@inflexa-ai/harness 0.45.1 → 0.46.0

package/dist/report-render/figures/forest.js

@@ -80,7 +80,7 @@ function deriveForest(block, rows, context) {
     if (read.isErr())
         return err(read.error);
     const order = channelOrder(block.encoding?.y ?? columns.value.term);
-    const ordered = orderCategories(context.blockId, read.value.length, (index) => read.value[index].term, read.value.map((entry) => entry.term), order, (index) => (order === undefined ? undefined : read.value[index].row[order.by]));
+    const ordered = orderCategories(context.blockId, read.value.length, (index) => read.value[index]?.term, read.value.map((entry) => entry.term), order, (index) => (order === undefined ? undefined : read.value[index]?.row[order.by]));
     if (ordered.isErr())
         return err(ordered.error);
     const byTerm = new Map(read.value.map((entry) => [String(entry.term), entry]));
@@ -154,10 +154,10 @@ function forestColumns(block, rows, context) {
     return ok({
         term: channelColumn(term),
         estimate: estimate.value,
-        ...(optional.low !== undefined ? { low: optional.low } : {}),
-        ...(optional.high !== undefined ? { high: optional.high } : {}),
-        ...(optional.p !== undefined ? { p: optional.p } : {}),
-        ...(optional.size !== undefined ? { size: optional.size } : {}),
+        low: optional.low,
+        high: optional.high,
+        p: optional.p,
+        size: optional.size,
     });
 }
 /**
@@ -313,8 +313,10 @@ export function termLines(term) {
     if (lines.length <= TERM_LINES)
         return lines.join("\n");
     const kept = lines.slice(0, TERM_LINES);
-    const last = kept[TERM_LINES - 1];
-    kept[TERM_LINES - 1] = `${last.length < TERM_LINE_CHARACTERS ? last : last.slice(0, TERM_LINE_CHARACTERS - 1)}…`;
+    const last = kept[kept.length - 1];
+    if (last === undefined)
+        return lines.join("\n");
+    kept[kept.length - 1] = `${last.length < TERM_LINE_CHARACTERS ? last : last.slice(0, TERM_LINE_CHARACTERS - 1)}…`;
     return kept.join("\n");
 }
 /** The estimated width in pixels of the widest text of one column at the page text size. */

