Added scripts to restore submission from spreadsheet. ops-1163 #1165
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amnonkhen
changed the title
amnonkhen
reviewed
Aug 23, 2023
| json.dump(global_uuid_mapping, f, indent=4, separators=(', ', ': ')) | ||
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| def main(project_uuid, token, spreadsheet_path, submission_uuid): | ||
| ingest_api = IngestApi('https://api.ingest.archive.data.humancellatlas.org/') |
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Don't use a hard coded ingest api url.
If you leave it blank, it is taken from the INGEST_API environment variable.
Add a note in the readme to set the correct variable prior to running the script.
Suggested change
| ingest_api = IngestApi('https://api.ingest.archive.data.humancellatlas.org/') | |
| ingest_api = IngestApi() |
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| if __name__ == '__main__': | ||
| main(sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4]) |
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Consider using some argument parsing here.
amnonkhen
reviewed
Aug 23, 2023
Co-authored-by: Amnon Khen <[email protected]>
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Applied the feedback |
amnonkhen
reviewed
Aug 30, 2023
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| project_uuid = os.getenv('project_uuid') | ||
| mongodb_uri = os.getenv('mongodb_uri') or 'mongodb://localhost:27017/' | ||
| map_json_path = os.getenv('map_json_path') or 'uuid_mapping.json' |
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env variables should be uppercase
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| mongodb_uri = os.getenv('mongodb_uri') or 'mongodb://localhost:27017/' | ||
| map_json_path = os.getenv('map_json_path') or 'uuid_mapping.json' |
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use the default function argument of getenv
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Applied feedback - Please @amnonkhen re-review |
amnonkhen
approved these changes
Sep 12, 2023
amnonkhen
approved these changes
Oct 16, 2023
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Added scripts with instructions to fix the issue described in #1163