Offline-review findings: table sorting, settings, labels, histogram titles (#8)

* Rename Integrity risk column to Structural liabilities

Aligns the structural-integrity column with the Antibody Sequence Liabilities block: same None/Present semantics, now styled and ranked as a score. The PColumn spec name is unchanged so downstream Lead Selection joins keep resolving it.

* Fix results-table sorting and simplify block settings

Sorting now works: the results-table state is persisted in BlockData and passed to createPlDataTableV3, so AG-Grid sorts re-derive rows server-side instead of leaving placeholder cells. A v1 to v2 data migration seeds the new tableState and drops the now-removed manual heavy/light chain inputs, which are auto-detected from the structure. Also rewrites the advanced confidence-threshold tooltips to lead with what changing them does.

* Render the histogram chart title via graph-maker

Histogram pages stay in a PlBlockPage with no-body-gutters and no page heading; the page label is carried by graph-maker's own chart title, which is part of its v-model state. inheritAttrs is disabled so the config title spread onto the component cannot also render as a PlBlockPage heading.

* Add changeset for the offline-review fixes

Bumps the block so the corrected long description republishes: the central registry currently serves a stale generic description because the last docs edit shipped without a version bump.

Author: xnacly

.changeset/implement-offline-review-findings.md

@@ -0,0 +1,8 @@
+---
+"@platforma-open/milaboratories.3d-structure-based-liabilities": patch
+"@platforma-open/milaboratories.3d-structure-based-liabilities.model": patch
+"@platforma-open/milaboratories.3d-structure-based-liabilities.ui": patch
+"@platforma-open/milaboratories.3d-structure-based-liabilities.workflow": patch
+---
+
+Fix results-table sorting, remove the manual heavy/light chain inputs (now auto-detected), clarify the advanced threshold tooltips, rename the "Integrity risk" column to "Structural liabilities", and restore the histogram page titles.

model/src/index.ts

@@ -14,24 +14,35 @@ import {
   ArrayColumnProvider,
   BlockModelV3,
   buildDatasetOptions,
+  createPlDataTableStateV2,
   createPlDataTableV3,
   DataModelBuilder,
   getAxisId,
   isPColumnSpec,
   parseResourceMap,
 } from "@platforma-sdk/model";
-import type { BlockArgs, BlockData, DetectedMode } from "./types";
+import type { BlockArgs, BlockData, BlockDataV1, DetectedMode } from "./types";
 
 export type { NumberingScheme, DetectedMode, BlockData, BlockArgs } from "./types";
 
-const dataModel = new DataModelBuilder().from<BlockData>("v1").init(() => ({
-  dataset: undefined,
-  heavyChainId: "",
-  lightChainId: "",
-  frConfThresh: 4.0,
-  cdrConfThresh: 6.0,
-  customBlockLabel: "",
-}));
+const dataModel = new DataModelBuilder()
+  .from<BlockDataV1>("v1")
+  // v1 -> v2: drop the removed manual chain fields and seed the persisted
+  // results-table state so existing block instances gain sortable tables.
+  .migrate<BlockData>("v2", (v1) => ({
+    dataset: v1.dataset,
+    frConfThresh: v1.frConfThresh,
+    cdrConfThresh: v1.cdrConfThresh,
+    customBlockLabel: v1.customBlockLabel,
+    tableState: createPlDataTableStateV2(),
+  }))
+  .init(() => ({
+    dataset: undefined,
+    frConfThresh: 4.0,
+    cdrConfThresh: 6.0,
+    customBlockLabel: "",
+    tableState: createPlDataTableStateV2(),
+  }));
 