package/dist/report-render/figures/gsea.js

@@ -17,10 +17,11 @@
  * (`drawnVertices`). The thinning keeps each vertex where the shape of a curve changes, thus the drawn line
  * follows the table.
  */
+import { textOf } from "../../lib/unknown-text.js";
 import { err, ok } from "neverthrow";
 import { channelColumn, channelOrder, channelTransform } from "../../contracts/report-blocks.js";
 import { TOOLBOX_BAND_PX } from "../chart-toolbox.js";
-import { CHART_BODY_PX, GUIDE_LINE_WIDTH_PX, MUTED_CHART_COLOR } from "../design.js";
+import { CHART_BODY_PX, CHART_INK, GUIDE_LINE_WIDTH_PX, MUTED_CHART_COLOR } from "../design.js";
 import { categoricalPalette, categoryName, chartProblem, columnPresent, firstAppearance, guideLine, guideMarkLine, statisticsGraphic, toNumber, valueAxis, valueAxisTitle, } from "./common.js";
 /**
  * The count of vertices that the thinning aims at for one curve, before it adds the vertices of shape.
@@ -83,9 +84,10 @@ function deriveGsea(block, rows, context) {
         return err(table.error);
     const { sets, metric } = table.value;
     const palette = categoricalPalette(sets.length);
-    const colorOf = (index) => palette[index % palette.length];
+    const colorOf = (index) => palette[index % palette.length] ?? CHART_INK;
     const legendLines = sets.length > 1 ? sets.length : 0;
     const grids = panelGrids(legendLines);
+    const topPanel = grids[0];
     const range = rankRange(sets, metric);
     const metricTitle = valueAxisTitle(context.labels, columns.value.metric, METRIC_TITLE);
     const deviations = sets.map((set) => maximumDeviation(set.score));
@@ -117,7 +119,7 @@ function deriveGsea(block, rows, context) {
             { ...valueAxis("y", metricTitle), gridIndex: 2, splitNumber: 3 },
         ],
         series: [...top, ...middle, bottom],
-        graphic: statisticsText(context, grids[0], corner),
+        graphic: topPanel === undefined ? [] : statisticsText(context, topPanel, corner),
         legend: legendLines > 0
             ? { data: sets.map((set) => set.name), orient: "vertical", left: percent(GRID_LEFT), bottom: 0, itemGap: LEGEND_GAP_PX }
             : { show: false },
@@ -154,7 +156,7 @@ function gseaColumns(encoding, rows, context) {
         score: column("y"),
         hit: column("hit"),
         metric: column("metric"),
-        ...(encoding.group !== undefined ? { set: channelColumn(encoding.group) } : {}),
+        set: encoding.group === undefined ? undefined : channelColumn(encoding.group),
     });
 }
 /**
@@ -276,14 +278,22 @@ function drawnVertices(curve, kept) {
 }
 /** True when the curve turns at one inner vertex. */
 function turns(curve, index) {
-    const before = curve[index].value - curve[index - 1].value;
-    const after = curve[index + 1].value - curve[index].value;
-    return before * after < 0;
+    const at = curve[index];
+    const before = curve[index - 1];
+    const after = curve[index + 1];
+    if (at === undefined || before === undefined || after === undefined)
+        return false;
+    return (at.value - before.value) * (after.value - at.value) < 0;
 }
 /** True when the sign of the curve changes between one inner vertex and a neighbor. */
 function crossesZero(curve, index) {
-    const sign = Math.sign(curve[index].value);
-    return sign !== Math.sign(curve[index - 1].value) || sign !== Math.sign(curve[index + 1].value);
+    const at = curve[index];
+    if (at === undefined)
+        return false;
+    const sign = Math.sign(at.value);
+    const before = curve[index - 1];
+    const after = curve[index + 1];
+    return before === undefined || sign !== Math.sign(before.value) || after === undefined || sign !== Math.sign(after.value);
 }
 /**
  * The running score of one set in the top panel, with its dashed mark from zero to its maximum deviation. The
@@ -379,8 +389,8 @@ function panelGrids(legendLines) {
  * empty, and a set that dips under zero leaves the bottom left empty.
  */
 function statisticsText(context, panel, corner) {
-    const top = Number.parseFloat(String(panel.top));
-    const height = Number.parseFloat(String(panel.height));
+    const top = Number.parseFloat(textOf(panel.top));
+    const height = Number.parseFloat(textOf(panel.height));
     return statisticsGraphic(context.statistics, corner).map((element) => corner === "top-right"
         ? { ...element, right: percent(GRID_RIGHT + STATISTICS_INSET), top: percent(top + STATISTICS_INSET) }
         : { ...element, left: percent(GRID_LEFT + STATISTICS_INSET), bottom: percent(100 - top - height + STATISTICS_INSET) });

package/dist/report-render/figures/heatmap.js

@@ -103,14 +103,18 @@ function cellKey(cell) {
 }
 function deriveHeatmap(block, rows, context) {
     const encoding = block.encoding ?? {};
-    for (const member of ["x", "y", "value"]) {
-        if (encoding[member] === undefined) {
-            return err(chartProblem(block.id, `The heatmap chart needs a column for the "${member}" channel.`));
-        }
-    }
     const xChannel = encoding.x;
     const yChannel = encoding.y;
     const valueChannel = encoding.value;
+    if (xChannel === undefined) {
+        return err(chartProblem(block.id, 'The heatmap chart needs a column for the "x" channel.'));
+    }
+    if (yChannel === undefined) {
+        return err(chartProblem(block.id, 'The heatmap chart needs a column for the "y" channel.'));
+    }
+    if (valueChannel === undefined) {
+        return err(chartProblem(block.id, 'The heatmap chart needs a column for the "value" channel.'));
+    }
     if (channelOrder(valueChannel) !== undefined) {
         return err(chartProblem(block.id, 'The "value" channel draws no category axis, thus it takes no "orderBy".'));
     }
@@ -146,7 +150,7 @@ function deriveHeatmap(block, rows, context) {
         if (cells.has(key)) {
             return err(chartProblem(block.id, `The heatmap holds the pair (${String(row[x.value])}, ${String(row[y.value])}) more than one time.`));
         }
-        cells.set(key, values[index]);
+        cells.set(key, values[index] ?? null);
     }
     const data = [];
     const finite = [];
@@ -167,7 +171,7 @@ function deriveHeatmap(block, rows, context) {
         data: xCategories.map(String),
         ...axisNameFields("x", xTitle),
         ...LINELESS_AXIS,
-        ...(hidden ? { axisLabel: { show: false } } : {}),
+        axisLabel: hidden ? { show: false } : undefined,
     };
     const yAxis = {
         type: "category",
@@ -310,11 +314,11 @@ function axisOrder(block, rows, context, axis, column, channel) {
  * beside its row. The tree of y reads down, as the matrix reads down.
  */
 function leafAxis(gridIndex, count, inverse) {
-    return { type: "value", gridIndex, min: -0.5, max: count - 0.5, ...(inverse ? { inverse: true } : {}), show: false };
+    return { type: "value", gridIndex, min: -0.5, max: count - 0.5, inverse: inverse ? true : undefined, show: false };
 }
 /** The hidden value axis of the heights of a dendrogram. The tree of y turns it, thus the root sits at the left and the leaves face the row names. */
 function heightAxis(gridIndex, height, inverse) {
-    return { type: "value", gridIndex, min: 0, max: height > 0 ? height : 1, ...(inverse ? { inverse: true } : {}), show: false };
+    return { type: "value", gridIndex, min: 0, max: height > 0 ? height : 1, inverse: inverse ? true : undefined, show: false };
 }
 /** The branches of one dendrogram: one elbow of lines for each edge, in the order of the tree table. */
 function dendrogramSeries(gridIndex, tree, axis) {

