diff --git a/steps/identify_bad_antennas.cwl b/steps/identify_bad_antennas.cwl
index 3bdc91f282d311feebe3eb858fadb06dd9da1932..822e98504644a58e55e7455f562a2ad58ef70dbc 100644
--- a/steps/identify_bad_antennas.cwl
+++ b/steps/identify_bad_antennas.cwl
@@ -7,14 +7,10 @@ baseCommand:
- python3
inputs:
- id: msin
- type: Directory[]
+ type: Directory
doc: MS to compare with
inputBinding:
position: 0
- - id: filter
- type: string?
- default: '*&'
- doc: Filter these baselines for the comparison
label: identifyBadAntennas.py
arguments:
@@ -22,25 +18,26 @@ arguments:
- |
import sys
import json
- from identifyBadAntennas import main as identifyBadAntennas
+ from identifyBadAntennas_CWL import main as identifyBadAntennas
- mss = sys.argv[1:]
+ ms = sys.argv[1]
filter = '$(inputs.filter)'
- output = identifyBadAntennas(mss, filter)
+ output = identifyBadAntennas(ms)
- filter_out = output['filter']
- cwl_output = {"filter_out": filter_out}
+ flaggedants = output['flaggedants']
+ cwl_output = {"flaggedants": flaggedants}
with open('./out.json', 'w') as fp:
json.dump(cwl_output, fp)
+
outputs:
- - id: filter_out
+ - id: flaggedants
type: string
outputBinding:
loadContents: true
glob: 'out.json'
- outputEval: $(JSON.parse(self[0].contents).filter_out)
+ outputEval: $(JSON.parse(self[0].contents).flaggedants)
- id: logfile
type: File?
outputBinding:
diff --git a/steps/identify_bad_antennas_join.cwl b/steps/identify_bad_antennas_join.cwl
new file mode 100644
index 0000000000000000000000000000000000000000..8745f75fb0249d7969293af8d7f97b39f9c11344
--- /dev/null
+++ b/steps/identify_bad_antennas_join.cwl
@@ -0,0 +1,54 @@
+class: CommandLineTool
+cwlVersion: v1.0
+$namespaces:
+ sbg: 'https://www.sevenbridges.com/'
+id: identify_bad_antennas_join
+baseCommand:
+ - python3
+inputs:
+ - id: flaggedants
+ type: string[]?
+ default: []
+ doc: list of flagged antennas
+ - id: filter
+ type: string?
+ default: '*&'
+ doc: Filter these baselines for the comparison
+
+label: identifyBadAntennas_join
+arguments:
+ - '-c'
+ - |
+
+ flaggedants_list = sys.argv[1:]
+ filter = '$(inputs.filter)'
+
+ flagged_antenna_list = set.intersection(*map(set, flaggedants_list))
+
+ for flagged_antenna in flagged_antenna_list:
+ filter += ';!' + flagged_antenna + '*&&*'
+
+ print('Identified bad antennas: ' + str(flagged_antenna_list))
+
+ cwl_output = {"filter": str(filter)}
+
+ with open('./out.json', 'w') as fp:
+ json.dump(cwl_output, fp)
+
+outputs:
+ - id: filter_out
+ type: string
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).filter)
+ - id: logfile
+ type: File?
