Merge pull request #70 from databio/dev

updated bedhost docs

docs/bedhost/build_image.md

@@ -0,0 +1,38 @@
+# Build the container locally
+
+Running with `uvicorn` provides auto-reload. To configure, this assumes you have previously set up `databio/secrets`. 
+
+1. Source `.env` file to populate the environment variables referenced in the configuration file.
+2. Start `bedhost` using `uvicorn` and pass the configuration file via the `BEDBASE_CONFIG` env var.
+
+
+```console
+source ../bedbase.org/environment/production.env
+BEDBASE_CONFIG=../bedbase.org/config/api.bedbase.org.yaml uvicorn bedhost.main:app --reload
+```
+
+You can change the database you're connecting to by using a different config file:
+- Using a local config: `BEDBASE_CONFIG=../bbconf/tests/data/config.yaml uvicorn bedhost.main:app --reload`
+- With new database: `BEDBASE_CONFIG=../bedbase.org/config/bedbase2.yaml uvicorn bedhost.main:app --reload`
+
+Now, you can access the service at [http://127.0.0.1:8000](http://127.0.0.1:8000). Example endpoints:
+- http://127.0.0.1:8000/v1/bed/bbad85f21962bb8d972444f7f9a3a932/metadata?full=true
+- http://127.0.0.1:8000/v1/bed/bbad85f21962bb8d972444f7f9a3a932/metadata/plots?full=true
+- http://127.0.0.1:8000/v1/objects/bed.bbad85f21962bb8d972444f7f9a3a932.chrombins
+- http://127.0.0.1:8000/v1/bed/list?limit=10&offset=0
+
+
+## Running the server in Docker
+
+### Building image
+
+- Primary image: `docker build -t databio/bedhost -f .Dockerfile .`
+- Dev image `docker build -t databio/bedhost:dev -f dev.Dockerfile .`
+- Test image: `docker build -t databio/bedhost:dev -f test.Dockerfile .`
+
+Existing images can be found [at dockerhub](https://hub.docker.com/r/databio/bedhost).
+
+
+## Deploying updates automatically
+
+- [Deploying bedbase](./deployment.md).

docs/bedhost/deployment.md

@@ -0,0 +1,64 @@
+# Deploying bedbase.org
+
+This repository deploys the API for bedbase. It will run these services:
+
+1. production API: https://api.bedbase.org/
+2. dev API: https://api-dev.bedbase.org/
+
+This repo will deploy a new service by following these steps:
+
+1. Build an image by packaging the bedhost image (from dockerhub) with the bbconf file in this repository.
+2. Push that image to AWS.
+3. Deploy it to yeti cluster with aws task def.
+
+## Build the container
+
+Here we use the `databio/bedhost` container on dockerhub, and just add the configuration file in this repo to it, so build is super fast.
+
+```
+docker build -t databio/bedhost-configured -f Dockerfiles/primary.Dockerfile .
+```
+
+Or for dev:
+
+```
+docker build -t databio/bedhost-configured-dev -f Dockerfiles/dev1.Dockerfile .
+```
+
+## Run it locally to test
+
+First, source the .env file to set env vars in the calling environment.
+Then, use `--env-file` to pass those env vars through to the container
+
+```
+source environment/production.env
+docker run --rm --network="host" \
+  --env-file environment/docker.env \
+  databio/bedhost-configured-dev
+```
+
+Here's another example for running the container:
+
+```
+docker run --rm --init -p 8000:8000 --name bedstat-rest-server \
+  --network="host" \
+  --volume ~/code/bedbase.org/config/api.bedbase.org.yaml:/bedbase.yaml \
+  --env-file ../bedbase.org/environment/docker.env \
+  --env BEDBASE_CONFIG=/bedbase.yaml \
+  databio/bedhost  uvicorn bedhost.main:app --reload
+```
+
+## Building the Amazon-tagged version
+
+You could build and push to ECR like this if you need it... but the github action will do this for you.
+
+Authenticate with AWS ECR:
+```
+aws ecr get-login-password --region us-east-1 | docker login --username AWS --password-stdin 235728444054.dkr.ecr.us-east-1.amazonaws.com
+```
+
+Build/tag/push image:
+```
+docker build -t 235728444054.dkr.ecr.us-east-1.amazonaws.com/bedhost -f Dockerfiles/primary.Dockerfile .
+docker push 235728444054.dkr.ecr.us-east-1.amazonaws.com/bedhost
+```

mkdocs.yml

@@ -48,6 +48,8 @@ nav:
       - BEDhost API guide:
         - BEDhost: bedhost/README.md
         - Developer Guide: bedhost/dev-guide.md
+        - Build image: bedhost/build_image.md
+        - Deploy API: bedhost/deployment.md
         - Changelog: bedhost/changelog.md
       - BBConf:
         - BBConf: bbconf/README.md