From cdf73381424d458b0997bef74384f984b08d9b83 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Thu, 28 Nov 2019 11:16:44 +0100
Subject: [PATCH] Add LoSoTo Duplicate step
Former-commit-id: e98ca4e4ba7f5b62b9304e3571685989bd4e78be
---
.gitlab-ci.yml | 6 +++++
steps/LoSoTo.Duplicate.cwl | 48 ++++++++++++++++++++++++++++++++++
test_jobs/losoto_duplicate.cwl | 7 +++++
3 files changed, 61 insertions(+)
create mode 100644 steps/LoSoTo.Duplicate.cwl
create mode 100644 test_jobs/losoto_duplicate.cwl
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index c6e83769..5585ff5f 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -68,6 +68,12 @@ losoto_abs:
script:
- cwl-runner --no-container steps/LoSoTo.Abs.cwl test_jobs/losoto_abs.json
+losoto_duplicate:
+ stage: test_steps
+ allow_failure: true
+ scripts:
+ - cwl-runner --no-container steps/LoSoTo.Duplicate.cwl test_jobs/losoto_duplicate.json
+
losoto_plot:
stage: test_steps
allow_failure: true
diff --git a/steps/LoSoTo.Duplicate.cwl b/steps/LoSoTo.Duplicate.cwl
new file mode 100644
index 00000000..777f6a6b
--- /dev/null
+++ b/steps/LoSoTo.Duplicate.cwl
@@ -0,0 +1,48 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_duplicate
+
+doc: |
+ Duplicate a table
+
+requirements:
+ InlineJavascriptRequirement: {}
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: 'parset.config'
+ entry: |
+ [duplicate]
+ soltab = $(inputs.soltab)
+ operation = DUPLICATE
+ $(inputs.soltabOut !== null? 'soltabOut=' + inputs.soltabOut: '')
+
+ - entryname: $(inputs.input_h5parm.basename)
+ entry: $(inputs.input_h5parm)
+ writable: true
+
+baseCommand: "losoto"
+
+arguments:
+ - $(inputs.input_h5parm.basename)
+ - parset.config
+
+hints:
+ DockerRequirement:
+ dockerPull: lofareosc/prefactor-ci:master
+
+inputs:
+ - id: input_h5parm
+ type: File
+ - id: soltab
+ type: string
+ doc: "Solution table"
+ - id: soltabOut
+ type: string?
+ doc: Output table name. By default choose next available from table type.
+outputs:
+ - id: output_h5parm
+ type: File
+ outputBinding:
+ glob: $(inputs.input_h5parm.basename)
diff --git a/test_jobs/losoto_duplicate.cwl b/test_jobs/losoto_duplicate.cwl
new file mode 100644
index 00000000..ff1cfa0f
--- /dev/null
+++ b/test_jobs/losoto_duplicate.cwl
@@ -0,0 +1,7 @@
+{
+ "input_h5parm": {
+ "class": "File",
+ "path": "/data/example.h5"
+ },
+ "soltab": "sol000/amplitude000"
+}
--
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