From 46594b9d390d7d882cc1b61ef160a7fb408abe68 Mon Sep 17 00:00:00 2001
From: Pranav Anbarasu <pranavanba@gmail.com>
Date: Thu, 3 Oct 2024 23:55:08 +0000
Subject: [PATCH] Upload intermediate summaries (output concepts) files to
 internal Synapse location for use in validation of staging i2b2 summaries
 data

---
 config/config.yml                             |  1 +
 .../upload-intermediate-summaries-files.R     | 24 +++++++++++++++++++
 2 files changed, 25 insertions(+)
 create mode 100644 scripts/write-output/upload-intermediate-summaries-files.R

diff --git a/config/config.yml b/config/config.yml
index 865e102..bc42486 100644
--- a/config/config.yml
+++ b/config/config.yml
@@ -18,6 +18,7 @@ staging:
   s3basekey: main/archive/2024-06-13/
   selectedVarsFileID: syn53503994
   outputConceptsDir: ./temp-output-concepts
+  tempOutputConceptSynID: syn53822708
 
 prod:
   inherits: staging
diff --git a/scripts/write-output/upload-intermediate-summaries-files.R b/scripts/write-output/upload-intermediate-summaries-files.R
new file mode 100644
index 0000000..45d9556
--- /dev/null
+++ b/scripts/write-output/upload-intermediate-summaries-files.R
@@ -0,0 +1,24 @@
+# Generate a TSV manifest file of intermediate summaries files (intermediate output concepts files)
+synapserutils::generate_sync_manifest(
+  directory_path = outputConceptsDir, 
+  parent_id = tempOutputConceptSynID, 
+  manifest_path = "temp-output-concepts-manifest.tsv"
+)
+
+# Exclude the final output_concepts.csv file from the manifest and write the
+# modified manifest file to a CSV file
+read.delim("temp-output-concepts-manifest.tsv") %>% 
+  dplyr::filter(!grepl("output_concepts.csv", path)) %>% 
+  write.csv(file = "temp-output-concepts-manifest.csv", row.names = FALSE, quote = FALSE)
+
+login <- synapser::synLogin()
+
+# Store each file listed in the CSV manifest file at its specified parent Synapse ID
+synapserutils::syncToSynapse(manifestFile = "temp-output-concepts-manifest.csv")
+
+# synclient <- reticulate::import("synapseclient")
+# syn_temp <- synclient$Synapse()
+# syn <- syn_temp$login()
+# 
+# synutils <- reticulate::import("synapseutils")
+# synutils$syncToSynapse(syn = syn, manifestFile = "temp-output-concepts-manifest.csv")