Merge a22985a into 70b793a

.travis.yml

@@ -4,10 +4,15 @@ cache: packages
 warnings_are_errors: false
 r_packages: devtools
 r_github_packages: 
-  - pepkit/pepr
+  #- pepkit/pepr
   - databio/simpleCache
+  - r-lib/covr
 bioc_packages: 
   - GenomicRanges
   - BiocStyle
   - BiocFileCache
+before_install:
+  - Rscript -e 'install.packages("devtools");devtools::install_github(repo = "pepkit/pepr",ref = "dev")'
+after_success:
+  - Rscript -e 'covr::coveralls()'
 

DESCRIPTION

@@ -1,23 +1,23 @@
 Package: BiocProject
 Title: Bioconductor Management with Portable Encapsulated Project (PEP) Objects
-Version: 0.2
-Authors@R: c(person("Michal", "Stolarczyk", email = "mjs5kd@virginia.edu",role = c("aut", "cre")), 
+Version: 0.2.1
+Authors@R: c(person("Michal", "Stolarczyk", email = "michal@virginia.edu",role = c("aut", "cre")), 
 	person("Nathan", "Sheffield", email = "nathan@code.databio.org",role = c("aut")))
 Description: A Bioconductor-oriented project management class. It wraps the
 	generic pepr R package for project metadata. BiocProject allows you to read 
 	in project metadata and data for an entire project with a single line of R code.
-License: GPL-3
+License: BSD_2_clause + file LICENSE
 Encoding: UTF-8
 LazyData: true
-Depends: S4Vectors, pepr, methods
+Depends: S4Vectors, pepr, methods, glue, RCurl
 Suggests:
     knitr,
     rmarkdown,
     testthat,
     yaml
 Enhances: BiocFileCache, simpleCache, GenomicRanges
 biocViews: DataImport, DataRepresentation
-RoxygenNote: 6.1.1
-URL: https://github.com/pepkit/BiocProject
-BugReports: https://github.com/pepkit/BiocProject
+RoxygenNote: 7.0.2
+URL: http://code.databio.org/BiocProject/
+BugReports: https://github.com/pepkit/BiocProject/issues
 VignetteBuilder: knitr

LICENSE

@@ -0,0 +1,2 @@
+YEAR: 2018
+COPYRIGHT HOLDER: Nathan Sheffield

NAMESPACE

@@ -1,13 +1,24 @@
 # Generated by roxygen2: do not edit by hand
 
 export(.insertPEP)
+export(.pyToR)
 export(.setShowMethod)
-export(.updateList)
+export(.unionList)
 export(BiocProject)
+export(gatherPipelineInterfaces)
+export(getOutputsBySample)
+export(getProjectOutputs)
+export(pipelineInterfacesBySample)
+export(readSchema)
 exportMethods(config)
 exportMethods(getProject)
 exportMethods(is)
-exportMethods(samples)
+exportMethods(sampleTable)
 import(S4Vectors)
 import(methods)
 import(pepr)
+importFrom(RCurl,getURLContent)
+importFrom(glue,glue)
+importFrom(methods,new)
+importFrom(pepr,checkSection)
+importFrom(pepr,config)

NEWS.md

@@ -1,3 +1,13 @@
+# BiocProject 0.2.1 - unreleased
+
+## Added
+
+* pipeline interface support, including functions: `getPipelineInterfaces`, `outputsByPipeline`, `outputsByProtocol`, `getPipelines`,`getProtocolMappings` and `samplesByProtocol`
+
+## Changed
+
+* the `bioconductor` section can be provided in either in the pipeline interface or in the project config. The project config location is given the priority 
+
 # BiocProject 0.2 - 2019-04-19
 
 ## Added

R/constants.R

@@ -8,7 +8,19 @@
 #   FUNCTION_ARGS:
 #       <arg1>: <val1>
 #       <arg2>: <val2>
-MAIN_SECTION = "bioconductor"
+BIOC_SECTION = "bioconductor"
 FUNCTION_ARGS = "funcArgs"
 FUNCTION_PATH = "readFunPath"
 FUNCTION_NAME = "readFunName"
+
+# other constants
+S_PIP_SECTION = "sample_pipeline"
+P_PIP_SECTION = "project_pipeline"
+PROTO_MAP_SECTION = "protocol_mapping"
+COLL_MAP_SECTION = "collator_mappings"
+OUTPUT_SCHEMA_SECTION = "output_schema"
+LOOPER_SECTION = "looper"
+PIP_IFACE_NAME = "pipeline_interfaces"
+PIP_IFACE_KEY = "pipeline_interfaces_key"
+SCHEMA_SAMPLE_OUTS = c("properties", "samples", "items", "properties")
+PIP_IFACE_SECTION = c(LOOPER_SECTION, PIP_IFACE_NAME)

