Integrate change

Former-commit-id: 0dbfc43c

lofar-cwl/steps/check_ateam_separation.cwl

@@ -39,6 +39,6 @@ outputs:
 label: check_Ateam_separation
 hints:
   - class: DockerRequirement
-    dockerPull: lofareosc/prefactor
+    dockerPull: lofareosc/prefactor:HBAcalibrator
   - class: InlineJavascriptRequirement
 stdout: Ateam_separation.log

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=
@@ -50,7 +51,7 @@ outputs:
 label: make_sourcedb_ateam
 hints:
   - class: DockerRequirement
-    dockerPull: 'lofareosc/prefactor:latest'
+    dockerPull: 'lofareosc/prefactor:HBAcalibrator'
 stdout: make_sourcedb_ateam.log
 requirements:
   - class: InlineJavascriptRequirement

steps/blsmooth.cwl

@@ -82,7 +82,7 @@ outputs:
       glob: $(inputs.msin.basename)
 hints:
  - class: DockerRequirement
-   dockerPull: lofareosc/prefactor-ci:master
+   dockerPull: lofareosc/prefactor:HBAcalibrator-ci:master
 requirements:
  - class: InitialWorkDirRequirement
    listing:

steps/check_ateam_separation.cwl

@@ -39,6 +39,6 @@ outputs:
 label: check_Ateam_separation
 hints:
   - class: DockerRequirement
-    dockerPull: lofareosc/prefactor
+    dockerPull: lofareosc/prefactor:HBAcalibrator
   - class: InlineJavascriptRequirement
 stdout: Ateam_separation.log

steps/find_skymodel_cal.cwl

@@ -12,9 +12,13 @@ inputs:
       inputBinding:
         position: 0
     - id: skymodels
+<<<<<<< HEAD
       type:
         - Directory?
         - File?
+=======
+      type: Directory?
+>>>>>>> 648aff693fcd8267a3f707ad8fc9609715cddaa2
       doc: Directory containing the sky models
     - id: skymodels_extension
       type: string?
@@ -46,9 +50,9 @@ arguments:
         skymodels = skymodels["path"]
     output = {}
     if extension != 'null':
-        output = find_skymodel(mss, skymodels, './', extension)
+        output = find_skymodel(mss, skymodels, extension)
     else:
-        output = find_skymodel(mss, skymodels, './')
+        output = find_skymodel(mss, skymodels)
 
     skymodel_path = output['SkymodelCal']
     skymodel_name = output['SkymodelName']
@@ -77,4 +81,8 @@ requirements:
 
 hints:
   DockerRequirement:
+<<<<<<< HEAD
     dockerPull: lofareosc/prefactor:latest
+=======
+    dockerPull: lofareosc/prefactor-ci:master
+>>>>>>> 648aff693fcd8267a3f707ad8fc9609715cddaa2

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 +216,18 @@ steps:
     label: make_sourcedb_ateam
     'sbg:x': -500
     'sbg:y': 300
+  - id: find_skymodel_cal
+    in:
+      - id: msin
+        source: msin
+      - id: skymodels
+        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
\ No newline at end of file
+  - class: ScatterFeatureRequirement