Port /data/entity/{id}/componentOf to content-node

deploy/nginx/common/routes-core.conf

@@ -381,11 +381,13 @@ location ~ ^/ContentService/data/participants/[^/]+/?$ {
 }
 
 # The other forms of a physical entity -- the same reference entity, modified,
-# elsewhere or in another species. Java's query kept as written; nothing found
-# is Java's 404. Byte-identical to Java over 25 ids covering every class that
-# appears (EWAS by reference type, simple entities, drugs), bar a 404 body's
-# url, as above. /entity/{id}/in-depth and the rest stay with Java.
-location ~ ^/ContentService/data/entity/[^/]+/otherForms/?$ {
+# elsewhere or in another species -- and what an entity or event is part of
+# (/componentOf). Java's queries kept as written; nothing found is Java's 404.
+# otherForms byte-identical to Java over 25 ids covering every class that
+# appears (EWAS by reference type, simple entities, drugs); componentOf over
+# 21, ATP's megabyte, every id form, events and every class of entity among
+# them; both bar a 404 body's url, as above. /entity/{id}/in-depth is above.
+location ~ ^/ContentService/data/entity/[^/]+/(otherForms|componentOf)/?$ {
     include /etc/nginx/common/content-node-proxy.conf;
 }
 

projects/website-angular/src/scripts/proxy-order.spec.ts

@@ -142,9 +142,15 @@ describe('the dev server proxy', () => {
     });
   }
 
-  it('sends the other forms of an entity to the content service', async () => {
-    await expectContentNode('/ContentService/data/entity/R-HSA-199420/otherForms');
-  });
+  for (const url of [
+    '/ContentService/data/entity/R-HSA-199420/otherForms',
+    '/ContentService/data/entity/R-HSA-199420/componentOf',
+    '/ContentService/data/entity/199420/componentOf/',
+  ]) {
+    it(`sends ${url} to the content service`, async () => {
+      await expectContentNode(url);
+    });
+  }
 
   for (const url of [
     '/ContentService/data/database/version',
@@ -321,8 +327,8 @@ describe('the dev server proxy', () => {
     '/ContentService/data/complexes/UniProt/P00533/x',
     // Only the participants and their reference entities are ported.
     '/ContentService/data/participants/R-HSA-5672965/participatingPhysicalEntities',
-    // Only the other forms and in-depth of an entity are ported.
-    '/ContentService/data/entity/R-HSA-199420/componentOf',
+    // Only these of an entity are ported: not a path below them.
+    '/ContentService/data/entity/R-HSA-199420/componentOf/x',
     // Only the locations are ported, not their neighbours under /detail.
     '/ContentService/data/detail/R-HSA-199420/getReverseGraph',
     '/ContentService/data/detail/R-HSA-109581/getSubGraph',

proxy.conf.js

@@ -186,7 +186,8 @@ module.exports = {
   '^/ContentService/data/database/(version|name)/?(\\?|$)': contentNode,
   '^/ContentService/data/pathways/top/[^/?]+/?(\\?|$)': contentNode,
   // The other forms of a physical entity: the details panel and the popup.
-  '^/ContentService/data/entity/[^/?]+/otherForms/?(\\?|$)': contentNode,
+  // What an entity or event is part of: the details page's table.
+  '^/ContentService/data/entity/[^/?]+/(otherForms|componentOf)/?(\\?|$)': contentNode,
   // Every place an object appears in the Pathway Browser: the details page's
   // locations tree. Only this one of Java's /data/detail/{id}/... paths.
   '^/ContentService/data/detail/[^/?]+/locationsInPWB/?(\\?|$)': contentNode,

specs/006-content-service-to-node/tasks.md

@@ -81,7 +81,7 @@ Each port follows the eight steps in [plan.md](plan.md#how-one-endpoint-is-porte
 - [x] T074 `GET /data/schema/{className}` — #511
 - [x] T074b `GET /data/schema/{className}/reference` — #512
 - [x] T075 `GET /data/complex/{id}/subunits`, `GET /data/complexes/{resource}/{identifier}` — #514
-- [ ] T076 `GET /data/entity/{id}/componentOf`
+- [x] T076 `GET /data/entity/{id}/componentOf` — #515
 - [ ] T077 `GET /data/participants/{id}/participatingPhysicalEntities`
 - [ ] T078 `GET /data/pathway/{id}/containedEvents`, `GET /data/pathway/{id}/containedEvents/{attributeName}` — Java maps the whole hasEvent subgraph into Events (Neo4jTemplate.findAll over `RETURN e, COLLECT(r), COLLECT(p)`), and `{attributeName}` reads a getter by reflection: do with T070/T072's getter table
 - [x] T079 `GET /data/pathways/low/entity/{id}/allForms`, `GET /data/pathways/low/diagram/entity/{id}`, `GET /data/pathways/low/diagram/entity/{id}/allForms` — #513

