diff --git a/sts_synindex_internal.R b/sts_synindex_internal.R index 205b698..7bf70b5 100644 --- a/sts_synindex_internal.R +++ b/sts_synindex_internal.R @@ -112,9 +112,11 @@ latest_commit_tree_url <- latest_commit$html_url %>% stringr::str_replace("commi # Index each file in Synapse if(nrow(synapse_manifest_to_upload) > 0){ for(file_number in seq_len(nrow(synapse_manifest_to_upload))){ - tmp <- synapse_manifest_to_upload[file_number, c("path", "parent", "s3_file_key")] + tmp <- + synapse_manifest_to_upload[file_number, c("path", "parent", "s3_file_key")] - absolute_file_path <- tools::file_path_as_absolute(tmp$path) + absolute_file_path <- + tools::file_path_as_absolute(tmp$path) temp_syn_obj <- synapser::synCreateExternalS3FileHandle( @@ -125,15 +127,16 @@ if(nrow(synapse_manifest_to_upload) > 0){ new_fileName <- stringr::str_replace_all(temp_syn_obj$fileName, ':', '_colon_') - f <- File(dataFileHandleId = temp_syn_obj$id, - parentId = tmp$parent, - name = new_fileName) - - f <- synStore(f, - activityName = "Indexing", - activityDescription = "Indexing internal parquet datasets", - used = PARQUET_FOLDER, - executed = latest_commit_tree_url) + f <- + synapser::File(dataFileHandleId = temp_syn_obj$id, + parentId = tmp$parent, + name = new_fileName) + f <- + synapser::synStore(f, + activityName = "Indexing", + activityDescription = "Indexing internal parquet datasets", + used = PARQUET_FOLDER, + executed = latest_commit_tree_url) } }