@jbrowse/cli 5.0.0-beta.10 → 5.0.0-beta.13

package/dist/commands/validate/index.js

@@ -24,7 +24,7 @@ what it cannot draw in a corner notice rather than refusing the track.
 This command runs the display's own rule list over every "marks" list in the
 file: an error where a mark draws nothing, never draws or a step cannot run,
 and a warning where a slot waits unread or the marks draw in an arrangement
-the author may not have meant. With --json each finding carries the stable
+the author may not have meant. With --json each finding has the stable
 "rule" id of the rule that made it.
 
 Types registered by plugins are not known to this command, so they come through

package/dist/commands/validate/markRules/colorScale.js

@@ -21,8 +21,8 @@ export const IDENTITY_SCALE = 'identity';
 const CATEGORICAL_PRESET = { scale: 'categorical' };
 /**
  * The fields whose values have names, an order and colours of their own on
- * every display, beneath each display's own presets. Red forward and blue
- * reverse is what the synteny ribbons paint too. The SV classes are
+ * every display, beneath each display's own presets. The synteny ribbons
+ * paint strand from this range too. The SV classes are
  * `svClassOf`'s, deletion red and duplication blue as dbVar and gnomAD-SV
  * paint them, insertion the pileup's purple, and the rest kept apart under
  * deuteranopia and protanopia. A record with no class files under `''`, so
@@ -166,6 +166,37 @@ export function scaleEndProblems({ domainMin, domainMax, domainQuantile }, { rev
 export function noticeLines(setting, problems) {
     return problems.map(({ slot, message }) => `${setting}.${slot}: ${message}`);
 }
+function numberOf(value) {
+    return typeof value === 'number' ? value : undefined;
+}
+function stringOf(value) {
+    return typeof value === 'string' ? value : undefined;
+}
+function listOf(value) {
+    return Array.isArray(value) ? value : undefined;
+}
+/** A quantitative scale's ends among the members `member` reads, each a number or unset. */
+export function scaleEndsOf(member) {
+    return {
+        domainMin: numberOf(member('domainMin')),
+        domainMax: numberOf(member('domainMax')),
+        domainQuantile: numberOf(member('domainQuantile')),
+    };
+}
+/**
+ * The members `colorProblems` reads among the ones `member` reads, each of the
+ * type it reads or unset, so a config snapshot and a config node answer alike.
+ */
+export function colorSlotsOf(member) {
+    return {
+        ...scaleEndsOf(member),
+        field: stringOf(member('field')) ?? '',
+        scale: stringOf(member('scale')),
+        domain: listOf(member('domain')),
+        range: listOf(member('range')),
+        labels: listOf(member('labels')),
+    };
+}
 function pinned(entry) {
     return entry !== '' && Number.isFinite(Number(entry));
 }

