Merge pull request #27 from pranavanba/main

Update script path for git commit metadata
Sage-Bionetworks · Apr 17, 2024 · c3dab47 · c3dab47
2 parents 93a88d7 + 3ee2c20
commit c3dab47
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Showing 4 changed files with 4 additions and 4 deletions.
diff --git a/scripts/deidentification/deidentification.R b/scripts/deidentification/deidentification.R
@@ -128,7 +128,7 @@ for (i in seq_along(deidentified_results$values_to_review)) {
 
 # Index each file in Synapse
 latest_commit <- gh::gh("/repos/:owner/:repo/commits/main", owner = "Sage-Bionetworks", repo = "recover-parquet-external")
-latest_commit_file_url <- paste0(latest_commit$html_url %>% stringr::str_replace("commit", "blob"), "/deidentification.R")
+latest_commit_file_url <- paste0(latest_commit$html_url %>% stringr::str_replace("commit", "blob"), "/scripts/deidentification/deidentification.R")
 
 for (i in seq_along(list.files('./dictionaries/new_to_review/'))) {
   synStore(File(path = list.files('./dictionaries/new_to_review', full.names = T)[i],

diff --git a/scripts/main/archive-to-current.R b/scripts/main/archive-to-current.R
@@ -105,7 +105,7 @@ if (!is.null(synFindEntityId(validated_date, config::get("PARQUET_FOLDER_ARCHIVE
   # 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$html_url %>% stringr::str_replace("commit", "tree")
-  latest_commit_this_file <- paste0(latest_commit$html_url %>% stringr::str_replace("commit", "blob"), "/archive-to-current.R")
+  latest_commit_this_file <- paste0(latest_commit$html_url %>% stringr::str_replace("commit", "blob"), "/scripts/main/archive-to-current.R")
 
   if(nrow(synapse_manifest_to_upload) > 0){
     for(file_number in seq_len(nrow(synapse_manifest_to_upload))){

diff --git a/scripts/main/staging_to_archive.R b/scripts/main/staging_to_archive.R
@@ -102,7 +102,7 @@ if (!is.null(synFindEntityId(validated_date, config::get("PARQUET_FOLDER_ARCHIVE
   # 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$html_url %>% stringr::str_replace("commit", "tree")
-  latest_commit_this_file <- paste0(latest_commit$html_url %>% stringr::str_replace("commit", "blob"), "/staging_to_archive.R")
+  latest_commit_this_file <- paste0(latest_commit$html_url %>% stringr::str_replace("commit", "blob"), "/scripts/main/staging_to_archive.R")
 
   if(nrow(synapse_manifest_to_upload) > 0){
     for(file_number in seq_len(nrow(synapse_manifest_to_upload))){

diff --git a/scripts/main/sts_synindex_external.R b/scripts/main/sts_synindex_external.R
@@ -214,7 +214,7 @@ if (nrow(synapse_fileview)>0) {
 
 # Index each file in Synapse
 latest_commit <- gh::gh("/repos/:owner/:repo/commits/main", owner = "Sage-Bionetworks", repo = "recover-parquet-external")
-latest_commit_this_file <- paste0(latest_commit$html_url %>% stringr::str_replace("commit", "blob"), "/sts_synindex_external.R")
+latest_commit_this_file <- paste0(latest_commit$html_url %>% stringr::str_replace("commit", "blob"), "/scripts/main/sts_synindex_external.R")
 
 act <- synapser::Activity(name = "Indexing",
                           description = "Indexing external parquet datasets",