From 72bb624b2aa1e5dee2fba545551b7a81d33f7b14 Mon Sep 17 00:00:00 2001
From: Alexander Drabent <alex@tls-tautenburg.de>
Date: Fri, 28 May 2021 11:31:39 +0200
Subject: [PATCH] bugfix missing frequencies
---
lofar-cwl/steps/applybeam.cwl | 2 +-
lofar-cwl/steps/check_ateam_separation.cwl | 42 ----------------------
lofar-cwl/steps/dpppconcat.cwl | 15 +++++---
steps/check_ateam_separation.cwl | 5 ++-
steps/filter_ms_group.cwl | 32 +++++++++++++----
subworkflow/concat.cwl | 5 ++-
workflows/prefactor_calibrator/prep.cwl | 2 +-
workflows/prefactor_target/prep.cwl | 2 +-
8 files changed, 46 insertions(+), 59 deletions(-)
delete mode 100755 lofar-cwl/steps/check_ateam_separation.cwl
diff --git a/lofar-cwl/steps/applybeam.cwl b/lofar-cwl/steps/applybeam.cwl
index 099f62ce..a69a628f 100644
--- a/lofar-cwl/steps/applybeam.cwl
+++ b/lofar-cwl/steps/applybeam.cwl
@@ -2,7 +2,7 @@ class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
-id: applycal
+id: applybeam
baseCommand:
- DPPP
inputs:
diff --git a/lofar-cwl/steps/check_ateam_separation.cwl b/lofar-cwl/steps/check_ateam_separation.cwl
deleted file mode 100755
index c8d801c9..00000000
--- a/lofar-cwl/steps/check_ateam_separation.cwl
+++ /dev/null
@@ -1,42 +0,0 @@
-class: CommandLineTool
-cwlVersion: v1.0
-id: check_ateam_separation
-baseCommand:
- - python3
- - /usr/local/bin/check_Ateam_separation.py
-inputs:
- - id: ms
- type:
- - Directory
- - type: array
- items: Directory
- inputBinding:
- position: 0
- doc: Input measurement set
- - default: Ateam_separation.png
- id: output_image_name
- type: string?
- inputBinding:
- position: 2
- prefix: '--outputimage'
- - id: min_separation
- type: int
- inputBinding:
- position: 1
- prefix: '--min_separation'
-outputs:
- - id: output_imag
- doc: Output image
- type: File?
- outputBinding:
- glob: $(inputs.output_image_name)
- - id: logfile
- type: File?
- outputBinding:
- glob: Ateam_separation.log
-label: check_Ateam_separation
-hints:
- - class: DockerRequirement
- dockerPull: lofareosc/prefactor:HBAcalibrator
- - class: InlineJavascriptRequirement
-stdout: Ateam_separation.log
diff --git a/lofar-cwl/steps/dpppconcat.cwl b/lofar-cwl/steps/dpppconcat.cwl
index 34b78840..0fca5fbf 100644
--- a/lofar-cwl/steps/dpppconcat.cwl
+++ b/lofar-cwl/steps/dpppconcat.cwl
@@ -8,13 +8,16 @@ baseCommand:
inputs:
- id: msin
type: 'Directory[]'
+ doc: Input Measurement Set
+ - id: msin_fname
+ doc: Input Measurement Set string (including dummy.ms)
+ type: 'string[]'
inputBinding:
position: 0
prefix: msin=
separate: false
itemSeparator: ','
- valueFrom: $(concatenate_path(self))
- doc: Input Measurement Set
+ valueFrom: "[$(self.join(','))]"
- id: msout_name
type: string
inputBinding:
@@ -87,7 +90,7 @@ inputs:
- id: missingdata
type: boolean
inputBinding:
- prefix: msout.missingdata=True
+ prefix: msin.missingdata=True
separate: false
shellQuote: false
position: 0
@@ -127,7 +130,7 @@ outputs:
glob: concat*.log
arguments:
- 'steps=[filter,avg,count]'
- - msout.orderms=False
+ - msin.orderms=False
- avg.type=average
requirements:
- class: ShellCommandRequirement
@@ -137,5 +140,9 @@ requirements:
hints:
- class: DockerRequirement
dockerPull: 'lofareosc/prefactor:HBAcalibrator'
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.msin)
+ writable: false
stdout: concat.log
stderr: concat_err.log
