From 08ed6f10a631a1d4e8c22a722c62d3ec018d709c Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Fri, 10 Jan 2020 14:49:57 +0100
Subject: [PATCH] Add Flagextend
Former-commit-id: ed15f74f40f6440539a66e38d3da643f3288fc30
---
.gitlab-ci.yml | 5 +++
steps/LoSoTo.Flagextend.cwl | 71 ++++++++++++++++++++++++++++++++
test_jobs/losoto_flagextend.json | 6 +++
3 files changed, 82 insertions(+)
create mode 100644 steps/LoSoTo.Flagextend.cwl
create mode 100644 test_jobs/losoto_flagextend.json
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index e82264fd..b73a4ece 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -114,6 +114,11 @@ losoto_clip:
allow_failure: true
script:
- cwl-runner --no-container steps/LoSoTo.Clip.cwl test_jobs/losoto_clip.json
+losoto_flagextend:
+ stage: test_steps
+ allow_failure: true
+ script:
+ - cwl-runner --no-container steps/LoSoTo.Flagextend.cwl test_jobs/losoto_flagextend.json
losoto_faraday:
stage: test_steps
diff --git a/steps/LoSoTo.Flagextend.cwl b/steps/LoSoTo.Flagextend.cwl
new file mode 100644
index 00000000..330b2fb9
--- /dev/null
+++ b/steps/LoSoTo.Flagextend.cwl
@@ -0,0 +1,71 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_flagextend
+
+$namespaces:
+ lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+doc: |
+ This operation for LoSoTo implement a extend flag procedure.
+ It can work in multi dimensional space and for each datum check if the
+ surrounding data are flagged to a certain %, then flag also that datum.
+ The size of the surrounding footprint can be tuned
+
+requirements:
+ InlineJavascriptRequirement:
+ expressionLib:
+ - { $include: utils.js}
+ InitialWorkDirRequirement:
+ listing:
+ - entryname: 'parset.config'
+ entry: $(get_losoto_config('FLAGEXTEND').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: axesToExt
+ type: string[]
+ doc: Axes used to find close flags.
+ - id: size
+ type: int[]
+ doc: |
+ Size of the window (diameter), per axis. If 0 is given then the entire
+ length of the axis is assumed.
+ Must be a vector of same length of Axes.
+ - id: percent
+ type: float?
+ doc: Percent of flagged data around the point to flag it, by default 50.
+ - id: maxCycles
+ type: int?
+ doc: Number of independent cycles of flag expansion, by default 3.
+ - id: ncpu
+ type: int?
+ doc: Number of CPU used, by default all available.
+
+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_flagextend.json b/test_jobs/losoto_flagextend.json
new file mode 100644
index 00000000..a90d48b5
--- /dev/null
+++ b/test_jobs/losoto_flagextend.json
@@ -0,0 +1,6 @@
+{
+ "input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"},
+ "soltab": "sol000/phase000",
+ "axesToExt": ["time"],
+ "size": [0]
+}
--
GitLab