diff --git a/lofar-cwl/steps/makesourcedb.cwl b/lofar-cwl/steps/makesourcedb.cwl
index eb5c2e7c7b8f09c0a2c97ea4512bb241cff17fb5..30c09253d64705615c090b4c8020e3c7002cf523 100755
--- a/lofar-cwl/steps/makesourcedb.cwl
+++ b/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=
diff --git a/steps/find_skymodel_cal.cwl b/steps/find_skymodel_cal.cwl
index 51a1dc4a8f7500fccac5cef763cd15d50ecaa505..6bfc52d0c8a70250bbb4b768d0db8d96e0ac1629 100644
--- a/steps/find_skymodel_cal.cwl
+++ b/steps/find_skymodel_cal.cwl
@@ -5,44 +5,25 @@ $namespaces:
id: find_skymodel_cal_py
baseCommand:
- python3
+ - /usr/local/bin/find_skymodel_cal.py
inputs:
- - id: msin
- type: Directory
- doc: MS containing the calibrator
- inputBinding:
- position: 0
- - id: skymodels
- type: Directory
- doc: Directory containing the sky models
- - id: skymodels_extension
- type: string?
- doc: path extension of the sky models
-
-label: find_skymodel_cal.py
-arguments:
- - '-c'
- - |
- import sys
-
- from unittest.mock import MagicMock
- sys.modules['lofarpipe.support.data_map'] = MagicMock()
-
-
- from find_skymodel_cal import main as find_skymodel
- import json
- mss = sys.argv[1:]
- skymodels = "$(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)
+ - id: ms
+ type:
+ - Directory
+ - type: array
+ items: Directory
+ inputBinding:
+ position: 0
+ doc: Input measurement set
+ - id: DirSkymodelCal
+ type:
+ - Directory
+ - string
+ default: '/data/skymodels'
+ doc: Directory containing the sky models
+ 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
diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl
index 1e84665e1833386275e3616214bdc46f7311ed9b..942787c9f84caba18e8902e8be34cddba821865a 100644
--- a/workflows/HBA_calibrator.cwl
+++ b/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
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index d71d33b4f9c7e92ff00c9efeb6060db7e44141d0..3355c043ed1de9c944ccf877aa727ed346959b1d 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/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
diff --git a/workflows/prefactor_calibrator/prep.cwl b/workflows/prefactor_calibrator/prep.cwl
index 511b6adb67fcff295edf29c1745ed69b90018331..ebe7e9cad1cbc2622653fdb036e70ee1900afa0f 100644
--- a/workflows/prefactor_calibrator/prep.cwl
+++ b/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
\ No newline at end of file
+ - class: ScatterFeatureRequirement