From 3e61c70943a082c2f3b5f2ee4a1b3494fe809648 Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Tue, 29 Oct 2019 11:29:47 +0100
Subject: [PATCH] Add predict step test
---
.gitlab-ci.yml | 6 ++++++
steps/predict.cwl | 29 +++++++++++++++--------------
test_jobs/predict.json | 10 ++++++++++
3 files changed, 31 insertions(+), 14 deletions(-)
create mode 100644 test_jobs/predict.json
diff --git a/.gitlab-ci.yml b/.gitlab-ci.yml
index ab043a38..26c089f1 100644
--- a/.gitlab-ci.yml
+++ b/.gitlab-ci.yml
@@ -94,6 +94,12 @@ ddecal:
script:
- cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/ddecal.cwl test_jobs/ddecal.json
+predict:
+ stage: test_steps
+ allow_failure: true
+ script:
+ - cwltool --no-container --preserve-environment LD_LIBRARY_PATH --preserve-environment PATH --preserve-environment PYTHONPATH steps/predict.cwl test_jobs/predict.json
+
prefactor_calibrator:
stage: integration_test
script:
diff --git a/steps/predict.cwl b/steps/predict.cwl
index e20f0151..972cce51 100644
--- a/steps/predict.cwl
+++ b/steps/predict.cwl
@@ -7,6 +7,11 @@ baseCommand: [DPPP]
requirements:
InlineJavascriptRequirement: {}
+
+ InitialWorkDirRequirement:
+ listing:
+ - entry: $(inputs.msin)
+ writable: true
hints:
DockerRequirement:
@@ -16,16 +21,17 @@ arguments:
- steps=[predict]
- predict.beammode=array_factor
- predict.usechannelfreq=False
+ - msout=.
inputs:
- id: msin
- type: Directory?
+ type: Directory
doc: Input Measurement Set
inputBinding:
prefix: msin=
separate: false
- id: msin_datacolumn
type: string
- default: SMOOTHED_DATA
+ default: DATA
doc: Input data Column
inputBinding:
prefix: msin.datacolumn=
@@ -33,16 +39,17 @@ inputs:
- id: msout_datacolumn
type: string
default: MODEL_DATA
- - id: source_db
- type: "[File, Directory]"
+ - id: sources_db
+ type: [File, Directory]
inputBinding:
prefix: predict.sourcedb=
separate: false
- - id: skymodel
+ - id: sources
type: string[]
+ default: null
inputBinding:
prefix: predict.sources=
- valueFrom: [$(self)]
+ valueFrom: "[$(self)]"
separate: false
itemSeparator: ','
- id: usebeammodel
@@ -50,17 +57,11 @@ inputs:
default: false
inputBinding:
prefix: predict.usebeammodel=True
- - 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)
+ glob: $(inputs.msin.basename)
diff --git a/test_jobs/predict.json b/test_jobs/predict.json
new file mode 100644
index 00000000..2a493f87
--- /dev/null
+++ b/test_jobs/predict.json
@@ -0,0 +1,10 @@
+{
+ "msin": {
+ "class": "Directory",
+ "path": "/data/L570745_SB001_uv_first10.MS"
+ },
+ "sources_db": {
+ "class": "File",
+ "path": "/data/A-Team_lowres.sourcedb"
+ }
+}
--
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