diff --git a/steps/DPPP.cwl b/steps/DPPP.cwl
index d86b709fef3e84628a494c1dc2aa3dfc3f83ff04..70d824f02518f594ecf5d9b8975041b1febee5bc 100755
--- a/steps/DPPP.cwl
+++ b/steps/DPPP.cwl
@@ -1,42 +1,35 @@
-#!/usr/bin/env cwl-runner
-
class: CommandLineTool
cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
id: dppp
-baseCommand: [DPPP]
-
-requirements:
- InlineJavascriptRequirement: {}
-
-hints:
- DockerRequirement:
- dockerPull: lofareosc/prefactor-ci:master
-
-arguments: []
-
+baseCommand:
+ - DPPP
inputs:
- id: parset
type: File?
inputBinding:
- position: -1
+ position: -1
- id: msin
type: Directory?
- doc: Input Measurement Set
inputBinding:
- prefix: msin=
- separate: false
- - id: msout_name
+ position: 0
+ prefix: msin=
+ separate: false
+ doc: Input Measurement Set
+ - default: out.MS
+ id: msout_name
type: string
- doc: Output Measurement Set
- default: out.MS
inputBinding:
- prefix: msout=
- separate: false
+ position: 0
+ prefix: msout=
+ separate: false
+ doc: Output Measurement Set
- id: secondary_files
- type: File[]?
+ type: 'File[]?'
doc: Secondary files needed for the step
- id: secondary_directories
- type: Directory[]?
+ type: 'Directory[]?'
doc: Secondary directories needed for the step
- id: output_file_names
type: Any
@@ -49,11 +42,10 @@ outputs:
doc: Output Measurement Set
type: Directory
outputBinding:
- glob: $(inputs.msout_name=="."?inputs.msin:inputs.msout_name)
+ glob: '$(inputs.msout_name=="."?inputs.msin:inputs.msout_name)'
- id: secondary_output_files
doc: Secondary output files
type: Any
-
outputBinding:
outputEval: |-
${
@@ -68,7 +60,6 @@ outputs:
}
return output
}
-
- id: secondary_output_directories
doc: Secondary output directories
type: Any
@@ -86,3 +77,13 @@ outputs:
}
return output
}
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: DPPP.log
+hints:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor
+stdout: DPPP.log
+requirements:
+ - class: InlineJavascriptRequirement
diff --git a/steps/check_ateam_separation.cwl b/steps/check_ateam_separation.cwl
index 0257dd38226dba7c0be4b1ac447eed45a68f2281..b7583f38f70d4b56414704f9c316b980ec5cd7f8 100755
--- a/steps/check_ateam_separation.cwl
+++ b/steps/check_ateam_separation.cwl
@@ -1,17 +1,11 @@
-#!/usr/bin/env cwl-runner
-
class: CommandLineTool
cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
id: check_ateam_separation
-
-requirements:
- - class: DockerRequirement
- dockerPull: lofareosc/prefactor-ci:master
- - class: InlineJavascriptRequirement
-
-
baseCommand:
- - check_Ateam_separation.py
+ - python3
+ - /usr/local/bin/check_Ateam_separation.py
inputs:
- id: ms
type:
@@ -21,20 +15,30 @@ inputs:
inputBinding:
position: 0
doc: Input measurement set
- - id: output_image_path
+ - default: ateam_separation.png
+ id: output_image_name
type: string?
- default: 'output/ateam_separation.png'
inputBinding:
+ position: 2
prefix: '--outputimage'
- id: min_separation
- type: float?
+ type: float
inputBinding:
- position: 0
+ position: 1
prefix: '--min_separation'
outputs:
- id: output_imag
doc: Output image
type: File?
outputBinding:
- glob: $(inputs.output_image_path)
+ glob: $(inputs.output_image_name)
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: Ateam_separation.log
label: check_Ateam_separation
+requirements:
+ - class: DockerRequirement
+ dockerPull: lofareosc/prefactor
+ - class: InlineJavascriptRequirement
+stdout: Ateam_separation.log
diff --git a/steps/makesourcedb.cwl b/steps/makesourcedb.cwl
index d2d43a39e2a86a1bc38259dc15d7d886e0c12652..eb5c2e7c7b8f09c0a2c97ea4512bb241cff17fb5 100755
--- a/steps/makesourcedb.cwl
+++ b/steps/makesourcedb.cwl
@@ -1,5 +1,3 @@
-#!/usr/bin/env cwl-runner
-
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
@@ -8,38 +6,51 @@ id: make_sourcedb
baseCommand:
- makesourcedb
inputs:
- - id: error_tolerance
- type: float?
