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Refactor: Schema Definition in TypeScript with Zod (#181)
* Create health router * Dictionary Routes moved into router Note: Changes route `/diff/` to `/dictionaries/diff` * Comments and minor changes * Refactor clients for external services into `/external` directory * Enforce TS strict and fix type issues * Major version bump, add immer and zod * Remove explicit paths declaration and rules redundant with strict * Copyright year update * Dictionary Schema defined with Zod * Move dictionary model to `/db` dir and base off new types * Move diff code to a service * Clean types, validate request inputs * Update types and db code reference * Move express handler wrappers to /routers dir * Clean up types, use immer for immutable changes * Handle ZodErrors thrown during requests * Use new types * Put `/diff` first to ensure it does not get blocked by `/:id` requests * Small type fixes * Update tests and fixtures to work with latest type validations * Provide some basic schema examples * Remove unused meta-schema * Move /diff to its own router * Organize all imports * Diff request path back to original * Organize Imports * Mocha Testing Config separate from npm scripts * Explicitly set `noImplicitAny` to enforce array.map type inference on unions * Move Reference Types to their own file * Refactor references utilities to use proper reference types * Move reference test fixtures and fix linebreak normalization tests * Proper formatting for beta version Co-authored-by: Anders Richardsson <[email protected]> * Comment clarification and typo correction Co-authored-by: Anders Richardsson <[email protected]> --------- Co-authored-by: Anders Richardsson <[email protected]>
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‎.mocharc.json

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{
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"extension": ["ts"],
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"require": "ts-node/register",
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"spec": "test/**/*.ts",
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"timeout": 35000
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}

