Content-node specs that fail on wrong code; Java's index failures

tools/content-node/citation.spec.ts

@@ -285,18 +285,24 @@ describe('StaticCitation', () => {
 
 vi.mock('./graph.ts', async () => ({
   read: async (cypher, params) => {
-    if (cypher.includes('DBInfo')) return [{ version: 97 }];
-    globalThis.graphAsked = params;
-    return globalThis.graphRows ?? [];
+    // The release as the service reads it: releaseNumber, not another property.
+    if (cypher === 'MATCH (n:DBInfo) RETURN n.releaseNumber AS version LIMIT 1')
+      return [{ version: 97 }];
+    const shared = globalThis as { graphAsked?: unknown; graphRows?: unknown[] };
+    shared.graphAsked = params;
+    return shared.graphRows ?? [];
   },
   configured: () => true,
   close: async () => {},
   envSetting: (key, fallback = '') => process.env[key] || fallback,
 }));
 
+/** What the stand-in graph answers, and what it was last asked. */
+const graph = globalThis as { graphAsked?: unknown; graphRows?: unknown[] };
+
 describe('the citation endpoints', () => {
-  let base;
-  let server;
+  let base: string;
+  let server: Server;
   let pmc: Server;
   let pmcAsked: (string | undefined)[] = [];
 
@@ -343,11 +349,11 @@ describe('the citation endpoints', () => {
   });
 
   it('/pathway/{id} is {} for an id that is no event, and export an empty 200', async () => {
-    globalThis.graphRows = [];
+    graph.graphRows = [];
     const pathway = await fetch(`${base}/ContentService/citation/pathway/R-HSA-9?dateAccessed=d`);
     expect([pathway.status, await pathway.text()]).toEqual([200, '{}']);
     // The id from the path, not the path's own words.
-    expect(globalThis.graphAsked).toEqual({ id: 'R-HSA-9' });
+    expect(graph.graphAsked).toEqual({ id: 'R-HSA-9' });
     const exported = await fetch(
       `${base}/ContentService/citation/export?isPathway=true&id=xyz&ext=bib&dateAccessed=d`
     );
@@ -358,6 +364,74 @@ describe('the citation endpoints', () => {
     ]);
   });
 
+  // An event as graph-core's enhanced query loads it, with nothing related.
+  const eventRow = (schemaClass: string, labels: string[]) => ({
+    root: {
+      id: 1,
+      labels: ['DatabaseObject', 'Event', ...labels],
+      props: {
+        dbId: 9,
+        stId: 'R-HSA-9',
+        displayName: 'An event',
+        releaseDate: '2020-06-15',
+        doi: '10.3180/R-HSA-9.1',
+        schemaClass,
+      },
+    },
+    order: [],
+    nodes: [],
+    relationships: [],
+  });
+
+  it("/pathway/{id} cites the event by the id as given; only a pathway's by its DOI", async () => {
+    try {
+      graph.graphRows = [eventRow('Pathway', ['Pathway'])];
+      const pathway = await (
+        await fetch(`${base}/ContentService/citation/pathway/9?dateAccessed=d`)
+      ).json();
+      // Asked by a versioned stable id, neither its stId nor its dbId: the
+      // link names the id as given.
+      graph.graphRows = [eventRow('Reaction', ['ReactionLikeEvent', 'Reaction'])];
+      const reaction = await (
+        await fetch(`${base}/ContentService/citation/pathway/R-HSA-9.1?dateAccessed=d`)
+      ).json();
+      expect([pathway, reaction]).toEqual([
+        {
+          imageCitation:
+            'Image Citation for An event. Reactome, 97, https://doi.org/10.3180/R-HSA-9.1 (d)',
+          pathwayCitation:
+            'The Reactome Consortium (2020). An event. Reactome, 97, https://doi.org/10.3180/R-HSA-9.1 (d)',
+        },
+        {
+          imageCitation:
+            'Image Citation for An event. Reactome, 97, https://reactome.org/content/detail/R-HSA-9.1 (d)',
+          pathwayCitation:
+            'The Reactome Consortium (2020). An event. Reactome, 97, https://reactome.org/content/detail/R-HSA-9.1 (d)',
+        },
+      ]);
+    } finally {
+      graph.graphRows = [];
+    }
+  });
+
+  it('export writes each format as its own type and extension', async () => {
+    for (const [ext, type, extension] of [
+      ['bib', 'application/x-bibtex; charset=utf-8', 'bib'],
+      ['ris', 'application/x-research-info-systems; charset=utf-8', 'ris'],
+      ['txt', 'text/plain; charset=utf-8', 'txt'],
+    ]) {
+      const response = await fetch(
+        `${base}/ContentService/citation/export?isPathway=false&id=12345&ext=${ext}&dateAccessed=d`
+      );
+      expect([
+        ext,
+        response.status,
+        response.headers.get('content-type'),
+        response.headers.get('content-disposition'),
+      ]).toEqual([ext, 200, type, `attachment; filename="reactome_citation_12345.${extension}"`]);
+    }
+  });
+
   it('/static/{id} is "unable to fetch" for an answer Java cannot read', async () => {
     globalThis.pmcAnswer = { resultList: { result: [{ ...europePmc, journalInfo: [] }] } };
     try {
@@ -474,7 +548,7 @@ describe('the citation endpoints', () => {
 
