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Add existing-data tag to ticket#4133

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eliottBo wants to merge 239 commits intomasterClinical-Genomics/cg:masterfrom existing-data-tagClinical-Genomics/cg:existing-data-tagCopy head branch name to clipboard

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Commits on Jul 5, 2024

• Add initial structure and models for a workflow (#3391)

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• Restructure order validation modules (#3405)

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Commits on Jul 11, 2024

• Add validation logic skeleton (#3410)(patch)

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Commits on Jul 16, 2024

• Add Tomte order validation rules (#3426)

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Commits on Jul 17, 2024

• Add well validation (#3437)

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Commits on Jul 29, 2024

• Fix typing and add blueprint for converting errors (#3476) (patch)

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• Refactor validators and utils

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• Refactor validators and utils

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• Fix structure for common validators

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• Fix naming

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• Validate unique sample names (#3480)

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• Validate unique case names (#3482)

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Commits on Jul 30, 2024

• Add application validation (#3484) (patch)

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• Validate father sex (#3488)

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• Add application workflow compatibility check (#3489) (patch)

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• Validate mother sex (#3490)

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• Validate father in same case as child (#3492)

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Commits on Jul 31, 2024

• Merge branch 'master' into improve-order-flow-main

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• Add application is not archived validation (#3497) (patch)

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• Rename validation rules (#3498) (patch)

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• Add gene panel validation (#3499) (patch)

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Commits on Aug 1, 2024

• Add no repeated panels validation (#3501) (patch)

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• Add elution buffer check for skip rc (#3502) (patch)

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• Validate mother in same case as child (#3493)

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• Validate pedigree (#3495)

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Commits on Aug 2, 2024

• Add subject_id different from case name validation (#3505) (patch)

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• Add subject_id different from sample name validation (#3503) (patch)

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Commits on Aug 5, 2024

• Validate concentration required if skip rc (#3508) (patch)

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Commits on Aug 6, 2024

• Validate container name requirement (#3527) (patch)

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Commits on Aug 7, 2024

• Validate well position requirement (#3528) (patch)

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Commits on Aug 8, 2024

• Add integration test for OrderValidationService (#3538) (patch)

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Commits on Aug 9, 2024

• Add validation for concentration intervals (#3509) (patch)

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• Validate volume interval (#3532) (patch)

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• Implement convert errors method (#3543) (patch)

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• Add string length constraint (#3548) (patch)

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Commits on Aug 12, 2024

• Type hint

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Commits on Aug 13, 2024

• Use list indices instead of case/sample names (#3552) (patch)

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Commits on Aug 14, 2024

• Add type hints (#3554) (patch)

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Commits on Aug 15, 2024

• Operate on new samples and cases (#3567)

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• Patch unique names rules (#3572)

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• Validate case name is unique (#3573)

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Commits on Aug 16, 2024

• Add case internal id existence check (#3577) (patch)

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• Validate existing samples do in fact exist (#3578)

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• Add status required check (#3579) (patch)

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• (Improve order flow) Validate sex required for new samples (#3580) (patch)

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• Source not required for existing samples (#3582) (patch)

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• Validate existing fathers (#3583)

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• Fix mother validation for existing samples (#3584)

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• Fix pedigree validation for existing cases and samples (#3585)

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• Consider old cases when validating father's sex (#3586) (patch)

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• (Improve order flow) Remove delivery type from Case (#3587) (patch)

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• Make source optionable (#3588) (patch)

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Commits on Aug 19, 2024

• Map order errors to response (#3589)

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• (Improve order flow) Add order validation response test (#3594) (patch)

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• Add microsalt order validation skeleton (#3595)

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• Do not instantiate with a model validator

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• (Improve order flow) Add order validation rules for microsalt (#3597)

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• Fix fixture

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• Shuffle error models (#3599)

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Commits on Aug 20, 2024

• (Improve order flow) Add sample application exists validation (#3600) (patch)