- inputBinding:
- position: 0
- separate: false
- id: sky_model
- type: File
+ type:
+ - File
+ - string
inputBinding:
position: 0
prefix: in=
separate: false
- - default: out.sourcedb
+ - default: Ateam.sourcedb
id: output_file_name
type: string?
inputBinding:
- position: 0
+ position: 1
prefix: out=
separate: false
+ valueFrom: Ateam.sourcedb
- default: blob
id: outtype
type: string?
inputBinding:
- position: 0
+ position: 2
prefix: outtype=
separate: false
+ - default: <
+ id: format
+ type: string?
+ inputBinding:
+ position: 3
+ prefix: format=
+ separate: false
outputs:
- - id: output
- type: [Directory, File]
+ - id: sourcedb
+ type:
+ - Directory
+ - File
outputBinding:
glob: $(inputs.output_file_name)
+ - id: log
+ type: File?
+ outputBinding:
+ glob: make_sourcedb_ateam.log
label: make_sourcedb_ateam
hints:
- class: DockerRequirement
- dockerPull: lofareosc/prefactor-ci:master
+ dockerPull: 'lofareosc/prefactor:latest'
+stdout: make_sourcedb_ateam.log
+requirements:
- class: InlineJavascriptRequirement
diff --git a/subworkflow/ndppp_prep_cal.cwl b/subworkflow/ndppp_prep_cal.cwl
index b495d85a1a3491b70e28d8e90dee66e70581674b..1ef432a24e3e6455cbee216d24982c0cdfd3ae1d 100644
--- a/subworkflow/ndppp_prep_cal.cwl
+++ b/subworkflow/ndppp_prep_cal.cwl
@@ -33,6 +33,10 @@ inputs:
type: Directory?
'sbg:x': 2129.6337890625
'sbg:y': 149.5590362548828
+ - id: skymodel
+ type: File
+ 'sbg:x': 1428.3411865234375
+ 'sbg:y': 273.64007568359375
outputs:
- id: msout
outputSource:
@@ -40,12 +44,12 @@ outputs:
type: Directory
'sbg:x': 2856.537841796875
'sbg:y': 53.67763900756836
- - id: demix_parmdb
+ - id: logfile
outputSource:
- - filter_demix_parmdb/output
- type: Directory
- 'sbg:x': 3071.909912109375
- 'sbg:y': -170.69992065429688
+ - dppp/logfile
+ type: File?
+ 'sbg:x': 2857.9423828125
+ 'sbg:y': 253.50680541992188
steps:
- id: flagbaseline
in:
@@ -107,10 +111,10 @@ steps:
'sbg:y': -42.28850555419922
- id: flagedge
in:
- - id: step_name
- default: flagedge
- id: steps
default: []
+ - id: step_name
+ default: flagedge
- id: chan
default: '[0..nchan/32-1,31*nchan/32..nchan-1]'
out:
@@ -155,6 +159,8 @@ steps:
- id: steps
source:
- flagamp/augmented_steps
+ - id: skymodel
+ source: skymodel
out:
- id: augmented_steps
run: ../steps/DP3.DemixerStepGenerator.cwl
@@ -197,26 +203,11 @@ steps:
- id: msout
- id: secondary_output_files
- id: secondary_output_directories
+ - id: logfile
run: ../steps/DPPP.cwl
'sbg:x': 2548.738037109375
'sbg:y': -37.388668060302734
- - id: filter_demix_parmdb
- in:
- - id: inputs
- source: dppp/secondary_output_directories
- - id: step_name
- default: demixstepgenerator
- valueFrom: demixstepgenerator
- - id: key_name
- valueFrom: instrumentmodel
- out:
- - id: output
- run: ../steps/DirSelector.cwl
- label: DirSelector
- 'sbg:x': 2838.8115234375
- 'sbg:y': -151.54710388183594
requirements:
- class: SubworkflowFeatureRequirement
- class: StepInputExpressionRequirement
- class: InlineJavascriptRequirement
-
diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl
index 04dcaede5f9ca54b385167cf1472cae7055fd3af..3ebbe019c1750bb60717dbba5f91923c6c8dc89b 100644
--- a/workflows/HBA_calibrator.cwl
+++ b/workflows/HBA_calibrator.cwl
@@ -5,28 +5,98 @@ label: HBA.cwl
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- - id: msin_calibrator
+ - id: msin
type: 'Directory[]'
- 'sbg:x': -245
- 'sbg:y': -44
+ 'sbg:x': -524.25
+ 'sbg:y': -397.7361145019531
+ - id: raw_data
+ type: boolean?