specs/010-java-services/contracts/operation-homes.md

@@ -28,7 +28,7 @@ The decision record of FR-001 and FR-002. It covers every operation in the two s
 | GET    | `/data/discover/{identifier}`                             | node — to port         | graph or search index                                                                         |
 | GET    | `/data/diseases`                                          | node — to port         | graph or search index                                                                         |
 | GET    | `/data/diseases/doid`                                     | node — to port         | graph or search index                                                                         |
-| GET    | `/data/entity/{id}/componentOf`                           | node — to port         | graph or search index                                                                         |
+| GET    | `/data/entity/{id}/componentOf`                           | node — ported          | graph or search index                                                                         |
 | GET    | `/data/entity/{id}/in-depth`                              | node — ported          | graph or search index                                                                         |
 | GET    | `/data/entity/{id}/otherForms`                            | node — ported          | graph or search index                                                                         |
 | GET    | `/data/event/{id}/ancestors`                              | node — ported          | graph or search index                                                                         |

tools/content-node/component-of.spec.mjs

@@ -0,0 +1,116 @@
+// @vitest-environment node
+//
+// /data/entity/{id}/componentOf -- what an entity or event is part of: the
+// complexes, sets and reactions above it, grouped by the relationship -- with
+// a stand-in graph. PhysicalEntityController over graph-core's
+// ComponentOfLinkageRepository, whose query is kept as written; rows come in
+// the order Neo4j gives them, unsorted, as in Java. The rows here are invented.
+import { afterAll, beforeAll, describe, expect, it, vi } from 'vitest';
+
+const asked = [];
+let rows = [];
+vi.mock('./graph.mjs', () => ({
+  read: async (cypher, params) => {
+    asked.push([cypher, params]);
+    return rows;
+  },
+  configured: () => true,
+  close: async () => {},
+  envSetting: () => '',
+}));
+
+const { app } = await import('./service.mjs');
+
+let base;
+let server;
+beforeAll(async () => {
+  await new Promise((resolve) => {
+    server = app().listen(0, '127.0.0.1', resolve);
+  });
+  base = `http://127.0.0.1:${server.address().port}`;
+});
+afterAll(() => new Promise((resolve) => server.close(resolve)));
+
+const get = (id) => fetch(`${base}/ContentService/data/entity/${id}/componentOf`);
+const last = () => asked[asked.length - 1];
+const oneLine = (cypher) => cypher.replace(/\s+/g, ' ').trim();
+
+describe('/data/entity/{id}/componentOf', () => {
+  it("runs graph-core's query as written and writes each group as Java does", async () => {
+    rows = [
+      {
+        type: 'output',
+        schemaClasses: ['Reaction', ''],
+        names: ['B', 'A'],
+        stIds: ['R-HSA-2', ''],
+        species: ['Homo sapiens', ''],
+      },
+      {
+        type: 'hasComponent',
+        schemaClasses: ['Complex'],
+        names: ['C'],
+        stIds: ['R-HSA-3'],
+        species: ['Homo sapiens'],
+      },
+    ];
+    asked.length = 0;
+    const response = await get('R-HSA-1');
+    expect(await response.text()).toBe(
+      '[{"type":"output","names":["B","A"],"stIds":["R-HSA-2",""],"schemaClasses":["Reaction",""],"species":["Homo sapiens",""]},' +
+        '{"type":"hasComponent","names":["C"],"stIds":["R-HSA-3"],"schemaClasses":["Complex"],"species":["Homo sapiens"]}]'
+    );
+    expect(oneLine(last()[0])).toBe(
+      "MATCH (n:DatabaseObject{stId: $id})<-[r:hasEvent|input|output|hasComponent|hasMember|hasCandidate|repeatedUnit|proteinMarker|RNAMarker]-(m) RETURN DISTINCT(TYPE(r)) AS type, COLLECT(COALESCE(m.schemaClass, '')) AS schemaClasses, COLLECT(COALESCE(m.displayName, '')) AS names, COLLECT(COALESCE(m.stId, '')) AS stIds, COLLECT(COALESCE(m.speciesName, '')) as species"
+    );
+    expect(last()[1]).toEqual({ id: 'R-HSA-1' });
+  });
+
+  it('reads the id as Spring reads a path variable: decoded, a matrix parameter cut', async () => {
+    rows = [
+      {
+        type: 'input',
+        schemaClasses: ['Reaction'],
+        names: ['A'],
+        stIds: ['R-HSA-2'],
+        species: ['H'],
+      },
+    ];
+    asked.length = 0;
+    await get('R-HSA-69620;x=1');
+    expect(last()[1]).toEqual({ id: 'R-HSA-69620' });
+  });
+
+  it('matches a dbId as a number', async () => {
+    rows = [
+      {
+        type: 'input',
+        schemaClasses: ['Reaction'],
+        names: ['A'],
+        stIds: ['R-HSA-2'],
+        species: ['H'],
+      },
+    ];
+    asked.length = 0;
+    await get('199420');
+    expect(oneLine(last()[0])).toMatch(/^MATCH \(n:DatabaseObject\{dbId: toInteger\(\$id\)\}\)<-/);
+  });
+
+  it('is a 404 naming the id, for one that is neither or is part of nothing', async () => {
+    rows = [];
+    for (const id of ['xyz', 'R-HSA-162582']) {
+      const response = await get(id);
+      const body = await response.json();
+      expect([id, response.status, body]).toEqual([
+        id,
+        404,
+        {
+          code: 404,
+          reason: 'NOT_FOUND',
+          url: expect.stringMatching(/\/componentOf$/),
+          messages: [`Id: ${id} has not been found in the System`],
+          targets: null,
+        },
+      ]);
+    }
+  });
+});

