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.
## 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
### Added - One sample per case rule for RNA Fusion cases
## Description The old validation used pydantic models such as `OrderIn`, and samples for each ordertype that new ones have replaced, therefore they need to be deleted. They are still called in many tests set to fail. The tests are still kept as they need to be translated into the new validation. This PR attempts to remove the pydantic models and fix the tests. Many changes are involved, so I separated the PR with an incomplete working set of changes. ### Added - Fixtures for taxprofiler order - Store fixture for order integration tests (includes all application and a maf order. To be expanded with organisms and everything needed for the tests) ### Changed - Fixed integration tests for Balsamic, Fastq, Fuffy, and Metagenome ### Fixed - Removed completely unused models --------- Co-authored-by: Isak Ohlsson Ångnell <40887124+islean@users.noreply.github.com>
remove organism existence validation
### Added - Rule preventing more than two samples in any Balsamic case - Rule preventing a double tumour pair in any Balsamic case - Rule preventing a double normal pair in any Balsamic case
Fix MIP, PACBIO and RML integration ttests
### Fixed - Index sequence mismatch is not highlighted when the index sequenced is simply missing
Fix integration tests for RNAFUSION, TAXPROFILER and TOMTE
Remove OrderIn model and old tests
### Fixed - lab_code, original_lab_address and region code are set as in master - Länssjukhuset Sundsvall added to BE original labs
Move the service in cg/services/order_validation_service/ to cg/services/orders/validation/. Similarly done in the tests
Remove skipping from previously failing tests
### Added - Logging of the errors happening during submission
### Fixed - Default index sequence is set for RML and Fluffy orders
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