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CDCgov / trusted-intermediary

Bringing together healthcare providers by reducing the connection burden.
Apache License 2.0
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CDC Trusted Intermediary

This document provides instructions for setting up the environment, running the application, and performing various tasks such as compiling, testing, and contributing to the project.

Requirements

Any distribution of the Java 17 JDK.

Using and Running

To run the application directly, execute...

./gradlew clean run

This runs the web API on port 8080. The app reads/writes data to a local file (unless you have a DB configured)

You can view the API documentation at /openapi.

Generating and using a token

  1. Run brew install mike-engel/jwt-cli/jwt-cli
  2. Replace PATH_TO_FILE_ON_YOUR_MACHINE in this command with the actual path, then run it: jwt encode --exp='+5min' --jti $(uuidgen) --alg RS256 --no-iat -S @/PATH_TO_FILE_ON_YOUR_MACHINE/trusted-intermediary/mock_credentials/organization-trusted-intermediary-private-key-local.pem
  3. Copy token from terminal and paste into your postman body with the key client_assertion
  4. Add a key to the body with the key scope and value of trusted-intermediary
  5. Body type should be x-wwww-form-urlencoded
  6. You should be able to run the post call against the v1/auth/token endpoint to receive a bearer token to be used in this step

Development

Additional Requirements

The additional requirements needed to contribute towards development are...

Generating .env File

To set up the necessary environment variables, run the generate_env.sh script. This script creates a .env file in the resource folder with the required configuration

  1. Navigate to the project directory.

  2. Run the generate_env.sh script:

    ./generate_env.sh

  3. If you run TI using Docker rather than Gradle, update the DB and port values in the .env file (the alternate values are in comments)

Using a local database

Use docker-compose.postgres.yml to run your local DB. In IntelliJ, you can click the play arrow to start it

docker-postgres.png

Apply all outstanding migrations:

liquibase update --changelog-file ./etor/databaseMigrations/root.yml --url jdbc:postgresql://localhost:5433/intermediary --username intermediary --password 'changeIT!' --label-filter '!azure'

If running in Windows, use double quotes instead:

liquibase update --changelog-file ./etor/databaseMigrations/root.yml --url jdbc:postgresql://localhost:5433/intermediary --username intermediary --password "changeIT!" --label-filter "!azure"

Compiling

To compile the application, execute...

./gradlew shadowJar

Once compiled, the built artifact is /app/build/libs/app-all.jar.

Testing

Unit Tests

To run the unit tests, execute...

./gradlew clean allUnitTests

End-to-end Tests

End-to-end tests are designed to interact with the API and verify that its overall flow operates correctly. They require that the API to be running already. The end-to-end tests use whatever database configuration is already in place - if you're using the local filesystem, so will the e2e tests (this is how they work on github), and if you're using a DB, so will the tests

To run them, execute...

./gradlew e2e:clean e2e:test

The previous command requires the API to be running already. To help streamline the execution of this flow, a helper Bash script can be executed...

./e2e-execute.sh

This will start the API, wait for it to respond, run the end-to-end tests against that running API, and then stop the API.

These tests are located under the e2e Gradle sub-project directory. Like any Gradle project, there are the main and test directories. The test directory contains the tests. The main directory contains our custom framework that helps us interact with the API.

Automated ReportStream Integration/End-to-End Test

These tests cover the integration between ReportStream and TI. They run automatically every weekday via Github actions. See the rs-e2e readme for more details.

Load Testing

Load tests are completed with Locust.io. Run the load tests by running...

./gradle-load-execute.sh

./docker-load-execute.sh

Currently, we are migrating to using Azure. Local load testing is using gradle, however a docker load test is available to mimic the Azure environment settings until the azure migration is complete.

This will run the API for you, so no need to run it manually.

Note:

If you are already running the API, stop it before running the load tests or the cleanup steps won't work.

The load tests will also spin up (and clean up) a local test DB on port 5434 that should not interfere with the local dev DB.

The locustfile.py that specifies the load test is located at ./operations/locustfile.py.

If you want to run the load test in an interactive mode, run...

locust -f ./operations/locustfile.py

The terminal will start a local web interface, and you can enter the swarm parameters for the test and the local url where the app is running (usually http://localhost:8080). You can also set time limits for the tests under 'Advanced Settings'.

Debugging

Attached JVM Config for IntelliJ

The project comes with an attached remote jvm configuration for debuging the container. If you check your remote JVM settings, under Run/Edit Configurations, you will see the Debug TI. If you want to add a new remote JVM configuration, follow the steps below, under "Docker Container Debugging Using Java Debug Wire Protocal"

Docker Container Debugging Using Java Debug Wire Protocal (JDWP)

Go into the Dockerfile file and change CMD ["java", "-jar", "app.jar"] to CMD ["java", "-agentlib:jdwp=transport=dt_socket,address=*:6006,server=y,suspend=n", "-jar", "app.jar"]

Steps

  1. In Intellij, click on Run and select Edit Configurations img.png
  2. Create a new Remote JVM Debug img_1.png
  3. Set up the configuration for the remote JVM debug to look like this. img_3.png
  4. In your code, set your breakpoint, and then start your docker container with docker-compose up --build
  5. Once your docker container is running, in order to attach, select Run again.
  6. Select Debug (not Attach to Process) img_3.png
  7. Select your Docker Debug that you set up in step 3 img_4.png
  8. A console window will pop up that will show you that it is connected to Docker, and at that point, you can interact with your container and then step through the code at your breakpoints. img_5.png

Deploying

Environments

We have a number of environments that are split between CDC and non-CDC Azure Entra domains and subscriptions.

