diff --git a/lofar-cwl/steps/applytarget.cwl b/lofar-cwl/steps/applytarget.cwl
index cb0f811446763fa75295a8d44b278878bc205e10..883ab2ec974c6c31646ce09126c38d3e594a8fa0 100644
--- a/lofar-cwl/steps/applytarget.cwl
+++ b/lofar-cwl/steps/applytarget.cwl
@@ -55,6 +55,13 @@ inputs:
Type of correction to perform. When using H5Parm, this is for now the name
of the soltab; the type will be deduced from the metadata in that soltab,
except for full Jones, in which case correction should be 'fulljones'.
+ - default: 'sol000'
+ id: solset
+ type: string
+ inputBinding:
+ position: 0
+ prefix: applycal.solset=
+ separate: false
- id: storagemanager
type: string
default: ""
diff --git a/lofar-cwl/steps/dpppconcat.cwl b/lofar-cwl/steps/dpppconcat.cwl
index b7e20eb0e4872ec5675527f06632a4c98562fc53..e4570f06b1db4bb7acb293e838ce4497d39ec9cf 100644
--- a/lofar-cwl/steps/dpppconcat.cwl
+++ b/lofar-cwl/steps/dpppconcat.cwl
@@ -9,11 +9,11 @@ inputs:
- id: msin
type: 'Directory[]'
inputBinding:
+ position: 0
prefix: msin=
separate: false
itemSeparator: ','
- shellQuote: false
- position: 0
+ valueFrom: $(concatenate_path(self))
doc: Input Measurement Set
- id: msout_name
type: string
@@ -44,7 +44,7 @@ inputs:
inputBinding:
prefix: filter.baseline=
separate: false
- shellQuote: false
+ shellQuote: true
position: 0
valueFrom: $(self)
default: null
@@ -96,7 +96,7 @@ inputs:
inputBinding:
prefix: msin.baseline=
separate: false
- shellQuote: false
+ shellQuote: true
position: 0
default: '*'
- id: avg_timeresolution
@@ -128,9 +128,12 @@ outputs:
arguments:
- 'steps=[filter,avg]'
- msout.orderms=False
+ - avg.type=average
requirements:
- class: ShellCommandRequirement
- class: InlineJavascriptRequirement
+ expressionLib:
+ - { $include: 'utils.js' }
hints:
- class: DockerRequirement
dockerPull: 'lofareosc/prefactor:HBAcalibrator'
diff --git a/steps/add_missing_stations.cwl b/steps/add_missing_stations.cwl
index ea4ecec182845c166e39e8a0f8e82576cb24eca4..d2258e1771c70c2055aaf01b9b0ead31285cc0ae 100644
--- a/steps/add_missing_stations.cwl
+++ b/steps/add_missing_stations.cwl
@@ -1,6 +1,7 @@
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
+ lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
id: add_missing_stations
baseCommand:
@@ -17,13 +18,14 @@ inputs:
type: File
inputBinding:
position: 0
- prefix: '--refh5parm'
+ prefix: '--refh5'
doc: External H5parm from which the full list of antennas is used from.
- id: solset
type: string?
inputBinding:
position: 0
prefix: '--solset'
+ default: 'sol000'
doc: Input calibration solutions
- id: refsolset
type: string?
@@ -31,35 +33,41 @@ inputs:
position: 0
prefix: '--refsolset'
doc: Input calibration solutions of the reference h5parm file
+ default: 'sol000'
- id: soltab_in
type: string?
inputBinding:
position: 0
prefix: '--soltab_in'
doc: Input solution table
+ default: 'phase000'
- id: soltab_out
type: string?
inputBinding:
position: 0
prefix: '--soltab_out'
doc: Output solution table (has to be different from input solution table)
+ default: 'GSMphase'
- id: filter
type: string?
inputBinding:
position: 0
prefix: '--filter'
doc: Filter these antenna string from the processing
+ default: '[CR]S*&'
- id: bad_antennas
type: string?
