Fix CIDConflict

[mzueva]

Greptile Summary

This PR fixes unstable Content IDs (CIDs) caused by non-deterministic Tengo map iteration in the import workflow templates, and migrates model/ and ui/ from the legacy vite + vue-tsc build pipeline to @milaboratories/ts-builder.

• CID fix: All import templates replace the unordered for key, file in map / for key, value in map idiom with for key in maps.getKeys(map) to guarantee sorted, deterministic iteration — affecting input-file frame registration and column-rename expression ordering. import-immunoSeq.tpl.tengo is partially fixed (column mapping only); the input-file loop still uses maps.forEach, which may reproduce the instability for that format.
• Build migration: model/ and ui/ adopt ts-builder scripts (build, watch, type-check), standardised tsconfig inheritance via @milaboratories/ts-configs, and an explicit exports field in model/package.json; dependency versions across the whole workspace are bumped to the latest SDK releases.

Confidence Score: 3/5

The build migration and most workflow fixes are clean, but import-immunoSeq.tpl.tengo input-file iteration was not migrated to the sorted pattern, leaving immunoSeq imports potentially still vulnerable to the CID instability this PR targets.

The maps.forEach left in import-immunoSeq.tpl.tengo for input-file ordering means the stated goal of the PR is only partially achieved for that format — users who re-import immunoSeq data could still see CID conflicts. The self-alias guard omission in import-custom.tpl.tengo is a narrower risk but could produce a runtime error if a user creates a passthrough mapping.

workflow/src/import-immunoSeq.tpl.tengo (input-file loop not migrated to sorted iteration), workflow/src/import-custom.tpl.tengo (missing self-alias guard)

Important Files Changed

Filename	Overview
workflow/src/import-common.tpl.tengo	Both input-file and column-mapping loops switched to maps.getKeys sorted iteration; self-alias guard added to renameExpressions. Core fix is correct and complete.
workflow/src/import-immunoSeq.tpl.tengo	Column-mapping loop fixed to use maps.getKeys, but input-file iteration still uses maps.forEach — diverges from the sorted-iteration pattern applied everywhere else and may still produce unstable CIDs for immunoSeq imports.
workflow/src/import-qiagen.tpl.tengo	Both input-file and column-mapping loops migrated to sorted maps.getKeys iteration. Change is consistent with the fix pattern.
workflow/src/import-custom.tpl.tengo	Both loops converted to maps.getKeys; maps import added. Missing the self-alias guard that import-common received, which could fail if a user maps a column to its own name.
workflow/src/infer-columns-custom.lib.tengo	Two map-iteration loops (customMapping and columnMapping) migrated to maps.getKeys for deterministic ordering; minor comment/whitespace cleanup.
model/package.json	Build pipeline migrated from vite + vite-plugin-dts to @milaboratories/ts-builder; exports field added; dependencies updated to match newer SDK versions.
ui/package.json	Build pipeline migrated to ts-builder; vue-tsc, vite, @vitejs/plugin-vue removed; @milaboratories/helpers and ts-configs added.

Flowchart

%%{init: {'theme': 'neutral'}}%%
flowchart TD
    A["inputFiles.inputs()"] --> B{Template}
    B -->|"import-common / import-qiagen / import-custom"| C["maps.getKeys sorted iteration ✅"]
    B -->|"import-immunoSeq"| D["maps.forEach non-deterministic ⚠️"]
    C --> E["Frame IDs stable"]
    D --> F["Frame IDs potentially unstable"]
    E --> G["maps.getKeys on columnMapping ✅"]
    F --> G
    G --> H["withColumns / filter / aggregate"]
    H --> I["save chain.tsv"]
    E --> J["Stable CID ✅"]
    F -.-> K["CID conflict risk ⚠️"]

Loading

Comments Outside Diff (1)

1. workflow/src/import-immunoSeq.tpl.tengo, line 27-34 (link)

   Input file iteration not migrated to sorted maps.getKeys

   Every other import template in this PR (import-common, import-qiagen, import-custom) switched from for key, file in inputFiles.inputs() to for key in maps.getKeys(inputMap) to guarantee deterministic ordering. import-immunoSeq.tpl.tengo still uses maps.forEach, which iterates in hash/insertion order and produces non-deterministic frame IDs, leaving immunoSeq imports exposed to the same unstable-CID problem this PR sets out to fix.

   Prompt To Fix With AI

   This is a comment left during a code review.
   Path: workflow/src/import-immunoSeq.tpl.tengo
   Line: 27-34
   
   Comment:
   **Input file iteration not migrated to sorted `maps.getKeys`**
   
   Every other import template in this PR (`import-common`, `import-qiagen`, `import-custom`) switched from `for key, file in inputFiles.inputs()` to `for key in maps.getKeys(inputMap)` to guarantee deterministic ordering. `import-immunoSeq.tpl.tengo` still uses `maps.forEach`, which iterates in hash/insertion order and produces non-deterministic frame IDs, leaving immunoSeq imports exposed to the same unstable-CID problem this PR sets out to fix.
   
   How can I resolve this? If you propose a fix, please make it concise.

Prompt To Fix All With AI

Fix the following 2 code review issues. Work through them one at a time, proposing concise fixes.

---

### Issue 1 of 2
workflow/src/import-immunoSeq.tpl.tengo:27-34
**Input file iteration not migrated to sorted `maps.getKeys`**

Every other import template in this PR (`import-common`, `import-qiagen`, `import-custom`) switched from `for key, file in inputFiles.inputs()` to `for key in maps.getKeys(inputMap)` to guarantee deterministic ordering. `import-immunoSeq.tpl.tengo` still uses `maps.forEach`, which iterates in hash/insertion order and produces non-deterministic frame IDs, leaving immunoSeq imports exposed to the same unstable-CID problem this PR sets out to fix.

### Issue 2 of 2
workflow/src/import-custom.tpl.tengo:38-44
**Missing self-alias guard on column rename**

`import-common.tpl.tengo` received an explicit check (`if canonical != original`) to skip self-aliasing, because passing `col("x").alias("x")` to `withColumns` creates a duplicate column and causes a runtime error. `import-custom.tpl.tengo` uses the same loop pattern but lacks the guard. If a user's custom mapping maps a canonical name to the same source column, the workflow will fail.

```suggestion
    // Rename original columns to canonical IDs
    renameExpressions := []
    for canonical in maps.getKeys(columnsInfo.columnMapping) {
        original := columnsInfo.columnMapping[canonical]
        if original != undefined && canonical != original {
            renameExpressions = append(renameExpressions, pt.col(original).alias(canonical))
        }
    }
    if len(renameExpressions) > 0 {
        df = df.withColumns(renameExpressions...)
    }
```

_{Reviews (1): Last reviewed commit: "Fix CIDConflict" | Re-trigger Greptile}

Greptile also left 1 inline comment on this PR.

[gemini-code-assist]

Code Review

This pull request addresses unstable CIDs by implementing sorted map iteration across several Tengo templates to ensure deterministic output. Additionally, it migrates the model and ui packages from a legacy Vite/vue-tsc build pipeline to @milaboratories/ts-builder and updates various SDK dependencies. Feedback suggests adding explanatory comments to the new iteration logic in import-custom.tpl.tengo and import-qiagen.tpl.tengo to maintain consistency with documentation provided in other workflow files.