R/functions.R

@@ -41,6 +41,7 @@
 #' If the \code{autoLoad} is set to \code{FALSE} the data will not be loaded 
 #' and empty \code{\link[pepr]{Project-class}} object will be returned.
 #' 
+#' @note The \code{bioconductor} section can be read from the project config file or pipeline interface. The former is given the priority
 #' 
 #' @section Further reading: 
 #' Browse the 
@@ -49,7 +50,7 @@
 #'
 #'
 #' @param file a character vector with a path to the PEP config file
-#' @param subproject a character vector with a name of the subproject
+#' @param amendments a character vector with a name of the subproject
 #' to be activated
 #' @param func a anonymous function that reads and/or processess the data, 
 #' it must take 
@@ -63,14 +64,18 @@
 #'  the \code{bioconductor} section in the config file.
 #' @param autoLoad a logical indicating whether the data should be loaded
 #'  automatically. See \code{Details} for more information.
+#' @param pipelineName a string indicating the name of the pipeline in the 
+#'  pipeline interface. It is used for the \code{bioconductor} section 
+#'  selection. If none provided and there's no \code{bioconductor} section in 
+#'  the config file, the first pipeline in the pipeline interface will be used. 
 #'
 #' @return an object of \code{\link[S4Vectors]{Annotated-class}} that is 
 #' returned by the user provided function with 
 #' the \code{\link[pepr]{Project-class}} object inserted into the first 
 #' element of the list in its medatada slot 
 #' 
 #' @examples 
-#' projectConfig = system.file("extdata", "example_peps-master",
+#' projectConfig = system.file("extdata", "example_peps-cfg2",
 #' "example_BiocProject", "project_config.yaml", package="BiocProject")
 #' bp=BiocProject(projectConfig)
 #' 
@@ -81,27 +86,31 @@
 #' @seealso \url{https://pepkit.github.io/}
 #' @import pepr
 #' @export BiocProject
-BiocProject = function(file, subproject = NULL, autoLoad = TRUE, func = NULL, 
-                        funcArgs = NULL) {
-    p = pepr::Project(file=file, subproject=subproject)
+BiocProject = function(file, amendments = NULL, autoLoad = TRUE, func = NULL, 
+                        funcArgs = NULL, projectLevel = FALSE) {
+    p = pepr::Project(file=file, amendments = amendments)
     # prevent PEP (Project object) input. This prevents BiocProject object
     # failing when the user provides the Project object
     if(is.null(funcArgs)){
         funcArgs = list()
     }else{
-        if (length(.findProjectInList(funcArgs)) > 0) 
+        if (length(.findProjectInList(funcArgs)) > 0) {
+            warning("Project object was found in the arguments list. It will be removed.")
             funcArgs = funcArgs[-.findProjectInList(funcArgs)]
+        }
     }
     args = append(list(p), funcArgs)
-    if(pepr::checkSection(pepr::config(p), c(MAIN_SECTION, FUNCTION_ARGS))){
-        args = .updateList(config(p)[[MAIN_SECTION]][[FUNCTION_ARGS]],args)
+    cfg = .getBiocConfig(p, projectLevel)
+    if(is.null(cfg))
+        cfg = pepr::config(p)
+    if(pepr::.checkSection(cfg, c(BIOC_SECTION, FUNCTION_ARGS))){
+        args = .unionList(config(p)[[BIOC_SECTION]][[FUNCTION_ARGS]],args)
         argsNames = names(args)
         project = args[[.findProjectInList(args)]]
         argsNames = append("",argsNames[-.findProjectInList(args)])
         args = append(list(p), args[[-.findProjectInList(args)]])
         names(args) = argsNames
     }
-
     if (!is.null(func)) {
         # use the anonymous function if provided
         if (is.function(func)) {
@@ -116,14 +125,14 @@ 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
-            if(!pepr::checkSection(pepr::config(p), MAIN_SECTION)){
+            # check if the config consists of BIOC_SECTION section
+            if(!pepr::.checkSection(cfg, BIOC_SECTION)){
                 message("No data was read. Returning a Project object")
                 warning("The config YAML is missing the '",
-                        MAIN_SECTION,"' section.")
+                        BIOC_SECTION,"' section.")
                 return(p)
             }    
-            funcName = pepr::config(p)[[MAIN_SECTION]][[FUNCTION_NAME]]
+            funcName = cfg[[BIOC_SECTION]][[FUNCTION_NAME]]
             # check if the function name was provided
             # and if it exists in the environment
             if (!is.null(funcName) && exists(funcName)) {
@@ -132,7 +141,8 @@ BiocProject = function(file, subproject = NULL, autoLoad = TRUE, func = NULL,
                 message("Used function '", funcName, "' from the environment")
                 return(.insertPEP(readData, p))
             }else{
-                if (!is.null(funcName) && length(grep("(\\:){2,3}", funcName)) != 0) {
+                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]]
@@ -147,10 +157,10 @@ BiocProject = function(file, subproject = NULL, autoLoad = TRUE, func = NULL,
                 # trying to source the file specified 
                 # in the config.yaml FUNCTION_PATH
                 funcPath = pepr::.expandPath(
-                    pepr::config(p)[[MAIN_SECTION]][[FUNCTION_PATH]])
+                    cfg[[BIOC_SECTION]][[FUNCTION_PATH]])
                 if (!is.null(funcPath)){
                     if (!file.exists(funcPath))
-                        funcPath = .makeAbsPath(funcPath,dirname(p@file))
+                        funcPath = .makeAbsPath(funcPath, dirname(p@file))
                     if (!file.exists(funcPath))
                         stop(
                             "The function does not exist in the environment and file '",
@@ -193,54 +203,4 @@ BiocProject = function(file, subproject = NULL, autoLoad = TRUE, func = NULL,
             return(p)
         }
     }
-}
-
-#' Insert a PEP metadata in a metadata slot of Annotated
-#' 
-#' This function inserts the PEP (\code{\link[pepr]{Project-class}}) 
-#' 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}}
-#' 
-#' @return an object of the same class as the object argument but enriched
-#'  with the metadata from the pep argument
-#' 
-#' @examples 
-#' # If the object is of class Annotated
-#' object = S4Vectors::List(result="test")
-#' result = .insertPEP(object, pepr::Project())
-#' metadata(result)
-#' 
-#' # If the object is not of class Annotated
-#' object1 = "test"
-#' result1 = .insertPEP(object1, pepr::Project())
-#' metadata(result1)
-#' @import S4Vectors methods
-#' @export
-.insertPEP = function(object, pep) {
-    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)
-    } 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)
-        object = result
-    }
-    .setShowMethod(object)
-    object
-}
+}

