DEV - Improve order flow main #3815
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Add parent models and Tomte models for the new validation flow.
Split logic into modules based on workflow
### Fixed - Some typing and a blueprint method for converting pydantic errors to our own custom errors.
### Added - Validation that the provided applications exist in the database
### Added - Check that the application provided is compatible with the chosen workflow.
### Added - Applications are validated not to be archived.
### Fixed - Standardised rule naming.
### Added - Added validation making sure that the gene panels exist in status db
### Added - Adds validation ensuring gene panels are not specified more than once.
### Added - Buffer validation for orders attempting to skip reception control
### Added - Validation ensuring that the subject id is not the same as the case name.
### Added - Validation ensuring that the sample name and subject id can not be the same.
### Added - Validation that the concentration is provided for all samples when skip reception control is attempted.
### Added - Container names are required when using well plates.
### Added - Validation that well position is filled in for samples in a well plate.
### Fixed - Response from StoreMicrobialFastqOrderService specifies project
Rework order fixtures
### Added - Validation rules ensuring only one priority and application is allowed per pool.
### Changed - The OrderSubmitterRegistry is a StoringServiceRegistry - The OrderSubmitters are removed - The OrdersAPI needs no Store in its init - The OrdersAPI needs a StoringServiceRegistry instead of a SubmitterRegistry - The OrdersAPI needs an OrderValidationService
diitaz93
reviewed
Jan 10, 2025
diitaz93
reviewed
Jan 10, 2025
diitaz93
reviewed
Jan 13, 2025
## Description Closes Clinical-Genomics/improve-order-flow#102 Fixes the sample name validation rule for Mutant orders to exclude control samples from the name check ### Added - Validation function `validate_non_control_sample_names_available` that verifies that sample names used in an order are not in the store excluding control samples - Utils function `get_sample_name_not_available_errors` used in new validation function - Mutant order fixture - aliases to group samples with organism and samples orders with control samples - tests for new validation functions ### Changed - Refactored validation function `validate_sample_names_available` to use the new utils function ### Fixed - Changed some balsamic structure in the order validation service - Reverted some deletions in json order fixtures from previous prs
### Added - Index sequences stored in backend ### Fixed - Index validation added
### Added - Tests for the order rules ### Fixed - connect_to_ticket removed from Order - user_id is made into a private attribute
## Description Closes Clinical-Genomics/improve-order-flow#119 Adds MAF cases to a fictitious MAF order
### Fixed - Removed old ValidateFastqOrderService
Remove old pacbio validation
remove metagenome old validation
### Fixed - Removed old microbial validation service
remove pool old validation
### Fixed - Removed old case order validation
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