From 9080c3fdfb717e10e1f2cdb40f59cbbcc0e7245f Mon Sep 17 00:00:00 2001
From: mancini <mancini@astron.nl>
Date: Wed, 25 Mar 2020 17:37:18 +0100
Subject: [PATCH] Refactor find skymodel cal
Former-commit-id: 33381e1da842be3181cddf899f9e0adb0f293a2e
Former-commit-id: 26f182cb05ad5123e3a237c51f1db0c0ead04f4d
---
steps/find_skymodel_cal.cwl | 33 +++++++++++++++++++++++++++------
1 file changed, 27 insertions(+), 6 deletions(-)
diff --git a/steps/find_skymodel_cal.cwl b/steps/find_skymodel_cal.cwl
index 51a1dc4a..936a3959 100644
--- a/steps/find_skymodel_cal.cwl
+++ b/steps/find_skymodel_cal.cwl
@@ -7,12 +7,14 @@ baseCommand:
- python3
inputs:
- id: msin
- type: Directory
+ type: Directory[]
doc: MS containing the calibrator
inputBinding:
position: 0
- id: skymodels
- type: Directory
+ type:
+ - Directory?
+ - File?
doc: Directory containing the sky models
- id: skymodels_extension
type: string?
@@ -23,6 +25,9 @@ arguments:
- '-c'
- |
import sys
+ import os
+ import shutil
+ null = None
from unittest.mock import MagicMock
sys.modules['lofarpipe.support.data_map'] = MagicMock()
@@ -31,16 +36,26 @@ arguments:
from find_skymodel_cal import main as find_skymodel
import json
mss = sys.argv[1:]
- skymodels = "$(inputs.skymodels.path)"
+ print(mss)
+ skymodels = $(inputs.skymodels)
extension = "$(inputs.skymodels_extension)"
+ if skymodels is None:
+ skymodels = "/data/skymodels"
+ else:
+ skymodels = skymodels["path"]
output = {}
if extension != 'null':
output = find_skymodel(mss, skymodels, './', extension)
else:
output = find_skymodel(mss, skymodels, './')
- cwl_output = {'class': 'File', 'path': output['SkymodelCal']}
+ skymodel_path = output['SkymodelCal']
+ skymodel_name = output['SkymodelName']
+ skymodel_path = shutil.copy(skymodel_path, os.getcwd())
+ cwl_output = {"file":{'class': 'File', 'path': skymodel_path},
+ "skymodel_name": skymodel_name}
+
with open('./out.json', 'w') as fp:
json.dump(cwl_output, fp)
outputs:
@@ -49,11 +64,17 @@ outputs:
outputBinding:
loadContents: true
glob: 'out.json'
- outputEval: $(JSON.parse(self[0].contents))
+ outputEval: $(JSON.parse(self[0].contents).file)
+ - id: model_name
+ type: string
+ outputBinding:
+ loadContents: true
+ glob: 'out.json'
+ outputEval: $(JSON.parse(self[0].contents).skymodel_name)
requirements:
- class: InlineJavascriptRequirement
hints:
DockerRequirement:
- dockerPull: lofareosc/prefactor-ci:master
+ dockerPull: lofareosc/prefactor:latest
--
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