From 7a31fba64ac00b2273943eb9378e8de8f3f4834b Mon Sep 17 00:00:00 2001
From: Anh Nguyet Vu <32753274+anngvu@users.noreply.github.com>
Date: Wed, 17 Jul 2024 14:52:57 -0600
Subject: [PATCH] Downclimb in develop (#180)

* Revert "change people functions to synapser (#168)"

This reverts commit 4320d35b99b48466de41c5337e0ff6dd8da5b2f4.

* Update README
---
 .github/workflows/R-CMD-check.yaml | 15 +++------------
 DESCRIPTION                        |  5 +----
 R/add_publication_from_unpaywall.R | 16 ++++++++++++++++
 R/basic_utils.R                    | 18 ------------------
 R/login.R                          | 10 ++++++----
 R/update_people_table.R            | 12 +++++-------
 README.md                          | 12 +++++++++---
 man/dot-store_rows.Rd              |  2 +-
 8 files changed, 41 insertions(+), 49 deletions(-)

diff --git a/.github/workflows/R-CMD-check.yaml b/.github/workflows/R-CMD-check.yaml
index 0cbf1669..b2ebad68 100644
--- a/.github/workflows/R-CMD-check.yaml
+++ b/.github/workflows/R-CMD-check.yaml
@@ -18,8 +18,8 @@ jobs:
       fail-fast: false
       matrix:
         config:
-          - {os: macOS-13,   r: 'release'}
-          - {os: windows-2022, r: 'release'}
+          - {os: macOS-latest,   r: 'release'}
+          - {os: windows-latest, 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@v4
+      - uses: actions/checkout@v2
 
       - uses: r-lib/actions/setup-pandoc@v2
 
@@ -40,18 +40,9 @@ 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:
diff --git a/DESCRIPTION b/DESCRIPTION
index 526aaaba..9e74f721 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -40,8 +40,7 @@ Imports:
     emoji,
     plyr,
     readxl,
-    yaml,
-    synapser (>= 1.0.0)
+    yaml
 URL: https://github.com/nf-osi/nfportalutils
 BugReports: https://github.com/nf-osi/nfportalutils/issues
 Suggests: 
@@ -51,5 +50,3 @@ Suggests:
     withr
 Config/testthat/edition: 2
 VignetteBuilder: knitr
-Remotes:  
-    github::Sage-Bionetworks/synapser
diff --git a/R/add_publication_from_unpaywall.R b/R/add_publication_from_unpaywall.R
index b4269b2d..28c33b3d 100644
--- a/R/add_publication_from_unpaywall.R
+++ b/R/add_publication_from_unpaywall.R
@@ -130,4 +130,20 @@ 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)
+# }
 
diff --git a/R/basic_utils.R b/R/basic_utils.R
index b80d51c7..99308fcb 100644
--- a/R/basic_utils.R
+++ b/R/basic_utils.R
@@ -82,21 +82,3 @@ 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)
-# }
-
diff --git a/R/login.R b/R/login.R
index 9225a677..374fa970 100644
--- a/R/login.R
+++ b/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{
@@ -22,7 +22,9 @@ syn_login <- function(authtoken = Sys.getenv("SYNAPSE_AUTH_TOKEN")){
 #' @returns A message.
 #' @keywords internal
 .check_login <- function(){
-  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.)')
+  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.)')
   }
 }
diff --git a/R/update_people_table.R b/R/update_people_table.R
index e575f70f..d1fee286 100644
--- a/R/update_people_table.R
+++ b/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
@@ -15,8 +15,7 @@ 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 <- synapser::synTableQuery(old_people_query, includeRowIdAndRowVersion	= F)$asDataFrame() %>%
-    tibble::as_tibble() %>%
+  old_people <- .syn$tableQuery(old_people_query)$asDataFrame() %>%
     dplyr::distinct()
 
   old_ids <- old_people[[{{people_column}}]]
@@ -24,8 +23,7 @@ add_people_from_table <- function(people_table_id, people_column, source_table_i
   #get ids from new source table
   new_people_query <- glue::glue("select {source_column} from {source_table_id}")
 
-  new_people <- synapser::synTableQuery(new_people_query, includeRowIdAndRowVersion	= F)$asDataFrame() %>%
-    tibble::as_tibble() %>%
+  new_people <- .syn$tableQuery(new_people_query)$asDataFrame() %>%
     dplyr::distinct() %>%
     dplyr::filter(!(!!rlang::sym(source_column)) %in% old_ids) %>%   #filter out existing ids
     purrr::pluck(source_column)
@@ -34,7 +32,7 @@ add_people_from_table <- function(people_table_id, people_column, source_table_i
 
   new_rows <- tibble::tibble(!!people_column := new_people)
 
-  schema <- synapser::synGet(people_table_id)
+  schema <- .syn$get(people_table_id)
 
   if(dry_run == F){
     .store_rows(schema, new_rows)
diff --git a/README.md b/README.md
index 586697ab..88690d7c 100644
--- a/README.md
+++ b/README.md
@@ -20,14 +20,20 @@ You can install `nfportalutils` from here:
 remotes::install_github("nf-osi/nfportalutils")
 ```
 
+The package interops with the [Python synapse client](https://github.com/Sage-Bionetworks/synapsePythonClient) via reticulate.
+You will have to download the Python synapse client first.
 
-
-## Additional Notes for Users
+## For Users
 
 - View function reference on docs site at [Reference](https://nf-osi.github.io/nfportalutils/reference/index.html). 
 - An alternative to viewing vignettes as Articles on the [docs site](https://nf-osi.github.io/nfportalutils/index.html) is to download them with pkg install and load with e.g. `vignette("annotate-nf-processed-data", package = "nfportalutils")` to view.
 
-## Additional Notes for Contributors 
+## For Contributors 
+
+### General picture
+- Again, default development happens in `develop`.
+- But we have a side branch called `develop-synapser` where interop tries to transition to `synapser`. 
+However, current coexistence makes development a bit tricky so consult first before trying new developments there.
 
 ### Contrib workflow
 - Branch of `develop` and make changes
diff --git a/man/dot-store_rows.Rd b/man/dot-store_rows.Rd
index 22394c72..bbbaa84d 100644
--- a/man/dot-store_rows.Rd
+++ b/man/dot-store_rows.Rd
@@ -1,5 +1,5 @@
 % Generated by roxygen2: do not edit by hand
-% Please edit documentation in R/basic_utils.R
+% Please edit documentation in R/add_publication_from_unpaywall.R
 \name{.store_rows}
 \alias{.store_rows}
 \title{Adds a row to a table.}