From 67c5cdfed03ff904dff3ced9c6e92411af9d978c Mon Sep 17 00:00:00 2001 From: Adam Wright Date: Fri, 9 Oct 2026 13:55:22 +0000 Subject: [PATCH 1/2] Test the diagram's elements against real pathways The diagram service turns Reactome's layout and graph files into the elements cytoscape draws -- some 700 lines no test touched. These check it against two real pathways, stored as fixtures exactly as the release serves them: R-HSA-9679191 (drugs, entity sets, links) and R-HSA-2206292 (a disease diagram, normal entities faded and affected ones crossed out). What a drawn diagram has to be, whatever the pathway: every element its own id, no line to something not drawn, every entity of the layout drawn as its kind, every reaction a node; and a drug marked a drug, a crossed-out entity crossed, a faded one faded and replaced by something drawn. Each was shown to catch a fault: dropping the drug class, the crossed class, a link's source, or the fade each fails exactly one test. Sub-pathway labels are laid out in a rendered cytoscape graph, which measures text on a canvas jsdom does not have; the spec gives it one that measures and draws nothing. The fixtures are left out of Prettier. Co-Authored-By: Claude Opus 5.5 --- .prettierignore | 4 + .../services/diagram.service.elements.spec.ts | 160 ++++++++++++++++++ .../fixtures/R-HSA-2206292.graph.json | 1 + .../lib/services/fixtures/R-HSA-2206292.json | 1 + .../fixtures/R-HSA-9679191.graph.json | 1 + .../lib/services/fixtures/R-HSA-9679191.json | 1 + .../ngx-reactome-diagram/tsconfig.spec.json | 1 + 7 files changed, 169 insertions(+) create mode 100644 projects/ngx-reactome-diagram/src/lib/services/diagram.service.elements.spec.ts create mode 100644 projects/ngx-reactome-diagram/src/lib/services/fixtures/R-HSA-2206292.graph.json create mode 100644 projects/ngx-reactome-diagram/src/lib/services/fixtures/R-HSA-2206292.json create mode 100644 projects/ngx-reactome-diagram/src/lib/services/fixtures/R-HSA-9679191.graph.json create mode 100644 projects/ngx-reactome-diagram/src/lib/services/fixtures/R-HSA-9679191.json diff --git a/.prettierignore b/.prettierignore index 96e0fb1..8ab1caa 100644 --- a/.prettierignore +++ b/.prettierignore @@ -13,3 +13,7 @@ package-lock.json # edited by hand, so an upgrade would skip or ask about it. Specs are its output. .specify specs + +# Real Reactome layout and graph files, stored as test fixtures exactly as +# served (minified). Reformatting them would multiply their size for nothing. +**/fixtures/*.json diff --git a/projects/ngx-reactome-diagram/src/lib/services/diagram.service.elements.spec.ts b/projects/ngx-reactome-diagram/src/lib/services/diagram.service.elements.spec.ts new file mode 100644 index 0000000..5ea24ca --- /dev/null +++ b/projects/ngx-reactome-diagram/src/lib/services/diagram.service.elements.spec.ts @@ -0,0 +1,160 @@ +import { TestBed } from '@angular/core/testing'; +import { provideHttpClient } from '@angular/common/http'; +import { HttpTestingController, provideHttpClientTesting } from '@angular/common/http/testing'; +import { firstValueFrom } from 'rxjs'; +import type cytoscape from 'cytoscape'; + +import { DIAGRAM_CONFIG_TOKEN, DiagramService } from './diagram.service'; +import therapeutics from './fixtures/R-HSA-9679191.json'; +import therapeuticsGraph from './fixtures/R-HSA-9679191.graph.json'; +import mpsVII from './fixtures/R-HSA-2206292.json'; +import mpsVIIGraph from './fixtures/R-HSA-2206292.graph.json'; + +/** + * What the diagram is drawn from: Reactome's layout and graph files, turned + * into cytoscape elements. Checked against real pathways, stored as fixtures + * from the Reactome release (download/current/diagram/.json and + * .graph.json), rather than hand-made data that only has the shapes its + * author thought of. + * + * - R-HSA-9679191, Potential therapeutics for SARS: drugs, entity sets, + * complexes and links. + * - R-HSA-2206292, MPS VII - Sly syndrome: a disease diagram, with the normal + * entities faded out and the affected ones crossed out. + */ + +type Layout = typeof therapeutics | typeof mpsVII; + +const BASE = 'https://example.org/diagram'; + +async function elementsOf( + id: string, + layout: Layout, + graph: object +): Promise { + const service = TestBed.inject(DiagramService); + const http = TestBed.inject(HttpTestingController); + // The service writes into what it is given; give it its own copy. + const loaded = firstValueFrom(service.getDiagram(id)); + http.expectOne(`${BASE}/${id}.json`).flush(structuredClone(layout)); + http.expectOne(`${BASE}/${id}.graph.json`).flush(structuredClone(graph)); + return loaded; +} + +/** The element drawn for this id; a missing one fails the test by name. */ +function drawn( + byId: Map, + id: number +) { + const element = byId.get(String(id)); + if (!element) throw new Error(`nothing is drawn for ${id}`); + return element; +} + +const all = (e: cytoscape.ElementsDefinition) => [...e.nodes, ...e.edges]; +const classesOf = (d: cytoscape.ElementDefinition) => + typeof d.classes === 'string' ? d.classes.split(' ') : (d.classes ?? []); + +describe('DiagramService, drawing real pathways', () => { + beforeEach(() => { + TestBed.configureTestingModule({ + providers: [ + provideHttpClient(), + provideHttpClientTesting(), + { provide: DIAGRAM_CONFIG_TOKEN, useValue: { diagramUrl: BASE } }, + ], + }); + // Sub-pathway labels are spread apart in a rendered cytoscape graph, which + // measures their text on a canvas; jsdom has none. A context that measures + // a character as 6px and draws nothing is enough for the layout to run. + vi.spyOn(HTMLCanvasElement.prototype, 'getContext').mockImplementation( + () => + new Proxy( + {}, + { + get: (_target, name) => + name === 'measureText' + ? (text: string) => ({ width: text.length * 6 }) + : () => ({ addColorStop: () => undefined, data: [] }), + set: () => true, + } + ) as never + ); + }); + afterEach(() => vi.restoreAllMocks()); + + for (const [id, layout, graph] of [ + ['R-HSA-9679191', therapeutics, therapeuticsGraph], + ['R-HSA-2206292', mpsVII, mpsVIIGraph], + ] as const) { + describe(id, () => { + it('gives every element its own id', async () => { + const ids = all(await elementsOf(id, layout, graph)).map((e) => e.data.id); + const repeated = ids.filter((x, i) => ids.indexOf(x) !== i); + expect(repeated).toEqual([]); + }); + + it('joins every line to something that is drawn', async () => { + const elements = await elementsOf(id, layout, graph); + const nodes = new Set(elements.nodes.map((n) => n.data.id)); + const dangling = elements.edges + .filter((e) => !nodes.has(e.data.source) || !nodes.has(e.data.target)) + .map((e) => `${e.data.id}: ${e.data.source} -> ${e.data.target}`); + expect(dangling).toEqual([]); + }); + + it('draws every entity of the layout, as its kind', async () => { + const service = TestBed.inject(DiagramService); + const byId = new Map( + (await elementsOf(id, layout, graph)).nodes.map((n) => [n.data.id, n]) + ); + for (const entity of layout.nodes) { + const node = drawn(byId, entity.id); + const kind = service.nodeTypeMap.get(entity.renderableClass); + if (!kind) throw new Error(`an unknown kind: ${entity.renderableClass}`); + expect(classesOf(node), `${entity.renderableClass} ${entity.id}`).toEqual( + expect.arrayContaining([...kind]) + ); + expect(node.data['reactomeId']).toBe(entity.reactomeId); + } + }); + + it('draws every reaction as a node of its own', async () => { + const nodes = new Set((await elementsOf(id, layout, graph)).nodes.map((n) => n.data.id)); + const missing = layout.edges.map((r) => String(r.id)).filter((r) => !nodes.has(r)); + expect(missing).toEqual([]); + }); + }); + } + + it('marks a drug as a drug', async () => { + const elements = await elementsOf('R-HSA-9679191', therapeutics, therapeuticsGraph); + const byId = new Map(elements.nodes.map((n) => [n.data.id, n])); + const drugs = therapeutics.nodes.filter((n) => n.renderableClass.endsWith('Drug')); + expect(drugs.length, 'the pathway has drugs').toBeGreaterThan(0); + for (const drug of drugs) { + expect(classesOf(drawn(byId, drug.id)), `${drug.renderableClass} ${drug.id}`).toContain( + 