MILAB-6463: select graph PFrame columns via the discover engine#1708
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🦋 Changeset detectedLatest commit: 22830cc The changes in this PR will be included in the next version bump. This PR includes changesets to release 15 packages
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This pull request refactors the compatible column discovery logic in getRelatedColumns to utilize the spec-driver discover engine (ColumnCollectionBuilder) instead of the previous heuristic-based approach. Feedback suggests explicitly adding rootColumns as a source to the ColumnCollectionBuilder to prevent potential errors and silent fallbacks to conservative mode when those columns are not yet registered in the context sources.
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Codecov Report❌ Patch coverage is
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## main #1708 +/- ##
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Coverage 55.28% 55.28%
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Files 312 313 +1
Lines 17508 17575 +67
Branches 3819 3835 +16
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- Misses 6595 6622 +27
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getRelatedColumns gates its partial-axis-match candidates through the spec-driver discover engine, dropping result-pool columns that share only a low-cardinality context axis (e.g. pl7.app/sampleId) with the block but cannot actually join it — the cause of "axes sets are disjoint" errors. Block columns and linkers are always kept; an unavailable verdict keeps the column.
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Problem
getRelatedColumns(used bycreatePFrameForGraphs, which builds the PFrame behind every block's graphs) selected related result-pool columns with a partial-axis-match heuristic. A column that shared a single low-cardinality context axis with the block (e.g.pl7.app/sampleId) was admitted, and its other, foreign axis was then seeded into the candidate set — dragging in an entire disconnected column universe. The resulting PFrame fails on join withSpecError … some of axes sets are disjoint.Concretely, in
clonotype-spacean IG-anchored graph PFrame pulled in a redefined-clonotype universe (a sibling block's columns sharing onlysampleId), and the multi-sequence-alignment join crashed.Fix
Decide column membership with the spec-driver discover engine (
ColumnCollectionBuilder,enrichmentmode) instead of the JS heuristic:enrichmentmode rejects a hit that would introduce a floating/disconnected axis.Column assembly (
enrichCompatible) is unchanged; only the selection step changed.Behavior verified (clonotype-space, all input anchors)
SpecError).Known deviations from the previous heuristic (documented inline, for follow-up)
These are inherent to selecting via discover while still assembling with
enrichCompatible, and are noted as code comments ingetRelatedColumns:enrichCompatible'sblockAxesheuristic, so a hit needing a non-trivial qualification to integrate may not be qualified.allAxes"hanging" set) are not rediscovered — discovery anchors onrootColumnsonly.rootColumnspec; very large block column sets may stress the spec-driver (QuickJS) deadline.Scope / testing note
createPFrameForGraphsruns for every block's graphs. This was verified end-to-end onclonotype-spaceacross all three anchors; it should go through the monorepo test suite before merge given the broad reach.Greptile Summary
This PR fixes a disjoint-axis
SpecErrorincreatePFrameForGraphsby replacing a loose JS heuristic ingetRelatedColumnswith the spec-driver discover engine (enrichmentmode). The old heuristic admitted result-pool columns that shared any single axis with the block, which could drag in entire disconnected universes; the new path only accepts columns that the discover engine can integrate without leaving a floating axis.candidatesnow contains all predicate-matching result-pool columns, and membership is decided byAnchoredColumnCollection.findColumns({ mode: "enrichment" }); root columns (anchors) and linkers that share an axis with the block are unconditionally kept.integrableIdsis leftundefinedand only block columns + directly-connected linkers are returned — rather than re-admitting the full candidate set.Confidence Score: 3/5
The core fix is sound and verified end-to-end on clonotype-space, but the outer catch silently suppresses all discover-engine errors — including the QuickJS deadline explicitly called out as a risk for large column sets — which could produce unexpectedly empty graphs in production with no diagnostic trail.
