Merge pull request #6 from pranavanba/add-provenance-to-synstore

RMHDR-200 Add provenance arguments to synStore()

sts_synindex_external.R

@@ -209,26 +209,33 @@ synapse_manifest_to_upload <-
          s3_file_key = gsub("cohort_", "cohort=", s3_file_key))
 
 # Index each file in Synapse
+latest_commit <- gh::gh("/repos/:owner/:repo/commits/main", owner = "Sage-Bionetworks", repo = "recover-parquet-external")
+latest_commit_tree_url <- latest_commit$html_url %>% stringr::str_replace("commit", "tree")
+
 if(nrow(synapse_manifest_to_upload) > 0){
   for(file_number in seq_len(nrow(synapse_manifest_to_upload))){
     tmp <- synapse_manifest_to_upload[file_number, c("path", "parent", "s3_file_key")]
 
     absolute_file_path <- tools::file_path_as_absolute(tmp$path)
-
+    
     temp_syn_obj <- 
       synapser::synCreateExternalS3FileHandle(
         bucket_name = PARQUET_BUCKET_EXTERNAL,
         s3_file_key = tmp$s3_file_key,
         file_path = absolute_file_path,
         parent = tmp$parent)
-
+    
     new_fileName <- stringr::str_replace_all(temp_syn_obj$fileName, ':', '_colon_')
-
-    f <- 
-      synStore(
-        File(dataFileHandleId = temp_syn_obj$id,
-             parentId = tmp$parent,
-             name = new_fileName))
-
+
+    f <- File(dataFileHandleId = temp_syn_obj$id,
+              parentId = tmp$parent,
+              name = new_fileName)
+
+    f <- synStore(f, 
+                  activity = "Indexing", 
+                  activityDescription = "Indexing external parquet datasets", 
+                  used = PARQUET_FOLDER_INTERNAL, 
+                  executed = latest_commit_tree_url)
+
   }
 }