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• Validate microsalt app compatibility (#3602)

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• Add microsalt max one sample per well validation (#3604)

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• Validate plate samples have a well assigned (#3605)

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• (Improve order flow) Add microsalt validate application not archived (#3603) (patch)

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• Fix placement of Tomte rule (#3608) (patch)

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• Add validation of internal_ids for Microsalt (#3610) (patch)

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Commits on Aug 21, 2024

• (Improve order flow) Add validation of repeated sample names for Microsalt (#3611) (patch)

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• Validate volume interval for microSALT (#3612) (patch)

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• Add organism exists validation for microSALT (#3613) (patch)

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• Add mip dna skeleton (#3615)

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• Add extraction method validation (#3616) (patch)

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• Ensure buffer is set for new samples (#3617)

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• Merge master

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• Add dev endpoints (#3619)

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• Remove tomte from general rules (#3621)

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Commits on Aug 22, 2024

• Split rules based on type they operate on (#3623)

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• Refactor util methods (#3624) (patch)

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Commits on Aug 23, 2024

• Patch min string length (#3630) (patch)

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Commits on Aug 26, 2024

• Patch tissue block typing (#3633) (patch)

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• Add empty string to None conversion (#3632) (patch)

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• Add mip dna rules (#3625)

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• Type panels as string (#3639) (patch)

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Commits on Aug 28, 2024

• Add models for existing samples and cases (#3648) (patch)

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• Add mutant order validation skeleton (#3653)

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• Add MutantSample model (#3654) (patch)

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• (Improve order flow) Remove existing sample rule for microsalt (#3652)

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• Add mutant rules (#3656)

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• Add mutant validation rule and refactor tests

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Commits on Aug 29, 2024

• Add balsamic (#3662)

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• Add missing import

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• Fix mutant rules structure

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• Add balsamic base validation rules (#3663)

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• Remove unnecessary rules (#3664) (patch)

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• Populate needed values (#3666) (patch)

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Commits on Aug 30, 2024

• Make sure internal_id None is disregarded (#3667) (patch)

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• Add balsamic sample sex validation (#3665)

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• Fix models to reflect new samples (#3671) (patch)

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Commits on Sep 2, 2024

• Patch indexing

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• (Improve order flow) Remove unused validation rule (#3674) (patch)

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Commits on Sep 4, 2024

• (Improve order flow) Add Balsamic validation rules (#3683) (patch)

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Commits on Sep 10, 2024

• Add well position validation for sample rules (#3699)

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Commits on Sep 12, 2024

• Add well position validation for case_sample (#3704)

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• Add validation tube names samples order (#3710)

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Commits on Sep 13, 2024

• Add validation tube names case (#3716)

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• patch ContainerNameRepeatedError error message (#3720)

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Commits on Sep 19, 2024

• Improve Order Flow, Add Container Name Validation #3723 (#3736)

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• Improve Order Flow: Add Required Volume Validation #3722 (#3741)

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Commits on Sep 30, 2024

• (Improve order flow) Refactor order flow tests (#3748) (patch)

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Commits on Oct 7, 2024

• Merge branch 'master' into improve-order-flow-main

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• Merge branch 'master' into improve-order-flow-main

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Commits on Oct 8, 2024

• Merge branch 'master' into improve-order-flow-main

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• Merge branch 'master' into improve-order-flow-main

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Commits on Oct 9, 2024

• Merge branch 'master' into improve-order-flow-main

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Commits on Oct 14, 2024

• Merge branch 'master' into improve-order-flow-main

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• Merge branch 'master' into improve-order-flow-main

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• Merge branch 'master' into improve-order-flow-main

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Commits on Oct 15, 2024

• Add sample error mapping (#3840) (patch)

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• Merge branch 'master' into improve-order-flow-main

