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Reference specific package name for function calls #4

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merged 1 commit into from
Apr 9, 2024
Merged

Reference specific package name for function calls #4

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25 changes: 14 additions & 11 deletions sts_synindex_internal.R
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Original file line number Diff line number Diff line change
Expand Up @@ -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(
Expand All @@ -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)
}
}
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