[WIP] feat: group file with same name and add new popover functionality

[diegomayorga-dept]

Title*

Group paired-read FASTQ files into one sample card/row in Data Collections

Type of Change*

• New feature
• Bug fix
• Documentation update
• Refactoring
• Hotfix
• Security patch
• UI/UX improvement

Description

In the Data Collections explorer, every S3 object rendered as its own card / table row. Multi-lane paired-read samples therefore showed up as 2–8 separate "samples" — e.g. WI-Jan-2024-S005_L001_R1, _L001_R2, _L002_R1, _L002_R2 appeared as four cards instead of one. This obscured the sample-level view lab users care about.

This PR collapses all files that share a sample base name into one display unit per sample:

• New utility getSampleGroupId() (packages/front-end/src/app/utils/data-collections-to-sample-sheet.ts) extracts a sample id from <sample>(_L<digits>)?_R[12](_<set>)?.f(ast)?q[.gz], collapsing all lanes of a sample. It reuses the existing getFileNameWithoutExt and is case-insensitive. Non-paired files (.txt, .fasta, index reads _I1/_I2, etc.) return null and stay as solo cards.
• Explorer (packages/front-end/src/app/components/EGDataCollectionsExplorer.vue): introduces an internal DisplayGroup type and buildDisplayGroups(); each batch section now carries groups. Cards and table rows iterate groups. Grouping is scoped per S3 folder so identically-named samples in different folders don't merge.
  • Card label = sample id; meta shows N files for groups (file size unchanged for solos).
  • Selection, drag-and-drop, and lasso operate atomically on all keys in a group; checkbox is tri-state (all / partial / none).
  • Tags shown are the union across the group; status counts, "X samples" header, and "Select all (N)" count groups; expiry is the soonest across the group; the permanent lock shows for any-permanent with "Some files…" tooltip text when partial.
• Analysis history popover (packages/front-end/src/app/components/EGFileAnalysisHistoryTooltip.vue): additive groupFiles prop renders a new "Files (N)" section between the header and Analysis History, listing each file's type pill (FASTQ/FASTA/Other) + filename + size. Run usages are deduped by RunId across the group. Single-file callers are unchanged.
• Removed the now-dead toggleKey emit and its parent handler in EGDataCollectionsPage.vue, since card/row clicks now toggle whole groups via update:selectedKeys.

Testing*

• Unit tests — new packages/front-end/test/app/utils/data-collections-sample-grouping.test.ts with 9 cases for getSampleGroupId: multi-lane, single-lane, no trailing set number, .fq/.fq.gz extensions, case-insensitive _r1_, non-paired files (null), index reads _I1/_I2 (null), lane-without-direction (null), and lane-in-sample-name preservation. All 4 utils suites pass (35 tests).
• Type check — production source (.ts/.vue) emits no new TypeScript errors. Lint clean on the touched .ts files.
• Manual E2E — seed a lab with a 4-file multi-lane sample (S005), a 2-file single-lane pair (S006), and a non-paired file (notes.txt); confirm 3 cards ("4 files", "2 files", file size), group select/lasso/drag-tag operate on all keys, popover "Files (N)" section renders, partial-permanent lock + tooltip, and the table view mirrors card behavior.

Impact

• UI-only change to the Data Collections explorer and its analysis popover; no API, schema, or backend changes.
• Parent (EGDataCollectionsPage) data shape (visibleFiles and the per-key maps) is unchanged; only the internal rendering and the now-removed toggleKey event differ.
• No new dependencies.

Additional Information

• Grouping rule confirmed with design: all lanes of a sample collapse into one card; card meta shows just N files (no date — "Jan-2024" in the mockup was part of the test filename).
• Edge-case decisions: tags = union (not intersection); batch = primary key's batch with first-non-null fallback (no "mixed" marker in v1); permanent = lock shown if any file in the group is permanent.

Checklist*

• No new errors or warnings have been introduced.
• All tests pass successfully and new tests added as necessary.
• Documentation has been updated accordingly.
• Code adheres to the coding and style guidelines of the project.
• Code has been commented in particularly hard-to-understand areas.

[Kevin Loftus (kevin-loftus-dept)]

Everything looks great except for some odd changes in the laboratory-service.ts log calls.

[Kevin Loftus (kevin-loftus-dept)]

I think these 11234 and 123 changes in this file may have been left in by mistake, can you remove them?