From d56091985a9a933a86d320267647dc7a15a68389 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Fri, 10 Jan 2020 13:37:36 +0100
Subject: [PATCH] Add LoSoTo Faraday
Former-commit-id: a488792f38e20485ca183c3c3662472d45c6099d
---
.gitlab-ci.yml | 10 ++++--
steps/LoSoTo.Faraday.cwl | 61 +++++++++++++++++++++++++++++++++++
test_jobs/losoto_faraday.json | 5 +++
3 files changed, 74 insertions(+), 2 deletions(-)
create mode 100644 steps/LoSoTo.Faraday.cwl
create mode 100644 test_jobs/losoto_faraday.json
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index a03cf0d5..78e53fe0 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -111,6 +111,12 @@ losoto_clip:
script:
- cwl-runner --no-container steps/LoSoTo.Clip.cwl test_jobs/losoto_clip.json
+losoto_faraday:
+ stage: test_steps
+ allow_failure: true
+ script:
+ - cwl-runner --no-container steps/LoSoTo.Faraday.cwl test_jobs/losoto_faraday.json
+
losoto_residual:
stage: test_steps
allow_failure: true
@@ -122,7 +128,7 @@ losoto_polalign:
allow_failure: true
script:
- cwl-runner --no-container steps/LoSoTo.Polalign.cwl test_jobs/losoto_polalign.json
-
+
parset_selector:
stage: test_steps
@@ -135,7 +141,7 @@ file_selector:
allow_failure: true
script:
- cwl-runner steps/FileSelector.cwl test_jobs/file_selector.json
-
+
NDPPP:
stage: test_steps
diff --git a/steps/LoSoTo.Faraday.cwl b/steps/LoSoTo.Faraday.cwl
new file mode 100644
index 00000000..e3092536
--- /dev/null
+++ b/steps/LoSoTo.Faraday.cwl
@@ -0,0 +1,61 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_faraday
+
+$namespaces:
+ lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+doc: |
+ Faraday rotation extraction from either a rotation table or a
+ circular phase (of which the operation get the polarisation difference).
+
+
+requirements:
+ InlineJavascriptRequirement:
+ expressionLib:
+ - { $include: utils.js}
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: 'parset.config'
+ entry: $(get_losoto_config('FARADAY').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: refAnt
+ type: string?
+ doc: Reference antenna, by default the first.
+ - id: maxResidual
+ type: float?
+ doc: |
+ Max average residual in radians before flagging datapoint,
+ by default 1. If 0: no check.
+
+
+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_faraday.json b/test_jobs/losoto_faraday.json
new file mode 100644
index 00000000..3632d7f1
--- /dev/null
+++ b/test_jobs/losoto_faraday.json
@@ -0,0 +1,5 @@
+{
+ "input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"},
+ "soltab": "sol000/phase000",
+ "ncpu": 1
+}
--
GitLab