Internal

The Internal environment is designed to be the Wild West, meaning anyone can push changes without restrictions. It allows for testing various configurations without the requirement that only stable builds be pushed. Use the Internal environment if you want to test something in a deployed environment in a non-CDC Azure Entra domain and subscription. See below:

Before starting...

Remember to ping the Engineering Channel to make sure someone is not already using the enviroment.

To deploy to the Internal environment...

  1. Check with the team that no one is already using it.

  2. Find the internal branch and delete it inGitHub.

  3. Delete your local internal branch if needed.

    git branch -D internal

  4. From the branch you want to test, create a new internal branch.

    git checkout -b internal

  5. Push the branch to GitHub.

    git push --set-upstream origin internal

Then the deploy will run. Remember that you now have the internal branch checked out locally. If you make subsequent code changes, you will make them on the internal branch instead of your original branch.

Dev

The Dev environment is similar to the Internal environment but deploys to a CDC Azure Entra domain and subscription. It is also meant to be the Wild West. Dev deploys similarly to the Internal environment, but you interact with the dev branch.

Staging

The Staging environment is production-like and meant to be stable. It deploys to a CDC Azure Entra domain and subscription. Deployments occur when a commit is made to the main branch. main is a protected branch and requires PR reviews before merge.

Prod

The Production environment is the real deal. It deploys to a CDC Azure Entra domain and subscription. Deployments occur when a release is published.

Initial Azure and GitHub Configuration

There is minimal set-up to do to get Terraform setup before you can run the Terraform commands in a new Azure environment in the Flexion Entra domain. For example, the internal environment. This does not apply to the CDC Entra domains and subscriptions.

  1. Create a resource group.
  2. Create a storage account inside the aforementioned resource group.
  3. Within the new storage account, create a Container.
  4. Within Azure Entra...
    1. Create an App Registration.
    2. Add federated credentials to the App Registration
      • repo:CDCgov/trusted-intermediary:ref:refs/heads/main (for terraform apply).
      • repo:CDCgov/trusted-intermediary:environment:staging (for staging webapp deploy).
      • And presumably other repo paths needed in the future for other environments and branches.
    3. Within your Subscription, assign the Contributor role to the previously created App Registration.
  5. Add GitHub Action secrets to your GitHub repository.
    • A secret with the tenant ID from Azure Entra directory.
    • A secret with the ID from the subscription that everything should be deployed into.
    • A secret with the ID of the App Registration created previously.
  6. Create a copy of one of the environments under the operations folder.
    1. Name the copy off of the name of the new environment. Ex: internal
    2. Edit the main.tf file with the names of the resources previously created: resource_group_name, storage_account_name, container_name. Also update the environment to match the new folder name.
  7. Create a GitHub Action workflow so that automatic deploys can occur. You can take inspiration from our Internal environment deployment. Make sure you set the AZURE_CLIENT_ID, AZURE_TENANT_ID, and AZURE_SUBSCRIPTION_ID based on the secrets created previously.

Interacting with Deployed Environments

The PR and Internal environment is available on the public Internet and able to be interacted with directly.

The Dev, Staging, and Prod environment are deployed inside a Vnet and require special steps to interact with these.

Application

The application basically has a firewall in place. You need to add (and remove when you're done) your IP address to the firewall allow list.

  1. Log into CyberArk and then into Azure with your -SU account.
  2. Navigate to the environment's app service.
  3. Click on Networking in the left pane.
  4. Click on the "Enabled with access restrictions" link under "Inbound traffic configuration".
  5. Add a new rule to allow your public IP address. Provide an appropriate name with your name. The priority will need a lower number than the existing denies. It will look like your IP address with a /32 appended. E.g. 192.168.0.1/32.
  6. Click "Save".

You will now be able to interact with that environment's application.

Note:

Don't forget to remove your rule and save when you are done.

Database

You will need to connect to the VPN for the given environment first, and then you can interact with the database. Notion contains the instructions for connecting to the VPN. After connecting, you can follow the database documentation to gain access.

Pre-Commit Hooks

We use pre-commit to run some hooks on every commit. These hooks do linting to ensure things are in a good spot before a commit is made. Please install pre-commit and then install the hooks.

pre-commit install

Contributing

Anyone is encouraged to contribute to the repository by forking and submitting a pull request. (If you are new to GitHub, you might start with a basic tutorial.) By contributing to this project, you grant a world-wide, royalty-free, perpetual, irrevocable, non-exclusive, transferable license to all users under the terms of the Apache Software License v2 or later.

