diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..40b878d --- /dev/null +++ b/.dockerignore @@ -0,0 +1 @@ +node_modules/ \ No newline at end of file diff --git a/.editorconfig b/.editorconfig new file mode 100644 index 0000000..1fd9498 --- /dev/null +++ b/.editorconfig @@ -0,0 +1,23 @@ +# https://editorconfig.org + + # Taken from Facebook's config + + # top-most EditorConfig file + root = true + + [*] + charset = utf-8 + # Unix-style newlines with a newline ending every file + end_of_line = lf + insert_final_newline = true + indent_size = 2 + indent_style = space + max_line_length = 80 + trim_trailing_whitespace = true + + [*.md] + max_line_length = 0 + trim_trailing_whitespace = false + + [COMMIT_EDITMSG] + max_line_length = 0 \ No newline at end of file diff --git a/.env-example b/.env-example new file mode 100644 index 0000000..ff8ec36 --- /dev/null +++ b/.env-example @@ -0,0 +1,29 @@ +# Basic config used whether running in the local Docker env or in the cloud +LOG_LEVEL=debug +DMSP_BASE_URL=https://doi.org/10.11111/ZZ + +# If you are running this system locally and want to run "offline" you should +# set this variable to `true` +USE_MOCK_DATA=false + +# If you want access to live data you will need to set the above variable to `false` +# and then provide fill out the following variables +AWS_REGION=us-west-2 + +# JSON Web Token (JWT) settings +JWT_SECRET=ihef93hgf9-u3hgfi3hfte4g4tg4tg4 +JWT_TTL=1hr + +# DMPHub API +DMPHUB_AUTH_URL=https://auth.mydomain.edu +DMPHUB_API_BASE_URL=https://api.mydomain.edu +DMPHUB_API_CLIENT_ID=1234567890 +DMPHUB_API_CLIENT_SECRET=zyxwvutsrq + +# MySQL database connections +MYSQL_CONNECTION_LIMIT=5 +MYSQL_HOST=localhost +MYSQL_PORT=3306 +MYSQL_DATABASE=dmsp +MYSQL_USER=root +MYSQL_PASSWORD= diff --git a/.gitignore b/.gitignore index f49edc8..2748a46 100644 --- a/.gitignore +++ b/.gitignore @@ -1,14 +1,23 @@ # Ignore the Dotenv file .env +# Ignore the local data-migration log. +data-migrations/processed.log + # Skip all of the dependencies in node_modules node_modules/ # Skip the compile distribution files dist/ -# testing -/coverage +# Skip the Jest code coverage folder +coverage/ + +# Ignore the persisted data sources for the local Docker dev env +docker/ + +# Ignore VS Code files, like the launch.json file +.vscode/ -# Visual Studio Code -.vscode +# OS specific files +.DS_Store diff --git a/CHANGELOG.md b/CHANGELOG.md new file mode 100644 index 0000000..1662d8b --- /dev/null +++ b/CHANGELOG.md @@ -0,0 +1,34 @@ + +### Added +- Schema, Mocks, Models and Resolvers for Affiliations and tests for the Models and Resolvers +- Added new DataSource for the DmptoolApi with endpoints for Affiliations and a new mock for this data source for use in tests + +### Updated +- Updated schemas.ts, resolvers.ts, mocks.ts and codegen.ts to use new Affiliation files +- Updated express.ts middleware file to pull in and initialize the new DmptoolApi datasource + +## v0.1 +Initial Apollo Server build + +### Added +- Added unit tests for User model and contributorRole resolver, and added @types/pino +- Added editor config +- initial Apollo server config +- Initial Schema for ContributorRole +- Initial Schema for DMSP +- Resolvers for ContributorRole +- Initial resolver to fetch a single DMSP from the DMPHub API +- Initial DMPHub API data source +- Initial MySQL data source +- Custom GraphQL scalars for ROR, ORCID and DMSP IDs +- Mechanism for Apollo to use mocks when a resolver has not yet been implemented +- Mocks for User +- Data migration mechanism `./data-migrations/process.sh` +- Documentation! +- Local Docker Compose config +- Pino logger with ECS formatter +- Plugin to log request/response lifecycle events +- Add Logger to the context and then used it in the resolvers + +### Updated +- Made some updates to auth code based on testing out recent changes with frontend [#34] \ No newline at end of file diff --git a/Dockerfile b/Dockerfile new file mode 100644 index 0000000..d8f0b27 --- /dev/null +++ b/Dockerfile @@ -0,0 +1,26 @@ +# Dockerfile +# preferred node version chosen here (22.1.0-alpine3.19 as of 05/04/2024) +FROM public.ecr.aws/docker/library/node:22.1.0-alpine3.19 + +# Create the directory on the node image +# where our Next.js app will live +RUN mkdir -p /app + +# Set /app as the working directory in container +WORKDIR /app + +# Copy package.json and package-lock.json +# to the /app working directory +COPY package*.json tsconfig.json codegen.ts .env ./ + +# Copy the rest of our Apollo Server folder into /app +COPY . . + +# Install dependencies in /app +RUN npm install + +# Ensure port 3000 is accessible to our system +EXPOSE 4000 + +# Command to run the Next.js app in development mode +CMD ["npm", "run", "dev"] diff --git a/Dockerfile.aws b/Dockerfile.aws new file mode 100644 index 0000000..3d5da21 --- /dev/null +++ b/Dockerfile.aws @@ -0,0 +1,20 @@ +# syntax = docker/dockerfile:1 + +# This version of the Dockerfile is used by the buildspec.yaml within the AWS environment +FROM public.ecr.aws/docker/library/node:current-alpine + +# Create the directory on the node image where our Apollo server will live +RUN mkdir -p /dist + +# Copy package.json and package-lock.json to the /app working directory +COPY package*.json ./ + +# Build the node_modules for production mode +RUN npm install + +# The app was built in the CodeBuild buildspec.yaml, so just copy dist/ in +COPY dist/ ./dist + +EXPOSE 4000 + +CMD ["node", "dist/index.js"] diff --git a/README.md b/README.md index c8ac147..744e10a 100644 --- a/README.md +++ b/README.md @@ -2,4 +2,65 @@ Apollo Server to support GraphQL interactions with the UI and external partners. -To run locally: `npm start` +Our Apollo server installation consists of: +- Data Sources: Code used to communicate with external APIs, databases, file systems, etc. +- GraphQL Schemas: The definition of our Graph including types, queries and mutations +- Resolvers: The code that processes incoming queries and uses the available data sources to generate the results +- Mocks: Stub or placeholder data that can be returned when a resolver has not yet been developed + +## Installation +- Make a local copy of the example dotenv file: `cp .env-example .env` +- Setup MySQL: + - If you are running on a Mac: + - If you have homebrew installed, run `brew install mysql` and then start it `brew services start mysql` + - Initialize the Database and the dataMigrations table: `./data-migrations/database-init.sh` + - Run all database migrations: `./data-migrations/process.sh` +- Install all of the dependencies: `npm install` +- Generate the Typescript types: `npm run generate` +- Startup the application in development mode: `npm run dev` +- Navigate to `http://localhost:4000` in your browser + +## Running current database migrations +- See the readme file in the `data-migrations` directory for instructions on running data migrations in your local environment. + +## Adding a new query/mutation +You should always start by updating an existing GraphQL Schema file or adding a new one to the `src/schemas` directory. + +Please include comments everywhere. These comments appear in the GraphQL explorer and help others undertand how to interact with the query or mutation. + +If you added a new schema file, make sure you update the `src/schemas.ts` file to pull in the new file when the server starts up. + +Once the schema has been added, you will need to run `npm run generate` this kicks off a script that builds out Typescript Types for the new schema and queries. + +### Create a new Model +You will need to create a Model if your new query/mutation will need to transform the response from the data source in any way prior to sending it to the caller or to the data source. + +For example: +- If my data source returns a property called `funder_id` and I want to send a boolean flag called `isFunder` to the caller, I perform the logic in a Model. +- If I simply want to rename a property prior to returning it to the client like the data source returning `identifier` but needing to send `DMPId` to the caller. + +Make sure that you transform the raw response from the data source into your Model in your new resolver. +For example: +``` +const response = await someDataSource.query('test'); +return new MyModel(response); +``` + +### Create a Mock +If you will be unable to create the corresponding resolver(s) at this point because of time constraints or because the data source is not yet ready, then you should add a new Mock file to the `src/schemas/` directory (or update and existing one with your changes). If you add a new mock be sure to update the `src/mocks.ts` to pull in your new mock when the server starts up. + +Note that mocks should represent the data structure that will be returned from your resolver to the caller. NOT the dtat structure that the resolver receives from the data source! + +### Create a Resolver +If your data source is ready and you have the bandwidth, add a new Resolver to the `src/resolvers/` directory (or update one with your new query/mutation). If you add a new Resolver be sure to update the `src/resolvers.ts` file to make sure it is included when the server starts up. + +### Add tests +You MUST add tests if you added or modified a Model! To do so, find the corresponding file (or add a new one) in the `src/models/__tests_/` directory. + +Resolver tests are not yet particularly useful. We will be updating this to add these integration tests in the near future. + +## Useful commands +- To run the Codegen utility to generate our Typescript types: `npm run generate` +- To run the server in development mode: `npm run dev` +- To run the server normally: `npm start` +- To build the application: `npm run build` diff --git a/buildspec.yaml b/buildspec.yaml new file mode 100644 index 0000000..9df026e --- /dev/null +++ b/buildspec.yaml @@ -0,0 +1,79 @@ +# Build specifications for AWS CodeBuild +# See: https://docs.aws.amazon.com/codebuild/latest/userguide/build-spec-ref.html + +# Each input artifact is extracted to its own directory by CodePipeline, the locations of which +# are stored in environment variables. The directory for the primary source artifact (this repo) +# is made available with $CODEBUILD_SRC_DIR. The directory for the DMPTool push artifacts is +# made available with $CODEBUILD_SRC_DIR_dmptool-commit. +# Do not change version. This is the version of aws buildspec, not the version of your buldspec file. +version: 0.2 + +phases: + install: + runtime-versions: + # Apollo gives error when building on < 21 + nodejs: 21 + commands: + # Install any libraries necessary for testing and compilation + # - echo Installing Mocha... + # - npm install -g mocha + pre_build: + commands: + # Set some ENV variables here because CF only allows a limit of 1000 characters in the + # EnvironmentVariable config for the Pipeline action :( + - export AWS_VERSION=$(aws --version) + + # Fetch the ECR repository name + - echo $ECR_REPOSITORY_URI >> .ecr + - export SHORT_ECR_URI=$(awk '{gsub("$ECR_REPOSITORY_NAME", "");print}' .ecr) + - rm .ecr + + # Set the repository URI to your ECR image and add an image tag with the first seven characters of the Git + # commit ID of the source. + - echo Logging in to Amazon ECR ... + - aws ecr get-login-password --region $AWS_REGION | docker login --username AWS --password-stdin $SHORT_ECR_URI + - IMAGE_TAG=${COMMIT_HASH:=apollo-latest} + + # Install MySQL so we can run DB migrations + # - dnf -y install mariadb105 + build: + commands: + - echo "Running build in ${NODE_ENV} mode - started on `date`" + - cd $CODEBUILD_SRC_DIR + + # - echo Checking for DB migrations + # - cd $CODEBUILD_SRC_DIR + # - cd data-migrations && ./process-aws.sh $NODE_ENV && cd .. + + # Install all of the dependencies (including dev so we can compile TS) + - npm install --production=false + + # Generate all of the GraphQL schema types + - npm run generate + + # Run any tests here + # - npm run test + + # Build the Apollo server which writes to the ./dist dir + - npm run build + + - echo Building the Docker image... + - docker build -f Dockerfile.aws -t $SHORT_ECR_URI:apollo-latest . + - docker tag $ECR_REPOSITORY_URI:apollo-latest $SHORT_ECR_URI:$IMAGE_TAG + post_build: + commands: + # Push the Docker image to the ECR repository. Fargate will pick it up an deploy automatically + - echo Build completed on `date` + - echo Pushing the Docker images... + - cd $CODEBUILD_SRC_DIR + - docker push $SHORT_ECR_URI:apollo-latest + - docker push $SHORT_ECR_URI:$IMAGE_TAG + + - echo Writing image definitions file... + - printf '[{"name":"%s","imageUri":"%s"}]' $TASK_DEFINITION_CONTAINER_NAME $ECR_REPOSITORY_URI:$IMAGE_TAG > imagedefinitions.json + + - echo Build completed on `date` + +artifacts: + # The Deploy step is expecting this name + files: imagedefinitions.json diff --git a/codegen.ts b/codegen.ts new file mode 100644 index 0000000..327326b --- /dev/null +++ b/codegen.ts @@ -0,0 +1,20 @@ +import type { CodegenConfig } from "@graphql-codegen/cli"; + +const config: CodegenConfig = { + schema: "./src/schemas/*.ts", + generates: { + "./src/types.ts": { + plugins: ["typescript", "typescript-resolvers"], + config: { + contextType: "./context#MyContext", + enumsAsTypes: true, + mappers: { + Dmsp: "./models/Dmsp#DmspModel", + ContributorRole: "./models/ContributorRole#ContributorRoleModel", + }, + }, + }, + }, +}; + +export default config; diff --git a/data-migrations/2024-05-02-1530-create-contributor-roles.sql b/data-migrations/2024-05-02-1530-create-contributor-roles.sql new file mode 100644 index 0000000..1444b5c --- /dev/null +++ b/data-migrations/2024-05-02-1530-create-contributor-roles.sql @@ -0,0 +1,11 @@ +CREATE TABLE `contributorRoles` ( + `id` int NOT NULL AUTO_INCREMENT, + `label` varchar(255) NOT NULL, + `url` varchar(255) NOT NULL, + `description` text, + `displayOrder` int NOT NULL, + `created` timestamp DEFAULT CURRENT_TIMESTAMP, + `modified` timestamp DEFAULT CURRENT_TIMESTAMP, + PRIMARY KEY (`id`), + CONSTRAINT unique_contributor_role_url UNIQUE (`url`) +) ENGINE=InnoDB AUTO_INCREMENT=1 DEFAULT CHARSET=utf8mb3; diff --git a/data-migrations/2024-05-03-1414-seed-contributor-roles.sql b/data-migrations/2024-05-03-1414-seed-contributor-roles.sql new file mode 100644 index 0000000..c253d8b --- /dev/null +++ b/data-migrations/2024-05-03-1414-seed-contributor-roles.sql @@ -0,0 +1,6 @@ +INSERT INTO contributorRoles (label, url, description, displayOrder) +VALUES + ('Data Manager', 'https://credit.niso.org/contributor-roles/data-curation/', 'An individual engaged in management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use.', 3), + ('Principal Investigator (PI)', 'https://credit.niso.org/contributor-roles/investigation/', 'An individual conducting a research and investigation process, specifically performing the experiments, or data/evidence collection.', 1), + ('Project Administrator', 'https://credit.niso.org/contributor-roles/project-administration/', 'An individual with management and coordination responsibility for the research activity planning and execution.', 2), + ('Other', 'http://dmptool.org/contributor_roles/other', '', 4); diff --git a/data-migrations/2024-06-04-1103-create-user-table.sql b/data-migrations/2024-06-04-1103-create-user-table.sql new file mode 100644 index 0000000..fb2caac --- /dev/null +++ b/data-migrations/2024-06-04-1103-create-user-table.sql @@ -0,0 +1,7 @@ +CREATE TABLE `users` ( + `id` INT AUTO_INCREMENT PRIMARY KEY, + `email` varchar(255) NOT NULL, + `password` varchar(255) NOT NULL, + `created` TIMESTAMP DEFAULT CURRENT_TIMESTAMP, + `modified` TIMESTAMP DEFAULT CURRENT_TIMESTAMP +) \ No newline at end of file diff --git a/data-migrations/2024-06-04-1255-update-user-table.sql b/data-migrations/2024-06-04-1255-update-user-table.sql new file mode 100644 index 0000000..3b28acf --- /dev/null +++ b/data-migrations/2024-06-04-1255-update-user-table.sql @@ -0,0 +1,8 @@ +ALTER TABLE `users` + ADD COLUMN `role` VARCHAR(16) AFTER `password`; + +ALTER TABLE `users` + ADD COLUMN `givenName` VARCHAR(255) AFTER `role`; + +ALTER TABLE `users` + ADD COLUMN `surName` VARCHAR(255) AFTER `givenName`; diff --git a/data-migrations/2024-06-07-1259-create-oauthClients.sql b/data-migrations/2024-06-07-1259-create-oauthClients.sql new file mode 100644 index 0000000..563bc8b --- /dev/null +++ b/data-migrations/2024-06-07-1259-create-oauthClients.sql @@ -0,0 +1,12 @@ +CREATE TABLE `oauthClients` ( + `id` INT AUTO_INCREMENT PRIMARY KEY, + `name` varchar(255) NOT NULL, + `redirectUris` text NOT NULL, + `grants` varchar(255) NOT NULL, + `clientId` varchar(255) NOT NULL, + `clientSecret` varchar(255) NOT NULL, + `userId` INT NOT NULL, + `created_at` TIMESTAMP DEFAULT CURRENT_TIMESTAMP, + `modified` TIMESTAMP DEFAULT CURRENT_TIMESTAMP, + CONSTRAINT unique_contributor_name UNIQUE (`name`) +); diff --git a/data-migrations/2024-06-07-1311-create-oauthCodes.sql b/data-migrations/2024-06-07-1311-create-oauthCodes.sql new file mode 100644 index 0000000..d18d812 --- /dev/null +++ b/data-migrations/2024-06-07-1311-create-oauthCodes.sql @@ -0,0 +1,11 @@ +CREATE TABLE `oauthCodes` ( + `code` varchar(255) PRIMARY KEY, + `redirectUri` varchar(255) NOT NULL, + `scope` varchar(255) NOT NULL, + `clientId` varchar(255) NOT NULL, + `userId` INT NOT NULL, + `codeChallenge` varchar(255), + `codeChallengeMethod` varchar(255), + `created_at` TIMESTAMP DEFAULT CURRENT_TIMESTAMP, + `modified` TIMESTAMP DEFAULT CURRENT_TIMESTAMP +) ENGINE=InnoDB AUTO_INCREMENT=1 DEFAULT CHARSET=utf8mb3; diff --git a/data-migrations/2024-06-07-1408-create-oauthTokens.sql b/data-migrations/2024-06-07-1408-create-oauthTokens.sql new file mode 100644 index 0000000..c1262ca --- /dev/null +++ b/data-migrations/2024-06-07-1408-create-oauthTokens.sql @@ -0,0 +1,11 @@ +CREATE TABLE `oauthTokens` ( + `token` varchar(255) PRIMARY KEY, + `expiresAt` DateTime, + `refreshToken` varchar(255), + `refreshTokenExpiresAt` DateTime, + `scope` varchar(255), + `clientId` varchar(255) NOT NULL, + `userId` INT NOT NULL, + `created_at` TIMESTAMP DEFAULT CURRENT_TIMESTAMP, + `modified` TIMESTAMP DEFAULT CURRENT_TIMESTAMP +) ENGINE=InnoDB AUTO_INCREMENT=1 DEFAULT CHARSET=utf8mb3; diff --git a/data-migrations/2024-06-07-1418-create-oauthRefreshTokens.sql b/data-migrations/2024-06-07-1418-create-oauthRefreshTokens.sql new file mode 100644 index 0000000..d763552 --- /dev/null +++ b/data-migrations/2024-06-07-1418-create-oauthRefreshTokens.sql @@ -0,0 +1,8 @@ +CREATE TABLE `oauthRefreshTokens` ( + `token` varchar(255) PRIMARY KEY, + `expiresAt` DateTime NOT NULL, + `clientId` varchar(255) NOT NULL, + `userId` INT NOT NULL, + `created_at` TIMESTAMP DEFAULT CURRENT_TIMESTAMP, + `modified` TIMESTAMP DEFAULT CURRENT_TIMESTAMP +) ENGINE=InnoDB AUTO_INCREMENT=1 DEFAULT CHARSET=utf8mb3; diff --git a/data-migrations/2024-06-07-1436-seed-users.sql b/data-migrations/2024-06-07-1436-seed-users.sql new file mode 100644 index 0000000..6eab695 --- /dev/null +++ b/data-migrations/2024-06-07-1436-seed-users.sql @@ -0,0 +1,12 @@ + +# TODO: Switch this to a script so that it uses the appropriate SALT! + +INSERT INTO `users` + (`email`, `password`, `givenName`, `surName`, `role`) +VALUES + ('orgA.user@example.com', '$2a$10$HeRb8Z2NK86pjJp300/flOt.xKK2hSkT1eLydo0KKNX8xrpLr3S7u', 'Harry', 'Potter', 'RESEARCHER'), + ('orgB.user@example.com', '$2a$10$HeRb8Z2NK86pjJp300/flOt.xKK2hSkT1eLydo0KKNX8xrpLr3S7u', 'Lucious', 'Malfoy', 'RESEARCHER'), + ('orgA.admin@example.com', '$2a$10$HeRb8Z2NK86pjJp300/flOt.xKK2hSkT1eLydo0KKNX8xrpLr3S7u', 'Alastor', 'Moody', 'ADMIN'), + ('orgB.admin@example.com', '$2a$10$HeRb8Z2NK86pjJp300/flOt.xKK2hSkT1eLydo0KKNX8xrpLr3S7u', 'Minerva', 'McGonagall', 'ADMIN'), + ('funder.admin@example.com', '$2a$10$HeRb8Z2NK86pjJp300/flOt.xKK2hSkT1eLydo0KKNX8xrpLr3S7u', 'Severus', 'Snape', 'ADMIN'), + ('super@example.com', '$2a$10$HeRb8Z2NK86pjJp300/flOt.xKK2hSkT1eLydo0KKNX8xrpLr3S7u', 'Albus', 'Dumbledore', 'SUPER_ADMIN'); diff --git a/data-migrations/2024-06-07-1437-seed-oauthClients.sql b/data-migrations/2024-06-07-1437-seed-oauthClients.sql new file mode 100644 index 0000000..14dfb9e --- /dev/null +++ b/data-migrations/2024-06-07-1437-seed-oauthClients.sql @@ -0,0 +1,7 @@ +INSERT INTO oauthClients + (name, redirectUris, grants, clientId, clientSecret, userId) +(SELECT + 'tester', 'http://localhost:3000/auth/callback', 'client_credentials, authorization_code', + '1234567890', UUID(), `users`.`id` +FROM users +WHERE users.email = 'orgA.admin@example.com'); diff --git a/data-migrations/2024-07-30-1334-add-affiliation-to-users.sql b/data-migrations/2024-07-30-1334-add-affiliation-to-users.sql new file mode 100644 index 0000000..cadb340 --- /dev/null +++ b/data-migrations/2024-07-30-1334-add-affiliation-to-users.sql @@ -0,0 +1,2 @@ +ALTER TABLE `users` + ADD COLUMN `affiliationId` VARCHAR(255) AFTER `surName`; diff --git a/data-migrations/2024-07-30-1338-seed-user-affiliations.sql b/data-migrations/2024-07-30-1338-seed-user-affiliations.sql new file mode 100644 index 0000000..dd27bb9 --- /dev/null +++ b/data-migrations/2024-07-30-1338-seed-user-affiliations.sql @@ -0,0 +1,4 @@ +UPDATE users SET affiliationId = 'https://ror.org/01nrxwf90' WHERE email LIKE '%A.%'; +UPDATE users SET affiliationId = 'https://ror.org/01tm6cn81' WHERE email LIKE '%B.%'; +UPDATE users SET affiliationId = 'https://ror.org/01cwqze88' WHERE email LIKE '%funder.%'; +UPDATE users SET affiliationId = 'https://ror.org/00dmfq477' WHERE affiliationId IS NULL; diff --git a/data-migrations/README.md b/data-migrations/README.md new file mode 100644 index 0000000..332b704 --- /dev/null +++ b/data-migrations/README.md @@ -0,0 +1,33 @@ +# Data Migrations + +This directory contains all of the necessary data migrations to build and alter a local instance of the application's database. We use a pattern similar to the one used by Rails. + +The `process.sh` file should be used to modify your local DB. When you run it, it will: +- Detect any `*.sql` files in this directory +- Run those SQL scripts against your local DB (using the credentials defined in your `.env` file if run locally or SSM if run from the Cloud9 Bastion instance) +- Update the `dataMigrations` table with the name(s) of file that was processed. + +The script checks the file names recorded in the `dataMigrations` table to determine whether or not it should run the migration. That means that you can delete the file name from this table and run the script if you need to rerun a migration for some reason. + +Migration file names start with a date and timestamp to ensure that they are run in the correct order. + +The `process-aws.sh` file is meant to be run from the AWS Clou9 instance only! + +## Running from the Cloud9 bastion server + +### Cloud9 initialization +First clone the Apollo server repository so that we have access to the latest DB migrations: +- `git clone https://github.com/CDLUC3/dmsp_backend_prototype.git` + +Checkout the version you want to work with (e.g. development) +- `cd ~/dmsp_backend_prototype/dmsp_backend_prototype` +- `git pull origin [branch]` +- `git checkout [branch]` + +Then run the initialization script to install the necessary packages to be able to run MySQL commands +- `~/dmsp_backend_prototype/data-migrations/bastion-init.sh` + +### Running the DB migrations +Make sure you are on the correct branch. Then run the following: +- `cd ~/dmsp_backend_prototype/data-migrations` +- `./process-aws.sh [ENV]` diff --git a/data-migrations/bastion-init.sh b/data-migrations/bastion-init.sh new file mode 100755 index 0000000..3b47b88 --- /dev/null +++ b/data-migrations/bastion-init.sh @@ -0,0 +1,5 @@ +echo 'Initializing Bastion to run MySQL data migrations' + +sudo yum install -y vim curl +sudo yum groupinstall -y "Development Tools" +sudo yum install -y mariadb105-devel diff --git a/data-migrations/database-init.sh b/data-migrations/database-init.sh new file mode 100755 index 0000000..e279b24 --- /dev/null +++ b/data-migrations/database-init.sh @@ -0,0 +1,23 @@ +# Load the Dotenv file +. .env + +CREATE_DATABASE="CREATE DATABASE IF NOT EXISTS ${MYSQL_DATABASE} + CHARACTER SET utf8mb4 + COLLATE utf8mb4_unicode_ci;" + +MIGRATIONS_TABLE="CREATE TABLE dataMigrations ( + migrationFile varchar(255) NOT NULL, + created timestamp DEFAULT CURRENT_TIMESTAMP, + PRIMARY KEY (migrationFile), + CONSTRAINT unique_migration_files UNIQUE (migrationFile) +) ENGINE=InnoDB AUTO_INCREMENT=1 DEFAULT CHARSET=utf8mb3;" + +echo "-h${MYSQL_HOST} -P${MYSQL_PORT} -u${MYSQL_USER} -p ${MYSQL_PASSWORD}" + +# Create the Database +echo "Creating database ${MYSQL_DATABASE} ..." +mysql -h${MYSQL_HOST} -P${MYSQL_PORT} -u${MYSQL_USER} -p ${MYSQL_PASSWORD} <<< ${CREATE_DATABASE} + +# Create the dataMigrations table which will be used going forward to store the migrations we have run +echo "Creating the dataMigrations table ..." +mysql -h${MYSQL_HOST} -P${MYSQL_PORT} -u${MYSQL_USER} -p ${MYSQL_PASSWORD} ${MYSQL_DATABASE} <<< ${MIGRATIONS_TABLE} diff --git a/data-migrations/process-aws.sh b/data-migrations/process-aws.sh new file mode 100755 index 0000000..61c0cc6 --- /dev/null +++ b/data-migrations/process-aws.sh @@ -0,0 +1,76 @@ +#!/bin/bash + +# ================================================================== +# = This script is meant to be run from the Cloud9 Bastion instance +# ================================================================== +if [ $# -ne 1 ]; then + echo 'Wrong number of arguments. Expecting 1: the env (e.g. `./process-aws.sh dev`)' + exit 1 +fi + +# Get the DB info from SSM +MYSQL_HOST=$(echo `aws ssm get-parameter --name /uc3/dmp/hub/${1}/DbHost | jq .Parameter.Value | sed -e "s/\"//g"`) +MYSQL_PORT=$(echo `aws ssm get-parameter --name /uc3/dmp/hub/${1}/DbPort | jq .Parameter.Value | sed -e "s/\"//g"`) +MYSQL_DATABASE=$(echo `aws ssm get-parameter --name /uc3/dmp/hub/${1}/DbName | jq .Parameter.Value | sed -e "s/\"//g"`) +MYSQL_USER=$(echo `aws ssm get-parameter --name /uc3/dmp/hub/${1}/DbUsername --with-decryption | jq .Parameter.Value | sed -e "s/\"//g"`) +MYSQL_PASSWORD=$(echo `aws ssm get-parameter --name /uc3/dmp/hub/${1}/DbPassword --with-decryption | jq .Parameter.Value | sed -e "s/\"//g"`) +MYSQL_ARGS="-h ${MYSQL_HOST} -P ${MYSQL_PORT} -u ${MYSQL_USER} -p${MYSQL_PASSWORD}" + +CREATE_DATABASE="CREATE DATABASE IF NOT EXISTS ${MYSQL_DATABASE} + CHARACTER SET utf8mb4 + COLLATE utf8mb4_unicode_ci;" + +MIGRATIONS_TABLE="CREATE TABLE dataMigrations ( + migrationFile varchar(255) NOT NULL, + created timestamp DEFAULT CURRENT_TIMESTAMP, + PRIMARY KEY (migrationFile), + CONSTRAINT unique_migration_files UNIQUE (migrationFile) +) ENGINE=InnoDB AUTO_INCREMENT=1 DEFAULT CHARSET=utf8mb3;" + +process_migration() { + # See if the migration was already processed + echo "Checking to see if $2 has been run ..." + EXISTS=$(mysql ${MYSQL_ARGS} -N ${MYSQL_DATABASE} <<< "SELECT * FROM dataMigrations WHERE migrationFile = '$2';") + if [ -z "$EXISTS" ]; then + # If not run it + echo "NEW MIGRATION - $2. Processing migration ..." + mysql ${MYSQL_ARGS} ${MYSQL_DATABASE} < $2 + WAS_PROCESSED=$? + + # If it worked then update the data-migrations table so we don't run it again! + if [ $WAS_PROCESSED -eq 0 ]; then + mysql ${MYSQL_ARGS} ${MYSQL_DATABASE} <<< "INSERT INTO dataMigrations (migrationFile) VALUES ('$2');" + echo " done" + else + echo " Something went wrong!" + fi + else + echo " already processed." + fi +} + +# Check to see if we have already run the migration file +echo "Checking to see if the database has been initialized" +mysql ${MYSQL_ARGS} -N ${MYSQL_DATABASE} <<< "SELECT * FROM dataMigrations WHERE migrationFile;" +INIT_CHECK=$? + +# If the above failed, then it's a brand new DB, so we need to create the migrations table +if [ $INIT_CHECK -eq 1 ]; then + echo " it has not, creating database ${MYSQL_DATABASE} ..." + mysql ${MYSQL_ARGS} <<< $CREATE_DATABASE + echo ' initializing dataMigrations table ...' + echo '' + mysql ${MYSQL_ARGS} ${MYSQL_DATABASE} <<< $MIGRATIONS_TABLE +else + echo ' it has.' +fi +echo '' + +# Run this script to process any new SQL migrations on youor local DB. +for i in ./data-migrations/*.sql; do + [ -f "$i" ] || break + + process_migration $i + echo '' + echo '' +done diff --git a/data-migrations/process.sh b/data-migrations/process.sh new file mode 100755 index 0000000..f71ccdf --- /dev/null +++ b/data-migrations/process.sh @@ -0,0 +1,49 @@ +#!