package/dist/commands/validate/markRules/markProblems.js

@@ -1,8 +1,8 @@
 // Generated by scripts/generateMarkRules.ts from plugins/marks/src/LinearMarkDisplay/markProblems.ts: do not edit, `pnpm autogen` rewrites it.
 import { AUTO_BIN } from './autoBin.js';
 import { FEATURE_FIELD_PRESETS, aggregateFieldName, colorProblems, fieldScaleOf, isJexl, SHAPE_NAMES, isNamedColor, paintedScale, scaleEndProblems, universalPresetOf, } from './markRuleFacts.js';
-import { MARK_SPECS, rampResolvesPerRegion, readsValue } from './markSpecs.js';
-import { DEFAULT_AGGREGATE_OP, BIN_OVERLAP_FIELD, DEFAULT_BIN_AS, DEFAULT_BIN_FIELD, DEFAULT_COVERAGE_AS, DEFAULT_FORMULA_AS, DEFAULT_LINE_INTERPOLATE, DEFAULT_ROW_PROPORTION, DEFAULT_LINK_SHAPE, DEFAULT_MARK_TYPE, CELLS_FIELDS, DEFAULT_PILEUP_AS, DEFAULT_PILEUP_FIELDS, DEFAULT_TEXT_FIELD, DEFAULT_X2, MATE_FIELDS, } from './markVocabulary.js';
+import { MARK_SPECS, readsValue } from './markSpecs.js';
+import { DEFAULT_AGGREGATE_OP, BIN_OVERLAP_FIELD, DEFAULT_BIN_AS, DEFAULT_BIN_FIELD, DEFAULT_COVERAGE_AS, DEFAULT_FORMULA_AS, DEFAULT_LINE_INTERPOLATE, DEFAULT_ROW_PROPORTION, DEFAULT_LINK_SHAPE, DEFAULT_MARK_TYPE, CELLS_FIELDS, DEFAULT_PILEUP_AS, DEFAULT_PILEUP_FIELDS, DEFAULT_TEXT_FIELD, DEFAULT_X2, MATE_FIELDS, MAX_THRESHOLD_CUTS, } from './markVocabulary.js';
 import { stepChannels } from './stepChannels.js';
 /**
  * The level of every rule of the list, by the stable id a report and a test
@@ -27,6 +27,8 @@ export const MARK_RULES = {
     'threshold-cuts': 'warning',
     /** A threshold colour naming no cut, so every value paints one colour. */
     'threshold-no-cuts': 'warning',
+    /** A threshold colour naming more cuts than it paints, so a value past the eighth takes the ninth colour. */
+    'threshold-cut-count': 'warning',
     /** A threshold `range` not one colour longer than its cuts. */
     'threshold-range': 'warning',
     /** A `domain` on a linear or log colour, whose ends are `domainMin` and `domainMax`. */
@@ -39,8 +41,6 @@ export const MARK_RULES = {
     'field-spells-constant': 'warning',
     /** A colour's or a shape's `labels` naming values its `domain` does not list, or no categorical scale's. */
     'labels-domain': 'warning',
-    /** A text's colour ramp with an open end, whose colours then differ from one region to the next. */
-    'unpinned-text-ramp': 'warning',
     /** A `minBpPerPx` not below the mark's `maxBpPerPx`, so the mark never draws. */
     'empty-zoom-range': 'error',
     /** A `filter` or `formula` whose `expr` is not a `jexl:` expression. */
@@ -59,6 +59,8 @@ export const MARK_RULES = {
     'step-field-expression': 'error',
     /** A `y` naming a field that no `aggregate` or `coverage` step before it writes. */
     'unwritten-y': 'error',
+    /** Another channel naming a field that no `aggregate` or `coverage` step before it writes, so it reads no value; the field a `facet` or `rows` splits on counts as written. */
+    'unwritten-field': 'warning',
     /** A mark other than a span drawn beside one that stacks rows, standing in the first of them. */
     'value-beside-rows': 'warning',
     /** Two `pileup` steps packing one plot, whose rows share numbers. */
@@ -120,11 +122,6 @@ function stepsOf(mark) {
 function colorScaleOf({ scale, field = '' }) {
     return paintedScale({ scale, field }, fieldScaleOf(FEATURE_FIELD_PRESETS, field));
 }
-function rampColor(mark) {
-    const color = mark.encoding?.color ?? {};
-    const painted = colorScaleOf(color);
-    return painted === 'linear' || painted === 'log' ? color : undefined;
-}
 function sizeFieldOf(size) {
     return typeof size === 'string'
         ? size
@@ -381,7 +378,34 @@ function stepProblems(steps, list = 'transform') {
     }
     return problems;
 }
-function ownProblems(mark, display, section) {
+// Each field a mark's channels read besides `y`, by the slot naming it: the
+// channels its type reads, a colour's or a shape's field where it is a scale,
+// a text's field as its default leaves it, and a link's size field.
+function channelFields(mark, spec) {
+    const encoding = mark.encoding ?? {};
+    const { x, x2, row, color = {}, shape, text = DEFAULT_TEXT_FIELD } = encoding;
+    const reads = (channel) => spec.channels.includes(channel);
+    const named = [
+        ['encoding.x', x],
+        ['encoding.x2', typeof x2 === 'string' ? x2 : x2?.pos],
+        ['encoding.x2.chrom', typeof x2 === 'object' ? x2.chrom : undefined],
+        ['encoding.row', reads('row') ? row : undefined],
+        [
+            'encoding.color.field',
+            reads('color') && colorScaleOf(color) !== 'none'
+                ? fieldOf(color)
+                : undefined,
+        ],