'drug' + ); + } + }); + + it('crosses out what the disease removes, and fades what it replaces', async () => { + const elements = await elementsOf('R-HSA-2206292', mpsVII, mpsVIIGraph); + const byId = new Map(elements.nodes.map((n) => [n.data.id, n])); + + const crossed = mpsVII.nodes.filter((n) => 'isCrossed' in n && n.isCrossed); + expect(crossed.length, 'the pathway crosses something out').toBeGreaterThan(0); + for (const n of crossed) expect(classesOf(drawn(byId, n.id))).toContain('crossed'); + + const faded = mpsVII.nodes.filter((n) => 'isFadeOut' in n && n.isFadeOut && !n.isCrossed); + expect(faded.length, 'the pathway fades something out').toBeGreaterThan(0); + for (const n of faded) { + const node = drawn(byId, n.id); + expect(node.data['isFadeOut'], `${n.id} is faded`).toBe(true); + // What stands in for it, when anything does, is something drawn. + const by = node.data['replacedBy'] as string | undefined; + if (by) expect(byId.has(by), `${n.id} is replaced by ${by}`).toBe(true); + } + }); +}); diff --git a/projects/ngx-reactome-diagram/src/lib/services/fixtures/R-HSA-2206292.graph.json b/projects/ngx-reactome-diagram/src/lib/services/fixtures/R-HSA-2206292.graph.json new file mode 100644 index 0000000..48b7490 --- /dev/null +++ b/projects/ngx-reactome-diagram/src/lib/services/fixtures/R-HSA-2206292.graph.json @@ -0,0 +1 @@ +{"dbId":2206292,"stId":"R-HSA-2206292","speciesName":"Homo sapiens","nodes":[{"dbId":2162224,"stId":"R-ALL-2162224","displayName":"GlcA-\u03b21,3-GlcNAc [lysosomal 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\ No newline at end of file diff --git a/projects/ngx-reactome-diagram/tsconfig.spec.json b/projects/ngx-reactome-diagram/tsconfig.spec.json index 610066d..1fc2173 100644 --- a/projects/ngx-reactome-diagram/tsconfig.spec.json +++ b/projects/ngx-reactome-diagram/tsconfig.spec.json @@ -3,6 +3,7 @@ "extends": "../../tsconfig.json", "compilerOptions": { "outDir": "../../out-tsc/spec", + "resolveJsonModule": true, "types": ["vitest/globals"] }, "include": ["**/*.spec.ts", "**/*.d.ts"] From 4498fd440765aaa32bdb433d7b6f1b429b00a341 Mon Sep 17 00:00:00 2001 From: Adam Wright Date: Fri, 9 Oct 2026 14:03:01 +0000 Subject: [PATCH 2/2] Make the diagram tests unable to pass by accident From review: - Only 2 of the 34 faded entities in MPS VII have a replacement, so the check passed with replacements gone entirely. It now covers faded reactions too and requires that some have one; crossed-out entities must not be faded. Shown failing with no replacement set. - The expected classes were read from the service's own map, so a wrong entry there passed. They are written out now; shown failing with Gene drawn as RNA. - R-HSA-69620, Cell Cycle Checkpoints, is added: sub-pathway labels, a gene, an RNA and an embedded pathway. Each label is drawn once and placed apart from the others; shown failing with one label lost. - Unanswered requests fail the test; only the canvas stub is restored, not every mock; and its comment says why it is needed even with no sub-pathways. Co-Authored-By: Claude Opus 5.5 --- .prettierignore | 4 +- .../services/diagram.service.elements.spec.ts | 93 +++++++++++++++---- .../services/fixtures/R-HSA-69620.graph.json | 1 + .../lib/services/fixtures/R-HSA-69620.json | 1 + 4 files changed, 81 insertions(+), 18 deletions(-) create mode 100644 projects/ngx-reactome-diagram/src/lib/services/fixtures/R-HSA-69620.graph.json create mode 100644 projects/ngx-reactome-diagram/src/lib/services/fixtures/R-HSA-69620.json diff --git a/.prettierignore b/.prettierignore index 8ab1caa..b437b52 100644 --- a/.prettierignore +++ b/.prettierignore @@ -14,6 +14,6 @@ package-lock.json .specify specs -# Real Reactome layout and graph files, stored as test fixtures exactly as -# served (minified). Reformatting them would multiply their size for nothing. +# Real Reactome layout and graph files, stored as test fixtures (minified +# from what the release serves). Reformatting them would multiply their size. **/fixtures/*.json