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Commits on Oct 23, 2024

• Merge branch 'master' into improve-order-flow-main

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Commits on Oct 29, 2024

• Merge branch 'master' into improve-order-flow-main

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Commits on Nov 6, 2024

• Merge branch 'master' into improve-order-flow-main

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• add fastq order and sample models (#3913)

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• add models and constants for RML (#3919)

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• removed deprecated fields in microsalt sample (#3920)

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• (Improve order flow) Rework application validation (#3904) (patch)

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Commits on Nov 15, 2024

• Add RNAFusion case and sample models (#3938)

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• (Improve order flow) Add metagenome classes (#3925) (patch)

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• (Improve order flow) Patch repeated case sample name rule (#3941) (patch)

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• Merge branch 'master' into improve-order-flow-main

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Commits on Nov 18, 2024

• improve order flow - Microbial fastq order classes (#3951)

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Commits on Nov 19, 2024

• patch microbial fastq sample (#3954)

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• Improve order flow - Add RnaFusion Rules (#3947)

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Commits on Nov 20, 2024

• add subject and sex validation to human samples (#3956)

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Commits on Nov 25, 2024

• rename validate_required_volume for validate_volume_required (#3963)

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• refactor sample validate_volume_required

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• Merge branch 'master' into improve-order-flow-main

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• add services and rules (#3966)

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Commits on Nov 26, 2024

• Merge branch 'master' into improve-order-flow-main

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• add pacbio models (#3969)

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• Patch library prep imports (#3974) (patch)

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Commits on Nov 27, 2024

• (Improve order flow) Update test endpoint (#3978) (patch)

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Commits on Dec 3, 2024

• Merge branch 'master' into improve-order-flow-main

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• add pacbio service (#3994)

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Commits on Dec 4, 2024

• Add validation case name different from sample name (#3995)(patch)

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Commits on Dec 5, 2024

• Improve-order-flow: Add Fluffy (#3934)

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• (Improve order flow) Add fastq rules (#3986) (patch)

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Commits on Dec 6, 2024

• Add validation if mip all samples unknown (#4001)(patch)

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• Add mip-rna order validation (#3914)

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Commits on Dec 9, 2024

• add Balsamic umi models (#4009)

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• (Improve order flow) Add metagenome rules (#3943)

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• Merge branch 'master' into improve-order-flow-main

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Commits on Dec 10, 2024

• Add taxprofiler rules and models (#4010)

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Commits on Dec 11, 2024

• (Improve order flow) Fix other alias (#3996) (patch)

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• Merge branch 'refs/heads/master' into improve-order-flow-main

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Commits on Dec 12, 2024

• Add RML validation rules (#4004)

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Commits on Dec 13, 2024

• add rule sample name different from case name (#4022)

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Commits on Dec 16, 2024

• Merge branch 'master' into improve-order-flow-main

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• Merge branch 'master' into improve-order-flow-main

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• Improve order flow storing main (#3976) (minor)

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• (Improve order flow) Refactor validation services (#4024) (minor)

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• Patch elution buffer other option (#4027) (patch)

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Commits on Dec 17, 2024

• Merge branch 'master' into improve-order-flow-main

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Commits on Dec 19, 2024

• rework microbial fastq store (#4026)

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• (Improve order flow) Make ticket id a private attribute (#4032) (patch)

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• (Improve order flow) Patch control parsing (#4033) (patch)

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• Make type of ticket clear in store services (#4034)

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Commits on Dec 20, 2024

• refactor fastq and microbial fastq storing services (#4037)

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• Patch setting ticket id (#4038) (patch)

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• rework pacbio store service (#4039)

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• Merge branch 'master' into improve-order-flow-main

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Commits on Jan 2, 2025

• (Improve order flow) Patch pedigree validation (#4036) (patch)

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• (Improve order flow) Rework store case order service (#4035) (minor)

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Commits on Jan 3, 2025

• Fix ExistingSample (#4045) (patch)

