Merge 2d8299a into 40cb416

.gitignore

@@ -2,3 +2,12 @@
 .Rhistory
 .RData
 .Ruserdata
+*DS_Store
+*DS_Store?
+._*
+.Spotlight-V100
+.Trashes
+ehthumbs.db
+Thumbs.db
+pepr.Rproj
+docs

.travis.yml

@@ -1,6 +1,6 @@
-language: R
+language: r
+os: "linux"
 warnings_are_errors: false
-sudo: false
 cache: packages
 r_packages: devtools
 r_github_packages: 

DESCRIPTION

@@ -1,10 +1,10 @@
 Package: pepr
 Type: Package
 Title: Reading Portable Encapsulated Projects
-Version: 0.2.2
+Version: 0.3.0
 Date: 2019-06-21
 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org",
-    role = c("aut", "cre")),person("Michal","Stolarczyk",email="mjs5kd@virginia.edu",role=c("ctb")))
+    role = c("aut", "cph")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut","cre")))
 Maintainer: Nathan Sheffield <nathan@code.databio.org>
 Description: Reads standardized project configuration files into R.
 Imports:
@@ -19,4 +19,4 @@ Suggests:
 VignetteBuilder: knitr
 License: BSD_2_clause + file LICENSE
 BugReports: https://github.com/pepkit/pepr
-RoxygenNote: 6.1.1
+RoxygenNote: 7.0.2

NAMESPACE

@@ -3,16 +3,17 @@
 export(.expandPath)
 export(.listifyDF)
 export(.printNestedList)
-export(.sanitizeConfig)
 export(.strformat)
+export(Config)
 export(Project)
-export(activateSubproject)
+export(activateAmendments)
 export(config)
 export(fetchSamples)
 export(getSample)
 export(getSubsample)
-export(listSubprojects)
-export(samples)
+export(listAmendments)
+export(makeSectionsAbsolute)
+export(sampleTable)
 exportClasses(Config)
 exportClasses(Project)
 exportMethods(checkSection)