 type ScoresCtx = BlockRenderCtx<unknown, unknown>;
 type ScoresPColumn = PColumn<PColumnDataUniversal | undefined>;
@@ -105,8 +116,6 @@ export const platforma = BlockModelV3.create(dataModel)
     }
     return {
       primaryRef: data.dataset.primary,
-      heavyChainId: data.heavyChainId,
-      lightChainId: data.lightChainId,
       frConfThresh: data.frConfThresh,
       cdrConfThresh: data.cdrConfThresh,
     };
@@ -158,6 +167,7 @@ export const platforma = BlockModelV3.create(dataModel)
     const mode = resolveMode(ctx);
     return createPlDataTableV3(ctx, {
       columns: variants,
+      tableState: ctx.data.tableState,
       displayOptions: mode
         ? {
             visibility: [

model/src/types.ts

@@ -1,4 +1,4 @@
-import type { DatasetSelection } from "@platforma-sdk/model";
+import type { DatasetSelection, PlDataTableStateV2 } from "@platforma-sdk/model";
 
 /** Numbering schemes the runtime can interpret. The block is now hardcoded
  *  to IMGT at the workflow layer because every supported upstream emits
@@ -13,22 +13,32 @@ export type DetectedMode = "TAP" | "TNP";
 export type BlockData = {
   /** Predicted-structures dataset picked via `PlDatasetSelector`. */
   dataset?: DatasetSelection;
-  /** Manual heavy/light chain mapping, used only when a PDB carries no
-   *  REMARK 99 PLATFORMA CDR records to auto-detect them. */
-  heavyChainId: string;
-  lightChainId: string;
   /** Confidence-gating thresholds (Å) for framework and CDR regions. */
   frConfThresh: number;
   cdrConfThresh: number;
   /** User-set block label; empty falls back to the derived default. */
   customBlockLabel: string;
+  /** Results-table sort / filter / column state. Persisted in the model and
+   *  fed into `createPlDataTableV3` so sorting re-derives rows server-side
+   *  instead of leaving AG-Grid with unsortable placeholder cells. */
+  tableState: PlDataTableStateV2;
+};
+
+/** Pre-v2 shape: carried manual `heavyChainId`/`lightChainId` (now
+ *  auto-detected, removed) and no persisted `tableState`. Kept so the v1 -> v2
+ *  migration can map existing block instances onto the current shape. */
+export type BlockDataV1 = {
+  dataset?: DatasetSelection;
+  heavyChainId: string;
+  lightChainId: string;
+  frConfThresh: number;
+  cdrConfThresh: number;
+  customBlockLabel: string;
 };
 
 /** Projection consumed by the workflow. */
 export type BlockArgs = {
   primaryRef: NonNullable<DatasetSelection["primary"]>;
-  heavyChainId: string;
-  lightChainId: string;
   frConfThresh: number;
   cdrConfThresh: number;
 };

ui/src/components/HistogramPage.vue

@@ -6,10 +6,18 @@ import { PlBlockPage } from "@platforma-sdk/ui-vue";
 import { computed } from "vue";
 import type { ThresholdBands } from "../pages/histogramConfigs";
 
+// The page wrappers spread the whole config; keys that aren't declared props
+// (title / columnName / fillColor) feed makeGraphState, not this component.
+// Drop them rather than let `title` fall through to PlBlockPage as a second
+// page heading: graph-maker's own title (from its v-model state) is the only
+// title we want.
+defineOptions({ inheritAttrs: false });
+
 const props = defineProps<{
-  // No page heading rendered. The section nav already labels the page;
-  // the threshold legend lives inside graph-maker's titleLineSlot so it
-  // sits next to the chart title bar instead of pushing the chart down.
+  // No PlBlockPage title: the chart's own title (graph-maker v-model state)
+  // carries the page label. Threshold lines are drawn by graph-maker from the
+  // value column's `pl7.app/graph/thresholds` annotation; the legend below
+  // maps the bands those lines delimit.
   notReadyTitle?: string;
   thresholds?: ThresholdBands;
   pFrame: OutputWithStatus<PFrameHandle>;
@@ -36,7 +44,7 @@ const hasLegend = computed(() => {
 </script>
 