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• Merge branch 'master' into improve-order-flow-main

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Commits on Jan 7, 2025

• (Improve order flow) Set family name in lims (#4050) (patch)

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• Merge branch 'master' into improve-order-flow-main

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Commits on Jan 8, 2025

• (Improve order flow) Rework store metagenome order service (#4048) (patch)

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• (Improve order flow) Rework microbial storing service (#4052) (patch)

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• (Improve order flow) Add buffer required rule (#4056) (patch)

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Commits on Jan 9, 2025

• Rework pool store service (#4059)

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• Merge branch 'master' into improve-order-flow-main

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• Patch microbial fastq response (#4061) (patch)

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Commits on Jan 10, 2025

• Fix fixture structure (#4067)

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• (Improve order flow) Add pool rules (#4066) (patch)

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• (Improve order flow) Remove submitters (#4062) (minor)

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• Fix docstrings and type hints of sample rules

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Commits on Jan 14, 2025

• add new mutant validation rule (#4075)

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• (Improve order flow) Fix index validation (#4073) (patch)

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• Merge master

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• Fix test

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• (Improve order flow) Clean up the Order model (#4082) (patch)

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• add support for MAF orders in storing fastq orders (#4083)

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• Merge branch 'master' into improve-order-flow-main

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Commits on Jan 15, 2025

• Remove old fastq validation (#4087) (patch)

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• Remove old pacbio validation (#4088)

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• remove metagenome old validation (#4091)

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• (Improve order flow) Remove old microbial validation (#4090) (patch)

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• remove pool old validation (#4093)

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• (Improve order flow) Remove old case validation (#4096) (patch)

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Commits on Jan 16, 2025

• (Improve order flow) RNAFusion One sample per case rule (#4095) (patch)

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• removing old sample and order models pt 1 (#4097)

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• remove organism validation (#4103)

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• (Improve order flow) Add balsamic sample errors (#4102) (patch)

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• remove organism validation (#4105)

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• Fix index sequence mismatch stacking (#4104) (patch)

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• Finish integration tests (#4107)

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Commits on Jan 17, 2025

• remove old models and old tests (#4109)

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• (Improve order flow) Add mutant fields (#4108) (patch)

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• move new validation service to orders (#4110)

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• move new validation service to orders (#4111)

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• (Improve order flow) Add error logging (#4114) (patch)

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• (Improve order flow) Set default index sequence (#4113) (patch)

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• remove directory for balsamic specific rules (#4116)

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• move orderAPI to services and rename to submitter (#4119)

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• Merge master

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• Fix linting

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• Fix volume rule (#4120) (patch)

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• Add utility functions for order data validation and ticket tag generation

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• Integrate ticket tag generation into TicketHandler

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• Add unit test for ticket tag generation in OrderSubmitter

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• Merge branch 'master' into improve-order-flow-main

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• Add existing cases should belong to customer rule (#4123) (patch)

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• Refactor ticket tag generation and enhance unit tests for accuracy

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• Add existing samples should belong to collaboration rule (#4124) (patch)

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Commits on Jan 21, 2025

• enhance order submission integration tests (#4121)

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• (Improve order flow) Fix delivery types (#4126) (patch)

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• Rename function and update references in ticket tag generation

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• Add fixture for MIP DNA order with existing samples

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• Update internal_id for existing sample in MIP DNA order fixture

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• Revert pre commit to master (#4128) (patch)

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• (Improve order flow) Override microbial dump (#4127) (patch)

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• Fix repeated case name rule (#4129) (patch)

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• Remove pacbio volume interval rule (#4130) (patch)

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• Make panels optional for existing cases (#4131) (patch)

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• Remove Balsamic-QC support

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• add test for validation pool (#4132)

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• Test mutant validator (#4134)

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• Merge branch 'improve-order-flow-main' into existing-data-tag

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• Rename order data check function and improve tag assignment logic

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