/bin/bash + +# ============================================================= +# = This script is meant to be run in the AWS CodeBuild step! = +# ============================================================= +. .env + +# Run the migration using the env variable defined in the dotenv file +if [ -z "${MYSQL_PASSWORD}" ]; then + MYSQL_ARGS="-h ${MYSQL_HOST} -P ${MYSQL_PORT} -u ${MYSQL_USER}" +else + MYSQL_ARGS="-h ${MYSQL_HOST} -P ${MYSQL_PORT} -u ${MYSQL_USER} -p${MYSQL_PASSWORD}" +fi + +echo $MYSQL_ARGS + +process_migration() { + # See if the migration was already processed + echo "Checking to see if $1 has been run ..." + EXISTS=$(mysql ${MYSQL_ARGS} -N ${MYSQL_DATABASE} <<< "SELECT * FROM dataMigrations WHERE migrationFile = '$1';") + if [ -z "$EXISTS" ]; then + # If not run it + echo "NEW MIGRATION - $1. Processing migration ..." + echo " mysql ${MYSQL_ARGS} ${MYSQL_DATABASE} < $1" + + mysql ${MYSQL_ARGS} ${MYSQL_DATABASE} < $1 + WAS_PROCESSED=$? + + # If it worked then update the data-migrations table so we don't run it again! + if [ $WAS_PROCESSED -eq 0 ]; then + mysql ${MYSQL_ARGS} ${MYSQL_DATABASE} <<< "INSERT INTO dataMigrations (migrationFile) VALUES ('$1');" + echo " done" + else + echo " Something went wrong!" + exit 1 + fi + else + echo " already processed." + fi +} + +# Run this script to process any new SQL migrations on youor local DB. +for i in ./data-migrations/*.sql; do + [ -f "$i" ] || break + + process_migration $i + echo '' + echo '' +done diff --git a/docker-compose.yaml b/docker-compose.yaml new file mode 100644 index 0000000..281a62b --- /dev/null +++ b/docker-compose.yaml @@ -0,0 +1,25 @@ +# NOTE:: +# The services, settings and environment setup in this compose file is for DEVELOPMENT ONLY! +# +# It is intended to run the Apollo server in an "offline" mode. All data will be mocked. +# +services: + apollo: + build: + context: . + dockerfile: Dockerfile + ports: + - "4000:4000" + - "3006:3006" + expose: + - "4000" + # environment: + # - USE_MOCK_DATA=true + # - LOG_LEVEL=info + # - DMSP_BASE_URL=https://localhost:3000/10.11111/ZZ + env_file: + - .env + environment: + MYSQL_HOST: 'host.docker.internal' + volumes: + - .:/app diff --git a/docs/.DS_Store b/docs/.DS_Store new file mode 100644 index 0000000..5008ddf Binary files /dev/null and b/docs/.DS_Store differ diff --git a/docs/authentication-overview.epgz b/docs/authentication-overview.epgz new file mode 100644 index 0000000..5451779 Binary files /dev/null and b/docs/authentication-overview.epgz differ diff --git a/docs/authentication-overview.png b/docs/authentication-overview.png new file mode 100644 index 0000000..41259dc Binary files /dev/null and b/docs/authentication-overview.png differ diff --git a/eslint.config.mjs b/eslint.config.mjs new file mode 100644 index 0000000..0760943 --- /dev/null +++ b/eslint.config.mjs @@ -0,0 +1,20 @@ +// @ts-check + +import globals from "globals"; +import eslint from '@eslint/js'; +import tseslint from 'typescript-eslint'; + +export default tseslint.config( + { + files: ["**/*.{js,mjs,cjs,ts}"], + ignores: ['src/types.ts'], + }, + { + languageOptions: { + globals: globals.browser + } + }, + eslint.configs.recommended, + ...tseslint.configs.recommended, + ...tseslint.configs.strict, +); diff --git a/jest.config.ts b/jest.config.ts new file mode 100644 index 0000000..32dcdc4 --- /dev/null +++ b/jest.config.ts @@ -0,0 +1,200 @@ +/** + * For a detailed explanation regarding each configuration property, visit: + * https://jestjs.io/docs/configuration + */ + +import type {Config} from 'jest'; + +const config: Config = { + // All imported modules in your tests should be mocked automatically + // automock: false, + + // Stop running tests after `n` failures + // bail: 0, + + // The directory where Jest should store its cached dependency information + // cacheDirectory: "/private/var/folders/_r/5bm_9p6n4tg90cqfqfpk0d0jb0nfj9/T/jest_nvg5d5", + + // Automatically clear mock calls, instances, contexts and results before every test + clearMocks: true, + + // Indicates whether the coverage information should be collected while executing the test + collectCoverage: true, + + // An array of glob patterns indicating a set of files for which coverage information should be collected + // collectCoverageFrom: undefined, + + // The directory where Jest should output its coverage files + coverageDirectory: "coverage", + + // An array of regexp pattern strings used to skip coverage collection + coveragePathIgnorePatterns: [ + "/node_modules/", + "/src/mocks/" + ], + + // Indicates which provider should be used to instrument code for coverage + coverageProvider: "v8", + + // A list of reporter names that Jest uses when writing coverage reports + // coverageReporters: [ + // "json", + // "text", + // "lcov", + // "clover" + // ], + + // An object that configures minimum threshold enforcement for coverage results + // coverageThreshold: undefined, + + // A path to a custom dependency extractor + // dependencyExtractor: undefined, + + // Make calling deprecated APIs throw helpful error messages + // errorOnDeprecated: false, + + // The default configuration for fake timers + // fakeTimers: { + // "enableGlobally": false + // }, + + // Force coverage collection from ignored files using an array of glob patterns + // forceCoverageMatch: [], + + // A path to a module which exports an async function that is triggered once before all test suites + // globalSetup: undefined, + + // A path to a module which exports an async function that is triggered once after all test suites + // globalTeardown: undefined, + + // A set of global variables that need to be available in all test environments + // globals: {}, + + // The maximum amount of workers used to run your tests. Can be specified as % or a number. E.g. maxWorkers: 10% will use 10% of your CPU amount + 1 as the maximum worker number. maxWorkers: 2 will use a maximum of 2 workers. + // maxWorkers: "50%", + + // An array of directory names to be searched recursively up from the requiring module's location + // moduleDirectories: [ + // "node_modules" + // ], + + // An array of file extensions your modules use + // moduleFileExtensions: [ + // "js", + // "mjs", + // "cjs", + // "jsx", + // "ts", + // "tsx", + // "json", + // "node" + // ], + + // A map from regular expressions to module names or to arrays of module names that allow to stub out resources with a single module + // moduleNameMapper: {}, + + // An array of regexp pattern strings, matched against all module paths before considered 'visible' to the module loader + // modulePathIgnorePatterns: [], + + // Activates notifications for test results + // notify: false, + + // An enum that specifies notification mode. Requires { notify: true } + // notifyMode: "failure-change", + + // A preset that is used as a base for Jest's configuration + preset: 'ts-jest', + + // Run tests from one or more projects + // projects: undefined, + + // Use this configuration option to add custom reporters to Jest + // reporters: undefined, + + // Automatically reset mock state before every test + // resetMocks: false, + + // Reset the module registry before running each individual test + // resetModules: false, + + // A path to a custom resolver + // resolver: undefined, + + // Automatically restore mock state and implementation before every test + // restoreMocks: false, + + // The root directory that Jest should scan for tests and modules within + // rootDir: undefined, + + // A list of paths to directories that Jest should use to search for files in + // roots: [ + // "" + // ], + + // Allows you to use a custom runner instead of Jest's default test runner + // runner: "jest-runner", + + // The paths to modules that run some code to configure or set up the testing environment before each test + setupFiles: ['./src/__tests__/setup.ts'], + + // A list of paths to modules that run some code to configure or set up the testing framework before each test + // setupFilesAfterEnv: [], + + // The number of seconds after which a test is considered as slow and reported as such in the results. + // slowTestThreshold: 5, + + // A list of paths to snapshot serializer modules Jest should use for snapshot testing + // snapshotSerializers: [], + + // The test environment that will be used for testing + // testEnvironment: "jest-environment-node", + + // Options that will be passed to the testEnvironment + // testEnvironmentOptions: {}, + + // Adds a location field to test results + // testLocationInResults: false, + + // The glob patterns Jest uses to detect test files + testMatch: [ + // "**/__tests__/**/*.[jt]s?(x)", + "**/?(*.)+(spec|test).[tj]s?(x)", + ], + + // An array of regexp pattern strings that are matched against all test paths, matched tests are skipped + // testPathIgnorePatterns: [ + // "/node_modules/" + // ], + + // The regexp pattern or array of patterns that Jest uses to detect test files + // testRegex: [], + + // This option allows the use of a custom results processor + // testResultsProcessor: undefined, + + // This option allows use of a custom test runner + // testRunner: "jest-circus/runner", + + // A map from regular expressions to paths to transformers + // transform: undefined, + + // An array of regexp pattern strings that are matched against all source file paths, matched files will skip transformation + // transformIgnorePatterns: [ + // "/node_modules/", + // "\\.pnp\\.[^\\/]+$" + // ], + + // An array of regexp pattern strings that are matched against all modules before the module loader will automatically return a mock for them + // unmockedModulePathPatterns: undefined, + + // Indicates whether each individual test should be reported during the run + // verbose: undefined, + + // An array of regexp patterns that are matched against all source file paths before re-running tests in watch mode + // watchPathIgnorePatterns: [], + + // Whether to use watchman for file crawling + // watchman: true, +}; + +export default config; diff --git a/package-lock.json b/package-lock.json index 8eb1f5f..2e6f7cf 100644 --- a/package-lock.json +++ b/package-lock.json @@ -7,31 +7,110 @@ "": { "name": "dmsp_apollo", "version": "1.0.0", - "license": "ISC", + "license": "MIT", "dependencies": { + "@apollo/datasource-rest": "^6.0.1", "@apollo/server": "^4.10.0", - "aws-sdk": "^2.1568.0", + "@elastic/ecs-pino-format": "^1.5.0", + "@graphql-tools/merge": "^9.0.3", + "@graphql-tools/mock": "^9.0.0", + "@graphql-tools/schema": "^10.0.0", + "@node-oauth/express-oauth-server": "^4.0.0", + "aws-sdk": "^2.1598.0", + "bcryptjs": "^2.4.3", + "casual": "^1.6.2", "dotenv": "^16.4.5", - "graphql": "^16.8.1" + "express": "^4.19.2", + "express-jwt": "^8.4.1", + "graphql": "^16.8.1", + "graphql-tag": "^2.12.6", + "http-cache-semantics": "^4.1.1", + "jsonwebtoken": "^9.0.2", + "mysql2": "^3.9.7", + "oauth2-server": "^3.1.1", + "pino": "^9.0.0", + "uuid": "^9.0.1", + "uuid-random": "^1.3.2" }, "devDependencies": { - "@types/node": "^20.11.23", - "typescript": "^5.3.3" + "@eslint/js": "^9.6.0", + "@graphql-codegen/cli": "^4.0.1", + "@graphql-codegen/typescript": "^4.0.1", + "@graphql-codegen/typescript-resolvers": "^4.0.1", + "@types/bcryptjs": "^2.4.6", + "@types/eslint__js": "^8.42.3", + "@types/express": "^4.17.21", + "@types/express-oauth-server": "^2.0.7", + "@types/jest": "^29.5.12", + "@types/oauth2-server": "^3.0.16", + "@types/pino": "^7.0.5", + "eslint": "^8.57.0", + "globals": "^15.6.0", + "jest": "^29.7.0", + "jest-mock": "^29.7.0", + "nodemon": "^3.1.0", + "ts-jest": "^29.1.4", + "ts-node-dev": "^2.0.0", + "typescript": "^5.5.2", + "typescript-eslint": "^7.14.1" + }, + "engines": { + "node": ">=21.6.2", + "npm": ">=10.2.4" + } + }, + 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"https://github.com/sponsors/sindresorhus" + } } } } diff --git a/package.json b/package.json index 584ffa7..3b0c55c 100644 --- a/package.json +++ b/package.json @@ -5,20 +5,71 @@ "main": "index.js", "scripts": { "compile": "tsc", - "start": "npm run compile && node ./dist/index.js" + "copy-graphql": "mkdir ./dist/schemas && cp ./src/schemas/*.graphql ./dist/schemas/", + "build": "rm -rf ./dist && npm run compile", + "generate": "graphql-codegen", + "dev": "ts-node-dev --respawn ./src/index.ts", + "test": "jest --coverage", + "test-tsc": "jest -c ./jest.tsc.config.js", + "lint": "npx eslint .", + "start": "npm run build && nodemon ./dist/index.js", + "aws_start": "node ./dist/index.js" }, + "repository": { + "type": "git", + "url": "https://github.com/CDLUC3/dmsp_backend_prototype.git" + }, + "author": "University of California Curation Center (UC3)", "keywords": [], - "author": "", - "license": "ISC", - "type": "module", + "license": "MIT", + "engines": { + "node": ">=21.6.2", + "npm": ">=10.2.4" + }, "dependencies": { + "@apollo/datasource-rest": "^6.0.1", "@apollo/server": "^4.10.0", - "aws-sdk": "^2.1568.0", + "@elastic/ecs-pino-format": "^1.5.0", + "@graphql-tools/merge": "^9.0.3", + "@graphql-tools/mock": "^9.0.0", + "@graphql-tools/schema": "^10.0.0", + "@node-oauth/express-oauth-server": "^4.0.0", + "aws-sdk": "^2.1598.0", + "bcryptjs": "^2.4.3", + "casual": "^1.6.2", "dotenv": "^16.4.5", - "graphql": "^16.8.1" + "express": "^4.19.2", + "express-jwt": "^8.4.1", + "graphql": "^16.8.1", + "graphql-tag": "^2.12.6", + "http-cache-semantics": "^4.1.1", + "jsonwebtoken": "^9.0.2", + "mysql2": "^3.9.7", + "oauth2-server": "^3.1.1", + "pino": "^9.0.0", + "uuid": "^9.0.1", + "uuid-random": "^1.3.2" }, "devDependencies": { - "@types/node": "^20.11.23", - "typescript": "^5.3.3" + "@eslint/js": "^9.6.0", + "@graphql-codegen/cli": "^4.0.1", + "@graphql-codegen/typescript": "^4.0.1", + "@graphql-codegen/typescript-resolvers": "^4.0.1", + "@types/bcryptjs": "^2.4.6", + "@types/eslint__js": "^8.42.3", + "@types/express": "^4.17.21", + "@types/express-oauth-server": "^2.0.7", + "@types/jest": "^29.5.12", + "@types/oauth2-server": "^3.0.16", + "@types/pino": "^7.0.5", + "eslint": "^8.57.0", + "globals": "^15.6.0", + "jest": "^29.7.0", + "jest-mock": "^29.7.0", + "nodemon": "^3.1.0", + "ts-jest": "^29.1.4", + "ts-node-dev": "^2.0.0", + "typescript": "^5.5.2", + "typescript-eslint": "^7.14.1" } } diff --git a/src/DynamoDBService.ts b/src/DynamoDBService.ts deleted file mode 100644 index 845864b..0000000 --- a/src/DynamoDBService.ts +++ /dev/null @@ -1,46 +0,0 @@ -import * as dotenv from 'dotenv'; -import { DocumentClient } from 'aws-sdk/lib/dynamodb/document_client.js'; -import AWS from './awsConfig.js'; - -// Pull in the environment variables from either the .env file or the ENV variables -dotenv.config(); - -interface Key { - PK: string; - SK: string; -} - -// Establish the DynamoDB Table names based on the environment -export const dynamoDBTables = { - dmps: process.env.DMPS_TABLE !== undefined ? process.env.DMPS_TABLE : 'dmps-local', -} - -// Generic DynamoDB service. The caller defines which table when initializing the service -export class DynamoDBService { - private dynamoDB: DocumentClient; - private tableName: string; - - constructor(tableName: string) { - this.dynamoDB = new AWS.DynamoDB.DocumentClient(); - this.tableName = tableName; - } - - async getItem(params: Key): Promise { - try { - const { Item } = await this.dynamoDB.get({ TableName: this.tableName, Key: params }).promise(); - return Item; - } catch (error) { - if (error instanceof Error) { - switch (error.name) { - case 'ResourceNotFoundException': - throw new Error('Item not found'); - default: - console.error('Error fetching item from DynamoDB:', error); - throw new Error('Error fetching item from DynamoDB'); - } - } else { - console.log(error); - } - } - } -} diff --git a/src/GraphqlTypeDefs.ts b/src/GraphqlTypeDefs.ts deleted file mode 100644 index 144a768..0000000 --- a/src/GraphqlTypeDefs.ts +++ /dev/null @@ -1,271 +0,0 @@ -// A schema is a collection of type definitions (hence "typeDefs") -// that together define the "shape" of queries that are executed against -// your data. -const typeDefs = `#graphql - "A Data Management and Sharing Plan (DMSP)" - type DMP { - # Required - contact: Contact! - created: String! - dataset: [Dataset!]! - dmp_id: Identifier! - modified: String! - project: [Project!]! - title: String! - - # Optional - contributor: [Contributor] - cost: [Cost] - description: String - dmphub_provenance_id: String - dmphub_versions: [Version!] - dmproadmap_featured: String - dmproadmap_privacy: String - dmproadmap_template: Template - dmproadmap_related_identifiers: [RelatedIdentifier!] - dmproadmap_research_facilities: [ResearchFacility!] - ethical_issues_exist: String - ethical_issues_description: String - ethical_issues_report: String - language: String - } - - "The primary contact for the DMSP" - type Contact { - # Required - name: String! - mbox: String! - contact_id: Identifier! - - # Optional - dmproadmap_affiliation: Affiliation - } - - "A contributor to the research project" - type Contributor { - # Required - name: String! - role: [String!]! - - # Optional - contributor_id: Identifier - dmproadmap_affiliation: Affiliation - mbox: String - } - - "Anticipated costs for the research project" - type Cost { - title: String! - - description: String - currency_code: String - value: Int - } - - "An insitutional or organizational affiliation of a contributor" - type Affiliation { - name: String! - - affiliation_id: Identifier - } - - type Identifier { - type: String! - identifier: String! - } - - "The research project associated with the DMSP" - type Project { - title: String! - - description: String - start: String - end: String - funding: [Funding!] - } - - #A funding source for the research project (often tied to the DMSP)" - type Funding { - funding_status: String! - name: String! - - dmproadmap_opportunity_number: String - dmproadmap_project_number: String - funder_id: Identifier - grant_id: Identifier - } - - "Anticipated research output (represents an 'actual' research output when the dataset_id is popuated)" - type Dataset { - title: String! - - type: String - description: String - data_quality_assurance: [String!] - dataset_id: Identifier - issued: String - keyword: [String!] - language: String - personal_data: String - sensitive_data: String - preservation_statement: String - distribution: [Distribution!] - metadata: [MetadataStandard!] - security_and_privacy: [SecurityPrivacyStatement!] - technical_resource: [TechnicalResource!] - } - - "A distribution of the research output" - type Distribution { - title: String! - data_access: String! - - access_url: String - available_until: String - byte_size: Int - description: String - download_url: String - format: [String!] - license: [License!] - host: Host - } - - "The repository associated with the distribution (e.g. Zenodo, GitHub, GeneBank, etc.)" - type Host { - title: String! - url: String! - - availability: String - backup_frequency: String - backup_type: String - certified_with: String - description: String - dmproadmap_host_id: Identifier - geo_location: String - pid_system: [String!] - storage_type: String - support_versioning: String - } - - "Licenses for the research output distribution" - type License { - license_ref: String! - start_date: String! - } - - "Metadata standards used for the research output" - type MetadataStandard { - metadata_standard_id: Identifier! - - description: String - language: String - } - - "A description of the security and privacy considerations for the research output" - type SecurityPrivacyStatement { - title: String! - - description: String - } - - "A technical resource involved in the production of the research output (e.g. an electron microscope or telescope)" - type TechnicalResource { - name: String! - - description: String - dmproadmap_technical_resource_id: Identifier - } - - "A place involved with the production of the research project (e.g. a lab, field station, observatory, etc.)" - type ResearchFacility { - name: String! - type: String! - - facility_id: Identifier - } - - "Identifiers for works related to the DMSP" - type RelatedIdentifier { - descriptor: String! - identifier: String! - type: String! - work_type: String! - } - - "The template used to produce the DMSP (specific to the dmphub_provenance)" - type Template { - id: String! - title: String! - } - - "A version of the DMSP" - type Version { - timestamp: String! - url: String! - } - - # The "Query" type is special: it lists all of the available queries that - # clients can execute, along with the return type for each. In this - # case, the "books" query returns an array of zero or more Books (defined above). - type Query { - books: [Book] - - getDMP(PK: String!, SK: String): DMP - dmps: [DMP] - } - - - type Mutation { - createDMP(input: DMPInput!): DMP - updateDMP(PK: String!, input: DMPInput!): DMP - deleteDMP(PK: String!): String - } - - - input DMPInput { - title: String! - modified: String! - created: String! - contact: ContactInput! - dmp_id: DMPIDInput! - project: [ProjectInput!]! - dataset: [DatasetInput!]! - } - - input ContactInput { - name: String! - dmproadmap_affiliation: AffiliationInput! - mbox: String! - contact_id: ContactIDInput! - } - - input AffiliationInput { - name: String! - affiliation_id: AffiliationIDInput! - } - - input AffiliationIDInput { - type: String! - identifier: String! - } - - input ContactIDInput { - type: String! - identifier: String! - } - - input DMPIDInput { - identifier: String! - type: String! - } - - input ProjectInput { - title: String! - } - - input DatasetInput { - title: String! - } -`; - -export default typeDefs; diff --git a/src/__tests__/helpers.ts b/src/__tests__/helpers.ts new file mode 100644 index 0000000..fed40b4 --- /dev/null +++ b/src/__tests__/helpers.ts @@ -0,0 +1,44 @@ +import { validateDmspId } from '../resolvers/scalars/dmspId'; +import { validateOrcid } from '../resolvers/scalars/orcid'; +import { validateRor } from '../resolvers/scalars/ror'; + +const emailRegex = new RegExp(/^[a-zA-Z0–9._-]+@[a-zA-Z0–9.-]+\.[a-zA-Z]{2,4}$/); +const timestampRegex = new RegExp(/[0-9]{4}-[0-9]{2}-[0-9]{2}\s([0-9]{2}:){2}[0-9]{2}/); +const urlRegex = new RegExp(/(https:\/\/www\.|http:\/\/www\.|https:\/\/|http:\/\/)?[a-zA-Z0-9]{2,}(\.[a-zA-Z0-9]{2,})(\.[a-zA-Z0-9]{2,})?/); + +// Assertion helpers +export function assertDmspId(val) { + try { + return validateDmspId(val).length > 0; + } catch { + return false; + } +} + +export function assertEmailAddress(val) { + return emailRegex.test(val); +} + +export function assertOrcid(val) { + try { + return validateOrcid(val).length > 0; + } catch { + return false; + } +} + +export function assertRor(val) { + try { + return validateRor(val).length > 0; + } catch { + return false; + } +} + +export function assertTimestamp(val) { + return timestampRegex.test(val) +} + +export function assertUrl(val) { + return urlRegex.test(val); +} diff --git a/src/__tests__/mockApolloContext.ts b/src/__tests__/mockApolloContext.ts new file mode 100644 index 0000000..7a97728 --- /dev/null +++ b/src/__tests__/mockApolloContext.ts @@ -0,0 +1,40 @@ +import { RESTDataSource } from "@apollo/datasource-rest"; +import { GraphQLFieldResolver } from 'graphql'; + +export interface ResolverSource { + +}; +export interface ResolverArgs { + +}; +export interface ResolverContext { + +}; +export interface ResolverInfo { + +}; +export type ContributorRolesResolver = GraphQLFieldResolver; + +// Mock the DMPHubAPI data source +export class MockDMPHubAPI extends RESTDataSource { + getData = jest.fn(); + getDMSPs = jest.fn(); + handleResponse = jest.fn(); + getDMSP = jest.fn(); + baseURL = ''; + + // Mocking the private properties + token = jest.fn(); + dmspIdWithoutProtocol = jest.fn(); +} + +export class mockDMPToolAPI extends RESTDataSource { + getAffiliation = jest.fn(); + getAffiliations = jest.fn(); + handleResponse = jest.fn(); + baseURL = ''; + + // Mocking the private properties + token = jest.fn(); + removeProtocol = jest.fn(); +} diff --git a/src/__tests__/mockApolloServer.ts b/src/__tests__/mockApolloServer.ts new file mode 100644 index 0000000..6687a8e --- /dev/null +++ b/src/__tests__/mockApolloServer.ts @@ -0,0 +1,18 @@ +import { ApolloServer } from '@apollo/server'; +import { addMocksToSchema } from '@graphql-tools/mock'; +import { makeExecutableSchema } from '@graphql-tools/schema'; + +import { MyContext } from '../context'; +import { typeDefs } from '../schema'; +import { resolvers } from '../resolver'; +import { mocks } from '../mocks'; + +// Test server using mocks +const server = new ApolloServer({ + schema: addMocksToSchema({ + schema: makeExecutableSchema({ typeDefs, resolvers }), + mocks, + }), +}); + +export default server; diff --git a/src/__tests__/mockLogger.ts b/src/__tests__/mockLogger.ts new file mode 100644 index 0000000..4344ab4 --- /dev/null +++ b/src/__tests__/mockLogger.ts @@ -0,0 +1,15 @@ +import pino from 'pino'; + +// Mock a Pino Logger +const mockLogger = { + level: jest.fn(), + fatal: jest.fn(), + error: jest.fn(), + warn: jest.fn(), + info: jest.fn(), + debug: jest.fn(), + trace: jest.fn(), + child: jest.fn().mockReturnThis(), +} as unknown as pino.Logger; + +export default mockLogger; diff --git a/src/__tests__/setup.ts b/src/__tests__/setup.ts new file mode 100644 index 0000000..071bf5a --- /dev/null +++ b/src/__tests__/setup.ts @@ -0,0 +1,32 @@ +import mockLogger from "./mockLogger"; + +// Mock the Pino logger +jest.mock('pino', () => () => mockLogger); + +// Always mock out our config files +jest.mock('../config/generalConfig', () => ({ + generalConfig: { + jwtSecret: 'testing', + jwtTtl: 5, + } +})); + +jest.mock('../config/oauthConfig', () => ({ + oauthConfig: { + authorizationCodeLifetime: 10, + accessTokenLifetime: 30, + refreshTokenLifetime: 30, + } +})) + +// Mock the MySQL connection +jest.mock('../datasources/mySQLDataSource', () => { + return { + __esModule: true, + MySQLDataSource: { + getInstance: jest.fn().mockReturnValue({ + query: jest.fn(), + }), + }, + }; +}); diff --git a/src/awsConfig.ts b/src/awsConfig.ts deleted file mode 100644 index 916f046..0000000 --- a/src/awsConfig.ts +++ /dev/null @@ -1,12 +0,0 @@ -import AWS from 'aws-sdk'; - -// JS SDK v3 does not support global configuration. -// Codemod has attempted to pass values to each service client in this file. -// You may need to update clients outside of this file, if they use global config. -AWS.config.update({ - region: process.env.AWS_REGION, - // accessKeyId: 'your-access-key-id', - // secretAccessKey: 'your-secret-access-key', -}); - -export default AWS; diff --git a/src/config.ts b/src/config.ts new file mode 100644 index 0000000..56def40 --- /dev/null +++ b/src/config.ts @@ -0,0 +1,49 @@ +import * as dotenv from 'dotenv'; +import { addMocksToSchema } from '@graphql-tools/mock'; +import { makeExecutableSchema } from '@graphql-tools/schema'; +import { ApolloServerPluginDrainHttpServer } from '@apollo/server/plugin/drainHttpServer'; +import { ApolloServerPluginLandingPageLocalDefault } from '@apollo/server/plugin/landingPage/default'; +import { ApolloServerPluginLandingPageDisabled } from '@apollo/server/plugin/disabled'; + +import { typeDefs } from './schema'; +import { resolvers } from './resolver'; +import { mocks } from './mocks'; +import { loggerPlugin } from './plugins/logger'; + +dotenv.config(); + +// Base Apollo server configuration +function baseConfig() { + // If we are running in offline mode then we will use mocks + if (['true', '1'].includes(process.env?.USE_MOCK_DATA?.toString()?.toLowerCase())) { + return { + schema: addMocksToSchema({ + schema: makeExecutableSchema({ typeDefs, resolvers }), + mocks, + preserveResolvers: true + }), + }; + } + // Otherwise use the normal resolvers connected to our data sources + return { typeDefs, resolvers }; +} + +// Standard Apollo server configuration regarless of whether we are using mock data or not +export function serverConfig(logger, httpServer) { + return { ...baseConfig(), ...