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Master merge from develop#135

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dasunpubudumal merged 87 commits intomastersanger/tol-lab-share:masterfrom developsanger/tol-lab-share:developCopy head branch name to clipboardJul 29, 2024

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Commits on Jun 11, 2024

• Bump more-itertools from 10.2.0 to 10.3.0

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Commits on Jun 14, 2024

• Change limber to sequencescape on Rabbit

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Commits on Jun 17, 2024

• Bump flake8 from 7.0.0 to 7.1.0

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Commits on Jun 21, 2024

• Bump python-snappy from 0.7.1 to 0.7.2

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Commits on Jun 24, 2024

• Bump types-requests from 2.32.0.20240602 to 2.32.0.20240622

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• Bump coverage from 7.5.3 to 7.5.4

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Commits on Jun 25, 2024

• Bump mypy from 1.10.0 to 1.10.1

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Commits on Jul 2, 2024

• Merge pull request #114 from sanger/dependabot/pip/more-itertools-10.3.0

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• Bump responses from 0.25.2 to 0.25.3

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• Merge pull request #115 from sanger/dependabot/pip/flake8-7.1.0

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• Merge pull request #116 from sanger/dependabot/pip/responses-0.25.3

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• Bump urllib3 from 2.2.1 to 2.2.2

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• Merge pull request #117 from sanger/dependabot/pip/urllib3-2.2.2

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• Merge pull request #118 from sanger/dependabot/pip/python-snappy-0.7.2

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• Merge pull request #119 from sanger/dependabot/pip/types-requests-2.32.0.20240622

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• Merge pull request #120 from sanger/dependabot/pip/coverage-7.5.4

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• Merge pull request #122 from sanger/dependabot/pip/mypy-1.10.1

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Commits on Jul 4, 2024

• Add processor for CreateAliquot.

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Commits on Jul 6, 2024

• Bump certifi from 2024.6.2 to 2024.7.4

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Commits on Jul 8, 2024

• Merge remote-tracking branch 'origin/95-y24-094-setup-a-connection-between-tol-lab-share-and-multilims-warehouse-rmq' into 96-y24-095-define-a-new-message-processor-in-tol-lab-share-to-consume-volu…

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• chore: Update .gitignore to exclude PyCharm files

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• Merge pull request #123 from sanger/95-y24-094-setup-a-connection-between-tol-lab-share-and-multilims-warehouse-rmq

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• Merge remote-tracking branch 'origin/develop' into 96-y24-095-define-a-new-message-processor-in-tol-lab-share-to-consume-volume-tracking-messages

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• feat: Add new message processor for CreateAliquot in tol-lab-share and connect to the publisher

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Commits on Jul 9, 2024

• Making mypy and the other linters happy

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• Making linter happy

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• Update insertSize schema change

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• feat: Update RabbitMQ server details for warehouse

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• Making the linters happy

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Commits on Jul 10, 2024

• Updating warehouse_publisher.py to publish messages to the warehouse RMQ to persist aliquots

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• Updating warehouse_publisher.py to publish messages to the warehouse RMQ to persist aliquots

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• Rolling back publisher.py changes as a new file has been created for warehouse rmq tests (warehouse_publisher.py)

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• Adding some logging

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• feat: Add TractionToWarehouseMessage to consumed messages

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• feat: Add TractionVolumeTrackingMessage root record

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• Updates to tests

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• Naming conflict fixed

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• fix: Correct type annotation in VALID_TRACTION_TO_WAREHOUSE_MESSAGE

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• Added tests to the message mapper

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• create_aliquot_processor.py implementation for process method

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• Making linters happy

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• Adding tests for the processor

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• feat: Implement valid message processing for TractionToWarehouseMessage

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• test: Add test for processing warehouse message in CreateAliquotProcessor

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Commits on Jul 11, 2024

• feat: Update CreateAliquotProcessor to process valid TractionToWarehouseMessage

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• feat: Add tests for CreateAliquotProcessor to process valid TractionToWarehouseMessage

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• feat: Add error logging when mlwh has errors

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• refactor: Simplify error handling in CreateAliquotProcessor

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• Update routing key in publish function of create_aliquot_message

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• refactor: Remove unused encoder_config_for method in CreateAliquotInWarehouseMessage

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• refactor: Update json method return type annotation to use quotes

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• Started adding demo scripts to test volume tracking work

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• chore: Update RabbitMQ credentials in traction_publisher.py

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• refactor: Refactor how mapping is done

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• refactor: Simplify mapping in TractionToWarehouseMapper

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• [skip ci] refactoring logs

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• Preparations for e2e testing locally

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Commits on Jul 12, 2024

• Bump coverage from 7.5.4 to 7.6.0

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• Bump types-requests from 2.32.0.20240622 to 2.32.0.20240712

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• refactor: Update create_aliquot_message.py to include a to_dict method

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• refactor: Update to_string method in CreateAliquotInWarehouseMessage

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• Documentation improvements

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Commits on Jul 15, 2024

• refactor: Update instantiation method in CreateAliquotProcessor

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• Minor refactorings

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• Some refactoring on root file

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• refactor: Update TractionToWarehouseMapper to TractionCreateAliquotToWarehouseMapper

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• refactor: Update RABBITMQ_ROUTING_KEY_CREATE_ALIQUOT format in __init__.py

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• refactor: Update environment variable name in rabbit.py and create_aliquot_message.py

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• refactor: Update TractionToWarehouseMessage import in __init__.py

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Commits on Jul 17, 2024

• Update SETUP_DOCKER.md

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• Update schemas/create-aliquot-in-mlwh/1-create-aliquot-in-mlwh.avsc

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• Some refactoring on root file

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• Merge remote-tracking branch 'origin/96-y24-095-define-a-new-message-processor-in-tol-lab-share-to-consume-volume-tracking-messages' into 96-y24-095-define-a-new-message-processor-in-tol-lab-share-…

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• Syncing the UAT schema

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Commits on Jul 18, 2024

• Merge pull request #125 from sanger/96-y24-095-define-a-new-message-processor-in-tol-lab-share-to-consume-volume-tracking-messages

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Commits on Jul 22, 2024

• Merge pull request #124 from sanger/dependabot/pip/certifi-2024.7.4

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• Merge pull request #126 from sanger/dependabot/pip/coverage-7.6.0

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• Merge pull request #127 from sanger/dependabot/pip/types-requests-2.32.0.20240712

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Commits on Jul 23, 2024

• Renaming limsUuid to aliquotUuid

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• Updating schema side changes

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• Updating warehouse side changes

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Commits on Jul 24, 2024

• Updating warehouse side changes

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• Updating routing key for warehouse

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• Merge pull request #133 from sanger/fix-schema-keys

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Commits on Jul 29, 2024

• chore: Bump up the release version to 2.1.0

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• chore: Revert release version to 2.0.0

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• chore: Update release version to 2.1.0

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