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As a production member,
I want to restrict the species selection to validated organisms and require a reference for non-validated organisms,
So that we ensure data consistency, reduce errors, and streamline the typing workflow.
Work Impact
Is there currently a workaround for this issue? If so, what is it?
Customers manually enter species names in the “Other species” column, which can lead to misspellings and inconsistencies.
We rely on customers to provide references for new species, but there is no validation process.
How much time would be saved by implementing this feature on a weekly basis?
For MWR, we in production are required to produce a passing QC result in the microsite QC report. This requires us to manually check the suggested species of a sample using Kraken, which takes perhaps 10 minutes per sample. However, after that, we also have to rerun the whole analysis for the sample, which takes hours.
How many users are affected by this issue?
The bioinformatics production team and all users handling microbial typing requests.
Are customers affected by this issue?
Yes, customers experience inconsistent handling of non-validated organisms, which can lead to uncertainty in typing results.
Acceptance Criteria
The “Species” column allows only a predefined list of validated organisms or Other. The validated set of organisms, and their reference genomes are list here:
Rename the validated organism so that:
The internal ID is the short name
The Name is the full-length name
Remove the duplicated K. pneumoniae entry, keep the one with NC_016845.1 as the reference genome.
If a validated organism is chosen, we use the value of the reference for the organism in StausDB
If “Other” is selected in the order form or the order portal, a reference must be provided.
The “Other species” column is removed from the order form.
StatusDB only stores validated organisms and references for better data management.
Orders do not create new entries in the "Organism" table
Notes
Additional information.
Dependencies.
Related user stories.
The text was updated successfully, but these errors were encountered:
As a production member,
I want to restrict the species selection to validated organisms and require a reference for non-validated organisms,
So that we ensure data consistency, reduce errors, and streamline the typing workflow.
Work Impact
Acceptance Criteria
Notes
The text was updated successfully, but these errors were encountered: