[DUOS-2041][risk=no] Documentation Updates (#1775)

* updating docs for running under compose and cypress

.gitignore

@@ -39,5 +39,7 @@ public/config.json
 
 
 # Server
+ca-bundle.crt
 server.crt
-server.key
+server.key
+site.conf

DEVNOTES.md

@@ -0,0 +1,111 @@
+# Local Development
+
+1. We use [node@16](https://github.com/nvm-sh/nvm#installing-and-updating):
+
+```
+curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.1/install.sh | bash
+nvm install 16
+```
+2. Install deps:
+
+```
+npm install
+```
+
+3. Install configs for an environment. This example is for the perf environment, but you can use values from any environment by looking at the deployed configs in https://duos-k8s.dsde-{%ENV%}.broadinstitute.org/config.json where {%ENV%} is any of `dev`, `staging`, `perf`, `alpha`, or `prod` 
+Remember to set the `env` value appropriately. We use `local` for running via npm, but under docker, we use a real env like `dev` 
+```
+cp config/perf.json public/config.json
+```
+
+Ensure that your `/etc/hosts` file has an entry for `local.broadinstitute.org`
+```properties
+127.0.0.1	local.broadinstitute.org
+```
+
+Download cert files from vault (requires vault access - see [DUOS team members](https://github.com/orgs/DataBiosphere/teams/duos) for more specifics):
+```shell
+vault login -method=github token=$(cat ~/.github-token)
+vault read --format=json <vault path>/server.key | jq -r .data.value > server.key
+vault read --format=json <vault path>/server.crt | jq -r .data.value > server.crt
+vault read --format=json <vault path>/ca-bundle.crt | jq -r .data.chain > ca-bundle.crt
+```
+
+Create a `site.conf` file in the project root directory using https://github.com/broadinstitute/terra-helmfile/blob/master/charts/duos/templates/_site.conf.tpl as a model. 
+
+Create a local environment file, `.env.local`
+```properties
+HOST=local.broadinstitute.org
+HTTPS=true
+SSL_CRT_FILE=server.crt
+SSL_KEY_FILE=server.key
+```
+
+4. Start development server:
+
+```shell
+npm start
+```
+### Running under Docker
+
+Update your local `docker-compose.yaml` file to mount the preferred `config.json` file in app volumes.
+Remember to set the `env` value appropriately in `config.json`. We use `local` for running via npm, but under docker, we use a real env like `dev`
+
+```dockerfile
+    volumes:
+      - ./public/config.json:/usr/share/nginx/html/config.json
+``` 
+
+Build and run:
+
+```shell
+docker build . -t duos
+docker compose up -d
+```
+
+# Testing
+
+## Cypress Tests
+
+We use Cypress for all component and integration testing. Each suite
+of tests is run separately for all PRs via github actions. Local
+testing can be run headless or viewed interactively.
+
+Cypress integration tests run locally require a different `baseUrl` than those
+run in Github Actions. Modify your local `cypress.config.js` file so
+that the `e2e.baseUrl` looks like this:
+```shell
+    baseUrl: 'https://local.broadinstitute.org:3000/',
+```
+This is not necessary for component tests.
+
+### Headless
+To run cypress integration tests, first start up the app in one terminal
+and in another terminal window, spin up the tests headless:
+
+```shell
+npm start
+npm run cypress:run
+```
+
+To run cypress component tests headless:
+
+```shell
+npm run cypress:run:component
+```
+
+### Interactive
+To run cypress integration tests, first start up the app in one terminal
+and in another terminal window, spin up the tests for viewing:
+
+```shell
+npm start
+npm run cypress:open
+```
+
+To run cypress component tests in a browser:
+
+```shell
+npm run cypress:open:component
+```
+

README.md

@@ -18,35 +18,5 @@ The Data Use Oversight system ensures that researchers using genomics data honor
 
 ![What is DUOS](https://github.com/DataBiosphere/duos-ui/blob/develop/public/images/what_is_duos.svg)
 
-### Developers
-
-1. We use [node@16](https://github.com/nvm-sh/nvm#installing-and-updating):
-
-```
-curl -o- https://raw.githubusercontent.com/nvm-sh/nvm/v0.39.1/install.sh | bash
-nvm install 16
-```
-2. Install deps:
-
-```
-npm install
-```
-
-3. Install configs for an environment. This example is for the perf environment, but you can use values from any environment by looking at the deployed configs in https://duos-k8s.dsde-{%ENV%}.broadinstitute.org/config.json where {%ENV%} is any of `dev`, `staging`, `perf`, `alpha`, or `prod` 
-
-```
-cp config/perf.json public/config.json
-```
-4. Start development server:
-
-```
-npm start
-```
-### Running under Docker
-
-Update your local environment configuration file and mount that to `/usr/share/nginx/html/config.json`
-
-```
-docker build . -t duos
-docker run -v ${PWD}/path/to/config.json:/usr/share/nginx/html/config.json:ro -p 80:8080 duos:latest
-```
+### Local Development
+See [DEVNOTES.md](DEVNOTES.md) for instructions on setting up an environment for local development.

docker-compose.yaml

@@ -1,19 +1,52 @@
 # This is an example compose file that can be used for local development.
 # Modify the config file in `volumes` to point to the desired environment, default id dev.
-#
+# Ensure that the following configuration files have been created in the correct locations:
+#   * public/config.json
+#   * ca-bundle.crt
+#   * server.crt
+#   * server.key
+#   * site.conf
+# Ensure that /etc/hosts contains an entry for:
+# 	127.0.0.1	local.broadinstitute.org
 # Build:
 #   docker build . -t duos
 # Run:
-#   docker-compose up
+#   docker compose up -d
 # Test
-#   http://localhost:3000/
+#   https://local.broadinstitute.org/
 version: '3.8'
 services:
   app:
     image: duos:latest
     container_name: duos
     ports:
-      - 3000:8080
+      - 8080:8080
     volumes:
-      - ./config/perf.json:/usr/share/nginx/html/config.json
+      - ./public/config.json:/usr/share/nginx/html/config.json
     command: ["nginx", "-g", "daemon off;"]
+    restart: always
+
+  proxy:
+    image: broadinstitute/openidc-proxy:tcell_3_1_0
+    container_name: duos-proxy
+    hostname: local.broadinstitute.org
+    links:
+      - app:app
+    ports:
+      - 80:8080
+      - 443:443
+    volumes:
+      - ./server.crt:/etc/ssl/certs/server.crt:ro
+      - ./server.key:/etc/ssl/private/server.key:ro
+      - ./ca-bundle.crt:/etc/ssl/certs/ca-bundle.crt:ro
+      - ./site.conf:/etc/apache2/sites-available/site.conf:ro
+    environment:
+      AUTH_TYPE: AuthType None
+      LOG_LEVEL: warn
+      OIDC_CLAIM: Require all granted
+      PROXY_PATH: /
+      PROXY_URL: http://app:8080/
+      SERVER_NAME: local.broadinstitute.org
+      SERVER_NAME_INT: local.broadinstitute.org
+      ENABLE_TCELL: 'no'
+    restart: always