recent changes, finish prep step

Former-commit-id: 9e2c9bca

lofar-cwl/steps/makesourcedb.cwl

@@ -10,6 +10,7 @@ inputs:
     type:
       - File
       - string
+    default: '/data/skymodels/Ateam_LBA_CC.skymodel'
     inputBinding:
       position: 0
       prefix: in=

steps/find_skymodel_cal.cwl

@@ -5,44 +5,25 @@ $namespaces:
 id: find_skymodel_cal_py
 baseCommand:
   - python3
+  - /usr/local/bin/find_skymodel_cal.py
 inputs:
-    - id: msin
-      type: Directory
-      doc: MS containing the calibrator
+  - id: ms
+    type:
+      - Directory
+      - type: array
+        items: Directory
     inputBinding:
       position: 0
-    - id: skymodels
-      type: Directory
+    doc: Input measurement set
+  - id: DirSkymodelCal
+    type:
+      - Directory
+      - string
+    default: '/data/skymodels'
     doc: Directory containing the sky models
-    - id: skymodels_extension
-      type: string?
-      doc: path extension of the sky models
-
-label: find_skymodel_cal.py
-arguments:
-  - '-c'
-  - |
-    import sys
-
-    from unittest.mock import MagicMock
-    sys.modules['lofarpipe.support.data_map'] = MagicMock()
-
-
-    from find_skymodel_cal import main as find_skymodel
-    import json
-    mss = sys.argv[1:]
-    skymodels = "$(inputs.skymodels.path)"
-
-    extension = "$(inputs.skymodels_extension)"
-    output = {}
-    if extension != 'null':
-        output = find_skymodel(mss, skymodels, './', extension)
-    else:
-        output = find_skymodel(mss, skymodels, './')
-
-    cwl_output = {'class': 'File', 'path': output['SkymodelCal']}
-    with open('./out.json', 'w') as fp:
-        json.dump(cwl_output, fp)
+    inputBinding:
+      position: 1
+      prefix: '--DirSky'
 outputs:
   - id: output_models
     type: File
@@ -50,10 +31,10 @@ outputs:
         loadContents: true
         glob: 'out.json'
         outputEval: $(JSON.parse(self[0].contents))
-
+label: find_skymodel_cal.py
 requirements:
   - class: InlineJavascriptRequirement
 
 hints:
   DockerRequirement:
-    dockerPull: lofareosc/prefactor-ci:master
+    dockerPull: lofareosc/prefactor

workflows/HBA_calibrator.cwl

@@ -160,17 +160,15 @@ inputs:
     'sbg:y': 1200
   - id: max_separation_arcmin
     type: float?
-    default: 1
+    default: 1.0
     'sbg:x': -1000
     'sbg:y': 1300
   - id: calibrator_path_skymodel
-    type: string?
-    default: /data/skymodels
+    type: Directory?
     'sbg:x': -1000
     'sbg:y': 1400
   - id: A-Team_skymodel
-    type: string?
-    default: /data/skymodels/Ateam_LBA_CC.skymodel
+    type: File?
     'sbg:x': -1000
     'sbg:y': 1500
   - id: cal_solutions
@@ -320,4 +318,3 @@ steps:
     'sbg:y': 0
 requirements:
   - class: SubworkflowFeatureRequirement
-  - class: ScatterFeatureRequirement

workflows/prefactor_calibrator.cwl

@@ -160,17 +160,15 @@ inputs:
     'sbg:y': 1200
   - id: max_separation_arcmin
     type: float?
-    default: 1
+    default: 1.0
     'sbg:x': -1000
     'sbg:y': 1300
   - id: calibrator_path_skymodel
-    type: string?
-    default: /data/skymodels
+    type: Directory?
     'sbg:x': -1000
     'sbg:y': 1400
   - id: A-Team_skymodel
-    type: string?
-    default: /data/skymodels/Ateam_LBA_CC.skymodel
+    type: File?
     'sbg:x': -1000
     'sbg:y': 1500
   - id: cal_solutions

workflows/prefactor_calibrator/prep.cwl

@@ -70,22 +70,28 @@ inputs:
     type: int?
     'sbg:x': -1000
     'sbg:y': 600
-  - id: A-Team_skymodel
-    type: string?
-    default: /data/skymodels/Ateam_LBA_CC.skymodel
+  - id: max_separation_arcmin
+    type: float?
     'sbg:x': -1000
     'sbg:y': 700
+  - id: calibrator_path_skymodel
+    type: Directory?
+    'sbg:x': -1000
+    'sbg:y': 800
+  - id: A-Team_skymodel
+    type: File?
+    'sbg:x': -1000
+    'sbg:y': 900
   - id: elevation
     type: string
-    default: '0deg..20deg'
+    default: 0deg..20deg
     'sbg:x': -1000
-    'sbg:y': 800
+    'sbg:y': 1000
   - id: amplmin
     type: float
-    default: 1e-30
+    default: 1.e-30
     'sbg:x': -1000
-    'sbg:y': 800
-
+    'sbg:y': 1100
 outputs:
   - id: check_Ateam_separation.png
     outputSource:
@@ -128,10 +134,12 @@ steps:
     in:
       - id: baselines_to_flag
         default: []
-        source: flag_baselines
-      - id: ntimechunk
-        default: 10
-        source: max_dppp_threads
+        source:
+          - flag_baselines
+      - id: elevation_to_flag
+        source: elevation
+      - id: min_amplitude_to_flag
+        source: amplmin
       - id: memoryperc
         default: 20
         source: memoryperc
@@ -143,7 +151,8 @@ steps:
         source: demix
       - id: msin
         linkMerge: merge_flattened
-        source: msin
+        source:
+          - msin
       - id: msin_baseline
         default: '*'
         source: filter_baselines
@@ -166,12 +175,12 @@ steps:
         source: process_baselines_cal
       - id: target_source
         source: demix_target
+      - id: ntimechunk
+        default: 10
+        source: max_dppp_threads
       - id: subtract_sources
-        source: demix_sources
-      - id: elevation_to_flag
-        source: elevation
-      - id: min_amplitude_to_flag
-        source: amplmin
+        source:
+          - demix_sources
     out:
       - id: msout
       - id: logfile
@@ -207,6 +216,20 @@ steps:
     label: make_sourcedb_ateam
     'sbg:x': -500
     'sbg:y': 300
+  - id: find_skymodel_cal
+    in:
+      - id: ms
+        source: msin
+      - id: max_seperation_arcmin
+        source: max_separation_arcmin
+      - id: DirSkymodelCal
+        source: calibrator_path_skymodel
+    out:
+      - id: output_models
+    run: ../../steps/find_skymodel_cal.cwl
+    label: find_skymodel_cal
+    'sbg:x': -500
+    'sbg:y': 500
 requirements:
   - class: SubworkflowFeatureRequirement
   - class: ScatterFeatureRequirement