e2e: recordings from Release 98; replay keys a query's parameters in order

e2e/analysis-results.spec.ts

@@ -173,6 +173,10 @@ test.describe('Analysis results', () => {
   // arrays changed in place, so the selection never counted as made, and the
   // stepper would not move on to the analysis.
   test('a dragged tissue counts as chosen', async ({ page }) => {
+    // Reaching the last step submits the analysis. Held unanswered: this is
+    // about the stepper, and an answered submission moves the form past the
+    // step this looks for.
+    await page.route('**/AnalysisService/identifiers/url**', () => {});
     await page.goto('/PathwayBrowser?analysisTab=tissue');
     const [available, selected] = [
       page.locator('.tissue-list').nth(0),
@@ -214,7 +218,7 @@ test.describe('Analysis summary', () => {
         status: 200,
         contentType: 'text/event-stream',
         body:
-          'event: start\ndata: {"release": "97", "analysis_type": "OVERREPRESENTATION", "disclosure": "aggregate"}\n\n' +
+          'event: start\ndata: {"release": "98", "analysis_type": "OVERREPRESENTATION", "disclosure": "aggregate"}\n\n' +
           `event: token\ndata: {"text": "Summary number ${asked}."}\n\n` +
           'event: done\ndata: {"state": "summarised"}\n\n',
       });
@@ -279,7 +283,7 @@ test.describe('Continuing a summary in the chat', () => {
         status: 200,
         contentType: 'text/event-stream',
         body:
-          'event: start\ndata: {"release": "97", "analysis_type": "OVERREPRESENTATION", "disclosure": "aggregate"}\n\n' +
+          'event: start\ndata: {"release": "98", "analysis_type": "OVERREPRESENTATION", "disclosure": "aggregate"}\n\n' +
           'event: token\ndata: {"text": "A summary to continue."}\n\n' +
           'event: done\ndata: {"state": "summarised"}\n\n',
       });
@@ -327,7 +331,7 @@ test.describe('Continuing a summary after the person-check lapsed', () => {
             status: 200,
             contentType: 'text/event-stream',
             body:
-              'event: start\ndata: {"release": "97", "analysis_type": "OVERREPRESENTATION", "disclosure": "aggregate"}\n\n' +
+              'event: start\ndata: {"release": "98", "analysis_type": "OVERREPRESENTATION", "disclosure": "aggregate"}\n\n' +
               'event: token\ndata: {"text": "A summary to continue."}\n\n' +
               'event: done\ndata: {"state": "summarised"}\n\n',
           })

e2e/analysis-token-spinner.spec.ts

@@ -10,7 +10,7 @@ import { test, expect } from './support/backend';
  */
 
 // An existing result, read only: nothing is submitted. It ends in "=".
-const TOKEN = 'MjAyNjA5MjUxNDM3NThfMTM=';
+const TOKEN = 'MjAyNjExMDIxNDQwMTVfOQ==';
 const LOAD = 60_000;
 
 test('the Analyze button stops spinning once a linked result is shown', async ({ page }) => {

e2e/analysis.spec.ts

@@ -503,7 +503,7 @@ test.describe('Quantitative analysis: adding a dataset', () => {
       route.fulfill({
         contentType: 'application/json',
         body: JSON.stringify({
-          release: '97',
+          release: '98',
           method_name: 'Camera',
           results: [],
           reactome_links: [],

e2e/diagram-load-errors.spec.ts

@@ -14,7 +14,7 @@ const LOAD = 60_000;
 const PATHWAY = 'R-HSA-69620';
 // An existing result, read only: nothing is submitted. It finds entities in
 // R-HSA-69620.
-const TOKEN = 'MjAyNjA5MjUxNDM3NThfMTM=';
+const TOKEN = 'MjAyNjExMDIxNDQwMTVfOQ==';
 // CHEK1 occurs in Cell Cycle Checkpoints.
 const FLAG = 'CHEK1';
 

e2e/downloads.spec.ts

@@ -1,6 +1,7 @@
 import { renderServiceAvailable } from './fixtures/serves';
 import { type Page, type Download } from '@playwright/test';
 import { test, expect } from './support/backend';
+import { copyOf } from './support/release-files';
 import { readFileSync } from 'node:fs';
 import { unzipSync, strFromU8 } from 'fflate';
 