inputBinding:
position: 0
prefix: '--bad_antennas'
doc: Antenna string to be processed
+ default: '[CR]S*&'
outputs:
- id: outh5parm
type: File
outputBinding:
glob: $(inputs.h5parm.basename)
+ format: 'lofar:#H5Parm'
- id: log
type: File[]
outputBinding:
@@ -77,3 +85,5 @@ requirements:
listing:
- entry: $(inputs.h5parm)
writable: true
+$schema:
+ - 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/steps/filter_ms_group.cwl b/steps/filter_ms_group.cwl
index 2d3b54179f9f809c1ac428bd7a0523116338c592..d51dcf695a9e51a0b748b14c56842b4e76d64284 100644
--- a/steps/filter_ms_group.cwl
+++ b/steps/filter_ms_group.cwl
@@ -34,12 +34,13 @@ requirements:
entry: |
import sys
import json
- import os.path as path
+ import os
+
group_id = "$(inputs.group_id)"
json_file = sys.argv[1]
ms_list = sys.argv[2:]
- ms_by_name = { ms.split(path.sep)[-1]:
+ ms_by_name = { ms.split(os.path.sep)[-1]:
{'class':'Directory', 'path': ms} for ms in ms_list}
output_file = 'selected_ms.json'
@@ -47,7 +48,7 @@ requirements:
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[ms_name] for ms_name in selected_ms]
+ selected_ms = [ms_by_name[os.path.basename(ms_name)] for ms_name in selected_ms]
with open(output_file, 'w') as f_stream:
diff --git a/steps/find_skymodel_target.cwl b/steps/find_skymodel_target.cwl
index e7aa0b88802fe6ac1df453565e6b9202e26a88bd..36191f1c6d89c1fa6240eb81698c211f4c8f481b 100644
--- a/steps/find_skymodel_target.cwl
+++ b/steps/find_skymodel_target.cwl
@@ -52,7 +52,7 @@ arguments:
output = download_skymodel_target(mss, SkymodelPath, Radius, DoDownload, Source)
- if SkymodelPath != "target.skymodel":
+ if "target.skymodel" not in SkymodelPath:
shutil.copyfile(SkymodelPath, "target.skymodel")
outputs:
diff --git a/steps/h5parmcat.cwl b/steps/h5parmcat.cwl
index f14f7e38892ff91bf78c80ada21c9d5b3b713fa7..2770fc827f22878db2d626da6f0ff81fa6189535 100644
--- a/steps/h5parmcat.cwl
+++ b/steps/h5parmcat.cwl
@@ -90,7 +90,7 @@ requirements:
hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor:HBAcalibrator
-stdout: parm_collector_output.log
-stderr: parm_collector_output_err.log
+stdout: h5parm_collector_output.log
+stderr: h5parm_collector_output_err.log
$schema:
- 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
diff --git a/steps/identify_bad_antennas.cwl b/steps/identify_bad_antennas.cwl
index a4cb554ed344c28119c6938e329e50d992ff1114..3bdc91f282d311feebe3eb858fadb06dd9da1932 100644
--- a/steps/identify_bad_antennas.cwl
+++ b/steps/identify_bad_antennas.cwl
@@ -48,12 +48,12 @@ outputs:
requirements:
- class: InlineJavascriptRequirement
-
-hints:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.msin)
writable: true
+hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor:HBAcalibrator
-stdout: identifyBadAntennas.log
\ No newline at end of file
+stdout: identifyBadAntennas.log
+stderr: identifyBadAntennas_err.log
\ No newline at end of file
diff --git a/subworkflow/ndppp_prep_targ.cwl b/subworkflow/ndppp_prep_targ.cwl
index 09f71d9c4d90b43d91534df8f3c13ec5d3733509..45d923d9430a8745aa6aace52a5759d98ee54cf8 100644
--- a/subworkflow/ndppp_prep_targ.cwl
+++ b/subworkflow/ndppp_prep_targ.cwl
@@ -472,3 +472,4 @@ steps:
requirements:
- class: SubworkflowFeatureRequirement
- class: InlineJavascriptRequirement
+ - class: StepInputExpressionRequirement
diff --git a/workflows/prefactor_target/finalize.cwl b/workflows/prefactor_target/finalize.cwl
index 7864e5663bb8168241526a2a70bb2f69bbf75f8f..d660be8dc63f1d616f0b97690c22da731ba0cc4f 100644
--- a/workflows/prefactor_target/finalize.cwl
+++ b/workflows/prefactor_target/finalize.cwl
@@ -72,6 +72,7 @@ steps:
source: insolutions
- id: soltab_in
source: gsmcal_step
+ valueFrom: $(self+'000')
- id: soltab_out
default: 'TGSSphase'
- id: filter
@@ -171,3 +172,5 @@ steps:
requirements:
- class: SubworkflowFeatureRequirement
- class: ScatterFeatureRequirement
+ - class: StepInputExpressionRequirement
+ - class: InlineJavascriptRequirement
\ No newline at end of file