+ outputBinding:
+ glob: identifyBadAntennas.log
+
+requirements:
+ - class: InlineJavascriptRequirement
+
+stdout: identifyBadAntennas.log
+stderr: identifyBadAntennas_err.log
\ No newline at end of file
diff --git a/workflows/prefactor_target/gsmcal.cwl b/workflows/prefactor_target/gsmcal.cwl
index 7685881345f03c6a2c18abf2d432b996171ccddf..77c4193ab20c8f3405745713baf9c4d0b8e5413a 100644
--- a/workflows/prefactor_target/gsmcal.cwl
+++ b/workflows/prefactor_target/gsmcal.cwl
@@ -73,7 +73,7 @@ outputs:
'sbg:y': 200
- id: bad_antennas
outputSource:
- - identifybadantennas/filter_out
+ - identifybadantennas_join/filter_out
type: string
'sbg:x': 1500
'sbg:y': 400
@@ -96,7 +96,7 @@ outputs:
'sbg:y': 800
- id: logfiles
outputSource:
- - identifybadantennas/logfile
+ - concat_logfiles_identify/output
- sort_times_into_freqGroups/logfile
- find_skymodel_target/logfile
- make_sourcedb_target/log
@@ -112,17 +112,31 @@ steps:
- id: identifybadantennas
in:
- id: msin
- source:
- - msin
- - id: filter
- source: filter_baselines
+ source: msin
out:
- - id: filter_out
+ - id: flaggedants
- id: logfile
run: ../../steps/identify_bad_antennas.cwl
label: identifybadantennas
+ scatter:
+ - msin
'sbg:x': -200
'sbg:y': -300
+ - id: identifybadantennas_join
+ in:
+ - id: flaggedants
+ source: identifybadantennas/flaggedants
+ - id: filter
+ source: filter_baselines
+ out:
+ - id: filter_out
+ - id: logfile
+ run: ../../steps/identify_bad_antennas_join.cwl
+ label: identifybadantennas_join
+ scatter:
+ - msin
+ 'sbg:x': 0
+ 'sbg:y': -300
- id: sort_times_into_freqGroups
in:
- id: msin
@@ -170,10 +184,10 @@ steps:
in:
- id: sky_model
source: find_skymodel_target/skymodel
- - id: logname
- default: make_sourcedb_target.log
- id: output_file_name
default: target.sourcedb
+ - id: logname
+ default: make_sourcedb_target.log
out:
- id: sourcedb
- id: log
@@ -253,6 +267,21 @@ steps:
label: concat_logfiles_unflagged
'sbg:x': 1200
'sbg:y': 900
+ - id: concat_logfiles_identify
+ in:
+ - id: file_list
+ linkMerge: merge_flattened
+ source:
+ - identifybadantennas/logfile
+ - identifybadantennas_join/logfile
+ - id: file_prefix
+ default: identifyBadAntennas
+ out:
+ - id: output
+ run: ../../steps/concatenate_files.cwl
+ label: concat_logfiles_identify
+ 'sbg:x': 1200
+ 'sbg:y': -100
- id: concat
in:
- id: msin
@@ -263,7 +292,7 @@ steps:
- id: groups_specification
source: sort_times_into_freqGroups/filenames
- id: filter_baselines
- source: identifybadantennas/filter_out
+ source: identifybadantennas_join/filter_out
- id: avg_timeresolution_concat
source: avg_timeresolution_concat
- id: avg_freqresolution_concat
@@ -271,9 +300,9 @@ steps:
- id: min_unflagged_fraction
source: min_unflagged_fraction
out:
+ - id: msout_old
- id: unflagged_fraction
- id: msout
- - id: msout_old
- id: dpppconcat.log
- id: check_unflagged_fraction.log
run: ../../subworkflow/concat.cwl
@@ -335,9 +364,11 @@ steps:
- id: plot_unflagged
in:
- id: msin
- source: concat/msout_old
+ source:
+ - concat/msout_old
- id: unflagged_fraction
- source: concat/unflagged_fraction
+ source:
+ - concat/unflagged_fraction
out:
- id: output_imag
- id: logfile
@@ -370,6 +401,7 @@ steps:
out:
- id: output_plots
- id: logfile
+ - id: parset
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_P
'sbg:x': 1000
@@ -400,6 +432,7 @@ steps:
out:
- id: output_plots
- id: logfile
+ - id: parset
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_P2
'sbg:x': 1000
@@ -431,6 +464,7 @@ steps:
out:
- id: output_plots
- id: logfile
+ - id: parset
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_Pd
'sbg:x': 1000
@@ -461,6 +495,7 @@ steps:
out:
- id: output_plots
- id: logfile
+ - id: parset
run: ../../lofar-cwl/steps/LoSoTo.Plot.cwl
label: losoto_plot_Pd2
'sbg:x': 1000
@@ -470,3 +505,4 @@ requirements:
- class: InlineJavascriptRequirement
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
+ - class: MultipleInputFeatureRequirement