Merge branch 'master' into 'losoto_replicateonaxis'

# Conflicts:
#   .gitlab-ci.yml

.gitlab-ci.yml

@@ -65,6 +65,17 @@ losoto_replicateonaxis:
   script:
     - cwl-runner --no-container steps/LoSoTo.Replicateonaxis.cwl test_jobs/losoto_axisreplicate.json
 
+losoto_reset:
+  stage: test_steps
+  allow_failure: true
+  script:
+    - cwl-runner --no-container steps/LoSoTo.Reset.cwl test_jobs/losoto_reset.json
+
+losoto_residual:
+  stage: test_steps
+  allow_failure: true
+  script:
+    - cwl-runner --no-container steps/LoSoTo.Residual.cwl test_jobs/losoto_residual.json
 
 parset_selector:
   stage: test_steps

steps/LoSoTo.Reset.cwl

+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_reset
+
+doc: Subtract/divide two tables or a clock/tec/tec3rd/rm from a phase.
+
+requirements:
+  InlineJavascriptRequirement: {}
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: 'parset.config'
+        entry: |
+          [reset]
+          soltab = $(inputs.soltab)
+          operation = RESET
+          $(inputs.dataVal !== null? 'dataVal=' + inputs.dataVal: '')
+
+      - entryname: $(inputs.input_h5parm.basename)
+        entry: $(inputs.input_h5parm)
+        writable: true
+
+baseCommand: "losoto"
+
+arguments:
+  - $(inputs.input_h5parm.basename)
+  - parset.config
+
+hints:
+  DockerRequirement:
+    dockerPull: lofareosc/prefactor-ci:master
+
+inputs:
+  - id: input_h5parm
+    type: File
+  - id: soltab
+    type: string
+    doc: "Solution table"
+  - id: dataVal
+    type: float?
+    doc: |
+      If given set values to this number, otherwise uses 1 for amplitude and 0
+      for all other soltab types.
+outputs:
+  - id: output_h5parm
+    type: File
+    outputBinding:
+      glob: $(inputs.input_h5parm.basename)

steps/LoSoTo.Residual.cwl

+#!/usr/bin/env cwl-runner
+
+class: CommandLineTool
+cwlVersion: v1.0
+id: losoto_abs
+
+doc: Subtract/divide two tables or a clock/tec/tec3rd/rm from a phase.
+
+requirements:
+  InitialWorkDirRequirement:
+    listing:
+      - entryname: 'parset.config'
+        entry: |
+          [residuals]
+          soltab = $(inputs.soltab)
+          operation=RESIDUALS
+          soltabsToSub=$(inputs.soltabsToSub)
+          ratio=$(inputs.ratio)
+
+      - entryname: $(inputs.input_h5parm.basename)
+        entry: $(inputs.input_h5parm)
+        writable: true
+
+baseCommand: "losoto"
+
+arguments:
+  - $(inputs.input_h5parm.basename)
+  - parset.config
+
+hints:
+  DockerRequirement:
+    dockerPull: lofareosc/prefactor-ci:master
+
+inputs:
+  - id: input_h5parm
+    type: File
+  - id: soltab
+    type: string
+    doc: "Solution table"
+  - id: soltabsToSub
+    type: string[]
+    doc: List of soltabs to subtract
+  - id: ratio
+    type: boolean?
+    default: false
+    doc: Return the ratio instead of subtracting.
+
+outputs:
+  - id: output_h5parm
+    type: File
+    outputBinding:
+      glob: $(inputs.input_h5parm.basename)

test_jobs/losoto_reset.json

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

test_jobs/losoto_residual.json

+{
+    "input_h5parm": {
+            "class": "File",
+            "path": "/data/example.h5"
+        },
+    "soltab": "sol000/amplitude000",
+    "soltabsToSub": ["amplitude000"]
+}