Merge pull request #28 from pepkit/dev

Release 0.2

.travis.yml

@@ -9,4 +9,5 @@ r_github_packages:
 bioc_packages: 
   - GenomicRanges
   - BiocStyle
-  - BiocFileCache
+  - BiocFileCache
+

DESCRIPTION

@@ -1,6 +1,6 @@
 Package: BiocProject
 Title: Bioconductor Management with Portable Encapsulated Project (PEP) Objects
-Version: 0.1.1
+Version: 0.1.2
 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

NAMESPACE

@@ -1,6 +1,7 @@
 # Generated by roxygen2: do not edit by hand
 
 export(.insertPEP)
+export(.setShowMethod)
 export(.updateList)
 export(BiocProject)
 exportMethods(config)

NEWS.md

@@ -1,4 +1,16 @@
-# BiocProject 0.1.1  - 2019-02-15
+# BiocProject 0.1.2 - unreleased
+
+## Added
+
+* the native `show` methods are redefined for the objects returned by `BiocProject::BiocProject` function, so that they display the PEP component of the object `metadata`
+* `BiocProject` function now handles the case when multiple data processing functions are defined in the config file. The last one is used if there's no match in `readFunName` and any of the functions sourced from the file specified in `readFunPath`
+
+## Changed
+
+* updates in the vignettes related to changes of metadata keys in the Project config
+* when the data processing function function is read from file, it is used within a newly created environment so that it is not left in the `.GlobalEnv` after the `BiocProject` function execution
+
+# BiocProject 0.1.1 - 2019-02-15
 
 ## Added
 
@@ -11,7 +23,7 @@
 * when errors are encountered, BiocProject now returns a PEP (`pepr::Project`) along with the error message in a `S4Vectors::List` object
 * the `bioconductor` section of the config file now follows the Bioconductor coding style (`camelCaps`)
 
-# BiocProject 0.1  - 2019-01-28
+# BiocProject 0.1 - 2019-01-28
 
 ## Added
 
@@ -22,22 +34,22 @@
 
 * **complete concept redesign**: no `BiocProject` class. The objects returned by the custom data reading function have to be of class `Annotated` and the `PEP` is inserted as the first element of its `metadata()` list
 
-# BiocProject 0.0.4  - 2019-01-25
+# BiocProject 0.0.4 - 2019-01-25
 
 ## 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
+# BiocProject 0.0.3 - 2018-12-21
 
 ## Changed
 
 * the default values for all optional arguments are `NULL`
 * change `lambda function` to `anonymous function`
 
-# BiocProject 0.0.2  - 2018-12-01
+# BiocProject 0.0.2 - 2018-12-01
 
 ## Changed
 
@@ -46,7 +58,7 @@
 * errors and warnings (if any) are returned instead of the data
 * if the object constructor can't find the function file, the message is more informative
 