diff --git a/steps/check_ateam_separation.cwl b/steps/check_ateam_separation.cwl
index 516beb61..00275869 100644
--- a/steps/check_ateam_separation.cwl
+++ b/steps/check_ateam_separation.cwl
@@ -1,11 +1,10 @@
class: CommandLineTool
cwlVersion: v1.0
-$namespaces:
- sbg: 'https://www.sevenbridges.com/'
id: check_ateam_separation
baseCommand:
- python3
- - /usr/local/bin/check_Ateam_separation.py
+ - -m
+ - check_Ateam_separation
inputs:
- id: ms
type:
diff --git a/steps/filter_ms_group.cwl b/steps/filter_ms_group.cwl
index d51dcf69..e09eec16 100644
--- a/steps/filter_ms_group.cwl
+++ b/steps/filter_ms_group.cwl
@@ -22,8 +22,14 @@ outputs:
type: Directory[]
outputBinding:
loadContents: true
- glob: selected_ms.json
+ glob: 'selected_ms.json'
outputEval: '$(JSON.parse(self[0].contents))'
+ - id: selected_ms
+ type: string[]
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).selected_ms)
label: filter_ms_group
requirements:
@@ -39,20 +45,34 @@ requirements:
group_id = "$(inputs.group_id)"
json_file = sys.argv[1]
ms_list = sys.argv[2:]
-
+
ms_by_name = { ms.split(os.path.sep)[-1]:
{'class':'Directory', 'path': ms} for ms in ms_list}
-
+
output_file = 'selected_ms.json'
with open(json_file, 'r') as f_stream:
selected_ms = json.load(f_stream)[group_id]
- print(selected_ms, ms_by_name)
- selected_ms = [ms_by_name[os.path.basename(ms_name)] for ms_name in selected_ms]
+
+ selected_ms = [os.path.basename(ms_name) for ms_name in selected_ms]
+ cwl_output = {'selected_ms': selected_ms}
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
+ selected_ms = [ms_by_name[ms_name] for ms_name in selected_ms if ms_name != 'dummy.ms']
with open(output_file, 'w') as f_stream:
json.dump(selected_ms, f_stream)
-
+
+
+hints:
+ - class: InitialWorkDirRequirement
+ listing:
+ - entry: $(inputs.measurement_sets)
+ writable: true
+stdout: filter_ms_by_group.log
+stderr: filter_ms_by_group_err.log
\ No newline at end of file
diff --git a/subworkflow/concat.cwl b/subworkflow/concat.cwl
index c1c00803..d2224d34 100644
--- a/subworkflow/concat.cwl
+++ b/subworkflow/concat.cwl
@@ -58,6 +58,7 @@ steps:
- msin
out:
- id: output
+ - id: selected_ms
run: ../steps/filter_ms_group.cwl
label: filter_ms_group
'sbg:x': -500
@@ -66,7 +67,9 @@ steps:
in:
- id: msin
source:
- - filter_ms_group/output
+ - msin
+ - id: msin_fname
+ source: filter_ms_group/selected_ms
- id: msout_name
source: group_id
- id: msin_datacolumn
diff --git a/workflows/prefactor_calibrator/prep.cwl b/workflows/prefactor_calibrator/prep.cwl
index 57ff28b8..4d40b75b 100644
--- a/workflows/prefactor_calibrator/prep.cwl
+++ b/workflows/prefactor_calibrator/prep.cwl
@@ -311,7 +311,7 @@ steps:
out:
- id: output_imag
- id: logfile
- run: ../../lofar-cwl/steps/check_ateam_separation.cwl
+ run: ../../steps/check_ateam_separation.cwl
label: check_Ateam_separation
'sbg:x': 254.234375
'sbg:y': 1440
diff --git a/workflows/prefactor_target/prep.cwl b/workflows/prefactor_target/prep.cwl
index a068460a..73a796aa 100644
--- a/workflows/prefactor_target/prep.cwl
+++ b/workflows/prefactor_target/prep.cwl
@@ -225,7 +225,7 @@ steps:
out:
- id: output_imag
- id: logfile
- run: ../../lofar-cwl/steps/check_ateam_separation.cwl
+ run: ../../steps/check_ateam_separation.cwl
label: check_Ateam_separation
'sbg:x': -500
'sbg:y': -300
--
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