{ + plugins: [ + // The LoggerPlugin is used by Apollo server to record events in the request/response + // lifecycle as well as handling any GraphQL errors + loggerPlugin(logger), + ApolloServerPluginDrainHttpServer({ httpServer }), + // If we are in production disable the default Explorer landing page + process.env.NODE_ENV === 'production' + ? ApolloServerPluginLandingPageDisabled() + : ApolloServerPluginLandingPageLocalDefault() + ], + // Mitigation for an issue that causes Apollo server v4 to return a 200 when a query + // includes invalid variables. + // See: https://www.apollographql.com/docs/apollo-server/migration/#known-regressions + status400ForVariableCoercionErrors: true + }}; +} diff --git a/src/config/generalConfig.ts b/src/config/generalConfig.ts new file mode 100644 index 0000000..af9dc48 --- /dev/null +++ b/src/config/generalConfig.ts @@ -0,0 +1,8 @@ +import { verifyCriticalEnvVariable } from "../utils/helpers"; + +verifyCriticalEnvVariable('JWT_SECRET'); + +export const generalConfig = { + jwtSecret: process.env.JWT_SECRET, + jwtTtl: process.env.JWT_TTL || '1hr', +} \ No newline at end of file diff --git a/src/config/mysqlConfig.ts b/src/config/mysqlConfig.ts new file mode 100644 index 0000000..1fc4b05 --- /dev/null +++ b/src/config/mysqlConfig.ts @@ -0,0 +1,20 @@ +import * as dotenv from 'dotenv'; +import { verifyCriticalEnvVariable } from "../utils/helpers"; +import { PoolConfig } from '../datasources/mySQLDataSource'; + +dotenv.config(); + +if (process.env.NODE_ENV === 'production') { + verifyCriticalEnvVariable('MYSQL_HOST'); + verifyCriticalEnvVariable('MYSQL_USER'); + verifyCriticalEnvVariable('MYSQL_PASSWORD'); +} + +export const mysqlConfig: PoolConfig = { + connectionLimit: Number(process.env.MYSQL_CONNECTION_LIMIT) || 5, + host: process.env.MYSQL_HOST, + port: Number(process.env.MYSQL_PORT) || 3306, + database: process.env.MYSQL_DATABASE || 'dmsp', + user: process.env.MYSQL_USER, + password: process.env.MYSQL_PASSWORD, +}; diff --git a/src/config/oauthConfig.ts b/src/config/oauthConfig.ts new file mode 100644 index 0000000..8a9fb0d --- /dev/null +++ b/src/config/oauthConfig.ts @@ -0,0 +1,15 @@ + +// FUTURE AUTH OPTIONS for Google, ORCID, etc. +// TODO: Update this to add our credentials for external OAuth + +// export const SomeExternalSystemConfig = { +// clientID: process.env.CLIENT_ID as string, +// clientSecret: process.env.CLIENT_SECRET as string, +// redirectUri: process.env.REDIRECT_URI as string, +// } + +export const oauthConfig = { + authorizationCodeLifetime: 600, // 10 minutes + accessTokenLifetime: 3600, // 1 hour + refreshTokenLifetime: 604800, // 7 days +}; diff --git a/src/context.ts b/src/context.ts new file mode 100644 index 0000000..a6e52cf --- /dev/null +++ b/src/context.ts @@ -0,0 +1,17 @@ +import { Logger } from 'pino'; +import { DMPHubAPI } from './datasources/dmphubAPI'; +import { DMPToolAPI } from './datasources/dmptoolAPI'; +import { MySQLDataSource } from './datasources/mySQLDataSource'; +import { User } from './models/User'; + +export type MyContext = { + token?: string | undefined; + user: User | undefined; + logger: Logger; + + dataSources: { + dmphubAPIDataSource: DMPHubAPI; + dmptoolAPIDataSource: DMPToolAPI; + sqlDataSource: MySQLDataSource; + }; +} diff --git a/src/controllers/healthcheck.ts b/src/controllers/healthcheck.ts new file mode 100644 index 0000000..6fdb228 --- /dev/null +++ b/src/controllers/healthcheck.ts @@ -0,0 +1,21 @@ +// Healthcheck endpoint for our load balancer. +// Be sure to call this BEFORE defining CORS settings since our AWS load +// balancer does not allow us to define headers! +export function healthcheck(apolloServer, response, logger) { + apolloServer.executeOperation({ query: '{ __typename }' }) + .then((data) => { + if (data.body.kind === 'single') { + if (data.body.singleResult.errors) { + const msgs = data.body.singleResult.errors.map((err) => err.message); + logger.error(`ERROR: Healthcheck - ${msgs.join(', ')}`); + response.status(400).send(JSON.stringify(data.body.singleResult.errors)); + } else { + response.status(200).send(JSON.stringify(data.body.singleResult.data)); + } + } + }) + .catch((error) => { + logger.error(`ERROR: Healthcheck - ${error.message}`); + response.status(400).send(JSON.stringify(error)); + }); +} \ No newline at end of file diff --git a/src/controllers/signinController.ts b/src/controllers/signinController.ts new file mode 100644 index 0000000..9b1654a --- /dev/null +++ b/src/controllers/signinController.ts @@ -0,0 +1,26 @@ +import { Request, Response } from 'express'; +import { logger, formatLogMessage } from '../logger'; +import { User } from '../models/User'; +import { generateToken } from '../services/tokenService'; + +export const signinController = async (req: Request, res: Response) => { + let user = new User(req.body); + try { + user = await user.login() || null; + + if (user) { + const token = generateToken(user); + if (token) { + res.status(200).json({ success: true, token }); + } else { + throw new Error('Login failed'); + } + + } else { + res.status(401).json({ success: false, message: 'Invalid credentials' }); + } + } catch (err) { + formatLogMessage(logger, { err }).error('Signin error') + res.status(500).json({ success: false, message: 'Internal server error' }); + } +}; diff --git a/src/controllers/signupController.ts b/src/controllers/signupController.ts new file mode 100644 index 0000000..814e77a --- /dev/null +++ b/src/controllers/signupController.ts @@ -0,0 +1,28 @@ +import { Request, Response } from 'express'; +import { logger, formatLogMessage } from '../logger'; +import { User } from '../models/User'; +import { generateToken } from '../services/tokenService'; + +export const signupController = async (req: Request, res: Response) => { + let user: User = new User(req.body); + try { + user = await user.register() || null; + if (user) { + if (user.errors.length >= 1) { + res.status(400).json({ success: false, message: user.errors?.join('| ') }); + } else { + const token = generateToken(user); + if (token) { + res.status(200).json({ success: true, token }); + } else { + throw new Error('Signup failed'); + } + } + } else { + res.status(500).json({ success: false, message: 'Unable to create the account at this time.' }); + } + } catch (err) { + formatLogMessage(logger, { msg: `Signup error. userId: ${user.id}, error: ${err?.message}` }); + res.status(500).json({ success: false, message: 'Internal server error' }); + } +}; diff --git a/src/datasources/dmphubAPI.ts b/src/datasources/dmphubAPI.ts new file mode 100644 index 0000000..04f06e3 --- /dev/null +++ b/src/datasources/dmphubAPI.ts @@ -0,0 +1,74 @@ +import AWS from 'aws-sdk'; +import { RESTDataSource } from "@apollo/datasource-rest"; +import type { KeyValueCache } from '@apollo/utils.keyvaluecache'; +import { logger, formatLogMessage } from '../logger'; +import { DmspModel as Dmsp } from "../models/Dmsp" +import { JWTToken } from '../services/tokenService'; + +// JS SDK v3 does not support global configuration. +// Codemod has attempted to pass values to each service client in this file. +// You may need to update clients outside of this file, if they use global config. +AWS.config.update({ + region: process.env.AWS_REGION, + // accessKeyId: 'your-access-key-id', + // secretAccessKey: 'your-secret-access-key', +}); + +export class DMPHubAPI extends RESTDataSource { + override baseURL = process.env.DMPHUB_API_BASE_URL; + + private token: JWTToken; + + constructor(options: { cache: KeyValueCache, token: JWTToken }) { + super(options); + + this.token = options.token; + } + + // Remove the protocol from the DMSP ID and encode it but preserve the `/` characters + dmspIdWithoutProtocol(dmspId) { + return dmspId.toString().replace(/^(https?:\/\/|https?%3A%2F%2F)/i, '').replace(/%2F/g, '/'); + } + + + // TODO: Pass the sessionId along to the API so it can be added to the API logs + // Search for DMSPs + getDMSPs() { + return this.get("dmps"); + } + + // TODO: Use the Fetcher to set the API auth token + // See: https://www.apollographql.com/docs/apollo-server/data/fetching-rest#intercepting-fetches + + // Standard response handler + handleResponse(response, resultAsArray = false) { + const success = response?.status >= 200 && response.status <= 300; + const errors = response?.errors || []; + const dmsps = response?.items?.map((dmsp) => dmsp['dmp']) || []; + + const ret = { + code: response?.status, + success: success, + message: success ? 'Ok' : errors.join(', ') + }; + if (resultAsArray) { + ret['dmsps'] = dmsps + } else { + ret['dmsp'] = dmsps[0]; + } + return ret; + } + + // Fetch a specific DMSP by its DMP ID + async getDMSP(dmspID: string) { + formatLogMessage(logger).info(`Calling DMPHub: ${this.baseURL}/dmps/${dmspID}`) + try { + const id = this.dmspIdWithoutProtocol(dmspID); + const response = await this.get(`dmps/${encodeURI(id)}`); + return this.handleResponse(response); + } catch(err) { + formatLogMessage(logger, { err }).error('Error calling DMPHub API getDMSP.') + throw(err); + } + } +} diff --git a/src/datasources/dmptoolAPI.ts b/src/datasources/dmptoolAPI.ts new file mode 100644 index 0000000..51d232b --- /dev/null +++ b/src/datasources/dmptoolAPI.ts @@ -0,0 +1,131 @@ +import { Buffer } from "buffer"; +import { AugmentedRequest, RESTDataSource } from "@apollo/datasource-rest"; +import type { KeyValueCache } from '@apollo/utils.keyvaluecache'; +import { logger, formatLogMessage } from '../logger'; +import { AffiliationModel, AffiliationSearchModel } from "../models/Affiliation" +import { JWTToken } from '../services/tokenService'; + +// Singleton class that retrieves an Auth token from the API +class Authorizer extends RESTDataSource { + static #instance: Authorizer; + + override baseURL = process.env.DMPHUB_AUTH_URL; + + public env: string; + public oauth2Token: string; + + private creds: string; + private expiry: Date; + + constructor() { + super(); + + this.env = this.baseURL.includes('uc3prd') ? 'dev' : (this.baseURL.includes('uc3stg') ? 'stg' : 'dev'); + // Base64 encode the credentials for the auth request + const hdr = `${process.env.DMPHUB_API_CLIENT_ID}:${process.env.DMPHUB_API_CLIENT_SECRET}`; + this.creds = Buffer.from(hdr, 'binary').toString('base64'); + this.authenticate(); + } + + // Singleton function to ensure we aren't reauthenticating every time + public static get instance(): Authorizer { + if (!Authorizer.#instance) { + Authorizer.#instance = new Authorizer(); + } + + return Authorizer.#instance; + } + + // Call the authenticate method and set this class' expiry timestamp + async authenticate() { + const response = await this.post(`/oauth2/token`); + formatLogMessage(logger).info(`Authenticating with DMPHub`); + this.oauth2Token = response.access_token; + + const currentDate = new Date(); + this.expiry = new Date(currentDate.getTime() + 600 * 1000); + } + + // Check if the current token has expired + hasExpired() { + const currentDate = new Date(); + return currentDate >= this.expiry; + } + + // Attach all of the necessary HTTP headers and the body prior to calling the token endpoint + override willSendRequest(_path: string, request: AugmentedRequest) { + request.headers['authorization'] =`Basic ${this.creds}`; + request.headers['content-type'] = 'application/x-www-form-urlencoded'; + request.body = `grant_type=client_credentials&scope=${this.baseURL}/${this.env}.read ${this.baseURL}/${this.env}.write`; + } +} + +// DataSource that interacts with the DMPHub API. This file is similar to the DdmphubAPI.ts. It has +// been separated out because these endpoints will eventually be replaced with queries to +// OpenSearch once that has been deployed. +export class DMPToolAPI extends RESTDataSource { + override baseURL = process.env.DMPHUB_API_BASE_URL; + + private token: JWTToken; + private authorizer: Authorizer; + + constructor(options: { cache: KeyValueCache, token: JWTToken }) { + super(options); + + this.token = options.token; + + this.authorizer = Authorizer.instance; + } + + // Add the Authorization token to the headers prior to the request + override willSendRequest(_path: string, request: AugmentedRequest) { + // Check the current token's expiry. If it has expired re-authenticate + if (this.authorizer.hasExpired) { + this.authorizer.authenticate(); + } + request.headers['authorization'] = `Bearer ${this.authorizer.oauth2Token}`; + }; + + // Remove the protocol from the DMSP ID and encode it but preserve the `/` characters + removeProtocol(id) { + return id.toString().replace(/^(https?:\/\/|https?%3A%2F%2F)/i, '').replace(/%2F/g, '/'); + } + + // Retrieve a single affiliation record + async getAffiliation(affiliationId: string) { + try { + const id = this.removeProtocol(affiliationId); + formatLogMessage(logger).info(`Calling DMPHub: ${this.baseURL}/affiliations/${id}`) + + const response = await this.get(`affiliations/${encodeURI(id)}`); + if (response) { + const affiliation = new AffiliationModel(response); + return affiliation ? affiliation : null; + } + return null; + } catch(err) { + formatLogMessage(logger, { err }).error('Error calling DMPHub API getAffiliation.') + throw(err); + } + } + + // Perform a search for affiliation records + async getAffiliations({ name, funderOnly = false }: { name: string, funderOnly?: boolean } ) { + try { + const sanitizedName = encodeURI(name); + const funderBool = funderOnly ? (funderOnly === true) : false; + const queryString = `search=${sanitizedName}&funderOnly=${funderBool}`; + formatLogMessage(logger).info(`Calling DMPHub: ${this.baseURL}/affiliations?${queryString}`) + + const response = await this.get(`affiliations?${queryString}`); + if (response) { + const affiliations = response.map((rec) => new AffiliationSearchModel(rec)) || []; + return affiliations ? affiliations : []; + } + return null; + } catch(err) { + formatLogMessage(logger, { err }).error('Error calling DMPHub API getAffiliation.') + throw(err); + } + } +} diff --git a/src/datasources/mySQLDataSource.ts b/src/datasources/mySQLDataSource.ts new file mode 100644 index 0000000..f402435 --- /dev/null +++ b/src/datasources/mySQLDataSource.ts @@ -0,0 +1,63 @@ +import * as mysql from 'mysql2/promise'; +import { mysqlConfig } from "../config/mysqlConfig"; +import { logger, formatLogMessage } from '../logger'; + +export type PoolConfig = { + connectionLimit: number; + host: string; + port: number; + database: string; + user: string; + password: string; +} + +// Singleton MySQL Connection Pool +export class MySQLDataSource { + private static instance: MySQLDataSource; + private pool: mysql.Pool; + + // Create a new connection pool + private constructor() { + try { + this.pool = mysql.createPool({ + ...mysqlConfig, + waitForConnections: true, + queueLimit: 0, + multipleStatements: false, + }); + } catch (err) { + formatLogMessage(logger, { err, message: 'Unable to establish the MySQL connection pool.' }) + } + } + + // Retrieve the instance of this class + public static getInstance(): MySQLDataSource { + if (!MySQLDataSource.instance) { + MySQLDataSource.instance = new MySQLDataSource(); + } + return MySQLDataSource.instance; + } + + // Retrieve the MySQL connection + public async getConnection(): Promise { + return this.pool.getConnection(); + } + + // Execute a SQL query + // eslint-disable-next-line @typescript-eslint/no-explicit-any + public async query(sql: string, values?: string[]): Promise { + try { + const vals = values.map((val) => (typeof val === 'string') ? val.trim() : val); + const [rows] = await this.pool.execute(sql, vals); + return rows; + } catch (err) { + formatLogMessage(logger, { err, message: 'Uable to process SQL query!' }) + throw err; + } + } + + // Release the MySQL connection pool + public async close(): Promise { + await this.pool.end(); + } +} \ No newline at end of file diff --git a/src/index.js b/src/index.js deleted file mode 100644 index e69de29..0000000 diff --git a/src/index.ts b/src/index.ts index dbeb861..6e01483 100644 --- a/src/index.ts +++ b/src/index.ts @@ -1,22 +1,60 @@ import { ApolloServer } from '@apollo/server'; -import { startStandaloneServer } from '@apollo/server/standalone'; - -import typeDefs from './GraphqlTypeDefs.js'; -import resolvers from './resolvers.js'; - -// The ApolloServer constructor requires two parameters: your schema -// definition and your set of resolvers. -const server = new ApolloServer({ - typeDefs, - resolvers, -}); - -// Passing an ApolloServer instance to the `startStandaloneServer` function: -// 1. creates an Express app -// 2. installs your ApolloServer instance as middleware -// 3. prepares your app to handle incoming requests -const { url } = await startStandaloneServer(server, { - listen: { port: 4000 }, -}); - -console.log(`🚀 Server ready at: ${url}`); +import express from 'express'; +import http from 'http'; +import cors from 'cors'; +import { logger } from './logger'; +import { serverConfig } from './config'; +import { healthcheck } from './controllers/healthcheck'; +import { attachApolloServer } from './middleware/express'; +import router from './router'; +import { MySQLDataSource } from './datasources/mySQLDataSource'; + +// TODO: Make this configurable and pass in as ENV variable +const PORT = 4000; + +// Required logic for integrating with Express +const app = express(); +// Our httpServer handles incoming requests to our Express app. +const httpServer = http.createServer(app); + +const apolloServer = new ApolloServer(serverConfig(logger, httpServer)); + +const startServer = async () => { + await apolloServer.start(); + const { cache } = apolloServer; + + // Healthcheck endpoint (declare this BEFORE Oauth2 and CORS definition due to AWS ALB limitations) + app.get('/up', (_request, response) => healthcheck(apolloServer, response, logger)); + + // Express middleware + app.use( + cors(), + express.urlencoded({ extended: false }), + express.json({ limit: '50mb' }), + ) + + // Attach Apollo server to all of the GraphQL calls + app.use('/graphql', attachApolloServer(apolloServer, cache, logger)) + + // Pass off to the Router for other handling + app.use('/', router); + + httpServer.listen({ port: 4000 }, () => { + console.log(`Server running on port ${PORT}`); + console.log(`GraphQL endpoint: http://localhost:${PORT}/graphql`) + }) +} + +// Handle graceful shutdown +const shutdown = async () => { + console.log('Shutting down server...'); + const pool = MySQLDataSource.getInstance(); + await pool.close(); + process.exit(0); +}; +process.on('SIGINT', shutdown); +process.on('SIGTERM', shutdown); + +startServer().catch((error) => { + console.log('Error starting server:', error) +}) diff --git a/src/logger.ts b/src/logger.ts new file mode 100644 index 0000000..2f12fa4 --- /dev/null +++ b/src/logger.ts @@ -0,0 +1,23 @@ +import pino, { Logger } from 'pino'; +import { ecsFormat } from '@elastic/ecs-pino-format'; + +const logLevel = process.env.LOG_LEVEL || 'info'; + +/* + * Logger using Pino and the Elastic Common Schema format to facilitate + * standardization across all log messaging. This format will allow us + * to more easily debug and track requests in OpenSearch. + */ +export const logger: Logger = pino({ level: logLevel, ...ecsFormat }) + +// Add the additional args to the ECS logger so that they are queryable fields. +// At least you should send the sessionId if available and the error (if applicable) +// eslint-disable-next-line @typescript-eslint/no-invalid-void-type +export function formatLogMessage(logger: Logger, args: object | void): Logger { + if (args) { + // Add the args to the ECS logger + return logger.child({ ...args }); + } + // Otherwise there were no additional arfs, so return the logger as-is + return logger; +} diff --git a/src/middleware/authMiddleware.ts b/src/middleware/authMiddleware.ts new file mode 100644 index 0000000..1601a99 --- /dev/null +++ b/src/middleware/authMiddleware.ts @@ -0,0 +1,22 @@ +import { Request, Response, NextFunction } from 'express'; +import jwt from 'jsonwebtoken'; +import { generalConfig } from '../config/generalConfig'; + +export const authMiddleware = (req: Request, res: Response, next: NextFunction) => { + const authHeader = req.headers.authorization; + + if (!authHeader) { + return res.status(401).json({ error: 'No token provided' }); + } + + const token = authHeader.split(' ')[1]; + + try { + const decoded = jwt.verify(token, generalConfig.jwtSecret as string); + // eslint-disable-next-line @typescript-eslint/no-explicit-any + (req as any).user = decoded; + next(); + } catch (error) { + res.status(401).json({ error: 'Invalid token' }); + } +}; diff --git a/src/middleware/cors.ts b/src/middleware/cors.ts new file mode 100644 index 0000000..f00ea35 --- /dev/null +++ b/src/middleware/cors.ts @@ -0,0 +1,5 @@ +import cors from 'cors'; + +export function handleCors() { + return cors(); +} diff --git a/src/middleware/express.ts b/src/middleware/express.ts new file mode 100644 index 0000000..46bbabd --- /dev/null +++ b/src/middleware/express.ts @@ -0,0 +1,29 @@ +import { expressMiddleware } from '@apollo/server/express4'; +import { DMPHubAPI } from '../datasources/dmphubAPI'; +import { DMPToolAPI } from '../datasources/dmptoolAPI'; +import { MySQLDataSource } from '../datasources/mySQLDataSource'; +import { JWTToken, verifyToken } from '../services/tokenService'; + +export function attachApolloServer(apolloServer, cache, logger) { + // expressMiddleware accepts the same arguments: + // an Apollo Server instance and optional configuration options + return expressMiddleware(apolloServer, { + context: async ({ req }) => { + // Extract the token from the incoming request so we can pass it on to the resolvers + const authHeader: string = req?.headers?.authorization || ''; + const authHdr: string = authHeader.split(' ')[1] || null; + const token: JWTToken = authHeader ? verifyToken(authHdr, logger) : null; + + return { + token, + // Pass the logger in so it is available to our resolvers and dataSources + logger, + dataSources: { + dmphubAPIDataSource: await new DMPHubAPI({ cache, token }), + dmptoolAPIDataSource: await new DMPToolAPI({ cache, token }), + sqlDataSource: await MySQLDataSource.getInstance(), + }, + } + }, + }); +} diff --git a/src/middleware/oauthServer.ts b/src/middleware/oauthServer.ts new file mode 100644 index 0000000..7cfd636 --- /dev/null +++ b/src/middleware/oauthServer.ts @@ -0,0 +1,116 @@ +import { Request, Response } from 'express'; +import { Request as OAuth2Request, Response as OAuth2Response } from '@node-oauth/oauth2-server'; +import OAuth2Server from '@node-oauth/oauth2-server'; +import { logger, formatLogMessage } from '../logger'; +import { OAuthClient } from '../models/OAuthClient'; +import { OAuthCode } from '../models/OAuthCode'; +import { OAuthRefreshToken } from '../models/OAuthRefreshToken'; +import { OAuthToken } from '../models/OAuthToken'; +import { User } from '../models/User'; +import { AuthorizationCode, Client, Token } from 'oauth2-server' + +const model = { + // Fetch the OAuth2 client from the DB + getClient: async function(clientId: string, clientSecret: string) { + return await OAuthClient.findOne(clientId, clientSecret); + }, + + // Fetch the authorization code from the DB + getAuthorizationCode: async function(authorizationCode: string) { + return await OAuthCode.findOne(authorizationCode); + }, + + // Save the authorization code in the DB + saveAuthorizationCode: async function(code: AuthorizationCode, client: Client, user: User) { + try { + code.client = client; + code.user = user; + return await code.save(); + } catch(err) { + formatLogMessage(logger, { err }).error('Error oauthServer.saveAuthorizationCode') + return null; + } + }, + + // Set the expiry date on the authorization code to the current time + revokeAuthorizationCode: async function(code: AuthorizationCode) { + try { + return await code.revoke(); + } catch(err) { + formatLogMessage(logger, { err }).error('Error oauthServer.revokeAuthorizationCode') + return null; + } + }, + + // Verify that the scope requested is allowed by the access token + verifyScope: async function(token: Token, scope: string | string[]) { + const scopeArray: string[] = Array.isArray(scope) ? scope : [scope]; + return await scopeArray.every((item) => token.scope.includes(item)); + }, + + // Verify that the User has authorized the scope for the OAuth2 client + validateScope: async function(user: User, client: Client, scope: string[]) { + const token = await OAuthToken.findByClientUser(client, user); + return scope.every((item) => token.scope.includes(item)); + }, + + // Fetch the access token from the DB + getAccessToken: async function(accessToken: string) { + try { + return await OAuthToken.findOne(accessToken); + } catch(err) { + formatLogMessage(logger, { err }).error('Error oauthServer.getAccessToken') + return null; + } + }, + + // Save the access token in the DB + saveToken: async function(token: Token, client: Client, user: User) { + try { + token.client = client; + token.user = user; + return await token.save(); + } catch (err) { + formatLogMessage(logger, { err }).error('Error oauthServer.saveToken') + return null; + } + }, + + // Set the expiry date on the access token to the current time + revokeToken: async function(token: Token) { + try { + return await token.revoke(); + } catch (err) { + formatLogMessage(logger, { err }).error('Error oauthServer.revokeToken') + return null; + } + }, + + // Fetch the refresh token from the DB + getRefreshToken: async function(refreshToken: string) { + return await OAuthRefreshToken.findOne(refreshToken); + }, +}; + +export function castRequest(req: Request): OAuth2Request { + return new OAuth2Request({ + headers: req.headers, + method: req.method, + query: req.query, + body: req.body, + }); +} + +export function castResponse(res: Response): OAuth2Response { + return new OAuth2Response({ + headers: res.getHeaders(), + //body: res.get('Content-Type') === 'application/json' ? res['body'] : undefined, + status: res.statusCode, + redirect: res.get('Location'), + }); +} + +export const oauthServer = new OAuth2Server({ + model, + allowBearerTokensInQueryString: true, +}); diff --git a/src/mocks.ts b/src/mocks.ts new file mode 100644 index 0000000..3061d4f --- /dev/null +++ b/src/mocks.ts @@ -0,0 +1,42 @@ +import casual from 'casual'; +import { DMSP_BASE_URL, validateDmspId } from './resolvers/scalars/dmspId'; +import { validateOrcid } from './resolvers/scalars/orcid'; +import { ROR_DOMAIN, validateRor } from './resolvers/scalars/ror'; +import { mock as affiliationMock } from './mocks/affiliation'; +import { mock as userMock } from './mocks/user'; +import { mock as contributorRoleMock } from './mocks/contributorRole'; + +// Mock resolvers for our custom Scalars +function mockOrcid() { + return validateOrcid(casual.card_number().toString().match(/[0-9]{4}/g).join('-')); +} +function mockRor() { + return validateRor(`${ROR_DOMAIN}${casual.rgb_hex.replace('#', '')}`); +} +function mockDmspId() { + return