package/dist/report-render/figures/index.d.ts

@@ -47,7 +47,7 @@ export type FigureMember = keyof ChartEncoding | "statistics" | "track" | "trees
  * The resolved track of a figure: the rows of the second table, its declared column order, and the columns
  * that the block names in it. The labels and the meanings are the declarations of the track binding.
  */
-export interface FigureTrack {
+export type FigureTrack = {
     readonly rows: readonly ChartRow[];
     readonly columns?: readonly string[];
     readonly start: string;
@@ -56,13 +56,13 @@ export interface FigureTrack {
     readonly length?: string;
     readonly labels: ColumnLabels;
     readonly meanings: ColumnMeanings;
-}
+};
 /**
  * The resolved tree of one category axis: the edge rows of the tree table, its declared column order, and the
  * three columns that the block names in it. The labels and the meanings are the declarations of the tree
  * binding.
  */
-export interface FigureTree {
+export type FigureTree = {
     readonly rows: readonly ChartRow[];
     readonly columns?: readonly string[];
     readonly parent: string;
@@ -70,7 +70,7 @@ export interface FigureTree {
     readonly height: string;
     readonly labels: ColumnLabels;
     readonly meanings: ColumnMeanings;
-}
+};
 /**
  * The parts of a preset that a figure hands to the composition machinery: the semantic axis titles, and the
  * per-row classification where the figure splits the rows itself. `colorOnTop` draws the points of a
@@ -81,12 +81,12 @@ export interface FigureTree {
  * items of the composition output states it, because the page builds each item from the cells and never
  * from the rewrite.
  */
-export interface FigureComposeExtras {
+export type FigureComposeExtras = {
     readonly preset?: PresetAxisTitles;
     readonly classification?: PresetClassification;
     readonly colorOnTop?: boolean;
     readonly keepsRowsInline?: boolean;
-}
+};
 /**
  * What one figure reads beside its block and its rows.
  *
@@ -103,7 +103,7 @@ export interface FigureComposeExtras {
  *   figure that puts a series before the result keeps the whole chart inline, because the page fills the
  *   leading series from the descriptors of the composition.
  */
-export interface FigureContext {
+export type FigureContext = {
     readonly blockId: string;
     readonly labels: ColumnLabels;
     readonly meanings: ColumnMeanings;
@@ -116,14 +116,14 @@ export interface FigureContext {
     };
     readonly textPx: number;
     readonly compose: (composition: ChartComposition, extras?: FigureComposeExtras) => Result<EchartOption, RenderProblem>;
-}
+};
 /** The derivation of one figure: the raw option, before the layout discipline and the figure rules. */
 export type FigureDerivation = (block: ChartBlock, rows: readonly ChartRow[], context: FigureContext) => Result<EchartOption, RenderProblem>;
 /** One figure module: the members of the block that it reads, and its derivation. */
-export interface FigureModule {
+export type FigureModule = {
     readonly reads: ReadonlySet<FigureMember>;
     readonly derive: FigureDerivation;
-}
+};
 /** The figure module of each chart type that has one. */
 export type FigureRegistry = Readonly<Partial<Record<ChartType, FigureModule>>>;
 /** The registered figure modules. A module joins by one entry here, keyed by its chart type. */