‎package-lock.json

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‎package.json

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{
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"name": "lectern",
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"version": "1.14.0",
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"description": "Data Dictionary Management",
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"scripts": {
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"start": "npm run serve",
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"build": "npm run build-ts",
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"serve": "node dist/server.js",
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"watch-node": "nodemon dist/server.js",
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"test": "mocha --timeout 35000 --exit -r ts-node/register test/**/*.ts",
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"watch-test": "mocha --watch --timeout 35000 --exit -r ts-node/register test/**/*.ts",
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"build-ts": "tsc",
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"watch-ts": "tsc -w",
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"debug": "npm run build && npm run watch-debug",
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"serve-debug": "nodemon --inspect dist/server.js",
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"watch-debug": "nodemon --watch 'src/**/*.ts' --ignore 'src/**/*.spec.ts' --exec node --inspect-brk -r ts-node/register ./src/server.ts",
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"gitmoji-config": "gitmoji -g",
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"commit": "gitmoji -c"
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},
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"repository": {
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"type": "git",
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"url": "git+https://github.com/overture-stack/lectern.git"
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},
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"author": "andricDu",
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"license": "AGPL-3.0",
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"bugs": {
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"url": "https://github.com/overture-stack/lectern/issues"
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},
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"homepage": "https://github.com/overture-stack/lectern#readme",
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"devDependencies": {
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"@types/body-parser": "^1.19.2",
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"@types/chai": "^4.1.7",
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"@types/errorhandler": "0.0.32",
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"@types/express": "^4.17.13",
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"@types/jsonwebtoken": "^8.3.2",
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"@types/lodash": "^4.14.136",
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"@types/memoizee": "^0.4.7",
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"@types/mocha": "^5.2.7",
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"@types/ms": "^0.7.31",
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"@types/swagger-ui-express": "^3.0.1",
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"chai": "^4.3.6",
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"chai-http": "^4.3.0",
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"concurrently": "^5.3.0",
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"gitmoji-cli": "^4.8.0",
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"husky": "^3.1.0",
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"mocha": "^9.2.0",
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"nodemon": "^2.0.15",
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"prettier": "^2.8.0",
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"testcontainers": "^1.1.19",
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"ts-node": "^10.0.0",
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"typescript": "^5.0.0"
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},
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"dependencies": {
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"ajv": "^8.0.0",
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"axios": "^1.0.0",
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"body-parser": "^1.19.2",
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"dotenv": "^16.0.0",
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"errorhandler": "^1.5.1",
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"express": "^4.18.2",
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"jsonwebtoken": "^8.5.1",
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"lodash": "^4.17.21",
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"memoizee": "^0.4.15",
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"mongoose": "^7.0.0",
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"ms": "^2.1.3",
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"node-vault": "^0.9.22",
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"swagger-ui-express": "^4.3.0",
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"winston": "^3.6.0"
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},
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"prettier": {
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"printWidth": 120,
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"trailingComma": "all",
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"singleQuote": true,
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"arrowParens": "always",
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"useTabs": true
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}
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"name": "lectern",
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"version": "2.0.0-next.0",
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"description": "Data Dictionary Management",
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"scripts": {
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"start": "npm run serve",
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"build": "npm run build-ts",
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"serve": "node dist/server.js",
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"watch-node": "nodemon dist/server.js",
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"test": "mocha ",
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"watch-test": "mocha --watch",
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"build-ts": "tsc",
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"watch-ts": "tsc -w",
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"debug": "npm run build && npm run watch-debug",
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"serve-debug": "nodemon --inspect dist/server.js",
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"watch-debug": "nodemon --watch 'src/**/*.ts' --ignore 'src/**/*.spec.ts' --exec node --inspect -r ts-node/register ./src/server.ts",
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"gitmoji-config": "gitmoji -g",
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"commit": "gitmoji -c"
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},
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"repository": {
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"type": "git",
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"url": "git+https://github.com/overture-stack/lectern.git"
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},
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"author": "andricDu",
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"license": "AGPL-3.0",
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"bugs": {
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"url": "https://github.com/overture-stack/lectern/issues"
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},
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"homepage": "https://github.com/overture-stack/lectern#readme",
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"devDependencies": {
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"@types/body-parser": "^1.19.2",
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"@types/chai": "^4.1.7",
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"@types/errorhandler": "0.0.32",
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"@types/express": "^4.17.13",
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"@types/jsonwebtoken": "^8.3.2",
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"@types/lodash": "^4.14.136",
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"@types/memoizee": "^0.4.7",
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"@types/mocha": "^5.2.7",
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"@types/ms": "^0.7.31",
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"@types/swagger-ui-express": "^3.0.1",
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"chai": "^4.3.6",
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"chai-http": "^4.3.0",
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"concurrently": "^5.3.0",
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"gitmoji-cli": "^4.8.0",
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"husky": "^3.1.0",
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"mocha": "^9.2.0",
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"nodemon": "^2.0.15",
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"prettier": "^2.8.0",
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"testcontainers": "^1.1.19",
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"ts-node": "^10.0.0",
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"typescript": "^5.0.0"
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},
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"dependencies": {
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"ajv": "^8.0.0",
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"axios": "^1.0.0",
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"body-parser": "^1.19.2",
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"dotenv": "^16.0.0",
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"errorhandler": "^1.5.1",
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"express": "^4.18.2",
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"immer": "^10.0.2",
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"jsonwebtoken": "^8.5.1",
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"lodash": "^4.17.21",
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"memoizee": "^0.4.15",
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"mongoose": "^7.0.0",
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"ms": "^2.1.3",
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"node-vault": "^0.9.22",
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"swagger-ui-express": "^4.3.0",
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"winston": "^3.6.0",
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"zod": "^3.21.4"
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},
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"prettier": {
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"printWidth": 120,
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"trailingComma": "all",
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"singleQuote": true,
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"arrowParens": "always",
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"useTabs": true
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}
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}

‎samples/dictionary/simple.json

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{
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"name": "Simple",
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"version": "1.0",
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"schemas": [
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{
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"name": "primatives",
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"description": "Includes one field of each primative type without any restrictions. No Frills.",
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"fields": [
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{ "name": "boolean_field", "valueType": "boolean" },
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{ "name": "integer_field", "valueType": "integer" },
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{ "name": "number_field", "valueType": "number" },
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{ "name": "string_field", "valueType": "string" }
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]
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}
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]
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}

‎samples/schemas/primatives.json

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{
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"name": "primatives",
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"description": "Includes one field of each primative type without any restrictions. No Frills.",
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"fields": [
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{ "name": "boolean_field", "valueType": "boolean" },
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{ "name": "integer_field", "valueType": "integer" },
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{ "name": "number_field", "valueType": "number" },
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{ "name": "string_field", "valueType": "string" }
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]
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}

