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Change Log for LangQC Project

The format is based on Keep a Changelog and this project adheres to Semantic Versioning.

[Unreleased]

Added

  • Added .github/dependabot.yml file to auto-update GitHub actions
  • Clickable icon next to run names to change to the view of all wells in that run

[2.3.0] - 2024-07-30

Added

  • New endpoint for fetching statistics about a library pool
  • Pool composition table added to the QC View for any well. Folded away by default
  • Barcode names from MLWH are now available to front and back end code

Fixed

  • Well detail fetching errors now produce a visible warning that was previously lost

[2.2.0] - 2024-06-11

Added

  • New endpoint added to support potential email notifications when QC states are finalised. /products/qc?weeks={n}&seq_level={bool}&final={bool}. It returns recent QC events

Fixed

  • Warehouse schema updated to match breaking change in pac_bio_product_metrics table

[2.1.0] - 2024-04-15

Changed

  • To simplify object instantiation and fields' assignment for some of the response models, converted PacBioWell and PacBioWellFull models to pydantic dataclasses.
  • Changed the response model for filtered by either QC status or run wells from PacBioWell to PacBioWellSummary, the latter initially being identical the former. In order to propagate information about a study to the tabbed well summary view, added a new field, study_names, to the PacBioWellSummary model.
  • Added a new event to the tabbed well summary view, to the button with the well name. Mouse hover over this button displays study names associated with the well.
  • Changed the colour scheme of the above mentioned button from grey to orange if one of the studies associated with the well is the BIOSCAN study, which the QC team needs to deal with slightly differently.
  • Added a new QC state 'On hold external'. Semantically the new state is similar to the existing 'On hold' state. The intended purpose of the new QC state - to highlight the wells, which are waiting for a completion of some off-site process (example - deplexing at http://mbrave.net/).

Added

  • A new response model PacBioWellSummary, which replaces PacBioWell in the latest's capacity of the response model for a PacBio well summary.
  • A new field, study_names, a potentially empty sorted array of unique study names, is added to the response model for a PacBio well summary.

[2.0.0] - 2024-02-20

Changed

  • The correctness of data in the 'properties' column of the LangQC 'sub_product' database table is no longer guaranteed because of the changes introduced in v. 5.0.0 of https://github.com/wtsi-npg/npg_id_generation The column is made nullable and then dropped. The ORM for the LangQC database is updated accordingly.

  • The production code no longer depends on the npg_id_generation package, therefore this dependency was moved to the dev section of pyproject.toml. The package is still used by tests and test fixtures.

  • Upgraded some of dev dependencies: npg_id_generation to 5.0.1, alembic to 1.13.0 or later.

  • Regenerated poetry.lock file.

[1.5.1] - 2024-01-25

Changed

  • The 'Unknown' UI tab no longer displays the wells that have any sequencing QC state associated with it. This feature was requested by the users.

  • To increase code readability, renamed qc_state_for_product_exists method in lang_qc::db::helper::qc to product_has_qc_state.

  • Added method products_have_qc_state to lang_qc::db::helper::qc, used it to optimise (reduce the number of database queries) some of the existing back-end code.

Fixed

  • The client side JavaScript dependency, element-plus, is pinned to version 2.4.4. In mid-January 2024 this was the highest version that worked with our code. The version expression we had "^2.3.7" allowed for fetching the latest available version of this library.

[1.5.0]

Added

  • Back-end code for the 'Upcoming' tab. The 'Upcoming' tab is automatically appended to the collection of the UI tabs for filtering wells.

Changed

  • Increased the look-back period for the inbox query from 4 weeks to 12 weeks. Introduced a preliminary filtering by the QC state, which is now available in ml warehouse. Since the ml warehouse QC state might not be up-to-date, a final check against the LangQC database is retained.
  • Major upgrade of FastAPI, Pydantic and related dependencies.

[1.4.1] - 2023-08-23

Added

  • Display of the release version in UI.
  • A constraint for Claimed QC state, made it applicable for sequencing QC type only.

Changed

  • Split the code for creating and updating QC sates into PacBio-specific and sequencing platform independent. Converted all methods to self- contained functions, discontinued use of classes where no object state has to be maintained.

Fixed

  • UI - ensured uniqueness of the row key for the well table.
  • A bug in creating a new product record in the LangQC database. The bug affected records with undefined value of the plate number, which was pushed to the database as a 'None' string instead of NULL.

[1.4.0] - 2023-08-16

Added

  • Tests for bulk retrieval of QC states
  • Third dimension for describing wells added to QC Schema to support multi-plate runs

Changed

  • Browser URLs now use id_product to identify items to show in the QC Viewer instead of the combination of run, label (and plate number)
  • More strict validation of checksums (id_product) when sent to backend API

Fixed

  • A bug that disregarded the value of the sequencing_outcomes_only argument in what is now the get_qc_states_by_id_product_list function

[1.3.0] - 2023-08-02

Added

  • Instrument name and type and plate number concatenated with the well label is added to QC View and table of wells
  • Loading concentration is added to the QC View

Changed

  • plate_number and id_product is added to API JSON feeds for well data

[1.2.0] - 2023-07-12

Added

  • Display the library_tube_barcode / Pool name in the QC View
  • Calculate and display deplexing percentages when appropriate

Changed

  • Modified the search-by-run interface to allow multiple runs to be shown at once

[1.1.0] - 2023-05-30

Added

  • Bookmarkable URLs
  • Support for back/forward browser buttons
  • Dedicated per-run view via /ui/run/$RUN_NAME
  • Search box to jump to the per-run view (exact match only)
  • QC View well now links to SMRTLink to help users find demux data more easily

Changed

  • ORM for ML warehouse selectively cloned into this repo to remove dependency on unsupported code
  • Warehouse mapping updated to include additional PacBio-related columns

Fixed

Run table was rendering the same data for all tabs. Now it only renders once for the selected tab

[1.0.1] - 2022-03-14

Changed

UI colour scheme and layout, the former to make it more coherent, the latter to reduce unused white space on the top of the page.

[1.0.0] - 2022-03-06

First production release.