validateDmspId(`${DMSP_BASE_URL}${casual.rgb_hex.replace('#', '').toUpperCase()}`); +} + +const scalarMocks = { + // Mocks for generic scalars + Int: () => casual.integer(1, 1000), + Float: () => casual.double(1.0, 999.99), + String: () => casual.sentence, + + // Mocks for graphql-tools custom scalars + URL: () => casual.url, + DateTimeISO: () => casual.date('YYYY-MM-DD HH:mm:ss'), + EmailAddress: () => casual.email, + + // Mocks for custom scalars + Orcid: () => mockOrcid(), + Ror: () => mockRor(), + DmspId: () => mockDmspId(), +}; + +export const mocks = { + ...scalarMocks, + ...affiliationMock, + ...contributorRoleMock, + ...userMock +}; diff --git a/src/mocks/affiliation.ts b/src/mocks/affiliation.ts new file mode 100644 index 0000000..5a0444f --- /dev/null +++ b/src/mocks/affiliation.ts @@ -0,0 +1,287 @@ +import { AffiliationModel, AffiliationSearchModel } from '../models/Affiliation'; + +// Just define what is unique here. Any fields you skip will end up using the defaults +// for their respective type as defined in ./src/mocks.ts +export const data = [ + { + "id": "https://ror.org/01nrxwf90", + "provenance": "ROR", + "provenanceSyncDate": "2024-07-22T07:43:26Z", + "name": "University of Edinburgh", + "displayName": "University of Edinburgh (ed.ac.uk)", + "active": true, + "funder": true, + "fundref": "http://dx.doi.org/10.13039/501100000848", + "types": ["Education"], + "acronyms": [], + "aliases": [], + "labels": [], + "countryCode": "GB", + "countryName": "United Kingdom", + "domain": "ed.ac.uk", + "wikipediaURL": "http://en.wikipedia.org/wiki/University_of_Edinburgh", + "links": ["http://www.ed.ac.uk/home"], + "searchNames": [ + "University of Edinburgh", + "ed.ac.uk", + ], + "relationships": [ + { + "id": "https://ror.org/05a7t9b67", + "type": "Child", + "name": "Edinburgh Cancer Research", + }, + { + "id": "https://ror.org/009bsy196", + "type": "Related", + "name": "Edinburgh Royal Infirmary", + } + ], + "addresses": [ + { + "city": "Edinburgh", + "state": null, + "stateCode": null, + "countryGeonamesId": 2635167, + "lat": 55.95206, + "lng": -3.19648, + } + ] + }, + { + "id": "https://ror.org/01tm6cn81", + "provenance": "ROR", + "provenanceSyncDate": "2024-07-27T12:44:13Z", + "name": "University of Gothenburg", + "displayName": "University of Gothenburg (gu.se)", + "active": true, + "funder": false, + "fundref": null, + "types": ["Education"], + "acronyms": [], + "aliases": [], + "labels": [ + { + "label": "Göteborgin yliopisto", + "iso639": "fi", + }, + { + "label": "Göteborgs universitet", + "iso639": "sv", + } + ], + "countryCode": "SE", + "countryName": "Sweden", + "domain": "gu.se", + "wikipediaURL": "http://en.wikipedia.org/wiki/University_of_Gothenburg", + "links": ["http://www.gu.se/english"], + "relationships": [ + { + "id": "https://ror.org/04vgqjj36", + "type": "Related", + "name": "Sahlgrenska University Hospital", + } + ], + "searchNames": [ + "Göteborgs universitet", + "Göteborgin yliopisto", + "University of Gothenburg", + "gu.se", + ], + "addresses": [ + { + "city": "Gothenburg", + "state": null, + "stateCode": null, + "countryGeonamesId": 2661886, + "lat": 57.70716, + "lng": 11.96679, + } + ] + }, + { + "id": "https://ror.org/00dmfq477", + "provenance": "ROR", + "provenanceSyncDate": "2024-07-30T15:12:45Z", + "name": "University of California Office of the President", + "displayName": "University of California Office of the President (ucop.edu)", + "active": true, + "funder": true, + "fundref": "http://dx.doi.org/10.13039/100014576", + "types": ["Education"], + "acronyms": ["UCOP"], + "aliases": [], + "countryCode": "US", + "countryName": "United States", + "domain": "ucop.edu", + "wikipediaURL": null, + "links": ["https://www.ucop.edu"], + "searchNames": [ + "University of California, Office of the President", + "ucop.edu", + "ucop", + ], + "relationships": [ + { + "id": "https://ror.org/033jnv181", + "type": "Parent", + "name": "United States Department of Health and Human Services", + } + ], + "addresses": [ + { + "city": "Oakland", + "state": "California", + "stateCode": "MD", + "countryGeonamesId": 6252001, + "lat": 37.80437, + "lng": -122.2708, + } + ] + }, + { + "id": "https://ror.org/01cwqze88", + "provenance": "ROR", + "provenanceSyncDate": "2024-07-30T15:12:45Z", + "name": "National Institutes of Health", + "displayName": "National Institutes of Health (nih.gov)", + "active": true, + "funder": true, + "fundref": "http://dx.doi.org/10.13039/100000002", + "types": ["Government"], + "acronyms": ["NIH"], + "aliases": [], + "countryCode": "US", + "countryName": "United States", + "domain": "nih.gov", + "wikipediaURL": "http://en.wikipedia.org/wiki/National_Institutes_of_Health", + "links": ["http://www.nih.gov/"], + "searchNames": [ + "National Institutes of Health", + "nih.gov", + ], + "relationships": [ + { + "id": "https://ror.org/033jnv181", + "type": "Parent", + "name": "United States Department of Health and Human Services", + } + ], + "addresses": [ + { + "city": "Bethesda", + "state": "Maryland", + "stateCode": "MD", + "countryGeonamesId": 6252001, + "lat": 38.98067, + "lng": -77.10026, + } + ] + }, + { + "id": "https://dmptool.org/orgs/12345", + "provenance": "DMPTool", + "provenanceSyncDate": "2021-03-07T12:13:41Z", + "name": "Example University", + "displayName": "Example University (example.edu)", + "active": true, + "funder": false, + "fundref": null, + "types": ["Education"], + "acronyms": ["EU"], + "aliases": ["Example"], + "countryCode": "US", + "countryName": "United States", + "domain": "example.edu", + "wikipediaURL": null, + "links": ["http://www.example.edu/library/"], + "searchNames": [ + "Example University", + "example.edu", + ], + }, +] + +export const searchData = [ + { + "id": "https://ror.org/01nrxwf90", + "fetchId": "ror.org/01nrxwf90", + "name": "University of Edinburgh", + "displayName": "University of Edinburgh (ed.ac.uk)", + "funder": true, + "fundref": "http://dx.doi.org/10.13039/501100000848", + "aliases": [], + "countryCode": "gb", + "countryName": "United Kingdom", + "links": ["ed.ac.uk", "http://www.ed.ac.uk/home"], + "locales": [], + }, + { + "id": "https://ror.org/01tm6cn81", + "fetchId": "ror.org/01tm6cn81", + "name": "University of Gothenburg", + "displayName": "University of Gothenburg (gu.se)", + "funder": false, + "fundref": "", + "aliases": [], + "countryCode": "se", + "countryName": "Sweden", + "links": ["gu.se", "http://www.gu.se/english"], + "locales": [ + { + "label": "Göteborgin yliopisto (gu.se)", + "iso639": "fi", + }, + { + "label": "Göteborgs universitet (gu.se)", + "iso639": "sv", + } + ], + }, + { + "id": "https://ror.org/01cwqze88", + "fetchId": "ror.org/01cwqze88", + "name": "National Institutes of Health", + "displayName": "National Institutes of Health (nih.gov)", + "funder": true, + "fundref": "http://dx.doi.org/10.13039/100000002", + "aliases": ["NIH"], + "countryCode": "us", + "countryName": "United States", + "links": ["http://www.nih.gov/"], + "locales": [], + }, + { + "id": "https://ror.org/00dmfq477", + "fetchId": "ror.org/00dmfq477", + "name": "University of California Office of the President", + "displayName": "University of California Office of the President (ucop.edu)", + "funder": true, + "fundref": "http://dx.doi.org/10.13039/100014576", + "aliases": ["UCOP"], + "countryCode": "us", + "countryName": "United States", + "links": ["https://www.ucop.edu"], + "locales": [], + }, + { + "id": "https://dmptool.org/orgs/12345", + "fetchId": "dmptool.org/orgs/12345", + "name": "Example University", + "displayName": "Example University (example.edu)", + "funder": false, + "fundref": "", + "aliases": ["EU"], + "countryCode": "us", + "countryName": "United States", + "links": ["http://www.example.edu/library/"], + "locales": [], + }, +] + +export const mock = { + // Return a random item from the data array + Affiliation: () => new AffiliationModel(data[Math.floor(Math.random() * data.length)]), + + Affiliations: () => searchData.map((rec) => new AffiliationSearchModel(rec)), +} diff --git a/src/mocks/contributorRole.ts b/src/mocks/contributorRole.ts new file mode 100644 index 0000000..956dacf --- /dev/null +++ b/src/mocks/contributorRole.ts @@ -0,0 +1,37 @@ +// Just define what is unique here. Any fields you skip will end up using the defaults +// for their respective type as defined in ./src/mocks.ts +const data = [ + { + id: 1, + url: 'https://credit.niso.org/contributor-roles/investigation/', + label: 'Principal Investigator (PI)', + description: 'An individual conducting a research and investigation process, specifically performing the experiments, or data/evidence collection.', + displayOrder: 1, + }, + { + id: 2, + url: 'https://credit.niso.org/contributor-roles/project-administration/', + label: 'Project Administrator', + description: 'An individual with management and coordination responsibility for the research activity planning and execution.', + displayOrder: 2, + }, + { + id: 3, + url: 'https://credit.niso.org/contributor-roles/data-curation/', + label: 'Data Manager', + description: 'An individual engaged in management activities to annotate (produce metadata), scrub data and maintain research data (including software code, where it is necessary for interpreting the data itself) for initial use and later re-use.', + displayOrder: 3, + }, + { + id: 4, + url: `${process.env.DMSP_BASE_URL}/contributor_roles/other`, + label: 'Other', + description: 'An individual associated with the research project that does not fall under one of the other primary roles.', + displayOrder: 4, + }, +] + +export const mock = { + // Return a random item from the data array + ContributorRole: () => data[Math.floor(Math.random() * data.length)] +} diff --git a/src/mocks/user.ts b/src/mocks/user.ts new file mode 100644 index 0000000..499e1ba --- /dev/null +++ b/src/mocks/user.ts @@ -0,0 +1,12 @@ +import casual from 'casual'; + +export const mock = { + // User account mock + User: () => ({ + id: casual.integer(1, 10000), + givenName: casual.first_name, + surName: casual.last_name, + email: casual.email, + role: casual.integer(0, 1) == 1 ? 'ADMIN' : 'RESEARCHER' + }) +}; diff --git a/src/models/Affiliation.ts b/src/models/Affiliation.ts new file mode 100644 index 0000000..866ca3c --- /dev/null +++ b/src/models/Affiliation.ts @@ -0,0 +1,167 @@ +// Represents an Institution, Organization or Company +export class AffiliationModel { + public id!: string; + public provenance!: string; + public provenanceSyncDate!: string; + public name!: string; + public displayName!: string; + public active!: boolean; + public funder!: boolean; + public fundref: string; + public types: string[]; + public acronyms: string[]; + public aliases: string[]; + public locales: AffiliationLocale[]; + public countryCode: string; + public countryName: string; + public domain: string; + public wikipediaURL: string; + public links: string[]; + public relationships: AffiliationRelationship[]; + public addresses: AffiliationAddress[]; + + private externalIds: ExternalId[]; + + // Initialize a new Affiliation + constructor(options) { + // This is our opportunity to convert ruby variable names over to JS + this.provenance = options._SOURCE || 'dmptool'; + this.provenanceSyncDate = options._SOURCE_SYNCED_AT || new Date().toUTCString(); + this.id = options.ID || options.id; + this.types = options.types || []; + this.name = options.name; + this.displayName = options.label || options.displayName || options.name; + this.active = options.active === 1; + this.funder = options.funder === 1; + this.acronyms = options.acronyms || []; + this.aliases = options.aliases || []; + this.countryCode = options.country?.country_code || options.countryCode; + this.countryName = options.country?.country_name || options.countryName; + this.domain = options.domain; + this.links = options.links || []; + + // If there are any labels/locales defined, initialize them + this.locales = []; + if(Array.isArray(options.locales)) { + this.locales = options.labels.map((lbl) => new AffiliationLocale(lbl)); + } + + // If there are any addresses defined, initialize them + this.addresses = []; + if(Array.isArray(options.addresses)) { + this.addresses = options.addresses.map((addr) => new AffiliationAddress(addr)); + } + + // If there are any relationships defined, initialize them + this.relationships = []; + if(Array.isArray(options.relationships)) { + this.relationships = options.relationships.map((rel) => new AffiliationRelationship(rel)); + } + + // If there are any external_ids defined, initialize them and set the FundRef ID + this.externalIds = []; + if (options.hasOwnProperty('external_ids')) { + this.externalIds = Object.keys(options.external_ids).map((key) => { + return new ExternalId({ + type: key, + ...options.external_ids[key] + }) + }); + this.fundref = this.externalIds?.find(id => id.type === 'fundref')?.id; + } + } +} + +// Represents an external identifier like FundRef, GRID, ISSN, etc. +class ExternalId { + public type!: string; + public id!: string; + + constructor(options) { + const allIds = Array.isArray(options.all) ? options.all : [options.all] + + this.type = options.type?.toLowerCase(); + this.id = options.preferred ? options.preferred : allIds[0]; + } +} + +// Represents the city, state, country and Lat+Long for the affiliation +export class AffiliationAddress { + public city: string; + public state: string; + public stateCode: string; + public countryGeonamesId: number; + public lat: number; + public lng: number; + + constructor(options) { + this.city = options.city; + this.state = options.state; + this.stateCode = options.state_code; + this.countryGeonamesId = options.country_geonames_id; + this.lat = options.lat; + this.lng = options.lng + } +} + +// Represents a relationship between 2 affiliations +export class AffiliationRelationship { + public id!: string; + public type!: string; + public name: string; + + constructor(options) { + this.id = options.id; + this.type = options.type; + this.name = options.label || options.name; + } +} + +export class AffiliationLocale { + public label!: string; + public locale!: string; + + constructor(options) { + this.label = options.label; + this.locale = options.iso639; + } +} + +// A pared down version of the full Affiliation object. This type is returned by +// our index searches +export class AffiliationSearchModel { + public id!: string; + public fetchId!: string; + public name!: string; + public displayName!: string; + public funder!: boolean; + public fundref: string; + public aliases: string[]; + public countryCode: string; + public countryName: string; + public links: string[]; + public locales: AffiliationLocale[]; + + // Initialize a new AffiliationSearch result + constructor(options) { + const suffix = options.domain || options.countryName; + + // This is our opportunity to convert ruby variable names over to JS + this.id = options.ror_url || options.id; + this.fetchId = this.id?.replace(/https?:\/\//g, ''); + this.name = options.name; + this.displayName = suffix ? `${options.name} (${suffix})` : options.name; + this.funder = options.hasOwnProperty('fundref_id'); + this.fundref = options.fundref_url || options.fundref; + this.aliases = options.aliases || []; + this.countryCode = options.countryCode; + this.countryName = options.countryName; + this.links = options.links || [options.domain]; + + // If there are any labels/locales defined, initialize them + this.locales = []; + if(Array.isArray(options.locales)) { + this.locales = options.labels?.map((lbl) => new AffiliationLocale(lbl)); + } + } +} diff --git a/src/models/ContributorRole.ts b/src/models/ContributorRole.ts new file mode 100644 index 0000000..ee16ee7 --- /dev/null +++ b/src/models/ContributorRole.ts @@ -0,0 +1,9 @@ +export type ContributorRoleModel = { + id: number; + displayOrder: number; + url: string; + label: string; + description: string; + created: string; + modified: string; +}; diff --git a/src/models/Dmsp.ts b/src/models/Dmsp.ts new file mode 100644 index 0000000..d4a9903 --- /dev/null +++ b/src/models/Dmsp.ts @@ -0,0 +1,38 @@ +import { ContributorRoleModel } from './ContributorRole'; + +export type DmspModel = { + primaryContact: PrimaryContact; + created: string; + modified: string; + title: string; + + contributors: [Contributor]; + description: string; + isFeatured: string; + visibility: string; + hasEthicalConcerns: string; + ethicalConcernsDescription: string; + ethicalConcernsReportURL: string; + language: string; +} + +type PrimaryContact = { + orcid: string; + name: string; + mbox: string; + affiliation: Affiliation; +} + +type Contributor = { + orcid: string; + name: string; + mbox: string; + role: [ContributorRoleModel] + affiliation: Affiliation; +} + +type Affiliation = { + ror: string; + name: string; + affiliation_id: string; +} diff --git a/src/models/OAuthClient.ts b/src/models/OAuthClient.ts new file mode 100644 index 0000000..c386c92 --- /dev/null +++ b/src/models/OAuthClient.ts @@ -0,0 +1,153 @@ +import { Client } from 'oauth2-server'; +import { v6 as uuidv6 } from 'uuid'; +import uuidRandom from 'uuid-random'; +import { stringToArray } from '../utils/helpers'; +import { User } from './User'; +import { MySQLDataSource } from '../datasources/mySQLDataSource'; +import { logger, formatLogMessage } from '../logger'; + +export class OAuthClient implements Client { + private mysql: MySQLDataSource; + + public id: string; + public name: string; + public redirectUris: string[]; + // eslint-disable-next-line @typescript-eslint/no-explicit-any + public grants: any[]; + public clientId: string; + public clientSecret: string; + public user: User; + public errors: string[]; + + // Initialize a new client + constructor(options) { + this.mysql = MySQLDataSource.getInstance(); + + this.id = options.id; + this.name = options.name; + this.redirectUris = stringToArray(options.redirectUris, ',') || []; + this.grants = stringToArray(options.grants, ',') || []; + this.clientId = options.clientId; + this.clientSecret = options.clientSecret; + this.user = options.user; + this.errors = []; + } + + // Find the OAuth2 Client by it's Client ID and Secret + static async findOne(clientId: string, clientSecret: string): Promise { + const mysql = MySQLDataSource.getInstance(); + const sql = 'SELECT * FROM oauthClients WHERE clientId = ? AND clientSecret = ?'; + try { + const [rows] = await mysql.query(sql, [clientId, clientSecret]); + const user = await User.findById(rows[0].userId); + + return rows.length === 0 ? null : new OAuthClient({ + ...OAuthClient._SqlFieldsToProperties(rows[0]), + user: user, + }); + } catch (err) { + formatLogMessage(logger, { err }).error('Error trying to find OAuthClient by id'); + throw err; + } + } + + // Find the OAuth2 Client by it's id + static async findById(oauthClientId: string): Promise { + const mysql = MySQLDataSource.getInstance(); + const sql = 'SELECT * FROM oauthClients WHERE id = ?'; + try { + const [rows] = await mysql.query(sql, [oauthClientId]); + const user = await User.findById(rows[0].userId); + + return rows.length === 0 ? null : new OAuthClient({ + ...OAuthClient._SqlFieldsToProperties(rows[0]), + user: user, + }); + } catch (err) { + formatLogMessage(logger, { err }).error('Error trying to find OAuthClient by id'); + throw err; + } + } + + // Function to help ensure data integrity + cleanup(): void { + this.name = this.name?.toLowerCase(); + this.redirectUris = this.redirectUris || []; + this.grants = this.grants || []; + this.clientId = this.clientId || this.generateClientId(); + this.clientSecret = this.clientSecret || this.generateClientSecret(); + } + + // Generate a random ClientId + generateClientId(): string { + return uuidv6(256); + } + + // Generate a random ClientSecret + generateClientSecret(): string { + return uuidRandom(); + } + + // Register/Save a new OAuthClient + async save(): Promise { + this.cleanup(); + + let sql = ` + INSERT INTO oauthClients (name, redirectUris, grants, clientId, clientSecret, userId) + VALUES(?,?,?,?,?,?) + `; + const vals = [ + this.name, + this.redirectUris?.join(', '), + this.grants?.join(', '), + this.clientId, + this.clientSecret, + this.user?.id?.toString(), + ]; + + // If the OAuthClient already has an id then update it instead + if (this.id) { + vals.push(this.id); + vals.push(new Date().toISOString()); + sql = ` + UPDATE oauthClients + SET name = ?, redirectUris = ?, grants = ?, clientId = ?, clientSecret = ?, userId = ?, modified = ? + WHERE id = ? + `; + } + + try { + const [result] = await this.mysql.query(sql, vals); + // eslint-disable-next-line @typescript-eslint/no-explicit-any + this.id = (result as any).insertId; + formatLogMessage(logger).debug(`OAuth Client was saved: ${result.insertId}`); + return true; + } catch (err) { + formatLogMessage(logger, { err }).error('Error saving OAuthClient'); + throw err; + } + } + + // Register/Save a new OAuthClient + async delete(): Promise { + try { + await this.mysql.query(`DELETE FROM oauthClients WHERE id = ?`, [this.id]); + formatLogMessage(logger).debug(`OAuth Client was deleted: ${this.id}`); + return true; + } catch (err) { + formatLogMessage(logger, { err }).error('Error deleting OAuthClient'); + throw err; + } + } + + static _SqlFieldsToProperties(row) { + return { + id: row.id, + name: row.name, + redirectUris: stringToArray(row.redirectUris, ','), + grants: stringToArray(row.grants, ','), + clientId: row.clientId, + clientSecret: row.clientSecret, + } + } +} diff --git a/src/models/OAuthCode.ts b/src/models/OAuthCode.ts new file mode 100644 index 0000000..03c00b2 --- /dev/null +++ b/src/models/OAuthCode.ts @@ -0,0 +1,177 @@ +import { AuthorizationCode } from 'oauth2-server'; +import { v4 as uuidv4 } from 'uuid'; +import { oauthConfig } from '../config/oauthConfig'; +import { stringToArray } from '../utils/helpers'; +import { OAuthClient } from './OAuthClient'; +import { OAuthToken } from './OAuthToken' +import { User } from '../models/User'; +import { MySQLDataSource } from '../datasources/mySQLDataSource'; +import { logger, formatLogMessage } from '../logger'; + +export class OAuthCode implements AuthorizationCode { + private mysql: MySQLDataSource; + + public authorizationCode: string; + public expiresAt: Date | undefined; + public redirectUri: string; + public scope: string | string[]; + public client: OAuthClient; + public user: User; + public codeChallenge?: string | undefined; + public codeChallengeMethod?: string | undefined; + public errors: string[]; + + // Initialize a new authorization code + constructor(options) { + this.mysql = MySQLDataSource.getInstance(); + + this.authorizationCode = options.authorizationCode; + this.expiresAt = options.expiresAt; + this.redirectUri = options.redirectUri; + this.scope = stringToArray(options.scope, ','); + this.client = options.client; + this.user = options.user; + this.codeChallenge = options.codeChallenge; + this.codeChallengeMethod = options.codeChallengeMethod; + this.errors = []; + } + + // Locate the authorization code by its id + static async findOne(authorizationCode: string): Promise { + try { + const mysql = MySQLDataSource.getInstance(); + const [rows] = await mysql.query('SELECT * FROM oauthCodes WHERE code = ?', [authorizationCode]); + if (rows.length === 0) { + return null; + } + // eslint-disable-next-line @typescript-eslint/no-explicit-any + const row = (rows as any[])[0]; + const client = await OAuthClient.findById(row.clientId); + const user = await User.findById(row.userId); + if (!client || !user) { + return null; + } + return new OAuthCode({ + ...OAuthToken._SqlFieldsToProperties(row), + client: await OAuthClient.findById(row.clientId), + user: await User.findById(row.userId), + }); + + } catch(err) { + formatLogMessage(logger, { err }).error('Unable to fetch AuthorizationCode from OAuthCodes'); + throw(err); + } + } + + // Validate the authorization code and issue an access token + static async exchangeCodeForToken(authorizationCode: string): Promise { + const authCode = await OAuthCode.findOne(authorizationCode) + + if(authCode.validate()) { + const accessToken = new OAuthToken({ client: authCode.client, user: authCode.user }); + if (accessToken) { + // TODO: We will want to modify the TTL based on the grant type + accessToken.save(); + return accessToken; + } + return null; + } + throw new Error('Invalid authorization code'); + } + + // Ensure data integrity + cleanup(): void { + this.authorizationCode = this.authorizationCode || this.generateAuthorizationCode(); + this.expiresAt = this.expiresAt || this.generateExpiryDate(); + this.redirectUri = this.redirectUri || 'http://localhost:3000'; + this.scope = this.scope || ['read']; + } + + // Generate the token TTL + generateExpiryDate(): Date { + const currentDate = new Date(); + return new Date(currentDate.getTime() + oauthConfig.authorizationCodeLifetime * 1000); + } + + // Generate a new unique authorization code + generateAuthorizationCode(): string { + return uuidv4(); + } + + // Ensure that the authorization code has not expired + async validate(): Promise { + if (this.authorizationCode) { + // Make sure it still exists in the database! and the payload matches (not tampered with) + const existing = await OAuthCode.findOne(this.authorizationCode); + if (existing && existing === this) { + // Make sure it is not expired + const currentDate = new Date(); + return this.expiresAt > currentDate; + } + return false; + } + return false; + } + + // Save the authorization code to the DB + async save(): Promise { + this.cleanup(); + + const sql = ` + INSERT INTO oauthCodes + (code, expiresAt, redirectUri, scope, userId, clientId, codeChallenge, codeChallengeMethod) + VALUES (?, ?, ?) + `; + const vals = [ + this.authorizationCode, + this.expiresAt.toISOString(), + this.redirectUri, + stringToArray(this.scope, ',').join(', '), + this.client.id.toString(), + this.user.id.toString(), + this.codeChallenge, + this.codeChallengeMethod, + ]; + + try { + const [result] = await this.mysql.query(sql, vals); + if (result[0]) { + formatLogMessage(logger) + .debug(`Authorization code created: User: ${this.user.id}, Code: ${result.insertId}`); + return true; + } + return false; + } catch(err) { + formatLogMessage(logger, { err }).error('Error saving OAuthCode'); + throw err; + } + } + + // Set the authorization code expiry to now + async revoke(): Promise { + const currentDate = new Date(); + const sql = `UPDATE oauthCodes SET expiresAt = ?, modified = ? WHERE code = ?