tools/content-node/service.mjs

@@ -1310,6 +1310,52 @@ export const endpoints = [
       };
     },
   },
+  {
+    path: '/ContentService/data/entity/{id}/componentOf',
+    // PTEN: the reactions it comes out of and goes into, and the complexes and
+    // sets it is part of.
+    sample: 'R-HSA-199420',
+    differs: [/^\/ContentService\/data\/entity\/[^/]+\/componentOf: \.url: /],
+    /**
+     * What an entity or event is directly part of -- the reactions, complexes,
+     * sets and pathways above it -- one group per relationship, each with the
+     * names, stable ids, classes and species of its members, '' for what one
+     * lacks. The details page's "Component of" table.
+     *
+     * graph-core's ComponentOfLinkageRepository.getComponentsOf, kept as
+     * written: the groups and their members come in the order Neo4j gives
+     * them, unsorted (ComponentOf.sortByName is never called). The id is read as graph-core reads it
+     * (graphCoreId); none found, or part of nothing, is Java's 404.
+     */
+    handler: async (request) => {
+      const raw = pathId(rawSegment(request, 4));
+      const missing = () => notFound(request, `Id: ${raw} has not been found in the System`);
+      const id = await graphCoreId(raw);
+      if (!id) return missing();
+      const rows = await read(
+        `MATCH (n:DatabaseObject${id.object})<-[r:hasEvent|input|output|hasComponent|hasMember|hasCandidate|repeatedUnit|proteinMarker|RNAMarker]-(m)
+         RETURN DISTINCT(TYPE(r)) AS type,
+                COLLECT(COALESCE(m.schemaClass, '')) AS schemaClasses,
+                COLLECT(COALESCE(m.displayName, '')) AS names,
+                COLLECT(COALESCE(m.stId, '')) AS stIds,
+                COLLECT(COALESCE(m.speciesName, '')) as species`,
+        id.params
+      );
+      if (rows.length === 0) return missing();
+      return {
+        status: 200,
+        // ComponentOf's fields in declaration order; none is ever empty.
+        body: rows.map(({ type, names, stIds, schemaClasses, species }) => ({
+          type,
+          names,
+          stIds,
+          schemaClasses,
+          species,
+        })),
+        type: 'application/json',
+      };
+    },
+  },
   {
     path: '/ContentService/data/complex/{id}/subunits',
     // A set: 354 entities under it -- complexes, sets, proteins and small molecules.