Merge pull request #59 from CDLUC3/development

Initial sync of development to main

Author: briri

.dockerignore

@@ -0,0 +1 @@
+node_modules/

.editorconfig

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+# 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

.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=

.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

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]

Dockerfile

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+# 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"]

Dockerfile.aws

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+# 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"]

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`

buildspec.yaml

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+# 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

codegen.ts

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+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;