Commit b5821d05 authored by mancini's avatar mancini

Merge commit 'c116d304'

parents 655821cf c116d304
......@@ -159,6 +159,12 @@ ddecal:
script:
- cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/ddecal.cwl test_jobs/ddecal.json
gaincal:
stage: test_steps
allow_failure: true
script:
- cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/gaincal.cwl test_jobs/gaincal.json
predict:
stage: test_steps
allow_failure: true
......
......@@ -13,7 +13,7 @@ requirements:
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
baseCommand:
- aoflagger
......
......@@ -19,6 +19,7 @@ inputs:
'sbg:y': -88
- id: autoweight
type: boolean
default: true
'sbg:x': -113
'sbg:y': 290
outputs:
......
......@@ -88,7 +88,7 @@ outputs:
glob: DPPP.log
hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor
dockerPull: lofareosc/lofar-pipeline
stdout: DPPP.log
requirements:
- class: InlineJavascriptRequirement
......@@ -63,7 +63,7 @@ outputs:
label: H5parm_collector
hints:
- class: DockerRequirement
dockerPull: 'lofareosc/prefactor-ci:master'
dockerPull: 'lofareosc/lofar-pipeline-ci:latest'
stdout: $(inputs.outh5parmname)-parm_collector_output.log
requirements:
- class: InlineJavascriptRequirement
......
......@@ -30,7 +30,7 @@ arguments:
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
inputs:
- id: input_h5parm
......
......@@ -30,7 +30,7 @@ arguments:
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
inputs:
- id: input_h5parm
......
......@@ -31,7 +31,7 @@ arguments:
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
inputs:
- id: input_h5parm
......
......@@ -44,7 +44,7 @@ arguments:
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
inputs:
- id: input_h5parm
......
......@@ -42,7 +42,7 @@ arguments:
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
inputs:
- id: input_h5parm
......
......@@ -29,7 +29,7 @@ arguments:
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
inputs:
- id: input_h5parm
......
......@@ -29,7 +29,7 @@ arguments:
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
inputs:
- id: input_h5parm
......
class: CommandLineTool
cwlVersion: v1.0
$namespaces:
sbg: 'https://www.sevenbridges.com/'
id: applycal
baseCommand:
- DPPP
arguments:
- steps=[applycal]
inputs:
- id: msin
type: Directory
inputBinding:
position: 0
prefix: msin=
separate: false
doc: Input Measurement Set
- default: DATA
id: msin_datacolumn
type: string
inputBinding:
position: 0
prefix: msin.datacolumn=
separate: false
doc: Input data Column
- id: parmdb
type: File
doc: Path of parmdb in which the parameters are stored. This can also be an H5Parm file, in that case the filename has to end in '.h5'
inputBinding:
prefix: applycal.parmdb
- id: correction
default: gain
type:
type: enum
symbols:
- gain
- tec
- clock
- rotationangle
- rotation
- scalarphase
- scalaramplitude
- rotationmeasure
- fulljones
doc: |
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'.
inputBinding:
prefix: applycal.correction=
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
glob: $(inputs.msin.basename)
requirements:
- class: InitialWorkDirRequirement
listing:
- entry: $(inputs.msin)
writable: true
- class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
dockerPull: lofareosc/lofar-pipeline-ci:latest
......@@ -39,6 +39,6 @@ outputs:
label: check_Ateam_separation
hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor
dockerPull: lofareosc/lofar-pipeline
- class: InlineJavascriptRequirement
stdout: Ateam_separation.log
......@@ -10,7 +10,7 @@ requirements:
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
arguments:
- steps=[ddecal]
......
#!/usr/bin/env cwl-runner
class: CommandLineTool
cwlVersion: v1.0
id: gaincal
baseCommand: [DPPP]
requirements:
InlineJavascriptRequirement: {}
hints:
DockerRequirement:
dockerPull: lofareosc/lofar-pipeline-ci:latest
arguments:
- steps=[gaincal]
inputs:
- id: msin
type: Directory?
doc: Input Measurement Set
inputBinding:
prefix: msin=
separate: false
- id: caltype
doc: |
The type of calibration that needs to be performed.
type:
type: enum
symbols:
- diagonal
- fulljones
- phaseonly
- scalarphase
- amplitude
- scalaramplitude
- tec
- tecandphase
inputBinding:
prefix: gaincal.caltype=
separate: false
- id: sourcedb
type: File
inputBinding:
prefix: gaincal.sourcedb=
separate: false
- id: usebeammodel
type: boolean
default: true
inputBinding:
prefix: gaincal.usebeammodel=true
separate: false
- id: solint
type: int
default: 1
doc: |
Number of time slots on which a solution is assumed to be constant (same as CellSize.Time in BBS).
0 means all time slots. Note that for larger settings of solint, and specially for solint = 0,
the memory usage of gaincal will be large (all visibilities for a solint should fit in memory).
- id: msin_datacolumn
type: string?
default: DATA
doc: Input data Column
inputBinding:
prefix: msin.datacolumn=
separate: false
- id: onebeamperpatch
type: boolean
doc: Input data Column
default: true
inputBinding:
prefix: gaincal.onebeamperpatch=True
separate: false
- id: msin_modelcolum
type: string
default: MODEL_DATA
doc: Model data Column
inputBinding:
prefix: msin.modelcolumn=
separate: false
- id: output_name_h5parm
type: string
default: instrument.h5
inputBinding:
prefix: gaincal.parmdb=
separate: false
- id: msout_name
type: string
doc: Output Measurement Set
default: out.MS
inputBinding:
prefix: msout=
separate: false
outputs:
- id: msout
doc: Output Measurement Set
type: Directory
outputBinding:
glob: $(inputs.msout_name=="."?inputs.msin:inputs.msout_name)
- id: h5parm
doc: Filename of output H5Parm (to be read by e.g. losoto)
type: File
format: lofar:#H5Parm
outputBinding:
glob: $(inputs.output_name_h5parm)
$namespaces:
lofar: https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
$schema:
- https://git.astron.nl/eosc/ontologies/raw/master/schema/lofar.owl
......@@ -43,7 +43,7 @@ outputs:
label: interpolate_visibilities
hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
requirements:
- class: InitialWorkDirRequirement
......
......@@ -50,7 +50,7 @@ outputs:
label: make_sourcedb_ateam
hints:
- class: DockerRequirement
dockerPull: 'lofareosc/prefactor:latest'
dockerPull: 'lofareosc/lofar-pipeline:latest'
stdout: make_sourcedb_ateam.log
requirements:
- class: InlineJavascriptRequirement
......@@ -51,7 +51,7 @@ label: ms_concat
requirements:
- class: ShellCommandRequirement
- class: DockerRequirement
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
- class: InlineJavascriptRequirement
- class: InitialWorkDirRequirement
listing:
......
......@@ -17,7 +17,7 @@ requirements:
- $import: RadioDatatypes.yaml
hints:
DockerRequirement:
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
baseCommand:
- python3
......
......@@ -68,4 +68,4 @@ requirements:
- class: InlineJavascriptRequirement
hints:
- class: DockerRequirement
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
......@@ -39,4 +39,4 @@ outputs:
label: WSClean
requirements:
- class: DockerRequirement
dockerPull: lofareosc/prefactor-ci:master
dockerPull: lofareosc/lofar-pipeline-ci:latest
{
"msin": {
"class": "Directory",
"path": "/data/L570745_SB001_uv_MODEL.MS"
},
"sourcedb": {"class":"File", "path":"/data/A-Team_lowres.sourcedb"},
"sourcename": "TauA",
"caltype": "diagonal"
}
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