feat: pre filter read run popup depending on the workflow type (#706)

[frano-m]

Closes #706.

This pull request introduces several enhancements and refactors to the ENA Sequencing Data selection workflow, focusing on improving user experience when filtering and selecting sequencing runs. The main changes include support for pre-selecting column filters based on query method and sequencing data type, improved button rendering logic, and better state management for filters. Additionally, a new column is added to the sequencing runs table.

Improvements to filtering and table state management:

• Added logic to pre-select column filters in the sequencing runs table when browsing by taxonomy ID, based on the sequencing data type (single or paired). This ensures users see relevant data immediately when browsing all sequences. [1] [2] [3]
• Refactored table state to maintain separate column filter states for different ENA query methods (by accession or by taxonomy ID), preventing filter leakage between modes. [1] [2] [3]

User interface enhancements:

• Improved button text rendering in both the collection and data selectors, making button labels clearer and context-aware based on the number of selected rows or available sequences. [1] [2]
• Added a loading indicator to the data selector for better feedback during data fetches.

Table and data model updates:

• Introduced a new column, First Public, to the sequencing runs table for additional metadata visibility. [1] [2] [3]
• Updated types and props to use consistent enums and improved typings for sequencing data types and query methods. [1] [2] [3] [4]

Miscellaneous:

• Minor refactorings and cleanup, such as removing unused imports and improving code comments for maintainability.

These changes collectively make the workflow for selecting ENA sequencing data more intuitive, maintainable, and responsive to user actions.

[Copilot]

Pull Request Overview

This pull request enhances the ENA Sequencing Data selection workflow by introducing pre-filtering capabilities and improving user experience. The main changes include support for dual query methods (by accession or taxonomy ID), automatic pre-selection of column filters based on sequencing data type, and improved state management to prevent filter leakage between different query modes.

• Refactored the ENA data fetching logic into two separate hooks for querying by accession and taxonomy ID
• Added automatic pre-filtering of sequencing runs table based on sequencing data type when browsing by taxonomy ID
• Improved button text rendering and added loading indicators for better user feedback

Reviewed Changes

Copilot reviewed 27 out of 31 changed files in this pull request and generated 1 comment.

Show a summary per file

File	Description
types.ts	Defines new enums for ENA query methods and sequencing data types
sequencingStep.tsx	Refactors to use separate hooks for different ENA query methods and manages query method state
enaSequencingData.tsx	Updates props interface and component to work with separated ENA hooks
useENADataByTaxonomyId/	New hook and utilities for fetching ENA data by taxonomy ID with pre-fetch logic
useENADataByAccession/	Refactored existing hook to focus only on accession-based queries
dataSelector.tsx	Enhanced with loading indicators and improved button text rendering
collectionSelector.tsx	Added pre-selection logic for column filters and improved button text
useTable/hook.ts	Enhanced to maintain separate column filter states for different query methods
Column definitions	Added new "First Public" column to the sequencing runs table

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