`; + const vals = [currentDate.toISOString(), currentDate.toISOString(), this.authorizationCode]; + try { + await this.mysql.query(sql, vals); + formatLogMessage(logger).debug(`Authorization code was revoked: ${this.authorizationCode}`); + return true; + } catch (err) { + formatLogMessage(logger, { err }).error('Error revoking OAuthCode'); + throw err; + } + } + + // Convert the DB fields to properties of this call (except client and user) + static _SqlFieldsToProperties(row) { + const scopeArray = typeof row.scope === 'string' ? row.scope.split(' ') : row.scope; + return { + authorizationCode: row.code, + expiresAt: new Date(row.expiresAt), + redirectUri: row.redirectUri, + scope: scopeArray, + codeChallenge: row.codeChallenge, + codeChallengeMethod: row.codeChallengeMethod, + } + } +} diff --git a/src/models/OAuthRefreshToken.ts b/src/models/OAuthRefreshToken.ts new file mode 100644 index 0000000..5e67168 --- /dev/null +++ b/src/models/OAuthRefreshToken.ts @@ -0,0 +1,138 @@ +import { RefreshToken } from 'oauth2-server'; +import { v4 as uuidv4 } from 'uuid'; +import { OAuthClient } from './OAuthClient'; +import { User } from './User'; +import { oauthConfig } from '../config/oauthConfig'; +import { MySQLDataSource } from '../datasources/mySQLDataSource'; +import { logger, formatLogMessage } from '../logger'; + +export class OAuthRefreshToken implements RefreshToken { + private mysql: MySQLDataSource; + + public refreshToken: string | undefined; + public refreshTokenExpiresAt?: Date | undefined; + public client: OAuthClient; + public user: User; + public errors: string[]; + + // Initialize a new refresh token + constructor(options) { + this.mysql = MySQLDataSource.getInstance(); + + this.refreshToken = options.refreshToken; + this.refreshTokenExpiresAt = options.refreshTokenExpiresAt; + this.client = options.client; + this.user = options.user; + this.errors = []; + } + + // Locate and refresh token by its id + static async findOne(refreshToken: string): Promise { + try { + const mysql = MySQLDataSource.getInstance(); + const [rows] = await mysql.query('SELECT * FROM oauthRefreshTokens WHERE token = ?', [refreshToken]); + if (rows.length === 0) { + return null; + } + // eslint-disable-next-line @typescript-eslint/no-explicit-any + const row = (rows as any[])[0]; + const client = await OAuthClient.findById(row.clientId); + const user = await User.findById(row.userId); + if (!client || !user) { + return null; + } + return new OAuthRefreshToken({ + ...OAuthRefreshToken._SqlFieldsToProperties(row), + client: await OAuthClient.findById(row.clientId), + user: await User.findById(row.userId), + }); + } catch(err) { + formatLogMessage(logger, { err }) + .error(`Unable to fetch RefreshToken from OAuthRefreshToken by token: ${refreshToken}`); + throw(err); + } + } + + // Ensure data integrity + cleanup(): void { + this.refreshToken = this.refreshToken || this.generateRefreshToken(); + this.refreshTokenExpiresAt = this.refreshTokenExpiresAt || this.generateExpiryDate(false); + } + + // Generate the token + generateRefreshToken(): string { + return uuidv4(); + } + + // Generate the TTL Expiry date + generateExpiryDate(forAccessToken = true): Date { + const currentDate = new Date(); + const ttlSeconds = forAccessToken ? oauthConfig.accessTokenLifetime : oauthConfig.refreshTokenLifetime; + return new Date(currentDate.getTime() + ttlSeconds * 1000); + } + + // Make sure the token has not been revoked and that it has not expired + async validate(): Promise { + if (this.refreshToken) { + // Make sure it still exists in the database! and the payload matches (not tampered with) + const existing = await OAuthRefreshToken.findOne(this.refreshToken); + if (existing && existing === this) { + // Make sure it is not expired + const currentDate = new Date(); + return this.refreshTokenExpiresAt > currentDate; + } + return false; + } + return false; + } + + // Save the Token to the DB + async save(): Promise { + this.cleanup(); + + const sql = `INSERT INTO oauthRefreshTokens (token, expiresAt, clientId, userId) VALUES (?, ?, ?, ?)`; + const vals = [ + this.refreshToken, + this.refreshTokenExpiresAt.toISOString(), + this.client.id.toString(), + this.user.id.toString() + ] + try { + await this.mysql.query(sql, vals); + // TODO: Fix this Type issue, we should able to define one here); + formatLogMessage(logger) + .debug(`OAuthRefreshToken was created: User: ${this.user.id}, token: ${this.refreshToken}`); + return true; + } catch (err) { + formatLogMessage(logger, { err }).error('Error saving OAuthRefreshToken'); + throw err; + } + } + + // Set the Expiry for the token to now + async revoke(): Promise { + const currentDate = new Date(); + const sql = ` + UPDATE oauthRefreshTokens SET refreshTokenExpiresAt = ?, modified = ? + WHERE token = ? + `; + const vals = [currentDate.toISOString(), currentDate.toISOString(), this.refreshToken]; + try { + await this.mysql.query(sql, vals); + // TODO: Fix this Type issue, we should able to define one here + formatLogMessage(logger).debug(`Refresh token was revoked: ${this.refreshToken}`); + return true; + } catch (err) { + formatLogMessage(logger, { err }).error('Error revoking OAuthRefreshToken'); + throw err; + } + } + + // Convert the DB fields to properties of this call (except client and user) + static _SqlFieldsToProperties(row) { + return { + refreshToken: row.refreshToken, + refreshTokenExpiresAt: new Date(row.refreshTokenExpiresAt), + } + } +} diff --git a/src/models/OAuthToken.ts b/src/models/OAuthToken.ts new file mode 100644 index 0000000..6483a25 --- /dev/null +++ b/src/models/OAuthToken.ts @@ -0,0 +1,185 @@ +import { Client, Token } from 'oauth2-server'; +import { v4 as uuidv4 } from 'uuid'; +import { OAuthClient } from './OAuthClient'; +import { OAuthRefreshToken } from './OAuthRefreshToken'; +import { User } from './User'; +import { oauthConfig } from '../config/oauthConfig'; +import { stringToArray } from '../utils/helpers'; +import { generateToken } from '../services/tokenService'; +import { MySQLDataSource } from '../datasources/mySQLDataSource'; +import { logger, formatLogMessage } from '../logger'; + +export class OAuthToken implements Token { + private mysql: MySQLDataSource; + + public accessToken: string; + public accessTokenExpiresAt?: Date | undefined; + public refreshToken?: string | undefined; + public refreshTokenExpiresAt?: Date | undefined; + public scope?: string[]; + public client: OAuthClient; + public user: User; + public errors: string[]; + + // Initialize a new access token + constructor(options) { + this.mysql = MySQLDataSource.getInstance(); + + this.accessToken = options.accessToken; + this.accessTokenExpiresAt = options.accessToken; + this.refreshToken = options.refreshToken; + this.refreshTokenExpiresAt = options.refreshTokenExpiresAt; + this.scope = options.scope || []; + this.client = options.client; + this.user = options.user; + this.errors = []; + } + + // Locate and access token by its id + static async findOne(accessToken: string): Promise { + try { + const mysql = MySQLDataSource.getInstance(); + const [rows] = await mysql.query('SELECT * FROM oauthTokens WHERE code = ?', [accessToken]); + if (rows.length === 0) { + return null; + } + // eslint-disable-next-line @typescript-eslint/no-explicit-any + const row = (rows as any[])[0]; + const client = await OAuthClient.findById(row.clientId); + const user = await User.findById(row.userId); + if (!client || !user) { + return null; + } + return new OAuthToken({ + ...OAuthToken._SqlFieldsToProperties(row), + client: await OAuthClient.findById(row.clientId), + user: await User.findById(row.userId), + }); + } catch(err) { + formatLogMessage(logger, { err }) + .error(`Unable to fetch AccessToken from OAuthToken by token: ${accessToken}`); + throw(err); + } + } + + // Locate an access token by the Client and User + static async findByClientUser(client: Client, user: User): Promise { + try { + const mysql = MySQLDataSource.getInstance(); + const sql = 'SELECT * FROM oauthTokens WHERE clientId = ? AND userId = ?' + const [rows] = await mysql.query(sql, [client.id, user.id.toString()]); + if (rows.length === 0) { + return null; + } + return new OAuthToken({ + ...OAuthToken._SqlFieldsToProperties(rows[0]), + client: client, + user, + }); + } catch(err) { + formatLogMessage(logger, { err }) + .error(`Unable to fetch AccessToken from OAuthToken for client: ${client.id}, user: ${user.id}`); + throw(err); + } + } + + // Ensure data integrity + async cleanup(): Promise { + this.accessToken = this.accessToken || generateToken(this.user); + this.accessTokenExpiresAt = this.accessTokenExpiresAt || this.generateExpiryDate(); + this.refreshToken = this.refreshToken || await this.generateRefreshToken(); + this.refreshTokenExpiresAt = this.refreshTokenExpiresAt || this.generateExpiryDate(false); + this.scope = stringToArray(this.scope, ',', ['read']); + } + + // Generate the token + async generateRefreshToken(): Promise { + const refreshToken = await new OAuthRefreshToken({ + refreshToken: uuidv4(), + client: this.client, + user: this.user, + }); + return refreshToken.refreshToken; + } + + // Generate the TTL Expiry date + generateExpiryDate(forAccessToken = true): Date { + const currentDate = new Date(); + const ttlSeconds = forAccessToken ? oauthConfig.accessTokenLifetime : oauthConfig.refreshTokenLifetime; + return new Date(currentDate.getTime() + ttlSeconds * 1000); + } + + // Make sure the token has not been revoked and that it has not expired + async validate(): Promise { + if (this.accessToken) { + // Make sure it still exists in the database! and the payload matches (not tampered with) + const existing = await OAuthToken.findOne(this.accessToken); + if (existing && existing === this) { + // Make sure it is not expired + const currentDate = new Date(); + return this.accessTokenExpiresAt > currentDate; + } + return false; + } + return false; + } + + // Save the Token to the DB + async save(): Promise { + this.cleanup(); + + const sql = ` + INSERT INTO oauthTokens + (token, expiresAt, refreshToken, refreshTokenExpiresAt, scope, clientId, userId) + VALUES (?, ?, ?, ?, ?, ?, ?) + `; + const vals = [ + this.accessToken, + this.accessTokenExpiresAt.toISOString(), + this.refreshToken, + this.refreshTokenExpiresAt.toISOString(), + stringToArray(this.scope, ',').join(', '), + this.client.id.toString(), + this.user.id.toString() + ] + try { + await this.mysql.query(sql, vals); + formatLogMessage(logger) + .debug(`OAuthToken was created: User: ${this.user.id}, token: ${this.accessToken}`); + return true; + } catch (err) { + formatLogMessage(logger, { err }).error('Error saving OAuthToken'); + throw err; + } + } + + // Set the Expiry for the token to now + async revoke(): Promise { + const currentDate = new Date(); + const sql = ` + UPDATE oauthTokens SET expiresAt = ?, refreshToken = NULL, refreshTokenExpiresAt = NULL + WHERE token = ? + `; + const vals = [currentDate.toISOString(), this.accessToken]; + try { + await this.mysql.query(sql, vals); + formatLogMessage(logger).debug(`Access token was revoked: ${this.accessToken}`); + return true; + } catch (err) { + formatLogMessage(logger, { err }).error('Error revoking OAuthToken'); + throw err; + } + } + + // Convert the DB fields to properties of this call (except client and user) + static _SqlFieldsToProperties(row) { + const scopeArray = typeof row.scope === 'string' ? row.scope.split(' ') : row.scope; + return { + accessToken: row.token, + accessTokenExpiresAt: row.expiresAt ? new Date(row.expiresAt) : null, + refreshToken: row.refreshToken, + refreshTokenExpiresAt: row.refreshTokenExpiresAt ? new Date(row.refreshTokenExpiresAt) : null, + scope: scopeArray, + } + } +} diff --git a/src/models/User.ts b/src/models/User.ts new file mode 100644 index 0000000..a920926 --- /dev/null +++ b/src/models/User.ts @@ -0,0 +1,189 @@ +import bcrypt from 'bcryptjs'; +import { MySQLDataSource } from '../datasources/mySQLDataSource'; +import { capitalizeFirstLetter, validateEmail } from '../utils/helpers'; +import { Falsey } from 'oauth2-server'; +import { logger, formatLogMessage } from '../logger'; + +// TODO: Is this the right place to create our Pool? +// const mysql = new MysqlDataSource({ config: mysqlConfig }); + +export enum UserRole { + Researcher = 'RESEARCHER', + Admin = 'ADMIN', + SuperAdmin = 'SUPER_ADMIN', +} + +export class User { + private mysql: MySQLDataSource; + + public id?: number; + public email: string; + public password: string; + public role: UserRole; + public givenName?: string; + public surName?: string; + public orcid?: string; + public errors: string[]; + public affiliationId: string; + public created: string; + public modified: string; + + // Initialize a new User + constructor(options) { + this.mysql = MySQLDataSource.getInstance(); + this.id = options.id; + this.email = options.email; + this.password = options.password; + this.role = options.role; + this.givenName = options.givenName; + this.surName = options.surName; + this.orcid = options.orcid; + this.affiliationId = options.affiliationId; + this.created = options.created || new Date().toUTCString(); + this.modified = options.modified || new Date().toUTCString(); + this.errors = []; + + this.cleanup(); + } + + // Ensure data integrity + cleanup() { + this.email = this.email?.trim()?.replace('%40', '@'); + this.role = this.role || UserRole.Researcher; + this.givenName = capitalizeFirstLetter(this.givenName); + this.surName = capitalizeFirstLetter(this.surName); + } + + // Verify that the email does not already exist and that the required fields have values + async validateNewUser(): Promise { + // check if email is already taken + const existing = await User.findByEmail(this.email); + + if (existing) { + this.errors.push('Email address already in use'); + } else { + if (!validateEmail(this.email)) { + this.errors.push('Invalid email address'); + } + if (!this.password) { + this.errors.push('Password is required'); + } else { + this.validatePassword(); + } + } + + return this.errors.length === 0; + } + + // Validate the password format + validatePassword(): boolean { + const specialCharsRegex = /[`!@#$%^&*_+\-=?~\s]/; + // eslint-disable-next-line no-useless-escape + const badSpecialCharsRegex = /[\(\)\{\}\[\]\|\\:;"'<>\,\.\/]/ + + // Test the string against the regular expression + if ( + this.password?.length >= 8 && + /[A-Z]/.test(this.password) && + /[a-z]/.test(this.password) && + /\d/.test(this.password) && + specialCharsRegex.test(this.password) && + !badSpecialCharsRegex.test(this.password) + ) { + return true; + } + this.errors.push(`Invalid password format. + Passwords must be greater than 8 characters, and contain at least + one number, + one upper case letter, + one lower case letter, and + one of the following special character (\`, !, @, #, $, %, ^, &, *, -, _, =, +, ?, ~)`); + return false; + } + + async hashPassword(password): Promise { + const salt = await bcrypt.genSalt(10); + return await bcrypt.hash(password, salt); + } + + // Find the User by their Id + static async findById(userId: string): Promise { + const mysql = MySQLDataSource.getInstance(); + const sql = 'SELECT id, email, givenName, surName, role, affiliationId, created, modified \ + FROM users WHERE id = ?'; + formatLogMessage(logger)?.debug(`User.findById: ${userId}`); + try { + const [rows] = await mysql.query(sql, [userId]); + return rows?.id ? new User(rows) : null; + } catch (err) { + formatLogMessage(logger, { err })?.error(`Error trying to find User by id ${userId}`); + throw err; + } + } + + // Find the User by their email address + static async findByEmail(email: string): Promise { + const mysql = MySQLDataSource.getInstance(); + const sql = 'SELECT id, email, givenName, surName, role, affiliationId, created, modified \ + from users where email = ?'; + + formatLogMessage(logger)?.debug(`User.findByEmail: ${email}`); + try { + const [rows] = await mysql.query(sql, [email]); + return rows?.id ? new User(rows) : null; + } catch (err) { + formatLogMessage(logger, { err })?.error(`Error trying to find User by email: ${email}`); + throw err; + } + } + + // Login making sure that the passwords match + async login(): Promise { + this.cleanup(); + const email = this.email || ''; + + if (!validateEmail(email) || !this.validatePassword()) { + return null; + } + + try { + formatLogMessage(logger)?.debug(`User.login: ${this.email}`); + const user = await User.findByEmail(email) || null; + if (user && await bcrypt.compare(this.password, user?.password)) { + return user; + } + return null; + } catch (err) { + formatLogMessage(logger, { err })?.error(`Error logging in User: ${this.email}`); + return null; + } + } + + // Register the User if the data is valid + async register(): Promise { + this.cleanup(); + await this.validateNewUser(); + + if (this.errors.length === 0) { + const passwordHash = await this.hashPassword(this.password); + this.password = passwordHash + + const mysql = MySQLDataSource.getInstance(); + const sql = 'INSERT INTO users (email, password, role, givenName, surName) VALUES(?,?,?,?,?)'; + formatLogMessage(logger)?.debug(`User.register: ${this.email}`); + try { + const vals = [this.email, this.password, this.role, this.givenName, this.surName] + const result = await mysql.query(sql, vals); + + logger.debug(`User was created: ${this.email}, id: ${result.insertId}`); + return await User.findById(result.insertId); + } catch (err) { + formatLogMessage(logger, { err })?.error(`Error creating User: ${this.email}`); + return null; + } + } else { + formatLogMessage(logger)?.debug(`Invalid user: ${this.email}`); + return this; + } + } +} diff --git a/src/models/__tests__/Affiliation.spec.ts b/src/models/__tests__/Affiliation.spec.ts new file mode 100644 index 0000000..13c8d68 --- /dev/null +++ b/src/models/__tests__/Affiliation.spec.ts @@ -0,0 +1,218 @@ +import { AffiliationModel, AffiliationSearchModel } from '../Affiliation'; + +const rawAffiliationSearchRecord = { + "PK": "AFFILIATION", + "SK": "advancedphotonsciencesunitedstates", + "aliases": ["Photon Sciences", "APS"], + "countryCode": "us", + "countryName": "United States", + "fundref_id": "100006389", + "fundref_url": "https://api.crossref.org/funders/100006389", + "links": [ "photonsci.com" ], + "name": "Advanced Photon Sciences (United States)", + "ror_id": "00182ep39", + "ror_url": "https://ror.org/00182ep39", + "searchName": "advancedphotonsciencesunitedstates" +}; + +const rawAffiliationRecord = { + "RESOURCE_TYPE": "AFFILIATION", + "ID": "https://ror.org/00dmfq477", + "acronyms": [ "UCOP" ], + "aliases": ["UC Office of the President"], + "active": 1, + "addresses": [ + { + "city": "Oakland", + "country_geonames_id": 6252001, + "geonames_city": { + "city": "Oakland", + "geonames_admin1": { + "ascii_name": "California", + "code": "US.CA", + "id": 5332921, + "name": "California" + }, + "geonames_admin2": { + "ascii_name": "Alameda", + "code": "US.CA.001", + "id": 5322745, + "name": "Alameda" + }, + "id": 5378538, + "license": { + "attribution": "Data from geonames.org under a CC-BY 3.0 license", + "license": "http://creativecommons.org/licenses/by/3.0/" + } + }, + "lat": 37.80437, + "lng": -122.2708, + "state": "California", + "state_code": "US-CA" + } + ], + "country": { "country_code": "US", "country_name": "United States" }, + "domain": "ucop.edu", + "external_ids": { + "FundRef": { "all": [ "100014576" ], "preferred": "100014576" }, + "ISNI": { "all": [ "0000 0004 0615 4051" ], "preferred": "0000 0004 0615 4051" } + }, + "lables": [ + { + "label": "Oficina del Presidente de la Universidad de California", + "iso639": "es" + } + ], + "funder": 1, + "label": "University of California Office of the President (ucop.edu)", + "links": [ "https://www.ucop.edu" ], + "name": "University of California Office of the President", + "parents": [ "https://ror.org/00pjdza24" ], + "relationships": [ + { + "id": "https://ror.org/00pjdza24", + "label": "University of California System", + "type": "Parent" + } + ], + "searchable_names": [ + "university of california office of the president", + "ucop.edu", + "UCOP" + ], + "types": [ "Education" ], + "_SOURCE": "ROR", + "_SOURCE_SYNCED_AT": "2024-07-23T00:04:11Z", +} + +describe('Affiliation constructor', () => { + it('should set the expected defaults', () => { + const affiliation = new AffiliationModel({}); + expect(affiliation.provenance).toEqual('dmptool'); + expect(affiliation.provenanceSyncDate === undefined).toBe(false); + expect(affiliation.active).toBe(false); + expect(affiliation.funder).toBe(false); + expect(affiliation.types).toEqual([]); + expect(affiliation.acronyms).toEqual([]); + expect(affiliation.aliases).toEqual([]); + expect(affiliation.links).toEqual([]); + expect(affiliation.addresses).toEqual([]); + expect(affiliation.relationships).toEqual([]); + expect(affiliation.id).toBe(undefined); + expect(affiliation.name).toBe(undefined); + expect(affiliation.displayName).toBe(undefined); + expect(affiliation.countryCode).toBe(undefined); + expect(affiliation.countryName).toBe(undefined); + expect(affiliation.domain).toBe(undefined); + }); + + it('should set the expected properties', () => { + const affiliation = new AffiliationModel(rawAffiliationRecord); + expect(affiliation.id).toEqual(rawAffiliationRecord.ID); + expect(affiliation.provenance).toEqual(rawAffiliationRecord._SOURCE); + expect(affiliation.provenanceSyncDate).toEqual(rawAffiliationRecord._SOURCE_SYNCED_AT); + expect(affiliation.types).toEqual(Array.isArray(rawAffiliationRecord.types) ? rawAffiliationRecord.types : []); + expect(affiliation.name).toEqual(rawAffiliationRecord.name); + expect(affiliation.displayName).toEqual(rawAffiliationRecord.label); + expect(affiliation.active).toEqual(rawAffiliationRecord.active === 1); + expect(affiliation.funder).toEqual(rawAffiliationRecord.funder === 1); + expect(affiliation.acronyms).toEqual(Array.isArray(rawAffiliationRecord.acronyms) ? rawAffiliationRecord.acronyms : []); + expect(affiliation.aliases).toEqual(Array.isArray(rawAffiliationRecord.aliases) ? rawAffiliationRecord.aliases : []); + expect(affiliation.countryCode).toEqual(rawAffiliationRecord.country?.country_code); + expect(affiliation.countryName).toEqual(rawAffiliationRecord.country?.country_name); + expect(affiliation.domain).toEqual(rawAffiliationRecord.domain); + expect(affiliation.links).toEqual(Array.isArray(rawAffiliationRecord.links) ? rawAffiliationRecord.links : []); + }); + + it('should ignore unexpected properties', () => { + const affiliation = new AffiliationModel(rawAffiliationRecord); + expect(affiliation.id).toEqual(rawAffiliationRecord.ID); + expect(affiliation['test']).toBeUndefined(); + }); + + it('should include an AffiliationAddress for each addresses entry', () => { + const affiliation = new AffiliationModel(rawAffiliationRecord); + expect(affiliation.id).toEqual(rawAffiliationRecord.ID); + affiliation.addresses.forEach(address => { + const addrs = rawAffiliationRecord.addresses.find((a) => a.lat === address.lat && a.lng === address.lng); + expect(addrs.city).toEqual(address.city); + expect(addrs.state).toEqual(address.state); + expect(addrs.state_code).toEqual(address.stateCode); + expect(addrs.country_geonames_id).toEqual(address.countryGeonamesId); + expect(addrs.lat).toEqual(address.lat); + expect(addrs.lng).toEqual(address.lng); + }); + }); + + it('should include an AffiliationRelationship for each relationships entry', () => { + const affiliation = new AffiliationModel(rawAffiliationRecord); + expect(affiliation.id).toEqual(rawAffiliationRecord.ID); + affiliation.relationships.forEach(relation => { + const relations = rawAffiliationRecord.relationships.find((r) => r.id === relation.id); + expect(relations.type).toEqual(relation.type); + expect(relations.label).toEqual(relation.name); + }); + }); + + it('should include an AffiliationLocale for each locale entry', () => { + const affiliation = new AffiliationModel(rawAffiliationRecord); + expect(affiliation.id).toEqual(rawAffiliationRecord.ID); + affiliation.locales.forEach(locale => { + const locales = rawAffiliationRecord.lables.find((l) => l.iso639 === locale.locale); + expect(locales.iso639).toEqual(locale.locale); + expect(locales.label).toEqual(locale.label); + }); + }); + + it('should handle Fundref as the `preferred` id in the `external_id`', () => { + const props = { "external_ids": [{ "type": "FundRef", "preferred": "9999999999" }] }; + const affiliation = new AffiliationModel(props); + expect(affiliation.fundref).toEqual(props.external_ids[0].preferred); + }); + + it('should handle Fundref as the 1st `all` entry when it is an Array', () => { + const props = { "external_ids": [{ "type": "FundRef", "all": ["9999999999", "000000000"] }] }; + const affiliation = new AffiliationModel(props); + expect(affiliation.fundref).toEqual(props.external_ids[0].all[0]); + }); + + it('should handle Fundref as the `all` entry what it is a string', () => { + const props = { "external_ids": [{ "type": "FundRef", "all": "9999999999" }] }; + const affiliation = new AffiliationModel(props); + expect(affiliation.fundref).toEqual(props.external_ids[0].all); + }); + + it('handles relationship with a `name` instead of `label', () => { + const props = { "relationships": [{ "type": "Tester", "name": "TEST" }] }; + const affiliation = new AffiliationModel(props); + expect(affiliation.relationships[0].name).toEqual(props.relationships[0].name); + }); +}); + +describe('AffiliationSearch constructor', () => { + it('should set the expected defaults', () => { + const affiliation = new AffiliationSearchModel({}); + expect(affiliation.id).toBe(undefined); + expect(affiliation.fetchId).toBe(undefined); + expect(affiliation.name).toBe(undefined); + expect(affiliation.funder).toBe(false); + expect(affiliation.fundref).toBe(undefined); + expect(affiliation.aliases).toEqual([]); + expect(affiliation.countryCode).toBe(undefined); + expect(affiliation.countryName).toBe(undefined); + expect(affiliation.links).toEqual([]); + }); + + it('should set the expected properties', () => { + const affiliation = new AffiliationSearchModel(rawAffiliationSearchRecord); + expect(affiliation.id).toEqual(rawAffiliationSearchRecord.ror_url); + expect(affiliation.fetchId).toEqual(affiliation.id.replace(/https?:\/\//g, '')); + expect(affiliation.name).toEqual(rawAffiliationSearchRecord.name); + expect(affiliation.funder).toEqual(rawAffiliationSearchRecord.hasOwnProperty('fundref_id')); + expect(affiliation.fundref).toEqual(rawAffiliationSearchRecord.fundref_url); + expect(affiliation.aliases).toEqual(Array.isArray(rawAffiliationSearchRecord.aliases) ? rawAffiliationSearchRecord.aliases : []); + expect(affiliation.countryCode).toEqual(rawAffiliationSearchRecord.countryCode); + expect(affiliation.countryName).toEqual(rawAffiliationSearchRecord.countryName); + expect(affiliation.links).toEqual(Array.isArray(rawAffiliationSearchRecord.links) ? rawAffiliationSearchRecord.links : []); + }); +}); diff --git a/src/models/__tests__/User.spec.ts b/src/models/__tests__/User.spec.ts new file mode 100644 index 0000000..38830e8 --- /dev/null +++ b/src/models/__tests__/User.spec.ts @@ -0,0 +1,435 @@ +import { User, UserRole } from '../User'; +import bcrypt from 'bcryptjs'; +import casual from 'casual'; +import { MySQLDataSource } from '../../datasources/mySQLDataSource'; +import { logger, formatLogMessage } from '../../logger'; + +jest.mock('../../datasources/mySQLDataSource', () => { + return { + __esModule: true, + MySQLDataSource: { + getInstance: jest.fn().mockReturnValue({ + query: jest.fn(), // Initialize the query mock function + }), + }, + }; +}); + +jest.mock('../../logger', () => ({ + __esModule: true, + formatLogMessage: jest.fn() +})) + +const userProps = { + email: 'test.user@example.com', + password: 'abcdefghijklmnop', +} +const mockUser = { id: 1, email: 'test@test.com', name: 'John Doe' }; +let mockQuery: jest.MockedFunction; + +describe('constructor', () => { + it('should set the expected properties', () => { + const props = { + id: casual.integer(1, 99999), + email: 'test@test.com', + password: 'password123', + role: UserRole.Admin, + givenName: casual.first_name, + surName: casual.last_name, + orcid: '0000-0000-0000-000X', + } + + const user = new User({ ...userProps, ...props }); + expect(user.id).toEqual(props.id); + expect(user.email).toEqual(props.email); + expect(user.password).toEqual(props.password); + expect(user.givenName).toEqual(props.givenName); + expect(user.surName).toEqual(props.surName); + expect(user.orcid).toEqual(props.orcid); + expect(user.role).toEqual(props.role); + }); + + it('should ignore unexpected properties', () => { + const user = new User({ ...userProps, test: 'blah' }); + expect(user.email).toEqual(userProps.email); + expect(user.password).toEqual(userProps.password); + expect(user['test']).toBeUndefined(); + }); +}); + +describe('cleanup standardizes the format of properties', () => { + it('should properly format the properties', () => { + const user = new User({ email: 'TESTer@exaMPle.cOm', givenName: ' Test ', surName: ' user ' }); + user.cleanup(); + expect(user.email).toEqual('TESTer@exaMPle.cOm'); + expect(user.givenName).toEqual('Test'); + expect(user.surName).toEqual('User'); + expect(user.role).toEqual(UserRole.Researcher); + }); +}); + +describe('validate a new User', () => { + beforeEach(() => { + jest.resetAllMocks(); + + // Cast getInstance to a jest.Mock type to use mockReturnValue + (MySQLDataSource.getInstance as jest.Mock).mockReturnValue({ + query: jest.fn(), // Initialize the query mock function here + }); + + const instance = MySQLDataSource.getInstance(); + mockQuery = instance.query as jest.MockedFunction; + }); + + afterEach(() => { + jest.clearAllMocks(); + }); + + it('should return true when we have a new user with a valid password', async () => { + mockQuery.mockResolvedValueOnce([{}, []]); + + const user = new User({ + email: 'test.user@example.com', + password: '@bcd3fGhijklmnop', + }); + + const isValid = await user.validateNewUser(); + expect(isValid).toBe(true); + }); + + it('should return false when we have a new user with an invalid password', async () => { + mockQuery.mockResolvedValueOnce([{}, []]); + + const user = new User({ + email: 'test.user@example.com', + password: 'abcde', + }); + + const isValid = await user.validateNewUser(); + expect(isValid).toBe(false); + }); + + it('should return false when we have an existing user', async () => { + mockQuery.mockResolvedValueOnce([mockUser, []]); + + const user = new User({ + email: 'test@test.com', + password: '@bcd3fGhijklmnop', + }); + + const isValid = await user.validateNewUser(); + expect(isValid).toBe(false); + }); + + it('should return false when we have a new user without a valid email format', async () => { + mockQuery.mockResolvedValueOnce([mockUser, []]); + + const user = new User({ + email: 'test.user', + password: '@bcd3fGhijklmnop', + }); + + const isValid = await user.validateNewUser(); + expect(isValid).toBe(false); + }); +}); + +describe('password validation', () => { + beforeEach(() => { + jest.resetAllMocks(); + + // Cast getInstance to a jest.Mock type to use mockReturnValue + (MySQLDataSource.getInstance as jest.Mock).mockReturnValue({ + query: jest.fn(), // Initialize the query mock function here + }); + + const instance = MySQLDataSource.getInstance(); + mockQuery = instance.query as jest.MockedFunction; + }); + + afterEach(() => { + jest.clearAllMocks(); + }); + + it('should return true for a valid passwords', () => { + expect(new User({ password: 'AbcdefgH1!' }).validatePassword()).toBe(true); + expect(new User({ password: 'AbcdefgH1@#$%^&*-_+=?' }).validatePassword()).toBe(true); + expect(new User({ password: 'Abcdef gH1#' }).validatePassword()).toBe(true); + expect(new User({ password: ' AbcdefgH1$' }).validatePassword()).toBe(true); + expect(new User({ password: 'AbcdefgH1! ' }).validatePassword()).toBe(true); + }); + + it('should allow all of the approved special characters', () => { + const chars = ['~', '`', '!', '@', '#', '$', '%', '^', '&', '*', '-', "_", '+', '=', '?', ' ']; + for (let i = 0; i < chars.length; i++) { + const valid = new User({ password: `Abcd3Fgh1jkL${chars[i]}` }).validatePassword(); + if (!valid) { + + console.log(`Failed when testing character ${chars[i]}`); + } + expect(valid).toBe(true); + }; + }); + + it('should fail for a new user with a password that is too short', async () => { + mockQuery.mockResolvedValueOnce([{}, []]); + + const user = new User({ + email: 'test.user@example.com', + password: 'abcde', + }); + + await user.validateNewUser(); + + expect(user.errors.length === 1); + expect(user.errors[0].includes('Invalid password')); + }); + + it('should fail for a new user if the password does not contain at least 1 uppercase letter', async () => { + mockQuery.mockResolvedValueOnce([{}, []]); + + const user = new User({ password: 'abcd3fgh1jk' }); + + await user.validateNewUser(); + + expect(user.errors.length === 1); + expect(user.errors[0].includes('Invalid password')); + }); + + + it('should return error if password is missing', async () => { + mockQuery.mockResolvedValueOnce([{}, []]); + + const user = new User({ + email: 'test.user@example.com', + password: null, + }); + + await user.validateNewUser(); + + expect(user.errors.length === 1); + expect(user.errors[0].includes('Password is required')); + }); + + it('should fail for a new user if the password does not contain at least 1 lowercase letter', async () => { + mockQuery.mockResolvedValueOnce([{}, []]); + + const user = new User({ + email: 'test.user@example.com', + password: 'ABCD3FGH1JKL', + }); + + await user.validateNewUser(); + + expect(user.errors.length === 1); + expect(user.errors[0].includes('Invalid password')); + }); + + it('should fail for a new user if the password does not contain at least 1 number letter', async () => { + mockQuery.mockResolvedValueOnce([{}, []]); + + const user = new User({ + email: 'test.user@example.com', + password: 'Abcd$Fgh#jkL', + }); + + await user.validateNewUser(); + expect(user.errors.length === 1); + expect(user.errors[0].includes('Invalid password')); + }); + + it('should fail for a new user if the password does not contain at least 1 special character', async () => { + mockQuery.mockResolvedValueOnce([{}, []]); + + const user = new User({ + email: 'test.user@example.com', + password: 'Abcd3Fgh1jkL', + }); + + await user.validateNewUser(); + + expect(user.errors.length === 1); + expect(user.errors[0].includes('Invalid password')); + }); + + it('should fail for a new user if it contains special characters that are not allowed', () => { + mockQuery.mockResolvedValueOnce([{}, []]); + + const badChars = ['(', ')', '{', '[', '}', ']', '|', '\\', ':', ';', '"', "'", '<', ',', '>', '.', '/']; + for (let i = 0; i < badChars.length; i++) { + const user = new User({ + email: 'test.user@example.com', + password: `Abcd3Fgh1jkL$${badChars[i]}`, + }); + + const valid = user.validatePassword(); + if (valid) { + console.log(`Failed when testing character ${badChars[i]}`); + } + expect(valid).toBe(false) + }; + + }); +}); + +describe('login()', () => { + + beforeEach(() => { + jest.resetAllMocks(); + + const bcryptCompare = jest.fn().mockResolvedValue(true); + (bcrypt.compare as jest.Mock) = bcryptCompare; + + const bcryptSalt = jest.fn().mockReturnValue('abc'); + (bcrypt.genSalt as jest.Mock) = bcryptSalt; + + const bcryptPassword = jest.fn().mockReturnValue('test.user@example.com'); + (bcrypt.hash as jest.Mock) = bcryptPassword; + + // Cast getInstance to a jest.Mock type to use mockReturnValue + (MySQLDataSource.getInstance as jest.Mock).mockReturnValue({ + query: jest.fn(), // Initialize the query mock function here + }); + + const instance = MySQLDataSource.getInstance(); + mockQuery = instance.query as jest.MockedFunction; + }); + + afterEach(() => { + jest.clearAllMocks(); + }); + + it('should not return null if user exists and its password matches with encrypted one', async () => { + const user = new User({ email: 'testFOOO@test.com', password: '@bcd3fGhij12klmnop' }); + const hashedPwd = await user.hashPassword('@bcd3fGhij12klmnop') + + mockQuery.mockResolvedValueOnce([{ id: 1, email: 'testFOOO@test.com', password: hashedPwd }, []]); + const response = await user.login(); + expect(response).not.toBeNull(); + }); + + it('should return an error when there is an invalid email', async () => { + const mockedUser = { id: 1, email: 'test.user@example.com', name: '@bcd3fGhijklmnop' }; + mockQuery.mockResolvedValueOnce([mockedUser, []]); + + const user = new User({ + email: 'example.com', + password: '@bcd3fGhijklmnop', + }); + + const response = await user.login(); + expect(user.errors.length === 1); + expect(response).toBe(null); + }); + + it('should return an error when there is an invalid password', async () => { + const mockedUser = { id: 1, email: 'test.user@example.com', name: '@bcd3fGhijklmnop' }; + mockQuery.mockResolvedValueOnce([mockedUser, []]); + + const user = new User({ + email: 'test.user@example.com', + password: 'abc', + }); + + const response = await user.login(); + expect(user.errors.length === 1); + expect(response).toBe(null); + }); + + it('should return null when findEmail() throws an error', async () => { + mockQuery.mockRejectedValueOnce('Something went wrong') + + const user = new User({ + email: 'test.user@example.com', + password: 'abc', + }); + + const response = await user.login(); + expect(response).toBeNull(); + }); +}); + +describe('register()', () => { + const bcryptSalt = jest.fn().mockReturnValue('abc'); + (bcrypt.genSalt as jest.Mock) = bcryptSalt; + + const bcryptPassword = jest.fn().mockReturnValue('test.user@example.com'); + (bcrypt.hash as jest.Mock) = bcryptPassword; + + beforeEach(() => { + jest.resetAllMocks(); + + // Cast getInstance to a jest.Mock type to use mockReturnValue + (MySQLDataSource.getInstance as jest.Mock).mockReturnValue({ + query: jest.fn(), // Initialize the query mock function here + }); + + const instance = MySQLDataSource.getInstance(); + mockQuery = instance.query as jest.MockedFunction; + }); + + afterEach(() => { + jest.clearAllMocks(); + }) + + it('should not return null if user exists and its password matches with encrypted one', async () => { + const mockedUser = { id: 1, email: 'test.user@example.com', name: '@bcd3fGhijklmnop' }; + // First call to Mock mysql query from findByEmail() + mockQuery.mockResolvedValueOnce([mockedUser, []]); + // Second call to Mock mysql query from register() + mockQuery.mockResolvedValueOnce({ id: 1 }); + // Third call to Mock mysql query from findById() + mockQuery.mockResolvedValueOnce([mockedUser, []]); + + const user = new User({ + email: 'test.user@example.com', + password: '@bcd3fGhijklmnop', + givenName: 'Test', + surName: 'simple' + }); + + const response = await user.register(); + expect(response).not.toBeNull(); + }); + + it('should return user object if there was an error creating user', async () => { + const mockedUser = { id: 1, email: 'test.user@example.com', name: '@bcd3fGhijklmnop' }; + // First call to Mock mysql query from findByEmail() + mockQuery.mockResolvedValueOnce([mockedUser, []]); + // Second call to Mock mysql query from register() + mockQuery.mockRejectedValueOnce('There was an error creating user'); + // Third call to Mock mysql query from findById() + mockQuery.mockResolvedValueOnce([mockedUser, []]); + + const user = new User({ + email: 'test.user@example.com', + password: '@bcd3fGhijklmnop', + givenName: 'Test', + surName: 'simple' + }); + + + const response = await user.register(); + expect(response).toBe(user); + }); + + it('should return null if there are errors validating the user', async () => { + const mockedUser = { id: 1, email: 'test.user@example.com', name: '@bcd3fGhijklmnop' }; + // First call to Mock mysql query from findByEmail() + mockQuery.mockResolvedValueOnce([{}, []]); + // Second call to Mock mysql query from register() + mockQuery.mockRejectedValueOnce('There was an error creating user'); + // Third call to Mock mysql query from findById() + mockQuery.mockResolvedValueOnce([mockedUser, []]); + + const user = new User({ + email: 'test.user@example.com', + password: '@bcd3fGhijklmnop', + givenName: 'Test', + surName: 'simple' + }); + + const response = await user.register(); + expect(response).toBeNull(); + }); +}); \ No newline at end of file diff --git a/src/plugins/__tests__/logger.spec.ts b/src/plugins/__tests__/logger.spec.ts new file mode 100644 index 0000000..f7d91a3 --- /dev/null +++ b/src/plugins/__tests__/logger.spec.ts @@ -0,0 +1,196 @@ +import { GraphQLError, GraphQLResolveInfo } from 'graphql'; +import { + GraphQLRequestContextDidEncounterSubsequentErrors, + GraphQLRequestContextWillSendSubsequentPayload, +} from '@apollo/server/dist/esm/externalTypes/requestPipeline'; +import { + BaseContext, + GraphQLRequestContext, + GraphQLRequestContextDidEncounterErrors, + GraphQLRequestContextDidResolveOperation, + GraphQLRequestContextDidResolveSource, + GraphQLRequestContextExecutionDidStart, + GraphQLRequestContextResponseForOperation, + GraphQLRequestContextValidationDidStart, + GraphQLRequestContextWillSendResponse, + GraphQLRequestExecutionListener, + GraphQLRequestListenerDidResolveField, + GraphQLExperimentalFormattedSubsequentIncrementalExecutionResult, + GraphQLRequestListener, +} from '@apollo/server'; +import mockLogger from '../../__tests__/mockLogger'; +import { loggerPlugin } from '../logger'; + +const mockIntrospectionRequestContext = { + request: { operationName: 'IntrospectionQuery' } +} as undefined as GraphQLRequestContext; + +const mockHealthCheckRequestContext = { + request: { query: '{ __typename }' }, +} as undefined as GraphQLRequestContext; + +const mockRequestContext = { + request: { + operationName: 'Me', + query: '{ User(id: 123) { id } }', + variables: [], + http: { method: 'PUT' }, + }, + response: { http: { status: 200 } }, +} as undefined as GraphQLRequestContext; + +const mockResolverInfo = { + fieldName: 'fieldName', + parentType: { name: 'parentTypeName' } +} as undefined as GraphQLResolveInfo; + +const mockRequestError = { + error: new Error(), +} + +// Define spies +let debugSpy: jest.SpyInstance; +let errorSpy: jest.SpyInstance; +let infoSpy: jest.SpyInstance; + +const logger = loggerPlugin(mockLogger); + +describe('loggerPlugin', () => { + beforeEach(() => { + debugSpy = jest.spyOn(mockLogger, 'debug'); + errorSpy = jest.spyOn(mockLogger, 'error'); + infoSpy = jest.spyOn(mockLogger, 'info'); + jest.clearAllMocks(); + }); + + afterEach(() => { + debugSpy.mockRestore(); + errorSpy.mockRestore(); + infoSpy.mockRestore(); + }); + + test('invalidRequestWasReceived logs the expected error message', async () => { + await logger.invalidRequestWasReceived(mockRequestError); + expect(errorSpy).toHaveBeenCalledWith('Invalid request error!'); + }); + + test('unexpectedErrorProcessingRequest logs the expected error message', async () => { + await logger.unexpectedErrorProcessingRequest({ + requestContext: mockRequestContext, + error: mockRequestError.error + }); + expect(errorSpy).toHaveBeenCalledWith('Server error!'); + }); + + describe('requestDidStart', () => { + test('skips introspection queries', async() => { + expect(await logger.requestDidStart(mockIntrospectionRequestContext)).toEqual({}); + }); + + test('skips healthcheck queries', async() => { + expect(await logger.requestDidStart(mockHealthCheckRequestContext)).toEqual({}); + }); + + test('logs the expected message', async () => { + await logger.requestDidStart(mockRequestContext); + expect(infoSpy).toHaveBeenCalledWith('Request started'); + }); + + test('returns a GraphQLRequestListener', async () => { + const listener = await logger.requestDidStart(mockRequestContext); + expect(typeof listener).toEqual('object'); + expect(listener).toHaveProperty('didResolveSource'); + }); + }); + + describe('GraphQLRequestListener', () => { + test('didResolveSource logs expected message', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + listener.didResolveSource(mockRequestContext as GraphQLRequestContextDidResolveSource); + expect(debugSpy).toHaveBeenCalledWith('Resolved source'); + }); + + test('parsingDidStart logs expected message', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + listener.parsingDidStart(mockRequestContext as GraphQLRequestContextDidResolveSource); + expect(debugSpy).toHaveBeenCalledWith('Parsing started'); + }); + + test('validationDidStart logs expected message', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + listener.validationDidStart(mockRequestContext as GraphQLRequestContextValidationDidStart); + expect(debugSpy).toHaveBeenCalledWith('Validation started'); + }); + + test('didResolveOperation logs expected message', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + listener.didResolveOperation(mockRequestContext as GraphQLRequestContextDidResolveOperation); + expect(debugSpy).toHaveBeenCalledWith('Resolved operation'); + }); + + test('responseForOperation logs expected message', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + listener.responseForOperation(mockRequestContext as GraphQLRequestContextResponseForOperation); + expect(debugSpy).toHaveBeenCalledWith('Ready to start operation'); + }); + + test('didEncounterErrors logs expected message', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + listener.didEncounterErrors(mockRequestContext as GraphQLRequestContextDidEncounterErrors); + expect(errorSpy).toHaveBeenCalledWith('Encountered errors!'); + }); + + test('didEncounterSubsequentErrors logs expected message', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + listener.didEncounterSubsequentErrors( + mockRequestContext as GraphQLRequestContextDidEncounterSubsequentErrors, + [] as GraphQLError[] + ); + expect(errorSpy).toHaveBeenCalledWith('Encountered subsequent errors!'); + }); + + test('willSendResponse logs expected message', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + listener.willSendResponse(mockRequestContext as GraphQLRequestContextWillSendResponse); + expect(infoSpy).toHaveBeenCalledWith('Ready to send response'); + }); + + test('willSendSubsequentPayload logs expected message', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + listener.willSendSubsequentPayload( + mockRequestContext as GraphQLRequestContextWillSendSubsequentPayload, + {} as GraphQLExperimentalFormattedSubsequentIncrementalExecutionResult + ); + expect(infoSpy).toHaveBeenCalledWith('Ready to send subsequent responses'); + }); + + test('executionDidStart logs expected message', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + listener.executionDidStart(mockRequestContext as GraphQLRequestContextExecutionDidStart); + expect(debugSpy).toHaveBeenCalledWith('Operation execution started'); + }); + + test('willResolveField logs expected error', async () => { + const listener = await logger.requestDidStart(mockRequestContext) as GraphQLRequestListener; + const fieldListener = await listener.executionDidStart( + mockRequestContext as GraphQLRequestContextExecutionDidStart + ) as GraphQLRequestExecutionListener; + + const mockGraphQLResolverParams = { + source: null, + args: {}, + contextValue: {}, + info: mockResolverInfo + } + + const resp = fieldListener.willResolveField(mockGraphQLResolverParams) as GraphQLRequestListenerDidResolveField + resp(mockRequestError.error, {}); + expect(debugSpy).toHaveBeenCalledWith( + expect.stringMatching(/Field parentTypeName.fieldName took [\d]+ns/i) + ); + expect(errorSpy).toHaveBeenCalledWith( + expect.stringMatching(/Field parentTypeName.fieldName failed/i) + ); + }); + }); +}); diff --git a/src/plugins/logger.ts b/src/plugins/logger.ts new file mode 100644 index 0000000..20c8a61 --- /dev/null +++ b/src/plugins/logger.ts @@ -0,0 +1,136 @@ +import { Logger } from 'pino'; + +import { + ApolloServerPlugin, + BaseContext, + GraphQLRequestListener, + GraphQLRequestContext, + GraphQLResponse +} from "@apollo/server"; + +// Extract the inmportant information from the incoming request so that it is logged +function setupLogger(loggerInstance: Logger, context = null, errors = null) { + const hdrs = context?.request?.http?.headers || new Map(); + const errs = errors instanceof Array ? errors : [errors]; + + return loggerInstance.child({ + httpMethod: context?.request?.http?.method, + httpReferer: hdrs?.get('referer'), + httpSecFetchSite: hdrs?.get('sec-fetch-site'), + httpUserAgent: hdrs?.get('user-agent'), + // TODO: We will eventually want to update this to include the nextJS session id + operationName: context?.request?.operationName, + variables: context?.request?.variables, + query: context?.request?.query, + status: context?.response?.http?.status, + err: errs + }); +} + +// Initialize the Logging plugin that Apollo will use on each request/response +export function loggerPlugin(logger: Logger): ApolloServerPlugin { + return { + // Fires any time Apollo server is going to respond with a 'Bad Request' error + async invalidRequestWasReceived(requestError) { + setupLogger(logger, {}, requestError.error).error('Invalid request error!'); + }, + + // Fires when Apollo server is going to respond with a 'Server' error + async unexpectedErrorProcessingRequest({ + requestContext, + error, + }: { + requestContext: GraphQLRequestContext; + error: Error; + }): Promise { + setupLogger(logger, requestContext?.request, error).error('Server error!'); + }, + + // Fires whenever a GraphQL request is received from a client. + async requestDidStart(initialContext: GraphQLRequestContext): Promise> { + // Skip schema introspection queries. They run incessantly in the Apollo server explorer! + if (initialContext?.request?.operationName === 'IntrospectionQuery') { + return {}; + } + // Skip healthcheck requests + if (initialContext?.request?.query === '{ __typename }') { + return {}; + } + + setupLogger(logger, initialContext).info('Request started'); + + return { + // Fires when Apollo Server was able to understand the incoming request + async didResolveSource(context) { + setupLogger(logger, context).debug('Resolved source'); + }, + + // Fires whenever Apollo Server starts parsing the query/mutation + async parsingDidStart(context) { + setupLogger(logger, context).debug('Parsing started'); + }, + + // Fires whenever Apollo Server will validates the query/mutation + async validationDidStart(context) { + setupLogger(logger, context).debug('Validation started'); + }, + + // Fires whenever Apollo Server figures out what query/mutation to use + async didResolveOperation(context) { + setupLogger(logger, context).debug('Resolved operation'); + }, + + // Fires right before Apollo server starts to process the operation + async responseForOperation(context): Promise { + setupLogger(logger, context).debug('Ready to start operation'); + // This is an opportunity to interrupt the operation! + // If its return value resolves to a non-null GraphQLResponse, that result + // is used instead of executing the query + return null; + }, + + // Fires once Apollo server has figured out what it needs to do + async executionDidStart(context) { + const localLogger = setupLogger(logger, context); + localLogger.debug('Operation execution started'); + + return { + willResolveField({ info }) { + const start = process.hrtime.bigint(); + const fld = `${info?.parentType?.name}.${info?.fieldName}`; + + return (error) => { + const end = process.hrtime.bigint(); + localLogger.debug(`Field ${fld} took ${end - start}ns`); + + if (error) { + localLogger.error(`Field ${fld} failed with ${error}`); + } + }; + }, + }; + }, + + // Fires if Apollo server encountered any errors when processing the operation + async didEncounterErrors(context) { + setupLogger(logger, context, context?.errors).error('Encountered errors!'); + }, + + // Fires only when using incremental delivery methods like @defer + async didEncounterSubsequentErrors(context, requestErrors) { + setupLogger(logger, context, requestErrors).error('Encountered subsequent errors!'); + }, + + // Fires right before Apollo server sends its response + async willSendResponse(context) { + setupLogger(logger, context).info('Ready to send response'); + }, + + // Fires only when using incremental delivery methods like @defer + async willSendSubsequentPayload(context) { + setupLogger(logger, context).info('Ready to send subsequent responses'); + }, + }; + }, + }; +} \ No newline at end of file diff --git a/src/resolver.ts b/src/resolver.ts new file mode 100644 index 0000000..69dd5ed --- /dev/null +++ b/src/resolver.ts @@ -0,0 +1,25 @@ +import { mergeResolvers } from '@graphql-tools/merge'; +import { IResolvers } from '@graphql-tools/utils'; + +import { dmspIdScalar } from './resolvers/scalars/dmspId'; +import { orcidScalar } from './resolvers/scalars/orcid'; +import { rorScalar } from './resolvers/scalars/ror'; + +import { resolvers as affiliationResolvers } from './resolvers/affiliation'; +import { resolvers as contributorRoleResolvers } from './resolvers/contributorRole'; +import { resolvers as dmspResolvers } from './resolvers/dmsp'; +import { resolvers as userResolvers } from './resolvers/user'; + +const scalarResolvers = { + DmspId: dmspIdScalar, + Orcid: orcidScalar, + Ror: rorScalar +} + +export const resolvers: IResolvers = mergeResolvers([ + scalarResolvers, + affiliationResolvers, + dmspResolvers, + contributorRoleResolvers, + userResolvers, +]); \ No newline at end of file diff --git a/src/resolvers.ts b/src/resolvers.ts deleted file mode 100644 index 075b5c6..0000000 --- a/src/resolvers.ts +++ /dev/null @@ -1,30 +0,0 @@ -import { dynamoDBTables, DynamoDBService } from './DynamoDBService.js'; - -interface DMP { - PK: string; - SK: string; - title: string; - modified: string; - created: string; - // ... other fields -} - -interface DMPKey { - PK: string; - SK: string; -} - -const dmpDBService = new DynamoDBService(dynamoDBTables.dmps); // Replace with your actual DynamoDB table name - -const resolvers = { - Query: { - // Get the DMSP - getDMP: async (_: any, { PK, SK }: { PK: string, SK: string }): Promise => { - SK = SK == undefined ? 