New project - other resources (#184)

* Issue #149

* Update

* Update

* Docs

DESCRIPTION

@@ -14,7 +14,7 @@ License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
 Roxygen: list(markdown = TRUE)
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports: 
     dplyr,
     data.table,

R/new_project.R

@@ -18,7 +18,10 @@
 #' @param institution Affiliated institution(s), **semicolon-sep if multiple**, e.g. "Stanford University; University of California, San Francisco".
 #' @param funder The funding agency. The relevant funder team will be made admin.
 #' @param initiative Title of funding initiative, e.g. "Young Investigator Award".
-#' @param datasets (Optional) Datasets for which folders will be created under main data folder ("Raw Data").
+#' @param datasets (Optional) List of datasets for which folders will be created under main data folder ("Raw Data").
+#' Attributes set on the list items become annotations on the dataset folders.
+#' @param other_resources (Optional) List of non-data resource types for which folders will be created.
+#' Attributes set on the list items become annotations on these folders.
 #' @param publicview Whether to put this project in the public view instead of staying private (registered or non-registered users can see project).
 #' @param webview Whether to open web browser to view newly created project. Defaults to FALSE.
 #' @param ... Additional arguments. Not used.
@@ -33,6 +36,7 @@ new_project <- function(name,
                         funder,
                         initiative,
                         datasets = NULL,
+                        other_resources = NULL,
                         publicview = FALSE,
                         webview = FALSE,
                         ...) {
@@ -73,6 +77,19 @@ new_project <- function(name,
   }
 
   # ASSETS ---------------------------------------------------------------------#
+
+  # Folder structure looks something like this,
+  # where * elements are conditionally present on data given:
+  #├── Analysis
+  #├── Milestone Reports
+  #├── Protocols*
+  #├── Raw Data
+  #│   ├── IHC dataset*
+  #│   └── RNA-seq dataset*
+  #└── Scripts*
+
+  # Note that all protocol files, etc. is expected to live in a single protocol folder and not further nested.
+
   # Create default upper-level folders
   folders <- add_default_folders(project)
   data_folder <- folders[["Raw Data"]]
@@ -82,6 +99,11 @@ new_project <- function(name,
     make_folder(parent = data_folder$properties$id, folders = datasets)
   }
 
+  # Create homes for non-data resources alongside "Raw Data"
+  if(length(other_resources)) {
+    make_folder(parent = project, folders = other_resources)
+  }
+
   # Add Project Files and Metadata fileview, add NF schema; currently doesn't add facets
   fv <- add_default_fileview(project)