From 4e620bb28c459d7b6fedded34bf560b63e398111 Mon Sep 17 00:00:00 2001
From: Timo Millenaar <tmillenaar@gmail.com>
Date: Thu, 22 Aug 2024 13:36:34 +0200
Subject: [PATCH] Make input_storage_manager and already_compressed part of
summary instead of top level of output json for improved atdb parsing
---
download_and_compress_pipeline.cwl | 32 ++----------------------------
steps/format_metrics.cwl | 6 ++++++
2 files changed, 8 insertions(+), 30 deletions(-)
diff --git a/download_and_compress_pipeline.cwl b/download_and_compress_pipeline.cwl
index 9a40513..6ad92e4 100644
--- a/download_and_compress_pipeline.cwl
+++ b/download_and_compress_pipeline.cwl
@@ -47,13 +47,6 @@ outputs:
type: File
outputSource:
- combine/inspect_file
-- id: input_storage_manager
- type: string[]
- outputSource: compress/input_storage_manager
-- id: already_compressed
- type: boolean[]
- outputSource: already_compressed/already_compressed
-
steps:
- id: fetch_data
@@ -115,30 +108,9 @@ steps:
source: compress/applied_fixes
- id: unfixable_issues
source: compress/unfixable_issues
+ - id: input_storage_manager
+ source: compress/input_storage_manager
run: steps/format_metrics.cwl
out:
- formatted_quality
- control
-
-- id: already_compressed
- run:
- class: ExpressionTool
- requirements:
- - class: InlineJavascriptRequirement
- inputs:
- - id: input_storage_manager
- type: string[]
- outputs:
- - id: already_compressed
- type: boolean[]
- expression: |
- ${
- return {
- already_compressed: inputs.input_storage_manager == "DyscoStorageManager"
- };
- }
- in:
- - id: input_storage_manager
- source: compress/input_storage_manager
- out:
- - id: already_compressed
\ No newline at end of file
diff --git a/steps/format_metrics.cwl b/steps/format_metrics.cwl
index fe3538c..7863218 100644
--- a/steps/format_metrics.cwl
+++ b/steps/format_metrics.cwl
@@ -27,6 +27,10 @@ inputs:
items:
type: array
items: string
+- id: input_storage_manager
+ type:
+ type: array
+ items: string
outputs:
- id: formatted_quality
@@ -44,6 +48,8 @@ expression: |
quality['summary']['applied_fixes'] = inputs.applied_fixes[0];
quality['summary']['unfixable_issues'] = inputs.unfixable_issues[0];
+ quality['summary']['input_storage_manager'] = inputs.input_storage_manager;
+ quality['summary']['already_compressed'] = inputs.input_storage_manager.map(value => value === "DyscoStorageManager");
var control = {
'keep_input': inputs.msin.map((file, index) => {
--
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