feat(core): remove DataTrack from schema and compiler

src/compiler/compile.ts

@@ -1,6 +1,6 @@
 import type { GoslingSpec, TemplateTrackDef, VisUnitApiData } from '@gosling-lang/gosling-schema';
 import type { HiGlassSpec } from '@gosling-lang/higlass-schema';
-import { traverseToFixSpecDownstream, overrideDataTemplates } from './spec-preprocess';
+import { traverseToFixSpecDownstream } from './spec-preprocess';
 import { replaceTrackTemplates } from '../core/utils/template';
 import { getRelativeTrackInfo, type Size } from './bounding-box';
 import type { CompleteThemeDeep } from '../core/utils/theme';
@@ -33,9 +33,6 @@ export function compile(
     // Make sure to keep the original spec as-is
     const specCopy = JSON.parse(JSON.stringify(spec));
 
-    // Override default visual encoding (i.e., `DataTrack` => `BasicSingleTrack`)
-    overrideDataTemplates(specCopy);
-
     // Replace track templates with raw gosling specs (i.e., `TemplateTrack` => `SingleTrack | OverlaidTrack`)
     replaceTrackTemplates(specCopy, templates);
 

src/compiler/spec-preprocess.test.ts

@@ -1,6 +1,6 @@
 import type { GoslingSpec, SingleView, Track } from '@gosling-lang/gosling-schema';
 import { getBoundingBox, getRelativeTrackInfo } from './bounding-box';
-import { traverseToFixSpecDownstream, overrideDataTemplates, convertToFlatTracks } from './spec-preprocess';
+import { traverseToFixSpecDownstream, convertToFlatTracks } from './spec-preprocess';
 import { getTheme } from '../core/utils/theme';
 
 describe('Fix Spec Downstream', () => {
@@ -259,36 +259,6 @@ describe('Spec Preprocess', () => {
         expect(spec.tracks[1].static).toEqual(false);
     });
 
-    it('override template (higlass-vector)', () => {
-        const spec: GoslingSpec = {
-            tracks: [{ data: { type: 'vector', url: '', column: 'c', value: 'v' }, overrideTemplate: true } as Track]
-        };
-        overrideDataTemplates(spec);
-        expect(spec.tracks[0]).toHaveProperty('mark');
-    });
-
-    it('override template (higlass-multivec)', () => {
-        {
-            const spec: GoslingSpec = {
-                tracks: [
-                    {
-                        data: { type: 'multivec', url: '', row: 'r', column: 'c', value: 'v' },
-                        overrideTemplate: true
-                    } as Track
-                ]
-            };
-            overrideDataTemplates(spec);
-            expect(spec.tracks[0]).toHaveProperty('mark');
-        }
-        {
-            const spec: GoslingSpec = {
-                tracks: [{ data: { type: 'multivec', url: '', row: 'r', column: 'c', value: 'v' } } as Track]
-            };
-            overrideDataTemplates(spec);
-            expect(spec.tracks[0]).not.toHaveProperty('mark'); // overrideTemplate is not set, so do not override templates
-        }
-    });
-
     it('Convert To FlatTracks', () => {
         const dummySpec: Track = { data: { type: 'csv', url: '' }, mark: 'bar', width: 10, height: 10 };
         {

