EVA-3635 - Fixes from Testing #53
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tcezard
commented
Aug 21, 2024
| # Validation is mandatory so if submit is requested then VALIDATE must have run before or be requested as well | ||
| if SUBMIT in tasks: | ||
| if not sub_config.get(READY_FOR_SUBMISSION_TO_EVA, False): | ||
| return True | ||
| submission_id = sub_config.get(SUB_CLI_CONFIG_KEY_SUBMISSION_ID, None) | ||
| if submission_id: | ||
| try: | ||
| submission_status = SubmissionWSClient().get_submission_status(submission_id) | ||
| submission_status = SubmissionWSClient(username, password).get_submission_status(submission_id) |
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Passing the username and password is required because the auth is a global variable and subsequent call will not have the username/password if it is initially created without them.
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I can't remember, did you check whether it worked without the global auth?
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I did try briefly and it didn't work first time so didn't push it since it wasn't pat of this ticket
Raise if metadata spreadsheet is not provided Remove requirement for VCF file type since it has been removed from the metadata Output logs for main nextflow steps to help debug Add debug option to main CLI Lower some docker validator log message to debug
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apriltuesday
approved these changes
Aug 29, 2024
| # Validation is mandatory so if submit is requested then VALIDATE must have run before or be requested as well | ||
| if SUBMIT in tasks: | ||
| if not sub_config.get(READY_FOR_SUBMISSION_TO_EVA, False): | ||
| return True | ||
| submission_id = sub_config.get(SUB_CLI_CONFIG_KEY_SUBMISSION_ID, None) | ||
| if submission_id: | ||
| try: | ||
| submission_status = SubmissionWSClient().get_submission_status(submission_id) | ||
| submission_status = SubmissionWSClient(username, password).get_submission_status(submission_id) |
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I can't remember, did you check whether it worked without the global auth?
nitin-ebi
approved these changes
Aug 30, 2024
Co-authored-by: April Shen <april.tuesday@gmail.com>
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Ensure all relative path are made into full path
Raise if metadata spreadsheet is not provided
Remove requirement for VCF file type since it has been removed from the metadata Output logs for main nextflow steps to help debug
Add debug option to main CLI
Lower some docker validator log message to debug