@@ -315,14 +316,26 @@ test.describe('Diagram downloads', () => {
   });
 
   test('a figure that cannot be made says so, rather than doing nothing', async ({ page }) => {
-    // Circadian clock builds six of its shapes out of <foreignObject>, which is
+    // Circadian clock built six of its shapes out of <foreignObject>, which is
     // how a design tool exports a conic gradient. Chromium taints a canvas the
-    // moment one is drawn onto it and refuses toDataURL, so this illustration
-    // cannot be turned into a picture in any browser.
+    // moment one is drawn onto it and refuses toDataURL, so such an
+    // illustration cannot be turned into a picture in any browser.
     //
     // That part is not fixable here. What was fixable: the click produced no
     // file, no message and no sign it had registered, because every client-side
     // exporter reported failure with console.error and nothing else.
+    //
+    // Release 98's copy was redrawn without them, so the test puts one back.
+    await page.route(/\/ehld\/R-HSA-9909396\.svg$/, (route) =>
+      route.fulfill({
+        contentType: 'image/svg+xml',
+        headers: { 'access-control-allow-origin': '*' },
+        body: readFileSync(copyOf(route.request().url()), 'utf8').replace(
+          '</svg>',
+          '<foreignObject width="10" height="10"><div xmlns="http://www.w3.org/1999/xhtml"></div></foreignObject></svg>'
+        ),
+      })
+    );
     await openDownloadTab(page, 'R-HSA-9909396');
     await page.locator('.container.diagram').getByText('PNG', { exact: true }).first().click();
 
@@ -862,4 +875,24 @@ test.describe('The render page, without the render service', () => {
     await expect(render).not.toHaveAttribute('data-render-error', new RegExp(TOKEN));
     await expect(render).not.toHaveAttribute('data-render-ready', 'true');
   });
+
+  // The reaction's own layout is never coloured, so the figure it draws
+  // carries no analysis, whatever the address asked for.
+  test('says the reaction view carries no analysis', async ({ page, request }) => {
+    test.skip(
+      !(await servesReactionDiagram(request)),
+      'this backend does not serve a reaction its own diagram'
+    );
+    await holdAnalysisForUniprot(page);
+    await page.goto(`/PathwayBrowser/render/${REACTION}?layout=reaction&analysis=${TOKEN}`);
+    await expect(page.locator('cr-render[data-render-ready="true"]')).toHaveCount(1, {
+      timeout: 120_000,
+    });
+    const state = await page.evaluate(
+      () =>
+        (window as unknown as { __renderState: { view: string; analysis: unknown } }).__renderState
+    );
+    expect(state.view).toBe('reaction');
+    expect(state.analysis).toBeNull();
+  });
 });

e2e/embed-diagram.spec.ts

@@ -689,7 +689,7 @@ test.describe('the embeddable diagram, told what to show', () => {
   const FLAG = 'CHEK1';
   // An existing result, read only: nothing is submitted. It finds entities in
   // R-HSA-69620.
-  const TOKEN = 'MjAyNjA5MjUxNDM3NThfMTM=';
+  const TOKEN = 'MjAyNjExMDIxNDQwMTVfOQ==';
   // Drawn in the R-HSA-69620 diagram: CDKN1A,CDKN1B, a DefinedSet.
   const ENTITY = 'R-HSA-182558';
 

e2e/embed-legacy-api.spec.ts

@@ -19,7 +19,7 @@ const LOAD = 90_000;
 const ENTITY = 'R-HSA-182558';
 const FLAG = 'CHEK1';
 // An existing result, read only: nothing is submitted.
-const TOKEN = 'MjAyNjA5MjUxNDM3NThfMTM=';
+const TOKEN = 'MjAyNjExMDIxNDQwMTVfOQ==';
 
 type Widget = Record<string, (...args: unknown[]) => void>;
 type LegacyGlobals = {

e2e/har/b222bde7a9b5e9cf54863cc84f8de6fb8149a276.json → e2e/har/055649fae1a8a87a05b6b145343d872749beda70.json