   it("/pathway/{id} is Java's 500 for an event it cannot cite", async () => {
     // A reaction with no release date: Java's getReleaseDate().substring NPEs.
-    globalThis.graphRows = [
+    graph.graphRows = [
       {
         root: {
           id: 1,
@@ -494,7 +568,7 @@ describe('the citation endpoints', () => {
         ['Something unexpected happened and the error has been reported.'],
       ]);
     } finally {
-      globalThis.graphRows = [];
+      graph.graphRows = [];
     }
   });
 

tools/content-node/contained-events.spec.mjs

@@ -44,8 +44,14 @@ vi.mock('./graph.ts', () => ({
     asked.push([cypher, params]);
     if (cypher.includes('[r:hasEvent*1..100]'))
       return params.stId === 'R-HSA-100' || params.dbId ? (records ?? RECORDS) : [];
-    for (const [type, rows] of Object.entries(lazy))
-      if (cypher.includes(`[r:${type}]`)) return rows;
+    // A lazy load by what it asks: `${type} ${direction} ${dbId}`, so one in
+    // the wrong direction, or of another event, finds nothing.
+    const load = /\{dbId:\$dbId\}\)(<-|-)\[r:(\w+)\](->|-)/.exec(cypher);
+    if (load)
+      return (
+        lazy[`${load[2]} ${load[1] === '<-' ? 'INCOMING' : 'OUTGOING'} ${Number(params.dbId)}`] ??
+        []
+      );
     return [];
   },
   configured: () => true,
@@ -113,22 +119,24 @@ describe('/data/pathway/{id}/containedEvents/{attributeName}', () => {
     expect(await response.text()).toBe('[R-HSA-200, R-HSA-300]');
   });
 
-  it('loads what findAll did not bring, outgoing relationships too', async () => {
-    lazy = {
-      compartment: [
-        {
-          m: {
-            id: 9,
-            labels: ['DatabaseObject', 'Compartment'],
-            props: { dbId: 70101, displayName: 'cytosol', schemaClass: 'Compartment' },
-          },
-          n: null,
+  it("loads what findAll did not bring, outgoing relationships too, each event's own", async () => {
+    const compartment = (id, dbId, displayName) => [
+      {
+        m: {
+          id,
+          labels: ['DatabaseObject', 'Compartment'],
+          props: { dbId, displayName, schemaClass: 'Compartment' },
         },
-      ],
+        n: null,
+      },
+    ];
+    lazy = {
+      'compartment OUTGOING 200': compartment(9, 70101, 'cytosol'),
+      'compartment OUTGOING 300': compartment(10, 7660, 'nucleoplasm'),
     };
     const response = await get('R-HSA-100/containedEvents/compartment');
     expect(await response.text()).toBe(
-      '[70101\tcytosol\tCompartment\n, 70101\tcytosol\tCompartment\n]'
+      '[70101\tcytosol\tCompartment\n, 7660\tnucleoplasm\tCompartment\n]'
     );
     lazy = {};
   });

