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feat(new delivery flow)#3598

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ChrOertlin merged 85 commits intomasterClinical-Genomics/cg:masterfrom dev-new-delivery-serviceClinical-Genomics/cg:dev-new-delivery-serviceCopy head branch name to clipboardSep 10, 2024

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Commits

Commits on Aug 19, 2024

• initial commit

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Commits on Aug 21, 2024

• Merge branch 'master' into dev-new-delivery-service

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• add(fetch delivery files service) (#3601)

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• fix imports

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• initial commit

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• fixes

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• fix

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• add test

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Commits on Aug 22, 2024

• fix test

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• add exists assertion

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• add func call

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• initial commit

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• Update tests/fixture_plugins/delivery_fixtures/delivery_files_models_fixtures.py

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• Update tests/fixture_plugins/delivery_fixtures/delivery_files_models_fixtures.py

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• Apply suggestions from code review

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• review

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• Merge branch 'add-file-mover' into add-file-reformatters

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• feat(delivery file mover service) (#3622)

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• conflicsts

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Commits on Aug 26, 2024

• refactor logic

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• fix formatter

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• fix concatenation

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• tests

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Commits on Aug 27, 2024

• add tests for formatters

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• add test

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• review comments

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• setup factory

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• add supporting functions

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• make super call

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• Merge branch 'add-file-reformatters' into add-delivery-services

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• changes

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• simplifiy formatter

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• add docstring

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• solve imports

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• Merge branch 'add-file-reformatters' into add-delivery-services

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• add factory

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• add builder test

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Commits on Aug 29, 2024

• add(delivery file formatter) (#3626)

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• merge conflicts

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• cleanup

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• fix doc

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• cleanup

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• Apply suggestions from code review

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• typehints

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• merge

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• rename class

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• missing typehints

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• add(delivery service factory) (#3647)

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Commits on Sep 2, 2024

• Merge branch 'dev-new-delivery-service' of https://github.com/Clinical-Genomics/cg into dev-new-delivery-service

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Commits on Sep 3, 2024

• fix(new delivery service calls in CLI) (#3673)

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• Merge branch 'master' into dev-new-delivery-service

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• cases have no workflows

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• Merge branch 'dev-new-delivery-service' of https://github.com/Clinical-Genomics/cg into dev-new-delivery-service

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• add delivery type validation in factory

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• Merge branch 'master' into dev-new-delivery-service

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Commits on Sep 4, 2024

• Merge branch 'master' into dev-new-delivery-service

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• add error for analysis bundles

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• hanlde error better rysnc

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• remove concatenation from mutant

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• add delete ticket folder when already exists

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• fix mutant factory test

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Commits on Sep 5, 2024

• fix(clinical delivery call) (#3688)

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Commits on Sep 6, 2024

• refactor(rsync api) (#3694)

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Commits on Sep 9, 2024

• Merge branch 'master' into dev-new-delivery-service

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• add(CLI automatic delivery fastq workflow) (#3692)

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• fix

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• remove unused var

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• fix bug

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• simplify rsync

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• revert rsync changes

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• handle houskeeper error

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• homogenise naming

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• clarification docstring

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• clear imports

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• function hidden

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• add cli help

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Commits on Sep 10, 2024

• Apply suggestions from code review

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• named args

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• Merge branch 'master' into dev-new-delivery-service

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• Apply suggestions from code review

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• add delivery type sanitasion

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• typehints

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• Apply suggestions from code review

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• review

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• Update tests/services/file_delivery/rsync_service/conftest.py

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