+ default: false
+ 'sbg:x': -499.4583435058594
+ 'sbg:y': -700.1944580078125
+ - id: memoryperc
+ type: int?
+ default: 20
+ 'sbg:x': -519.2446899414062
+ 'sbg:y': -98.3177261352539
+ - id: demix
+ type: boolean?
+ default: false
+ 'sbg:x': -508.2083435058594
+ 'sbg:y': 359.7083435058594
+ - id: baselines_to_flag
+ type: 'string[]?'
+ default: []
+ 'sbg:x': -506.8194580078125
+ 'sbg:y': 503.4721984863281
+ - id: min_separation
+ type: float?
+ default: 30
+ 'sbg:x': -525
+ 'sbg:y': -249.46209716796875
+ - id: A-Team_sky_model
+ type: File?
+ 'sbg:x': -509
+ 'sbg:y': 679.407958984375
outputs:
- - id: solutions
+ - id: msout
outputSource:
- - prefactor/solutions
- type: File
- 'sbg:x': 99
- 'sbg:y': -44
+ - prefactor/msout
+ type: Directory[]
+ 'sbg:x': 289.5600891113281
+ 'sbg:y': -144.01869201660156
+ - id: make_sourcedb_ateam.log
+ outputSource:
+ - prefactor/make_sourcedb_ateam.log
+ type: File?
+ 'sbg:x': 317.4496154785156
+ 'sbg:y': 9.373631477355957
+ - id: logfile_prep_cal
+ outputSource:
+ - prefactor/logfile_prep_cal
+ type: File[]?
+ 'sbg:x': 315.0741882324219
+ 'sbg:y': 180.26284790039062
+ - id: check_Ateam_separation.png
+ outputSource:
+ - prefactor/check_Ateam_separation.png
+ type: File[]?
+ 'sbg:x': 287.6455078125
+ 'sbg:y': 344.1313171386719
+ - id: check_Ateam_separation.log
+ outputSource:
+ - prefactor/check_Ateam_separation.log
+ type: File[]?
+ 'sbg:x': 315.5941467285156
+ 'sbg:y': 494.9656982421875
steps:
- id: prefactor
in:
+ - id: raw_data
+ source: raw_data
+ - id: demix
+ source: demix
- id: msin
source:
- - msin_calibrator
+ - msin
+ - id: memoryperc
+ source: memoryperc
+ - id: baselines_to_flag
+ source:
+ - baselines_to_flag
+ - id: min_separation
+ source: min_separation
+ - id: A-Team_sky_model
+ source: A-Team_sky_model
out:
- - id: solutions
- run: ./prefactor_calibrator.cwl
+ - id: check_Ateam_separation.png
+ - id: check_Ateam_separation.log
+ - id: make_sourcedb_ateam.log
+ - id: msout
+ - id: logfile_prep_cal
+ run: ./prefactor_calibrator_test.cwl
label: prefactor_calibrator
- 'sbg:x': -72.39886474609375
- 'sbg:y': -44.5
+ 'sbg:x': -107.87364959716797
+ 'sbg:y': -53.743682861328125
requirements:
- class: SubworkflowFeatureRequirement
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index bd5f299b4b7ae640770d018b5c20495dfd1a4f72..9f8d3c6c58516fce1ecf3ab70d2615fe76d95e10 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/workflows/prefactor_calibrator.cwl
@@ -7,52 +7,56 @@ $namespaces:
inputs:
- id: raw_data
type: boolean
- 'sbg:x': -798
- 'sbg:y': -680
+ 'sbg:x': -634
+ 'sbg:y': -688
- id: demix
type: boolean
- 'sbg:x': -635
- 'sbg:y': -176
+ 'sbg:x': -639.3313598632812
+ 'sbg:y': -271
- id: msin
type: 'Directory[]'
- 'sbg:x': -828
- 'sbg:y': -600
+ 'sbg:x': -635
+ 'sbg:y': -543
- id: skymodels
type: Directory
- 'sbg:x': 5
- 'sbg:y': -819
- - id: min_amplitude_to_flag
- type: float
- 'sbg:x': -798
- 'sbg:y': -441
+ 'sbg:x': -123
+ 'sbg:y': -850
- id: memoryperc
type: int
- 'sbg:x': -643
- 'sbg:y': -357
+ 'sbg:x': -634
+ 'sbg:y': -411
- id: baselines_to_flag
type: 'string[]'
- 'sbg:x': -448
- 'sbg:y': -161
+ 'sbg:x': -635.8651123046875
+ 'sbg:y': -148
- id: uvw
type: File?