tools/content-node/diagram-search.spec.mjs

@@ -15,7 +15,13 @@ const objects = {
 };
 
 vi.mock('./graph.ts', () => ({
-  read: async (_cypher, params) => (objects[params.id] ? [objects[params.id]] : []),
+  // Only the object check as the service writes it: a wrong property (a
+  // diagram flag read from hasEHLD, say) finds nothing.
+  read: async (cypher, params) =>
+    cypher.includes('RETURN labels(n) AS labels, n.hasDiagram AS hasDiagram LIMIT 1') &&
+    objects[params.id]
+      ? [objects[params.id]]
+      : [],
   configured: () => true,
   close: async () => {},
   envSetting: (key, fallback = '') => process.env[key] || fallback,
@@ -254,9 +260,23 @@ describe('/diagram/{diagram}/occurrences/{instance}', () => {
     });
     const none = await get('diagram/R-HSA-68886/occurrences/R-HSA-141433');
     expect(await none.text()).toBe('{"diagramEntity":"R-HSA-68886","inDiagram":false}');
-    answer = () => ({ response: { numFound: 1, docs: [{ occurrences: ['R-HSA-68886:true:x'] }] } });
-    const short = await get('diagram/R-HSA-68886/occurrences/R-HSA-141433');
-    expect(short.status).toBe(500);
+    // Java's ArrayIndexOutOfBoundsException, with its own message
+    // (GlobalExceptionHandler.handleUnclassified): extractRawOccurrence reads
+    // [0], [2], [3], then [1], so three parts fail at 3, two at 2 -- and
+    // one at 2, not 1: the order is Java's, not the parts'.
+    for (const [occurrence, message] of [
+      ['R-HSA-68886:true:x', 'Index 3 out of bounds for length 3'],
+      ['R-HSA-68886:true', 'Index 2 out of bounds for length 2'],
+      ['R-HSA-68886', 'Index 2 out of bounds for length 1'],
+    ]) {
+      answer = () => ({ response: { numFound: 1, docs: [{ occurrences: [occurrence] }] } });
+      const short = await get('diagram/R-HSA-68886/occurrences/R-HSA-141433');
+      expect([occurrence, short.status, (await short.json()).messages]).toEqual([
+        occurrence,
+        500,
+        [message],
+      ]);
+    }
   });
 
   it('asks again in every scope, then is the 404', async () => {

tools/content-node/discover.spec.mjs

@@ -209,7 +209,9 @@ const graph =
     if (/AS related/.test(cypher))
       return [{ labels: (load[0] ?? LOADED).root.labels, related: load.length > 0 }];
     if (/MATCH \(n\)-\[r\]-\(m\)/.test(cypher)) return load;
-    if (/DBInfo/.test(cypher)) return [{ version: 97 }];
+    // The release as the service reads it: releaseNumber, not another property.
+    if (cypher === 'MATCH (n:DBInfo) RETURN n.releaseNumber AS version LIMIT 1')
+      return [{ version: 97 }];
     // The edit's author, with no stoichiometry on the relationship: once.
     if (/<-\[r:author\]-/.test(cypher) && Number(params.dbId) === 8)
       return [{ m: { dbId: 20, surname: 'Roe' }, n: null }];
@@ -285,5 +287,12 @@ describe("/data/discover/{identifier}: Java's errors", () => {
     const load = asked.find((cypher) => /MATCH \(n\)-\[r\]-\(m\)/.test(cypher));
     expect(load).toBeDefined();
     expect(load).not.toMatch(/ORDER BY|OPTIONAL/);
+    // The object by the id asked, and the three columns mapResult reads.
+    expect(load?.replace(/\s+/g, ' ')).toBe(
+      'MATCH (n:DatabaseObject) WHERE n.stId = $id WITH n LIMIT 1 MATCH (n)-[r]-(m) ' +
+        'RETURN {id: id(n), labels: labels(n), props: properties(n)} AS root, ' +
+        'COLLECT({id: id(r), type: type(r), start: id(startNode(r)), end: id(endNode(r)), props: properties(r)}) AS relationships, ' +
+        'COLLECT({id: id(m), labels: labels(m), props: properties(m)}) AS nodes'
+    );
   });
 });

