@platforma-open/milaboratories.sequence-properties.model 1.1.1 → 1.2.0

package/dist/types.d.ts

@@ -1,11 +1,16 @@
 import { PlDataTableStateV2, PlRef } from "@platforma-sdk/model";
+import { GraphMakerState } from "@milaboratories/graph-maker";
 
 //#region src/types.d.ts
-type BlockData = {
+type BlockDataV1 = {
   inputAnchor?: PlRef;
   tableState: PlDataTableStateV2;
   defaultBlockLabel?: string;
 };
+type BlockData = BlockDataV1 & {
+  graphStateScatter: GraphMakerState;
+  graphStateHistogram: GraphMakerState;
+};
 type BlockArgs = {
   inputAnchor: PlRef;
 };

package/dist/types.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"types.d.ts","names":[],"sources":["../src/types.ts"],"mappings":";;;KAEY,SAAA;EACV,WAAA,GAAc,KAAA;EACd,UAAA,EAAY,kBAAA;EAIZ,iBAAA;AAAA;AAAA,KAGU,SAAA;EACV,WAAA,EAAa,KAAA;AAAA;AAAA,KAGH,YAAA;AAAA,KAMA,gBAAA;AAAA,KAEA,YAAA;EACV,IAAA,GAAO,YAAA;EACP,QAAA,GAAW,gBAAA;EACX,YAAA;EACA,QAAA;AAAA"}
+{"version":3,"file":"types.d.ts","names":[],"sources":["../src/types.ts"],"mappings":";;;;KAKY,WAAA;EACV,WAAA,GAAc,KAAA;EACd,UAAA,EAAY,kBAAA;EAIZ,iBAAA;AAAA;AAAA,KAGU,SAAA,GAAY,WAAA;EACtB,iBAAA,EAAmB,eAAA;EACnB,mBAAA,EAAqB,eAAA;AAAA;AAAA,KAGX,SAAA;EACV,WAAA,EAAa,KAAA;AAAA;AAAA,KAGH,YAAA;AAAA,KAMA,gBAAA;AAAA,KAEA,YAAA;EACV,IAAA,GAAO,YAAA;EACP,QAAA,GAAW,gBAAA;EACX,YAAA;EACA,QAAA;AAAA"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@platforma-open/milaboratories.sequence-properties.model",
-  "version": "1.1.1",
+  "version": "1.2.0",
   "description": "Block model",
   "type": "module",
   "main": "dist/index.js",
@@ -14,13 +14,14 @@
     "./dist/*": "./dist/*"
   },
   "dependencies": {
+    "@milaboratories/graph-maker": "1.3.3",
     "@milaboratories/helpers": "^1.14.1",
     "@platforma-sdk/model": "1.69.0"
   },
   "devDependencies": {
     "@milaboratories/ts-builder": "1.3.2",
     "@milaboratories/ts-configs": "1.2.3",
-    "@platforma-sdk/block-tools": "2.7.16"
+    "@platforma-sdk/block-tools": "2.7.19"
   },
   "peerDependencies": {
     "@types/node": "*",

package/src/dataModel.ts

@@ -1,6 +1,31 @@
+import type { GraphMakerState } from "@milaboratories/graph-maker";
 import { createPlDataTableStateV2, DataModelBuilder } from "@platforma-sdk/model";
-import type { BlockData } from "./types";
+import type { BlockData, BlockDataV1 } from "./types";
 
-export const blockDataModel = new DataModelBuilder().from<BlockData>("Ver_2026_04_28").init(() => ({
-  tableState: createPlDataTableStateV2(),
-}));
+const DEFAULT_SCATTER_STATE: GraphMakerState = {
+  title: "",
+  template: "dots",
+  currentTab: null,
+};
+
+const DEFAULT_HISTOGRAM_STATE: GraphMakerState = {
+  title: "",
+  template: "bins",
+  currentTab: null,
+  layersSettings: {
+    bins: { fillColor: "#99e099" },
+  },
+};
+
+export const blockDataModel = new DataModelBuilder()
+  .from<BlockDataV1>("Ver_2026_04_28")
+  .migrate<BlockData>("Ver_2026_05_05", (v1) => ({
+    ...v1,
+    graphStateScatter: { ...DEFAULT_SCATTER_STATE },
+    graphStateHistogram: { ...DEFAULT_HISTOGRAM_STATE },
+  }))
+  .init(() => ({
+    tableState: createPlDataTableStateV2(),
+    graphStateScatter: { ...DEFAULT_SCATTER_STATE },
+    graphStateHistogram: { ...DEFAULT_HISTOGRAM_STATE },
+  }));