+        ['encoding.shape.field', reads('shape') ? fieldOf(shape) : undefined],
+        ['encoding.text', reads('text') ? text : undefined],
+        [
+            'encoding.size.field',
+            spec.size === 'channel' ? sizeFieldOf(encoding.size) : undefined,
+        ],
+    ];
+    return named.flatMap(([slot, field]) => field && !isJexl(field) ? [[slot, field]] : []);
+}
+function ownProblems(mark, display, section, split) {
     const type = markTypeOf(mark);
     const problems = [];
     const y = mark.encoding?.y;
@@ -430,6 +454,10 @@ function ownProblems(mark, display, section) {
         (color.domain ?? []).length === 0) {
         problems.push(found('threshold-no-cuts', 'encoding.color.domain', 'a threshold names its cut points in domain, and with none every value paints the first colour'));
     }
+    const cutCount = (color.domain ?? []).filter(cut => Number.isFinite(Number(cut))).length;
+    if (colorScaleOf(color) === 'threshold' && cutCount > MAX_THRESHOLD_CUTS) {
+        problems.push(found('threshold-cut-count', 'encoding.color.domain', `a threshold paints ${MAX_THRESHOLD_CUTS} cuts, and these ${cutCount} leave a value past the ${MAX_THRESHOLD_CUTS}th in the ${MAX_THRESHOLD_CUTS + 1}th colour`));
+    }
     problems.push(...shapeLabelProblems(mark.encoding?.shape));
     problems.push(...constantAsFieldProblems(mark.encoding));
     if (typeof size === 'object') {
@@ -437,14 +465,6 @@ function ownProblems(mark, display, section) {
             problems.push(found(rule, `encoding.size.${slot}`, message));
         }
     }
-    const ramp = rampColor(mark);
-    if (ramp) {
-        const { domainMin, domainMax } = ramp;
-        if (rampResolvesPerRegion(type) &&
-            (domainMin === undefined || domainMax === undefined)) {
-            problems.push(found('unpinned-text-ramp', `encoding.color.${domainMin === undefined ? 'domainMin' : 'domainMax'}`, `a ${type}'s ramp resolves an open end against each region's own extremes, so its colours agree across regions only with domainMin and domainMax both pinned`));
-        }
-    }
     const { minBpPerPx = 0, maxBpPerPx = 0 } = mark;
     if (minBpPerPx > 0 && maxBpPerPx > 0 && minBpPerPx >= maxBpPerPx) {
         problems.push(found('empty-zoom-range', 'minBpPerPx', `never draws: minBpPerPx ${minBpPerPx} is not below maxBpPerPx ${maxBpPerPx}`));
@@ -454,8 +474,19 @@ function ownProblems(mark, display, section) {
         problems.push(found('two-packings', 'transform', `packs rows of its own over the ${packsIn(section) ? "facet's" : "display's"} pileup, and the two share row numbers; one pileup packs every mark`));
     }
     const fields = madeFields([...display, ...section, ...stepsOf(mark)]);
-    if (fields && y && !isJexl(y) && !fields.has(y)) {
-        problems.push(found('unwritten-y', 'encoding.y', `reads "${y}", which no step before it writes; they leave ${[...fields].join(', ')}`));
+    if (fields) {
+        if (split) {
+            fields.add(split);
+        }
+        const leaves = `which no step before it writes; they leave ${[...fields].join(', ')}`;
+        if (y && !isJexl(y) && !fields.has(y)) {
+            problems.push(found('unwritten-y', 'encoding.y', `reads "${y}", ${leaves}`));
+        }
+        for (const [slot, field] of channelFields(mark, spec)) {
+            if (!fields.has(field)) {
+                problems.push(found('unwritten-field', slot, `reads "${field}", ${leaves}`));
+            }
+        }
     }
     return problems;
 }
@@ -468,6 +499,13 @@ function ownProblems(mark, display, section) {
 export function markProblems({ marks, facet, transform = [], rows, scales, }) {
     const faceted = named(facet?.field);
     const drawsRows = named(rows?.field) && !faceted;
+    // the field the sections or rows are split on, which every section's rows
+    // keep through the steps that make rows
+    const split = faceted
+        ? String(facet?.field)
+        : drawsRows
+            ? String(rows?.field)
+            : undefined;
     const section = readable(facet?.transform ?? []);
     const display = readable(transform);
     const shared = [...display, ...section];
@@ -489,7 +527,10 @@ export function markProblems({ marks, facet, transform = [], rows, scales, }) {
             : []),
         ...(drawsRows ? packingsUnderRows(marks, transform, section) : []),
         ...marks.flatMap((mark, i) => mark
-            ? ownProblems(mark, display, section).map(p => ({ mark: i, ...p }))
+            ? ownProblems(mark, display, section, split).map(p => ({
+                mark: i,
+                ...p,
+            }))
             : []),
     ];
     for (const [i, mark] of marks.entries()) {

