Milab 6738 vdj import chain match

[mchernys]

• 093dfc2 chain matching fix
• eac8d71 pure pnpm run upgrade-sdk output, no hand-written changes
• 7430875 fixes the upgrade forced (3 small ones)
• f8dba62 changeset for the upgrade
• b6a6ed5 empty-import warning + stats table fix

Greptile Summary

This PR upgrades the Platforma SDK and block structure, broadens V(D)J chain matching, and adds user-facing detection of samples left without clonotypes.

• Makes Custom and ImmunoSeq locus matching case- and position-insensitive and makes QIAseq chain matching case-insensitive.
• Adds an emptyChainSamples model output and warning banner for samples whose summed clonotype count is zero.
• Allows the statistics table to render ready columns without waiting for missing column data.
• Refreshes the package facade, build variants, CI configuration, and SDK dependencies.

Important touched terms

• Receptor chain: A biological immunoglobulin or T-cell receptor chain such as IGHeavy, IGLight, TCRAlpha, or TCRBeta. Matching now normalizes case across the changed importers.
• Locus: The chain-identifying token in a gene call, such as IGH, IGK, TRA, or TRB. Custom and ImmunoSeq now search for this token anywhere in the uppercased gene value.
• Clonotype: A distinct immune-receptor sequence represented in imported data. The model now totals clonotype counts across imported chains to identify empty samples.
• P-column: Platforma's typed column representation for result data. Statistics columns are now requested with dontWaitAllData, and only ready columns are passed to the table.
• Block facade: The published TypeScript/JavaScript entry point exposing the block contract, data types, model, and pack pointer. It is regenerated under structure version 2.
• Block pointer: Metadata locating the packaged block assets. The new facade exposes BlockPointer and ImportVdjBlockPointer using URLs derived from import.meta.url.
• Build variant: A combination of channel, software selection, and artifact location used by the refreshed build system. Root scripts now provide development and release variants through PL_BUILD_* variables.

Confidence Score: 5/5

The PR appears safe to merge, with no concrete blocking or independently actionable non-blocking defects established in the changed code.

The chain normalization follows the documented cross-format behavior, the warning and table changes are coherently connected to statistics outputs, and no accepted failures remain.

Important Files Changed

Filename	Overview
workflow/src/import-custom.tpl.tengo	Makes Custom locus matching case- and position-insensitive while retaining separate IGK/IGL handling.
workflow/src/import-immunoSeq.tpl.tengo	Replaces anchored, case-sensitive V-gene matching with normalized locus substring matching.
workflow/src/import-qiagen.tpl.tengo	Uppercases the normalized QIAseq chain column before exact locus comparisons.
model/src/index.ts	Adds partial-column table handling and computes zero-clonotype sample warnings from statistics p-columns.
ui/src/pages/MainPage.vue	Displays a capped warning listing samples with no imported clonotypes.
block/src/index.ts	Introduces the structure-v2 ESM facade, inferred block contract types, and URL-based block-pack pointer.
.github/workflows/build.yaml	Moves CI to the refreshed runner and development/release build-script matrix.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart LR
  A[Imported VDJ rows] --> B[Normalize chain-defining value]
  B --> C[Filter rows by requested receptor chain]
  C --> D[Generate per-chain clonotypes and statistics]
  D --> E[Expose statistics as p-columns]
  E --> F[Sum clonotype counts per sample]
  F --> G{Total is zero?}
  G -- Yes --> H[Show empty-sample warning]
  G -- No --> I[Render statistics table]

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