Add ReplicateOnAxis step

.gitlab-ci.yml

@@ -59,6 +59,12 @@ losoto_norm:
   script:
     - cwl-runner --no-container steps/LoSoTo.Norm.cwl test_jobs/losoto_norm.json
 
+losoto_replicateonaxis:
+  stage: test_steps
+  allow_failure: true
+  script:
+    - cwl-runner --no-container steps/LoSoTo.Replicateonaxis.cwl test_jobs/losoto_axisreplicate.json
+
 
 parset_selector:
   stage: test_steps

steps/LoSoTo.Replicateonaxis.cwl

+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_replicate_on_axis
+
+doc: |
+  Replace the values along a certain axis taking them from one specific axis
+  cell
+
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: "replicate_axis.py"
+        entry: |
+          import sys
+          from losoto.h5parm import openSoltab
+          from losoto.operations import replicateonaxis
+
+          soltab_address = "$(inputs.soltab)"
+          soltab = openSoltab(sys.argv[1], address=soltab_address)
+
+          axisReplicate = "$(inputs.axisReplicate)"
+          fromCell = "$(inputs.fromCell !== null ? inputs.fromCell : 0)"
+          updateWeights = "$(inputs.updateWeights? inputs.updateWeights : 'True')"
+
+          replicateonaxis.run(soltab, axisReplicate=axisReplicate,
+                                      fromCell=fromCell,
+                                      updateWeights=updateWeights)
+
+      - entryname: $(inputs.input_h5parm.basename)
+        entry: $(inputs.input_h5parm)
+        writable: true
+
+baseCommand: "python3"
+
+arguments:
+  - replicate_axis.py
+  - $(inputs.input_h5parm.basename)
+
+
+hints:
+  DockerRequirement:
+    dockerPull: lofareosc/prefactor-ci:master
+
+inputs:
+  - id: input_h5parm
+    type: File
+  - id: soltab
+    type: string
+    doc: "Solution table"
+  - id: axisReplicate
+    type: string
+    doc: Axis along which replicate the values.
+  - id: fromCell
+    type: string?
+    doc: A cell value in axisReplicate from which to copy the data values.
+  - id: updateWeights
+    type: boolean?
+    doc: |
+      If False then weights are untouched, if True they are replicated
+      like data. Default: True.
+
+outputs:
+  - id: output_h5parm
+    type: File
+    outputBinding:
+      glob: $(inputs.input_h5parm.basename)

test_jobs/losoto_replicateonaxis.json

+{
+    "input_h5parm": {
+            "class": "File",
+            "path": "/data/example.h5"
+        },
+    "soltab": "sol000/amplitude000",
+    "axisReplicate": "time",
+    "updateWeight": true
+}