R/config.R

@@ -0,0 +1,293 @@
+setMethod("initialize", "Config", function(.Object, data) {
+  .Object = methods::callNextMethod(.Object, data)  # calls list initialize
+  .Object = .reformat(.Object)
+  return(.Object)
+})
+
+
+#'  The constructor of a class representing PEP config
+#'
+#' @param file a character with project configuration yaml file
+#' @param amendments a character with the amendments names to be activated
+#'
+#' @return
+#' @examples
+#' projectConfig = system.file("extdata", "example_peps-cfg2",
+#' "example_amendments1", "project_config.yaml", package="pepr")
+#' c=Config(projectConfig)
+#' @export
+Config = function(file, amendments = NULL){
+  message("Loading config file: ", file)
+  cfg_data = .loadConfig(filename=file, amendments=amendments)
+  config = methods::new("Config",data=cfg_data)
+  config = makeSectionsAbsolute(config, REQ_ABS, file)
+  .listAmendments(config)
+  return(config)
+}
+
+
+#' Config objects are specialized list objects
+#'
+#' Config objects are used with the \code{\link{Project-class}} objects
+#'
+#' @exportClass Config
+setClass("Config", contains = "list")
+
+# Override the standard generic show function for our config-style lists
+setMethod(
+  "show",
+  signature = "Config", 
+  definition = function(object) {
+    cat("Config object. Class:", class(object), fill = T)
+    .printNestedList(object)
+    invisible(NULL)
+  }
+)
+
+
+#' Make sections absolute in the config
+#' 
+#' @export
+setGeneric("makeSectionsAbsolute", function(object, sections, cfgPath)
+  standardGeneric("makeSectionsAbsolute"))
+
+setMethod(
+  "makeSectionsAbsolute", 
+  signature = signature(
+    object="Config", 
+    sections="character", 
+    cfgPath="character"
+    ), 
+  definition = function(object, sections, cfgPath) {
+    # Enable creation of absolute path using given parent folder path.
+    absViaParent = pryr::partial(.makeAbsPath, parent=dirname(cfgPath))
+    for(section in sections){
+      if (section %in% names(object)){
+        absSectionVals = c()
+        for (iSection in object[section]){
+          absSection = absViaParent(iSection)
+          absSectionVals = append(absSectionVals, absSection)
+        }
+        object[section] = absSectionVals
+      }
+    }
+  return(object)
+  }
+)
+
+
+#' Check config spec version and reformat if needed
+#'
+#' @param object an object of \code{\link{Config-class}} 
+#' 
+#' @return an object of \code{\link{Config-class}} 
+setGeneric(".reformat", function(object)
+  standardGeneric(".reformat"))
+
+setMethod(
+  ".reformat", 
+  signature = "Config", 
+  definition = function(object) {
+    if (CFG_VERSION_KEY %in% names(object)){
+      split = str_split(object[[CFG_VERSION_KEY]],"\\.")[[1]]
+      if (length(split) < 3) stop("PEP version string is not tripartite")
+      majorVer = as.numeric(split[1])
+      if (majorVer < 2){
+        if (CFG_MODIFIERS_KEY %in% names(object)){
+          stop("Project configuration file subscribes to specification 
+               >= 2.0.0, since ",CFG_MODIFIERS_KEY," section is defined. Set ",
+               CFG_VERSION_KEY, " to 2.0.0 in your config")
+        } else{
+          stop("Config file reformatting is not supported. 
+               Reformat the config manually.")
+        }
+      }
+    } else{
+      stop("Config file is missing ", CFG_VERSION_KEY, " key. 
+           Add it to the config manually.")
+    }
+    return(object)
+  }
+)
+
+
+setGeneric("checkSection", function(object, sectionNames)
+  standardGeneric("checkSection"))
+
+#' Check for existence of a section in the Project config
+#' 
+#' This function checks for the section/nested sections in the config YAML file.
+#'  Returns \code{TRUE} if it exist(s) or \code{FALSE} otherwise.
+#' 
+#' Element indices can be used instead of the actual names, see \code{Examples}.
+#' 
+#' @param object object of \code{\link[pepr]{Config-class}}
+#' @param sectionNames the name of the section or names of the 
+#'        nested sections to look for
+#' 
+#' @return a logical indicating whether the section exists
+#' 
+#' @examples
+#' projectConfig = system.file("extdata", "example_peps-cfg2",
+#' "example_amendments1", "project_config.yaml", package="pepr")
+#' p=Project(projectConfig)
+#' checkSection(config(p),sectionNames = c("amendments","newLib"))
+#' checkSection(config(p),sectionNames = c("amendments",1))
+#' @export
+setMethod(
+  "checkSection",
+  signature = "Config",
+  definition = function(object, sectionNames) {
+    # try co convert the section name to numeric, return original name if 
+    # not possible this enables the outer method to check the sections 
+    # existance by index and by name at the same time
+    tryToNum = function(x){
+        convertedX = suppressWarnings(as.numeric(x))
+        ifelse(!is.na(convertedX), convertedX, x)
+    }
+    testList = object
+    counter = 1
+    while (!is.na(sectionNames[counter])) {
