From 521597ddd590ea631eff0e836f6724b4c236ef02 Mon Sep 17 00:00:00 2001 From: Isuru Liyanage Date: Tue, 11 Jan 2022 13:32:04 +0530 Subject: [PATCH 1/9] import ajv draft2019-9 module --- examples/objects/draft2019-9-recursive.json | 10 ++++++++ .../schemas/draft2019-9-recursive-schema.json | 24 +++++++++++++++++++ package-lock.json | 21 ++++++++++++---- package.json | 4 ++-- src/bio-validator.js | 8 ++++++- test/supportsDrafts2019-9Recursive.test.js | 19 +++++++++++++++ 6 files changed, 79 insertions(+), 7 deletions(-) create mode 100644 examples/objects/draft2019-9-recursive.json create mode 100644 examples/schemas/draft2019-9-recursive-schema.json create mode 100644 test/supportsDrafts2019-9Recursive.test.js diff --git a/examples/objects/draft2019-9-recursive.json b/examples/objects/draft2019-9-recursive.json new file mode 100644 index 0000000..45ff4a1 --- /dev/null +++ b/examples/objects/draft2019-9-recursive.json @@ -0,0 +1,10 @@ +{ + "sample_labels": [ + { + "label": "test1" + }, + { + "label": "test2" + } + ] +} diff --git a/examples/schemas/draft2019-9-recursive-schema.json b/examples/schemas/draft2019-9-recursive-schema.json new file mode 100644 index 0000000..d98b6cf --- /dev/null +++ b/examples/schemas/draft2019-9-recursive-schema.json @@ -0,0 +1,24 @@ +{ + "$schema": "https://json-schema.org/draft/2019-09/schema", + "$id": "test_schema_X", + "type": "object", + "required": ["sample_labels"], + "additionalProperties": false, + "properties": { + "sample_labels": { + "type": "array", + "minItems": 1, + "additionalProperties": false, + "items": { + "type": "object", + "required": ["label"], + "additionalProperties": false, + "properties": { + "label": { + "type": "string" + } + } + } + } + } +} diff --git a/package-lock.json b/package-lock.json index a3db8fd..cb62163 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,6 +1,6 @@ { "name": "biovalidator", - "version": "1.9.0", + "version": "1.9.1", "lockfileVersion": 1, "requires": true, "dependencies": { @@ -920,9 +920,9 @@ "dev": true }, "ajv": { - "version": "7.2.1", - "resolved": "https://registry.npmjs.org/ajv/-/ajv-7.2.1.tgz", - "integrity": "sha512-+nu0HDv7kNSOua9apAVc979qd932rrZeb3WOvoiD31A/p1mIE5/9bN2027pE2rOPYEdS3UHzsvof4hY+lM9/WQ==", + "version": "7.2.4", + "resolved": "https://registry.npmjs.org/ajv/-/ajv-7.2.4.tgz", + "integrity": "sha512-nBeQgg/ZZA3u3SYxyaDvpvDtgZ/EZPF547ARgZBrG9Bhu1vKDwAIjtIf+sDtJUKa2zOcEbmRLBRSyMraS/Oy1A==", "requires": { "fast-deep-equal": "^3.1.1", "json-schema-traverse": "^1.0.0", @@ -936,6 +936,19 @@ "integrity": "sha512-s1RBVF4HZd2UjGkb6t6uWoXjf6o7j7dXPQIL7vprcIT/67bTD6+5ocsU0UKShS2qWxueGDWuGfKHfOxHWrlTQg==", "requires": { "ajv": "^7.0.0" + }, + "dependencies": { + "ajv": { + "version": "7.2.4", + "resolved": "https://registry.npmjs.org/ajv/-/ajv-7.2.4.tgz", + "integrity": "sha512-nBeQgg/ZZA3u3SYxyaDvpvDtgZ/EZPF547ARgZBrG9Bhu1vKDwAIjtIf+sDtJUKa2zOcEbmRLBRSyMraS/Oy1A==", + "requires": { + "fast-deep-equal": "^3.1.1", + "json-schema-traverse": "^1.0.0", + "require-from-string": "^2.0.2", + "uri-js": "^4.2.2" + } + } } }, "ansi-align": { diff --git a/package.json b/package.json index c6a603d..2d62437 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "biovalidator", - "version": "1.9.1", + "version": "1.9.2", "description": "A nodejs JSON schema validator service. Extended from Ajv to include ontology validation.", "main": "src/server.js", "repository": "https://github.com/elixir-europe/biovalidator.git", @@ -19,7 +19,7 @@ "schema", "validator" ], - "author": "EMBL-EBI-SUBS, fpenim, ke4, haseeb-gh", + "author": "EMBL-EBI-AIT, fpenim, ke4, haseeb-gh", "license": "Apache-2.0", "dependencies": { "ajv": "~7.2.1", diff --git a/src/bio-validator.js b/src/bio-validator.js index c8a2170..21fca99 100644 --- a/src/bio-validator.js +++ b/src/bio-validator.js @@ -5,7 +5,9 @@ const Promise = require('bluebird'); const path = require("path"); const fs = require('fs'); -const Ajv = require("ajv").default; +// const Ajv = require("ajv").default; +const Ajv = require("ajv/dist/2019").default; +// import Ajv2019 from "ajv/dist/2019" const addFormats = require("ajv-formats"); const request = require("request-promise"); const AppError = require("./model/application-error"); @@ -105,7 +107,11 @@ class BioValidator { } constructAjv(customKeywordValidators) { + // const ajvInstance = new Ajv({allErrors: true, strict:false, loadSchema: this.generateLoadSchemaRefFn()}); const ajvInstance = new Ajv({allErrors: true, strict:false, loadSchema: this.generateLoadSchemaRefFn()}); + // const ajvInstance = new Ajv2019(); + const draft7MetaSchema = require("ajv/dist/refs/json-schema-draft-07.json") + ajvInstance.addMetaSchema(draft7MetaSchema) addFormats(ajvInstance); BioValidator._addCustomKeywordValidators(ajvInstance, customKeywordValidators); diff --git a/test/supportsDrafts2019-9Recursive.test.js b/test/supportsDrafts2019-9Recursive.test.js new file mode 100644 index 0000000..0cf7850 --- /dev/null +++ b/test/supportsDrafts2019-9Recursive.test.js @@ -0,0 +1,19 @@ +const fs = require("fs"); +const BioValidator = require('../src/bio-validator'); + +test("draft2019-9Recursive", () => { + let inputSchema = fs.readFileSync("examples/schemas/draft2019-9-recursive-schema.json"); + let jsonSchema = JSON.parse(inputSchema); + + let inputObj = fs.readFileSync("examples/objects/draft2019-9-recursive.json"); + let jsonObj = JSON.parse(inputObj); + + + + const validator = new BioValidator([]); + + return validator.validate(jsonSchema, jsonObj).then((data) => { + expect(data).toBeDefined(); + expect(data.length).toBe(0); + }); +}); From a6230ce40f38dd3e563084282070a72b80ec99c7 Mon Sep 17 00:00:00 2001 From: Isuru Liyanage Date: Tue, 11 Jan 2022 14:38:14 +0530 Subject: [PATCH 2/9] clean comments --- src/bio-validator.js | 4 ---- 1 file changed, 4 deletions(-) diff --git a/src/bio-validator.js b/src/bio-validator.js index 21fca99..00eb905 100644 --- a/src/bio-validator.js +++ b/src/bio-validator.js @@ -5,9 +5,7 @@ const Promise = require('bluebird'); const path = require("path"); const fs = require('fs'); -// const Ajv = require("ajv").default; const Ajv = require("ajv/dist/2019").default; -// import Ajv2019 from "ajv/dist/2019" const addFormats = require("ajv-formats"); const request = require("request-promise"); const AppError = require("./model/application-error"); @@ -107,9 +105,7 @@ class BioValidator { } constructAjv(customKeywordValidators) { - // const ajvInstance = new Ajv({allErrors: true, strict:false, loadSchema: this.generateLoadSchemaRefFn()}); const ajvInstance = new Ajv({allErrors: true, strict:false, loadSchema: this.generateLoadSchemaRefFn()}); - // const ajvInstance = new Ajv2019(); const draft7MetaSchema = require("ajv/dist/refs/json-schema-draft-07.json") ajvInstance.addMetaSchema(draft7MetaSchema) addFormats(ajvInstance); From 3072b3f59960e7d29b175f98a62c47e1b7849712 Mon Sep 17 00:00:00 2001 From: Isuru Liyanage Date: Mon, 14 Feb 2022 13:35:26 +0000 Subject: [PATCH 3/9] rename test files to reflect tests --- .../{draft2019-9-recursive.json => draft2019-9-support.json} | 0 ...-recursive-schema.json => draft2019-9-support-schema.json} | 0 ...ts2019-9Recursive.test.js => supportsDrafts2019-9.test.js} | 4 ++-- 3 files changed, 2 insertions(+), 2 deletions(-) rename examples/objects/{draft2019-9-recursive.json => draft2019-9-support.json} (100%) rename examples/schemas/{draft2019-9-recursive-schema.json => draft2019-9-support-schema.json} (100%) rename test/{supportsDrafts2019-9Recursive.test.js => supportsDrafts2019-9.test.js} (80%) diff --git a/examples/objects/draft2019-9-recursive.json b/examples/objects/draft2019-9-support.json similarity index 100% rename from examples/objects/draft2019-9-recursive.json rename to examples/objects/draft2019-9-support.json diff --git a/examples/schemas/draft2019-9-recursive-schema.json b/examples/schemas/draft2019-9-support-schema.json similarity index 100% rename from examples/schemas/draft2019-9-recursive-schema.json rename to examples/schemas/draft2019-9-support-schema.json diff --git a/test/supportsDrafts2019-9Recursive.test.js b/test/supportsDrafts2019-9.test.js similarity index 80% rename from test/supportsDrafts2019-9Recursive.test.js rename to test/supportsDrafts2019-9.test.js index 0cf7850..d1ff7df 100644 --- a/test/supportsDrafts2019-9Recursive.test.js +++ b/test/supportsDrafts2019-9.test.js @@ -2,10 +2,10 @@ const fs = require("fs"); const BioValidator = require('../src/bio-validator'); test("draft2019-9Recursive", () => { - let inputSchema = fs.readFileSync("examples/schemas/draft2019-9-recursive-schema.json"); + let inputSchema = fs.readFileSync("examples/schemas/draft2019-9-support-schema.json"); let jsonSchema = JSON.parse(inputSchema); - let inputObj = fs.readFileSync("examples/objects/draft2019-9-recursive.json"); + let inputObj = fs.readFileSync("examples/objects/draft2019-9-support.json"); let jsonObj = JSON.parse(inputObj); From 53ba897939d07641be95907f141ad65570704c33 Mon Sep 17 00:00:00 2001 From: Isuru Liyanage Date: Mon, 14 Feb 2022 13:38:00 +0000 Subject: [PATCH 4/9] add router to support base URL --- package-lock.json | 9512 ++++++++++++++++++++++++++++++++++++++++++--- package.json | 2 +- src/server.js | 10 +- 3 files changed, 8954 insertions(+), 570 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"nodemon": "^2.0.6", "ts-node": "^9.1.0", diff --git a/src/server.js b/src/server.js index 9749c7e..5b61318 100644 --- a/src/server.js +++ b/src/server.js @@ -8,9 +8,11 @@ const argv = require("yargs").argv; const npid = require("npid"); const app = express(); +const router = express.Router() const port = process.env.PORT || 3020; +const basePath = process.env.VALIDATOR_BASE_URL || '/'; -app.use(express.static('src/views')); +router.use(express.static('src/views')); app.use(bodyParser.json()); @@ -32,7 +34,7 @@ app.use(function(err, req, res, next) { } }); -app.post("/validate", (req, res) => { +router.post("/validate", (req, res) => { logger.log("debug", "Received POST request."); var inputSchema = req.body.schema; @@ -54,7 +56,7 @@ app.post("/validate", (req, res) => { } }); -app.get("/validate", (req, res) => { +router.get("/validate", (req, res) => { logger.log("silly", "Received GET request."); res.send({ @@ -66,6 +68,8 @@ app.get("/validate", (req, res) => { }); }); +app.use(basePath, router); + app.listen(port, () => { logger.log("info", ` -- Started server on port ${port} --`); if(argv.logPath) { logger.log("info", ` --> Log output: ${argv.logPath}`); } From 1bfaf50443e4365a55b90878b19fd98e2f5fd827 Mon Sep 17 00:00:00 2001 From: Isuru Liyanage Date: Wed, 25 May 2022 23:42:40 +0100 Subject: [PATCH 5/9] local schema directory --- .gitignore | 3 +- package-lock.json | 276 +++++++++++++++--- package.json | 1 + src/biovalidator.js | 205 +++++++++++++ src/cli/biovalidator-cli.js | 78 +++++ src/utils/file_utils.js | 26 ++ test/resources/ref_test_invalid.json | 6 + test/resources/ref_test_schema.json | 14 + test/resources/ref_test_valid.json | 7 + .../resources/schema_dir/ontology_schema.json | 17 ++ validator-cli2.js | 47 +++ 11 files changed, 642 insertions(+), 38 deletions(-) create mode 100644 src/biovalidator.js create mode 100644 src/cli/biovalidator-cli.js create mode 100644 src/utils/file_utils.js create mode 100644 test/resources/ref_test_invalid.json create mode 100644 test/resources/ref_test_schema.json create mode 100644 test/resources/ref_test_valid.json create mode 100644 test/resources/schema_dir/ontology_schema.json create mode 100755 validator-cli2.js diff --git a/.gitignore b/.gitignore index a38b2b3..47ab6ae 100644 --- a/.gitignore +++ b/.gitignore @@ -2,4 +2,5 @@ node_modules/ .idea/ .DS_Store log/ -*.iml \ No newline at end of file +*.iml +server.pid diff --git a/package-lock.json b/package-lock.json index 19b0c1e..dabed16 100644 --- a/package-lock.json +++ b/package-lock.json @@ -12,6 +12,7 @@ "ajv": "~7.2.1", "ajv-formats": "^1.5.1", "express": "^4.17.1", + "glob": "^8.0.3", "npid": "^0.4.0", "request": "^2.88.2", "request-promise": "^4.2.4", @@ -783,6 +784,26 @@ "node-notifier": "^8.0.0" } }, + "node_modules/@jest/reporters/node_modules/glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "dependencies": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + }, + "engines": { + "node": "*" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" + } + }, "node_modules/@jest/source-map": { "version": "26.6.2", "resolved": "https://registry.npmjs.org/@jest/source-map/-/source-map-26.6.2.tgz", @@ -1583,8 +1604,7 @@ "node_modules/balanced-match": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.0.tgz", - "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=", - "dev": true + "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=" }, "node_modules/base": { "version": "0.11.2", @@ -3133,8 +3153,7 @@ "node_modules/fs.realpath": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/fs.realpath/-/fs.realpath-1.0.0.tgz", - "integrity": "sha1-FQStJSMVjKpA20onh8sBQRmU6k8=", - "dev": true + "integrity": "sha1-FQStJSMVjKpA20onh8sBQRmU6k8=" }, "node_modules/fsevents": { "version": "2.2.1", @@ -3232,20 +3251,18 @@ } }, "node_modules/glob": { - "version": "7.1.6", - "resolved": "https://registry.npmjs.org/glob/-/glob-7.1.6.tgz", - "integrity": "sha512-LwaxwyZ72Lk7vZINtNNrywX0ZuLyStrdDtabefZKAY5ZGJhVtgdznluResxNmPitE0SAO+O26sWTHeKSI2wMBA==", - "dev": true, + "version": "8.0.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-8.0.3.tgz", + "integrity": "sha512-ull455NHSHI/Y1FqGaaYFaLGkNMMJbavMrEGFXG/PGrg6y7sutWHUHrz6gy6WEBH6akM1M414dWKCNs+IhKdiQ==", "dependencies": { "fs.realpath": "^1.0.0", "inflight": "^1.0.4", "inherits": "2", - "minimatch": "^3.0.4", - "once": "^1.3.0", - "path-is-absolute": "^1.0.0" + "minimatch": "^5.0.1", + "once": "^1.3.0" }, "engines": { - "node": "*" + "node": ">=12" }, "funding": { "url": "https://github.com/sponsors/isaacs" @@ -3263,6 +3280,25 @@ "node": ">= 6" } }, + "node_modules/glob/node_modules/brace-expansion": { + "version": "2.0.1", + "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.1.tgz", + "integrity": "sha512-XnAIvQ8eM+kC6aULx6wuQiwVsnzsi9d3WxzV3FpWTGA19F621kwdbsAcFKXgKUHZWsy+mY6iL1sHTxWEFCytDA==", + "dependencies": { + "balanced-match": "^1.0.0" + } + }, + "node_modules/glob/node_modules/minimatch": { + "version": "5.1.0", + "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-5.1.0.tgz", + "integrity": "sha512-9TPBGGak4nHfGZsPBohm9AWg6NoT7QTCehS3BIJABslyZbzxfV78QM2Y6+i741OPZIafFAaiiEMh5OyIrJPgtg==", + "dependencies": { + "brace-expansion": "^2.0.1" + }, + "engines": { + "node": ">=10" + } + }, "node_modules/global-dirs": { "version": "2.0.1", "resolved": "https://registry.npmjs.org/global-dirs/-/global-dirs-2.0.1.tgz", @@ -3618,7 +3654,6 @@ "version": "1.0.6", "resolved": "https://registry.npmjs.org/inflight/-/inflight-1.0.6.tgz", "integrity": "sha1-Sb1jMdfQLQwJvJEKEHW6gWW1bfk=", - "dev": true, "dependencies": { "once": "^1.3.0", "wrappy": "1" @@ -4254,6 +4289,26 @@ } } }, + "node_modules/jest-config/node_modules/glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "dependencies": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + }, + "engines": { + "node": "*" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" + } + }, "node_modules/jest-diff": { "version": "26.6.2", "resolved": "https://registry.npmjs.org/jest-diff/-/jest-diff-26.6.2.tgz", @@ -4631,6 +4686,26 @@ "node": "6.* || 8.* || >= 10.*" } }, + "node_modules/jest-runtime/node_modules/glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "dependencies": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + }, + "engines": { + "node": "*" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" + } + }, "node_modules/jest-runtime/node_modules/locate-path": { "version": "5.0.0", "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-5.0.0.tgz", @@ -5503,9 +5578,9 @@ } }, "node_modules/minimatch": { - "version": "3.0.4", - "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.0.4.tgz", - "integrity": "sha512-yJHVQEhyqPLUTgt9B83PXu6W3rx4MvvHvSUvToogpwoGDOUQ+yDrR0HRot+yOCdCO7u4hX3pWft6kWBBcqh0UA==", + "version": "3.1.2", + "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.2.tgz", + "integrity": "sha512-J7p63hRiAjw1NDEww1W7i37+ByIrOWO5XQQAzZ3VOcL0PNybwpfmV/N05zFAzwQ9USyEcX6t3UO+K5aqBQOIHw==", "dev": true, "dependencies": { "brace-expansion": "^1.1.7" @@ -6027,7 +6102,6 @@ "version": "1.4.0", "resolved": "https://registry.npmjs.org/once/-/once-1.4.0.tgz", "integrity": "sha1-WDsap3WWHUsROsF9nFC6753Xa9E=", - "dev": true, "dependencies": { "wrappy": "1" } @@ -6886,6 +6960,26 @@ "url": "https://github.com/sponsors/isaacs" } }, + "node_modules/rimraf/node_modules/glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "dependencies": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + }, + "engines": { + "node": "*" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" + } + }, "node_modules/rsvp": { "version": "4.8.5", "resolved": "https://registry.npmjs.org/rsvp/-/rsvp-4.8.5.tgz", @@ -7824,6 +7918,26 @@ "node": ">=8" } }, + "node_modules/test-exclude/node_modules/glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "dependencies": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + }, + "engines": { + "node": "*" + }, + "funding": { + "url": "https://github.com/sponsors/isaacs" + } + }, "node_modules/text-hex": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/text-hex/-/text-hex-1.0.0.tgz", @@ -8600,8 +8714,7 @@ "node_modules/wrappy": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=", - "dev": true + "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=" }, "node_modules/write-file-atomic": { "version": "3.0.3", @@ -9327,6 +9440,22 @@ "string-length": "^4.0.1", "terminal-link": "^2.0.0", "v8-to-istanbul": "^7.0.0" + }, + "dependencies": { + "glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "requires": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + } + } } }, "@jest/source-map": { @@ -9982,8 +10111,7 @@ "balanced-match": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.0.tgz", - "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=", - "dev": true + "integrity": "sha1-ibTRmasr7kneFk6gK4nORi1xt2c=" }, "base": { "version": "0.11.2", @@ -11232,8 +11360,7 @@ "fs.realpath": { "version": "1.0.0", "resolved": "https://registry.npmjs.org/fs.realpath/-/fs.realpath-1.0.0.tgz", - "integrity": "sha1-FQStJSMVjKpA20onh8sBQRmU6k8=", - "dev": true + "integrity": "sha1-FQStJSMVjKpA20onh8sBQRmU6k8=" }, "fsevents": { "version": "2.2.1", @@ -11306,17 +11433,33 @@ } }, "glob": { - "version": "7.1.6", - "resolved": "https://registry.npmjs.org/glob/-/glob-7.1.6.tgz", - "integrity": "sha512-LwaxwyZ72Lk7vZINtNNrywX0ZuLyStrdDtabefZKAY5ZGJhVtgdznluResxNmPitE0SAO+O26sWTHeKSI2wMBA==", - "dev": true, + "version": "8.0.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-8.0.3.tgz", + "integrity": "sha512-ull455NHSHI/Y1FqGaaYFaLGkNMMJbavMrEGFXG/PGrg6y7sutWHUHrz6gy6WEBH6akM1M414dWKCNs+IhKdiQ==", "requires": { "fs.realpath": "^1.0.0", "inflight": "^1.0.4", "inherits": "2", - "minimatch": "^3.0.4", - "once": "^1.3.0", - "path-is-absolute": "^1.0.0" + "minimatch": "^5.0.1", + "once": "^1.3.0" + }, + "dependencies": { + "brace-expansion": { + "version": "2.0.1", + "resolved": "https://registry.npmjs.org/brace-expansion/-/brace-expansion-2.0.1.tgz", + "integrity": "sha512-XnAIvQ8eM+kC6aULx6wuQiwVsnzsi9d3WxzV3FpWTGA19F621kwdbsAcFKXgKUHZWsy+mY6iL1sHTxWEFCytDA==", + "requires": { + "balanced-match": "^1.0.0" + } + }, + "minimatch": { + "version": "5.1.0", + "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-5.1.0.tgz", + "integrity": "sha512-9TPBGGak4nHfGZsPBohm9AWg6NoT7QTCehS3BIJABslyZbzxfV78QM2Y6+i741OPZIafFAaiiEMh5OyIrJPgtg==", + "requires": { + "brace-expansion": "^2.0.1" + } + } } }, "glob-parent": { @@ -11608,7 +11751,6 @@ "version": "1.0.6", "resolved": "https://registry.npmjs.org/inflight/-/inflight-1.0.6.tgz", "integrity": "sha1-Sb1jMdfQLQwJvJEKEHW6gWW1bfk=", - "dev": true, "requires": { "once": "^1.3.0", "wrappy": "1" @@ -12229,6 +12371,22 @@ "jest-validate": "^26.6.2", "micromatch": "^4.0.2", "pretty-format": "^26.6.2" + }, + "dependencies": { + "glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "requires": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + } + } } }, "jest-diff": { @@ -12533,6 +12691,20 @@ "integrity": "sha512-DyFP3BM/3YHTQOCUL/w0OZHR0lpKeGrxotcHWcqNEdnltqFwXVfhEBQ94eIo34AfQpo0rGki4cyIiftY06h2Fg==", "dev": true }, + "glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "requires": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + } + }, "locate-path": { "version": "5.0.0", "resolved": "https://registry.npmjs.org/locate-path/-/locate-path-5.0.0.tgz", @@ -13075,9 +13247,9 @@ "dev": true }, "minimatch": { - "version": "3.0.4", - "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.0.4.tgz", - "integrity": "sha512-yJHVQEhyqPLUTgt9B83PXu6W3rx4MvvHvSUvToogpwoGDOUQ+yDrR0HRot+yOCdCO7u4hX3pWft6kWBBcqh0UA==", + "version": "3.1.2", + "resolved": "https://registry.npmjs.org/minimatch/-/minimatch-3.1.2.tgz", + "integrity": "sha512-J7p63hRiAjw1NDEww1W7i37+ByIrOWO5XQQAzZ3VOcL0PNybwpfmV/N05zFAzwQ9USyEcX6t3UO+K5aqBQOIHw==", "dev": true, "requires": { "brace-expansion": "^1.1.7" @@ -13480,7 +13652,6 @@ "version": "1.4.0", "resolved": "https://registry.npmjs.org/once/-/once-1.4.0.tgz", "integrity": "sha1-WDsap3WWHUsROsF9nFC6753Xa9E=", - "dev": true, "requires": { "wrappy": "1" } @@ -14121,6 +14292,22 @@ "dev": true, "requires": { "glob": "^7.1.3" + }, + "dependencies": { + "glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "requires": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + } + } } }, "rsvp": { @@ -14876,6 +15063,22 @@ "@istanbuljs/schema": "^0.1.2", "glob": "^7.1.4", "minimatch": "^3.0.4" + }, + "dependencies": { + "glob": { + "version": "7.2.3", + "resolved": "https://registry.npmjs.org/glob/-/glob-7.2.3.tgz", + "integrity": "sha512-nFR0zLpU2YCaRxwoCJvL6UvCH2JFyFVIvwTLsIf21AuHlMskA1hhTdk+LlYJtOlYt9v6dvszD2BGRqBL+iQK9Q==", + "dev": true, + "requires": { + "fs.realpath": "^1.0.0", + "inflight": "^1.0.4", + "inherits": "2", + "minimatch": "^3.1.1", + "once": "^1.3.0", + "path-is-absolute": "^1.0.0" + } + } } }, "text-hex": { @@ -15498,8 +15701,7 @@ "wrappy": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=", - "dev": true + "integrity": "sha1-tSQ9jz7BqjXxNkYFvA0QNuMKtp8=" }, "write-file-atomic": { "version": "3.0.3", diff --git a/package.json b/package.json index cb011bd..a8c829f 100644 --- a/package.json +++ b/package.json @@ -25,6 +25,7 @@ "ajv": "~7.2.1", "ajv-formats": "^1.5.1", "express": "^4.17.1", + "glob": "^8.0.3", "npid": "^0.4.0", "request": "^2.88.2", "request-promise": "^4.2.4", diff --git a/src/biovalidator.js b/src/biovalidator.js new file mode 100644 index 0000000..fa6537b --- /dev/null +++ b/src/biovalidator.js @@ -0,0 +1,205 @@ +/** + * Created by rolando on 08/08/2018. + */ + +const Promise = require('bluebird'); +const path = require("path"); +const fs = require('fs'); +const Ajv = require("ajv/dist/2019").default; +const addFormats = require("ajv-formats"); +const request = require("request-promise"); +const AppError = require("./model/application-error"); +const {getFiles, readFile} = require("./utils/file_utils"); +const {isChildTermOf, isValidTerm, isValidTaxonomy} = require("./keywords"); +const GraphRestriction = require("./keywords/graph_restriction"); +const ValidationError = require("./model/validation-error"); +const logger = require("./winston"); + +const devMode = 0; +console.debug = devMode ? console.debug : () => { +}; + +const customKeywordValidators = [ + new isChildTermOf(null, "https://www.ebi.ac.uk/ols/api/search?q="), + new isValidTerm(null, "https://www.ebi.ac.uk/ols/api/search?q="), + new isValidTaxonomy(null), + new GraphRestriction(null, "https://www.ebi.ac.uk/ols/api") +]; + +class BioValidator2 { + constructor(localSchemaPath) { + this.validatorCache = {}; + this.cachedSchemas = {}; + this.preCompiledSchemaDirectory = localSchemaPath; + this.ajvInstance = this.constructAjv(); + } + + runValidation(inputSchema, inputObject) { + logger.log("silly", "Running validation..."); + return new Promise((resolve, reject) => { + this.validate(inputSchema, inputObject) + .then((validationResult) => { + if (validationResult.length === 0) { + resolve([]); + } else { + let ajvErrors = []; + validationResult.forEach(validationError => { + ajvErrors.push(validationError); + }); + + resolve(this.convertToValidationErrors(ajvErrors)); + } + } + ).catch((error) => { + if (error.errors) { + reject(new AppError(error.errors)); + } else { + logger.log("error", "An error ocurred while running the validation. Error : " + JSON.stringify(error)); + reject(new AppError("An error ocurred while running the validation.")); + } + }); + }); + } + + validate(inputSchema, inputObject) { + inputSchema["$async"] = true; + return new Promise((resolve, reject) => { + const compiledSchemaPromise = this.getValidationFunction(inputSchema); + + compiledSchemaPromise.then((validate) => { + Promise.resolve(validate(inputObject)) + .then((data) => { + if (validate.errors) { + resolve(validate.errors); + } else { + resolve([]); + } + } + ).catch((err) => { + if (!(err instanceof Ajv.ValidationError)) { + console.error("An error occurred while running the validation."); + reject(new AppError("An error occurred while running the validation.")); + } else { + console.debug("debug", this.ajvInstance.errorsText(err.errors, {dataVar: inputObject.alias})); + resolve(err.errors); + } + }); + }).catch((err) => { + console.error("async schema compiled encountered and error"); + console.error(err.stack); + reject(err); + }); + }); + } + + convertToValidationErrors(ajvErrorObjects) { + let localErrors = []; + ajvErrorObjects.forEach( (errorObject) => { + let tempValError = new ValidationError(errorObject); + let index = localErrors.findIndex(valError => (valError.dataPath === tempValError.dataPath)); + + if(index !== -1) { + localErrors[index].errors.push(tempValError.errors[0]); + } else { + localErrors.push(tempValError); + } + }); + return localErrors; + } + + getSchema(schemaUri) { + if (!this.cachedSchemas[schemaUri]) { + return new Promise((resolve, reject) => { + BioValidator.fetchSchema(schemaUri) + .then(schema => { + this.cachedSchemas[schemaUri] = schema; + resolve(schema); + }) + .catch(err => { + reject(err); + }) + }); + } else { + return Promise.resolve(this.cachedSchemas[schemaUri]); + } + } + + static fetchSchema(schemaUrl) { + return request({ + method: "GET", + url: schemaUrl, + json: true, + }); + } + + getValidationFunction(inputSchema) { + const schemaId = inputSchema['$id']; + + if (this.validatorCache[schemaId]) { + return Promise.resolve(this.validatorCache[schemaId]); + } else { + const compiledSchemaPromise = this.ajvInstance.compileAsync(inputSchema); + if (schemaId) { + this.validatorCache[schemaId] = compiledSchemaPromise; + } + return Promise.resolve(compiledSchemaPromise); + } + } + + constructAjv() { + const ajvInstance = new Ajv({allErrors: true, strict: false, loadSchema: this.generateLoadSchemaRefFn()}); + const draft7MetaSchema = require("ajv/dist/refs/json-schema-draft-07.json") + ajvInstance.addMetaSchema(draft7MetaSchema) + addFormats(ajvInstance); + + this.addCustomKeywordValidators(ajvInstance); + this.preCompileLocalSchemas(ajvInstance); + + return ajvInstance + } + + addCustomKeywordValidators(ajvInstance) { + customKeywordValidators.forEach(customKeywordValidator => { + ajvInstance = customKeywordValidator.configure(ajvInstance); + }); + + return ajvInstance; + } + + generateLoadSchemaRefFn() { + const cachedSchemas = this.cachedSchemas; + + return (uri) => { + if (cachedSchemas[uri]) { + return Promise.resolve(cachedSchemas[uri]); + } else { + return new Promise((resolve, reject) => { + request({ + method: "GET", + url: uri, + json: true + }).then(resp => { + const loadedSchema = resp; + loadedSchema["$async"] = true; + cachedSchemas[uri] = loadedSchema; + resolve(loadedSchema); + }).catch(err => { + reject(err); + }); + }); + } + }; + } + + preCompileLocalSchemas(ajv) { + let schemaFiles = getFiles(this.preCompiledSchemaDirectory); + for (let file of schemaFiles) { + let schema = readFile(file); + // ajv.addSchema(schema, schema["$id"]); + const validate = ajv.getSchema(schema["$id"] || ajv.compile(schema)); + this.cachedSchemas[schema["$id"]] = schema; + } + } +} + +module.exports = BioValidator2; diff --git a/src/cli/biovalidator-cli.js b/src/cli/biovalidator-cli.js new file mode 100644 index 0000000..b3ad11e --- /dev/null +++ b/src/cli/biovalidator-cli.js @@ -0,0 +1,78 @@ +const logger = require("../winston"); +const fs = require("fs"); +const {log_error, log_info } = require("../utils/logger"); +const BioValidator2 = require("../biovalidator"); + +class BioValidatorCLI2 { + constructor(pathToSchema, pathToJson, schemaDirectory) { + this.pathToSchema = pathToSchema + this.pathToJson = pathToJson + this.schemaDirectory = schemaDirectory; + } + + read_schema(pathToSchema) { + if (fs.existsSync(pathToSchema)) { + let schemaStr = fs.readFileSync(pathToSchema, 'utf-8') + return JSON.parse(schemaStr) + } else { + log_error("File '" + pathToSchema + "' does not exist!"); + process.exit(1); + } + } + + read_json(pathToJson) { + if (fs.existsSync(pathToJson)) { + let jsonStr = fs.readFileSync(pathToJson, 'utf-8') + return JSON.parse(jsonStr) + } else { + log_error("File '" + pathToJson + "' does not exist!"); + process.exit(1); + } + } + + validate() { + this.inputSchema = this.read_schema(this.pathToSchema) + this.jsonToValidate = this.read_json(this.pathToJson) + let biovalidator = new BioValidator2("/home/isuru/Projects/biovalidator/test/resources/schema_dir/*.json"); + + if (this.inputSchema && this.jsonToValidate) { + biovalidator.runValidation(this.inputSchema, this.jsonToValidate).then((output) => { + logger.log("silly", "Sent validation results."); + this.process_output(output); + }).catch((error) => { + console.error("console error: " + error); + logger.log("error", error); + }); + } else { + let appError = "Something is missing, both schema and object are required to execute validation."; + log_error(appError); + } + } + + process_output(output) { + if (output.length === 0) { + log_info("No validation errors reported."); + } else { + log_error("The validation process has found the following error(s):\n") + log_error(this.error_report(output)); + } + console.log("Validation finished."); + } + + error_report(jsonErrors) { + let errorOutput = ""; + jsonErrors.forEach( (errorObject) => { + const dataPath = errorObject.dataPath; + const errors = errorObject.errors; + let errorStr = ""; + errors.forEach( (error) => { + errorStr = errorStr.concat("\n\t", error); + }) + errorOutput = errorOutput.concat(dataPath + errorStr + "\n"); + }) + + return errorOutput; + } +} + +module.exports = BioValidatorCLI2; diff --git a/src/utils/file_utils.js b/src/utils/file_utils.js new file mode 100644 index 0000000..66258bd --- /dev/null +++ b/src/utils/file_utils.js @@ -0,0 +1,26 @@ +const fs = require('fs'); +const glob = require('glob'); + +function getFiles(filePattern) { + let files = []; + if (glob.hasMagic(filePattern)) { + const dataFiles = glob.sync(filePattern, {cwd: process.cwd()}) + files = files.concat(dataFiles); + } else { + files.push(filePattern); + } + + console.log(files) + console.log("files length: " + files.length) + return files; +} + +function readFile(filePath) { + let schema = fs.readFileSync(filePath).toString(); + let jsonSchema = JSON.parse(schema.toString()); + jsonSchema["$async"] = true; + + return jsonSchema; +} + +module.exports = { getFiles, readFile } diff --git a/test/resources/ref_test_invalid.json b/test/resources/ref_test_invalid.json new file mode 100644 index 0000000..83ebbea --- /dev/null +++ b/test/resources/ref_test_invalid.json @@ -0,0 +1,6 @@ +{ + "name": "human", + "ontology": { + "id": "NCBITaxon:9606" + } +} diff --git a/test/resources/ref_test_schema.json b/test/resources/ref_test_schema.json new file mode 100644 index 0000000..856759a --- /dev/null +++ b/test/resources/ref_test_schema.json @@ -0,0 +1,14 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "$id": "https://www.ebi.ac.uk/ait/schema/schema-ref-test", + "type": "object", + "properties": { + "name": { + "type": "string" + }, + "ontology": { + "$ref": "https://www.ebi.ac.uk/ait/schema/ontology" + } + }, + "required": ["name", "ontology"] +} diff --git a/test/resources/ref_test_valid.json b/test/resources/ref_test_valid.json new file mode 100644 index 0000000..29aad6b --- /dev/null +++ b/test/resources/ref_test_valid.json @@ -0,0 +1,7 @@ +{ + "name": "human", + "ontology": { + "id": "NCBITaxon:9606", + "label": "Homo sapiens" + } +} diff --git a/test/resources/schema_dir/ontology_schema.json b/test/resources/schema_dir/ontology_schema.json new file mode 100644 index 0000000..a196cb3 --- /dev/null +++ b/test/resources/schema_dir/ontology_schema.json @@ -0,0 +1,17 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "$id": "https://www.ebi.ac.uk/ait/schema/ontology", + "type": "object", + "properties": { + "id": { + "type": "string" + }, + "label": { + "type": "string" + } + }, + "required": [ + "id", + "label" + ] +} diff --git a/validator-cli2.js b/validator-cli2.js new file mode 100755 index 0000000..839f0d2 --- /dev/null +++ b/validator-cli2.js @@ -0,0 +1,47 @@ +const yargs = require('yargs/yargs') +const { hideBin } = require('yargs/helpers') + +function get_usage() { + let helpText = "\nBio-validator CLI (Command Line Interface)\n"; + helpText = helpText.concat("usage: node ./validator-cli.js [--schema=path/to/schema] [--json=path/to/json]") + return helpText +} + +function print_help() { + console.log(get_usage()) +} + +const argv = yargs(hideBin(process.argv)) + .usage(get_usage()) + .demandOption(['schema', 'json']) + .alias('s', 'schema') + .alias('j', 'json') + .describe('schema', 'path to the schema file') + .describe('json', 'path to the json file to validate') + .example('node ./validator-cli.js --json=valid.json --schema=test_schema.json', + 'Validates \'valid.json\' with \'test_schema.json\'.') + .argv + +const BioValidatorCLI2 = require("./src/cli/biovalidator-cli"); +const {log_error} = require("./src/utils/logger"); + +let schema = argv["schema"] +let json = argv["json"] +let schemaDir = argv["schemaDir"] +let isParameterMissing = false; + +if (!schema || schema === "" || typeof schema === "boolean") { + log_error("Schema parameter or its value is missing!"); + isParameterMissing = true; +} +if (!json || json === "" || typeof json === "boolean") { + log_error("Json parameter or its value is missing!"); + isParameterMissing = true; +} + +if (isParameterMissing || argv["help"]) { + print_help() +} else { + const bioValidator = new BioValidatorCLI2(schema, json, schemaDir); + bioValidator.validate() +} From 078e4c2128c32d64ee09d627d4652bbfaaae1273 Mon Sep 17 00:00:00 2001 From: Isuru Liyanage Date: Thu, 26 May 2022 10:54:29 +0100 Subject: [PATCH 6/9] reference from default directory or glob --- package-lock.json | 201 ++++++++++++++++++++++++++---- package.json | 1 - src/bio-validator.js | 165 ------------------------ src/{cli => }/biovalidator-cli.js | 12 +- src/biovalidator.js | 18 +-- src/cli/bio-validator-cli.js | 75 ----------- src/server.js | 10 +- src/utils/file_utils.js | 12 +- src/validator.js | 57 --------- test/async-validation.test.js | 17 +-- test/bio-validator-cli.test.js | 14 ++- test/bio-validator.test.js | 10 +- test/graphRestriction.test.js | 8 +- test/isChildTermOf.test.js | 4 +- test/isValidTaxonomy.test.js | 10 +- test/isValidTerm.test.js | 4 +- test/sample_checklists.test.js | 7 +- test/supportsDrafts2019-9.test.js | 4 +- test/validator.test.js | 11 +- validator-cli.js | 7 +- validator-cli2.js | 47 ------- 21 files changed, 259 insertions(+), 435 deletions(-) delete mode 100644 src/bio-validator.js rename src/{cli => }/biovalidator-cli.js (88%) delete mode 100644 src/cli/bio-validator-cli.js delete mode 100644 src/validator.js delete mode 100755 validator-cli2.js diff --git a/package-lock.json b/package-lock.json index dabed16..196aec8 100644 --- a/package-lock.json +++ b/package-lock.json @@ -22,7 +22,6 @@ }, "devDependencies": { "bufferutil": "^4.0.2", - "canvas": "^2.7.0", "jest": "^26.6.0", "nodemon": "^2.0.6", "ts-node": "^9.1.0", @@ -896,6 +895,8 @@ "resolved": "https://registry.npmjs.org/@mapbox/node-pre-gyp/-/node-pre-gyp-1.0.8.tgz", "integrity": "sha512-CMGKi28CF+qlbXh26hDe6NxCd7amqeAzEqnS6IHeO6LoaKyM/n+Xw3HT1COdq8cuioOdlKdqn/hCmqPUOMOywg==", "dev": true, + "optional": true, + "peer": true, "dependencies": { "detect-libc": "^1.0.3", "https-proxy-agent": "^5.0.0", @@ -916,6 +917,8 @@ "resolved": "https://registry.npmjs.org/nopt/-/nopt-5.0.0.tgz", "integrity": "sha512-Tbj67rffqceeLpcRXrT7vKAN8CwfPeIBgM7E6iBkmKLV7bEMwpGgYLGv0jACUsECaa/vuxP0IjEont6umdMgtQ==", "dev": true, + "optional": true, + "peer": true, "dependencies": { "abbrev": "1" }, @@ -931,6 +934,8 @@ "resolved": "https://registry.npmjs.org/semver/-/semver-7.3.5.tgz", "integrity": "sha512-PoeGJYh8HK4BTO/a9Tf6ZG3veo/A7ZVsYrSA6J8ny9nb3B1VrpkuN+z9OE5wfE5p6H4LchYZsegiQgbJD94ZFQ==", "dev": true, + "optional": true, + "peer": true, "dependencies": { "lru-cache": "^6.0.0" }, @@ -1172,6 +1177,8 @@ "resolved": "https://registry.npmjs.org/agent-base/-/agent-base-6.0.2.tgz", "integrity": "sha512-RZNwNclF7+MS/8bDg70amg32dyeZGZxiDuQmZxKLAlQjr3jGyLx+4Kkk58UO7D2QdgFIQCovuSuZESne6RG6XQ==", "dev": true, + "optional": true, + "peer": true, "dependencies": { "debug": "4" }, @@ -1184,6 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"sha1-hMbhWbgZBP3KWaDvRM2HDTElD5o=", - "dev": true + "dev": true, + "optional": true, + "peer": true }, "node_modules/depd": { "version": "1.1.2", @@ -2507,6 +2534,8 @@ "resolved": "https://registry.npmjs.org/detect-libc/-/detect-libc-1.0.3.tgz", "integrity": "sha1-+hN8S9aY7fVc1c0CrFWfkaTEups=", "dev": true, + "optional": true, + "peer": true, "bin": { "detect-libc": "bin/detect-libc.js" }, @@ -3143,6 +3172,8 @@ "resolved": "https://registry.npmjs.org/fs-minipass/-/fs-minipass-2.1.0.tgz", "integrity": "sha512-V/JgOLFCS+R6Vcq0slCuaeWEdNC3ouDlJMNIsacH2VtALiu9mV4LPrHc5cDl8k5aw6J8jwgWWpiTo5RYhmIzvg==", "dev": true, + "optional": true, + "peer": true, "dependencies": { "minipass": "^3.0.0" }, @@ -3180,6 +3211,8 @@ "resolved": "https://registry.npmjs.org/gauge/-/gauge-3.0.2.tgz", "integrity": "sha512-+5J6MS/5XksCuXq++uFRsnUd7Ovu1XenbeuIuNRJxYWjgQbPuFhT14lAvsWfqfAmnwluf1OwMjz39HjfLPci0Q==", "dev": true, + "optional": true, + "peer": true, "dependencies": { "aproba": "^1.0.3 || ^2.0.0", "color-support": "^1.1.2", @@ -3421,7 +3454,9 @@ "version": "2.0.1", "resolved": "https://registry.npmjs.org/has-unicode/-/has-unicode-2.0.1.tgz", "integrity": "sha1-4Ob+aijPUROIVeCG0Wkedx3iqLk=", - "dev": true + "dev": true, + "optional": true, + "peer": true }, "node_modules/has-value": { "version": "1.0.0", @@ -3559,6 +3594,8 @@ "resolved": "https://registry.npmjs.org/https-proxy-agent/-/https-proxy-agent-5.0.0.tgz", "integrity": "sha512-EkYm5BcKUGiduxzSt3Eppko+PiNWNEpa4ySk9vTC6wDsQJW9rHSa+UhGNJoRYp7bz6Ht1eaRIa6QaJqO5rCFbA==", "dev": true, + "optional": true, + "peer": true, "dependencies": { "agent-base": "6", "debug": "4" @@ -3572,6 +3609,8 @@ "resolved": "https://registry.npmjs.org/debug/-/debug-4.3.3.tgz", "integrity": "sha512-/zxw5+vh1Tfv+4Qn7a5nsbcJKPaSvCDhojn6FEl9vupwK2VCSDtEiEtqr8DFtzYFOdz63LBkxec7DYuc2jon6Q==", "dev": true, + "optional": true, + "peer": true, "dependencies": { "ms": "2.1.2" }, @@ -3588,7 +3627,9 @@ "version": "2.1.2", "resolved": 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"content-disposition": { "version": "0.5.3", @@ -10829,7 +10928,9 @@ "version": "1.0.0", "resolved": "https://registry.npmjs.org/delegates/-/delegates-1.0.0.tgz", "integrity": "sha1-hMbhWbgZBP3KWaDvRM2HDTElD5o=", - "dev": true + "dev": true, + "optional": true, + "peer": true }, "depd": { "version": "1.1.2", @@ -10845,7 +10946,9 @@ "version": "1.0.3", "resolved": "https://registry.npmjs.org/detect-libc/-/detect-libc-1.0.3.tgz", "integrity": "sha1-+hN8S9aY7fVc1c0CrFWfkaTEups=", - "dev": true + "dev": true, + "optional": true, + "peer": true }, "detect-newline": { "version": "3.1.0", @@ -11353,6 +11456,8 @@ "resolved": "https://registry.npmjs.org/fs-minipass/-/fs-minipass-2.1.0.tgz", "integrity": "sha512-V/JgOLFCS+R6Vcq0slCuaeWEdNC3ouDlJMNIsacH2VtALiu9mV4LPrHc5cDl8k5aw6J8jwgWWpiTo5RYhmIzvg==", "dev": true, + "optional": true, + "peer": true, "requires": { "minipass": "^3.0.0" } @@ -11380,6 +11485,8 @@ "resolved": "https://registry.npmjs.org/gauge/-/gauge-3.0.2.tgz", "integrity": 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"peer": true, "requires": { "minipass": "^3.0.0", "yallist": "^4.0.0" @@ -13305,7 +13424,9 @@ "version": "1.0.4", "resolved": "https://registry.npmjs.org/mkdirp/-/mkdirp-1.0.4.tgz", "integrity": "sha512-vVqVZQyf3WLx2Shd0qJ9xuvqgAyKPLAiqITEtqW0oIUjzo3PePDd6fW9iFz30ef7Ysp/oiWqbhszeGWW2T6Gzw==", - "dev": true + "dev": true, + "optional": true, + "peer": true }, "moment": { "version": "2.24.0", @@ -13321,7 +13442,9 @@ "version": "2.15.0", "resolved": "https://registry.npmjs.org/nan/-/nan-2.15.0.tgz", "integrity": "sha512-8ZtvEnA2c5aYCZYd1cvgdnU6cqwixRoYg70xPLWUws5ORTa/lnw+u4amixRS/Ac5U5mQVgp9pnlSUnbNWFaWZQ==", - "dev": true + "dev": true, + "optional": true, + "peer": true }, "nanomatch": { "version": "1.2.13", @@ -13364,6 +13487,8 @@ "resolved": "https://registry.npmjs.org/node-fetch/-/node-fetch-2.6.7.tgz", "integrity": "sha512-ZjMPFEfVx5j+y2yF35Kzx5sF7kDzxuDj6ziH4FFbOp87zKDZNx8yExJIb05OGF4Nlt9IHFIMBkRl41VdvcNdbQ==", "dev": true, + "optional": true, + "peer": true, "requires": { "whatwg-url": "^5.0.0" }, @@ -13372,19 +13497,25 @@ "version": "0.0.3", "resolved": "https://registry.npmjs.org/tr46/-/tr46-0.0.3.tgz", "integrity": "sha1-gYT9NH2snNwYWZLzpmIuFLnZq2o=", - "dev": true + "dev": true, + "optional": true, + "peer": true }, "webidl-conversions": { "version": "3.0.1", "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz", "integrity": "sha1-JFNCdeKnvGvnvIZhHMFq4KVlSHE=", - "dev": true + "dev": true, + "optional": true, + "peer": true }, "whatwg-url": { "version": "5.0.0", "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz", "integrity": "sha1-lmRU6HZUYuN2RNNib2dCzotwll0=", "dev": true, + "optional": true, + "peer": true, "requires": { "tr46": "~0.0.3", "webidl-conversions": "^3.0.0" @@ -13562,6 +13693,8 @@ "resolved": "https://registry.npmjs.org/npmlog/-/npmlog-5.0.1.tgz", "integrity": "sha512-AqZtDUWOMKs1G/8lwylVjrdYgqA4d9nu8hc+0gzRxlDb1I10+FHBGMXs6aiQHFdCUUlqH99MUMuLfzWDNDtfxw==", "dev": true, + "optional": true, + "peer": true, "requires": { "are-we-there-yet": "^2.0.0", "console-control-strings": "^1.1.0", @@ -13584,7 +13717,9 @@ "version": "4.1.1", "resolved": "https://registry.npmjs.org/object-assign/-/object-assign-4.1.1.tgz", "integrity": "sha1-IQmtx5ZYh8/AXLvUQsrIv7s2CGM=", - "dev": true + "dev": true, + "optional": true, + "peer": true }, "object-copy": { "version": "0.1.0", @@ -14612,13 +14747,17 @@ "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 + "dev": true, + "optional": true, + "peer": true }, "simple-get": { "version": "3.1.0", "resolved": "https://registry.npmjs.org/simple-get/-/simple-get-3.1.0.tgz", "integrity": "sha512-bCR6cP+aTdScaQCnQKbPKtJOKDp/hj9EDLJo3Nw4y1QksqaovlW/bnptB6/c1e+qmNIDHRK+oXFDdEqBT8WzUA==", "dev": true, + "optional": true, + "peer": true, "requires": { "decompress-response": "^4.2.0", "once": "^1.3.1", @@ -14630,6 +14769,8 @@ "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" } @@ -14638,7 +14779,9 @@ "version": "2.1.0", "resolved": "https://registry.npmjs.org/mimic-response/-/mimic-response-2.1.0.tgz", "integrity": "sha512-wXqjST+SLt7R009ySCglWBCFpjUygmCIfD790/kVbiGmUgfYGuB14PiTd5DwVxSV4NcYHjzMkoj5LjQZwTQLEA==", - "dev": true + "dev": true, + "optional": true, + "peer": true } } }, @@ -15029,6 +15172,8 @@ "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", @@ -15575,6 +15720,8 @@ "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" } diff --git a/package.json b/package.json index a8c829f..08b27bc 100644 --- a/package.json +++ b/package.json @@ -35,7 +35,6 @@ }, "devDependencies": { "bufferutil": "^4.0.2", - "canvas": "^2.7.0", "jest": "^26.6.0", "nodemon": "^2.0.6", "ts-node": "^9.1.0", diff --git a/src/bio-validator.js b/src/bio-validator.js deleted file mode 100644 index 00eb905..0000000 --- a/src/bio-validator.js +++ /dev/null @@ -1,165 +0,0 @@ -/** - * Created by rolando on 08/08/2018. - */ - -const Promise = require('bluebird'); -const path = require("path"); -const fs = require('fs'); -const Ajv = require("ajv/dist/2019").default; -const addFormats = require("ajv-formats"); -const request = require("request-promise"); -const AppError = require("./model/application-error"); - -const devMode = 0; -console.debug = devMode ? console.debug : () => { }; - - -/** - * - * Wraps the generic validator, outputs errors in custom format. - * - */ - -class BioValidator { - constructor(customKeywordValidators, baseSchemaPath){ - this.validatorCache = {}; - this.cachedSchemas = {}; - this.ajvInstance = this.constructAjv(customKeywordValidators); - this.baseSchemaPath = baseSchemaPath; - this.customKeywordValidators = customKeywordValidators; - } - - validate(inputSchema, inputObject) { - inputSchema["$async"] = true; - return new Promise((resolve, reject) => { - const compiledSchemaPromise = this.getValidationFunction(inputSchema); - - compiledSchemaPromise.then((validate) => { - Promise.resolve(validate(inputObject)) - .then((data) => { - if (validate.errors) { - resolve(validate.errors); - } else { - resolve([]); - } - } - ).catch((err) => { - if (!(err instanceof Ajv.ValidationError)) { - console.error("An error occurred while running the validation."); - reject(new AppError("An error occurred while running the validation.")); - } else { - console.debug("debug", this.ajvInstance.errorsText(err.errors, {dataVar: inputObject.alias})); - resolve(err.errors); - } - }); - }).catch((err) => { - console.error("async schema compiled encountered and error"); - console.error(err.stack); - reject(err); - }); - }); - } - - validateWithRemoteSchema(schemaUri, document) { - return this.getSchema(schemaUri) - .then(schema => {return this.validateSingleSchema(document, schema)}) - } - - getSchema(schemaUri) { - if(! this.cachedSchemas[schemaUri]) { - return new Promise((resolve, reject) => { - BioValidator.fetchSchema(schemaUri) - .then(schema => { - this.cachedSchemas[schemaUri] = schema; - resolve(schema); - }) - .catch(err => { - reject(err); - }) - }); - } else { - return Promise.resolve(this.cachedSchemas[schemaUri]); - } - } - - static fetchSchema(schemaUrl) { - return request({ - method: "GET", - url: schemaUrl, - json: true, - }); - } - - getValidationFunction(inputSchema) { - const schemaId = inputSchema['$id']; - - if(this.validatorCache[schemaId]) { - return Promise.resolve(this.validatorCache[schemaId]); - } else { - const compiledSchemaPromise = this.ajvInstance.compileAsync(inputSchema); - if(schemaId) { - this.validatorCache[schemaId] = compiledSchemaPromise; - } - return Promise.resolve(compiledSchemaPromise); - } - } - - constructAjv(customKeywordValidators) { - const ajvInstance = new Ajv({allErrors: true, strict:false, loadSchema: this.generateLoadSchemaRefFn()}); - const draft7MetaSchema = require("ajv/dist/refs/json-schema-draft-07.json") - ajvInstance.addMetaSchema(draft7MetaSchema) - addFormats(ajvInstance); - BioValidator._addCustomKeywordValidators(ajvInstance, customKeywordValidators); - - return ajvInstance - } - - static _addCustomKeywordValidators(ajvInstance, customKeywordValidators) { - customKeywordValidators.forEach(customKeywordValidator => { - ajvInstance = customKeywordValidator.configure(ajvInstance); - }); - - return ajvInstance; - } - - generateLoadSchemaRefFn() { - const cachedSchemas = this.cachedSchemas; - const baseSchemaPath = this.baseSchemaPath; - - const loadSchemaRefFn = (uri) => { - if(cachedSchemas[uri]) { - return Promise.resolve(cachedSchemas[uri]); - } else { - if (baseSchemaPath) { - let ref = path.join(baseSchemaPath, uri); - console.log('loading ref ' + ref); - let jsonSchema = fs.readFileSync(ref); - let loadedSchema = JSON.parse(jsonSchema); - loadedSchema["$async"] = true; - cachedSchemas[uri] = loadedSchema; - return Promise.resolve(loadedSchema); - } - else { - return new Promise((resolve, reject) => { - request({ - method: "GET", - url: uri, - json: true - }).then(resp => { - const loadedSchema = resp; - loadedSchema["$async"] = true; - cachedSchemas[uri] = loadedSchema; - resolve(loadedSchema); - }).catch(err => { - reject(err); - }); - }); - } - } - }; - - return loadSchemaRefFn; - } -} - -module.exports = BioValidator; diff --git a/src/cli/biovalidator-cli.js b/src/biovalidator-cli.js similarity index 88% rename from src/cli/biovalidator-cli.js rename to src/biovalidator-cli.js index b3ad11e..15f0504 100644 --- a/src/cli/biovalidator-cli.js +++ b/src/biovalidator-cli.js @@ -1,9 +1,9 @@ -const logger = require("../winston"); +const logger = require("./winston"); const fs = require("fs"); -const {log_error, log_info } = require("../utils/logger"); -const BioValidator2 = require("../biovalidator"); +const {log_error, log_info } = require("./utils/logger"); +const BioValidator = require("./biovalidator"); -class BioValidatorCLI2 { +class BioValidatorCLI { constructor(pathToSchema, pathToJson, schemaDirectory) { this.pathToSchema = pathToSchema this.pathToJson = pathToJson @@ -33,7 +33,7 @@ class BioValidatorCLI2 { validate() { this.inputSchema = this.read_schema(this.pathToSchema) this.jsonToValidate = this.read_json(this.pathToJson) - let biovalidator = new BioValidator2("/home/isuru/Projects/biovalidator/test/resources/schema_dir/*.json"); + let biovalidator = new BioValidator(this.schemaDirectory); if (this.inputSchema && this.jsonToValidate) { biovalidator.runValidation(this.inputSchema, this.jsonToValidate).then((output) => { @@ -75,4 +75,4 @@ class BioValidatorCLI2 { } } -module.exports = BioValidatorCLI2; +module.exports = BioValidatorCLI; diff --git a/src/biovalidator.js b/src/biovalidator.js index fa6537b..ab6a333 100644 --- a/src/biovalidator.js +++ b/src/biovalidator.js @@ -26,7 +26,7 @@ const customKeywordValidators = [ new GraphRestriction(null, "https://www.ebi.ac.uk/ols/api") ]; -class BioValidator2 { +class BioValidator { constructor(localSchemaPath) { this.validatorCache = {}; this.cachedSchemas = {}; @@ -192,14 +192,16 @@ class BioValidator2 { } preCompileLocalSchemas(ajv) { - let schemaFiles = getFiles(this.preCompiledSchemaDirectory); - for (let file of schemaFiles) { - let schema = readFile(file); - // ajv.addSchema(schema, schema["$id"]); - const validate = ajv.getSchema(schema["$id"] || ajv.compile(schema)); - this.cachedSchemas[schema["$id"]] = schema; + if (this.preCompiledSchemaDirectory) { + let schemaFiles = getFiles(this.preCompiledSchemaDirectory); + for (let file of schemaFiles) { + let schema = readFile(file); + // ajv.addSchema(schema, schema["$id"]); + const validate = ajv.getSchema(schema["$id"] || ajv.compile(schema)); + this.cachedSchemas[schema["$id"]] = schema; + } } } } -module.exports = BioValidator2; +module.exports = BioValidator; diff --git a/src/cli/bio-validator-cli.js