From 84009373c14218061d188fe4d9427b93bc3e7fe4 Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Tue, 23 May 2023 16:03:19 -0400 Subject: [PATCH 1/4] [wfpm v0.8.0] started a new version song-score-upload@2.9.3 from song-score-upload@2.9.2 which was released --- song-score-upload/main.nf | 2 +- song-score-upload/pkg.json | 2 +- song-score-upload/tests/checker.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/song-score-upload/main.nf b/song-score-upload/main.nf index 978f5ff..1c32d87 100755 --- a/song-score-upload/main.nf +++ b/song-score-upload/main.nf @@ -21,7 +21,7 @@ */ nextflow.enable.dsl = 2 -version = '2.9.2' +version = '2.9.3' // universal params go here, change default value as needed params.publish_dir = "" // set to empty string will disable publishDir diff --git a/song-score-upload/pkg.json b/song-score-upload/pkg.json index ab9f6b0..be5281e 100644 --- a/song-score-upload/pkg.json +++ b/song-score-upload/pkg.json @@ -1,6 +1,6 @@ { "name": "song-score-upload", - "version": "2.9.2", + "version": "2.9.3", "description": "SONG/SCORE upload", "main": "main.nf", "deprecated": false, diff --git a/song-score-upload/tests/checker.nf b/song-score-upload/tests/checker.nf index 2d30eec..910036c 100755 --- a/song-score-upload/tests/checker.nf +++ b/song-score-upload/tests/checker.nf @@ -25,7 +25,7 @@ */ nextflow.enable.dsl = 2 -version = '2.9.2' +version = '2.9.3' // universal params go here, change default value as needed params.max_retries = 5 // set to 0 will disable retry From a177aca3b47bbacc2197e1a81f8d2dafaa5e2ebe Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Tue, 23 May 2023 16:22:41 -0400 Subject: [PATCH 2/4] Bump score version --- process/score_upload.nf | 2 +- song-score-upload/main.nf | 2 +- song-score-upload/tests/checker.nf | 2 +- 3 files changed, 3 insertions(+), 3 deletions(-) diff --git a/process/score_upload.nf b/process/score_upload.nf index e2f644c..47e7c55 100644 --- a/process/score_upload.nf +++ b/process/score_upload.nf @@ -10,7 +10,7 @@ params.first_retry_wait_time = 1 // in seconds // required params w/ default params.container = "ghcr.io/overture-stack/score" -params.container_version = "5.8.1" +params.container_version = "5.9.0" params.transport_mem = 2 // Transport memory is in number of GBs // optional if secret mounted from pod else required diff --git a/song-score-upload/main.nf b/song-score-upload/main.nf index 1c32d87..87abfe3 100755 --- a/song-score-upload/main.nf +++ b/song-score-upload/main.nf @@ -50,7 +50,7 @@ params.score_transport_mem = 1 // GB 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 = "5.8.1" +params.score_container_version = "5.9.0" song_params = [ *:params, diff --git a/song-score-upload/tests/checker.nf b/song-score-upload/tests/checker.nf index 910036c..6ab78db 100755 --- a/song-score-upload/tests/checker.nf +++ b/song-score-upload/tests/checker.nf @@ -52,7 +52,7 @@ params.score_transport_mem = 1 // GB 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 = "5.8.1" +params.score_container_version = "5.9.0" song_params = [ *:params, From 7caac15301ceba081968918b75663979c435c27b Mon Sep 17 00:00:00 2001 From: edsu7 <22638361+edsu7@users.noreply.github.com> Date: Wed, 24 May 2023 11:01:20 -0400 Subject: [PATCH 3/4] bump version to `latest` --- .DS_Store | Bin 6148 -> 10244 bytes process/score_upload.nf | 2 +- process/song_manifest.nf | 2 +- process/song_publish.nf | 2 +- process/song_submit.nf | 2 +- song-score-upload/main.nf | 4 ++-- song-score-upload/tests/checker.nf | 4 ++-- 7 files changed, 8 insertions(+), 8 deletions(-) diff --git a/.DS_Store b/.DS_Store index 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optional if secret mounted from pod else required diff --git