feat: create paired-end workflow configuration step (#456) #497
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Pull Request Overview
This pull request introduces new user interface components for sequencing data selection, updates to the GTF step UI, and removes unused constants and imports. Key changes include the addition of the AccessionSelector and CollectionSelector components, enhancements to the GTFStep component (including an "Edit" button and updated typography), and support for a new SANGER_READ_RUN parameter.
Reviewed Changes
Copilot reviewed 62 out of 62 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| collectionSummary.tsx | Added a summary display for selected collections. |
| collectionSummary.styles.ts | Styled the summary paper and toolbar. |
| CollectionSelector/* | New dialog component for selecting sequencing runs. |
| UseTable/* | Hook for table configuration with new column definitions and accessor. |
| accessionSelector.tsx | New dialog component for filtering accessions with validation. |
| gtfStep.tsx | Updated GTFStep UI with revised callbacks and typography. |
| workflow.tsx | Adjusted workflow invocation with an explicit null for read runs. |
| README.md | Updated documentation to include the new SANGER_READ_RUN parameter. |
| onClick={onLaunch} | ||
| {...BUTTON_PROPS.PRIMARY_CONTAINED} | ||
| disabled={!value} | ||
| onClick={() => onStep()} |
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The onStep callback is used inconsistently: the 'Edit' button calls onStep with an index parameter while the 'Continue' button calls it without any arguments. This design may cause ambiguity for API consumers; consider defining separate callbacks (e.g., onEdit and onContinue) or using a consistent argument pattern.
| onClick={() => onStep()} | |
| onClick={() => onContinue()} |
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Closes #456.
This pull request introduces several updates and new features to the workflow configuration components, with a focus on enhancing user interfaces, adding support for new data types, and cleaning up unused code. The most significant changes include the addition of new dialog components for sequencing data selection, updates to the GTF step UI, and removal of unused constants and imports.
Enhancements to Sequencing Data Selection:
AccessionSelectorcomponent for selecting initial filtering options, including styled dialogs and form elements. ([[1]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-3826bd95e8b41bb348e73dfc5bbccea2858bda6555488379d5f9e3213bf580ebR1-R95),[[2]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-ed1df3928fd7b8051fa92eb44ef4adac9bc3c37245e59f853346b840648e895bR1-R10))CollectionSelectorcomponent with a table-based UI for selecting sequencing runs, including row selection and configuration logic. ([[1]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-3fe256b5e4682121975f73775458460923748c411b81fce960467a89742f78e4R1-R59),[[2]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-44a244e42a8831969c5e282196a35f1ac4b116d0a503c396753819db0cdc1e58R1-R31),[[3]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-729768a95b7f11be9d2ba63fb45e9dcf0e3e9d8569f35ccbfd76c03f37aa4a85R1-R24),[[4]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-744d4de7582f51fe941a4ebc734adf027cd889525d88b0a5ba04d7a460d4a383R1-R6),[[5]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-963b15643594690e86c2611f0c5aec47db7dcaf1964495ff7866b97fd45c5914R1-R12),[[6]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-7f515d7f76324364209c2a13ed18fb8aff983cbd7d2718eb8ab491e8296bc0c0R1-R6))Updates to GTF Step UI:
GTFStepcomponent to include an "Edit" button for completed steps and improved optional labels with dynamic content. ([app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/GTFStep/gtfStep.tsxL64-R82](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-ab497e102ce360031472573dbede5dd2457ecd5791cb002c52f8bf19d3a3ceaaL64-R82))GTFStepto directly reference typography variants instead of constants for better maintainability. ([app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/GTFStep/gtfStep.tsxL90-R111](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-ab497e102ce360031472573dbede5dd2457ecd5791cb002c52f8bf19d3a3ceaaL90-R111))Support for New Data Types:
SANGER_READ_RUNvariable for reference genome configurations. ([[1]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-b335630551682c19a781afebcf4d07bf978fb1f8ac04c6bf87428ed5106870f5L72-R88),[[2]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-e0b75ab8221e59e4a0d12e481c77dbab95b3376876f175cff03fd64ece76a56cR61))Code Cleanup and Refactoring:
TYPOGRAPHY_PROPSandBUTTON_PROPS, from several files to streamline the codebase. ([[1]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-5e0c534a0601fe9a6202e0699ed357706c860a650163c1d1d8dcec3897135f0eL1-L7),[[2]](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-ab497e102ce360031472573dbede5dd2457ecd5791cb002c52f8bf19d3a3ceaaL14-R25))GTFStepcomponent by removing unused props likelaunchStatusand replacing them with more relevant ones. ([app/components/Entity/components/ConfigureWorkflowInputs/components/Main/components/Stepper/components/Step/GTFStep/gtfStep.tsxL34-R36](https://github.com/galaxyproject/brc-analytics/pull/497/files#diff-ab497e102ce360031472573dbede5dd2457ecd5791cb002c52f8bf19d3a3ceaaL34-R36))These updates collectively improve the user experience for configuring workflows, enhance maintainability, and expand functionality to support new use cases.