From ce0ec3e36820b7859416fe6cf65c78296cfc0847 Mon Sep 17 00:00:00 2001 From: Hicham Date: Tue, 25 Mar 2025 17:17:07 +0100 Subject: [PATCH 1/4] docs: enrich repo files --- CONTRIBUTING.md | 30 ++++++++++ README.md | 129 ++++++++++++++++++++++++++++++------------- public/logo_C360.png | Bin 0 -> 30153 bytes 3 files changed, 120 insertions(+), 39 deletions(-) create mode 100644 CONTRIBUTING.md create mode 100644 public/logo_C360.png diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md new file mode 100644 index 000000000..6efe9205b --- /dev/null +++ b/CONTRIBUTING.md @@ -0,0 +1,30 @@ +## Contributing to Cohort360 + +As an open source project, **Cohort360** welcomes contributions of many forms: + * Creating an issue for bug report + * Readme improvements + * New feature you would like **Cohort360** to have + +To help make your contribution to this project successful, we do have a few guidelines in place. + +Each PR, no matter how small, should have a GitHub **issue** associated with it. + +Here's a quick checklist for a **good PR**: + +1. A GitHub Issue with a good description associated with the PR +2. One feature/change per PR +3. We use [conventional commits](https://www.conventionalcommits.org/en/v1.0.0/#summary) for more readability. This helps generate a well + organized changelog file +4. One commit per PR. If necessary, squash commits before pushing you branch +5. Rebased your branch on main (`git rebase`, not `git pull`) +6. Add a good descriptive commit message, with link to issue. + For example: + > feat(cohort): add amazing feature #issue-number +7. No changes to code not directly related to your PR/issue +8. Add tests to cover new code +9. Run tests locally before pushing changes + + +Once you have submitted your PR please monitor it for comments/feedback. + +We appreciate your help to make **Cohort360** an even better open source project! \ No newline at end of file diff --git a/README.md b/README.md index a71cf72e4..185d8fd1f 100644 --- a/README.md +++ b/README.md @@ -1,68 +1,119 @@ -
- Cohort360 logo -

A web application to find patients, build cohorts and visualize data.

-
+
+ Cohort360 logo +

Lookup patients, build cohorts and visualize data.

-# Cohort360 +
[![Actions Status](https://github.com/aphp/Cohort360-FrontEnd/workflows/cohort360-main-pipeline/badge.svg)](https://github.com/aphp/Cohort360-FrontEnd/actions) [![Quality Gate](https://sonarcloud.io/api/project_badges/measure?project=aphp_Cohort360&metric=alert_status)](https://sonarcloud.io/dashboard?id=aphp_Cohort360) +
+ +Report a bug +Β· +What's new ? +
+--- + + +
+ Table of Contents +
    +
  1. + Overview + +
    2. +
  2. + Project Setup + +
    3. +
  3. Partners
    4. +
  4. Contributing
    5. +
  5. License
    6. +
  6. Contact
    7. +
+
+ +## Overview + +**Cohort360** is a project that aims to provide health professionals with a set of tools to explore patients data. + +### πŸ”‘ Features + * Look patients up using a set of criteria + * Run search queries on medical texts + * Group patients sharing some criteria by creating cohorts + * Get insights on cohorts at frst glance + * Visualize patient data + * Export patient data for extensive analysis + +
+ ⬆️ back to top +
-## Architecture +### πŸ› οΈ Built With -- [ ] Add Architecture schema +* React +* ... -Cohort360 consists of a React front-end and a Django back-end (REST API). -This repository hosts the front-end, while the back-end will be available soon. +## πŸš€ Project setup -Both the front-end and the back-end depend on a third, possibly custom, party: an endpoint to query medical data and to create cohorts. -This third endpoint can be a FHIR API for example. This is the case for the first creators of Cohort360. +### 1. πŸ’  Requirements -## Installation +To run Cohort360 locally, you'll need the following applications running: +πŸ“Œ [Cohort360-backend](https://github.com/aphp/Cohort360-Back-end/blob/enrich_repo_files/README.md) +πŸ“Œ A FHIR API to retrieve medical data -### Requirements: +### 2. πŸ“₯ Get the code -* A running back-end server -* A running third party endpoint (FHIR API for example) -* An authentication server -* Node.js (16 or higher) installed + ```sh + git clone https://github.com/aphp/Cohort360-FrontEnd.git + ``` -### Running the front-end +### 3. πŸ”§ Configuration -1. First copy the `.env.example` file to `.env` and edit this file to match your configuration. -2. Run `npm install` -3. Run `npm audit fix` -4. Run `npm run build` +> precise what configuration is needed: env vars, extra files to create to hold special configurations -This will generate files in the `build` directory that can be exposed via a web server like Nginx, or a node server. +### 4. ▢️ Run the app -An example configuration with Nginx can be found [here](.templates/nginx.conf) +Start development server -## CI +```shell +npm start +``` -A [gitlab-ci.yml](.templates/.gitlab-ci.yml) is available in the `.templates` folder, alongside -a [nginx configuration](.templates/nginx.conf) example (useful for deployment). +All set up πŸŽ‰ + +Check the application running on [http://localhost:3000](http://localhost:3000) + +
+ ⬆️ back to top +
-## Deployment +## 🏒 Partners -A docker image is available to build via the [Dockerfile](Dockerfile). You only need to update the location of your nginx conf. + * AP-HP Clinical Data Warehouse + * Arkhn : [arkhn.org](https://arkhn.org/) + * Akimed : [www.akimed.io](https://www.akimed.io/) -## Start Contributing -A contributing guide will be published soon. +## 🀝 Contributing -## Partners +See [CONTRIBUTING.md](CONTRIBUTING.md) for detailed process about contributing to this repository. -* AP-HP Clinical Data Warehouse -* Arkhn : [arkhn.org](https://arkhn.org/) -* Akimed : [www.akimed.io](https://www.akimed.io/) +## πŸ“œ License -## Contributors +**Cohort360** is licensed under the Apache License - see the [LICENSE](LICENSE) file for details. -Coming soon... +## πŸ’¬ Contact -## License -Cohort360 is licensed under Apache License 2. +If you find this project useful, please consider starring the repository and report any encountered bugs or issues. +Write to us at: **open-source@cohort360.org** \ No newline at end of file diff --git a/public/logo_C360.png b/public/logo_C360.png new file 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ztVj3`SdPfP!q58JD~3-6Do{aKP7&Vqqacv06*NKfm1&ITNnb_xA@Y^5&VU?K!hT>Y zT4=#$U{ArU{`nQdr2-YW+=P{s(i-S^nd|Wh)Z(G5uz0m zfe?Zgh9gSTCJRAwbw8qXC7c3|f*e9f6*!YOXQ21wl$0_AXizb Date: Wed, 26 Mar 2025 17:26:59 +0100 Subject: [PATCH 2/4] docs: update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 185d8fd1f..107a8ed7a 100644 --- a/README.md +++ b/README.md @@ -1,6 +1,6 @@
Cohort360 logo -

