-
Notifications
You must be signed in to change notification settings - Fork 0
Commit
This commit does not belong to any branch on this repository, and may belong to a fork outside of the repository.
- Loading branch information
1 parent
e78aab4
commit ff1245c
Showing
2 changed files
with
107 additions
and
3 deletions.
There are no files selected for viewing
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
|
@@ -24,11 +24,20 @@ Team Members: [Yao Xiao](mailto:[email protected]), [Bowen Xu](mailto:bowenx | |
| - [Data Pipeline](#data-pipeline) | ||
| - [Model Training & Optimization](#model-training--optimization) | ||
| - [Frontend Interface](#frontend-interface) | ||
| - [Backend APIs](#backend-apis) | ||
| - [Backend Service](#backend-service) | ||
| - [Deployment](#deployment) | ||
| - [Future Steps](#future-steps) | ||
| - [References](#references) | ||
|
|
||
| Subdirectory READMEs: | ||
|
|
||
| - [/app](./app/README.md) | ||
| - [/deploy](./deploy/README.md) | ||
| - [/src/data-pipeline](./src/data-pipeline/README.md) | ||
| - [/src/embedding-model](./src/embedding-model/README.md) | ||
| - [/src/construct-qa](./src/construct-qa/README.md) | ||
| - [/src/finetune-model](./src/finetune-model/README.md) | ||
|
|
||
| ## Introduction | ||
|
|
||
| Clinical trial data includes structured information collected during research studies designed to evaluate the safety, efficacy, and outcomes of medical interventions, treatments, or devices on human participants. In recent years, this type of data has expanded rapidly, especially in large repositories like [ClinicalTrials.gov](https://clinicaltrials.gov/), creating immense opportunities to advance healthcare research and improve patient outcomes. However, the large volume and complexity of such data create challenges for researchers, clinicians, and patients in finding and understanding trials relevant to their specific needs. | ||
|
|
@@ -126,7 +135,7 @@ After selecting a specific trial from the retrieval results, users can proceed t | |
|
|
||
| There are many more UI/UX designs to enhance user experience that we will not cover here. Some of them include: responsive design for mobile devices, copy button for queries and responses, automatic scroll-into-view for sidebars and chat panels, GitHub-flavored markdown support, etc. | ||
|
|
||
| ## Backend APIs | ||
| ## Backend Service | ||
|
|
||
| See [/app](./app/README.md) for details about the application. | ||
|
|
||
|
|
||
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,8 +1,103 @@ | ||
| # App | ||
|
|
||
| ## Backend APIs | ||
| Make sure you are under the current directory and that you have `veritas-trial-service.json` under the `/secrets/` directory. To build and run our application locally, simply run: | ||
|
|
||
| ```bash | ||
| make | ||
| ``` | ||
|
|
||
| This command composes the backend and the frontend. This also requires proper access to the remotely deployed ChromaDB service. The frontend interface will be available at http://localhost:8080, and the backend service will be available at http://localhost:8001. | ||
|
|
||
| Alternatively, for development purposes, you may start the frontend and the backend separetely, First install necessarily dependencies. Make sure you have `node` and `pnpm` ready for the frontend, and `pipenv` ready for the backend. Run: | ||
|
|
||
| ```bash | ||
| make devinstall | ||
| ``` | ||
|
|
||
| Then in two different terminals, run the following two commands to start the frontend and the backend separately: | ||
|
|
||
| ```bash | ||
| make devfrontend | ||
| make devbackend | ||
| ``` | ||
|
|
||
| The `make devfrontend` command relies on the Vite server that supports live reload which makes frontend development much easier. The `make devbackend` builds the backend Docker container and starts its service. | ||
|
|
||
| ## Frontend Interface | ||
|
|
||
| > [!NOTE] | ||
| > Our frontend interface is temporarily deployed at: https://34.57.211.196.sslip.io/. The deployment will be removed after the end of the semester. | ||
| Our frontend is build with React and TypeScript with the Vite framework. As follows is the structure of our frontend: | ||
|
|
||
| ``` | ||
| ├── public/ > Public assets | ||
| ├── src | ||
| │ ├── components/ > React functional components | ||
| │ ├── api.ts > Wrappers for backend API calls | ||
| │ ├── App.tsx > Main application | ||
| │ ├── consts.ts > Constants | ||
| │ ├── global.css > Global style sheet | ||
| │ ├── main.tsx > Application entrypoint | ||
| │ ├── types.ts > Type definitions | ||
| │ ├── utils.ts > Utility functions | ||
| │ └── vite-env.d.ts | ||
| ├── .dockerignore | ||
| ├── .prettierignore | ||
| ├── Dockerfile | ||
| ├── eslint.config.js | ||
| ├── index.html | ||
| ├── package.json | ||
| ├── pnpm-lock.yaml | ||
| ├── tsconfig.app.json | ||
| ├── tsconfig.json | ||
| ├── tsconfig.node.json | ||
| └── vite.config.ts | ||
| ``` | ||
|
|
||
| The retrieval panel: | ||
|
|
||
|  | ||
|
|
||
| The chat session: | ||
|
|
||
|  | ||
|
|
||
| ## Backend Service | ||
|
|
||
| > [!NOTE] | ||
| > Our backend service is temporarily deployed at: https://34.57.211.196.sslip.io/api/. The deployment will be removed after the end of the semester. | ||
| Our backend is built with FastAPI in Python. As follows are the API specifications: | ||
|
|
||
|  | ||
|  | ||
|  | ||
|  | ||
|
|
||
| ## Continuous Integration Setup | ||
|
|
||
| We have continuous integration triggered per pull request targeting the main branch and per merged commit to the main branch. This includes: | ||
|
|
||
| - [Building](https://github.com/VeritasTrial/ac215_VeritasTrial/actions/workflows/build.yaml): Test that the images for the application can be successfully built. | ||
| - [Formatting and Linting](https://github.com/VeritasTrial/ac215_VeritasTrial/actions/workflows/lint.yaml): Check formatting and linting of the codebase to ensure code quality. This applies to both the frontend and the backend. The backend uses [black](https://black.readthedocs.io/en/stable/) for formatting, [ruff](https://docs.astral.sh/ruff/) for linting, and [mypy](https://mypy.readthedocs.io/en/stable/) for static type checking. The frontend uses [prettier](https://prettier.io/) for formatting, and [eslint](https://eslint.org/) and [typescript-eslint](https://typescript-eslint.io/) for linting and type checking. | ||
| - [Testing](https://github.com/VeritasTrial/ac215_VeritasTrial/actions/workflows/test.yaml): Test the codebase (backend only) and generate coverage report. | ||
|
|
||
| | CI success on merging to main | CI success on PR targetting main | | ||
| |:-----------------------------:|:--------------------------------:| | ||
| |  |  | | ||
|
|
||
| We have also configured the dependabot to automatically update the dependencies of our codebase and perform security checks. | ||
|
|
||
| ## Automated Test Implementation | ||
|
|
||
| To run our backend test suite, you need to create a local development environment. Run the following: | ||
|
|
||
| ```bash | ||
| make devtest | ||
| make devtestcov # Also generate coverage report | ||
| ``` | ||
|
|
||
| We use [pytest](https://docs.pytest.org/en/stable/) for testing and [coverage.py](https://coverage.readthedocs.io/en/7.6.7/) for coverage report. | ||
|
|
||
|  |