change people functions to synapser (#168)

* change people functions to synapser

* add synapser remote

* Add synapser update ci (#170)

* Respecify OS versions for Mac and Windows

* Add fallback deps install

* Upgrade step version

---------

Co-authored-by: Anh Nguyet Vu <[email protected]>

.github/workflows/R-CMD-check.yaml

@@ -18,8 +18,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release'}
+          - {os: macOS-13,   r: 'release'}
+          - {os: windows-2022, r: 'release'}
           - {os: ubuntu-latest,   r: 'devel', http-user-agent: 'release'}
           - {os: ubuntu-latest,   r: 'release'}
           - {os: ubuntu-latest,   r: 'oldrel-1'}
@@ -29,7 +29,7 @@ jobs:
       R_KEEP_PKG_SOURCE: yes
 
     steps:
-      - uses: actions/checkout@v2
+      - uses: actions/checkout@v4
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -40,9 +40,18 @@ jobs:
           use-public-rspm: true
 
       - uses: r-lib/actions/setup-r-dependencies@v2
+        id: install-deps
+        continue-on-error: true
         with:
           extra-packages: any::rcmdcheck
           needs: check
+
+      - name: If source build fails on macOS or Windows, fall back to typical install
+        if: steps.install-deps.outcome == 'failure'
+        shell: Rscript {0}
+        run: |
+          reticulate::install_miniconda()
+          install.packages("synapser", repos="http://ran.synapse.org")
 
       - uses: r-lib/actions/check-r-package@v2
         with:

DESCRIPTION

@@ -40,7 +40,8 @@ Imports:
     emoji,
     plyr,
     readxl,
-    yaml
+    yaml,
+    synapser (>= 1.0.0)
 URL: https://github.com/nf-osi/nfportalutils
 BugReports: https://github.com/nf-osi/nfportalutils/issues
 Suggests: 
@@ -50,3 +51,5 @@ Suggests:
     withr
 Config/testthat/edition: 2
 VignetteBuilder: knitr
+Remotes:  
+    github::Sage-Bionetworks/synapser

R/add_publication_from_unpaywall.R

@@ -130,20 +130,4 @@ add_publication_from_unpaywall <- function(publication_table_id,
       }
     }}
 
-#' Adds a row to a table.
-#' @param schema A synapse table Schema object.
-#' @param new_row A data frame of one or more rows that match the provided schema.
-#' @export
-.store_rows <- function(schema, new_row){
-
-  table <- .syn$store(synapseclient$Table(schema, new_row))
-
-}
-
-# .pluck_column_type_and_name <- function(column){
-#   coltype <- purrr::pluck(column, "columnType")
-#   name <- purrr::pluck(column, "name")
-#
-#   c(coltype, name)
-# }
 

R/basic_utils.R

@@ -82,3 +82,21 @@ walk <- function(syn_id, as_list = TRUE) {
 
 }
 
+
+#' Adds a row to a table.
+#' @param schema A synapse table Schema object.
+#' @param new_row A data frame of one or more rows that match the provided schema.
+#' @export
+.store_rows <- function(schema, new_row){
+
+  table <- synapser::synStore(synapser::Table(schema, new_row))
+
+}
+
+# .pluck_column_type_and_name <- function(column){
+#   coltype <- purrr::pluck(column, "columnType")
+#   name <- purrr::pluck(column, "name")
+#
+#   c(coltype, name)
+# }
+

R/login.R

@@ -1,9 +1,9 @@
 #' Logs into Synapse.
-#' 
+#'
 #' Wrapper around https://python-docs.synapse.org/build/html/index.html#synapseclient.Synapse.login
 #' Username and password authentication is not supported.
 #' Recommendation is to store `SYNAPSE_AUTH_TOKEN` in environment, so login can be used simply as `syn_login()`.
-#'  
+#'
 #' @param authtoken Uses `SYNAPSE_AUTH_TOKEN` environmental variable, or a personal access token (PAT) can be provided.
 #' @examples
 #' \dontrun{
@@ -22,9 +22,7 @@ syn_login <- function(authtoken = Sys.getenv("SYNAPSE_AUTH_TOKEN")){
 #' @returns A message.
 #' @keywords internal
 .check_login <- function(){
-  if(!exists(".syn")){
-    stop('Please run `nfportalutils::syn_login()` prior to running functions that require a connection to Synapse. (Alternatively, the Python `synapseclient` is unavailable.)')
-  }else if(capture.output(.syn) == "<pointer: 0x0>"){
-    stop('Please run `nfportalutils::syn_login()` prior to running functions that require a connection to Synapse. (Alternatively, the Python `synapseclient` is unavailable.)')
+  if(!exists(".syn") & !exists("syn")){
+    stop('Please run `nfportalutils::syn_login()` or `synapser::synLogin()` prior to running functions that require a connection to Synapse. (Alternatively, the Python `synapseclient` is unavailable.)')
   }
 }

R/update_people_table.R

@@ -1,7 +1,7 @@
 #' Update the People table from a source Table or View column
-#' 
+#'
 #' @param people_table_id The synapse id of the table used for referencing people.
-#' @param people_column Column name within the people table that contains the relevant people values. 
+#' @param people_column Column name within the people table that contains the relevant people values.
 #' @param source_table_id The synapse id of the source table.
 #' @param source_column Column name within the source table that contains the relevant source values.
 #' @inheritParams update_study_annotations
@@ -15,15 +15,17 @@ add_people_from_table <- function(people_table_id, people_column, source_table_i
   #get current people ids
   old_people_query <- glue::glue("select {people_column} from {people_table_id}")
 
-  old_people <- .syn$tableQuery(old_people_query)$asDataFrame() %>%
+  old_people <- synapser::synTableQuery(old_people_query, includeRowIdAndRowVersion	= F)$asDataFrame() %>%
+    tibble::as_tibble() %>%
     dplyr::distinct()
 
   old_ids <- old_people[[{{people_column}}]]
 
   #get ids from new source table
   new_people_query <- glue::glue("select {source_column} from {source_table_id}")
 
-  new_people <- .syn$tableQuery(new_people_query)$asDataFrame() %>%
+  new_people <- synapser::synTableQuery(new_people_query, includeRowIdAndRowVersion	= F)$asDataFrame() %>%
+    tibble::as_tibble() %>%
     dplyr::distinct() %>%
     dplyr::filter(!(!!rlang::sym(source_column)) %in% old_ids) %>%   #filter out existing ids
     purrr::pluck(source_column)
@@ -32,7 +34,7 @@ add_people_from_table <- function(people_table_id, people_column, source_table_i
 
   new_rows <- tibble::tibble(!!people_column := new_people)
 
-  schema <- .syn$get(people_table_id)
+  schema <- synapser::synGet(people_table_id)
 
   if(dry_run == F){
     .store_rows(schema, new_rows)