'VERSION#latest' : SK - const item = await dmpDBService.getItem({ PK: PK, SK: SK }); - return item as DMP; - }, - }, -}; - -export default resolvers; diff --git a/src/resolvers/affiliation.ts b/src/resolvers/affiliation.ts new file mode 100644 index 0000000..afc23e1 --- /dev/null +++ b/src/resolvers/affiliation.ts @@ -0,0 +1,42 @@ + +import { formatLogMessage } from '../logger'; +import { Resolvers } from "../types"; +import { MyContext } from '../context'; + +export const resolvers: Resolvers = { + Query: { + // returns an array of Affiliations + affiliations: async (_, options, { logger, dataSources }: MyContext) => { + const logMessage = `Resolving query affiliations(options: '${options}')`; + + return new Promise((resolve, reject) => { + dataSources.dmptoolAPIDataSource.getAffiliations(options) + .then(rows => { + formatLogMessage(logger).debug(logMessage); + resolve(rows) + }) + .catch(err => { + formatLogMessage(logger, { err, options }).error(`ERROR: ${logMessage} - ${err.message}`); + reject(err) + }); + }); + }, + + // Returns the specified Affiliation + affiliation: async (parent, { affiliationId }, { logger, dataSources }: MyContext) => { + const logMessage = `Resolving query affiliation(affiliationId: '${affiliationId}')`; + + return new Promise((resolve, reject) => { + dataSources.dmptoolAPIDataSource.getAffiliation(encodeURIComponent(affiliationId)) + .then(row => { + formatLogMessage(logger).debug(logMessage); + resolve(row); + }) + .catch(err => { + formatLogMessage(logger, { err, affiliationId }).error(`ERROR: ${logMessage} - ${err.message}`); + reject(err) + }); + }); + }, + } +} diff --git a/src/resolvers/contributorRole.ts b/src/resolvers/contributorRole.ts new file mode 100644 index 0000000..2071656 --- /dev/null +++ b/src/resolvers/contributorRole.ts @@ -0,0 +1,136 @@ + +import { formatLogMessage } from '../logger'; +import { Resolvers } from "../types"; +import { ContributorRoleModel } from "../models/ContributorRole"; +import { MyContext } from '../context'; + +// Extracting this particular query because we call it after mutations +async function fetchContributorRole(dataSources, contributorRoleId): Promise { + return new Promise((resolve, reject) => { + const sql = 'SELECT * FROM contributorRoles WHERE id = ?'; + dataSources.sqlDataSource.query(sql, [contributorRoleId]) + .then(rows => { + resolve(rows[0]) + }) + .catch(error => reject(error)); + }); +} + +// Generic error handler for mutations +function handleMutationError(logger, args) { + formatLogMessage(logger, args) + + return { + code: 400, + success: false, + message: args?.err?.message || 'Fatal error occurred while trying to run the query.', + contributorRole: null, + }; +} + +export const resolvers: Resolvers = { + Query: { + // returns an array of all contributor roles + contributorRoles: async (_, __, { logger, dataSources }: MyContext) => { + const logMessage = 'Resolving query contributorRoles'; + try { + const sql = 'SELECT * FROM contributorRoles ORDER BY label'; + const resp = await dataSources.sqlDataSource.query(sql, []); + + formatLogMessage(logger).debug(logMessage); + return resp; + } catch (err) { + handleMutationError(logger, { err }); + throw err; + } + }, + // returns a contributor role that matches the specified ID + contributorRoleById: async (_, { contributorRoleId }, { logger, dataSources }) => { + const logMessage = `Resolving query contributorRoleById(id: '${contributorRoleId}')` + try { + const resp = await fetchContributorRole(dataSources, contributorRoleId); + formatLogMessage(logger, { contributorRoleId }).debug(logMessage); + return resp[0]; + } catch (err) { + handleMutationError(logger, { err, contributorRoleId }); + throw err; + } + }, + // returns the contributor role that matches the specified URL + contributorRoleByURL: async (_, { contributorRoleURL }, { logger, dataSources }) => { + const logMessage = `Resolved query contirbutorRoleByURL(url: '${contributorRoleURL}')` + try { + const sql = 'SELECT * FROM contributorRoles WHERE url = ?'; + const resp = await dataSources.sqlDataSource.query(sql, [contributorRoleURL]) + + formatLogMessage(logger, { contributorRoleURL }).debug(logMessage); + return resp[0]; + } catch (err) { + handleMutationError(logger, { err, contributorRoleURL }); + throw err; + } + }, + }, + + Mutation: { + // add a new ContributorRole + addContributorRole: async (_, { url, label, displayOrder, description }, { logger, dataSources }) => { + const logArgs = { url, label, displayOrder, description }; + const logMessage = `Resolving mutation addContributorRole`; + + try { + const sql = 'INSERT INTO contributorRoles (url, label, description, displayOrder) VALUES (?, ?, ?)'; + const resp = await dataSources.sqlDataSource.query(sql, [url, label, description, displayOrder]); + + formatLogMessage(logger, logArgs).debug(logMessage); + + const contributor = await fetchContributorRole(dataSources, resp.id); + + return { + code: 201, + success: true, + message: `Successfully added ContributorRole ${resp.id}`, + contributorRole: contributor + }; + } catch (err) { + return handleMutationError(logger, { err, ...logArgs }); + } + }, + updateContributorRole: async (_, { id, url, label, displayOrder, description }, { logger, dataSources }) => { + const logArgs = { id, url, label, displayOrder, description }; + const logMessage = `Resolving mutation updateContributorRole`; + try { + const sql = 'UPDATE contributorRoles SET url = ?, label = ?, description = ?, displayOrder = ?) WHERE id = ?'; + await dataSources.sqlDataSource.query(sql, [url, label, description, displayOrder, id]); + + formatLogMessage(logger, logArgs).debug(logMessage); + return { + code: 200, + success: true, + message: `Successfully updated ContributorRole ${id}`, + contributorRole: fetchContributorRole(dataSources, id), + }; + } catch (err) { + return handleMutationError(logger, { err, ...logArgs }); + } + }, + removeContributorRole: async (_, { id }, { logger, dataSources }) => { + const logMessage = `Resolving mutation removeContributorRole`; + const original = fetchContributorRole(dataSources, id); + try { + const sql = 'DELETE FROM contributorRoles WHERE id = ?'; + await dataSources.sqlDataSource.query(sql, [id]); + + formatLogMessage(logger, { id }).debug(logMessage); + return { + code: 200, + success: true, + message: `Successfully removed ContributorRole ${id}`, + contributorRole: original, + }; + } catch (err) { + return handleMutationError(logger, { err, id }); + } + }, + }, +}; diff --git a/src/resolvers/dmsp.ts b/src/resolvers/dmsp.ts new file mode 100644 index 0000000..3635ae8 --- /dev/null +++ b/src/resolvers/dmsp.ts @@ -0,0 +1,23 @@ +import { formatLogMessage } from '../logger'; +import { Resolvers } from "../types"; + +export const resolvers: Resolvers = { + Query: { + // returns a DMSP that matches the specified DMP ID + dmspById: (_, { dmspId }, { logger, dataSources }) => { + const logMessage = `Resolving query dmspById(dmspId: '${dmspId}')`; + + return new Promise((resolve, reject) => { + dataSources.dmphubAPIDataSource.getDMSP(encodeURIComponent(dmspId)) + .then(rows => { + formatLogMessage(logger).debug(logMessage); + resolve(rows) + }) + .catch(err => { + formatLogMessage(logger, { err, dmspId }).error(`ERROR: ${logMessage} - ${err.message}`); + reject(err) + }); + }); + }, + }, +}; diff --git a/src/resolvers/scalars/dmspId.ts b/src/resolvers/scalars/dmspId.ts new file mode 100644 index 0000000..1dc3017 --- /dev/null +++ b/src/resolvers/scalars/dmspId.ts @@ -0,0 +1,35 @@ +import { GraphQLScalarType, Kind } from 'graphql'; + +export const DMSP_BASE_URL: string = process.env.DMSP_BASE_URL; +const DMSP_REGEX: RegExp = /^[0-9a-zA-Z]+$/; + +export function validateDmspId(val) { + const id = val.split(DMSP_BASE_URL)[1]; + if (val.startsWith(DMSP_BASE_URL) && id.match(DMSP_REGEX).length > 0) { + return val; + } + throw new Error(`Invalid DMSP ID format. Expected: "${DMSP_BASE_URL}A1B2C3D4"`); +}; + +// GraphQL Scalar definition for a DMSP ID +export const dmspIdScalar = new GraphQLScalarType({ + name: 'DmspId', + description: 'A Data Management and Sharing Plan\'s (DMSP) ID', + + serialize(dmspId) { + return validateDmspId(dmspId.toString()); + }, + + parseValue(value) { + return validateDmspId(value.toString()); + }, + + parseLiteral(ast) { + if (ast.kind === Kind.STRING) { + // Convert hard-coded AST string to string and then to DmspId + return validateDmspId(ast.value.toString()); + } + // Invalid hard-coded value (not a string) + return null; + }, +}); \ No newline at end of file diff --git a/src/resolvers/scalars/orcid.ts b/src/resolvers/scalars/orcid.ts new file mode 100644 index 0000000..a132651 --- /dev/null +++ b/src/resolvers/scalars/orcid.ts @@ -0,0 +1,38 @@ +import { GraphQLScalarType, Kind } from 'graphql'; + +export const ORCID_DOMAIN: string = 'https://orcid.org/'; +const ORCID_ID_REGEX: RegExp = /^([0-9a-zA-Z]{4}-){3}[0-9a-zA-Z]{4}$/; +const ORCID_URL_REGEX: RegExp = /^https?:\/\/orcid.org\/([0-9a-zA-Z]{4}-){3}[0-9a-zA-Z]{4}/; + +// Function to ensure the ORCID is properly formatted +export function validateOrcid(val) { + const match = val.startsWith('http') ? val.match(ORCID_URL_REGEX) : val.match(ORCID_ID_REGEX); + if (match.length > 0) { + // Prepend the ORCID URL to the id if it doesn't have it + return val.startsWith('http') ? val : `${ORCID_DOMAIN}${val}`; + } + throw new Error(`Invalid ORCID format. Expected: "https://orcid.org/0000-0000-0000-0000" or "0000-0000-0000-0000"`); +}; + +// GraphQL Scalar definition for a researcher ORCID +export const orcidScalar = new GraphQLScalarType({ + name: 'Orcid', + description: 'A researcher ORCID', + + serialize(orcid) { + return validateOrcid(orcid.toString()) + }, + + parseValue(value) { + return validateOrcid(value.toString()); + }, + + parseLiteral(ast) { + if (ast.kind === Kind.STRING) { + // Convert hard-coded AST string to string and then to Orcid + return validateOrcid(ast.value); + } + // Invalid hard-coded value (not a string) + return null; + }, +}); \ No newline at end of file diff --git a/src/resolvers/scalars/ror.ts b/src/resolvers/scalars/ror.ts new file mode 100644 index 0000000..8839a2a --- /dev/null +++ b/src/resolvers/scalars/ror.ts @@ -0,0 +1,37 @@ +import { GraphQLScalarType, Kind } from 'graphql'; + +export const ROR_DOMAIN: string = 'https://ror.org/'; +const ROR_ID_REGEX: RegExp = /^[0-9a-zA-Z]+$/; +const ROR_URL_REGEX: RegExp = /^https?:\/\/ror.org\/[0-9a-zA-Z]+/ + +export function validateRor(val) { + const match = val.startsWith('http') ? val.match(ROR_URL_REGEX) : val.match(ROR_ID_REGEX); + if (match.length > 0) { + // Prepend the ROR URL to the id if it doesn't have it + return val.startsWith('http') ? val : `${ROR_DOMAIN}${val}`; + } + throw new Error(`Invalid ROR format. Expected: "https://ror.org/abcd1234"`); +} + +// GraphQL Scalar definition for a researcher ORCID +export const rorScalar = new GraphQLScalarType({ + name: 'Ror', + description: 'An organization ROR ID', + + serialize(ror) { + return validateRor(ror.toString()) + }, + + parseValue(value) { + return validateRor(value.toString()); + }, + + parseLiteral(ast) { + if (ast.kind === Kind.STRING) { + // Convert hard-coded AST string to string and then to Ror + return validateRor(ast.value); + } + // Invalid hard-coded value (not a string) + return null; + }, +}); \ No newline at end of file diff --git a/src/resolvers/user.ts b/src/resolvers/user.ts new file mode 100644 index 0000000..e05cd2c --- /dev/null +++ b/src/resolvers/user.ts @@ -0,0 +1,75 @@ + +import { formatLogMessage } from '../logger'; +import { Resolvers } from "../types"; +import { MyContext } from '../context'; +import { User } from '../models/User'; + +export const resolvers: Resolvers = { + Query: { + // returns the current User + me: async (_, __, { logger, token }: MyContext) => { + const logMessage = 'Resolving query me'; + // Hard coding for testing for now. Change this out to get the email from the token + const user = null; + // const user = User.findByEmail('orgA.user@example.com'); + if (user) { + return user; + } + return { + code: 401, + success: false, + message: 'Unauthorized', + user: null, + }; + }, + + // Should only be callable by an Admin. Super returns all users, Admin gets only + // the users associated with their affiliationId + users: async (_, __, { logger, dataSources }) => { + const logMessage = `Resolving query users` + try { + const sql = 'SELECT id, givenName, surName, email, role, affiliationId, created, modified \ + FROM users ORDER BY created DESC' + const resp = await dataSources.sqlDataSource.query(sql); + formatLogMessage(logger).debug(logMessage); + return resp[0]; + } catch (err) { + return { + code: 500, + success: false, + message: 'Fatal error occurred while trying to run the query.', + users: null, + }; + } + }, + + // This query should only be available to Admins. Super can get any user and Admin can get + // only users associated with their affiliationId + user: async (_, { userId }, { logger }) => { + const logMessage = `Resolving query user for id ${userId}` + try { + const user = await User.findById(userId); + formatLogMessage(logger).debug(logMessage); + return user; + } catch (err) { + formatLogMessage(logger).error(`Error fetching user ${userId} - ${err.message}`); + return null; + } + }, + }, + + User: { + // Chained resolver to fetch the Affiliation info for the user + affiliation: async (parent: User, _, { logger, dataSources }) => { + const logMessage = 'Chaining resolver for affiliation'; + const rorId = parent.affiliationId.replace(/https?:\/\//g, '') + try { + formatLogMessage(logger).debug(logMessage); + return dataSources.dmptoolAPIDataSource.getAffiliation(rorId); + } catch(err) { + formatLogMessage(logger).error(`Error fetching affiliation ${rorId} for user ${parent.id} - ${err.message}`); + return null; + } + }, + }, +}; diff --git a/src/router.ts b/src/router.ts new file mode 100644 index 0000000..02b9828 --- /dev/null +++ b/src/router.ts @@ -0,0 +1,37 @@ +import express from 'express'; +import { expressjwt } from 'express-jwt'; +import { generalConfig } from './config/generalConfig'; +import { signinController } from './controllers/signinController'; +import { signupController } from './controllers/signupController'; +import { oauthServer, castRequest, castResponse } from './middleware/oauthServer'; + +const router = express.Router(); + +const authMiddleware = expressjwt({ + algorithms: ['HS256'], + credentialsRequired: false, + secret: generalConfig.jwtSecret as string, +}); + +// Support for email+password +router.post('/signin', (req, res) => signinController(req, res)); +router.post('/signup', (req, res, next) => signupController(req, res)); + +// Support for OAuth2 +router.get('/authorize', (req, res) => oauthServer.authorize(castRequest(req), castResponse(res))); +router.post('/authenticate', (req, res) => oauthServer.authenticate(castRequest(req), castResponse(res))); +router.post('/token', (req, res) => oauthServer.token(castRequest(req), castResponse(res))); + +// GraphQL operations +router.use('/graphql', authMiddleware); + +// Sample protected endpoint +router.post("/protected", authMiddleware, (req, res) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any + if (!(req as any).auth.admin) { + return res.sendStatus(401); + } + res.sendStatus(200); +}); + +export default router; diff --git a/src/schema.ts b/src/schema.ts new file mode 100644 index 0000000..f67e0e2 --- /dev/null +++ b/src/schema.ts @@ -0,0 +1,15 @@ +import { mergeTypeDefs } from '@graphql-tools/merge'; + +import { typeDefs as baseTypeDefs } from './schemas/base'; +import { typeDefs as affiliationTypeDefs } from './schemas/affiliation'; +import { typeDefs as contributorRoleTypeDefs } from './schemas/contributorRole'; +import { typeDefs as dmspTypeDefs } from './schemas/dmsp'; +import { typeDefs as userTypeDefs } from './schemas/user'; + +export const typeDefs = mergeTypeDefs([ + baseTypeDefs, + affiliationTypeDefs, + contributorRoleTypeDefs, + dmspTypeDefs, + userTypeDefs +]); diff --git a/src/schemas/affiliation.ts b/src/schemas/affiliation.ts new file mode 100644 index 0000000..b213a64 --- /dev/null +++ b/src/schemas/affiliation.ts @@ -0,0 +1,107 @@ +import gql from "graphql-tag"; + +export const typeDefs = gql` + extend type Query { + "Retrieve a specific Affiliation by its ID" + affiliation(affiliationId: String!): Affiliation + "Perform a search for Affiliations matching the specified name" + affiliations(name: String!, funderOnly: Boolean): [AffiliationSearch] + } + + "Search result - An abbreviated version of an Affiliation" + type AffiliationSearch { + "The unique identifer for the affiliation (typically the ROR id)" + id: String! + "The official name of the affiliation from the system of provenance" + name: String! + "The official display name" + displayName: String! + "Whether or not this affiliation is a funder" + funder: Boolean! + "The Crossref Funder id" + fundref: String + "Alias names and acronyms for the affiliation" + aliases: [String] + "The official ISO 2 character country code for the affiliation" + countryCode: String + "The country name for the affiliation" + countryName: String + "URL links associated with the affiliation" + links: [String] + "Localization options for the affiliation name" + locales: [AffiliationLocale] + } + + "A respresentation of an institution, organization or company" + type Affiliation { + "The unique identifer for the affiliation (typically the ROR id)" + id: String! + "Whether or not the affiliation is active. Inactive records shoould not appear in typeaheads!" + active: Boolean! + "The official name for the affiliation (defined by the system of provenance)" + name: String! + "The display name to help disambiguate similar names (typically with domain or country appended)" + displayName: String! + "Whether or not this affiliation is a funder" + funder: Boolean! + "The Crossref Funder id" + fundref: String + "Acronyms for the affiliation" + acronyms: [String] + "Alias names for the affiliation" + aliases: [String] + "The official homepage for the affiliation" + domain: String + "The official ISO 2 character country code for the affiliation" + countryCode: String + "The country name for the affiliation" + countryName: String + "Localization options for the affiliation name" + locales: [AffiliationLocale] + "URL links associated with the affiliation" + links: [String] + "The types of the affiliation (e.g. Company, Education, Government, etc.)" + types: [String] + "The URL for the affiliation's Wikipedia entry" + wikipediaURL: URL + "Other related affiliations" + relationships: [AffiliationRelationship] + "The address(es) for the affiliation" + addresses: [AffiliationAddress] + "The system the affiliation's data came from (e.g. ROR, DMPTool, etc.)" + provenance: String! + "The last time the data for the affiliation was synced with the system of provenance" + provenanceSyncDate: String! + } + + type AffiliationRelationship { + "The unique identifer for the related affiliation (typically the ROR id)" + id: String! + "The relationship type (e.g. Parent)" + type: String! + "The official name of the related affiliation" + name: String! + } + + type AffiliationAddress { + "The name of the affiliation's city" + city: String + "The name of the affiliation's state/province" + state: String + "The code of the affiliation's state/province" + stateCode: String + "The Geonames identify of the affiliation's country" + countryGeonamesId: Int + "The latitude coordinate" + lat: Float + "The longitude coordinate" + lng: Float + } + + type AffiliationLocale { + "The localized name of the affiliation" + label: String! + "The language code" + locale: String! + } +`; diff --git a/src/schemas/base.ts b/src/schemas/base.ts new file mode 100644 index 0000000..02d282c --- /dev/null +++ b/src/schemas/base.ts @@ -0,0 +1,23 @@ +import gql from "graphql-tag"; + +export const typeDefs = gql` + # Specialized scalars from graphql-tools: https://the-guild.dev/graphql/scalars/docs/scalars + scalar DateTimeISO + scalar EmailAddress + scalar URL + + # Our custom scalars + scalar Orcid + scalar Ror + scalar DmspId + + # Base Query and Mutation objects are defined here because names must be unique and each + # individual GraphQL file has its own Queries and Mutations, so we have those extend these + # base definitions + type Query { + _empty: String + } + type Mutation { + _empty: String + } +`; \ No newline at end of file diff --git a/src/schemas/contributorRole.ts b/src/schemas/contributorRole.ts new file mode 100644 index 0000000..6967a31 --- /dev/null +++ b/src/schemas/contributorRole.ts @@ -0,0 +1,51 @@ +import gql from "graphql-tag"; + +export const typeDefs = gql` + extend type Query { + "Get all of the contributor role types" + contributorRoles: [ContributorRole] + "Get the contributor role by it's id" + contributorRoleById(contributorRoleId: Int!): ContributorRole + "Get the contributor role by it's URL" + contributorRoleByURL(contributorRoleURL: URL!): ContributorRole + } + + extend type Mutation { + "Add a new contributor role (URL and label must be unique!)" + addContributorRole(url: URL!, label: String!, displayOrder: Int!, description: String): ContributorRoleMutationResponse + "Update the contributor role" + updateContributorRole(id: ID!, url: URL!, label: String!, displayOrder: Int!, description: String): ContributorRoleMutationResponse + "Delete the contributor role" + removeContributorRole(id: ID!): ContributorRoleMutationResponse + } + + type ContributorRoleMutationResponse { + "Similar to HTTP status code, represents the status of the mutation" + code: Int! + "Indicates whether the mutation was successful" + success: Boolean! + "Human-readable message for the UI" + message: String! + """ + The contributor role that was impacted by the mutation. + The new one if we were adding, the one that was updated when updating, or the one deletd when removing + """ + contributorRole: ContributorRole + } + + type ContributorRole { + id: Int! + "The order in which to display these items when displayed in the UI" + displayOrder: Int! + "The Ui label to display for the contributor role" + label: String! + "The URL for the contributor role" + url: URL! + "A longer description of the contributor role useful for tooltips" + description: String + "The timestamp of when the contributor role was created" + created: DateTimeISO! + "The timestamp of when the contributor role last modified" + modified: DateTimeISO! + } +`; \ No newline at end of file diff --git a/src/schemas/dmsp.ts b/src/schemas/dmsp.ts new file mode 100644 index 0000000..e271dc6 --- /dev/null +++ b/src/schemas/dmsp.ts @@ -0,0 +1,98 @@ +import gql from "graphql-tag"; + +export const typeDefs = gql` + extend type Query { + "Get the DMSP by its DMP ID" + dmspById(dmspId: DmspId!): SingleDmspResponse + } + + type SingleDmspResponse { + "Similar to HTTP status code, represents the status of the mutation" + code: Int! + "Indicates whether the mutation was successful" + success: Boolean! + "Human-readable message for the UI" + message: String! + "The DMSP" + dmsp: Dmsp + } + + type Dmsp { + contact: PrimaryContact! + created: DateTimeISO! + dmp_id: DmspIdentifier! + ethical_issues_exist: YesNoUnknown! + modified: DateTimeISO! + title: String! + + contributor: [Contributor] + description: String + dmproadmap_featured: String + dmproadmap_related_identifiers: [RelatedIdentifier] + dmproadmap_visibility: String + ethical_issues_description: String + ethical_issues_report: URL + language: String + } + + type PrimaryContact implements Person { + name: String! + mbox: String + dmproadmap_affiliation: DmpRoadmapAffiliation + + contact_id: Identifier + } + + type Contributor implements Person { + name: String! + mbox: String + dmproadmap_affiliation: DmpRoadmapAffiliation + + role: [String!]! + contributorId: PersonIdentifier + } + + type RelatedIdentifier { + descriptor: String! + identifier: URL! + type: String! + work_type: String! + } + + type DmpRoadmapAffiliation { + name: String! + affiliation_id: OrganizationIdentifier + } + + type DmspIdentifier { + type: String! + identifier: DmspId! + } + + type OrganizationIdentifier { + type: String! + identifier: Ror! + } + + type PersonIdentifier { + type: String! + identifier: Orcid! + } + + type Identifier { + type: String! + identifier: String! + } + + interface Person { + name: String! + mbox: String + dmproadmap_affiliation: DmpRoadmapAffiliation + } + + enum YesNoUnknown { + yes + no + unknown + } +`; \ No newline at end of file diff --git a/src/schemas/user.ts b/src/schemas/user.ts new file mode 100644 index 0000000..f7ef294 --- /dev/null +++ b/src/schemas/user.ts @@ -0,0 +1,27 @@ +import gql from "graphql-tag"; + +export const typeDefs = gql` + extend type Query { + me: User + users: [User] + user(userId: String!): User + } + + enum UserRole { + RESEARCHER + ADMIN + SUPER_ADMIN + } + + type User { + id: Int + givenName: String + surName: String + email: EmailAddress! + role: UserRole! + orcid: Orcid + created: DateTimeISO! + modified: DateTimeISO! + affiliation: Affiliation + } +`; \ No newline at end of file diff --git a/src/services/__tests__/tokenService.spec.ts b/src/services/__tests__/tokenService.spec.ts new file mode 100644 index 0000000..7ea3aca --- /dev/null +++ b/src/services/__tests__/tokenService.spec.ts @@ -0,0 +1,34 @@ +import { User, UserRole } from '../../models/User'; +import { generateToken, verifyToken } from '../tokenService'; + +describe('generateToken', () => { + test('it returns a new JWT', () => { + const user = new User({ id: 999, email: 'test@example.com', role: UserRole.Researcher }); + const token = generateToken(user); + expect(token).toBeDefined(); + }); + + test('it returns Falsey if the User has no id (it hasn\'t been saved)', () => { + const user = new User({ email: 'test@example.com', role: UserRole.Researcher }); + const token = generateToken(user); + expect(token).toBeFalsy(); + }); +}); + +describe('verifyToken', () => { + test('it can verify a valid token', () => { + const user = new User({ id: 999, email: 'test@example.com', role: UserRole.Researcher }); + const token = generateToken(user); + const decoded = verifyToken(token, null); + expect(decoded.id).toEqual(user.id); + expect(decoded.email).toEqual(user.email); + expect(decoded.role).toEqual(user.role); + }); + + test('it returns Falsey when the token cannot be validated', () => { + const user = new User({ id: 999, email: 'test@example.com', role: UserRole.Researcher }); + const token = generateToken(user); + const decoded = verifyToken(token.substring(10), null); + expect(decoded).toBeFalsy(); + }); +}); \ No newline at end of file diff --git a/src/services/tokenService.ts b/src/services/tokenService.ts new file mode 100644 index 0000000..ded1c44 --- /dev/null +++ b/src/services/tokenService.ts @@ -0,0 +1,41 @@ +import jwt, { JwtPayload } from 'jsonwebtoken'; +import { Logger } from 'pino'; +import { formatLogMessage } from '../logger'; +import { User } from '../models/User'; +import { generalConfig } from '../config/generalConfig'; +import { UserRole } from '../models/User'; + +export interface JWTToken extends JwtPayload { + id: number, + email: string, + givenName: string, + surName: string, + role: string, +} + +// Generate a JWT Token for the given User +export const generateToken = (user: User): string => { + if (generalConfig.jwtSecret && user && user.id && user.email) { + const payload: JWTToken = { + id: user.id, + email: user.email, + givenName: user.givenName, + surName: user.surName, + role: user.role.toString() || UserRole.Researcher, + } + return jwt.sign(payload, generalConfig.jwtSecret as string, { expiresIn: generalConfig.jwtTtl }); + } + return null; +}; + +// Verify the incoming JWT +export const verifyToken = (token: string, logger: Logger): JWTToken => { + try { + return jwt.verify(token, generalConfig.jwtSecret as string) as JWTToken; + } catch(err) { + if (logger) { + formatLogMessage(logger, { err }); + } + return null; + } +}; diff --git a/src/types.ts b/src/types.ts new file mode 100644 index 0000000..65ca7af --- /dev/null +++ b/src/types.ts @@ -0,0 +1,761 @@ +import { GraphQLResolveInfo, GraphQLScalarType, GraphQLScalarTypeConfig } from 'graphql'; +import { DmspModel } from './models/Dmsp'; +import { ContributorRoleModel } from './models/ContributorRole'; +import { MyContext } from './context'; +export type Maybe = T | null; +export type InputMaybe = Maybe; +export type Exact = { [K in keyof T]: T[K] }; +export type MakeOptional = Omit & { [SubKey in K]?: Maybe }; +export type MakeMaybe = Omit & { [SubKey in K]: Maybe }; +export type MakeEmpty = { [_ in K]?: never }; +export type Incremental = T | { [P in keyof T]?: P extends ' $fragmentName' | '__typename' ? T[P] : never }; +export type Omit = Pick>; +export type RequireFields = Omit & { [P in K]-?: NonNullable }; +/** All built-in and custom scalars, mapped to their actual values */ +export type Scalars = { + ID: { input: string; output: string; } + String: { input: string; output: string; } + Boolean: { input: boolean; output: boolean; } + Int: { input: number; output: number; } + Float: { input: number; output: number; } + DateTimeISO: { input: any; output: any; } + DmspId: { input: any; output: any; } + EmailAddress: { input: any; output: any; } + Orcid: { input: any; output: any; } + Ror: { input: any; output: any; } + URL: { input: any; output: any; } +}; + +/** A respresentation of an institution, organization or company */ +export type Affiliation = { + __typename?: 'Affiliation'; + /** Acronyms for the affiliation */ + acronyms?: Maybe>>; + /** Whether or not the affiliation is active. Inactive records shoould not appear in typeaheads! */ + active: Scalars['Boolean']['output']; + /** The address(es) for the affiliation */ + addresses?: Maybe>>; + /** Alias names for the affiliation */ + aliases?: Maybe>>; + /** The official ISO 2 character country code for the affiliation */ + countryCode?: Maybe; + /** The country name for the affiliation */ + countryName?: Maybe; + /** The display name to help disambiguate similar names (typically with domain or country appended) */ + displayName: Scalars['String']['output']; + /** The official homepage for the affiliation */ + domain?: Maybe; + /** Whether or not this affiliation is a funder */ + funder: Scalars['Boolean']['output']; + /** The Crossref Funder id */ + fundref?: Maybe; + /** The unique identifer for