Lookup patients, build cohorts and visualize data.

+

Explore patient data πŸ”, build cohorts πŸ‘₯ and export data πŸ“₯πŸ“Š Works with FHIR πŸ”₯


@@ -116,4 +116,4 @@ See [CONTRIBUTING.md](CONTRIBUTING.md) for detailed process about contributing t ## πŸ’¬ Contact If you find this project useful, please consider starring the repository and report any encountered bugs or issues. -Write to us at: **open-source@cohort360.org** \ No newline at end of file +Write to us at: **open-source@cohort360.org** From ab9535ab761fc90b26a3025406f36a17642568a7 Mon Sep 17 00:00:00 2001 From: Julien Dubiel Date: Wed, 26 Mar 2025 17:53:48 +0100 Subject: [PATCH 3/4] docs: update README.md --- README.md | 39 +++++++++++++++++---------------------- 1 file changed, 17 insertions(+), 22 deletions(-) diff --git a/README.md b/README.md index 107a8ed7a..9c74f91c3 100644 --- a/README.md +++ b/README.md @@ -24,6 +24,7 @@ Overview @@ -35,7 +36,6 @@
  • Run the app
    • -
  • Partners
  • Contributing
  • License
  • Contact
    • @@ -44,19 +44,20 @@ ## Overview -**Cohort360** is a project that aims to provide health professionals with a set of tools to explore patients data. - ### πŸ”‘ Features - * Look patients up using a set of criteria - * Run search queries on medical texts - * Group patients sharing some criteria by creating cohorts - * Get insights on cohorts at frst glance - * Visualize patient data - * Export patient data for extensive analysis -
    - ⬆️ back to top -
    +* Explore, visualize, and search patient data +* Run advanced search queries on textual documents +* Create patient cohorts using a dedicated, user-friendly query builder +* Build queries with data criteria, complexity, and temporal constraints +* Get insights into cohorts at a glance +* Export cohort data for in-depth analysis + +### Based on FHIR + +Cohort360 accesses health data through a FHIR server. + +FHIR is the world’s most widely used standard for exposing health data via APIs. ### πŸ› οΈ Built With @@ -74,13 +75,13 @@ To run Cohort360 locally, you'll need the following applications running: ### 2. πŸ“₯ Get the code - ```sh - git clone https://github.com/aphp/Cohort360-FrontEnd.git - ``` +```sh +git clone https://github.com/aphp/Cohort360-FrontEnd.git +``` ### 3. πŸ”§ Configuration -> precise what configuration is needed: env vars, extra files to create to hold special configurations +> To do : specify what configuration is needed: env vars, extra files to create to hold special configurations ### 4. ▢️ Run the app @@ -98,12 +99,6 @@ Check the application running on [http://localhost:3000](http://localhost:3000) ⬆️ back to top
    -## 🏒 Partners - - * AP-HP Clinical Data Warehouse - * Arkhn : [arkhn.org](https://arkhn.org/) - * Akimed : [www.akimed.io](https://www.akimed.io/) - ## 🀝 Contributing From e2e9c6c7822398516680f043414b9f1c0544cc9b Mon Sep 17 00:00:00 2001 From: Julien Dubiel Date: Wed, 26 Mar 2025 18:03:16 +0100 Subject: [PATCH 4/4] docs: update README.md --- README.md | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/README.md b/README.md index 9c74f91c3..90c1eb2ba 100644 --- a/README.md +++ b/README.md @@ -53,11 +53,11 @@ * Get insights into cohorts at a glance * Export cohort data for in-depth analysis -### Based on FHIR +### πŸ”₯ Based on FHIR Cohort360 accesses health data through a FHIR server. -FHIR is the world’s most widely used standard for exposing health data via APIs. +[FHIR](https://www.hl7.org/fhir/) is the world’s most widely used standard for exposing health data via APIs. ### πŸ› οΈ Built With