package/dist/commands/validate/markRules/markSpecs.js

@@ -12,46 +12,39 @@ export const MARK_SPECS = {
     bar: {
         channels: ['y', 'row', 'color'],
         value: 'required',
-        ramp: 'display',
         hit: 'rows',
     },
     point: {
         channels: ['y', 'row', 'color', 'shape'],
         value: 'required',
-        ramp: 'display',
         hit: 'index',
         size: 'constant',
     },
     rule: {
         channels: ['y', 'row', 'color'],
         value: 'required',
-        ramp: 'display',
         hit: 'rows',
         size: 'constant',
     },
     line: {
         channels: ['y', 'row', 'color'],
         value: 'required',
-        ramp: 'display',
         hit: 'rows',
         size: 'constant',
     },
     span: {
         channels: ['row', 'color'],
         value: 'none',
-        ramp: 'display',
         hit: 'rows',
     },
     text: {
         channels: ['y', 'row', 'color', 'text'],
         value: 'optional',
-        ramp: 'worker',
         hit: false,
     },
     link: {
         channels: ['y', 'row', 'color', 'size'],
         value: 'optional',
-        ramp: 'display',
         hit: 'index',
         farFoot: true,
         size: 'channel',
@@ -72,23 +65,18 @@ export function plotsValue(type) {
 export function hitsByIndex(type) {
     return specOf(type).hit === 'index';
 }
-/** Whether a mark type's ramp colour resolves per region, in the worker. */
-export function rampResolvesPerRegion(type) {
-    return specOf(type).ramp === 'worker';
-}
 /**
- * The lanes a mark asks the worker to fill: its type's channels, a ramp's raw
- * values beside the colour where the display resolves the ramp, and the hit
- * index where the mark answers a hover through one. The encoder fills whichever of
- * `color` and `colorValue` the colour declaration calls for.
+ * The lanes a mark asks the worker to fill: its type's channels, the colour
+ * lanes `colorLanesOf` chose for its declaration, and the hit index where the
+ * mark answers a hover through one.
  */
-export function markLanes(type) {
+export function markLanes(type, colorLanes) {
     const spec = specOf(type);
     return [
         ...spec.channels.flatMap((channel) => channel === 'shape'
             ? ['glyph']
-            : channel === 'color' && spec.ramp === 'display'
-                ? [channel, 'colorValue']
+            : channel === 'color'
+                ? colorLanes
                 : [channel]),
         ...(spec.farFoot ? ['x2Ref'] : []),
         ...(hitsByIndex(type) ? ['index'] : []),