The silent catch on a code path with a known stress trigger (large block column sets hitting QuickJS deadline) is the main concern: the graph silently loses enrichment columns and nothing surfaces to the operator. Combined with the potential ID-namespace mismatch and the still-heuristic linker path, the change needs the logging gap addressed and a broader test run before it can be considered fully safe.
sdk/model/src/pframe_utils/columns.ts — specifically the bare catch block around the discover-engine call and the linker-connectivity check.
Important Files Changed
getRelatedColumnswith the spec-driver discover engine (enrichment mode) for candidate filtering; linkers still use a JS heuristic; silent catch on discover failure has no logging; potential PObjectId namespace mismatch between integrableIds and candidates.Flowchart
%%{init: {'theme': 'neutral'}}%% flowchart TD A[getRelatedColumns called rootColumns + predicate] --> B[Build blockAxes from rootColumns axes] B --> C[Collect linkerColumns matching predicate] C --> D[getAvailableWithLinkersAxes expand blockAxes with connected linker axes] D --> E[Fetch candidates columns.getColumns predicate] E --> F{anchorSpecs non-empty?} F -- No --> G[integrableIds = undefined] F -- Yes --> H[ColumnCollectionBuilder .addSources ctx .build with anchors] H -- throws --> G H -- ok --> I[collection.findColumns mode: enrichment] I -- throws --> G I -- ok --> J[integrableIds = Set of discovered IDs collection.dispose] G --> K[Filter candidates] J --> K K --> L{rootIds.has c.id?} L -- Yes --> M[include] L -- No --> N{isLinkerColumn?} N -- Yes --> O{linkerConnectsToBlock? JS heuristic on blockAxes} O -- Yes --> M O -- No --> P[exclude] N -- No --> Q{integrableIds?.has c.id} Q -- true --> M Q -- false/undefined --> P M --> R[enrichCompatible assemble final PFrameDef]%%{init: {'theme': 'base', 'themeVariables': {"darkMode": true, "background": "#0d1117", "primaryColor": "#21262d", "primaryTextColor": "#e6edf3", "primaryBorderColor": "#8b949e", "lineColor": "#8b949e", "textColor": "#e6edf3", "edgeLabelBackground": "#161b22", "actorBkg": "#21262d", "actorBorder": "#8b949e", "actorTextColor": "#e6edf3", "actorLineColor": "#8b949e", "signalColor": "#8b949e", "signalTextColor": "#e6edf3", "noteBkgColor": "#373320", "noteBorderColor": "#d4a72c", "noteTextColor": "#f0e6c0", "labelBoxBkgColor": "#21262d", "labelBoxBorderColor": "#8b949e", "labelTextColor": "#e6edf3", "loopTextColor": "#e6edf3", "activationBkgColor": "#30363d", "activationBorderColor": "#8b949e"}}}%% flowchart TD A[getRelatedColumns called rootColumns + predicate] --> B[Build blockAxes from rootColumns axes] B --> C[Collect linkerColumns matching predicate] C --> D[getAvailableWithLinkersAxes expand blockAxes with connected linker axes] D --> E[Fetch candidates columns.getColumns predicate] E --> F{anchorSpecs non-empty?} F -- No --> G[integrableIds = undefined] F -- Yes --> H[ColumnCollectionBuilder .addSources ctx .build with anchors] H -- throws --> G H -- ok --> I[collection.findColumns mode: enrichment] I -- throws --> G I -- ok --> J[integrableIds = Set of discovered IDs collection.dispose] G --> K[Filter candidates] J --> K K --> L{rootIds.has c.id?} L -- Yes --> M[include] L -- No --> N{isLinkerColumn?} N -- Yes --> O{linkerConnectsToBlock? JS heuristic on blockAxes} O -- Yes --> M O -- No --> P[exclude] N -- No --> Q{integrableIds?.has c.id} Q -- true --> M Q -- false/undefined --> P M --> R[enrichCompatible assemble final PFrameDef]Prompt To Fix All With AI
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