the affiliation (typically the ROR id) */ + id: Scalars['String']['output']; + /** URL links associated with the affiliation */ + links?: Maybe>>; + /** Localization options for the affiliation name */ + locales?: Maybe>>; + /** The official name for the affiliation (defined by the system of provenance) */ + name: Scalars['String']['output']; + /** The system the affiliation's data came from (e.g. ROR, DMPTool, etc.) */ + provenance: Scalars['String']['output']; + /** The last time the data for the affiliation was synced with the system of provenance */ + provenanceSyncDate: Scalars['String']['output']; + /** Other related affiliations */ + relationships?: Maybe>>; + /** The types of the affiliation (e.g. Company, Education, Government, etc.) */ + types?: Maybe>>; + /** The URL for the affiliation's Wikipedia entry */ + wikipediaURL?: Maybe; +}; + +export type AffiliationAddress = { + __typename?: 'AffiliationAddress'; + /** The name of the affiliation's city */ + city?: Maybe; + /** The Geonames identify of the affiliation's country */ + countryGeonamesId?: Maybe; + /** The latitude coordinate */ + lat?: Maybe; + /** The longitude coordinate */ + lng?: Maybe; + /** The name of the affiliation's state/province */ + state?: Maybe; + /** The code of the affiliation's state/province */ + stateCode?: Maybe; +}; + +export type AffiliationLocale = { + __typename?: 'AffiliationLocale'; + /** The localized name of the affiliation */ + label: Scalars['String']['output']; + /** The language code */ + locale: Scalars['String']['output']; +}; + +export type AffiliationRelationship = { + __typename?: 'AffiliationRelationship'; + /** The unique identifer for the related affiliation (typically the ROR id) */ + id: Scalars['String']['output']; + /** The official name of the related affiliation */ + name: Scalars['String']['output']; + /** The relationship type (e.g. Parent) */ + type: Scalars['String']['output']; +}; + +/** Search result - An abbreviated version of an Affiliation */ +export type AffiliationSearch = { + __typename?: 'AffiliationSearch'; + /** Alias names and acronyms for the affiliation */ + aliases?: Maybe>>; + /** The official ISO 2 character country code for the affiliation */ + countryCode?: Maybe; + /** The country name for the affiliation */ + countryName?: Maybe; + /** The official display name */ + displayName: Scalars['String']['output']; + /** Whether or not this affiliation is a funder */ + funder: Scalars['Boolean']['output']; + /** The Crossref Funder id */ + fundref?: Maybe; + /** The unique identifer for the affiliation (typically the ROR id) */ + id: Scalars['String']['output']; + /** URL links associated with the affiliation */ + links?: Maybe>>; + /** Localization options for the affiliation name */ + locales?: Maybe>>; + /** The official name of the affiliation from the system of provenance */ + name: Scalars['String']['output']; +}; + +export type Contributor = Person & { + __typename?: 'Contributor'; + contributorId?: Maybe; + dmproadmap_affiliation?: Maybe; + mbox?: Maybe; + name: Scalars['String']['output']; + role: Array; +}; + +export type ContributorRole = { + __typename?: 'ContributorRole'; + /** The timestamp of when the contributor role was created */ + created: Scalars['DateTimeISO']['output']; + /** A longer description of the contributor role useful for tooltips */ + description?: Maybe; + /** The order in which to display these items when displayed in the UI */ + displayOrder: Scalars['Int']['output']; + id: Scalars['Int']['output']; + /** The Ui label to display for the contributor role */ + label: Scalars['String']['output']; + /** The timestamp of when the contributor role last modified */ + modified: Scalars['DateTimeISO']['output']; + /** The URL for the contributor role */ + url: Scalars['URL']['output']; +}; + +export type ContributorRoleMutationResponse = { + __typename?: 'ContributorRoleMutationResponse'; + /** Similar to HTTP status code, represents the status of the mutation */ + code: Scalars['Int']['output']; + /** + * The contributor role that was impacted by the mutation. + * The new one if we were adding, the one that was updated when updating, or the one deletd when removing + */ + contributorRole?: Maybe; + /** Human-readable message for the UI */ + message: Scalars['String']['output']; + /** Indicates whether the mutation was successful */ + success: Scalars['Boolean']['output']; +}; + +export type DmpRoadmapAffiliation = { + __typename?: 'DmpRoadmapAffiliation'; + affiliation_id?: Maybe; + name: Scalars['String']['output']; +}; + +export type Dmsp = { + __typename?: 'Dmsp'; + contact: PrimaryContact; + contributor?: Maybe>>; + created: Scalars['DateTimeISO']['output']; + description?: Maybe; + dmp_id: DmspIdentifier; + dmproadmap_featured?: Maybe; + dmproadmap_related_identifiers?: Maybe>>; + dmproadmap_visibility?: Maybe; + ethical_issues_description?: Maybe; + ethical_issues_exist: YesNoUnknown; + ethical_issues_report?: Maybe; + language?: Maybe; + modified: Scalars['DateTimeISO']['output']; + title: Scalars['String']['output']; +}; + +export type DmspIdentifier = { + __typename?: 'DmspIdentifier'; + identifier: Scalars['DmspId']['output']; + type: Scalars['String']['output']; +}; + +export type Identifier = { + __typename?: 'Identifier'; + identifier: Scalars['String']['output']; + type: Scalars['String']['output']; +}; + +export type Mutation = { + __typename?: 'Mutation'; + _empty?: Maybe; + /** Add a new contributor role (URL and label must be unique!) */ + addContributorRole?: Maybe; + /** Delete the contributor role */ + removeContributorRole?: Maybe; + /** Update the contributor role */ + updateContributorRole?: Maybe; +}; + + +export type MutationAddContributorRoleArgs = { + description?: InputMaybe; + displayOrder: Scalars['Int']['input']; + label: Scalars['String']['input']; + url: Scalars['URL']['input']; +}; + + +export type MutationRemoveContributorRoleArgs = { + id: Scalars['ID']['input']; +}; + + +export type MutationUpdateContributorRoleArgs = { + description?: InputMaybe; + displayOrder: Scalars['Int']['input']; + id: Scalars['ID']['input']; + label: Scalars['String']['input']; + url: Scalars['URL']['input']; +}; + +export type OrganizationIdentifier = { + __typename?: 'OrganizationIdentifier'; + identifier: Scalars['Ror']['output']; + type: Scalars['String']['output']; +}; + +export type Person = { + dmproadmap_affiliation?: Maybe; + mbox?: Maybe; + name: Scalars['String']['output']; +}; + +export type PersonIdentifier = { + __typename?: 'PersonIdentifier'; + identifier: Scalars['Orcid']['output']; + type: Scalars['String']['output']; +}; + +export type PrimaryContact = Person & { + __typename?: 'PrimaryContact'; + contact_id?: Maybe; + dmproadmap_affiliation?: Maybe; + mbox?: Maybe; + name: Scalars['String']['output']; +}; + +export type Query = { + __typename?: 'Query'; + _empty?: Maybe; + /** Retrieve a specific Affiliation by its ID */ + affiliation?: Maybe; + /** Perform a search for Affiliations matching the specified name */ + affiliations?: Maybe>>; + /** Get the contributor role by it's id */ + contributorRoleById?: Maybe; + /** Get the contributor role by it's URL */ + contributorRoleByURL?: Maybe; + /** Get all of the contributor role types */ + contributorRoles?: Maybe>>; + /** Get the DMSP by its DMP ID */ + dmspById?: Maybe; + me?: Maybe; + user?: Maybe; + users?: Maybe>>; +}; + + +export type QueryAffiliationArgs = { + affiliationId: Scalars['String']['input']; +}; + + +export type QueryAffiliationsArgs = { + funderOnly?: InputMaybe; + name: Scalars['String']['input']; +}; + + +export type QueryContributorRoleByIdArgs = { + contributorRoleId: Scalars['Int']['input']; +}; + + +export type QueryContributorRoleByUrlArgs = { + contributorRoleURL: Scalars['URL']['input']; +}; + + +export type QueryDmspByIdArgs = { + dmspId: Scalars['DmspId']['input']; +}; + + +export type QueryUserArgs = { + userId: Scalars['String']['input']; +}; + +export type RelatedIdentifier = { + __typename?: 'RelatedIdentifier'; + descriptor: Scalars['String']['output']; + identifier: Scalars['URL']['output']; + type: Scalars['String']['output']; + work_type: Scalars['String']['output']; +}; + +export type SingleDmspResponse = { + __typename?: 'SingleDmspResponse'; + /** Similar to HTTP status code, represents the status of the mutation */ + code: Scalars['Int']['output']; + /** The DMSP */ + dmsp?: Maybe; + /** Human-readable message for the UI */ + message: Scalars['String']['output']; + /** Indicates whether the mutation was successful */ + success: Scalars['Boolean']['output']; +}; + +export type User = { + __typename?: 'User'; + affiliation?: Maybe; + created: Scalars['DateTimeISO']['output']; + email: Scalars['EmailAddress']['output']; + givenName?: Maybe; + id?: Maybe; + modified: Scalars['DateTimeISO']['output']; + orcid?: Maybe; + role: UserRole; + surName?: Maybe; +}; + +export type UserRole = + | 'ADMIN' + | 'RESEARCHER' + | 'SUPER_ADMIN'; + +export type YesNoUnknown = + | 'no' + | 'unknown' + | 'yes'; + + + +export type ResolverTypeWrapper = Promise | T; + + +export type ResolverWithResolve = { + resolve: ResolverFn; +}; +export type Resolver = ResolverFn | ResolverWithResolve; + +export type ResolverFn = ( + parent: TParent, + args: TArgs, + context: TContext, + info: GraphQLResolveInfo +) => Promise | TResult; + +export type SubscriptionSubscribeFn = ( + parent: TParent, + args: TArgs, + context: TContext, + info: GraphQLResolveInfo +) => AsyncIterable | Promise>; + +export type SubscriptionResolveFn = ( + parent: TParent, + args: TArgs, + context: TContext, + info: GraphQLResolveInfo +) => TResult | Promise; + +export interface SubscriptionSubscriberObject { + subscribe: SubscriptionSubscribeFn<{ [key in TKey]: TResult }, TParent, TContext, TArgs>; + resolve?: SubscriptionResolveFn; +} + +export interface SubscriptionResolverObject { + subscribe: SubscriptionSubscribeFn; + resolve: SubscriptionResolveFn; +} + +export type SubscriptionObject = + | SubscriptionSubscriberObject + | SubscriptionResolverObject; + +export type SubscriptionResolver = + | ((...args: any[]) => SubscriptionObject) + | SubscriptionObject; + +export type TypeResolveFn = ( + parent: TParent, + context: TContext, + info: GraphQLResolveInfo +) => Maybe | Promise>; + +export type IsTypeOfResolverFn = (obj: T, context: TContext, info: GraphQLResolveInfo) => boolean | Promise; + +export type NextResolverFn = () => Promise; + +export type DirectiveResolverFn = ( + next: NextResolverFn, + parent: TParent, + args: TArgs, + context: TContext, + info: GraphQLResolveInfo +) => TResult | Promise; + + +/** Mapping of interface types */ +export type ResolversInterfaceTypes<_RefType extends Record> = { + Person: ( Contributor ) | ( PrimaryContact ); +}; + +/** Mapping between all available schema types and the resolvers types */ +export type ResolversTypes = { + Affiliation: ResolverTypeWrapper; + AffiliationAddress: ResolverTypeWrapper; + AffiliationLocale: ResolverTypeWrapper; + AffiliationRelationship: ResolverTypeWrapper; + AffiliationSearch: ResolverTypeWrapper; + Boolean: ResolverTypeWrapper; + Contributor: ResolverTypeWrapper; + ContributorRole: ResolverTypeWrapper; + ContributorRoleMutationResponse: ResolverTypeWrapper & { contributorRole?: Maybe }>; + DateTimeISO: ResolverTypeWrapper; + DmpRoadmapAffiliation: ResolverTypeWrapper; + Dmsp: ResolverTypeWrapper; + DmspId: ResolverTypeWrapper; + DmspIdentifier: ResolverTypeWrapper; + EmailAddress: ResolverTypeWrapper; + Float: ResolverTypeWrapper; + ID: ResolverTypeWrapper; + Identifier: ResolverTypeWrapper; + Int: ResolverTypeWrapper; + Mutation: ResolverTypeWrapper<{}>; + Orcid: ResolverTypeWrapper; + OrganizationIdentifier: ResolverTypeWrapper; + Person: ResolverTypeWrapper['Person']>; + PersonIdentifier: ResolverTypeWrapper; + PrimaryContact: ResolverTypeWrapper; + Query: ResolverTypeWrapper<{}>; + RelatedIdentifier: ResolverTypeWrapper; + Ror: ResolverTypeWrapper; + SingleDmspResponse: ResolverTypeWrapper & { dmsp?: Maybe }>; + String: ResolverTypeWrapper; + URL: ResolverTypeWrapper; + User: ResolverTypeWrapper; + UserRole: UserRole; + YesNoUnknown: YesNoUnknown; +}; + +/** Mapping between all available schema types and the resolvers parents */ +export type ResolversParentTypes = { + Affiliation: Affiliation; + AffiliationAddress: AffiliationAddress; + AffiliationLocale: AffiliationLocale; + AffiliationRelationship: AffiliationRelationship; + AffiliationSearch: AffiliationSearch; + Boolean: Scalars['Boolean']['output']; + Contributor: Contributor; + ContributorRole: ContributorRoleModel; + ContributorRoleMutationResponse: Omit & { contributorRole?: Maybe }; + DateTimeISO: Scalars['DateTimeISO']['output']; + DmpRoadmapAffiliation: DmpRoadmapAffiliation; + Dmsp: DmspModel; + DmspId: Scalars['DmspId']['output']; + DmspIdentifier: DmspIdentifier; + EmailAddress: Scalars['EmailAddress']['output']; + Float: Scalars['Float']['output']; + ID: Scalars['ID']['output']; + Identifier: Identifier; + Int: Scalars['Int']['output']; + Mutation: {}; + Orcid: Scalars['Orcid']['output']; + OrganizationIdentifier: OrganizationIdentifier; + Person: ResolversInterfaceTypes['Person']; + PersonIdentifier: PersonIdentifier; + PrimaryContact: PrimaryContact; + Query: {}; + RelatedIdentifier: RelatedIdentifier; + Ror: Scalars['Ror']['output']; + SingleDmspResponse: Omit & { dmsp?: Maybe }; + String: Scalars['String']['output']; + URL: Scalars['URL']['output']; + User: User; +}; + +export type AffiliationResolvers = { + acronyms?: Resolver>>, ParentType, ContextType>; + active?: Resolver; + addresses?: Resolver>>, ParentType, ContextType>; + aliases?: Resolver>>, ParentType, ContextType>; + countryCode?: Resolver, ParentType, ContextType>; + countryName?: Resolver, ParentType, ContextType>; + displayName?: Resolver; + domain?: Resolver, ParentType, ContextType>; + funder?: Resolver; + fundref?: Resolver, ParentType, ContextType>; + id?: Resolver; + links?: Resolver>>, ParentType, ContextType>; + locales?: Resolver>>, ParentType, ContextType>; + name?: Resolver; + provenance?: Resolver; + provenanceSyncDate?: Resolver; + relationships?: Resolver>>, ParentType, ContextType>; + types?: Resolver>>, ParentType, ContextType>; + wikipediaURL?: Resolver, ParentType, ContextType>; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type AffiliationAddressResolvers = { + city?: Resolver, ParentType, ContextType>; + countryGeonamesId?: Resolver, ParentType, ContextType>; + lat?: Resolver, ParentType, ContextType>; + lng?: Resolver, ParentType, ContextType>; + state?: Resolver, ParentType, ContextType>; + stateCode?: Resolver, ParentType, ContextType>; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type AffiliationLocaleResolvers = { + label?: Resolver; + locale?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type AffiliationRelationshipResolvers = { + id?: Resolver; + name?: Resolver; + type?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type AffiliationSearchResolvers = { + aliases?: Resolver>>, ParentType, ContextType>; + countryCode?: Resolver, ParentType, ContextType>; + countryName?: Resolver, ParentType, ContextType>; + displayName?: Resolver; + funder?: Resolver; + fundref?: Resolver, ParentType, ContextType>; + id?: Resolver; + links?: Resolver>>, ParentType, ContextType>; + locales?: Resolver>>, ParentType, ContextType>; + name?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type ContributorResolvers = { + contributorId?: Resolver, ParentType, ContextType>; + dmproadmap_affiliation?: Resolver, ParentType, ContextType>; + mbox?: Resolver, ParentType, ContextType>; + name?: Resolver; + role?: Resolver, ParentType, ContextType>; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type ContributorRoleResolvers = { + created?: Resolver; + description?: Resolver, ParentType, ContextType>; + displayOrder?: Resolver; + id?: Resolver; + label?: Resolver; + modified?: Resolver; + url?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type ContributorRoleMutationResponseResolvers = { + code?: Resolver; + contributorRole?: Resolver, ParentType, ContextType>; + message?: Resolver; + success?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export interface DateTimeIsoScalarConfig extends GraphQLScalarTypeConfig { + name: 'DateTimeISO'; +} + +export type DmpRoadmapAffiliationResolvers = { + affiliation_id?: Resolver, ParentType, ContextType>; + name?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type DmspResolvers = { + contact?: Resolver; + contributor?: Resolver>>, ParentType, ContextType>; + created?: Resolver; + description?: Resolver, ParentType, ContextType>; + dmp_id?: Resolver; + dmproadmap_featured?: Resolver, ParentType, ContextType>; + dmproadmap_related_identifiers?: Resolver>>, ParentType, ContextType>; + dmproadmap_visibility?: Resolver, ParentType, ContextType>; + ethical_issues_description?: Resolver, ParentType, ContextType>; + ethical_issues_exist?: Resolver; + ethical_issues_report?: Resolver, ParentType, ContextType>; + language?: Resolver, ParentType, ContextType>; + modified?: Resolver; + title?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export interface DmspIdScalarConfig extends GraphQLScalarTypeConfig { + name: 'DmspId'; +} + +export type DmspIdentifierResolvers = { + identifier?: Resolver; + type?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export interface EmailAddressScalarConfig extends GraphQLScalarTypeConfig { + name: 'EmailAddress'; +} + +export type IdentifierResolvers = { + identifier?: Resolver; + type?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type MutationResolvers = { + _empty?: Resolver, ParentType, ContextType>; + addContributorRole?: Resolver, ParentType, ContextType, RequireFields>; + removeContributorRole?: Resolver, ParentType, ContextType, RequireFields>; + updateContributorRole?: Resolver, ParentType, ContextType, RequireFields>; +}; + +export interface OrcidScalarConfig extends GraphQLScalarTypeConfig { + name: 'Orcid'; +} + +export type OrganizationIdentifierResolvers = { + identifier?: Resolver; + type?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type PersonResolvers = { + __resolveType: TypeResolveFn<'Contributor' | 'PrimaryContact', ParentType, ContextType>; + dmproadmap_affiliation?: Resolver, ParentType, ContextType>; + mbox?: Resolver, ParentType, ContextType>; + name?: Resolver; +}; + +export type PersonIdentifierResolvers = { + identifier?: Resolver; + type?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type PrimaryContactResolvers = { + contact_id?: Resolver, ParentType, ContextType>; + dmproadmap_affiliation?: Resolver, ParentType, ContextType>; + mbox?: Resolver, ParentType, ContextType>; + name?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type QueryResolvers = { + _empty?: Resolver, ParentType, ContextType>; + affiliation?: Resolver, ParentType, ContextType, RequireFields>; + affiliations?: Resolver>>, ParentType, ContextType, RequireFields>; + contributorRoleById?: Resolver, ParentType, ContextType, RequireFields>; + contributorRoleByURL?: Resolver, ParentType, ContextType, RequireFields>; + contributorRoles?: Resolver>>, ParentType, ContextType>; + dmspById?: Resolver, ParentType, ContextType, RequireFields>; + me?: Resolver, ParentType, ContextType>; + user?: Resolver, ParentType, ContextType, RequireFields>; + users?: Resolver>>, ParentType, ContextType>; +}; + +export type RelatedIdentifierResolvers = { + descriptor?: Resolver; + identifier?: Resolver; + type?: Resolver; + work_type?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export interface RorScalarConfig extends GraphQLScalarTypeConfig { + name: 'Ror'; +} + +export type SingleDmspResponseResolvers = { + code?: Resolver; + dmsp?: Resolver, ParentType, ContextType>; + message?: Resolver; + success?: Resolver; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export interface UrlScalarConfig extends GraphQLScalarTypeConfig { + name: 'URL'; +} + +export type UserResolvers = { + affiliation?: Resolver, ParentType, ContextType>; + created?: Resolver; + email?: Resolver; + givenName?: Resolver, ParentType, ContextType>; + id?: Resolver, ParentType, ContextType>; + modified?: Resolver; + orcid?: Resolver, ParentType, ContextType>; + role?: Resolver; + surName?: Resolver, ParentType, ContextType>; + __isTypeOf?: IsTypeOfResolverFn; +}; + +export type Resolvers = { + Affiliation?: AffiliationResolvers; + AffiliationAddress?: AffiliationAddressResolvers; + AffiliationLocale?: AffiliationLocaleResolvers; + AffiliationRelationship?: AffiliationRelationshipResolvers; + AffiliationSearch?: AffiliationSearchResolvers; + Contributor?: ContributorResolvers; + ContributorRole?: ContributorRoleResolvers; + ContributorRoleMutationResponse?: ContributorRoleMutationResponseResolvers; + DateTimeISO?: GraphQLScalarType; + DmpRoadmapAffiliation?: DmpRoadmapAffiliationResolvers; + Dmsp?: DmspResolvers; + DmspId?: GraphQLScalarType; + DmspIdentifier?: DmspIdentifierResolvers; + EmailAddress?: GraphQLScalarType; + Identifier?: IdentifierResolvers; + Mutation?: MutationResolvers; + Orcid?: GraphQLScalarType; + OrganizationIdentifier?: OrganizationIdentifierResolvers; + Person?: PersonResolvers; + PersonIdentifier?: PersonIdentifierResolvers; + PrimaryContact?: PrimaryContactResolvers; + Query?: QueryResolvers; + RelatedIdentifier?: RelatedIdentifierResolvers; + Ror?: GraphQLScalarType; + SingleDmspResponse?: SingleDmspResponseResolvers; + URL?: GraphQLScalarType; + User?: UserResolvers; +}; + diff --git a/src/utils/__tests__/graphQLErrors.spec.ts b/src/utils/__tests__/graphQLErrors.spec.ts new file mode 100644 index 0000000..2224406 --- /dev/null +++ b/src/utils/__tests__/graphQLErrors.spec.ts @@ -0,0 +1,25 @@ +import { GraphQLError } from 'graphql'; +import { + AuthenticationError, + AUTHENTICATION_ERROR_CODE, + DEFAULT_AUNAUTHORIZED_MESSAGE, + DEFAULT_FORBIDDEN_MESSAGE, + ForbiddenError, + FORBIDDEN_ERROR_CODE, +} from '../graphQLErrors'; + +describe('Authentication error', () => { + test('returns a GraphQLError with the default error message', () => { + const err = AuthenticationError(); + expect(err).toBeInstanceOf(GraphQLError); + expect(err.message).toEqual(DEFAULT_AUNAUTHORIZED_MESSAGE); + expect(err.extensions?.code).toEqual(AUTHENTICATION_ERROR_CODE); + }); + + test('it uses the error message provided', () => { + const err = ForbiddenError(); + expect(err).toBeInstanceOf(GraphQLError); + expect(err.message).toEqual(DEFAULT_FORBIDDEN_MESSAGE); + expect(err.extensions?.code).toEqual(FORBIDDEN_ERROR_CODE); + }); +}); diff --git a/src/utils/__tests__/helpers.spec.ts b/src/utils/__tests__/helpers.spec.ts new file mode 100644 index 0000000..1af72be --- /dev/null +++ b/src/utils/__tests__/helpers.spec.ts @@ -0,0 +1,64 @@ +import { + validateEmail, + capitalizeFirstLetter, + stringToArray, + verifyCriticalEnvVariable +} from '../helpers'; + +describe('Email validation', () => { + test('returns true if the value is a valid email', () => { + expect(validateEmail('test@example.com')).toBe(true); + expect(validateEmail('test-user@example.company')).toBe(true); + expect(validateEmail('test.user@example.co')).toBe(true); + expect(validateEmail('a@b.ab')).toBe(true); + }); + + test('returns true if the value is NOT an email', () => { + expect(validateEmail('test.example.com')).toBe(false); + expect(validateEmail('test-user@example')).toBe(false); + expect(validateEmail('@example.co')).toBe(false); + }); +}); + +describe('Capitalize the first letter of a string', () => { + test('it works', () => { + expect(capitalizeFirstLetter('test')).toEqual('Test'); + expect(capitalizeFirstLetter(' teSt ')).toEqual('TeSt'); + expect(capitalizeFirstLetter(' van gogh')).toEqual('Van gogh'); + expect(capitalizeFirstLetter('van Gogh')).toEqual('Van Gogh'); + }); + + test('it can handle an empty string', () => { + expect(capitalizeFirstLetter(' ')).toEqual(''); + }) +}); + +describe('Convert a string into an Array', () => { + test('returns the string as string[]', () => { + expect(stringToArray('foo bar baz')).toEqual(['foo', 'bar', 'baz']); + }); + test('returns the default', () => { + expect(stringToArray(null)).toEqual([]); + }); + test('allows us to define the delimiter', () => { + expect(stringToArray('foo, bar , baz', ',')).toEqual(['foo', 'bar', 'baz']); + }); + test('allows us to define the default response', () => { + expect(stringToArray(null, ',', ['test'])).toEqual(['test']); + }); +}); + +describe('Verify critical env variables', () => { + test('does not log an error if the specified variable exist', () => { + const logSpy = jest.spyOn(global.console, 'log').mockImplementation(() => { }); + verifyCriticalEnvVariable('NODE_ENV'); + expect(logSpy).not.toHaveBeenCalled(); + logSpy.mockRestore(); + }); + test('logs an error if the specified variable does not exist', () => { + const logSpy = jest.spyOn(global.console, 'log').mockImplementation(() => { }); + verifyCriticalEnvVariable('TEST_SECRET'); + expect(logSpy).toHaveBeenCalled(); + logSpy.mockRestore(); + }); +}); diff --git a/src/utils/graphQLErrors.ts b/src/utils/graphQLErrors.ts new file mode 100644 index 0000000..69c48da --- /dev/null +++ b/src/utils/graphQLErrors.ts @@ -0,0 +1,23 @@ +import { GraphQLError } from 'graphql'; + +export const AUTHENTICATION_ERROR_CODE: string = 'UNAUTHENTICATED'; +export const FORBIDDEN_ERROR_CODE: string = 'FORBIDDEN'; + +export const DEFAULT_AUNAUTHORIZED_MESSAGE: string = 'Unauthorized'; +export const DEFAULT_FORBIDDEN_MESSAGE: string = 'Forbidden'; + +export function AuthenticationError(errMessage = DEFAULT_AUNAUTHORIZED_MESSAGE) { + return new GraphQLError(errMessage, { + extensions: { + code: AUTHENTICATION_ERROR_CODE, + }, + }); +}; + +export function ForbiddenError(errMessage = DEFAULT_FORBIDDEN_MESSAGE) { + return new GraphQLError(errMessage, { + extensions: { + code: FORBIDDEN_ERROR_CODE, + }, + }); +}; diff --git a/src/utils/helpers.ts b/src/utils/helpers.ts new file mode 100644 index 0000000..1fa5496 --- /dev/null +++ b/src/utils/helpers.ts @@ -0,0 +1,33 @@ +// Convert a string into an Array (return the default or an empty array if it is null or undefined) +export function stringToArray(array: any, delimiter: string = ' ', defaultResponse: string[] = []): string[] { + if (typeof array === 'string') { + return array.split(delimiter).map((item) => item.trim()); + } + return array || defaultResponse; +} + +// Capitalize the first letter of the string. +export function capitalizeFirstLetter(str: string): string { + if (str) { + const val = str.trim(); + + if (val.length > 0) { + return val.charAt(0).toUpperCase() + val.slice(1); + } + return val; + } + return ''; +} + +// Email address validation +export function validateEmail(email: string): boolean { + const emailRegex = /^[^\s@]+@[^\s@]+\.[^\s@]+$/; + return emailRegex.test(email); +} + +// Helper that will log and error and terminate the Node process if a critical env variable is missing. +export function verifyCriticalEnvVariable(variable: string): void { + if (process.env[variable] === undefined) { + console.log(Error(`FATAL ERROR: No ${variable} defined in the environment!`)); + } +} diff --git a/tsconfig.json b/tsconfig.json index 0c9d0a4..94edbf5 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -1,16 +1,12 @@ { "compilerOptions": { - "rootDirs": ["src"], + "rootDir": "src", "outDir": "dist", - "lib": ["es2020"], "target": "es2020", - "module": "NodeNext", - "moduleResolution": "NodeNext", + "moduleResolution": "node", "esModuleInterop": true, - "types": ["node"], - - "strict": true, - "noImplicitAny": true, - "strictNullChecks": true, - } -} \ No newline at end of file + "module": "commonjs" + }, + "include": ["src", "src/__tests__"], + "exclude": ["node_modules"], +}