@@ -1 +1 @@
-[[{"dbId":9615710,"displayName":"Late endosomal microautophagy","stId":"R-HSA-9615710","name":["Late endosomal microautophagy"],"stIdVersion":"R-HSA-9615710.5","schemaClass":"Pathway","doi":"10.3180/R-HSA-9615710.1","speciesName":"Homo sapiens","releaseDate":"2019-06-12","hasDiagram":true,"hasEHLD":false,"diagramWidth":1630,"diagramHeight":919,"inferred":false,"inDisease":false},{"dbId":9612973,"displayName":"Autophagy","stId":"R-HSA-9612973","name":["Autophagy"],"stIdVersion":"R-HSA-9612973.4","schemaClass":"TopLevelPathway","speciesName":"Homo sapiens","releaseDate":"2019-06-12","hasDiagram":true,"hasEHLD":true,"diagramWidth":626,"diagramHeight":338,"inferred":false,"inDisease":false}]]
+[[{"dbId":9615710,"displayName":"Late endosomal microautophagy","stId":"R-HSA-9615710","name":["Late endosomal microautophagy"],"stIdVersion":"R-HSA-9615710.5","schemaClass":"Pathway","doi":"10.3180/R-HSA-9615710.1","speciesName":"Homo sapiens","releaseDate":"2019-06-12","hasDiagram":true,"hasEHLD":false,"diagramWidth":1630,"diagramHeight":919,"inferred":false,"inDisease":false},{"dbId":9612973,"displayName":"Autophagy","stId":"R-HSA-9612973","name":["Autophagy"],"stIdVersion":"R-HSA-9612973.5","schemaClass":"TopLevelPathway","speciesName":"Homo sapiens","releaseDate":"2019-06-12","hasDiagram":true,"hasEHLD":true,"diagramWidth":626,"diagramHeight":338,"inferred":false,"inDisease":false}]]

e2e/har/05aca34ac87a652f042e90854db6f4367f958841.json

@@ -0,0 +1 @@
+[[{"dbId":6796648,"displayName":"TP53 Regulates Transcription of DNA Repair Genes","stId":"R-HSA-6796648","name":["TP53 Regulates Transcription of DNA Repair Genes"],"stIdVersion":"R-HSA-6796648.5","schemaClass":"Pathway","doi":"10.3180/r-hsa-6796648.1","speciesName":"Homo sapiens","releaseDate":"2016-03-23","hasDiagram":true,"hasEHLD":false,"diagramWidth":1633,"diagramHeight":1133,"inferred":false,"inDisease":false},{"dbId":3700989,"displayName":"Transcriptional Regulation by TP53","stId":"R-HSA-3700989","name":["Transcriptional Regulation by TP53"],"stIdVersion":"R-HSA-3700989.8","oldStId":"REACT_355048","schemaClass":"Pathway","doi":"10.3180/r-hsa-3700989.4","speciesName":"Homo sapiens","releaseDate":"2015-03-19","hasDiagram":true,"hasEHLD":true,"diagramWidth":687,"diagramHeight":414,"inferred":false,"inDisease":false},{"dbId":212436,"displayName":"Generic Transcription Pathway","stId":"R-HSA-212436","name":["Generic Transcription Pathway"],"stIdVersion":"R-HSA-212436.15","oldStId":"REACT_12627","schemaClass":"Pathway","doi":"10.3180/REACT_12627.1","speciesName":"Homo sapiens","releaseDate":"2008-03-12","releaseStatus":"UPDATED","hasDiagram":true,"hasEHLD":false,"diagramWidth":2027,"diagramHeight":1176,"inferred":false,"inDisease":false},{"dbId":73857,"displayName":"RNA Polymerase II Transcription","stId":"R-HSA-73857","name":["RNA Polymerase II Transcription"],"stIdVersion":"R-HSA-73857.7","oldStId":"REACT_1366","schemaClass":"Pathway","doi":"10.3180/REACT_1366.1","speciesName":"Homo sapiens","releaseDate":"2004-07-06","releaseStatus":"UPDATED","hasDiagram":true,"hasEHLD":false,"diagramWidth":2900,"diagramHeight":1308,"inferred":false,"inDisease":false},{"dbId":74160,"displayName":"Gene expression (Transcription)","stId":"R-HSA-74160","name":["Gene expression (Transcription)"],"stIdVersion":"R-HSA-74160.11","oldStId":"REACT_71","schemaClass":"TopLevelPathway","speciesName":"Homo sapiens","releaseDate":"2004-07-06","releaseStatus":"UPDATED","hasDiagram":true,"hasEHLD":true,"diagramWidth":1046,"diagramHeight":355,"inferred":false,"inDisease":false}]]

e2e/har/05e27cf8614d5b31e0cc31da3a6379fbd5274bf1.json

@@ -0,0 +1 @@
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e2e/har/099f8655314630f7253a04cd298a033f6b31c0dd.json