tools/content-node/flag.spec.mjs

@@ -20,8 +20,15 @@ const species = {
 
 vi.mock('./graph.ts', () => ({
   read: async (cypher, params) => {
-    if (cypher.includes(':Species')) return [species[params.name] ?? []].flat();
-    return objects[params.id] ? [objects[params.id]] : [];
+    // Only the queries as the service writes them: the species by exact
+    // name among its names, and the object check reading hasDiagram.
+    if (cypher.includes(':Species'))
+      return cypher.includes('MATCH (n:Species) WHERE $name IN n.name RETURN')
+        ? [species[params.name] ?? []].flat()
+        : [];
+    return cypher.includes('n.hasDiagram AS hasDiagram') && objects[params.id]
+      ? [objects[params.id]]
+      : [];
   },
   configured: () => true,
   close: async () => {},
@@ -127,6 +134,18 @@ describe('/diagram/{pathwayId}/flag', () => {
     ]);
   });
 
+  it("is Java's index failure for an occurrence of fewer than four parts", async () => {
+    // extractRawOccurrence reads [0], [2], [3], then [1]: two parts fail at 2.
+    answer = () => ({
+      response: { numFound: 1, docs: [{ stId: 'R-HSA-9', occurrences: ['R-HSA-446203:true'] }] },
+    });
+    const response = await get('diagram/R-HSA-446203/flag?query=CTSA');
+    expect([response.status, (await response.json()).messages]).toEqual([
+      500,
+      ['Index 2 out of bounds for length 2'],
+    ]);
+  });
+
   it('flags through interactors when asked, and is the 404 for nothing', async () => {
     asked = [];
     answer = () => ({ response: { numFound: 0, docs: [] } });
@@ -147,6 +166,9 @@ describe('/diagram/{pathwayId}/flag', () => {
     expect([bad.status, (await bad.json()).messages]).toEqual([400, ["'xyz' cannot be found"]]);
     const blank = await get('diagram/R-HSA-446203/flag?query=CTSA&includeInteractors=%20');
     expect(blank.status).toBe(500);
+    expect((await blank.json()).messages).toEqual([
+      'Something unexpected happened and the error has been reported.',
+    ]);
     expect(asked).toHaveLength(0);
   });
 });
@@ -214,10 +236,24 @@ describe('/fireworks/flag', () => {
     ]);
   });
 
-  it("is Java's failure, not a guess, when two Species share the name", async () => {
+  it('is a failure, before Solr is asked, when two Species share the name', async () => {
     asked = [];
     const response = await get('fireworks/flag?query=x&species=Twice');
+    // Status only: Java's message here is Spring Data's
+    // IncorrectResultSizeDataAccessException, which has not been measured.
     expect(response.status).toBe(500);
     expect(asked).toHaveLength(0);
   });
+
+  it("is Java's index failure for an occurrence of fewer than four parts", async () => {
+    // fireworksFlagging reads [0], then [3]: one part fails at 3, not 1.
+    answer = () => ({
+      response: { numFound: 1, docs: [{ llps: ['R-HSA-1'], occurrences: ['R-HSA-1'] }] },
+    });
+    const response = await get('fireworks/flag?query=x&species=Mus%20musculus');
+    expect([response.status, (await response.json()).messages]).toEqual([
+      500,
+      ['Index 3 out of bounds for length 1'],
+    ]);
+  });
 });

tools/content-node/icon.spec.mjs

@@ -83,7 +83,10 @@ describe('searchEntry, as SolrConverter.buildEntry builds an Entry', () => {
   });
 
   it('fails, as Java does, on an entity with fewer than four parts', () => {
-    expect(() => searchEntry({ ...icon, iconPhysicalEntities: ['a#b#c#'] }, {})).toThrow();
+    // Its ArrayIndexOutOfBoundsException: read [0] to [3], three parts fail at 3.
+    expect(() => searchEntry({ ...icon, iconPhysicalEntities: ['a#b#c#'] }, {})).toThrow(
+      expect.objectContaining({ javaMessage: 'Index 3 out of bounds for length 3' })
+    );
   });
 
   it('id is the stId when there is one, else the dbId', () => {