‎src/app-health.ts

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/*
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* Copyright (c) 2020 The Ontario Institute for Cancer Research. All rights reserved
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* Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved
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*
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* This program and the accompanying materials are made available under the terms of
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* the GNU Affero General Public License v3.0. You should have received a copy of the

‎src/app.ts

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/*
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* Copyright (c) 2020 The Ontario Institute for Cancer Research. All rights reserved
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* Copyright (c) 2023 The Ontario Institute for Cancer Research. All rights reserved
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*
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* This program and the accompanying materials are made available under the terms of
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* the GNU Affero General Public License v3.0. You should have received a copy of the
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* ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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*/
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import express, { RequestHandler, Express } from 'express';
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import bodyParser from 'body-parser';
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import { AppConfig } from './config/appConfig';
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import * as dictionaryController from './controllers/dictionaryController';
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import { errorHandler } from './utils/errors';
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import express, { Express } from 'express';
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import * as swaggerUi from 'swagger-ui-express';
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import * as swagger from './config/swagger.json';
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import ego from './services/egoTokenService';
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import logger from './config/logger';
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import { dbHealth, Status } from './app-health';
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/**
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* Decorator to handle errors from async express route handlers
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*/
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const wrapAsync = (fn: RequestHandler<any, any, any, any>): RequestHandler => {
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return (req, res, next) => {
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const routePromise: any = fn(req, res, next);
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if (routePromise.catch) {
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routePromise.catch(next);
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}
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};
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};
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import { AppConfig } from './config/appConfig';
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import logger from './config/logger';
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import * as swagger from './config/swagger.json';
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import dictionaryRouter from './routers/dictionaryRouter';
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import diffRouter from './routers/diffRouter';
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import healthRouter from './routers/healthRouter';
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import { errorHandler } from './utils/errors';
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const App = (config: AppConfig): Express => {
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/**
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* Auth Decorator
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*/
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const egoDecorator = process.env.AUTH_ENABLED === 'true' ? ego() : wrapAsync;
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// Create Express server with mongoConfig
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const app = express();
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const serverPort = config.serverPort();
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}),
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);
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swagger['info']['version'] = process.env.npm_package_version;
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app.use(openApiPath, swaggerUi.serve, swaggerUi.setup(swagger));
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logger.info(`OpenAPI setup... done: http://localhost:${serverPort}${openApiPath}`);
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app.get('/health', (req, res) => {
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if (dbHealth.status == Status.OK) {
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const resBody = {
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appStatus: 'Up',
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dbStatus: dbHealth.status,
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};
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return res.status(200).send(resBody);
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} else {
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const resBody = {
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appStatus: 'Error/Unknown',
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dbStatus: dbHealth.status,
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};
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return res.status(500).send(resBody);
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}
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});
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// Root Handler:
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app.get('/', (_, res) => {
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const details = {
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app: 'Lectern',
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version: process.env.npm_package_version,
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commit: process.env.COMMIT_SHA,
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};
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res.send(details);
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});
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app.use('/health', healthRouter);
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app.use('/dictionaries', dictionaryRouter);
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app.use('/diff', diffRouter);
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app.get('/dictionaries', wrapAsync(dictionaryController.listDictionaries));
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app.post('/dictionaries', egoDecorator(dictionaryController.createDictionary));
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app.get('/dictionaries/:dictId', wrapAsync(dictionaryController.getDictionary));
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app.post('/dictionaries/:dictId/schemas', egoDecorator(dictionaryController.addSchema));
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app.put('/dictionaries/:dictId/schemas', egoDecorator(dictionaryController.updateSchema));
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app.get('/diff/', wrapAsync(dictionaryController.diffDictionaries));
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/**
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* Swagger Setup
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*/
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swagger.info.version = process.env.npm_package_version || '';
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app.use(openApiPath, swaggerUi.serve, swaggerUi.setup(swagger));
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logger.info(`Access swagger docs: http://localhost:${serverPort}${openApiPath}`);
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// Error handler must be added last to capture all thrown errors.
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app.use(errorHandler);
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return app;

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