package/src/index.ts

@@ -1,4 +1,9 @@
-import type { ColumnSource, InferOutputsType } from "@platforma-sdk/model";
+import type {
+  ColumnSource,
+  InferOutputsType,
+  PColumnIdAndSpec,
+  PFrameHandle,
+} from "@platforma-sdk/model";
 import {
   Annotation,
   ArrayColumnProvider,
@@ -55,6 +60,13 @@ export const platforma = BlockModelV3.create(blockDataModel)
     if (ctx.data.inputAnchor === undefined) return undefined;
     const ownCols = ctx.outputs?.resolve("propertiesPf")?.getPColumns();
     if (ownCols === undefined) return undefined;
+    // `coverageTier` is set in workflow/main.tpl.tengo and surfaced via the
+    // `info` JSON resource. Allowed values are defined in types.ts::WorkflowInfo.
+    // Gate on `info` so the table renders consistently with the chosen aa
+    // column rather than briefly without it while `info` is still resolving.
+    const info = ctx.outputs?.resolve("info")?.getDataAsJson<WorkflowInfo>();
+    if (info === undefined) return undefined;
+    const tier = info.coverageTier;
 
     // Build sources explicitly: upstream cols from the result pool minus
     // anything traced back to this block, plus this block's own cols from
@@ -78,12 +90,48 @@ export const platforma = BlockModelV3.create(blockDataModel)
         anchors: { main: ctx.data.inputAnchor },
         selector: { mode: "enrichment" },
       },
-      // UX policy (not in spec): default-show only this block's columns;
-      // demote upstream cols to optional to keep the table uncluttered.
-      // This block's cols fall through unmatched and keep the visibility
-      // stamped at workflow-time (`pl7.app/table/visibility`).
+      // Default-visible: this block's columns + a single source amino-acid
+      // sequence column matching the analysed coverage tier. Reviewer asked
+      // for one sequence next to the properties — full-chain VDJRegion when
+      // available (it contains the CDR3); CDR3 alone when that is all the
+      // input has; peptide for peptide mode. Chain A (heavy / alpha / gamma)
+      // only — chain B stays available via the column picker. Other upstream
+      // cols → optional. This block's cols fall through unmatched and keep
+      // their workflow-time `pl7.app/table/visibility` annotation.
       displayOptions: {
         visibility: [
+          {
+            match: (spec) => {
+              if (spec.domain?.["pl7.app/vdj/scClonotypeChain/index"] === "secondary") {
+                return false;
+              }
+              if (spec.domain?.["pl7.app/alphabet"] !== "aminoacid") return false;
+
+              const isVdj = spec.name === "pl7.app/vdj/sequence";
+              const isUniversal = spec.name === "pl7.app/sequence";
+              if (!isVdj && !isUniversal) return false;
+
+              const feature = isVdj
+                ? spec.domain?.["pl7.app/vdj/feature"]
+                : spec.domain?.["pl7.app/feature"];
+
+              if (tier === "peptide") {
+                return isUniversal && feature === "peptide";
+              }
+
+              const chain = spec.domain?.["pl7.app/vdj/scClonotypeChain"];
+              if (chain !== undefined && chain !== "A") return false;
+
+              if (tier === "full_chain") {
+                return feature === "VDJRegion" || feature === "VDJRegionInFrame";
+              }
+              if (tier === "cdr3_only" || tier === "partial") {
+                return feature === "CDR3";
+              }
+              return false;
+            },
+            visibility: "default",
+          },
           {
             match: (spec) =>
               !spec.annotations?.[Annotation.Trace]?.includes(
