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Commit 89ffab29 authored by alex's avatar alex
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Merge branch 'shallow_listing' into 'master' 

Shallow listing

See merge request eosc/prefactor3-cwl!35

Former-commit-id: 1ba6f2fa
Former-commit-id: 7c8ff63f
parents b05195fb a71af87b
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steps/check_ateam_separation.cwl
+ 3
− 3
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
id: check_ateam_separation
baseCommand:
- check_Ateam_separation.py
......@@ -26,7 +26,7 @@ inputs:
outputs:
- id: output_imag
doc: Output image
type: File?
type: File
outputBinding:
glob: $(inputs.output_image_name)
- id: output_json
......@@ -35,7 +35,7 @@ outputs:
outputBinding:
glob: '*.json'
- id: logfile
type: File?
type: File
outputBinding:
glob: Ateam_separation.log
label: check_Ateam_separation
......
steps/check_unflagged_fraction.cwl
+ 2
− 2
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: check_unflagged_fraction
......@@ -56,7 +56,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).unflagged_fraction)
- id: logfile
type: File[]?
type: File[]
outputBinding:
glob: 'check_unflagged_fraction*.log'
......
steps/collectlog.cwl
+ 1
− 1
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: collectlog
......
steps/compare_station_list.cwl
+ 3
− 3
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: compare_station_list
......@@ -51,7 +51,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).filter_out)
- id: logfile
type: File[]?
type: File[]
outputBinding:
glob: 'compareStationList*.log'
......@@ -59,7 +59,7 @@ requirements:
- class: InlineJavascriptRequirement
hints:
DockerRequirement:
- class: DockerRequirement
dockerPull: lofareosc/prefactor3-cwl
stdout: compareStationList.log
stderr: compareStationList_err.log
\ No newline at end of file
steps/concatenate_files.cwl
+ 1
− 1
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: concatfiles
......
steps/createRMh5parm.cwl
+ 13
− 13
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
id: createRMh5parm
label: createRMh5parm
baseCommand:
......@@ -19,77 +19,77 @@ inputs:
position: 2
doc: Input h5parm solutions file
- id: ionex_server
type: string
type: string?
doc: IONEX Server path
default: 'ftp://ftp.aiub.unibe.ch/CODE/'
inputBinding:
prefix: '--server'
position: 0
- id: ionex_prefix
type: string
type: string?
doc: IONEX Prefix
default: 'CODG'
inputBinding:
prefix: '--prefix'
position: 0
- id: ionex_path
type: string
type: string?
doc: IONEX path
default: './'
inputBinding:
prefix: '--path'
position: 0
- id: solset
type: string
type: string?
doc: solset in which IONEX solution are put
default: 'sol000'
inputBinding:
prefix: '--solsetName'
position: 0
- id: timestep
type: float
type: float?
doc: timestep in seconds
default: 300.
inputBinding:
prefix: '-t'
position: 0
- id: smart_interpol
type: float
type: float?
doc: float parameter describing how much of Earth rotation is taken in to account in interpolation of the IONEX files. 1.0 means time interpolation assumes ionosphere rotates in opposite direction of the Earth
default: 0.
inputBinding:
prefix: '-e'
position: 0
- id: proxyserver
type: string
type: string?
doc: Specify proxy server if necessary
default: null
inputBinding:
prefix: '--proxyserver'
position: 0
- id: proxyport
type: int
type: int?
doc: Specify proxy port if necessary
default: null
inputBinding:
prefix: '--proxyport'
position: 0
- id: proxytype
type: string
type: string?
doc: Specify proxy type if necessary
default: null
inputBinding:
prefix: '--proxytype'
position: 0
- id: proxyuser
type: string
type: string?
doc: Specify proxy user name if necessary
default: null
inputBinding:
prefix: '--proxyuser'
position: 0
- id: proxypass
type: string
type: string?
doc: Specify proxy server password if necessary
default: null
inputBinding:
......
steps/create_workflow_input.cwl
+ 1
− 1
View file @ 89ffab29
......@@ -3,7 +3,7 @@ $namespaces:
id: create_workflow_input
label: create_workflow_input
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
inputs:
- id: msin
type: Directory[]
......
steps/directory_listing.cwl
+ 1
− 1
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: directory_listing
......
steps/dppp_make_parset_cal.cwl 0 → 100755
+ 117
− 0