-# BiocProject 0.0.1  - 2018-11-20
+# BiocProject 0.0.1 - 2018-11-20
 
 ## Added
 

R/functions.R

@@ -83,15 +83,7 @@
 #' @export BiocProject
 BiocProject = function(file, subproject = NULL, autoLoad = TRUE, func = NULL, 
                         funcArgs = NULL) {
-    p = tryCatch(
-        expr = { 
-            pepr::Project(file=file, subproject=subproject)
-        },warning = function(w) {
-            message(w)
-            stop("There are warnings 
-                associated with the 'Project' object creation.")
-        }
-    )
+    p = pepr::Project(file=file, subproject=subproject)
     # prevent PEP (Project object) input. This prevents BiocProject object
     # failing when the user provides the Project object
     if(is.null(funcArgs)){
@@ -124,49 +116,69 @@ BiocProject = function(file, subproject = NULL, autoLoad = TRUE, func = NULL,
         if(!is.logical(autoLoad)) stop("'autoLoad' argument has to be a logical, 
                                     got '", class(autoLoad),"'")
         if (autoLoad) {
-        # check if the config consists of MAIN_SECTION section
+            # check if the config consists of MAIN_SECTION section
             if(!pepr::checkSection(pepr::config(p), MAIN_SECTION)){
                 message("No data was read. Returning a Project object")
                 warning("The config YAML is missing the '",
                         MAIN_SECTION,"' section.")
                 return(p)
             }    
-        funcName = pepr::config(p)[[MAIN_SECTION]][[FUNCTION_NAME]]
-        # check if the function name was provided
-        # and if it exists in the environment
+            funcName = pepr::config(p)[[MAIN_SECTION]][[FUNCTION_NAME]]
+            # check if the function name was provided
+            # and if it exists in the environment
             if (!is.null(funcName) && exists(funcName)) {
                 # function from config.yaml in environment
                 readData = .callBiocFun(funcName, args)
-                message("Used function ", funcName, " from the environment")
+                message("Used function '", funcName, "' from the environment")
                 return(.insertPEP(readData, p))
             }else{
                 if (!is.null(funcName) && length(grep("(\\:){2,3}", funcName)) != 0) {
                     # trying to access the function from the namespace that
                     # was specified in the config.yaml FUNCTION_NAME
                     splitted = strsplit(funcName, ":")[[1]]
                     nonEmpty = splitted[which(splitted != "")]
-                    funcName = utils::getFromNamespace(x=nonEmpty[2], ns=nonEmpty[1])
-                    readData = .callBiocFun(funcName, args)
-                    message("Used function ", funcName, " from the environment")
+                    funcCode = utils::getFromNamespace(nonEmpty[2], nonEmpty[1])
+                    readData = .callBiocFun(funcCode, args)
+                    message("Used function '", nonEmpty[2],
+                            "' from the package: ", nonEmpty[1])
                     return(.insertPEP(readData, p))
                 }
-                # function from config.yaml in read_fun_name not in environment,
-                # trying to source the file specified in
-                # the config.yaml FUNCTION_PATH
+                # function from config.yaml in FUNCTION_NAME not in environment,
+                # trying to source the file specified 
+                # in the config.yaml FUNCTION_PATH
                 funcPath = pepr::.expandPath(
                     pepr::config(p)[[MAIN_SECTION]][[FUNCTION_PATH]])
                 if (!is.null(funcPath)){
                     if (!file.exists(funcPath))
                         funcPath = .makeAbsPath(funcPath,dirname(p@file))
-                        if(!file.exists(funcPath))
+                    if (!file.exists(funcPath))
                         stop(
-                            "The function does not exist in the environment and file ",
+                            "The function does not exist in the environment and file '",
                             funcPath,
-                            " does not exist"
+                            "' does not exist"
                         )
-                    readFun = source(funcPath)$value
-                    message("Function read from file: ", funcPath)
-                    readData = .callBiocFun(readFun, args)
+                    # Load the sourced objects into a new environment, 
+                    # so they are not in the .GlobalEnv after the BiocProject 
+                    # function execution
+                    e = new.env()
+                    # only the last defined function is saved into the variable 
+                    # below so first we need to check whether the FUNCTION_NAME 
+                    # defines a preferred function. If it does not, then use the
+                    # lastFun. This is relevant in case multiple functions are
+                    # defined in the file specified in FUNCTION_PATH.
+                    lastFun = source(funcPath, local=e)$value
+                    # check again for the specified funcion name, maybe it is 
+                    # defined in the file which was just sourced
+                    if (!is.null(funcName) && exists(funcName, where=e)) {
+                        message("Function '", funcName,"' read from file '", funcPath, "'")
+                        readData = .callBiocFun(
+                            getFunction(funcName, where=e,mustFind=TRUE), args)
+                        return(.insertPEP(readData, p))
+                    }
+                    # the function indicated in FUNCTION_NAME was not found, 
+                    # use the last one in FUNCTION_PATH
+                    message("Multiple functions found in '", funcPath, "'. Using the last one.")
+                    readData = .callBiocFun(lastFun, args)
                     return(.insertPEP(readData, p))
                 }else{
                     warning("Can't find function in the environment and the value for '"
@@ -189,6 +201,12 @@ BiocProject = function(file, subproject = NULL, autoLoad = TRUE, func = NULL,
 #' into the metadata slot of objects that 
 #' extend the \code{\link[S4Vectors]{Annotated-class}}
 #' 
+#' Additionally, if the object extends the 
+#' \code{\link[S4Vectors]{Annotated-class}} (or is a list that will be
+#' automatically converted to a \code{\link[S4Vectors]{List}}) the show method 
+#' for its class is redefined to display the \code{\link[pepr]{Project-class}} 
+#' as the metadata.
+#' 
 #' @param object an object of \code{\link[S4Vectors]{Annotated-class}}
 #' @param pep an object of class \code{\link[pepr]{Project-class}}
 #' 
@@ -211,14 +229,18 @@ BiocProject = function(file, subproject = NULL, autoLoad = TRUE, func = NULL,
     if(!methods::is(pep, "Project")) 
         stop("the pep argument has to be of class 'Project', 
             got '", class(pep),"'")
+    # do we throw a warning/message saying what happens in the next line?
+    if(methods::is(object, "list"))
+        object = S4Vectors::List(object)
     if(methods::is(object, "Annotated")){
         S4Vectors::metadata(object) = list(PEP=pep)
-        object
-    }else{
-        warning("The 'object' argument has to be of class 'Annotated', got '",
-                class(object),"'")
+    } else{
+        warning("BiocProject expects data loading functions to return an 'Annotated' object, but your function returned a '",
+                class(object),"' object. To use an Annotated, this returned object has been placed in the first slot of a List")
         result = S4Vectors::List(result=object)
         S4Vectors::metadata(result) = list(PEP=pep)
-        result
+        object = result
     }
+    .setShowMethod(object)
+    object
 }

