From bb10ca12d9ee62f2cbfb485a0edfa79021d9811c Mon Sep 17 00:00:00 2001
From: Mattia Mancini <mancini@astron.nl>
Date: Fri, 21 Jul 2023 09:53:46 +0000
Subject: [PATCH] Improve LDV workflow
---
steps/format_quality.cwl | 27 ++++++++++++++
steps/list_directory_files.cwl | 20 ++++++++++
...calibrator.cwl => ldv_linc_calibrator.cwl} | 37 +++++++++++++++----
...efactor_target.cwl => ldv_linc_target.cwl} | 31 ++++++++++++----
4 files changed, 100 insertions(+), 15 deletions(-)
create mode 100644 steps/format_quality.cwl
create mode 100644 steps/list_directory_files.cwl
rename workflows/{ldv_prefactor_calibrator.cwl => ldv_linc_calibrator.cwl} (60%)
rename workflows/{ldv_prefactor_target.cwl => ldv_linc_target.cwl} (77%)
diff --git a/steps/format_quality.cwl b/steps/format_quality.cwl
new file mode 100644
index 00000000..926c9bde
--- /dev/null
+++ b/steps/format_quality.cwl
@@ -0,0 +1,27 @@
+class: ExpressionTool
+cwlVersion: v1.2
+inputs:
+- id: plots
+ type: File[]
+- id: summary
+ type: File
+
+outputs:
+- id: quality
+ type: Any
+expression: |
+ ${
+ return {
+ "quality": {
+ "plots": inputs.plots,
+ "details": {},
+ "sensitivity": "N/A",
+ "uv-coverage": "N/A",
+ "observing-conditions": "N/A",
+ "summary_file": inputs.summary
+ }
+ }
+ }
+
+requirements:
+- class: InlineJavascriptRequirement
diff --git a/steps/list_directory_files.cwl b/steps/list_directory_files.cwl
new file mode 100644
index 00000000..e60a3e59
--- /dev/null
+++ b/steps/list_directory_files.cwl
@@ -0,0 +1,20 @@
+id: listdirectory
+label: list_directory
+class: ExpressionTool
+cwlVersion: v1.2
+
+inputs:
+ - id: input
+ type: Directory
+ loadListing: shallow_listing
+outputs:
+ - id: output
+ type: File[]
+
+expression: |
+ ${
+ return {'output': inputs.input.listing}
+ }
+
+requirements:
+ - class: InlineJavascriptRequirement
diff --git a/workflows/ldv_prefactor_calibrator.cwl b/workflows/ldv_linc_calibrator.cwl
similarity index 60%
rename from workflows/ldv_prefactor_calibrator.cwl
rename to workflows/ldv_linc_calibrator.cwl
index 32892237..30ca3dd8 100644
--- a/workflows/ldv_prefactor_calibrator.cwl
+++ b/workflows/ldv_linc_calibrator.cwl
@@ -15,11 +15,11 @@ outputs:
- id: solutions
type: File
outputSource:
- - prefactor_calibrator/solutions
+ - linc_calibrator/solutions
- id: summary
type: File
outputSource:
- - prefactor_calibrator/summary
+ - linc_calibrator/summary
- id: inspection_plots
type: File
outputSource:
@@ -28,7 +28,28 @@ outputs:
type: File
outputSource:
- compress_logs/compressed
+- id: quality
+ type: Any
+ outputSource:
+ - format_quality/quality
+
steps:
+- id: format_quality
+ in:
+ - id: plots
+ source: list_inspection_plots/output
+ - id: summary
+ source: linc_calibrator/summary
+ run: ../steps/format_quality.cwl
+ out:
+ - id: quality
+- id: list_inspection_plots
+ in:
+ - id: input
+ source: linc_calibrator/inspection_plots
+ run: ../steps/list_directory_files.cwl
+ out:
+ - id: output
- id: fetch_data
in:
- id: surl_link
@@ -37,7 +58,7 @@ steps:
run: ../steps/fetch_data.cwl
out:
- id: uncompressed
-- id: prefactor_calibrator
+- id: linc_calibrator
in:
- id: msin
source: fetch_data/uncompressed
@@ -48,16 +69,16 @@ steps:
- id: inspection_plots
- id: log_files
- id: compress_inspection_plots
- in:
+ in:
- id: directory
- source: prefactor_calibrator/inspection_plots
+ source: linc_calibrator/inspection_plots
+ run: ../steps/compress.cwl
out:
- id: compressed
- run: ../steps/compress.cwl
- id: compress_logs
in:
- id: directory
- source: prefactor_calibrator/log_files
+ source: linc_calibrator/log_files
+ run: ../steps/compress.cwl
out:
- id: compressed
- run: ../steps/compress.cwl
\ No newline at end of file
diff --git a/workflows/ldv_prefactor_target.cwl b/workflows/ldv_linc_target.cwl
similarity index 77%
rename from workflows/ldv_prefactor_target.cwl
rename to workflows/ldv_linc_target.cwl
index fdd1b4c4..9a497356 100644
--- a/workflows/ldv_prefactor_target.cwl
+++ b/workflows/ldv_linc_target.cwl
@@ -23,11 +23,11 @@ outputs:
- id: cal_solutions
type: File
outputSource:
- - prefactor_target/solutions
+ - linc_target/solutions
- id: summary
type: File
outputSource:
- - prefactor_target/summary
+ - linc_target/summary
- id: calibrated_data
type: File[]
outputSource:
@@ -40,7 +40,18 @@ outputs:
type: File
outputSource:
- compress_logs/compressed
+ - id: quality
+ type: Any
+ outputSource:
+ - format_quality/quality
steps:
+ - id: format_quality
+ in:
+ - id: plots
+ source: list_inspection_plots/output
+ out:
+ - id: quality
+ run: ../steps/format_quality.cwl
- id: fetch_data
in:
- id: surl_link
@@ -56,7 +67,7 @@ steps:
run: ../steps/fetch_file.cwl
out:
- id: downloaded
- - id: prefactor_target
+ - id: linc_target
in:
- id: msin
source: fetch_data/uncompressed
@@ -76,15 +87,21 @@ steps:
- id: compress_inspection_plots
in:
- id: directory
- source: prefactor_target/inspection_plots
+ source: linc_target/inspection_plots
out:
- id: compressed
run: ../steps/compress.cwl
-
+ - id: list_inspection_plots
+ in:
+ - id: input
+ source: linc_target/inspection_plots
+ out:
+ - id: output
+ run: ../steps/list_directory_files.cwl
- id: split_calibrated_data
in:
- id: input
- source: prefactor_target/calibrated_data
+ source: linc_target/calibrated_data
out:
- id: output
run: ../steps/list_directory.cwl
@@ -99,7 +116,7 @@ steps:
- id: compress_logs
in:
- id: directory
- source: prefactor_target/log_files
+ source: linc_target/log_files
out:
- id: compressed
run: ../steps/compress.cwl
\ No newline at end of file
--
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