 <template>
-  <PlBlockPage>
+  <PlBlockPage no-body-gutters>
     <GraphMaker
       v-model="graphStateModel"
       chart-type="histogram"

ui/src/pages/MainPage.vue

@@ -2,7 +2,6 @@
 import type { PlStructureViewerProps } from "@milaboratories/structure-viewer";
 import { PlStructureViewer } from "@milaboratories/structure-viewer";
 import type { PFrameHandle, PTableKey } from "@platforma-sdk/model";
-import { createPlDataTableStateV2 } from "@platforma-sdk/model";
 import { defaultBlockLabelFor } from "@platforma-open/milaboratories.3d-structure-based-liabilities.model";
 import {
   PlAccordionSection,
@@ -14,7 +13,6 @@ import {
   PlMaskIcon24,
   PlNumberField,
   PlSlideModal,
-  PlTextField,
   usePlDataTableSettingsV2,
 } from "@platforma-sdk/ui-vue";
 import { computed, ref } from "vue";
@@ -33,9 +31,6 @@ const scoresTableSettings = usePlDataTableSettingsV2({
   model: () => app.model.outputs.scoresTable,
   sourceId: () => "scores-v2",
 });
-// v-model writes stay UI-local so AG-Grid state events don't re-fire the
-// model output handler.
-const scoresLocalState = ref(createPlDataTableStateV2());
 
 const pdbsMap = computed(() => app.model.outputs.clonotypePdbsMap);
 const clonotypeAxisId = computed(() => app.model.outputs.clonotypeAxisId);
@@ -111,30 +106,6 @@ const modalTitle = computed(() => {
         clearable
       />
 
-      <div class="field-grid field-grid--settings">
-        <PlTextField
-          v-model="app.model.data.heavyChainId"
-          label="Heavy chain"
-          placeholder="auto-detect"
-        >
-          <template #tooltip>
-            Which chain in the structure is the heavy chain. Leave empty to detect it automatically;
-            set a single chain letter (e.g. A) only if a structure has no chain annotation and
-            detection fails.
-          </template>
-        </PlTextField>
-        <PlTextField
-          v-model="app.model.data.lightChainId"
-          label="Light chain"
-          placeholder="auto-detect"
-        >
-          <template #tooltip>
-            Which chain in the structure is the light chain. Leave empty to detect it automatically;
-            set a single chain letter only if detection fails.
-          </template>
-        </PlTextField>
-      </div>
-
       <PlAccordionSection label="Advanced thresholds">
         <div class="field-grid">
           <PlNumberField
@@ -145,9 +116,11 @@ const modalTitle = computed(() => {
             :step="0.5"
           >
             <template #tooltip>
-              Predicted-error cutoff above which framework-region motifs are treated as too
-              uncertain to flag. Raise it for experimental crystal structures whose B-factors are
-              temperature factors rather than predicted error.
+              Framework-region residues whose predicted error exceeds this cutoff (Å) are dropped
+              before scoring, so their motifs are not flagged. Higher keeps and flags more residues,
+              including uncertain ones; lower trusts only high-confidence framework. Default 4 Å.
+              Raise it for experimental crystal structures, whose B-factors are temperature factors
+              rather than predicted error.
             </template>
           </PlNumberField>
           <PlNumberField
@@ -158,8 +131,10 @@ const modalTitle = computed(() => {
             :step="0.5"
           >
             <template #tooltip>
-              Same as the framework threshold, applied to the more flexible CDR loops, where
-              predicted structures are typically less certain.
+              Same gating as the framework threshold, applied to the CDR loops. CDRs are more
+              flexible and usually predicted with lower confidence, so this cutoff is looser by
+              default (6 Å). Higher flags motifs in more CDR residues; lower keeps only
+              high-confidence CDR positions.
             </template>
           </PlNumberField>
         </div>
@@ -184,7 +159,7 @@ const modalTitle = computed(() => {
     <!-- One row per clonotype. The open button on the clonotype-key cell pops
          the structure-viewer modal for that row. -->
     <PlAgDataTableV2
-      v-model="scoresLocalState"
+      v-model="app.model.data.tableState"
       :settings="scoresTableSettings"
       :show-cell-button-for-axis-id="clonotypeAxisId"
       :cell-button-invoke-rows-on-double-click="true"
@@ -230,10 +205,6 @@ const modalTitle = computed(() => {
   gap: 12px;
   margin-bottom: 8px;
 }
-.field-grid--settings {
-  margin-top: 12px;
-}
-
 .run-alert {
   margin-top: 12px;
 }