b/src/cli/bio-validator-cli.js deleted file mode 100644 index 2dfa773..0000000 --- a/src/cli/bio-validator-cli.js +++ /dev/null @@ -1,75 +0,0 @@ -const runValidation = require("../validator"); -const logger = require("../winston"); -const fs = require("fs"); -const {log_error, log_info } = require("../utils/logger"); - -class BioValidatorCLI { - constructor(pathToSchema, pathToJson) { - this.pathToSchema = pathToSchema - this.pathToJson = pathToJson - } - - read_schema(pathToSchema) { - if (fs.existsSync(pathToSchema)) { - let schemaStr = fs.readFileSync(pathToSchema, 'utf-8') - return JSON.parse(schemaStr) - } else { - log_error("File '" + pathToSchema + "' does not exist!"); - process.exit(1); - } - } - - read_json(pathToJson) { - if (fs.existsSync(pathToJson)) { - let jsonStr = fs.readFileSync(pathToJson, 'utf-8') - return JSON.parse(jsonStr) - } else { - log_error("File '" + pathToJson + "' does not exist!"); - process.exit(1); - } - } - - validate() { - this.inputSchema = this.read_schema(this.pathToSchema) - this.jsonToValidate = this.read_json(this.pathToJson) - if (this.inputSchema && this.jsonToValidate) { - runValidation(this.inputSchema, this.jsonToValidate).then((output) => { - logger.log("silly", "Sent validation results."); - this.process_output(output); - }).catch((error) => { - console.error("console error: " + error); - logger.log("error", error); - }); - } else { - let appError = "Something is missing, both schema and object are required to execute validation."; - log_error(appError); - } - } - - process_output(output) { - if (output.length === 0) { - log_info("No validation errors reported."); - } else { - log_error("The validation process has found the following error(s):\n") - log_error(this.error_report(output)); - } - console.log("Validation finished."); - } - - error_report(jsonErrors) { - let errorOutput = ""; - jsonErrors.forEach( (errorObject) => { - const dataPath = errorObject.dataPath; - const errors = errorObject.errors; - let errorStr = ""; - errors.forEach( (error) => { - errorStr = errorStr.concat("\n\t", error); - }) - errorOutput = errorOutput.concat(dataPath + errorStr + "\n"); - }) - - return errorOutput; - } -} - -module.exports = BioValidatorCLI; diff --git a/src/server.js b/src/server.js index 5b61318..275780b 100644 --- a/src/server.js +++ b/src/server.js @@ -1,8 +1,8 @@ const express = require("express"); const bodyParser = require("body-parser"); const logger = require("./winston"); -const runValidation = require("./validator"); const AppError = require("./model/application-error"); +const BioValidator = require("./biovalidator") const argv = require("yargs").argv; const npid = require("npid"); @@ -12,6 +12,8 @@ const router = express.Router() const port = process.env.PORT || 3020; const basePath = process.env.VALIDATOR_BASE_URL || '/'; +const biovalidator = new BioValidator(); + router.use(express.static('src/views')); app.use(bodyParser.json()); @@ -37,11 +39,11 @@ app.use(function(err, req, res, next) { router.post("/validate", (req, res) => { logger.log("debug", "Received POST request."); - var inputSchema = req.body.schema; - var inputObject = req.body.object; + let inputSchema = req.body.schema; + let inputObject = req.body.object; if (inputSchema && inputObject) { - runValidation(inputSchema, inputObject).then((output) => { + biovalidator.runValidation(inputSchema, inputObject).then((output) => { logger.log("silly", "Sent validation results."); res.status(200).send(output); }).catch((error) => { diff --git a/src/utils/file_utils.js b/src/utils/file_utils.js index 66258bd..f64857e 100644 --- a/src/utils/file_utils.js +++ b/src/utils/file_utils.js @@ -7,11 +7,15 @@ function getFiles(filePattern) { const dataFiles = glob.sync(filePattern, {cwd: process.cwd()}) files = files.concat(dataFiles); } else { - files.push(filePattern); + if (fs.lstatSync(filePattern).isDirectory()) { + fs.readdirSync(filePattern).forEach(file => { + files.push(filePattern + "/" + file); + }); + } else { + files.push(filePattern); + } } - console.log(files) - console.log("files length: " + files.length) return files; } @@ -23,4 +27,4 @@ function readFile(filePath) { return jsonSchema; } -module.exports = { getFiles, readFile } +module.exports = {getFiles, readFile} diff --git a/src/validator.js b/src/validator.js deleted file mode 100644 index c3acb9f..0000000 --- a/src/validator.js +++ /dev/null @@ -1,57 +0,0 @@ -const logger = require("./winston"); -const ValidationError = require("./model/validation-error"); -const AppError = require("./model/application-error"); -const BioValidator = require("./bio-validator"); -const GraphRestriction = require("./keywords/graph_restriction"); -const { isChildTermOf, isValidTerm, isValidTaxonomy } = require("./keywords"); - -const validator = new BioValidator([ - new isChildTermOf(null, "https://www.ebi.ac.uk/ols/api/search?q="), - new isValidTerm(null, "https://www.ebi.ac.uk/ols/api/search?q="), - new isValidTaxonomy(null), - new GraphRestriction(null, "https://www.ebi.ac.uk/ols/api") -]); - -function convertToValidationErrors(ajvErrorObjects) { - let localErrors = []; - ajvErrorObjects.forEach( (errorObject) => { - let tempValError = new ValidationError(errorObject); - let index = localErrors.findIndex(valError => (valError.dataPath === tempValError.dataPath)); - - if(index !== -1) { - localErrors[index].errors.push(tempValError.errors[0]); - } else { - localErrors.push(tempValError); - } - }); - return localErrors; -} - -function runValidation(inputSchema, inputObject) { - logger.log("silly", "Running validation..."); - return new Promise((resolve, reject) => { - validator.validate(inputSchema, inputObject) - .then((validationResult) => { - if (validationResult.length === 0) { - resolve([]); - } else { - let ajvErrors = []; - validationResult.forEach(validationError => { - ajvErrors.push(validationError); - }); - - resolve(convertToValidationErrors(ajvErrors)); - } - } - ).catch((error) => { - if (error.errors) { - reject(new AppError(error.errors)); - } else { - logger.log("error", "An error ocurred while running the validation. Error : " + JSON.stringify(error)); - reject(new AppError("An error ocurred while running the validation.")); - } - }); - }); -} - -module.exports = runValidation; diff --git a/test/async-validation.test.js b/test/async-validation.test.js index 52ee5ce..780c4ce 100644 --- a/test/async-validation.test.js +++ b/test/async-validation.test.js @@ -1,5 +1,6 @@ const fs = require("fs"); -const runValidation = require("../src/validator"); +const BioValidator = require("../src/biovalidator") +const biovalidator = new BioValidator(); test(" -> isChildTermOf Schema", () => { let inputSchema = fs.readFileSync("examples/schemas/isChildTerm-schema.json", "utf-8"); @@ -8,7 +9,7 @@ test(" -> isChildTermOf Schema", () => { let inputObj = fs.readFileSync("examples/objects/isChildTerm.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - return runValidation(jsonSchema, jsonObj).then( (data) => { + return biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data[0]).toBeDefined(); expect(data[0].dataPath).toBe("/attributes/age/0/terms/0/url"); @@ -22,7 +23,7 @@ test("FAANG Schema - FAANG \'organism\' sample", () => { let inputObj = fs.readFileSync("examples/objects/faang-organism-sample.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - return runValidation(jsonSchema, jsonObj).then( (data) => { + return biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(0); }); @@ -35,7 +36,7 @@ test("FAANG Schema - \'specimen\' sample", () => { let inputObj = fs.readFileSync("examples/objects/faang-specimen-sample.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - return runValidation(jsonSchema, jsonObj).then( (data) => { + return biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(0); }); @@ -48,7 +49,7 @@ test("FAANG Schema - \'pool of specimens\' sample", () => { let inputObj = fs.readFileSync("examples/objects/faang-poolOfSpecimens-sample.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - return runValidation(jsonSchema, jsonObj).then( (data) => { + return biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(0); }); @@ -61,7 +62,7 @@ test("FAANG Schema - \'cell specimen\' sample", () => { let inputObj = fs.readFileSync("examples/objects/faang-cellSpecimen-sample.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - return runValidation(jsonSchema, jsonObj).then( (data) => { + return biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(0); }); @@ -74,7 +75,7 @@ test("FAANG Schema - \'cell culture\' sample", () => { let inputObj = fs.readFileSync("examples/objects/faang-cellCulture-sample.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - return runValidation(jsonSchema, jsonObj).then( (data) => { + return biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(0); }); @@ -87,7 +88,7 @@ test("FAANG Schema - \'cell line\' sample", () => { let inputObj = fs.readFileSync("examples/objects/faang-cellLine-sample.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - return runValidation(jsonSchema, jsonObj).then( (data) => { + return biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(0); }); diff --git a/test/bio-validator-cli.test.js b/test/bio-validator-cli.test.js index 5518b8d..53c574c 100644 --- a/test/bio-validator-cli.test.js +++ b/test/bio-validator-cli.test.js @@ -1,4 +1,4 @@ -const BioValidatorCLI = require("../src/cli/bio-validator-cli") +const BioValidatorCLI = require("../src/biovalidator-cli") test("Using wrong parameters results with error", () => { const mockExit = jest.spyOn(process, 'exit').mockImplementation(() => {}); @@ -43,3 +43,15 @@ test( "Invalid JSON should result with validation error", () => { expect(errorOutput).toEqual(expectedErrorOutput) }); + +test("Should be able to reference schemas from a directory", () => { + const mockExit = jest.spyOn(process, 'exit').mockImplementation(() => {}); + + const schema = "test/resources/ref_test_schema.json"; + const data = "test/resources/ref_test_valid.json"; + const ref = "test/resources/schema_dir/*"; + const cli = new BioValidatorCLI(schema, data, ref); + cli.validate(); + + +}); diff --git a/test/bio-validator.test.js b/test/bio-validator.test.js index 6dd8d53..b293727 100644 --- a/test/bio-validator.test.js +++ b/test/bio-validator.test.js @@ -1,8 +1,8 @@ const fs = require("fs"); -const BioValidator = require('../src/bio-validator'); +const BioValidator = require('../src/biovalidator'); test("Empty Schema (empty object)", () => { - const validator = new BioValidator([]); + const validator = new BioValidator(); return validator.validate({}, {}).