- 'sbg:x': -360
- 'sbg:y': -851
+ 'sbg:x': -356.9723205566406
+ 'sbg:y': -804.0709838867188
- id: strategy
type: File?
- 'sbg:x': -430
+ 'sbg:x': -352
'sbg:y': -713
- id: propagate_solutions
type: boolean
- 'sbg:x': -99
- 'sbg:y': -698
+ 'sbg:x': -112
+ 'sbg:y': -737
- id: flagunconverged
type: boolean
- 'sbg:x': -167
- 'sbg:y': -396
+ 'sbg:x': -92
+ 'sbg:y': -400
- id: do_smooth
type: boolean
- 'sbg:x': -201
- 'sbg:y': -237
+ 'sbg:x': -89
+ 'sbg:y': -276
+ - id: min_separation
+ type: float?
+ 'sbg:x': -638.4987182617188
+ 'sbg:y': 31.238996505737305
+ - id: A-Team_sky_model
+ type: string
+ 'sbg:x': -889.9927978515625
+ 'sbg:y': -845.9927978515625
outputs:
- id: outh5parm
outputSource:
@@ -64,8 +68,26 @@ outputs:
outputSource:
- h5parm_collector/log
type: File
- 'sbg:x': 430.1015625
- 'sbg:y': -349.5
+ 'sbg:x': 481.1239318847656
+ 'sbg:y': -368.0228576660156
+ - id: output_imag
+ outputSource:
+ - check_ateam_separation/output_imag
+ type: File?
+ 'sbg:x': 486.94464111328125
+ 'sbg:y': -5.156437873840332
+ - id: logfile
+ outputSource:
+ - check_ateam_separation/logfile
+ type: File?
+ 'sbg:x': 492.1335754394531
+ 'sbg:y': 133
+ - id: log_1
+ outputSource:
+ - make_sourcedb/log
+ type: File?
+ 'sbg:x': 495.6245422363281
+ 'sbg:y': -1257.4857177734375
steps:
- id: ndppp_prep_cal
in:
@@ -77,7 +99,6 @@ steps:
default: 0deg..20deg
- id: min_amplitude_to_flag
default: 1.e-30
- source: min_amplitude_to_flag
- id: memoryperc
default: 20
source: memoryperc
@@ -89,6 +110,8 @@ steps:
linkMerge: merge_flattened
source:
- msin
+ - id: skymodel
+ source: make_sourcedb/sourcedb
out:
- id: msout
- id: demix_parmdb
@@ -153,6 +176,31 @@ steps:
label: H5parm_collector
'sbg:x': 292.1979675292969
'sbg:y': -543.7208251953125
+ - id: check_ateam_separation
+ in:
+ - id: ms
+ source:
+ - msin
+ - id: min_separation
+ source: min_separation
+ out:
+ - id: output_imag
+ - id: logfile
+ run: ../steps/check_ateam_separation.cwl
+ label: check_Ateam_separation
+ 'sbg:x': -331.452392578125
+ 'sbg:y': 23.596216201782227
+ - id: make_sourcedb
+ in:
+ - id: sky_model
+ source: A-Team_sky_model
+ out:
+ - id: sourcedb
+ - id: log
+ run: ../steps/makesourcedb.cwl
+ label: make_sourcedb_ateam
+ 'sbg:x': -628.7400512695312
+ 'sbg:y': -847.117919921875
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
diff --git a/workflows/prefactor_calibrator_test.cwl b/workflows/prefactor_calibrator_test.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..c57c29dff8a72d7eca670d7f13593d10effe6857
--- /dev/null
+++ b/workflows/prefactor_calibrator_test.cwl
@@ -0,0 +1,130 @@
+class: Workflow
+cwlVersion: v1.0
+id: prefactor_calibrator
+label: prefactor_calibrator
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+inputs:
+ - id: raw_data
+ type: boolean
+ 'sbg:x': -634
+ 'sbg:y': -688
+ - id: demix
+ type: boolean
+ 'sbg:x': -639.3313598632812
+ 'sbg:y': -271
+ - id: msin
+ type: 'Directory[]'
+ 'sbg:x': -635
+ 'sbg:y': -543
+ - id: memoryperc
+ type: int
+ 'sbg:x': -634
+ 'sbg:y': -411
+ - id: baselines_to_flag
+ type: 'string[]'
+ 'sbg:x': -635.8651123046875
+ 'sbg:y': -148
+ - id: min_separation
+ type: float?