ui/src/pages/histogramConfigs.ts

@@ -94,13 +94,13 @@ export const histogramConfigs = {
 
 /** Seed a graph-maker `bins` template from a histogram config. The `bins`
  * layer needs an explicit fillColor; the template's default ('white') is
- * invisible against the chart background. The chart title is left blank
- * because the section nav already labels the page; rendering `cfg.title`
- * here too duplicates it inside the chart frame. */
+ * invisible against the chart background. `title` is graph-maker's own chart
+ * title (part of its v-model state, editable in the chart), which carries the
+ * page label since the page renders no PlBlockPage heading of its own. */
 export function makeGraphState(cfg: HistogramConfig): GraphMakerState {
   return {
     template: "bins",
-    title: "",
+    title: cfg.title,
     currentTab: null,
     layersSettings: { bins: { fillColor: cfg.fillColor } },
   };

workflow/src/main.tpl.tengo

@@ -116,20 +116,12 @@ wf.body(func(args) {
 			arg("--clonotype-filter").arg("clonotype_filter.tsv")
 	}
 
-	// Empty strings fall through to the Python defaults.
-	withOptArg := func(c, flag, value) {
-		if is_undefined(value) || value == "" {
-			return c
-		}
-		return c.arg(flag).arg(value)
-	}
 	// Numbering scheme is hardcoded to IMGT: every supported upstream
 	// (3D Structure Prediction block, ImmuneBuilder predictions) emits
 	// IMGT-numbered structures, and our compactness anchors + canonical
-	// disulfide positions assume IMGT.
+	// disulfide positions assume IMGT. Heavy/light chains are auto-detected
+	// from the structure's REMARK records, so no chain flags are passed.
 	cmd = cmd.arg("--numbering-scheme").arg("imgt")
-	cmd = withOptArg(cmd, "--chain-h", args.heavyChainId)
-	cmd = withOptArg(cmd, "--chain-l", args.lightChainId)
 
 	result := cmd.
 		saveFile("per_clonotype.tsv").

workflow/src/specs.lib.tengo

@@ -211,14 +211,20 @@ scoresColumnSpecs := {
 			"pl7.app/table/orderPriority": "1050"
 		}
 	},
+	// Renamed from "Integrity risk" to match the "Structural liabilities"
+	// column in the Antibody Sequence Liabilities block: same None/Present
+	// semantics, styled and ranked as a score. The spec `name` is unchanged
+	// so downstream joins (Lead Selection) keep resolving it.
 	structuralIntegrityRisk: {
 		valueType: "String",
 		name: "pl7.app/liabilities/structuralIntegrityRisk",
 		annotations: {
-			"pl7.app/label": "Integrity risk",
-			"pl7.app/description": "Binary flag (None/Present) for hard-to-fix structural issues: broken/missing disulfides, exposed extra Cys, structural motifs.",
+			"pl7.app/label": "Structural liabilities",
+			"pl7.app/description": "Binary flag (None/Present) for hard-to-fix structural issues: broken/missing disulfides, exposed extra Cys, structural motifs. These require scaffold redesign rather than point substitutions.",
+			"pl7.app/isScore": "true",
 			"pl7.app/isDiscreteFilter": "true",
 			"pl7.app/discreteValues": INTEGRITY_DISCRETE_VALUES,
+			"pl7.app/score/rankingOrder": "decreasing",
 			"pl7.app/table/visibility": "default",
 			"pl7.app/table/orderPriority": "1040"
 		}