From e0d437030fc5884b981aee12f91cb6ab001bf6c4 Mon Sep 17 00:00:00 2001
From: Alexander Drabent <alex@tls-tautenburg.de>
Date: Fri, 8 May 2020 18:15:24 +0200
Subject: [PATCH] add stderr and Dysco
---
lofar-cwl/steps/applybeam.cwl | 12 +++-
lofar-cwl/steps/applycal.cwl | 12 +++-
lofar-cwl/steps/predict.cwl | 5 +-
subworkflow/apply_calibrate_bp.cwl | 94 +++++++++++++++++++++++++-----
subworkflow/apply_calibrate_fr.cwl | 19 +++++-
subworkflow/apply_calibrate_pa.cwl | 38 +++++++++++-
6 files changed, 155 insertions(+), 25 deletions(-)
diff --git a/lofar-cwl/steps/applybeam.cwl b/lofar-cwl/steps/applybeam.cwl
index 81559884..00f3f391 100644
--- a/lofar-cwl/steps/applybeam.cwl
+++ b/lofar-cwl/steps/applybeam.cwl
@@ -41,9 +41,14 @@ inputs:
except for full Jones, in which case correction should be 'fulljones'.
- id: storagemanager
type: string
- default: dysco
+ default: ""
inputBinding:
prefix: msout.storagemanager=
+ - id: databitrate
+ type: int?
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
- id: updateweights
type: string?
inputBinding:
@@ -76,10 +81,11 @@ outputs:
outputBinding:
glob: $(inputs.msin.basename)
- id: logfile
- type: File
+ type: File[]
outputBinding:
- glob: applycal_$(inputs.type).log
+ glob: 'applycal_$(inputs.type)*.log'
stdout: applycal_$(inputs.type).log
+stderr: applycal_$(inputs.type)_err.log
arguments:
- 'steps=[applybeam]'
- msout=.
diff --git a/lofar-cwl/steps/applycal.cwl b/lofar-cwl/steps/applycal.cwl
index 03f258d0..49b2f718 100644
--- a/lofar-cwl/steps/applycal.cwl
+++ b/lofar-cwl/steps/applycal.cwl
@@ -50,9 +50,14 @@ inputs:
except for full Jones, in which case correction should be 'fulljones'.
- id: storagemanager
type: string
- default: dysco
+ default: ""
inputBinding:
prefix: msout.storagemanager=
+ - id: databitrate
+ type: int?
+ inputBinding:
+ prefix: msout.storagemanager.databitrate=
+ separate: false
- id: updateweights
type: string?
inputBinding:
@@ -66,10 +71,11 @@ outputs:
outputBinding:
glob: $(inputs.msin.basename)
- id: logfile
- type: File
+ type: File[]
outputBinding:
- glob: applycal_$(inputs.correction).log
+ glob: 'applycal_$(inputs.correction)*.log'
stdout: applycal_$(inputs.correction).log
+stderr: applycal_$(inputs.correction)_err.log
arguments:
- 'steps=[applycal]'
- msout=.
diff --git a/lofar-cwl/steps/predict.cwl b/lofar-cwl/steps/predict.cwl
index 3364b3b5..dcd0781c 100644
--- a/lofar-cwl/steps/predict.cwl
+++ b/lofar-cwl/steps/predict.cwl
@@ -61,13 +61,12 @@ inputs:
prefix: msout.overwrite=True
- id: storagemanager
type: string
- default: "Dysco"
+ default: ""
inputBinding:
prefix: msout.storagemanager=
separate: false
- id: databitrate
- type: int
- default: 0
+ type: int?
inputBinding:
prefix: msout.storagemanager.databitrate=
separate: false
diff --git a/subworkflow/apply_calibrate_bp.cwl b/subworkflow/apply_calibrate_bp.cwl
index 357cb86a..66362f93 100644
--- a/subworkflow/apply_calibrate_bp.cwl
+++ b/subworkflow/apply_calibrate_bp.cwl
@@ -28,7 +28,7 @@ inputs:
outputs:
- id: apply_fr.log
outputSource:
- - applyFR/logfile
+ - concat_logfiles_applyFR/output
type: File
'sbg:x': 1000
'sbg:y': -300
@@ -46,7 +46,7 @@ outputs:
'sbg:y': -100
- id: apply_cal.log
outputSource:
- - applyBP/logfile
+ - concat_logfiles_applyBP/output
type: File
'sbg:x': 1000
'sbg:y': 0
@@ -64,7 +64,7 @@ outputs:
'sbg:y': 200
- id: apply_pa.log
outputSource:
- - applyPA/logfile
+ - concat_logfiles_applyPA/output
type: File
'sbg:x': 1000
'sbg:y': 300
@@ -79,6 +79,10 @@ steps:
source: input_h5parm
- id: msout_datacolumn
default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
- id: correction
default: polalign
out:
@@ -94,14 +98,18 @@ steps:
source: applyPA/msout
- id: msin_datacolumn
default: CORRECTED_DATA
- - id: updateweights
- default: 'True'
- id: parmdb
source: input_h5parm
- id: msout_datacolumn
default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
- id: correction
default: bandpass
+ - id: updateweights
+ default: 'True'
out:
- id: msout
- id: logfile
@@ -111,22 +119,26 @@ steps:
'sbg:y': 0
- id: applybeam
in:
+ - id: msin
+ source: applyBP/msout
- id: msin_datacolumn
default: CORRECTED_DATA
- id: msout_datacolumn
default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