src/compiler/spec-preprocess.ts

@@ -11,8 +11,6 @@ import type {
     DisplaceTransform
 } from '@gosling-lang/gosling-schema';
 import {
-    IsDataTemplate,
-    IsDataDeepTileset,
     IsSingleTrack,
     IsChannelDeep,
     IsOverlaidTrack,
@@ -461,107 +459,3 @@ export function traverseToFixSpecDownstream(spec: GoslingSpec | SingleView, pare
         });
     }
 }
-
-/**
- * Get an encoding template for the `higlass-vector` data type.
- * @param column
- * @param value
- */
-export function getVectorTemplate(column: string, value: string): SingleTrack {
-    return {
-        data: {
-            type: 'vector',
-            url: '',
-            column,
-            value
-        },
-        mark: 'bar',
-        x: { field: column, type: 'genomic', axis: 'top' },
-        y: { field: value, type: 'quantitative' },
-        width: 400,
-        height: 100
-    };
-}
-
-export function getMultivecTemplate(
-    row: string,
-    column: string,
-    value: string,
-    categories: string[] | undefined
-): SingleTrack {
-    return categories && categories.length < 10
-        ? {
-              data: {
-                  type: 'multivec',
-                  url: '',
-                  row,
-                  column,
-                  value,
-                  categories
-              },
-              mark: 'bar',
-              x: { field: column, type: 'genomic', axis: 'top' },
-              y: { field: value, type: 'quantitative' },
-              row: { field: row, type: 'nominal', legend: true },
-              color: { field: row, type: 'nominal' },
-              width: 400,
-              height: 100
-          }
-        : {
-              data: {
-                  type: 'multivec',
-                  url: '',
-                  row,
-                  column,
-                  value,
-                  categories
-              },
-              mark: 'rect',
-              x: { field: column, type: 'genomic', axis: 'top' },
-              row: { field: row, type: 'nominal', legend: true },
-              color: { field: value, type: 'quantitative' },
-              width: 400,
-              height: 100
-          };
-}
-
-/**
- * Override default visual encoding in each track for given data type.
- * @param spec
- */
-export function overrideDataTemplates(spec: GoslingSpec) {
-    traverseTracks(spec, (t, i, ts) => {
-        if (!('data' in t) || !t.data || !IsDataDeepTileset(t.data)) {
-            // if `data` is not specified, we can not provide a correct template.
-            return;
-        }
-
-        if ('alignment' in t) {
-            // This is an OverlaidTracks, so skip this.
-            return;
-        }
-
-        if (!IsDataTemplate(t)) {
-            // This is not partial specification that we need to use templates
-            return;
-        }
-
-        switch (t.data.type) {
-            case 'vector':
-            case 'bigwig':
-                ts[i] = Object.assign(getVectorTemplate(t.data.column ?? 'position', t.data.value ?? 'value'), t);
-                break;
-            case 'multivec':
-                ts[i] = Object.assign(
-                    getMultivecTemplate(
-                        t.data.row ?? 'category',
-                        t.data.column ?? 'position',
-                        t.data.value ?? 'value',
-                        t.data.categories
-                    ),
-                    t
-                );
-                break;
-        }
-    });
-}

src/core/utils/overlay.ts

@@ -6,14 +6,20 @@ import type {
     ChannelDeep,
     DataDeep
 } from '@gosling-lang/gosling-schema';
-import { IsChannelDeep, IsDataTrack, IsOverlaidTrack, IsSingleTrack, IsDummyTrack } from '@gosling-lang/gosling-schema';
+import {
+    IsChannelDeep,
+    IsOverlaidTrack,
+    IsSingleTrack,
+    IsDummyTrack,
+    IsTemplateTrack
+} from '@gosling-lang/gosling-schema';
 
 /**
  * Resolve superposed tracks into multiple track specifications.
  * Some options are corrected to ensure the resolved tracks use consistent visual properties, such as the existence of the axis for genomic coordinates.
  */
 export function resolveSuperposedTracks(track: Track): SingleTrack[] {
-    if (IsDataTrack(track) || IsDummyTrack(track)) {
+    if (IsTemplateTrack(track) || IsDummyTrack(track)) {
         // no BasicSingleTrack to return
         return [];
     }
@@ -69,7 +75,7 @@ export function resolveSuperposedTracks(track: Track): SingleTrack[] {
 export function spreadTracksByData(tracks: Track[]): Track[] {
     return ([] as Track[]).concat(
         ...tracks.map(t => {
-            if (IsDataTrack(t) || !IsOverlaidTrack(t) || t._overlay.length <= 1) {
+            if (!IsOverlaidTrack(t) || t._overlay.length <= 1) {
                 // no overlaid tracks to spread
                 return [t];
             }

src/core/utils/template.ts

@@ -303,6 +303,10 @@ export function replaceTrackTemplates(spec: GoslingSpec, templates: TemplateTrac
         if ('encoding' in viewBase) {
             delete viewBase.encoding;
         }
+        // Remove a template property since it is not a template anymore
+        if('template' in viewBase) {
+            delete viewBase.template;
+        }
         const convertedView: OverlaidTracks = {
             ...viewBase,
             alignment: 'overlay',

src/gosling-schema/gosling.schema.guards.ts

@@ -22,7 +22,6 @@ import type {
     MultivecData,
     MatrixData,
     VectorData,
-    DataTrack,
     BigWigData,
     SingleView,
     FlatTracks,
@@ -92,18 +91,10 @@ export function IsStackedTracks(_: SingleView): _ is StackedTracks {
     return !IsFlatTracks(_) && !IsOverlaidTracks(_);
 }
 
-export function IsDataTrack(_: Track): _ is DataTrack {
-    // !!! Track might not contain `mark` when it is superposed one
-    return !IsOverlaidTrack(_) && 'data' in _ && !('mark' in _);
-}
 export function IsDummyTrack(_: Track): _ is DummyTrack {
     return 'type' in _ && _.type == 'dummy-track';
 }
 
-export function IsDataTemplate(_: Partial<Track>): boolean {
-    return !!('data' in _ && 'overrideTemplate' in _ && _.overrideTemplate);
-}
-
 export function IsDataDeep(data: DataDeep | Datum[]): data is DataDeep {
     return typeof data === 'object';
 }