a/process/song_manifest.nf b/process/song_manifest.nf index 8854a21..43e45ad 100644 --- a/process/song_manifest.nf +++ b/process/song_manifest.nf @@ -12,7 +12,7 @@ params.first_retry_wait_time = 1 // in seconds // required params w/ default params.container = "ghcr.io/overture-stack/song-client" -params.container_version = "5.0.2" +params.container_version = "latest" // optional if secret mounted from pod else required params.api_token = "" // song/score API token for download process diff --git a/process/song_publish.nf b/process/song_publish.nf index 91539a7..7d1f77e 100644 --- a/process/song_publish.nf +++ b/process/song_publish.nf @@ -10,7 +10,7 @@ params.first_retry_wait_time = 1 // in seconds // required params w/ default params.container = "ghcr.io/overture-stack/song-client" -params.container_version = "5.0.2" +params.container_version = "latest" // optional if secret mounted from pod else required params.api_token = "" // song/score API token for download process diff --git a/process/song_submit.nf b/process/song_submit.nf index 4615b0a..4d322d6 100644 --- a/process/song_submit.nf +++ b/process/song_submit.nf @@ -10,7 +10,7 @@ params.first_retry_wait_time = 1 // in seconds // required params w/ default params.container = "ghcr.io/overture-stack/song-client" -params.container_version = "5.0.2" +params.container_version = "latest" // optional if secret mounted from pod else required params.api_token = "" // song/score API token for download process diff --git a/song-score-upload/main.nf b/song-score-upload/main.nf index 87abfe3..fc60560 100755 --- a/song-score-upload/main.nf +++ b/song-score-upload/main.nf @@ -42,7 +42,7 @@ params.song_mem = 1 // GB params.song_url = "https://song.rdpc-qa.cancercollaboratory.org" params.song_api_token = "" params.song_container = "ghcr.io/overture-stack/song-client" -params.song_container_version = "5.0.2" +params.song_container_version = "latest" params.score_cpus = 1 params.score_mem = 1 // GB @@ -50,7 +50,7 @@ params.score_transport_mem = 1 // GB 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 = "5.9.0" +params.score_container_version = "latest" song_params = [ *:params, diff --git a/song-score-upload/tests/checker.nf b/song-score-upload/tests/checker.nf index 6ab78db..fde67f9 100755 --- a/song-score-upload/tests/checker.nf +++ b/song-score-upload/tests/checker.nf @@ -44,7 +44,7 @@ params.song_mem = 1 // GB params.song_url = "https://song.rdpc-qa.cancercollaboratory.org" params.song_api_token = "" params.song_container = "ghcr.io/overture-stack/song-client" -params.song_container_version = "5.0.2" +params.song_container_version = "latest" params.score_cpus = 1 params.score_mem = 1 // GB @@ -52,7 +52,7 @@ params.score_transport_mem = 1 // GB 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 = "5.9.0" +params.score_container_version = "latest" song_params = [ *:params, 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 4/4] 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 GIT binary patch delta 1331 zcmdT?OHUI~6rQhCnHjCziqzU`$S4UQ6a@?TRvrQ(7^)OOe5GYZ9Vt`j32$sM>&PgblV?D+~QPpI24Hab~91Z}#Rm6BFDk?hW^W`^Zgk zpSfx73-^ut11DU_0)ZPo6rd1AC`LJ|P>mWiA&A{*MFp 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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} ${forceFlag} """ } diff --git a/song-score-upload/.DS_Store b/song-score-upload/.DS_Store new file mode 100644 index 0000000000000000000000000000000000000000..8211dfa223073c1cbeb3bf064e5a255118eb971e GIT binary patch literal 6148 zcmeHK%TB^T6g?L)V${gejY+?N#6PG67q0mLg#wK_QUW3_yZ2-KK396~%mkqbOEu=+ zfo z2^^nUh92?j`8fkjON%ck!CSKH73>ms`{2h4$g<$%;X-Ahlc3G2{rJ^%m! literal 0 HcmV?d00001 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,