package/dist/report-render/figures/index.js

@@ -49,7 +49,7 @@ export const FIGURE_PRESET_TYPES = [
 ];
 /** True when the chart type exists as a figure module alone. */
 export function isFigurePresetType(chartType) {
-    return FIGURE_PRESET_TYPES.includes(chartType);
+    return FIGURE_PRESET_TYPES_SET.has(chartType);
 }
 /**
  * The chart types that draw through a figure module alone: each figure preset, the heatmap, and the four
@@ -58,9 +58,11 @@ export function isFigurePresetType(chartType) {
  * each draw elements that no composition holds, thus none of them keeps an expansion beside its module.
  */
 export const MODULE_ONLY_TYPES = [...FIGURE_PRESET_TYPES, "heatmap", "volcano", "ma", "manhattan", "km"];
+const MODULE_ONLY_TYPES_SET = new Set(MODULE_ONLY_TYPES);
+const FIGURE_PRESET_TYPES_SET = new Set(FIGURE_PRESET_TYPES);
 /** True when the chart type draws through a figure module alone. */
 export function isModuleOnlyType(chartType) {
-    return MODULE_ONLY_TYPES.includes(chartType);
+    return MODULE_ONLY_TYPES_SET.has(chartType);
 }
 /** The registered figure modules. A module joins by one entry here, keyed by its chart type. */
 export const FIGURE_MODULES = {

package/dist/report-render/figures/km.js

@@ -85,7 +85,7 @@ function deriveKm(block, rows, context) {
     if (curves.isErr())
         return err(curves.error);
     const palette = categoricalPalette(curves.value.length);
-    const colorOf = (index) => palette[index % palette.length];
+    const colorOf = (index) => palette[index % palette.length] ?? CHART_INK;
     const end = timeEnd(curves.value);
     const step = timeStep(end);
     const ticks = timeTicks(end, step);
@@ -108,7 +108,7 @@ function deriveKm(block, rows, context) {
     const timeAxis = {
         ...valueAxis("x", valueAxisTitle(context.labels, columns.value.time), { min: 0, max: end }),
         interval: step,
-        ...(onTick(end, step) ? {} : { axisLabel: { showMaxLabel: false } }),
+        axisLabel: onTick(end, step) ? undefined : { showMaxLabel: false },
     };
     const survivalAxis = valueAxis("y", valueAxisTitle(context.labels, columns.value.survival), { min: 0, max: 1 });
     const plotGrid = { top: pct(layout.top), bottom: pct(layout.plotBottom), left: pct(left), right: pct(GRID_RIGHT) };
@@ -121,7 +121,7 @@ function deriveKm(block, rows, context) {
         xAxis: table ? [timeAxis, tableTimeAxis(end, step)] : timeAxis,
         yAxis: table ? [survivalAxis, tableGroupAxis(curves.value, colorOf)] : survivalAxis,
         series,
-        ...(graphic.length > 0 ? { graphic } : {}),
+        graphic,
     };
     return ok(layout.bodyPx > CHART_BODY_PX ? withFigureBody(option, layout.bodyPx) : option);
 }
@@ -175,11 +175,11 @@ function kmColumns(block, rows, context) {
     return ok({
         time: time.value,
         survival: survival.value,
-        ...(optional.group !== undefined ? { group: optional.group } : {}),
-        ...(optional.low !== undefined ? { low: optional.low } : {}),
-        ...(optional.high !== undefined ? { high: optional.high } : {}),
-        ...(optional.censor !== undefined ? { censor: optional.censor } : {}),
-        ...(optional.risk !== undefined ? { risk: optional.risk } : {}),
+        group: optional.group,
+        low: optional.low,
+        high: optional.high,
+        censor: optional.censor,
+        risk: optional.risk,
     });
 }
 /**
@@ -268,7 +268,8 @@ function curveSeries(curve, index, color, columns) {
     const name = categoryName(curve.name);
     const points = curve.points;
     const line = points.map((point) => [point.time, point.survival]);
-    if (points.length === 0 || points[0].time > 0)
+    const first = points[0];
+    if (first === undefined || first.time > 0)
         line.unshift([0, 1]);
     const series = [
         {