R/utils.R

@@ -132,3 +132,37 @@
     })))
 }
 
+#' Redefine the show method of the object
+#' 
+#' Adds the Project objects display to the default show method of an \code{\link[S4Vectors]{Annotated-class}}
+#' 
+#' The method is defined in the environment in which the function was called, see: \code{\link[base]{sys.parent}}
+#' 
+#' @param returnedObject object of \code{\link[S4Vectors]{Annotated-class}}
+#' 
+#' @return \code{FALSE} if the function was not set
+#'
+#' @export
+#'
+#' @examples
+#' x = S4Vectors::List(c("so","cool"))
+#' metadata(x) = list(PEP=pepr::Project())
+#' .setShowMethod(x)
+#' x
+.setShowMethod = function(returnedObject) {
+    oriClass = class(returnedObject)
+    if(!is(returnedObject,"Annotated")){
+        warning("The show method was not redefined for '", oriClass, "'")
+        return(FALSE)
+    }
+    oriShow =  selectMethod("show", oriClass)
+    # the new method is created only if the environment of the original one is locked.
+    # this way the method will not be redefined over and over again when the BiocProject functon is called.
+    if(environmentIsLocked(environment(oriShow)))
+        setMethod("show", signature = oriClass, definition = function(object){
+            do.call(oriShow, list(object))
+            pep = getProject(object)
+            cat("\nmetadata: ")
+            selectMethod("show","Project")(pep)
+        }, where = parent.frame())
+}

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

@@ -1,5 +1,5 @@
 metadata:
-  sample_annotation: sample_annotation.csv
+  sample_table: sample_table.csv
 
 bioconductor:
   readFunName: readBedFiles

inst/extdata/example_peps-master/example_BiocProject/project_config_resize.yaml

@@ -1,5 +1,5 @@
 metadata:
-  sample_annotation: sample_annotation.csv
+  sample_table: sample_table.csv
 
 bioconductor:
   readFunName: readBedFiles_resize

inst/extdata/example_peps-master/example_BiocProject/readBedFiles_resize.R

@@ -11,4 +11,4 @@ readBedFiles_resize = function(project, resize.width) {
   setwd(cwd)
   names(result) = sampleNames
   return(GenomicRanges::GRangesList(result))
-}
+}

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

@@ -1,5 +1,5 @@
 metadata:
-  sample_annotation: sample_annotation.csv
+  sample_table: sample_table.csv
 
 bioconductor:
   readFunName: readBedFilesExceptions

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

@@ -1,5 +1,5 @@
 metadata:
-  sample_annotation: sample_annotation.csv
+  sample_table: sample_table.csv
 
 bioconductor:
   readFunName: readRemoteData

inst/extdata/example_peps-master/example_BiocProject_remote/project_config_resize.yaml

@@ -1,5 +1,5 @@
 metadata:
-  sample_annotation: sample_annotation.csv
+  sample_table: sample_table.csv
 
 bioconductor:
   read_fun_name: readRemoteData_resize

inst/test_projects/faulty_project/project_config_no_function.yaml

@@ -1,7 +1,7 @@
 # This is a faulty PEP.
 # The readFunName and readFunPath values point to function that does not exist
 metadata:
-  sample_annotation: sample_annotation.csv
+  sample_table: sample_table.csv
 
 bioconductor:
   readFunName: readBedFiles_missing

inst/test_projects/faulty_project/project_config_no_section.yaml

@@ -1,4 +1,4 @@
 # This is a faulty PEP.
 # The bioconductor section does not exist
 metadata:
-  sample_annotation: sample_annotation.csv
+  sample_table: sample_table.csv

tests/testthat/test_all.R

@@ -187,11 +187,6 @@ test_that("BiocProject function throws a warning and returns a Project object
     expect_warning(expect_is(BiocProject(configFileNoSection),"Project"))
 })
 
-test_that("BiocProject function throws an error 
-          when nonexistent subproject is provided",{
-    expect_error(expect_warning(BiocProject(configFile, subproject = "test")))
-})
-
 context("Test Annotated methods")
 
 test_that("samples returns a correct object", {