R/methods_Annotated.R

@@ -22,7 +22,7 @@ setMethod(".is.project","Annotated",function(.Object){
 #' @return an object of \code{\link[pepr]{Project-class}}
 #' 
 #' @examples
-#' projectConfig = system.file("extdata", "example_peps-master",
+#' projectConfig = system.file("extdata", "example_peps-cfg2",
 #' "example_BiocProject", "project_config.yaml", package="BiocProject")
 #' p=BiocProject(projectConfig)
 #' getProject(p)
@@ -51,17 +51,17 @@ setMethod("getProject","Annotated",function(.Object){
 #'
 #' @return a data.table with the with metadata about samples
 #' @examples
-#' projectConfig = system.file("extdata", "example_peps-master",
+#' projectConfig = system.file("extdata", "example_peps-cfg2",
 #' "example_BiocProject", "project_config.yaml", package="BiocProject")
 #' p=BiocProject(projectConfig)
-#' samples(p)
+#' sampleTable(p)
 #' @import pepr
 #' @export
 setMethod(
-    f = "samples",
+    f = "sampleTable",
     signature = "Annotated",
     definition = function(object) {
-        pepr::samples(getProject(object))
+        pepr::sampleTable(getProject(object))
     })
 
 
@@ -76,7 +76,7 @@ setMethod(
 #' @return a list with the config file
 #'
 #' @examples
-#' projectConfig = system.file("extdata", "example_peps-master",
+#' projectConfig = system.file("extdata", "example_peps-cfg2",
 #' "example_BiocProject", "project_config.yaml", package="BiocProject")
 #' p=BiocProject(projectConfig)
 #' config(p)