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docs: enrich README.md (#1)
Co-authored-by: Hicham <[email protected]>
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‎.env

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# images
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## apps
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SJS_IMAGE=aphpid/cohort360-queryexecutor:latest
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QUERY_EXECUTOR_IMAGE=aphpid/cohort360-queryexecutor:latest
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BACK_IMAGE=aphpid/cohort360-backend:latest
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PORTAIL_IMAGE=aphpid/cohort360-administrationportal:latest
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FRONT_IMAGE=aphpid/cohort360-frontend:latest
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## 3rd party services
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FHIR_IMAGE=hapiproject/hapi:latest
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JWT_IMAGE=harbor.eds.aphp.fr/cohort360/jwt-server:mock
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KEYCLOAK_IMAGE=bitnami/keycloak:24.0.5
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REDIS_IMAGE=redis:7.2.5
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PSQL_CLIENT_IMAGE=jbergknoff/postgresql-client
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# network
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SJS_LOCAL_PORT=9804
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QUERY_EXECUTOR_LOCAL_PORT=9804
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BACK_LOCAL_PORT=8000
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PORTAIL_LOCAL_PORT=9807
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FRONT_LOCAL_PORT=9808
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FHIR_LOCAL_PORT=8081
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REDIS_LOCAL_PORT=9801
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PG_LOCAL_PORT=9802
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JWT_LOCAL_PORT=8883
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KEYCLOAK_LOCAL_PORT=9090
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# misc
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HEALTHCHECK_PERIOD=5s

‎.gitmodules

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[submodule "Cohort360-AdministrationPortal"]
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path = Cohort360-AdministrationPortal
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url = https://github.com/aphp/Cohort360-AdministrationPortal.git
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[submodule "Cohort360-Back-end"]
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path = Cohort360-Back-end
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url = git@github.com:aphp/Cohort360-Back-end.git
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path = Cohort360-Back-end
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url = https://github.com/aphp/Cohort360-Back-end.git
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[submodule "Cohort360-FrontEnd"]
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path = Cohort360-FrontEnd
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url = [email protected]:aphp/Cohort360-FrontEnd.git
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[submodule "Cohort360-AdministrationPortal"]
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path = Cohort360-AdministrationPortal
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url = [email protected]:aphp/Cohort360-AdministrationPortal.git
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url = https://github.com/aphp/Cohort360-FrontEnd.git
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[submodule "Cohort360-QueryExecutor"]
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path = Cohort360-QueryExecutor
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url = https://github.com/aphp/Cohort360-QueryExecutor.git
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url = https://github.com/aphp/Cohort360-QueryExecutor.git
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[submodule "fakedata/synthea"]
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path = fakedata/synthea
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url = https://github.com/synthetichealth/synthea.git
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path = fakedata/synthea
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url = https://github.com/synthetichealth/synthea.git

‎Cohort360-AdministrationPortal

Submodule Cohort360-AdministrationPortal updated 23 files

‎Cohort360-Back-end

Submodule Cohort360-Back-end updated 146 files

‎Cohort360-FrontEnd

Submodule Cohort360-FrontEnd updated 343 files

‎Cohort360-QueryExecutor

Submodule Cohort360-QueryExecutor updated 27 files

‎README.md

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## Quick start
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After cloning this respository:
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### Get the code
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Start by cloning this repository from a [stable release tag](https://github.com/aphp/Cohort360/releases):
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```
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git clone --depth 1 --branch <some-release-tag> https://github.com/aphp/Cohort360.git
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```
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Fetch the corresponding submodules repositories:
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```
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git submodule init
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git submodule update
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git submodule update --init --recursive --remote
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```
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With fake data generation
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### Spin it up
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Generate fake data with Synthea (for first time execution)
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```
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docker compose -f docker-compose.yaml -f docker-compose.fakedata.yaml up
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```
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Without fake data generation
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#### Track fake data generation
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Soon after you can go to [http://localhost:8080](http://localhost:8080) to check up the initialization progress
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> it may be very long if a lot of fake data patients are generated (default 200 records).
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Run without generating fake data (for later executions)
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```
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docker compose --env-file .env up
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```
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Soon after you can go to [http://localhost:8080](http://localhost:8080) to check up the initialization progress (it may be very long if a lot of fake data patients are generated (default 200)).
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Then you can go to the Cohort 360 application with the following urls :
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- main application : http://localhost:9808
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- admin portal : http://localhost:9807
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- keycloak authentication: http://172.28.0.20:8080
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### About fake data
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The default credentials are admin:admin
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The base instance contains no data you can use [Synthea](https://github.com/synthetichealth/synthea) to generate some fake data and upload them to the FHIR instance.
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After adding new organizations in FHIR, you **must manually** synchronize them in the backend of the application, for that:
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* Go to `http://localhost:8000/docs` default URL of the Django backend application
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* Login to acquire an access token using the endpoint `/auth/login/`
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* Make a request to the endpoint `PUT /fhir-perimeters/_sync/`
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## Fake data
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You should then have the patient data and organization available in the application.
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The base instance contains no data you can use [Synthea](https://github.com/synthetichealth/synthea) to generate some fake data and upload them to the FHIR instance.
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The current Docker Compose sets up an initialization Docker to populate the data it will proceed to generate data with **Synthea** (using a quick fixed fork) and synchronize the perimeters.
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After adding new Organizations in FHIR, you must manually synchronize them in the backend of the application, for that
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go to `http://localhost:8000/docs` (default url of the backend application), login (using the oidc secret found in the file `env/django.env` `OIDC_CLIENT_SECRET_1`) and then execute the query of the endpoint `PUT /fhir-perimeters/_sync/`. You should then have the patient data and organization available in the application.
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The current docker compose sets up an initialization docker to populate the data it will proceed to generate data with synthea (using a quick fixed fork) and synchronize the perimeters.
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## Give it a try
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Then you can visit different applications with the following URLs:
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- Main **Cohort360** app : http://localhost:9808
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- **Administration Portal** app : http://localhost:9807
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> (i) The default credentials are **`admin`**:**`admin`**
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‎conf/front.config.json

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},
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"system": {
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"codeDisplayJWT": "ArrowUp,ArrowDown,ArrowLeft,ArrowRight,a,z,e,r,t,y,Enter",
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"displayJwtLogin": true,
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"displayOidcLogin": false,
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"oidc": {
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"clientId": "cohort360",
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"issuer": "http://172.28.0.20:8080/realms/cohort/protocol/openid-connect/auth",
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"redirectUri": "http://localhost:9808",
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"responseType": "code",
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"scope": "openid",
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"state": "mlTPASu3bwdFmFUSK4G4ImecrsKW9pQ7SDdf7uB"
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"clientId": "",
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"issuer": "",
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"redirectUri": "",
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"responseType": "",
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"scope": "",
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"state": ""
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},
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"wsProtocol": "ws://"
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}

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