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.1
id: make_parset
label: define_parset
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: raw_data
type: boolean?
default: false
- id: demix
type: boolean?
default: false
- id: filter_baselines
type: string?
default: '[CR]S*&'
- id: memoryperc
type: int?
default: 20
- id: baselines_to_flag
type: 'string[]?'
default: []
- id: elevation_to_flag
type: string?
default: '0deg..15deg'
- id: min_amplitude_to_flag
type: float?
default: 1e-30
- id: timeresolution
type: int?
default: 4
- id: freqresolution
type: string?
default: '48.82kHz'
- id: process_baselines_cal
type: string?
default: '*&'
- id: demix_timestep
type: int?
default: 10
- id: demix_freqstep
type: int?
default: 16
- id: target_source
type: string?
default: ''
- id: subtract_sources
type: 'string[]?'
default:
- CasA
- CygA
- id: ntimechunk
type: int?
default: 10
outputs:
- id: output
type: File
outputBinding:
glob: DPPP.parset
baseCommand:
- cp
arguments:
- prefix: ''
shellQuote: false
position: 0
valueFrom: input.parset
- prefix: ''
shellQuote: false
position: 0
valueFrom: DPPP.parset
requirements:
- class: InlineJavascriptRequirement
- class: ShellCommandRequirement
- class: InitialWorkDirRequirement
listing:
- entryname: input.parset
entry: |+
steps = [$(inputs.raw_data?'flagedge,aoflag,':'')flagbaseline,flagelev,flagamp,$(inputs.demix?'demix,':'')filter,avg]
#
msout.storagemanager = "Dysco"
msout.storagemanager.databitrate = 0
#
filter.type = filter
filter.baseline = $(inputs.filter_baselines)
filter.remove = true
#
flagedge.type = preflagger
flagedge.chan = [0..nchan/32-1,31*nchan/32..nchan-1]
#
aoflag.type = aoflagger
aoflag.memoryperc = $(inputs.memoryperc)
aoflag.keepstatistics = false
#
flagbaseline.type = preflagger
flagbaseline.baseline = $(inputs.baselines_to_flag)
#
flagelev.type = preflagger
flagelev.elevation = $(inputs.elevation_to_flag)
#
flagamp.type = preflagger
flagamp.amplmin = $(inputs.min_amplitude_to_flag)
#
avg.type = average
avg.timeresolution = $(inputs.timeresolution)
avg.freqresolution = $(inputs.freqresolution)
#
demix.type = demixer
demix.baseline = $(inputs.process_baselines_cal)
demix.demixfreqstep = $(inputs.demix_freqstep)
demix.demixtimestep = $(inputs.demix_timestep)
demix.ignoretarget = False
demix.targetsource = $(inputs.target_source)
demix.subtractsources = $(inputs.subtract_sources)
demix.ntimechunk = $(inputs.ntimechunk)
demix.freqstep = 1
demix.timestep = 1
demix.instrumentmodel = instrument
steps/dppp_make_parset_target.cwl 0 → 100755
+ 166
− 0
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.1
id: make_parset
label: define_parset
$namespaces:
sbg: 'https://www.sevenbridges.com/'
inputs:
- id: raw_data
type: boolean?
default: false
- id: demix
type: boolean?
default: false
- id: apply_tec_correction
type: boolean?
default: false
- id: apply_rm_correction
type: boolean?
default: true
- id: apply_phase_correction
type: boolean?
default: false
- id: apply_clock_correction
type: boolean?
default: true
- id: apply_beam_correction
type: boolean?
default: true
- id: filter_baselines
type: string?
default: '[CR]S*&'
- id: memoryperc
type: int?
default: 20
- id: baselines_to_flag
type: 'string[]?'
default: []
- id: elevation_to_flag
type: string?
default: '0deg..15deg'
- id: min_amplitude_to_flag
type: float?
default: 1e-30
- id: updateweights
type: boolean?
default: true
- id: timeresolution
type: int?
default: 4
- id: freqresolution
type: string?
default: '48.82kHz'
- id: process_baselines_target
type: string?
default: '[CR]S*&'
- id: demix_timestep
type: int?
default: 10
- id: demix_freqstep
type: int?
default: 16
- id: target_source
type: string?
default: ''
- id: subtract_sources
type: 'string[]?'
default:
- CasA
- CygA
- id: ntimechunk
type: int?
default: 10
outputs:
- id: output
type: File
outputBinding:
glob: DPPP.parset
baseCommand:
- cp
arguments:
- prefix: ''
shellQuote: false
position: 0
valueFrom: input.parset
- prefix: ''
shellQuote: false
position: 0
valueFrom: DPPP.parset
requirements:
- class: InlineJavascriptRequirement
- class: ShellCommandRequirement
- class: InitialWorkDirRequirement
listing:
- entryname: input.parset
entry: |+
