From 10ca12bdc98c3150155b7941f7db95b0abaf5ffb Mon Sep 17 00:00:00 2001
From: edsu7 <22638361+edsu7@users.noreply.github.com>
Date: Fri, 26 May 2023 11:15:20 -0400
Subject: [PATCH] add force flag

---
 .DS_Store                          | Bin 10244 -> 10244 bytes
 process/score_upload.nf            |   5 +++--
 song-score-upload/.DS_Store        | Bin 0 -> 6148 bytes
 song-score-upload/main.nf          |   4 +++-
 song-score-upload/tests/checker.nf |   1 +
 5 files changed, 7 insertions(+), 3 deletions(-)
 create mode 100644 song-score-upload/.DS_Store

diff --git a/.DS_Store b/.DS_Store
index 7df21db5b14c164f6d37f3a1c3ebc4963285a75c..44c83ff0ce7a068aa9b237cba8d0ee21d2ca3eda 100644
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diff --git a/process/score_upload.nf b/process/score_upload.nf
index 8d2c4cc..61ef9be 100644
--- a/process/score_upload.nf
+++ b/process/score_upload.nf
@@ -15,7 +15,7 @@ params.transport_mem = 2 // Transport memory is in number of GBs
 
 // optional if secret mounted from pod else required
 params.api_token = "" // song/score API token for download process
-
+params.score_force = false
 // required params, no default
 // --song_url         song url for download process
 // --score_url        score url for download process
@@ -52,6 +52,7 @@ process scoreUpload {
 
     script:
         accessToken = params.api_token ? params.api_token : "`cat /tmp/rdpc_secret/secret`"
+        forceFlag = params.score_force ? "--force" : ""
         """
         export METADATA_URL=${params.song_url}
         export STORAGE_URL=${params.score_url}
@@ -59,6 +60,6 @@ process scoreUpload {
         export TRANSPORT_MEMORY=${params.transport_mem}
         export ACCESSTOKEN=${accessToken}
         
-        score-client upload --manifest ${manifest}
+        score-client upload --manifest ${manifest} ${forceFlag}
         """
 }
diff --git a/song-score-upload/.DS_Store b/song-score-upload/.DS_Store
new file mode 100644
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diff --git a/song-score-upload/main.nf b/song-score-upload/main.nf
index fc60560..87e6b55 100755
--- a/song-score-upload/main.nf
+++ b/song-score-upload/main.nf
@@ -51,6 +51,7 @@ params.score_url = "https://score.rdpc-qa.cancercollaboratory.org"
 params.score_api_token = ""
 params.score_container = "ghcr.io/overture-stack/score"
 params.score_container_version = "latest"
+params.score_force = false
 
 song_params = [
     *:params,
@@ -71,7 +72,8 @@ score_params = [
     'score_url': params.score_url,
     'score_container': params.score_container,
     'score_container_version': params.score_container_version,
-    'api_token': params.score_api_token ?: params.api_token
+    'api_token': params.score_api_token ?: params.api_token,
+    'score_force': params.score_force
 ]
 
 include { songSubmit as songSub } from './local_modules/song-submit' params(song_params)
diff --git a/song-score-upload/tests/checker.nf b/song-score-upload/tests/checker.nf
index fde67f9..7cf0ce1 100755
--- a/song-score-upload/tests/checker.nf
+++ b/song-score-upload/tests/checker.nf
@@ -53,6 +53,7 @@ params.score_url = "https://score.rdpc-qa.cancercollaboratory.org"
 params.score_api_token = ""
 params.score_container = "ghcr.io/overture-stack/score"
 params.score_container_version = "latest"
+params.score_force = false
 
 song_params = [
     *:params,