diff --git a/projects/ngx-reactome-diagram/src/lib/services/diagram.service.elements.spec.ts b/projects/ngx-reactome-diagram/src/lib/services/diagram.service.elements.spec.ts index 5ea24ca..c15c4a0 100644 --- a/projects/ngx-reactome-diagram/src/lib/services/diagram.service.elements.spec.ts +++ b/projects/ngx-reactome-diagram/src/lib/services/diagram.service.elements.spec.ts @@ -2,6 +2,7 @@ import { TestBed } from '@angular/core/testing'; import { provideHttpClient } from '@angular/common/http'; import { HttpTestingController, provideHttpClientTesting } from '@angular/common/http/testing'; import { firstValueFrom } from 'rxjs'; +import type { MockInstance } from 'vitest'; import type cytoscape from 'cytoscape'; import { DIAGRAM_CONFIG_TOKEN, DiagramService } from './diagram.service'; @@ -9,24 +10,48 @@ import therapeutics from './fixtures/R-HSA-9679191.json'; import therapeuticsGraph from './fixtures/R-HSA-9679191.graph.json'; import mpsVII from './fixtures/R-HSA-2206292.json'; import mpsVIIGraph from './fixtures/R-HSA-2206292.graph.json'; +import checkpoints from './fixtures/R-HSA-69620.json'; +import checkpointsGraph from './fixtures/R-HSA-69620.graph.json'; /** * What the diagram is drawn from: Reactome's layout and graph files, turned * into cytoscape elements. Checked against real pathways, stored as fixtures * from the Reactome release (download/current/diagram/.json and - * .graph.json), rather than hand-made data that only has the shapes its - * author thought of. + * .graph.json, minified), rather than hand-made data that only has the shapes + * its author thought of. * * - R-HSA-9679191, Potential therapeutics for SARS: drugs, entity sets, * complexes and links. * - R-HSA-2206292, MPS VII - Sly syndrome: a disease diagram, with the normal * entities faded out and the affected ones crossed out. + * - R-HSA-69620, Cell Cycle Checkpoints: sub-pathways, whose labels are laid + * out apart from one another, a gene, an RNA and an embedded pathway. */ -type Layout = typeof therapeutics | typeof mpsVII; +type Layout = typeof therapeutics | typeof mpsVII | typeof checkpoints; const BASE = 'https://example.org/diagram'; +/** + * The classes each kind of entity is drawn with -- what the style library's + * selectors match. Written out rather than read from the service's own map, so + * a wrong entry there fails here. + */ +const KINDS: Record = { + Protein: ['Protein', 'PhysicalEntity'], + Entity: ['GenomeEncodedEntity', 'PhysicalEntity'], + Gene: ['Gene', 'PhysicalEntity'], + RNA: ['RNA', 'PhysicalEntity'], + Complex: ['Complex', 'PhysicalEntity'], + EntitySet: ['EntitySet', 'PhysicalEntity'], + Chemical: ['Molecule', 'PhysicalEntity'], + ProteinDrug: ['Protein', 'PhysicalEntity', 'drug'], + ComplexDrug: ['Complex', 'PhysicalEntity', 'drug'], + ChemicalDrug: ['Molecule', 'PhysicalEntity', 'drug'], + EntitySetDrug: ['EntitySet', 'PhysicalEntity', 'drug'], + EncapsulatedNode: ['Interacting', 'Pathway'], +}; + async function elementsOf( id: string, layout: Layout, @@ -56,6 +81,8 @@ const classesOf = (d: cytoscape.ElementDefinition) => typeof d.classes === 'string' ? d.classes.split(' ') : (d.classes ?? []); describe('DiagramService, drawing real pathways', () => { + let canvas: MockInstance; + beforeEach(() => { TestBed.configureTestingModule({ providers: [ @@ -64,10 +91,12 @@ describe('DiagramService, drawing real pathways', () => { { provide: DIAGRAM_CONFIG_TOKEN, useValue: { diagramUrl: BASE } }, ], }); - // Sub-pathway labels are spread apart in a rendered cytoscape graph, which - // measures their text on a canvas; jsdom has none. A context that measures - // a character as 6px and draws nothing is enough for the layout to run. - vi.spyOn(HTMLCanvasElement.prototype, 'getContext').mockImplementation( + // Sub-pathway labels are laid out apart in a temporary rendered cytoscape + // graph, which measures their text on a canvas -- and is created even for a + // pathway with no sub-pathways. jsdom has no canvas: without this every + // test fails with "Could not create