From b8c8b58c146c88ae19b36b80d3499cf6313dffc7 Mon Sep 17 00:00:00 2001
From: alex <alex@tls-tautenburg.de>
Date: Mon, 7 Feb 2022 11:32:22 +0000
Subject: [PATCH] move to modeldatacolumns / tidy up deprecated variables
---
steps/ddecal.cwl | 19 +++++++------------
workflows/HBA_calibrator.cwl | 5 -----
workflows/HBA_target.cwl | 2 ++
workflows/LBA_calibrator.cwl | 5 -----
workflows/prefactor_calibrator.cwl | 3 ---
.../apply_calibrate_bp.cwl | 5 +++--
.../apply_calibrate_fr.cwl | 5 +++--
.../apply_calibrate_pa.cwl | 5 +++--
.../predict_calibrate.cwl | 5 +++--
workflows/prefactor_target/concat.cwl | 3 ---
workflows/prefactor_target/finalize.cwl | 4 +---
workflows/prefactor_target/gsmcal.cwl | 2 --
12 files changed, 22 insertions(+), 41 deletions(-)
diff --git a/steps/ddecal.cwl b/steps/ddecal.cwl
index 454afeea..7e4f0b83 100644
--- a/steps/ddecal.cwl
+++ b/steps/ddecal.cwl
@@ -35,14 +35,6 @@ inputs:
prefix: msin.datacolumn=
separate: false
- - id: msin_modelcolum
- type: string?
- default: MODEL_DATA
- doc: Model data Column
- inputBinding:
- prefix: msin.modelcolumn=
- separate: false
-
- id: output_name_h5parm
type: string?
default: instrument.h5
@@ -68,11 +60,14 @@ inputs:
default: true
inputBinding:
prefix: ddecal.propagateconvergedonly=True
- - id: usemodelcolumn
- type: boolean?
- default: true
+ - id: modeldatacolumns
+ type: string[]?
+ default: []
inputBinding:
- prefix: ddecal.usemodelcolumn=True
+ prefix: ddecal.modeldatacolumns=
+ separate: false
+ valueFrom: "[$(self.join(','))]"
+ shellQuote: false
- id: flagunconverged
type: boolean?
default: false
diff --git a/workflows/HBA_calibrator.cwl b/workflows/HBA_calibrator.cwl
index 602e998c..a989afee 100644
--- a/workflows/HBA_calibrator.cwl
+++ b/workflows/HBA_calibrator.cwl
@@ -88,9 +88,6 @@ inputs:
- id: tables2export
type: string?
default: clock
- - id: final_apply
- type: boolean?
- default: false
- id: max_dppp_threads
type: int?
default: 10
@@ -200,8 +197,6 @@ steps:
source: clock_smooth
- id: tables2export
source: tables2export
- - id: final_apply
- source: final_apply
- id: max_dppp_threads
source: max_dppp_threads
- id: memoryperc
diff --git a/workflows/HBA_target.cwl b/workflows/HBA_target.cwl
index bf2ea2df..f9a55072 100644
--- a/workflows/HBA_target.cwl
+++ b/workflows/HBA_target.cwl
@@ -276,6 +276,8 @@ steps:
source: clip_sources
- id: ncores
source: ncores
+ - id: gsmcal_step
+ source: gsmcal_step
out:
- id: logfiles
- id: msout
diff --git a/workflows/LBA_calibrator.cwl b/workflows/LBA_calibrator.cwl
index f8457969..baf35ae2 100644
--- a/workflows/LBA_calibrator.cwl
+++ b/workflows/LBA_calibrator.cwl
@@ -88,9 +88,6 @@ inputs:
- id: tables2export
type: string?
default: phaseOrig
- - id: final_apply
- type: boolean?
- default: false
- id: max_dppp_threads
type: int?
default: 10
@@ -200,8 +197,6 @@ steps:
source: clock_smooth
- id: tables2export
source: tables2export
- - id: final_apply
- source: final_apply
- id: max_dppp_threads
source: max_dppp_threads
- id: memoryperc
diff --git a/workflows/prefactor_calibrator.cwl b/workflows/prefactor_calibrator.cwl
index 775ffbba..637da953 100644
--- a/workflows/prefactor_calibrator.cwl
+++ b/workflows/prefactor_calibrator.cwl
@@ -87,9 +87,6 @@ inputs:
- id: tables2export
type: string?
default: clock
- - id: final_apply
- type: boolean?
