Bugfix/python #656
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Bugfix/python #656
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added 2 commits
March 10, 2021 13:43
…tations having text = None
rkm
requested changes
Mar 10, 2021
| @@ -144,11 +144,13 @@ def extract_file(input, output): | |||
| for root, dirs, files in os.walk(args.input, topdown=False): | |||
| for name in files: | |||
| extract_file(os.path.join(root, name), args.output_dir) | |||
| else: | |||
| elif mongodb != {}: | |||
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Is this a typo of mongo_db above? I'm not seeing mongodb defined anywhere
| # could be a SOPInstanceUID in Mongo | ||
| # except SOPInstanceUID is not in the Mongo index, | ||
| # only the DicomFilePath. | ||
| mongodb = Mongo.SmiPyMongoCollection(mongo_host) | ||
| mongodb.setImageCollection('SR') | ||
| mongojson = mongodb.DicomFilePathToJSON(args.input) | ||
| extract_mongojson(mongojson, output_dir) | ||
| else: | ||
| logging.error(f'Cannot find {args.input} in as file or in MongoDB') |
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might be useful to exit non-zero here so any scripts can hook-into this
rkm
approved these changes
Mar 10, 2021
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Proposed Changes
Handle missing MongoDB settings in default.yaml because settings are spread across two yaml files.
Allow a virtualenv to be specified instead of the default environment when running SRAnonTool.
Handle the output from the latest SemEHR anonymiser
Ignore None-type annotations
Types of changes
What types of changes does your code introduce? Tick all that apply.
[skip ci]Checklist
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