Remove synapse_func.py and use syn object

Sage-Bionetworks · Apr 19, 2021 · 4910256 · 4910256
1 parent 6ce6d82
commit 4910256
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Showing 4 changed files with 17 additions and 19 deletions.
diff --git a/R/app_server.R b/R/app_server.R
@@ -37,7 +37,7 @@ app_server <- function( input, output, session ) {
       ### login and update session; otherwise, notify to login to Synapse first
       tryCatch({
         syn$login(sessionToken = input$cookie)
-        values$tables <- get_tables()
+        values$tables <- get_tables(syn)
         # get controlled-vocabulary list
         values$cv_terms <- get_synapse_annotations("syn25322361", syn) %>%
           select(key, value, columnType) %>%

diff --git a/R/mod_validator.R b/R/mod_validator.R
@@ -283,6 +283,7 @@ mod_validator_server <- function(input, output, session, values){
       if (type == "dataset") {
         annotations <- dataset_annots(row)
         syn_id <- save_folder_to_synapse(
+          syn,
           synapseclient,
           name,
           parent_folder[["dataset"]],
@@ -297,6 +298,7 @@ mod_validator_server <- function(input, output, session, values){
 
         annotations <- file_annots(row, dataset_folder, tables$grants, tables$datasets)
         syn_id <- save_file_to_synapse(
+          syn,
           synapseclient,
           name,
           dataset_folder,
@@ -337,13 +339,13 @@ mod_validator_server <- function(input, output, session, values){
                                    tables$publications
                                  )
         )
-        syn_store(synapseclient$Table(portal_table[[type]], new_portal_row))
+        syn$store(synapseclient$Table(portal_table[[type]], new_portal_row))
       }
       #      output$diag <- DT::renderDT(new_portal_row)
       #      syn_store(synapseclient$Table(portal_table[[type]], new_portal_row))
 
       ### update stats on overview tab
-      values$tables <- get_tables()
+      values$tables <- get_tables(syn)
       # TODO: make this tables value a reactive
       # display_overview_stats(output, tables)
       # display_quickview(output, tables)

diff --git a/R/synapse_funcs.py b/R/synapse_funcs.py
diff --git a/R/utils.R b/R/utils.R
@@ -45,7 +45,7 @@ split_and_search <- function(annots, table, search_col, output_col,
 
 
 ## Save new entity to Synapse; Folder for dataset manifest, File for others
-save_file_to_synapse <- function(synapseclient, name,
+save_file_to_synapse <- function(syn, synapseclient, name,
                                  parent, annotations) {
   name <- syn_prettify(name)
 
@@ -57,22 +57,22 @@ save_file_to_synapse <- function(synapseclient, name,
     parent = parent,
     annotations = annotations
   )
-  new_file <- syn_store(new_file)
+  new_file <- syn$store(new_file)
 
   # remove dummy file
   file.remove(name)
 
   new_file$id
 }
-save_folder_to_synapse <- function(synapseclient, name,
+save_folder_to_synapse <- function(syn, synapseclient, name,
                                    parent, annotations) {
   name <- syn_prettify(name)
   new_folder <- synapseclient$Folder(
     name,
     parent = parent,
     annotations = annotations
   )
-  new_folder <- syn_store(new_folder)
+  new_folder <- syn$store(new_folder)
   new_folder$id
 }
 
@@ -164,27 +164,32 @@ publication_row <- function(syn_id, manifest, grants, datasets) {
 }
 
 #' Get Synapse tables used for the portal.
-get_tables <- function() {
+get_tables <- function(syn) {
   grants <- get_portal_table(
+    syn,
     portal_table[["grant"]],
     c("grantId", "grantName", "grantNumber", "grantInstitution",
       "themeId", "theme", "consortiumId", "consortium")
   )
   publications <- get_portal_table(
+    syn,
     portal_table[["publication"]],
     c("publicationId", "publicationTitle", "grantId", "grantNumber",
       "grantName", "themeId", "theme", "consortiumId", "consortium"
     )
   )
   datasets <- get_portal_table(
+    syn,
     portal_table[["dataset"]],
     c("datasetId", "datasetName", "datasetAlias")
   )
   tools <- get_portal_table(
+    syn,
     portal_table[["tool"]],
     c("toolId", "toolName")
   )
   files <- get_portal_table(
+    syn,
     portal_table[["file"]],
     c("fileName", "datasets", "parentId")
   )
@@ -198,9 +203,9 @@ get_tables <- function() {
 }
 
 #' Get selected coloumns from a Synapse table.
-get_portal_table <- function(table_id, cols) {
+get_portal_table <- function(syn, table_id, cols) {
   query <- sprintf("SELECT %s FROM %s", paste0(cols, collapse=","), table_id)
-  return(syn_table_query(query)$asDataFrame())
+  return(syn$tableQuery(query)$asDataFrame())
 }