steps = [$(inputs.raw_data?'flagedge,aoflag,':'')flagbaseline,flagelev,flagamp,$(inputs.demix?'demix,':'')filter,applyPA,applybandpass,$(inputs.apply_clock_correction?'applyclock,':'')$(inputs.apply_beam_correction?'applybeam,':'')$(inputs.apply_rm_correction?'applyRM,':'')$(inputs.apply_tec_correction?'applytec,':'')$(inputs.apply_phase_correction?'applyphase,':'')avg]
#
msout.storagemanager = "Dysco"
msout.storagemanager.databitrate = 0
#
filter.type = filter
filter.baseline = $(inputs.filter_baselines)
filter.remove = true
#
flagedge.type = preflagger
flagedge.chan = [0..nchan/32-1,31*nchan/32..nchan-1]
#
aoflag.type = aoflagger
aoflag.memoryperc = $(inputs.memoryperc)
aoflag.keepstatistics = false
#
flagbaseline.type = preflagger
flagbaseline.baseline = $(inputs.baselines_to_flag)
#
flagelev.type = preflagger
flagelev.elevation = $(inputs.elevation_to_flag)
#
flagamp.type = preflagger
flagamp.amplmin = $(inputs.min_amplitude_to_flag)
#
applyPA.type = applycal
applyPA.correction = polalign
applyPA.solset = calibrator
#
applybandpass.type = applycal
applybandpass.correction = bandpass
applybandpass.updateweights = $(inputs.updateweights?'True':'False')
applybandpass.solset = calibrator
#
applyclock.type = applycal
applyclock.correction = clock
applyclock.solset = calibrator
#
applytec.type = applycal
applytec.correction = tec
applytec.solset = calibrator
#
applyphase.type = applycal
applyphase.correction = phaseOrig
applyphase.solset = calibrator
#
applyRM.type = applycal
applyRM.correction = RMextract
applyRM.solset = target
#
applybeam.type = applybeam
applybeam.usechannelfreq = True
applybeam.updateweights = $(inputs.updateweights?'True':'False')
applybeam.invert = True
applybeam.beammode = element
#
avg.type = average
avg.timeresolution = $(inputs.timeresolution)
avg.freqresolution = $(inputs.freqresolution)
#
demix.type = demixer
demix.baseline = $(inputs.process_baselines_target)
demix.demixfreqstep = $(inputs.demix_freqstep)
demix.demixtimestep = $(inputs.demix_timestep)
demix.ignoretarget = False
demix.targetsource = $(inputs.target_source)
demix.subtractsources = $(inputs.subtract_sources)
demix.ntimechunk = $(inputs.ntimechunk)
demix.freqstep = 1
demix.timestep = 1
demix.instrumentmodel = instrument
steps/dppp_prep_cal.cwl 0 → 100755
+ 103
− 0
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: dppp
baseCommand:
- DP3
inputs:
- id: parset
type: File?
inputBinding:
position: -1
- id: msin
type: Directory?
inputBinding:
position: 0
prefix: msin=
separate: false
doc: Input Measurement Set
- id: msout_name
default: "."
type: string?
inputBinding:
position: 0
prefix: msout=
separate: false
doc: Output Measurement Set
- id: autoweight
default: false
type: boolean?
inputBinding:
position: 0
prefix: 'msin.autoweight=True'
- id: baseline
default: ''
type: string?
inputBinding:
position: 0
prefix: 'msin.baseline='
separate: false
- id: output_column
default: DATA
type: string?
inputBinding:
position: 0
prefix: 'msout.datacolumn='
separate: false
- id: input_column
default: DATA
type: string?
inputBinding:
position: 0
prefix: 'msin.datacolumn='
separate: false
- id: writefullresflag
type: boolean?
default: false
inputBinding:
prefix: msout.writefullresflag=True
- id: overwrite
type: boolean?
default: false
inputBinding:
prefix: msout.overwrite=True
- id: storagemanager
type: string?
default: ""
inputBinding:
prefix: msout.storagemanager=
separate: false
- id: databitrate
type: int?
default: 0
inputBinding:
prefix: msout.storagemanager.databitrate=
separate: false
- id: skymodel
type: File
inputBinding:
position: 0
prefix: demix.skymodel=
separate: false
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
glob: '$(inputs.msout_name=="." ? inputs.msin.basename : inputs.msout_name)'
- id: logfile
type: File[]
outputBinding:
glob: 'DPPP*.log'
hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor3-cwl
stdout: DPPP.log
stderr: DPPP_err.log
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.msin)
writable: true
steps/dppp_prep_target.cwl 0 → 100755
+ 141
− 0
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: dppp
baseCommand:
- DP3
inputs:
- id: parset
type: File?
inputBinding:
position: -1
- id: msin
type: Directory?
inputBinding:
position: 0
prefix: msin=
separate: false
doc: Input Measurement Set
- id: solutions
type: File?
doc: Input Solution Set
- id: msout_name
default: "."
type: string?
inputBinding:
position: 0