Please read CONTRIBUTING.md for additional details.

All comments, messages, pull requests, and other submissions received through CDC including this GitHub page may be subject to applicable federal law, including but not limited to the Federal Records Act, and may be archived. Learn more at http://www.cdc.gov/other/privacy.html.

Database

For database documentation: /docs/database.md

Setup with ReportStream

CDC-TI Setup

  1. Checkout main branch for CDCgov/trusted-intermediary
  2. Run ./generate_env.sh to generate .env file with required environment variables
  3. Run TI with ./gradlew clean run

ReportStream Setup

For Apple Silicon you will want to enable the Docker option for Use Rosetta for x86/amd64 emulation on Apple Silicon. After enabling this option it is recommended that you delete all docker images and containers and rebuild them with this option enabled.

  1. Checkout master branch for CDCgov/prime-reportstream
  2. Build RS (for more information please refer to the ReportStream docs):
    • If building for the first time, run: ./cleanslate in prime-reportstream/prime-router
    • Otherwise run: ./gradlew clean package in prime-reportstream root folder
    • If attempting to access the metadata endpoint in RS add the variable ETOR_TI_baseurl="http://host.docker.internal:8080" to prime-router/.vault/env/.env.local file before building the container
  3. Run RS with docker compose up -d. You may also use ./gradlew quickRun
  4. Run the RS setup script in this repository: /scripts/setup/setup-reportstream.sh
    • Before running the script, make sure to follow the instructions in /scripts/README.md
    • You can verify the script created vault secrets successfully by going to http://localhost:8200/ in your browser, use the token in prime-router/.vault/env/.env.local to authenticate, and then go to Secrets engines > secret/ to check the available secrets

Submit request to ReportStream

Locally
Orders

To test sending from a simulated hospital:

curl --header 'Content-Type: application/hl7-v2' --header 'Client: flexion.simulated-hospital' --header 'Authorization: Bearer dummy_token' --data-binary '@/path/to/orm_message.hl7' 'http://localhost:7071/api/waters'

To test sending from TI:

curl --header 'Content-Type: application/fhir+ndjson' --header 'Client: flexion.etor-service-sender' --header 'Authorization: Bearer dummy_token' --data-binary '@/path/to/oml_message.fhir' 'http://localhost:7071/api/waters'
Results

To test sending from a simulated lab:

curl --header 'Content-Type: application/hl7-v2' --header 'Client: flexion.simulated-lab' --header 'Authorization: Bearer dummy_token' --data-binary '@/path/to/oru_message.hl7' 'http://localhost:7071/api/waters'

To test sending from TI:

curl --header 'Content-Type: application/fhir+ndjson' --header 'Client: flexion.etor-service-sender' --header 'Authorization: Bearer dummy_token' --data-binary '@/path/to/oru_message.fhir' 'http://localhost:7071/api/waters'

After one or two minutes, check that hl7 files have been dropped to prime-reportstream/prime-router/build/sftp folder

Staging

In order to submit a request, you'll need to authenticate with ReportStream using JWT auth:

  1. Create a JWT for the sender (e.g. flexion.simulated-hospital) using the sender's private key, which should be stored in Keybase. You may use this CLI tool to create the JWT:

    jwt encode --exp='+5min' --jti $(uuidgen) --alg RS256 -k <sender> -i <sender> -s <sender> -a staging.prime.cdc.gov --no-iat -S @/path/to/sender_private.pem

  2. Use the generated JWT to authenticate with ReportStream and get the token, which will be in the access_token response

    curl --header 'Content-Type: application/x-www-form-urlencoded' --data 'scope=flexion.*.report' --data 'client_assertion=<jwt>' --data 'client_assertion_type=urn:ietf:params:oauth:client-assertion-type:jwt-bearer' --data 'grant_type=client_credentials' 'http://localhost:7071/api/token'

  3. Submit an Order or Result using the returned token in the 'Authorization: Bearer <token>' header

DORA Metrics

We use DORA Metrics to measure our DevOps performance. We currently are tracking Deployment Frequency, Change Fail Rate and Mean Time to Recovery.

The metrics are produced weekly using a Github Action and written into CSV files which are available for download in the workflow job's artifacts.

Related Documents

CDC Notices

Public Domain Standard Notice

This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.

License Standard Notice

The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later.

This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version.

This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details.

You should have received a copy of the Apache Software License along with this program. If not, see http://www.apache.org/licenses/LICENSE-2.0.html

The source code forked from other open source projects will inherit its license.

Privacy Standard Notice

This repository contains only non-sensitive, publicly available data and information. All material and community participation is covered by the Disclaimer and Code of Conduct. For more information about CDC's privacy policy, please visit http://www.cdc.gov/other/privacy.html.

Records Management Standard Notice

This repository is not a source of government records, but is a copy to increase collaboration and collaborative potential. All government records will be published through the CDC website.

Additional Standard Notices

Please refer to CDC's Template Repository for more information about contributing to this repository, public domain notices and disclaimers, and code of conduct.