+ - id: type
+ default: applybeam
- id: updateweights
default: 'true'
+ - id: usechannelfreq
+ default: 'false'
- id: invert
default: 'true'
- id: beammode
default: element
- - id: usechannelfreq
- default: 'false'
- - id: msin
- source: applyBP/msout
- - id: type
- default: applybeam
out:
- id: msout
- id: logfile
@@ -144,6 +156,10 @@ steps:
source: input_h5parm
- id: msout_datacolumn
default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
- id: correction
default: faraday
out:
@@ -176,10 +192,10 @@ steps:
default: SMOOTHED_DATA
- id: msin_modelcolum
default: MODEL_DATA
- - id: flagunconverged
- source: flagunconverged
- id: propagate_solutions
source: propagatesolutions
+ - id: flagunconverged
+ source: flagunconverged
- id: mode
default: diagonal
out:
@@ -202,4 +218,56 @@ steps:
label: concat_logfiles_calib_cal
'sbg:x': 700
'sbg:y': 200
+ - id: concat_logfiles_applyFR
+ in:
+ - id: file_list
+ source:
+ - applyFR/logfile
+ - id: file_prefix
+ default: applycal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applyFR
+ 'sbg:x': 400
+ 'sbg:y': 200
+ - id: concat_logfiles_applybeam
+ in:
+ - id: file_list
+ source:
+ - applybeam/logfile
+ - id: file_prefix
+ default: applybeam
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applybeam
+ 'sbg:x': 200
+ 'sbg:y': 200
+ - id: concat_logfiles_applyBP
+ in:
+ - id: file_list
+ source:
+ - applyBP/logfile
+ - id: file_prefix
+ default: applycal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applBP
+ 'sbg:x': 0
+ 'sbg:y': 200
+ - id: concat_logfiles_applyPA
+ in:
+ - id: file_list
+ source:
+ - applyPA/logfile
+ - id: file_prefix
+ default: applycal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applyPA
+ 'sbg:x': -200
+ 'sbg:y': 200
requirements: []
diff --git a/subworkflow/apply_calibrate_fr.cwl b/subworkflow/apply_calibrate_fr.cwl
index 80137502..3c20638a 100644
--- a/subworkflow/apply_calibrate_fr.cwl
+++ b/subworkflow/apply_calibrate_fr.cwl
@@ -40,7 +40,7 @@ outputs:
'sbg:y': -100
- id: apply_cal.log
outputSource:
- - applyFR/logfile
+ - concat_logfiles_applycal/output
type: File
'sbg:x': 1000
'sbg:y': 0
@@ -67,6 +67,10 @@ steps:
source: input_h5parm
- id: msout_datacolumn
default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
- id: correction
default: faraday
out:
@@ -125,4 +129,17 @@ steps:
label: concat_logfiles_calib_cal
'sbg:x': 700
'sbg:y': 200
+ - id: concat_logfiles_applycal
+ in:
+ - id: file_list
+ source:
+ - applyFR/logfile
+ - id: file_prefix
+ default: applycal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applycal
+ 'sbg:x': -200
+ 'sbg:y': 200
requirements: []
diff --git a/subworkflow/apply_calibrate_pa.cwl b/subworkflow/apply_calibrate_pa.cwl
index 3fe54c8d..c8f1ea5c 100644
--- a/subworkflow/apply_calibrate_pa.cwl
+++ b/subworkflow/apply_calibrate_pa.cwl
@@ -40,7 +40,7 @@ outputs:
'sbg:y': -100
- id: apply_cal.log
outputSource:
- - applyPA/logfile
+ - concat_logfiles_applycal/output
type: File
'sbg:x': 1000
'sbg:y': 0
@@ -58,7 +58,7 @@ outputs:
'sbg:y': 200
- id: applybeam.log
outputSource:
- - applybeam/logfile
+ - concat_logfiles_applybeam/output
type: File
'sbg:x': 1000
'sbg:y': 300
@@ -73,6 +73,10 @@ steps:
source: input_h5parm
- id: msout_datacolumn
default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
- id: correction
default: polalign
out:
@@ -88,6 +92,10 @@ steps:
default: CORRECTED_DATA
- id: msout_datacolumn
default: CORRECTED_DATA
+ - id: storagemanager
+ default: Dysco
+ - id: databitrate
+ default: 0
- id: updateweights
default: 'true'
- id: invert
@@ -156,4 +164,30 @@ steps:
label: concat_logfiles_calib_cal
'sbg:x': 700
'sbg:y': 200
+ - id: concat_logfiles_applybeam
+ in:
+ - id: file_list
+ source:
+ - applybeam/logfile
+ - id: file_prefix
+ default: applybeam
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applybeam
+ 'sbg:x': 0
+ 'sbg:y': 200
+ - id: concat_logfiles_applycal
+ in:
+ - id: file_list
+ source:
+ - applyPA/logfile
+ - id: file_prefix
+ default: applycal
+ out:
+ - id: output
+ run: ../steps/concatenate_files.cwl
+ label: concat_logfiles_applycal
+ 'sbg:x': -200
+ 'sbg:y': 200
requirements: []
--
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