package/dist/report-render/figures/label-room.d.ts

@@ -15,16 +15,16 @@ import { CHART_EXPORT_SIZES } from "../design.js";
 /** The gap between a point and its name, in pixels. */
 export declare const NAME_GAP_PX = 4;
 /** One box in data units, or in pixels. */
-export interface Box {
+export type Box = {
     readonly left: number;
     readonly right: number;
     readonly bottom: number;
     readonly top: number;
-}
+};
 /** True when two boxes share an area. */
 export declare function overlaps(a: Box, b: Box): boolean;
 /** The range of the two axes of a plot, in data units. */
-export interface PlotRange {
+export type PlotRange = {
     readonly x: {
         readonly min: number;
         readonly max: number;
@@ -33,13 +33,13 @@ export interface PlotRange {
         readonly min: number;
         readonly max: number;
     };
-}
+};
 /** One named point: its place in data units and its name. */
-export interface NamedPoint {
+export type NamedPoint = {
     readonly x: number;
     readonly y: number;
     readonly text: string;
-}
+};
 /** The four sides of a point where its name can sit, in the order that the figure tries them. */
 export declare const NAME_SIDES: readonly ["right", "left", "top", "bottom"];
 /** One side of a point. */
@@ -74,11 +74,11 @@ export declare function nameAnchors(names: readonly NamedPoint[], weights: reado
  * size. A smaller frame puts the names nearer to each other than the drawn plot does, thus a name that clears
  * its neighbors in the frame clears them in the drawn plot.
  */
-export interface NameFrame {
+export type NameFrame = {
     readonly widthPx: number;
     readonly heightPx: number;
     readonly textPx: number;
-}
+};
 /** The width of one text in pixels at one text size: the estimate of each figure that places its own text. */
 export declare function textWidthPx(text: string, textPx: number): number;
 /** The frame of the page: the plot inside the 900 by 400 pixel chart body of a window 1280 pixels wide. */
@@ -97,17 +97,17 @@ export declare const EXPORT_PLOT_FRAMES: Readonly<Record<keyof typeof CHART_EXPO
  */
 export type LeaderSide = "right" | "left" | "top";
 /** The anchor of one name in data units, and the side of the anchor where the text sits. */
-export interface LeaderName {
+export type LeaderName = {
     readonly x: number;
     readonly y: number;
     readonly side: LeaderSide;
-}
+};
 /** The points that no name can cover: the plotted pair of each row, and the diameter of the largest point. */
-export interface NameObstacles {
+export type NameObstacles = {
     readonly xs: readonly (number | null)[];
     readonly ys: readonly (number | null)[];
     readonly pointPx: number;
-}
+};
 /**
  * The anchor of each name, in the order of the names, or `undefined` for a name that finds no free place.
  *

package/dist/report-render/figures/label-room.js

@@ -90,7 +90,10 @@ export function pointNameSides(points, plot, pointPx) {
  */
 export function nameAnchors(names, weights, plot) {
     const length = plot.x.max - plot.x.min;
-    const order = names.map((_name, index) => index).sort((a, b) => weights[b] - weights[a] || a - b);
+    const order = weights
+        .map((weight, index) => ({ weight, index }))
+        .sort((a, b) => b.weight - a.weight || a.index - b.index)
+        .map((entry) => entry.index);
     const line = nameSize("", length).height;
     const out = names.map(() => undefined);
     // A box of no height covers nothing, and a grid of such cells has no key.
@@ -100,6 +103,8 @@ export function nameAnchors(names, weights, plot) {
     const lines = Math.ceil((plot.y.max - plot.y.min) / line);
     for (const index of order) {
         const name = names[index];
+        if (name === undefined)
+            continue;
         const { width, height } = nameSize(name.text, length);
         const boxAt = (y) => ({ left: name.x - width / 2, right: name.x + width / 2, bottom: y - height / 2, top: y + height / 2 });
         const free = (y, moved) => {
@@ -202,7 +207,7 @@ export function placeLeaderNames(names, obstacles, plot, sides, top, frame = COL
     for (let index = 0; index < obstacles.xs.length; index += 1) {
         const x = obstacles.xs[index];
         const y = obstacles.ys[index];
-        if (x === null || y === null)
+        if (x === null || x === undefined || y === null || y === undefined)
             continue;
         const point = { x: toX(x), y: toY(y) };
         const key = `${cellOf(point.x)}:${cellOf(point.y)}`;

package/dist/report-render/figures/locuszoom.d.ts

@@ -25,11 +25,11 @@
  */
 import type { FigureModule } from "./index.js";
 /** One LD bin: the r² range, lower end included, and its color. The highest bin includes 1. */
-export interface LdBin {
+export type LdBin = {
     readonly low: number;
     readonly high: number;
     readonly color: string;
-}
+};
 /** The five r² bins of LocusZoom, in ascending order, with its colors: navy, sky blue, green, orange, and red. */
 export declare const LD_BINS: readonly LdBin[];
 /** The gray of a variant with no r², and the name of its series and its legend entry. */