@@ -95,9 +143,56 @@ export const platforma = BlockModelV3.create(blockDataModel)
       },
     });
   })
+  .outputWithStatus("propertiesPfHandle", (ctx): PFrameHandle | undefined => {
+    const allPCols = ctx.outputs?.resolve("propertiesPf")?.getPColumns();
+    if (allPCols === undefined) return undefined;
+    // Drop the AA fraction column from the pframe entirely. Two-axis
+    // (variantKey × aminoAcid), at 50k peptides ~1M cells — enough to trip
+    // graph-maker's cell-count guard on its own. The picker already excludes
+    // it via `isNumericScalar` (axesSpec.length === 1), so the data was
+    // pure overhead.
+    const pCols = allPCols.filter((c) => c.spec.name !== "pl7.app/aaFraction");
+    // Use `ctx.createPFrame` instead of `createPFrameForGraphs`. The latter
+    // walks the result pool and pulls in this block's `exports.properties`
+    // — a `trace.inject`-stamped re-emission of every column already in
+    // `propertiesPf`, published for Lead Selection — so axis dropdowns
+    // show e.g. "Net Charge (pH7) / IG" twice. Same workaround chosen by
+    // cdr3-spectratype, batch-correction, cell-type-annotation, and
+    // dimensionality-reduction.
+    //
+    // Pull single-axis metadata anchored to the input dataset's two axes
+    // (idx 0 = sample, idx 1 = entity key) so sample groups / patient IDs /
+    // peptide abundance and similar cols remain available for grouping and
+    // filtering. Drop self-trace to keep our own exports out.
+    const inputAnchor = ctx.data.inputAnchor;
+    const upstreamMeta =
+      inputAnchor !== undefined
+        ? (
+            ctx.resultPool.getAnchoredPColumns({ main: inputAnchor }, [
+              { axes: [{ anchor: "main", idx: 0 }] },
+              { axes: [{ anchor: "main", idx: 1 }] },
+            ]) ?? []
+          ).filter(
+            (c) =>
+              !c.spec.annotations?.[Annotation.Trace]?.includes(
+                "milaboratories.sequence-properties",
+              ),
+          )
+        : [];
+    return ctx.createPFrame([...pCols, ...upstreamMeta]);
+  })
+  .output("propertiesPfCols", (ctx): PColumnIdAndSpec[] | undefined => {
+    const pCols = ctx.outputs?.resolve("propertiesPf")?.getPColumns();
+    if (pCols === undefined) return undefined;
+    return pCols.map((c) => ({ columnId: c.id, spec: c.spec }) satisfies PColumnIdAndSpec);
+  })
   .title(() => "Sequence Properties")
   .subtitle((ctx) => ctx.data.defaultBlockLabel ?? "")
-  .sections(() => [{ type: "link" as const, href: "/" as const, label: "Main" }])
+  .sections(() => [
+    { type: "link" as const, href: "/" as const, label: "Main" },
+    { type: "link" as const, href: "/scatter" as const, label: "Scatterplot" },
+    { type: "link" as const, href: "/histogram" as const, label: "Histogram" },
+  ])
   .done();
 
 export type BlockOutputs = InferOutputsType<typeof platforma>;

package/src/types.ts

@@ -1,6 +1,9 @@
+import type { GraphMakerState } from "@milaboratories/graph-maker";
 import type { PlDataTableStateV2, PlRef } from "@platforma-sdk/model";
 
-export type BlockData = {
+// Pre-Visualizations shape. Retained as the v1 type so the data-model
+// migration chain stays well-typed.
+export type BlockDataV1 = {
   inputAnchor?: PlRef;
   tableState: PlDataTableStateV2;
   // UI-only state. Tracks the selected input dataset's label so the block
@@ -9,6 +12,11 @@ export type BlockData = {
   defaultBlockLabel?: string;
 };
 
+export type BlockData = BlockDataV1 & {
+  graphStateScatter: GraphMakerState;
+  graphStateHistogram: GraphMakerState;
+};
+
 export type BlockArgs = {
   inputAnchor: PlRef;
 };