Merge branch 'develop' into patch/nf-anno-utils

R/basic_utils.R

@@ -53,7 +53,7 @@ dt_read <- function(file) {
 bare_syn_id <- function(uri) {
   not_na <- which(!is.na(uri))
   x <- uri[not_na]
-  syn <- regmatches(x, regexpr("syn[0-9]{8,12}", x))
+  syn <- regmatches(x, regexpr("syn[0-9]{7,12}", x))
   uri[not_na] <- syn
   return(uri)
 }
@@ -65,7 +65,6 @@ bare_syn_id <- function(uri) {
 #' @keywords internal
 is_valid_syn_id <- function(id) {
   result <- grepl("^syn[0-9]{4,}$", id)
-  result
 }
 
 #' Walk through a directory

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,
                         ...) {
@@ -73,13 +77,41 @@ 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"]]
+  data_folder_id <- folders[["Raw Data"]]$properties$id
+
+  # Bind JSON schema so children folders have NF's dataset schemas, see
+  # https://repo-prod.prod.sagebase.org/repo/v1/schema/type/registered/org.synapse.nf-superdataset
+  # and https://help.synapse.org/docs/JSON-Schemas.3107291536.html
+  bind_schema_request <- jsonlite::toJSON(list(entityId = data_folder_id,
+                                               `schema$id` = "org.synapse.nf-superdataset",
+                                               enableDerivedAnnotations = TRUE),
+                                          auto_unbox = TRUE)
+  binding_uri <- glue::glue("https://repo-prod.prod.sagebase.org/repo/v1/entity/{data_folder_id}/schema/binding")
+  try(.syn$restPUT(binding_uri, bind_schema_request))
 
   # Create data-specific folders in "Raw Data"
   if(length(datasets)) {
-    make_folder(parent = data_folder$properties$id, folders = datasets)
+    make_folder(parent = data_folder_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

R/register_study.R

@@ -60,7 +60,10 @@ add_new_study_meta <- function(id, study_meta) {
     "dataStatus",
     "grantDOI",
     "relatedStudies",
-    "studyFileviewId")]
+    "studyFileviewId",
+    "grantStartDate",
+    "grantEndDate",
+    "embargoEndDate")]
 
   if(is.null(study_meta$studyStatus) || is.na(study_meta$studyStatus)) study_meta$studyStatus <- "Active"
   if(is.null(study_meta$dataStatus) || is.na(study_meta$dataStatus)) study_meta$dataStatus <- "Data Pending"
@@ -95,7 +98,7 @@ add_study_summary <- function(study_id, summary, table_id = "syn16787123") {
   BASE_URL <- "https://repo-prod.prod.sagebase.org/repo/v1"
   url <- glue::glue("{BASE_URL}/entity/{table_id}/table/transaction/async/start")
 
-  studyId_col_model <- "82658"
+  studyId_col_model <- "82686"
   summary_col_model <- "82091"
 
   new_row <- list(etag = NULL,

R/wiki_mod.R

@@ -114,7 +114,7 @@ data_curator_app_subpage <- function(project_id, dry_run = TRUE) {
   subpage <- "NF Data Curator App"
   # Default buttons and links
   app_label <- "App"
-  app_url <- "https://shiny.synapse.org/users/rallaway/NF_data_curator"
+  app_url <- "https://dca.app.sagebionetworks.org/"
   app_btn <- button_widget(label = app_label, url = app_url)
 
   doc_label <- "Docs"