- default: false
- id: max_dppp_threads
type: int?
default: 10
diff --git a/workflows/prefactor_calibrator/apply_calibrate_bp.cwl b/workflows/prefactor_calibrator/apply_calibrate_bp.cwl
index 0553de82..b6817234 100644
--- a/workflows/prefactor_calibrator/apply_calibrate_bp.cwl
+++ b/workflows/prefactor_calibrator/apply_calibrate_bp.cwl
@@ -161,8 +161,9 @@ steps:
source: BLsmooth/msout
- id: msin_datacolumn
default: SMOOTHED_DATA
- - id: msin_modelcolum
- default: MODEL_DATA
+ - id: modeldatacolumns
+ default:
+ - 'MODEL_DATA'
- id: propagate_solutions
source: propagatesolutions
- id: flagunconverged
diff --git a/workflows/prefactor_calibrator/apply_calibrate_fr.cwl b/workflows/prefactor_calibrator/apply_calibrate_fr.cwl
index e1379163..d7bd6678 100644
--- a/workflows/prefactor_calibrator/apply_calibrate_fr.cwl
+++ b/workflows/prefactor_calibrator/apply_calibrate_fr.cwl
@@ -78,8 +78,9 @@ steps:
source: BLsmooth/msout
- id: msin_datacolumn
default: SMOOTHED_DATA
- - id: msin_modelcolum
- default: MODEL_DATA
+ - id: modeldatacolumns
+ default:
+ - 'MODEL_DATA'
- id: flagunconverged
source: flagunconverged
- id: propagate_solutions
diff --git a/workflows/prefactor_calibrator/apply_calibrate_pa.cwl b/workflows/prefactor_calibrator/apply_calibrate_pa.cwl
index 781f954f..dace8768 100644
--- a/workflows/prefactor_calibrator/apply_calibrate_pa.cwl
+++ b/workflows/prefactor_calibrator/apply_calibrate_pa.cwl
@@ -109,8 +109,9 @@ steps:
source: BLsmooth/msout
- id: msin_datacolumn
default: SMOOTHED_DATA
- - id: msin_modelcolum
- default: MODEL_DATA
+ - id: modeldatacolumns
+ default:
+ - 'MODEL_DATA'
- id: flagunconverged
source: flagunconverged
- id: propagate_solutions
diff --git a/workflows/prefactor_calibrator/predict_calibrate.cwl b/workflows/prefactor_calibrator/predict_calibrate.cwl
index 3956350e..99d585f5 100644
--- a/workflows/prefactor_calibrator/predict_calibrate.cwl
+++ b/workflows/prefactor_calibrator/predict_calibrate.cwl
@@ -79,8 +79,9 @@ steps:
source: predict/msout
- id: msin_datacolumn
default: SMOOTHED_DATA
- - id: msin_modelcolum
- default: MODEL_DATA
+ - id: modeldatacolumns
+ default:
+ - 'MODEL_DATA'
- id: propagate_solutions
source: propagatesolutions
- id: flagunconverged
diff --git a/workflows/prefactor_target/concat.cwl b/workflows/prefactor_target/concat.cwl
index 042327fe..d9e92bab 100644
--- a/workflows/prefactor_target/concat.cwl
+++ b/workflows/prefactor_target/concat.cwl
@@ -18,9 +18,6 @@ inputs:
- id: avg_freqresolution_concat
type: string?
default: '97.64kHz'
- - id: min_unflagged_fraction
- type: float?
- default: 0.5
outputs:
- id: flagged_fraction_dict
outputSource:
diff --git a/workflows/prefactor_target/finalize.cwl b/workflows/prefactor_target/finalize.cwl
index 33486c93..d62f9a1e 100644
--- a/workflows/prefactor_target/finalize.cwl
+++ b/workflows/prefactor_target/finalize.cwl
@@ -178,8 +178,6 @@ steps:
valueFrom: $(self.nameroot+'_wsclean.ms')
- id: msin_datacolumn
default: DATA
- - id: msout_datacolumn
- default: DATA
- id: overwrite
default: false
- id: storagemanager
@@ -267,7 +265,7 @@ steps:
default: 15asec
- id: auto_threshold
default: 5
- - id: size
+ - id: image_size
default: [2500,2500]
- id: niter
default: 10000
diff --git a/workflows/prefactor_target/gsmcal.cwl b/workflows/prefactor_target/gsmcal.cwl
index 0e769b6c..affefcec 100644
--- a/workflows/prefactor_target/gsmcal.cwl
+++ b/workflows/prefactor_target/gsmcal.cwl
@@ -311,8 +311,6 @@ steps:
source: avg_timeresolution_concat
- id: avg_freqresolution_concat
source: avg_freqresolution_concat
- - id: min_unflagged_fraction
- source: min_unflagged_fraction
out:
- id: msout
- id: flagged_fraction_dict
--
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