From b78104b74810abd5770f70e4e1f192570beeeab4 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Tue, 14 Jan 2020 11:38:35 +0100
Subject: [PATCH] Add splitleak
---
.gitlab-ci.yml | 6 ++++
steps/LoSoTo.Splitleak.cwl | 55 +++++++++++++++++++++++++++++++++
test_jobs/losoto_splitleak.json | 4 +++
3 files changed, 65 insertions(+)
create mode 100644 steps/LoSoTo.Splitleak.cwl
create mode 100644 test_jobs/losoto_splitleak.json
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ba19298f..d8a27290 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -155,6 +155,12 @@ losoto_residual:
script:
- cwl-runner --no-container steps/LoSoTo.Residual.cwl test_jobs/losoto_residual.json
+losoto_splitleak:
+ stage: test_steps
+ allow_failure: true
+ script:
+ - cwl-runner --no-container steps/LoSoTo.Splitleak.cwl test_jobs/losoto_splitleak.json
+
losoto_polalign:
stage: test_steps
allow_failure: true
diff --git a/steps/LoSoTo.Splitleak.cwl b/steps/LoSoTo.Splitleak.cwl
new file mode 100644
index 00000000..34059375
--- /dev/null
+++ b/steps/LoSoTo.Splitleak.cwl
@@ -0,0 +1,55 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_splitleak
+
+$namespaces:
+ lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+doc: Duplicate a table
+
+requirements:
+ InlineJavascriptRequirement:
+ expressionLib:
+ - { $include: utils.js}
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: 'parset.config'
+ entry: $(get_losoto_config('SPLITLEAK').join('\n'))
+
+ - entryname: $(inputs.input_h5parm.basename)
+ entry: $(inputs.input_h5parm)
+ writable: true
+
+baseCommand: "losoto"
+
+arguments:
+ - $(inputs.input_h5parm.basename)
+ - parset.config
+
+hints:
+ DockerRequirement:
+ dockerPull: lofareosc/lofar-pipeline-ci:latest
+
+inputs:
+ - id: input_h5parm
+ type: File
+ format: lofar:#H5Parm
+ - id: soltab
+ type: string
+ doc: "Solution table"
+ - id: soltabOutG
+ type: string?
+ doc: Output table name (diagonal component). By default choose next available from table type.
+ - id: soltabOutD
+ type: string?
+ doc: Output table name (leakage component). By default choose next available from table type.
+
+outputs:
+ - id: output_h5parm
+ type: File
+ format: lofar:#H5Parm
+ outputBinding:
+ glob: $(inputs.input_h5parm.basename)
+$schema:
+ - https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
diff --git a/test_jobs/losoto_splitleak.json b/test_jobs/losoto_splitleak.json
new file mode 100644
index 00000000..0b34257c
--- /dev/null
+++ b/test_jobs/losoto_splitleak.json
@@ -0,0 +1,4 @@
+{
+ "input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"},
+ "soltab": "sol000/amplitude000"
+}
--
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