EVA-3414 Store validation result and pass it to submit #14
Conversation
cli/eva_sub_cli.py
Outdated
| config_file_path = os.path.join(args.submission_dir, SUB_CLI_CONFIG_FILE) | ||
| sub_config = WritableConfig(config_file_path, version=__version__) | ||
|
|
||
| if args.task == RESUME: |
There was a problem hiding this comment.
Optional: From a design standpoint, if validation fails for a submission, I feel that issuing "resume" at that point should resume the validation. #standup
There was a problem hiding this comment.
I think I'd agree. We might want to discuss what is and what isn't resumable but if we have a generic resume option it should apply to all steps.
There was a problem hiding this comment.
This being said implementing a comprehensive resume strategy seems outside of the scope of this ticket.
There was a problem hiding this comment.
Tried to simplify resume option
cli/eva_sub_cli.py
Outdated
| config_file_path = os.path.join(args.submission_dir, SUB_CLI_CONFIG_FILE) | ||
| sub_config = WritableConfig(config_file_path, version=__version__) | ||
|
|
||
| if args.task == RESUME: |
There was a problem hiding this comment.
I think I'd agree. We might want to discuss what is and what isn't resumable but if we have a generic resume option it should apply to all steps.
cli/eva_sub_cli.py
Outdated
| if not args.vcf_files_mapping: | ||
| raise Exception(f"Please provide a CSV file which provides VCF and corresponding assembly information " | ||
| f"(use the --vcf_files_mapping switch)") | ||
| if not args.metadata_json and not args.metadata_xlsx: | ||
| raise Exception(f"Please provide the file that describes the project, analysis, samples and files " | ||
| f"using either --metadata_json or --metadata_xlsx") |
There was a problem hiding this comment.
This could probably be improved in a subsequent ticket but the upload does need to know where the VCF and metadata is.
cli/eva_sub_cli.py
Outdated
| config_file_path = os.path.join(args.submission_dir, SUB_CLI_CONFIG_FILE) | ||
| sub_config = WritableConfig(config_file_path, version=__version__) | ||
|
|
||
| if args.task == RESUME: |
There was a problem hiding this comment.
This being said implementing a comprehensive resume strategy seems outside of the scope of this ticket.
There was a problem hiding this comment.
I think these additions would be better suited to reporter.py so they apply to all subsequent validators we might implement.
cli/docker_validator.py
Outdated
| def update_config_with_validation_result(self): | ||
| self.sub_config.set(VALIDATION_RESULTS, value=self.results) | ||
| self.sub_config.set(READY_FOR_SUBMISSION_TO_EVA, value=self.verify_ready_for_submission_to_eva()) | ||
| self.sub_config.write() |
There was a problem hiding this comment.
I think I would model the writing of the config to the way it works in ELOAD
| SUBMIT = 'submit' | ||
| RESUME = 'resume' | ||
|
|
||
| logging_config.add_stdout_handler() |
There was a problem hiding this comment.
The call to add_stdout_handler should be made in the main function. This avoids having multiple handlers being added if this file is ever loaded as a library.
nitin-ebi
force-pushed
the
store_validation_result
branch
from
9499d91 to
8d84d55
Compare
No description provided.