@jbrowse/cli 5.0.0-beta.11 → 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/markVocabulary.js

@@ -39,7 +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

@@ -12,7 +12,7 @@ import { fileNameOf, isLooseTrackConfig, matchFormat, } from '@jbrowse/add-track
 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';
@@ -290,7 +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)
         : [];
@@ -344,18 +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));
@@ -385,19 +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.11';
+export const version = '5.0.0-beta.13';

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/cli",
-  "version": "5.0.0-beta.11",
+  "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.11",
-    "@jbrowse/text-indexing-core": "^5.0.0-beta.11",
-    "@jbrowse/cigar-utils": "^5.0.0-beta.11"
+    "@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"