@@ -0,0 +1 @@
+{"dbId":8948464,"displayName":"BCL2L1 gene [nucleoplasm]","stId":"R-HSA-8948464","stIdVersion":"R-HSA-8948464.1","maxDepth":1,"name":["BCL2L1 gene"],"speciesName":"Homo sapiens","compartment":[{"dbId":7660,"displayName":"nucleoplasm","accession":"0005654","databaseName":"GO","definition":"\"That part of the nuclear content other than the chromosomes or the nucleolus.\" [GOC:ma, ISBN:0124325653]","name":"nucleoplasm","url":"https://www.ebi.ac.uk/QuickGO/term/GO:0005654","className":"Compartment","schemaClass":"Compartment"}],"species":{"dbId":48887,"displayName":"Homo sapiens","name":["Homo sapiens","H. sapiens","Hs","human","man"],"taxId":"9606","abbreviation":"HSA","className":"Species","schemaClass":"Species"},"endCoordinate":-1,"referenceType":"ReferenceDNASequence","startCoordinate":1,"referenceEntity":{"dbId":8948435,"displayName":"ENSEMBL:ENSG00000171552 BCL2L1","stId":"ensembl:ENSG00000171552","databaseName":"ENSEMBL","identifier":"ENSG00000171552","url":"https://www.ensembl.org/id/ENSG00000171552","moleculeType":"Entity","physicalEntity":[8948464],"geneName":["BCL2L1","BCL2L","BCLX"],"className":"ReferenceDNASequence","schemaClass":"ReferenceDNASequence"},"className":"DNA Sequence","inDisease":false,"schemaClass":"EntityWithAccessionedSequence"}

e2e/har/370408447dc9a5ccca6add7c924405f25253e44b.json → e2e/har/0bda11740362a49052b2ddcfe4152f6890f68b3b.json

@@ -1 +1 @@
-{"R-HSA-109581":{"dbId":10104642,"displayName":"Apoptosis","stId":"R-MMU-109581","stIdVersion":"R-MMU-109581.1","isInDisease":false,"isInferred":true,"maxDepth":7,"name":["Apoptosis"],"releaseDate":"2026-06-17","speciesName":"Mus musculus","hasDiagram":true,"hasEHLD":false,"schemaClass":"Pathway","className":"Pathway"},"R-HSA-109606":{"dbId":10104982,"displayName":"Intrinsic Pathway for Apoptosis","stId":"R-MMU-109606","stIdVersion":"R-MMU-109606.1","isInDisease":false,"isInferred":true,"maxDepth":6,"name":["Intrinsic Pathway for Apoptosis"],"releaseDate":"2026-06-17","speciesName":"Mus musculus","hasDiagram":true,"hasEHLD":false,"schemaClass":"Pathway","className":"Pathway"},"R-HSA-5357801":{"dbId":10104644,"displayName":"Programmed Cell Death","stId":"R-MMU-5357801","stIdVersion":"R-MMU-5357801.1","isInDisease":false,"isInferred":true,"maxDepth":8,"name":["Programmed Cell Death"],"releaseDate":"2026-06-17","speciesName":"Mus musculus","hasDiagram":true,"hasEHLD":false,"schemaClass":"TopLevelPathway","className":"TopLevelPathway"}}
+{"R-HSA-109581":{"dbId":10117572,"displayName":"Apoptosis","stId":"R-MMU-109581","stIdVersion":"R-MMU-109581.1","isInDisease":false,"isInferred":true,"maxDepth":7,"name":["Apoptosis"],"releaseDate":"2026-09-16","speciesName":"Mus musculus","hasDiagram":true,"hasEHLD":false,"schemaClass":"Pathway","className":"Pathway"},"R-HSA-109606":{"dbId":10117912,"displayName":"Intrinsic Pathway for Apoptosis","stId":"R-MMU-109606","stIdVersion":"R-MMU-109606.1","isInDisease":false,"isInferred":true,"maxDepth":6,"name":["Intrinsic Pathway for Apoptosis"],"releaseDate":"2026-09-16","speciesName":"Mus musculus","hasDiagram":true,"hasEHLD":false,"schemaClass":"Pathway","className":"Pathway"},"R-HSA-5357801":{"dbId":10117574,"displayName":"Programmed Cell Death","stId":"R-MMU-5357801","stIdVersion":"R-MMU-5357801.1","isInDisease":false,"isInferred":true,"maxDepth":8,"name":["Programmed Cell Death"],"releaseDate":"2026-09-16","speciesName":"Mus musculus","hasDiagram":true,"hasEHLD":false,"schemaClass":"TopLevelPathway","className":"TopLevelPathway"}}