package/dist/commands/validate/markRules/markVocabulary.js

@@ -26,6 +26,8 @@ export const DEFAULT_LINK_SHAPE = 'dome';
 export const DEFAULT_LINK_STROKE_PX = 2;
 /** The fraction of its row a span fills where its `rowProportion` is left unwritten. */
 export const DEFAULT_ROW_PROPORTION = 1;
+/** The cuts a threshold colour paints, render-core's `MAX_COLOR_CUTS`. */
+export const MAX_THRESHOLD_CUTS = 8;
 export const SIZE_SCALES = ['linear', 'log'];
 export const MARK_SOURCES = ['features', 'density'];
 export const DEFAULT_MARK_SOURCE = 'features';
@@ -37,7 +39,7 @@ export const BIN_OVERLAP_FIELD = 'overlap';
 export const DEFAULT_COVERAGE_AS = 'coverage';
 export const DEFAULT_FLATTEN_FIELD = 'subfeatures';
 export const DEFAULT_CELLS_FIELD = 'seq';
-/** What a `cells` step writes: `state` on every cell, `base` on a mismatch or an insertion, `match` off a gap, `length` on an insertion. */
+/** What a `cells` step writes: `state` on every cell, `base` on a mismatch or an insertion, `match` off a gap or a reference `N`, `length` on an insertion. */
 export const CELLS_FIELDS = ['state', 'base', 'match', 'length'];
 export const DEFAULT_PILEUP_AS = 'row';
 export const DEFAULT_PILEUP_FIELDS = ['start', 'end'];

package/dist/commands/validate/schemaValidate.js

@@ -68,7 +68,7 @@ function describe(schema) {
     if (name === 'JexlString') {
         return 'a "jexl:" expression';
     }
-    if (name === 'CssColor') {
+    if (name === 'CssColor' || name === 'CssColorEntry') {
         return 'a CSS color (a name like "red", "#rrggbb", "rgb()" or "hsl()")';
     }
     if (name) {
@@ -378,7 +378,7 @@ function explain(data, errors, problems, depth) {
                 break;
             }
             case 'pattern':
-                emit(where, error.schemaPath.endsWith('/CssColor/pattern')
+                emit(where, /\/CssColor(?:Entry)?\/pattern$/.test(error.schemaPath)
                     ? `expected ${describe({ $ref: '#/$defs/CssColor' })}, got ${JSON.stringify(error.data)}`
                     : `expected a string matching /${String(parent.pattern)}/, got ${JSON.stringify(error.data)}`);
                 break;