canvas of type 2d". A context that + // measures a character as 6px and draws nothing lets the layout run. + canvas = vi.spyOn(HTMLCanvasElement.prototype, 'getContext').mockImplementation( () => new Proxy( {}, @@ -81,11 +110,16 @@ describe('DiagramService, drawing real pathways', () => { ) as never ); }); - afterEach(() => vi.restoreAllMocks()); + afterEach(() => { + // Nothing asked for that the test did not answer. + TestBed.inject(HttpTestingController).verify(); + canvas.mockRestore(); + }); for (const [id, layout, graph] of [ ['R-HSA-9679191', therapeutics, therapeuticsGraph], ['R-HSA-2206292', mpsVII, mpsVIIGraph], + ['R-HSA-69620', checkpoints, checkpointsGraph], ] as const) { describe(id, () => { it('gives every element its own id', async () => { @@ -104,16 +138,15 @@ describe('DiagramService, drawing real pathways', () => { }); it('draws every entity of the layout, as its kind', async () => { - const service = TestBed.inject(DiagramService); const byId = new Map( (await elementsOf(id, layout, graph)).nodes.map((n) => [n.data.id, n]) ); for (const entity of layout.nodes) { const node = drawn(byId, entity.id); - const kind = service.nodeTypeMap.get(entity.renderableClass); - if (!kind) throw new Error(`an unknown kind: ${entity.renderableClass}`); + const kind = KINDS[entity.renderableClass]; + if (!kind) throw new Error(`no expected classes for ${entity.renderableClass}`); expect(classesOf(node), `${entity.renderableClass} ${entity.id}`).toEqual( - expect.arrayContaining([...kind]) + expect.arrayContaining(kind) ); expect(node.data['reactomeId']).toBe(entity.reactomeId); } @@ -145,16 +178,44 @@ describe('DiagramService, drawing real pathways', () => { const crossed = mpsVII.nodes.filter((n) => 'isCrossed' in n && n.isCrossed); expect(crossed.length, 'the pathway crosses something out').toBeGreaterThan(0); - for (const n of crossed) expect(classesOf(drawn(byId, n.id))).toContain('crossed'); + for (const n of crossed) { + const node = drawn(byId, n.id); + expect(classesOf(node), `${n.id} is crossed out`).toContain('crossed'); + // Crossed out, not faded: it is the disease's change, drawn in front. + expect(node.data['isFadeOut'], `${n.id} is not faded`).toBe(false); + } - const faded = mpsVII.nodes.filter((n) => 'isFadeOut' in n && n.isFadeOut && !n.isCrossed); + // Faded entities and faded reactions alike. + const faded = [ + ...mpsVII.nodes.filter((n) => 'isFadeOut' in n && n.isFadeOut && !n.isCrossed), + ...mpsVII.edges.filter((r) => 'isFadeOut' in r && r.isFadeOut), + ]; expect(faded.length, 'the pathway fades something out').toBeGreaterThan(0); + const replaced: string[] = []; for (const n of faded) { const node = drawn(byId, n.id); expect(node.data['isFadeOut'], `${n.id} is faded`).toBe(true); - // What stands in for it, when anything does, is something drawn. const by = node.data['replacedBy'] as string | undefined; - if (by) expect(byId.has(by), `${n.id} is replaced by ${by}`).toBe(true); + if (by) { + expect(byId.has(by), `${n.id} is replaced by ${by}, which is drawn`).toBe(true); + replaced.push(`${n.id} -> ${by}`); + } + } + // Some of what is faded has the disease's version drawn in its place. + expect(replaced.length, 'faded elements that have a replacement').toBeGreaterThan(0); + }); + + it('labels each sub-pathway once, placed apart from the others', async () => { + const elements = await elementsOf('R-HSA-69620', checkpoints, checkpointsGraph); + const labels = elements.nodes.filter((n) => classesOf(n).includes('Shadow')); + expect(labels.map((n) => n.data['reactomeId'] as number).sort()).toEqual( + checkpoints.shadows.map((s) => s.reactomeId).sort() + ); + for (const label of labels) { + const { x, y } = label.position ?? { x: NaN, y: NaN }; + expect(Number.isFinite(x) && Number.isFinite(y), `${label.data.id} is placed`).toBe(true); } + const places = labels.map((n) => `${n.position?.x},${n.position?.y}`); + expect(new Set(places).size, 'no two labels in one place').toBe(labels.length); }); }); 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