prefix: msout=
separate: false
doc: Output Measurement Set
- id: autoweight
default: false
type: boolean?
inputBinding:
position: 0
prefix: 'msin.autoweight=True'
- id: baseline
default: ''
type: string?
inputBinding:
position: 0
prefix: 'msin.baseline='
separate: false
- id: output_column
default: DATA
type: string?
inputBinding:
position: 0
prefix: 'msout.datacolumn='
separate: false
- id: input_column
default: DATA
type: string?
inputBinding:
position: 0
prefix: 'msin.datacolumn='
separate: false
- id: writefullresflag
type: boolean?
default: false
inputBinding:
prefix: msout.writefullresflag=True
- id: overwrite
type: boolean?
default: false
inputBinding:
prefix: msout.overwrite=True
- id: storagemanager
type: string?
default: ""
inputBinding:
prefix: msout.storagemanager=
separate: false
- id: databitrate
type: int?
default: 0
inputBinding:
prefix: msout.storagemanager.databitrate=
separate: false
- id: apply_tec_correction
type: boolean?
default: false
inputBinding:
position: 0
prefix: 'applytec.parmdb='
separate: false
valueFrom: $(inputs.solutions.path)
- id: apply_rm_correction
type: boolean?
default: true
inputBinding:
position: 0
prefix: 'applyRM.parmdb='
separate: false
valueFrom: $(inputs.solutions.path)
- id: apply_phase_correction
type: boolean?
default: false
inputBinding:
position: 0
prefix: 'applyphase.parmdb='
separate: false
valueFrom: $(inputs.solutions.path)
- id: apply_clock_correction
type: boolean?
default: true
inputBinding:
position: 0
prefix: 'applyclock.parmdb='
separate: false
valueFrom: $(inputs.solutions.path)
- id: skymodel
type: File
inputBinding:
position: 0
prefix: demix.skymodel=
separate: false
arguments:
- applyPA.parmdb=$(inputs.solutions.path)
- applybandpass.parmdb=$(inputs.solutions.path)
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
glob: '$(inputs.msout_name=="." ? inputs.msin.basename : inputs.msout_name)'
- id: logfile
type: File[]
outputBinding:
glob: 'DPPP*.log'
hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor3-cwl
stdout: DPPP.log
stderr: DPPP_err.log
requirements:
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.msin)
writable: true
steps/filter_ms_group.cwl
+ 2
− 2
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
id: filter_ms_group
baseCommand:
- python3
......
steps/findRefAnt.cwl
+ 2
− 2
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: findRefAnt
......@@ -37,7 +37,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).flagged_fraction_dict)
- id: logfile
type: File?
type: File
outputBinding:
glob: findRefAnt.log
......
steps/findRefAnt_join.cwl
+ 3
− 3
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: findRefAnt_join
......@@ -30,11 +30,11 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).refant)
- id: flagged_fraction_antenna
type: File?
type: File
outputBinding:
glob: 'flagged_fraction_antenna.json'
- id: logfile
type: File?
type: File
outputBinding:
glob: findRefAnt.log
......
steps/find_skymodel_cal.cwl
+ 2
− 2
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: find_skymodel_cal_py
......@@ -43,7 +43,7 @@ outputs:
glob: 'out.json'
outputEval: $(JSON.parse(self[0].contents).skymodel_name)
- id: logfile
type: File?
type: File
outputBinding:
glob: find_skymodel_cal.log
......
steps/find_skymodel_target.cwl
+ 4
− 3
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: find_skymodel_target_py
......@@ -61,7 +61,7 @@ outputs:
outputBinding:
glob: target.skymodel
- id: logfile
type: File?
type: File
outputBinding:
glob: find_skymodel_target.log
......@@ -69,6 +69,7 @@ requirements:
- class: InlineJavascriptRequirement
hints:
DockerRequirement:
- class: DockerRequirement
dockerPull: lofareosc/prefactor3-cwl
stdout: find_skymodel_target.log
\ No newline at end of file
steps/get_targetname.cwl
+ 1
− 1
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
......
steps/h5parm_pointingname.cwl
+ 1
− 1
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
......
steps/h5parmcat.cwl
+ 1
− 1
View file @ 89ffab29
class: CommandLineTool
cwlVersion: v1.0
cwlVersion: v1.1
$namespaces:
lofar: 'https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl'
sbg: 'https://www.sevenbridges.com/'
......
  • alex @alex

    mentioned in commit bae94184

     ·

    mentioned in commit bae94184

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