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Add per-organization, versioned specification codes - #1561
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…b/civic-v2 into versioned-specification-codes
… EID tags on evaluations
… EID tags on evaluations
…b/civic-v2 into versioned-specification-codes
…alid specs for the given assertion
…and code descriptions
…ady been evaluated
…rength and oncogenic/benign group
…valuated on strength
…s/alerts on draft specs
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Closes #1348
This PR implements per-organization, versioned specification codes by adding three new tables:
This PR also implements a new form, the specification-submit form. This form is used to submit or revise evaluations. This is a multi-part form. First, it displays a set of available specifications based on which ones are applicable for the assertion, based on assertion type and previously evaluated specifications. Once a specification is selected, it displays details about the specification. A second form is then auto-generated based on the criteria available for the selected specification. For oncogenicity and pathogenicity evaluations, the criteria are displayed inside of a stepper component where each assessment group is a separate step. Selecting multiple criteria in an assessment group as "met" will cause a validation error. Selecting mutually exclusive codes as met will also cause a validation error. The form also displays an evaluation summary that displays the full list of criteria as tags., with colors to represent the chosen evaluation status. For clinical impact evaluations, the available criteria for the selected specification populate a drop down and one criteria can be selected. On submission, the a new submit_criteria_evaluation mutation is called which will either create a set of criteria evaluations (one for each criteria in the spec for oncogenicity/pathogenicity - or a single evaluation for clinical impact) if there are no existing evaluations for the spec or it will revise the exiting evaluation(s). For evaluations of clinical impact, a switch from one AMP/ASCO/CAP category to another is a revision to the selected specification criteria of the single evaluation - instead of a separate evaluation.
All evaluated specs are displayed on the assertion summary (one description item component per evaluated spec). For oncogenicity and pathogenicity these display tags for met codes. For these assertion types there is now also a new "Oncogenicity Evaluations" or "Pathogenicity Evaluations" tab, which shows the full details for each evaluated specification, its codes and evaluation results (status, modifier, justification, evidence items). Draft specifications are clearly marked with a "Draft" warning tag or warning banner, depending on context.
The revisions tab will have additional tabs, one for each evaluated specification. For onogenicity and pathogenicity, there is one subtab per criteria with any revisions to the evaluation for that specific criteria available there. For clinical impact, there is no subtab and the revisions to the single evaluation are shown.