diff --git a/examples/schemas/biosamples-schema.json b/examples/schemas/biosamples-schema.json index 0e2f312..2765180 100644 --- a/examples/schemas/biosamples-schema.json +++ b/examples/schemas/biosamples-schema.json @@ -1,5 +1,6 @@ { "$schema": "http://json-schema.org/draft-07/schema#", + "$id": "test/biosamples/schema", "title": "Sample", "description": "A BioSamples sample.", diff --git a/package-lock.json b/package-lock.json index 6b157f0..25d0803 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,6 +11,7 @@ "dependencies": { "ajv": "~7.2.1", "ajv-formats": "^1.5.1", + "canvas": "^2.8.0", "express": "^4.17.1", "glob": "^8.0.3", "npid": "^0.4.0", @@ -27,6 +28,7 @@ "bufferutil": "^4.0.2", "jest": "^26.6.0", "nodemon": "^2.0.6", + "supertest": "^6.3.3", "ts-node": "^9.1.0", "typescript": "^4.1.2", "utf-8-validate": "^5.0.3" @@ -897,9 +899,6 @@ "version": "1.0.8", "resolved": "https://registry.npmjs.org/@mapbox/node-pre-gyp/-/node-pre-gyp-1.0.8.tgz", "integrity": "sha512-CMGKi28CF+qlbXh26hDe6NxCd7amqeAzEqnS6IHeO6LoaKyM/n+Xw3HT1COdq8cuioOdlKdqn/hCmqPUOMOywg==", - 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"dev": true, - "optional": true, - "peer": true, "requires": { "minipass": "^3.0.0", "yallist": "^4.0.0" @@ -12435,10 +12587,7 @@ "mkdirp": { "version": "1.0.4", "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-1.0.4.tgz", - "integrity": "sha512-vVqVZQyf3WLx2Shd0qJ9xuvqgAyKPLAiqITEtqW0oIUjzo3PePDd6fW9iFz30ef7Ysp/oiWqbhszeGWW2T6Gzw==", - "dev": true, - "optional": true, - "peer": true + "integrity": "sha512-vVqVZQyf3WLx2Shd0qJ9xuvqgAyKPLAiqITEtqW0oIUjzo3PePDd6fW9iFz30ef7Ysp/oiWqbhszeGWW2T6Gzw==" }, "moment": { "version": "2.29.4", @@ -12453,10 +12602,7 @@ "nan": { "version": "2.15.0", "resolved": "https://registry.npmjs.org/nan/-/nan-2.15.0.tgz", - "integrity": "sha512-8ZtvEnA2c5aYCZYd1cvgdnU6cqwixRoYg70xPLWUws5ORTa/lnw+u4amixRS/Ac5U5mQVgp9pnlSUnbNWFaWZQ==", - "dev": true, - "optional": true, - "peer": true + "integrity": "sha512-8ZtvEnA2c5aYCZYd1cvgdnU6cqwixRoYg70xPLWUws5ORTa/lnw+u4amixRS/Ac5U5mQVgp9pnlSUnbNWFaWZQ==" }, "nanomatch": { "version": "1.2.13", @@ -12498,9 +12644,6 @@ "version": "2.6.7", "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz", "integrity": "sha512-ZjMPFEfVx5j+y2yF35Kzx5sF7kDzxuDj6ziH4FFbOp87zKDZNx8yExJIb05OGF4Nlt9IHFIMBkRl41VdvcNdbQ==", - 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"integrity": "sha512-VUJ49FC8U1OxwZLxIbTTrDvLnf/6TDgxZcK8wxR8zs13xpx7xbG60ndBlhNrFi2EMuFRoeDoJO7wthSLq42EjA==", - "dev": true + "integrity": "sha512-VUJ49FC8U1OxwZLxIbTTrDvLnf/6TDgxZcK8wxR8zs13xpx7xbG60ndBlhNrFi2EMuFRoeDoJO7wthSLq42EjA==" }, "simple-concat": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/simple-concat/-/simple-concat-1.0.1.tgz", - "integrity": "sha512-cSFtAPtRhljv69IK0hTVZQ+OfE9nePi/rtJmw5UjHeVyVroEqJXP1sFztKUy1qU+xvz3u/sfYJLa947b7nAN2Q==", - "dev": true, - "optional": true, - "peer": true + "integrity": "sha512-cSFtAPtRhljv69IK0hTVZQ+OfE9nePi/rtJmw5UjHeVyVroEqJXP1sFztKUy1qU+xvz3u/sfYJLa947b7nAN2Q==" }, "simple-get": { "version": "3.1.1", "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.1.tgz", "integrity": "sha512-CQ5LTKGfCpvE1K0n2us+kuMPbk/q0EKl82s4aheV9oXjFEz6W/Y7oQFVJuU6QG77hRT4Ghb5RURteF5vnWjupA==", - "dev": true, - "optional": true, - "peer": true, "requires": { "decompress-response": "^4.2.0", "once": "^1.3.1", @@ -13664,9 +13798,6 @@ "version": "4.2.1", "resolved": "https://registry.npmjs.org/decompress-response/-/decompress-response-4.2.1.tgz", "integrity": "sha512-jOSne2qbyE+/r8G1VU+G/82LBs2Fs4LAsTiLSHOCOMZQl2OKZ6i8i4IyHemTe+/yIXOtTcRQMzPcgyhoFlqPkw==", - "dev": true, - "optional": true, - "peer": true, "requires": { "mimic-response": "^2.0.0" } @@ -13674,10 +13805,7 @@ "mimic-response": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/mimic-response/-/mimic-response-2.1.0.tgz", - "integrity": "sha512-wXqjST+SLt7R009ySCglWBCFpjUygmCIfD790/kVbiGmUgfYGuB14PiTd5DwVxSV4NcYHjzMkoj5LjQZwTQLEA==", - "dev": true, - "optional": true, - "peer": true + "integrity": "sha512-wXqjST+SLt7R009ySCglWBCFpjUygmCIfD790/kVbiGmUgfYGuB14PiTd5DwVxSV4NcYHjzMkoj5LjQZwTQLEA==" } } }, @@ -14049,6 +14177,95 @@ "integrity": "sha512-BrpvfNAE3dcvq7ll3xVumzjKjZQ5tI1sEUIKr3Uoks0XUl45St3FlatVqef9prk4jRDzhW6WZg+3bk93y6pLjA==", "dev": true }, + "superagent": { + "version": "8.0.9", + "resolved": "https://registry.npmjs.org/superagent/-/superagent-8.0.9.tgz", + "integrity": "sha512-4C7Bh5pyHTvU33KpZgwrNKh/VQnvgtCSqPRfJAUdmrtSYePVzVg4E4OzsrbkhJj9O7SO6Bnv75K/F8XVZT8YHA==", + "dev": true, + "requires": { + "component-emitter": "^1.3.0", + "cookiejar": "^2.1.4", + "debug": "^4.3.4", + "fast-safe-stringify": "^2.1.1", + "form-data": "^4.0.0", + "formidable": "^2.1.2", + "methods": "^1.1.2", + "mime": "2.6.0", + "qs": "^6.11.0", + "semver": "^7.3.8" + }, + "dependencies": { + "combined-stream": { + "version": "1.0.8", + "resolved": "https://registry.npmjs.org/combined-stream/-/combined-stream-1.0.8.tgz", + "integrity": "sha512-FQN4MRfuJeHf7cBbBMJFXhKSDq+2kAArBlmRBvcvFE5BB1HZKXtSFASDhdlz9zOYwxh8lDdnvmMOe/+5cdoEdg==", + "dev": true, + "requires": { + "delayed-stream": "~1.0.0" + } + }, + "debug": { + "version": "4.3.4", + "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.4.tgz", + "integrity": "sha512-PRWFHuSU3eDtQJPvnNY7Jcket1j0t5OuOsFzPPzsekD52Zl8qUfFIPEiswXqIvHWGVHOgX+7G/vCNNhehwxfkQ==", + "dev": true, + "requires": { + "ms": "2.1.2" + } + }, + "form-data": { + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/form-data/-/form-data-4.0.0.tgz", + "integrity": "sha512-ETEklSGi5t0QMZuiXoA/Q6vcnxcLQP5vdugSpuAyi6SVGi2clPPp+xgEhuMaHC+zGgn31Kd235W35f7Hykkaww==", + "dev": true, + "requires": { + "asynckit": "^0.4.0", + "combined-stream": "^1.0.8", + "mime-types": "^2.1.12" + } + }, + "mime": { + "version": "2.6.0", + "resolved": "https://registry.npmjs.org/mime/-/mime-2.6.0.tgz", + "integrity": "sha512-USPkMeET31rOMiarsBNIHZKLGgvKc/LrjofAnBlOttf5ajRvqiRA8QsenbcooctK6d6Ts6aqZXBA+XbkKthiQg==", + "dev": true + }, + "ms": { + "version": "2.1.2", + "resolved": "https://registry.npmjs.org/ms/-/ms-2.1.2.tgz", + "integrity": "sha512-sGkPx+VjMtmA6MX27oA4FBFELFCZZ4S4XqeGOXCv68tT+jb3vk/RyaKWP0PTKyWtmLSM0b+adUTEvbs1PEaH2w==", + "dev": true + }, + "qs": { + "version": "6.11.0", + "resolved": "https://registry.npmjs.org/qs/-/qs-6.11.0.tgz", + "integrity": "sha512-MvjoMCJwEarSbUYk5O+nmoSzSutSsTwF85zcHPQ9OrlFoZOYIjaqBAJIqIXjptyD5vThxGq52Xu/MaJzRkIk4Q==", + "dev": true, + "requires": { + "side-channel": "^1.0.4" + } + }, + "semver": { + "version": "7.3.8", + "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.8.tgz", + "integrity": "sha512-NB1ctGL5rlHrPJtFDVIVzTyQylMLu9N9VICA6HSFJo8MCGVTMW6gfpicwKmmK/dAjTOrqu5l63JJOpDSrAis3A==", + "dev": true, + "requires": { + "lru-cache": "^6.0.0" + } + } + } + }, + "supertest": { + "version": "6.3.3", + "resolved": "https://registry.npmjs.org/supertest/-/supertest-6.3.3.tgz", + "integrity": "sha512-EMCG6G8gDu5qEqRQ3JjjPs6+FYT1a7Hv5ApHvtSghmOFJYtsU5S+pSb6Y2EUeCEY3CmEL3mmQ8YWlPOzQomabA==", + "dev": true, + "requires": { + "methods": "^1.1.2", + "superagent": "^8.0.5" + } + }, "supports-color": { "version": "7.2.0", "resolved": "https://registry.npmjs.org/supports-color/-/supports-color-7.2.0.tgz", @@ -14078,9 +14295,6 @@ "version": "6.1.11", "resolved": "https://registry.npmjs.org/tar/-/tar-6.1.11.tgz", "integrity": "sha512-an/KZQzQUkZCkuoAA64hM92X0Urb6VpRhAFllDzz44U2mcD5scmT3zBc4VgVpkugF580+DQn8eAFSyoQt0tznA==", - "dev": true, - "optional": true, - "peer": true, "requires": { "chownr": "^2.0.0", "fs-minipass": "^2.0.0", @@ -14561,9 +14775,6 @@ "version": "1.1.5", "resolved": "https://registry.npmjs.org/wide-align/-/wide-align-1.1.5.tgz", "integrity": "sha512-eDMORYaPNZ4sQIuuYPDHdQvf4gyCF9rEEV/yPxGfwPkRodwEgiMUUXTx/dex+Me0wxx53S+NgUHaP7y3MGlDmg==", - "dev": true, - "optional": true, - "peer": true, "requires": { "string-width": "^1.0.2 || 2 || 3 || 4" } @@ -14714,8 +14925,7 @@ "yallist": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz", - "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==", - "dev": true + "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==" }, "yargs": { "version": "16.2.0", diff --git a/package.json b/package.json index 09987c5..6642e73 100644 --- a/package.json +++ b/package.json @@ -40,6 +40,7 @@ "bufferutil": "^4.0.2", "jest": "^26.6.0", "nodemon": "^2.0.6", + "supertest": "^6.3.3", "ts-node": "^9.1.0", "typescript": "^4.1.2", "utf-8-validate": "^5.0.3" diff --git a/src/core/biovalidator-core.js b/src/core/biovalidator-core.js index 3aafff5..6238da6 100644 --- a/src/core/biovalidator-core.js +++ b/src/core/biovalidator-core.js @@ -51,7 +51,10 @@ class BioValidator { } getCachedSchema() { - this.ajvInstance.getSchema(""); + return { + "cachedSchema": Object.keys(this.validatorCache), + "referencedSchema": Object.keys(this.referencedSchemaCache) + }; } clearCachedSchema() { diff --git a/src/core/server.js b/src/core/server.js index bfe7249..c55c194 100644 --- a/src/core/server.js +++ b/src/core/server.js @@ -101,10 +101,8 @@ class BioValidatorServer { }); this.router.get("/cache", (req, res) => { - let cachedSchema = this.biovalidator.getCachedSchema(); // todo fill in the logic to get cached schema - res.send({ - "message": "This endpoint is not implemented yet" - }); + let cachedSchema = this.biovalidator.getCachedSchema(); + res.send(cachedSchema); }); this.router.delete("/cache", (req, res) => { @@ -118,7 +116,7 @@ class BioValidatorServer { } _startServer() { - this.app.listen(this.port, () => { + this.expressServer = this.app.listen(this.port, () => { logger.info(`---------------------------------------------`); logger.info(`------------ ELIXIR biovalidator ------------`); logger.info(`---------------------------------------------`); diff --git a/src/keywords/graphRestriction.js b/src/keywords/graphRestriction.js index 037c838..fc72175 100644 --- a/src/keywords/graphRestriction.js +++ b/src/keywords/graphRestriction.js @@ -87,6 +87,7 @@ class GraphRestriction { let olsResponsePromise; if(cachedOlsResponses[url]) { olsResponsePromise = Promise.resolve(cachedOlsResponses[url]); + logger.debug("Returning cached response for OLS request: " + url) } else { olsResponsePromise = request({ diff --git a/test/biovalidatorServer.test.js b/test/biovalidatorServer.test.js new file mode 100644 index 0000000..bd0e274 --- /dev/null +++ b/test/biovalidatorServer.test.js @@ -0,0 +1,59 @@ +const fs = require("fs"); +const npid = require("npid"); + +const BioValidatorServer = require('../src/core/server'); +const supertest = require('supertest'); +const server = new BioValidatorServer("3020", ""); +server.start() +const requestWithSupertest = supertest(server.app); + +describe('biovalidator server endpoints', () => { + afterAll(done => { + server.expressServer.close(); + npid.remove(server.pidPath); + done(); + }); + + it('GET /cache should initially return empty cache', async () => { + const res = await requestWithSupertest.get('/cache'); + expect(res.status).toEqual(200); + expect(res.type).toEqual(expect.stringContaining('json')); + expect(res.body).toHaveProperty('cachedSchema'); + expect(res.body).toEqual({"cachedSchema": [], "referencedSchema": []}) + }); + + it('GET /cache contains object after one hit', async () => { + + let inputSchema = JSON.parse(fs.readFileSync("examples/schemas/biosamples-schema.json", "utf-8")); + let inputData = JSON.parse(fs.readFileSync("examples/objects/faang-organism-sample.json", "utf-8")); + + let res = await requestWithSupertest.post('/validate') + .send({ + "schema": inputSchema, + "data": inputData + }); + + expect(res.status).toEqual(200); + expect(res.type).toEqual(expect.stringContaining('json')); + expect(res.body).toEqual([]) + + + res = await requestWithSupertest.get('/cache'); + expect(res.status).toEqual(200); + expect(res.type).toEqual(expect.stringContaining('json')); + expect(res.body).toHaveProperty('cachedSchema'); + expect(res.body).toEqual({"cachedSchema": ["test/biosamples/schema"], "referencedSchema": []}) + }); + + it('GET /cache should be empty after cache clear', async () => { + let res = await requestWithSupertest.delete('/cache'); + expect(res.status).toEqual(200); + + res = await requestWithSupertest.get('/cache'); + expect(res.status).toEqual(200); + expect(res.type).toEqual(expect.stringContaining('json')); + expect(res.body).toHaveProperty('cachedSchema'); + expect(res.body).toEqual({"cachedSchema": [], "referencedSchema": []}) + }); + +});