package/dist/commands/validate/validateConfig.js

@@ -8,10 +8,11 @@
 // loading normally with the setting doing nothing.
 //
 // Pure: no filesystem, no process exit. The command wrapper owns both.
+import { fileNameOf, isLooseTrackConfig, matchFormat, } from '@jbrowse/add-track-core';
 import { configManifest } from './configManifest.generated.js';
 import { displayDefaultsForTrackType } from './displayDefaultKeys.js';
 import { isRecord, liftToSnapshot } from './liftConfig.js';
-import { colorProblems, scaleEndProblems } from './markRules/colorScale.js';
+import { colorProblems, colorSlotsOf, scaleEndProblems, scaleEndsOf, } from './markRules/colorScale.js';
 import { markProblems } from './markRules/markProblems.js';
 import { hasDeclaredShape, rootConfigurationSlots, schemaProblems, } from './schemaValidate.js';
 import { didYouMean } from './suggest.js';
@@ -103,7 +104,7 @@ function checkPluggable(obj, group, groupLabel, where, report) {
 }
 function checkTrack(track, index, manifest, report, ctx) {
     const where = `tracks[${index}]`;
-    const loose = typeof track.uri === 'string' && !('adapter' in track);
+    const loose = isLooseTrackConfig(track);
     const trackId = track.trackId;
     if (typeof trackId === 'string' && trackId) {
         if (ctx.seenTrackIds.has(trackId)) {
@@ -129,6 +130,19 @@ function checkTrack(track, index, manifest, report, ctx) {
             }
         }
     }
+    if (loose) {
+        const file = fileNameOf(track.uri);
+        const spec = matchFormat(file)?.spec;
+        if (!spec || !('adapterType' in spec)) {
+            const message = `JBrowse infers no track from "${file}", so the track fails to load: give it an "adapter"`;
+            if (ctx.declaresPlugins) {
+                report.warn(`${where}.uri`, `${message}, unless a plugin it declares guesses this extension`);
+            }
+            else {
+                report.error(`${where}.uri`, message);
+            }
+        }
+    }
     checkPluggable(track, manifest.tracks, 'track', where, report);
     if (!loose) {
         checkPluggable(track.adapter, manifest.adapters, 'adapter', `${where}.adapter`, report);
@@ -276,7 +290,7 @@ function declaredEntries(lifted, display, slot, slots) {
         return (slots.find(s => s.name === slot)?.defaultEntries ?? []);
     }
     return Array.isArray(list)
-        ? list.map((entry, i) => hasDeclaredShape(written[i], `${SLOTS_POINTER}/${slot}/items`)
+        ? list.map((entry, i) => hasDeclaredShape([written[i]], `${SLOTS_POINTER}/${slot}`)
             ? entry
             : undefined)
         : [];
@@ -330,18 +344,9 @@ function pushOnce(report, problem) {
         report.problems.push(problem);
     }
 }
-function numberOf(value) {
-    return typeof value === 'number' ? value : undefined;
-}
-function scaleEndsOf(scale) {
-    return {
-        domainMin: numberOf(scale.domainMin),
-        domainMax: numberOf(scale.domainMax),
-        domainQuantile: numberOf(scale.domainQuantile),
-    };
-}
 function scalesOf(scales) {
-    return isRecord(scales.y) ? { y: scaleEndsOf(scales.y) } : {};
+    const { y } = scales;
+    return isRecord(y) ? { y: scaleEndsOf(name => y[name]) } : {};
 }
 function declaredMembers(written, slot) {
     const declared = new Set((slot.subSlots ?? []).map(s => s.name));
@@ -371,19 +376,15 @@ function checkScaleSlots(display, slots, where, report) {
         }
         const members = declaredMembers(written, slot);
         if (slot.fieldPresets) {
-            for (const problem of colorProblems({
-                ...scaleEndsOf(members),
-                field: typeof members.field === 'string' ? members.field : '',
-                scale: typeof members.scale === 'string' ? members.scale : undefined,
-                domain: Array.isArray(members.domain) ? members.domain : undefined,
-                range: Array.isArray(members.range) ? members.range : undefined,
-                labels: Array.isArray(members.labels) ? members.labels : undefined,
-            }, slot.fieldPresets)) {
+            for (const problem of colorProblems(colorSlotsOf(name => name === 'field'
+                ? (members.field ?? slot.fieldDefault)
+                : members[name]), slot.fieldPresets)) {
                 warn(`${where}.${slot.name}`, problem);
             }
         }
-        if (slot.name === 'scales' && isRecord(members.y)) {
-            for (const problem of scaleEndProblems(scaleEndsOf(members.y))) {
+        const { y } = members;
+        if (slot.name === 'scales' && isRecord(y)) {
+            for (const problem of scaleEndProblems(scaleEndsOf(name => y[name]))) {
                 warn(`${where}.scales.y`, problem);
             }
         }

package/dist/version.js

@@ -1 +1 @@
-export const version = '5.0.0-beta.10';
+export const version = '5.0.0-beta.13';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "5.0.0-beta.10",
+  "version": "5.0.0-beta.13",
   "type": "module",
   "description": "A command line tool for working with JBrowse 2",
   "keywords": [
@@ -31,9 +31,9 @@
     "cli-progress": "^3.12.0",
     "serve-handler": "^6.1.7",
     "tmp": "^0.2.7",
-    "@jbrowse/add-track-core": "^5.0.0-beta.10",
-    "@jbrowse/cigar-utils": "^5.0.0-beta.10",
-    "@jbrowse/text-indexing-core": "^5.0.0-beta.10"
+    "@jbrowse/cigar-utils": "^5.0.0-beta.13",
+    "@jbrowse/add-track-core": "^5.0.0-beta.13",
+    "@jbrowse/text-indexing-core": "^5.0.0-beta.13"
   },
   "publishConfig": {
     "access": "public"