From 65a69002d05309550233e315e02e1c189c57c170 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Mon, 13 Jan 2020 16:01:08 +0100
Subject: [PATCH] Add Interpolate step

Former-commit-id: c5d6ae5c9652efeadc79ecfe19f78bb4cba4dda4
---
 .gitlab-ci.yml                    |  5 ++
 steps/LoSoTo.Interpolate.cwl      | 82 +++++++++++++++++++++++++++++++
 test_jobs/losoto_interpolate.json |  7 +++
 3 files changed, 94 insertions(+)
 create mode 100644 steps/LoSoTo.Interpolate.cwl
 create mode 100644 test_jobs/losoto_interpolate.json

diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index 7c82d622..5e94a075 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -130,6 +130,11 @@ losoto_faraday:
   script:
     - cwl-runner --no-container steps/LoSoTo.Faraday.cwl test_jobs/losoto_faraday.json
 
+losoto_interpolate:
+  stage: test_steps
+  allow_failure: true
+  script:
+    - cwl-runner --no-container steps/LoSoTo.Interpolate.cwl test_jobs/losoto_interpolate.json
 losoto_residual:
   stage: test_steps
   allow_failure: true
diff --git a/steps/LoSoTo.Interpolate.cwl b/steps/LoSoTo.Interpolate.cwl
new file mode 100644
index 00000000..aa956ebf
--- /dev/null
+++ b/steps/LoSoTo.Interpolate.cwl
@@ -0,0 +1,82 @@
+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_interpolate
+
+$namespaces:
+  lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
+doc: |
+  This operation for LoSoTo implements regridding and linear interpolation of data for an axis.
+  WEIGHT: compliant
+
+
+
+
+requirements:
+  InlineJavascriptRequirement:
+    expressionLib:
+      - { $include: utils.js}
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: 'parset.config'
+        entry: $(get_losoto_config('INTERPOLATE').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: axisToRegrid
+    type: string
+    doc: Name of the axis for which regridding/interpolation will be done
+  - id: outSoltab
+    type: string
+    doc: Output sol tab name
+  - id: newdelta
+    type: string
+    doc: Fundamental width between samples after regridding. E.g., "100kHz" or "10s"
+
+  - id: delta
+    type: string?
+    doc: |
+      Fundamental width between samples in axisToRegrid. E.g., "100kHz" or "10s". If "",
+      it is calculated from the axisToRegrid values
+
+  - id: maxFlaggedWidth
+    type: int?
+    doc: |
+      Maximum allowable width in number of samples (after regridding) above which
+      interpolated values are flagged (e.g., maxFlaggedWidth = 5 would allow gaps of
+      5 samples or less to be interpolated across but gaps of 6 or more would be
+      flagged)
+  - id: log
+    type: boolean?
+    doc: Interpolation is done in log10 space, by default False
+
+
+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_interpolate.json b/test_jobs/losoto_interpolate.json
new file mode 100644
index 00000000..327302ee
--- /dev/null
+++ b/test_jobs/losoto_interpolate.json
@@ -0,0 +1,7 @@
+{
+  "input_h5parm": {"class": "File", "path": "/data/example.h5", "format": "lofar:#H5Parm"},
+  "soltab":  "sol000/phase000",
+  "axisToRegrid": "time",
+  "newdelta": "1s",
+  "outSoltab": "timeout"
+}
-- 
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