+      item = tryToNum(sectionNames[counter])
+      if((!is.list(testList)) || is.null(testList[[item]])){
+        return(FALSE)
+      }
+      testList = testList[[item]]
+      counter = counter + 1
+    }
+    return(TRUE)
+  }
+)
+
+
+#' View PEP config of the object of \code{\link{Project-class}}
+#'
+#' This method can be used to view the config slot of
+#' the \code{\link{Project-class}} class
+#'
+#' @param object an object of \code{\link{Project-class}}
+#'
+#' @return a list with the config file
+#'
+#' @examples
+#' projectConfig = system.file("extdata", "example_peps-cfg2",
+#' "example_amendments1", "project_config.yaml", package="pepr")
+#' p=Project(projectConfig)
+#' config(p)
+#'
+#' @export
+setGeneric("config", function(object)
+  standardGeneric("config"))
+
+setMethod(
+  "config",
+  signature = "Project",
+  definition = function(object) {
+    object@config
+  }
+)
+
+#' Load the config of a PEP
+#'
+#' Loads a PEP config file
+#'
+#' @param amendments amendments to activate
+#' @param filename file path to config file
+#' 
+#' @seealso \url{https://pepkit.github.io/}
+.loadConfig = function(filename=NULL, amendments=NULL) {
+  if (!file.exists(filename)) {
+    stop("Config file found: ", filename)
+  }
+  # Initialize config object
+  cfg_data = yaml::yaml.load_file(filename)
+  if (!is.list(cfg_data))
+    stop("The config file has to be a YAML formatted file.
+         See: http://yaml.org/start.html")
+  # Update based on imports inm the config file
+  cfg_data = .applyImports(cfg_data, filename)
+  # Update based on amendments if any specified
+  cfg_data = .applyAmendments(cfg_data, amendments)
+  # make bioconductor$readFunPath value absolute, used in BiocProject
+  if(!is.null(cfg_data$bioconductor$readFunPath)){
+    path = gsub("\\./","",cfg_data$bioconductor$readFunPath)
+    cfg_data$bioconductor$readFunPath = 
+      .makeAbsPath(path, parent=dirname(filename))
+  }
+  cfg_data$name = .inferProjectName(cfg_data, filename)
+  return(cfg_data)
+}
+
+.listAmendments = 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
+  # is preferred
+  if(!style == "message"){
+    printFun = pryr::partial(cat, fill=T)
+  }else{
+    printFun = message
+  }
+  if (length(names(cfg$amendments)) > 0) {
+    # If there are any show a cat and return if needed
+    printFun("  amendments: ", paste0(names(cfg$amendments), collapse=","))
+    invisible(names(cfg$amendments))
+  } else{
+    # Otherwise return NULL for testing purposes
+    NULL
+  }
+}
+
+#' Apply amendments
+#' 
+#' Overwrite and/or add Project attributes from the amendments section
+#'
+#' @param cfg config
+#' @param amendments 
+#'
+#' @return
+.applyAmendments = function(cfg, amendments=NULL) {
+  if (!is.null(amendments)) {
+    for (amendment in amendments){
+      if (is.null(cfg$amendments[[amendment]])) {
+        warning("Amendment not found: ", amendment)
+        message("Amendment was not activated")
+        return(cfg)
+      }
+      cfg = utils::modifyList(cfg, cfg$amendments[[amendment]])
+      message("Activating amendment: ", amendment)
+    }
+  }
+  return(cfg)
+}
+
+#' Function for recursive config data imports
+#'
+#' @param cfg_data config data, possibly including imports statement
+#' @param filename path to the file to get the imports for
+#'
+#' @return config data enriched in imported sections, if imports existed in the
+#'  input
+.applyImports = function(cfg_data, filename){
+  if (!CFG_IMPORTS_KEY %in% names(cfg_data))
+    return(cfg_data)
+  for(externalPath in cfg_data[[CFG_IMPORTS_KEY]]){
+    externalPath=.makeAbsPath(externalPath, parent = dirname(filename))
+    extCfg = .loadConfig(filename = externalPath)  
+    cfg_data = utils::modifyList(cfg_data, extCfg)
+    message("  Loaded external config file: ", externalPath)
+  }
+  return(cfg_data)
+}
+
+#' Infer project name
+#' 
+#' Based on dedicated config section or PEP enclosing dir
+#'
+#' @param cfg config data
+#' @param filename path to the config file
+#'
+#' @return
+.inferProjectName = function(cfg, filename){
+  if (!is.null(cfg$name)) return(cfg$name)
+  return(basename(dirname(normalizePath(filename))))
+}

R/constants.R

@@ -1,4 +1,15 @@
-kOldPipelinesSection = "pipelines_dir"
-kRelativeToOutputDirMetadataSections = c("results_subdir", "submission_subdir")
-
-kRelativeToConfigSections = c("metadata", "pipeline_config")
+# constant variables declarations
+CFG_SAMPLE_TABLE_KEY = "sample_table"
+CFG_SUBSAMPLE_TABLE_KEY = "subsample_table"
+REQ_ABS = c(CFG_SAMPLE_TABLE_KEY, CFG_SUBSAMPLE_TABLE_KEY)
+CFG_VERSION_KEY = "pep_version"
+CFG_MODIFIERS_KEY = "sample_modifiers"
+CFG_APPEND_KEY = "append"
+CFG_IMPLY_KEY = "imply"
+CFG_DERIVE_KEY = "derive"
+CFG_IMPLY_THEN_KEY = "then"
+CFG_IMPLY_IF_KEY = "if"
+CFG_DERIVE_ATTRS_KEY = "attributes"
+CFG_DERIVE_SOURCES_KEY = "sources"
+CFG_IMPORTS_KEY = "imports"
+CFG_DUPLICATE_KEY = "duplicate"