = BiocProject(configFile)
+```
+In case an error is caught, the erorr message is preserved and stored in the `.Data` slot of the `BiocProject` object, so it can be accessed the regular way:
+```{r}
+getData(bpExceptions)
+```
+# Further reading
+
+See this [More arguments than just a PEP in your function?](./2multipleArguments.html) vignette if you want to:
+
+* use an anonymous function instead of one defined *a priori*
 * use a function that requires more arguments than just a PEP
-* use a function that is a part of another `R` package
+
+See the [Working with remote data](./4remoteData.html) vignette to learn how to download the data from the Internet and store it conveniently in the `BiocProject` object.
+
+See the [Working with large datasets - simpleCache](./3simpleCache.html) vignette to learn how the `simpleCache` R package can be used to prevent copious and lengthy results recalculations when working with large datasets.

vignettes/2multipleArguments.Rmd

@@ -72,9 +72,9 @@ bpArgs =  BiocProject(file=ProjectConfigArgs, funcArgs=list(resize.width=100))
 The `funcArgs` argument gets a one element list and passes the `resize.width` argument to your custom data processing function.
 
 
-# How to use a anonymous function
+# How to use an anonymous function
 
-You can use a [anonymous function](https://en.wikipedia.org/wiki/Anonymous_function) (that is implemented in the `BiocProject` function call) to provide additional arguments to your function of interest. For example:
+You can use an [anonymous function](https://en.wikipedia.org/wiki/Anonymous_function) (that is implemented in the `BiocProject` function call) to provide additional arguments to your function of interest. For example:
 
 ```{r}
 bpAnonymous = BiocProject(file=ProjectConfigArgs, func=function(x){
@@ -83,7 +83,4 @@ bpAnonymous = BiocProject(file=ProjectConfigArgs, func=function(x){
   )
 #Inspect it
 bpAnonymous
-```
-
-
-
+```