Add pullProject() and saveProject()

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: pepr
 Type: Package
 Title: Reading Portable Encapsulated Projects
-Version: 0.5.0
-Date: 2023-11-16
+Version: 0.6.0
+Date: 2024-08-10
 Authors@R: c(person("Nathan", "Sheffield", email = "nathan@code.databio.org",
     role = c("aut", "cph","cre")),person("Michal","Stolarczyk",email="michal@virginia.edu",role=c("aut")))
 Maintainer: Nathan Sheffield <nathan@code.databio.org>
@@ -18,7 +18,9 @@ Imports:
     pryr,
     data.table,
     methods,
-    RCurl
+    RCurl,
+    tidyr,
+    httr
 Suggests:
     knitr,
     testthat,
@@ -27,5 +29,5 @@ Suggests:
 VignetteBuilder: knitr
 License: BSD_2_clause + file LICENSE
 BugReports: https://github.com/pepkit/pepr
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.2
 Encoding: UTF-8

NAMESPACE

@@ -18,16 +18,21 @@ export(getSample)
 export(getSubsample)
 export(listAmendments)
 export(makeSectionsAbsolute)
+export(pullProject)
 export(sampleTable)
+export(saveJWT)
+export(saveProject)
 exportClasses(Config)
 exportClasses(Project)
 exportMethods("$")
 exportMethods("[")
 exportMethods("[[")
 import(RCurl)
+import(httr)
 import(pryr)
 import(stringr)
 import(yaml)
 importFrom(methods,as)
 importFrom(methods,callNextMethod)
 importFrom(methods,is)
+importFrom(tidyr,unnest)

R/config.R

@@ -26,6 +26,11 @@ setMethod("initialize", "Config", function(.Object, data) {
 #' @export
 #' @rdname Config-class
 Config = function(file, amendments = NULL) {
+  ### if the config from the Project constructor is a list and not a filepath, it is from a PEP fetched from PEPhub
+  if (typeof(file) == 'list') {
+    config = methods::new("Config", data = file)
+    return(config)
+  }
   message("Loading config file: ", file)
   cfg_data = .loadConfig(filename = file, amendments = amendments)
   config = methods::new("Config", data = cfg_data)
@@ -58,7 +63,7 @@ setMethod(
 #' .expandList(x)
 #' @export
 #' @keywords internal
-.expandList <- function(x) {
+.expandList = function(x) {
   if (is.list(x))
     return(lapply(x, .expandList))
   if (length(x) > 1)
@@ -81,7 +86,7 @@ setMethod(
 #' .getSubscript(l, 1) == .getSubscript(l, "a")
 #' @export
 #' @keywords internal
-.getSubscript <- function(lst, i) {
+.getSubscript = function(lst, i) {
   if (is.character(i))
     return(grep(paste0("^", i, "$"), names(lst)))
   return(i)
@@ -135,7 +140,7 @@ setMethod("[[", "Config", function(x, i) {
 })
 
 
-.DollarNames.Config <- function(x, pattern = "")
+.DollarNames.Config = function(x, pattern = "")
   grep(paste0("^", pattern), grep(names(x), value = TRUE))
 
 #' @rdname select-config

R/constants.R

@@ -20,4 +20,5 @@ CFG_DUPLICATE_KEY = "duplicate"
 CFG_REMOVE_KEY = "remove"
 CFG_LOOPER_KEY = "looper"
 SAMPLE_NAME_ATTR = "sample_name"
-SUBSAMPLE_NAME_ATTR = "subsample_name"
+SUBSAMPLE_NAME_ATTR = "subsample_name"
+BASE_URL = "https://pephub-api.databio.org/api/v1/"

R/pepr.R

@@ -8,6 +8,8 @@
 #' @import yaml
 #' @import stringr
 #' @import pryr
+#' @import httr
+#' @importFrom tidyr unnest
 #'
 #' @references 
 #' GitHub: \url{https://github.com/pepkit/pepr}, Documentation: \url{https://code.databio.org/pepr/}