+ 'sbg:x': -638.4987182617188
+ 'sbg:y': 31.238996505737305
+ - id: A-Team_sky_model
+ type:
+ - string?
+ - File?
+ default: '/data/skymodels/Ateam_LBA_CC.skymodel'
+ 'sbg:x': -889.9927978515625
+ 'sbg:y': -845.9927978515625
+outputs:
+ - id: check_Ateam_separation.png
+ outputSource:
+ - check_ateam_separation/output_imag
+ type: File[]?
+ 'sbg:x': 68.06497955322266
+ 'sbg:y': -3.1985559463500977
+ - id: check_Ateam_separation.log
+ outputSource:
+ - check_ateam_separation/logfile
+ type: File[]?
+ 'sbg:x': 83.07220458984375
+ 'sbg:y': 136.60289001464844
+ - id: make_sourcedb_ateam.log
+ outputSource:
+ - make_sourcedb/log
+ type: File?
+ 'sbg:x': 71.66065216064453
+ 'sbg:y': -880.4981689453125
+ - id: msout
+ outputSource:
+ - ndppp_prep_cal/msout
+ type: Directory[]
+ 'sbg:x': 52.33274459838867
+ 'sbg:y': -546.0951538085938
+ - id: logfile_prep_cal
+ outputSource:
+ - ndppp_prep_cal/logfile
+ type: File[]?
+ 'sbg:x': 43.325523376464844
+ 'sbg:y': -371.35504150390625
+steps:
+ - id: ndppp_prep_cal
+ in:
+ - id: baselines_to_flag
+ default: []
+ source:
+ - baselines_to_flag
+ - id: elevation_to_flag
+ default: 0deg..20deg
+ - id: min_amplitude_to_flag
+ default: 1.e-30
+ - id: memoryperc
+ default: 20
+ source: memoryperc
+ - id: raw_data
+ source: raw_data
+ - id: demix
+ source: demix
+ - id: msin
+ linkMerge: merge_flattened
+ source:
+ - msin
+ - id: skymodel
+ source: make_sourcedb/sourcedb
+ out:
+ - id: msout
+ - id: logfile
+ run: ../subworkflow/ndppp_prep_cal.cwl
+ label: ndppp_prep_cal
+ scatter:
+ - msin
+ 'sbg:x': -359
+ 'sbg:y': -519
+ - id: check_ateam_separation
+ in:
+ - id: ms
+ source:
+ - msin
+ - id: min_separation
+ source: min_separation
+ out:
+ - id: output_imag
+ - id: logfile
+ run: ../steps/check_ateam_separation.cwl
+ label: check_Ateam_separation
+ 'sbg:x': -331.452392578125
+ 'sbg:y': 23.596216201782227
+ - id: make_sourcedb
+ in:
+ - id: sky_model
+ source: A-Team_sky_model
+ out:
+ - id: sourcedb
+ - id: log
+ run: ../steps/makesourcedb.cwl
+ label: make_sourcedb_ateam
+ 'sbg:x': -628.7400512695312
+ 'sbg:y': -847.117919921875
+requirements:
+ - class: SubworkflowFeatureRequirement
+ - class: ScatterFeatureRequirement