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(0); @@ -16,7 +16,7 @@ test("Attributes Schema", () => { let inputObj = fs.readFileSync("examples/objects/attributes.json"); let jsonObj = JSON.parse(inputObj); - const validator = new BioValidator([]); + const validator = new BioValidator(); return validator.validate(jsonSchema, jsonObj).then((data) => { expect(data).toBeDefined(); @@ -33,7 +33,7 @@ test("BioSamples Schema - FAANG \'organism\' sample", () => { let inputObj = fs.readFileSync("examples/objects/faang-organism-sample.json"); let jsonObj = JSON.parse(inputObj); - const validator = new BioValidator([]); + const validator = new BioValidator(); return validator.validate(jsonSchema, jsonObj).then((data) => { expect(data).toBeDefined(); @@ -47,7 +47,7 @@ test("Study Schema", () => { let inputObj = fs.readFileSync("examples/objects/study.json"); let jsonObj = JSON.parse(inputObj); - const validator = new BioValidator([]); + const validator = new BioValidator(); return validator.validate(jsonSchema, jsonObj).then((data) => { expect(data).toBeDefined(); diff --git a/test/graphRestriction.test.js b/test/graphRestriction.test.js index 7bc66bd..a9446f5 100644 --- a/test/graphRestriction.test.js +++ b/test/graphRestriction.test.js @@ -1,5 +1,5 @@ const fs = require("fs"); -const BioValidator = require('../src/bio-validator'); +const BioValidator = require('../src/biovalidator'); const GraphRestriction = require('../src/keywords/graph_restriction'); @@ -10,7 +10,7 @@ test(" -> graphRestriction 1 Schema", () => { let inputObj = fs.readFileSync("examples/objects/graphRestriction_pass.json"); let jsonObj = JSON.parse(inputObj); - const validator = new BioValidator([new GraphRestriction(null, "https://www.ebi.ac.uk/ols/api")]); + const validator = new BioValidator(); return validator.validate(jsonSchema, jsonObj).then((data) => { expect(data).toBeDefined(); @@ -26,7 +26,7 @@ test(" -> graphRestriction 2 Schema", () => { let jsonObj = JSON.parse(inputObj); - const validator = new BioValidator([new GraphRestriction(null, "https://www.ebi.ac.uk/ols/api")]); + const validator = new BioValidator(); return validator.validate(jsonSchema, jsonObj).then((data) => { expect(data).toBeDefined(); @@ -41,7 +41,7 @@ test(" -> graphRestriction 3 Schema", () => { let jsonObj = JSON.parse(inputObj); - const validator = new BioValidator([new GraphRestriction(null, "https://www.ebi.ac.uk/ols/api")]); + const validator = new BioValidator(); return validator.validate(jsonSchema, jsonObj).then((data) => { expect(data).toBeDefined(); diff --git a/test/isChildTermOf.test.js b/test/isChildTermOf.test.js index 1d92085..42f93c3 100644 --- a/test/isChildTermOf.test.js +++ b/test/isChildTermOf.test.js @@ -1,5 +1,5 @@ const fs = require("fs"); -const BioValidator = require('../src/bio-validator'); +const BioValidator = require('../src/biovalidator'); const IsChildTermOf = require('../src/keywords/ischildtermof'); test("isChildTermOf", () => { @@ -11,7 +11,7 @@ test("isChildTermOf", () => { - const validator = new BioValidator([new IsChildTermOf(null, "https://www.ebi.ac.uk/ols/api/search?q=")]); + const validator = new BioValidator(); return validator.validate(jsonSchema, jsonObj).then((data) => { expect(data).toBeDefined(); diff --git a/test/isValidTaxonomy.test.js b/test/isValidTaxonomy.test.js index cdbe6a1..5ad2811 100644 --- a/test/isValidTaxonomy.test.js +++ b/test/isValidTaxonomy.test.js @@ -1,5 +1,5 @@ const fs = require("fs"); -const BioValidator = require('../src/bio-validator'); +const BioValidator = require('../src/biovalidator'); const IsValidTaxonomy = require('../src/keywords/isvalidtaxonomy'); test("valid taxonomy expression should pass the validation", () => { @@ -9,9 +9,7 @@ test("valid taxonomy expression should pass the validation", () => { let inputObj = fs.readFileSync("examples/objects/isValidTaxonomy.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - const schemaValidator = new BioValidator( - [new IsValidTaxonomy(null)] - ); + const schemaValidator = new BioValidator(); return schemaValidator.validate(jsonSchema, jsonObj).then( (data) => { console.log(data); @@ -27,9 +25,7 @@ test("invalid taxonomy expresson should return an error", () => { let inputObj = fs.readFileSync("examples/objects/isInvalidTaxonomy.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - const schemaValidator = new BioValidator( - [new IsValidTaxonomy(null)] - ) + const schemaValidator = new BioValidator() return schemaValidator.validate(jsonSchema, jsonObj).then( (data) => { console.log(data); diff --git a/test/isValidTerm.test.js b/test/isValidTerm.test.js index ea578d7..a446165 100644 --- a/test/isValidTerm.test.js +++ b/test/isValidTerm.test.js @@ -1,5 +1,5 @@ const fs = require("fs"); -const BioValidator = require('../src/bio-validator'); +const BioValidator = require('../src/biovalidator'); const IsValidTerm = require('../src/keywords/isvalidterm'); test("isValidTerm", () => { @@ -9,7 +9,7 @@ test("isValidTerm", () => { const inputObj = fs.readFileSync("examples/objects/isValidTerm.json"); const jsonObj = JSON.parse(inputObj); - const validator = new BioValidator([new IsValidTerm(null, 'https://www.ebi.ac.uk/ols/api/search?q=')]); + const validator = new BioValidator(); return validator.validate(jsonSchema, jsonObj).then((data) => { expect(data).toBeDefined(); diff --git a/test/sample_checklists.test.js b/test/sample_checklists.test.js index f1f76f2..f748cc2 100644 --- a/test/sample_checklists.test.js +++ b/test/sample_checklists.test.js @@ -1,5 +1,6 @@ const fs = require("fs"); -const runValidation = require("../src/validator"); +const BioValidator = require("../src/biovalidator") +const biovalidator = new BioValidator(); const checklistFolder = "test/resources/ena_samples/checklists/"; const validObjectFolder = "test/resources/ena_samples/objects/valid/"; const invalidObjectFolder = "test/resources/ena_samples/objects/invalid/"; @@ -15,7 +16,7 @@ describe("Sample Checklist tests", () => { let inputObj = fs.readFileSync(validObjectFolder + samplePrefix + file); let jsonObj = JSON.parse(inputObj); - runValidation(jsonSchema, jsonObj).then( (data) => { + biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(0); }); @@ -73,7 +74,7 @@ describe("Sample Checklist tests", () => { let inputObj = fs.readFileSync(invalidObjectFolder + samplePrefix + file); let jsonObj = JSON.parse(inputObj); - runValidation(jsonSchema, jsonObj).then( (data) => { + biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); if (missingPropertyMap.get(file) != null) { expect(data.length).toBe(1); diff --git a/test/supportsDrafts2019-9.test.js b/test/supportsDrafts2019-9.test.js index d1ff7df..705a303 100644 --- a/test/supportsDrafts2019-9.test.js +++ b/test/supportsDrafts2019-9.test.js @@ -1,5 +1,5 @@ const fs = require("fs"); -const BioValidator = require('../src/bio-validator'); +const BioValidator = require('../src/biovalidator'); test("draft2019-9Recursive", () => { let inputSchema = fs.readFileSync("examples/schemas/draft2019-9-support-schema.json"); @@ -10,7 +10,7 @@ test("draft2019-9Recursive", () => { - const validator = new BioValidator([]); + const validator = new BioValidator(); return validator.validate(jsonSchema, jsonObj).then((data) => { expect(data).toBeDefined(); diff --git a/test/validator.test.js b/test/validator.test.js index d8a3c5a..7f6384f 100644 --- a/test/validator.test.js +++ b/test/validator.test.js @@ -1,8 +1,9 @@ const fs = require("fs"); -const runValidation = require("../src/validator"); +const BioValidator = require("../src/biovalidator") +const biovalidator = new BioValidator(); test("Empty Schema (empty object)", () => { - return runValidation({}, {}).then( (data) => { + return biovalidator.runValidation({}, {}).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(0); }); @@ -15,7 +16,7 @@ test("Attributes Schema", () => { let inputObj = fs.readFileSync("examples/objects/attributes.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - return runValidation(jsonSchema, jsonObj).then( (data) => { + return biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(1); expect(data[0].errors.length).toBe(1); @@ -30,7 +31,7 @@ test("BioSamples Schema - FAANG \'organism\' sample", () => { let inputObj = fs.readFileSync("examples/objects/faang-organism-sample.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - return runValidation(jsonSchema, jsonObj).then( (data) => { + return biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(0); }); @@ -43,7 +44,7 @@ test("Study Schema", () => { let inputObj = fs.readFileSync("examples/objects/study.json", "utf-8"); let jsonObj = JSON.parse(inputObj); - return runValidation(jsonSchema, jsonObj).then( (data) => { + return biovalidator.runValidation(jsonSchema, jsonObj).then( (data) => { expect(data).toBeDefined(); expect(data.length).toBe(2); }); diff --git a/validator-cli.js b/validator-cli.js index 29aea5f..227ea17 100755 --- a/validator-cli.js +++ b/validator-cli.js @@ -16,17 +16,20 @@ const argv = yargs(hideBin(process.argv)) .demandOption(['schema', 'json']) .alias('s', 'schema') .alias('j', 'json') + .alias('r', 'ref') .describe('schema', 'path to the schema file') .describe('json', 'path to the json file to validate') + .describe('ref', 'path to referenced schema directory, file or glob pattern') .example('node ./validator-cli.js --json=valid.json --schema=test_schema.json', 'Validates \'valid.json\' with \'test_schema.json\'.') .argv -const BioValidatorCLI = require("./src/cli/bio-validator-cli"); +const BioValidatorCLI = require("./src/biovalidator-cli"); const {log_error} = require("./src/utils/logger"); let schema = argv["schema"] let json = argv["json"] +let schemaRef = argv["ref"] let isParameterMissing = false; if (!schema || schema === "" || typeof schema === "boolean") { @@ -41,6 +44,6 @@ if (!json || json === "" || typeof json === "boolean") { if (isParameterMissing || argv["help"]) { print_help() } else { - const bioValidator = new BioValidatorCLI(schema, json); + const bioValidator = new BioValidatorCLI(schema, json, schemaRef); bioValidator.validate() } diff --git a/validator-cli2.js b/validator-cli2.js deleted file mode 100755 index 839f0d2..0000000 --- a/validator-cli2.js +++ /dev/null @@ -1,47 +0,0 @@ -const yargs = require('yargs/yargs') -const { hideBin } = require('yargs/helpers') - -function get_usage() { - let helpText = "\nBio-validator CLI (Command Line Interface)\n"; - helpText = helpText.concat("usage: node ./validator-cli.js [--schema=path/to/schema] [--json=path/to/json]") - return helpText -} - -function print_help() { - console.log(get_usage()) -} - -const argv = yargs(hideBin(process.argv)) - .usage(get_usage()) - .demandOption(['schema', 'json']) - .alias('s', 'schema') - .alias('j', 'json') - .describe('schema', 'path to the schema file') - .describe('json', 'path to the json file to validate') - .example('node ./validator-cli.js --json=valid.json --schema=test_schema.json', - 'Validates \'valid.json\' with \'test_schema.json\'.') - .argv - -const BioValidatorCLI2 = require("./src/cli/biovalidator-cli"); -const {log_error} = require("./src/utils/logger"); - -let schema = argv["schema"] -let json = argv["json"] -let schemaDir = argv["schemaDir"] -let isParameterMissing = false; - -if (!schema || schema === "" || typeof schema === "boolean") { - log_error("Schema parameter or its value is missing!"); - isParameterMissing = true; -} -if (!json || json === "" || typeof json === "boolean") { - log_error("Json parameter or its value is missing!"); - isParameterMissing = true; -} - -if (isParameterMissing || argv["help"]) { - print_help() -} else { - const bioValidator = new BioValidatorCLI2(schema, json, schemaDir); - bioValidator.validate() -} From 4a156f1fbd75f69f8f7a15d7f75c2b11016b9808 Mon Sep 17 00:00:00 2001 From: Isuru Liyanage Date: Thu, 26 May 2022 15:25:55 +0100 Subject: [PATCH 7/9] support multiple local ref --- src/biovalidator-cli.js | 6 ++--- src/biovalidator.js | 9 +++---- src/utils/file_utils.js | 30 +++++++++++++++-------- test/resources/ref_test_invalid.json | 10 +++++--- test/resources/ref_test_schema.json | 6 ++--- test/resources/ref_test_valid.json | 12 ++++++--- test/resources/schema_dir/duo_schema.json | 19 ++++++++++++++ 7 files changed, 64 insertions(+), 28 deletions(-) create mode 100644 test/resources/schema_dir/duo_schema.json diff --git a/src/biovalidator-cli.js b/src/biovalidator-cli.js index 15f0504..f72dc2f 100644 --- a/src/biovalidator-cli.js +++ b/src/biovalidator-cli.js @@ -4,10 +4,10 @@ const {log_error, log_info } = require("./utils/logger"); const BioValidator = require("./biovalidator"); class BioValidatorCLI { - constructor(pathToSchema, pathToJson, schemaDirectory) { + constructor(pathToSchema, pathToJson, pathToRefSchema) { this.pathToSchema = pathToSchema this.pathToJson = pathToJson - this.schemaDirectory = schemaDirectory; + this.pathToRefSchema = pathToRefSchema; } read_schema(pathToSchema) { @@ -33,7 +33,7 @@ class BioValidatorCLI { validate() { this.inputSchema = this.read_schema(this.pathToSchema) this.jsonToValidate = this.read_json(this.pathToJson) - let biovalidator = new BioValidator(this.schemaDirectory); + let biovalidator = new BioValidator(this.pathToRefSchema); if (this.inputSchema && this.jsonToValidate) { biovalidator.runValidation(this.inputSchema, this.jsonToValidate).then((output) => { diff --git a/src/biovalidator.js b/src/biovalidator.js index ab6a333..af43add 100644 --- a/src/biovalidator.js +++ b/src/biovalidator.js @@ -30,7 +30,7 @@ class BioValidator { constructor(localSchemaPath) { this.validatorCache = {}; this.cachedSchemas = {}; - this.preCompiledSchemaDirectory = localSchemaPath; + this.localSchemaPath = localSchemaPath; this.ajvInstance = this.constructAjv(); } @@ -192,12 +192,11 @@ class BioValidator { } preCompileLocalSchemas(ajv) { - if (this.preCompiledSchemaDirectory) { - let schemaFiles = getFiles(this.preCompiledSchemaDirectory); + if (this.localSchemaPath) { + let schemaFiles = getFiles(this.localSchemaPath); for (let file of schemaFiles) { let schema = readFile(file); - // ajv.addSchema(schema, schema["$id"]); - const validate = ajv.getSchema(schema["$id"] || ajv.compile(schema)); + ajv.getSchema(schema["$id"] || ajv.compile(schema)); this.cachedSchemas[schema["$id"]] = schema; } } diff --git a/src/utils/file_utils.js b/src/utils/file_utils.js index f64857e..e0979b6 100644 --- a/src/utils/file_utils.js +++ b/src/utils/file_utils.js @@ -3,6 +3,26 @@ const glob = require('glob'); function getFiles(filePattern) { let files = []; + if (Array.isArray(filePattern)) { + for (let fp of filePattern) { + addFiles(fp, files); + } + } else { + addFiles(filePattern, files); + } + + return new Set(files); +} + +function readFile(filePath) { + let schema = fs.readFileSync(filePath).toString(); + let jsonSchema = JSON.parse(schema.toString()); + jsonSchema["$async"] = true; + + return jsonSchema; +} + +function addFiles(filePattern, files) { if (glob.hasMagic(filePattern)) { const dataFiles = glob.sync(filePattern, {cwd: process.cwd()}) files = files.concat(dataFiles); @@ -15,16 +35,6 @@ function getFiles(filePattern) { files.push(filePattern); } } - - return files; -} - -function readFile(filePath) { - let schema = fs.readFileSync(filePath).toString(); - let jsonSchema = JSON.parse(schema.toString()); - jsonSchema["$async"] = true; - - return jsonSchema; } module.exports = {getFiles, readFile} diff --git a/test/resources/ref_test_invalid.json b/test/resources/ref_test_invalid.json index 83ebbea..8d6bd2e 100644 --- a/test/resources/ref_test_invalid.json +++ b/test/resources/ref_test_invalid.json @@ -1,6 +1,10 @@ { - "name": "human", - "ontology": { - "id": "NCBITaxon:9606" + "name": "BioBank cohort study", + "duo": { + "term": { + "id": "DUO:0000022" + }, + "modifier": "UK", + "description": "Only accessible for researchers based in UK" } } diff --git a/test/resources/ref_test_schema.json b/test/resources/ref_test_schema.json index 856759a..b4ea4ec 100644 --- a/test/resources/ref_test_schema.json +++ b/test/resources/ref_test_schema.json @@ -6,9 +6,9 @@ "name": { "type": "string" }, - "ontology": { - "$ref": "https://www.ebi.ac.uk/ait/schema/ontology" + "duo": { + "$ref": "https://www.ebi.ac.uk/ait/schema/duo" } }, - "required": ["name", "ontology"] + "required": ["name", "duo"] } diff --git a/test/resources/ref_test_valid.json b/test/resources/ref_test_valid.json index 29aad6b..4ddd605 100644 --- a/test/resources/ref_test_valid.json +++ b/test/resources/ref_test_valid.json @@ -1,7 +1,11 @@ { - "name": "human", - "ontology": { - "id": "NCBITaxon:9606", - "label": "Homo sapiens" + "name": "BioBank cohort study", + "duo": { + "term": { + "id": "DUO:0000022", + "label": "geographical restriction" + }, + "modifier": "UK", + "description": "Only accessible for researchers based in UK" } } diff --git a/test/resources/schema_dir/duo_schema.json b/test/resources/schema_dir/duo_schema.json new file mode 100644 index 0000000..36b2477 --- /dev/null +++ b/test/resources/schema_dir/duo_schema.json @@ -0,0 +1,19 @@ +{ + "$schema": "http://json-schema.org/draft-07/schema#", + "$id": "https://www.ebi.ac.uk/ait/schema/duo", + "type": "object", + "properties": { + "term": { + "$ref": "https://www.ebi.ac.uk/ait/schema/ontology" + }, + "modifier": { + "type": "string" + }, + "description": { + "type": "string" + } + }, + "required": [ + "term" + ] +} From ff13fca85bba344e13954f335a9d6f8c8e34d9f8 Mon Sep 17 00:00:00 2001 From: Isuru Liyanage Date: Fri, 27 May 2022 16:44:27 +0100 Subject: [PATCH 8/9] fix glob file add error --- src/biovalidator-cli.js | 5 ++--- src/biovalidator.js | 1 + src/utils/file_utils.js | 2 +- 3 files changed, 4 insertions(+), 4 deletions(-) diff --git a/src/biovalidator-cli.js b/src/biovalidator-cli.js index f72dc2f..32943ff 100644 --- a/src/biovalidator-cli.js +++ b/src/biovalidator-cli.js @@ -7,7 +7,7 @@ class BioValidatorCLI { constructor(pathToSchema, pathToJson, pathToRefSchema) { this.pathToSchema = pathToSchema this.pathToJson = pathToJson - this.pathToRefSchema = pathToRefSchema; + this.biovalidator = new BioValidator(pathToRefSchema); } read_schema(pathToSchema) { @@ -33,10 +33,9 @@ class BioValidatorCLI { validate() { this.inputSchema = this.read_schema(this.pathToSchema) this.jsonToValidate = this.read_json(this.pathToJson) - let biovalidator = new BioValidator(this.pathToRefSchema); if (this.inputSchema && this.jsonToValidate) { - biovalidator.runValidation(this.inputSchema, this.jsonToValidate).then((output) => { + this.biovalidator.runValidation(this.inputSchema, this.jsonToValidate).then((output) => { logger.log("silly", "Sent validation results."); this.process_output(output); }).catch((error) => { diff --git a/src/biovalidator.js b/src/biovalidator.js index af43add..084c819 100644 --- a/src/biovalidator.js +++ b/src/biovalidator.js @@ -184,6 +184,7 @@ class BioValidator { cachedSchemas[uri] = loadedSchema; resolve(loadedSchema); }).catch(err => { + console.log("Failed to retrieve remote schema: " + uri) reject(err); }); }); diff --git a/src/utils/file_utils.js b/src/utils/file_utils.js index e0979b6..9eb69ba 100644 --- a/src/utils/file_utils.js +++ b/src/utils/file_utils.js @@ -25,7 +25,7 @@ function readFile(filePath) { function addFiles(filePattern, files) { if (glob.hasMagic(filePattern)) { const dataFiles = glob.sync(filePattern, {cwd: process.cwd()}) - files = files.concat(dataFiles); + files.push(...dataFiles); } else { if (fs.lstatSync(filePattern).isDirectory()) { fs.readdirSync(filePattern).forEach(file => { From 4e64146f0c6c8015769c956de35284bb4ef4f72a Mon Sep 17 00:00:00 2001 From: Isuru Liyanage Date: Tue, 7 Jun 2022 09:43:22 +0100 Subject: [PATCH 9/9] preparing for new release v1.10.0 --- package.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/package.json b/package.json index 08b27bc..e1dca0e 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "biovalidator", - "version": "1.9.2", + "version": "1.10.0", "description": "A nodejs JSON schema validator service. Extended from Ajv to include ontology validation.", "main": "src/server.js", "repository": "https://github.com/elixir-europe/biovalidator.git",