refgenieserver
This folder contains code for an API to provide reference genomes. refgenieserver can do 2 things: archive an existing refgenie folder, and then serve it.
How to serve
Building container
In the same directory as the Dockerfile:
docker build -t refgenieserverim .
Running container for development:
You can run it directly after installing with pip install, like this:
refgenieserver serve -c refgenie.yaml -p 5000
Better, though, is to use the container. Mount a directory of files to serve at /genomes:
docker run --rm -p 80:80 --name refgenieservercon \
-v $(pwd)/files:/genomes \
refgenieserverim refgenieserver serve -c refgenie.yaml
Running container for production:
Run the container from the image you just built:
docker run --rm -d -p 80:80 \
-v /path/to/genomes_archive:/genomes \
--name refgenieservercon \
refgenieserverim refgenieserver serve -c /genomes/genome_config.yaml
Make sure the genome_config.yaml filename matches what you've named your configuration file! We use -d to detach so it's in background. You shouldn't need to mount the app (-v /path/to/refgenieserver:/app) because in this case we're running it directly. Terminate container when finished:
docker stop refgenieservercon
Interacting with the API web server
Navigate to http://localhost/ to see the server in action.
You can see the automatic docs and interactive swagger openAPI interface at http://localhost/docs. That will also tell you all the endpoints, etc.
Monitoring for errors
Attach to container to see debug output:
docker attach refgenieservercon
Grab errors:
docker events | grep -oP "(?<=die )[^ ]+"
View those error codes:
docker logs <error_code>
Enter an interactive shell to explore the container contents:
docker exec -it refgenieservercon sh
How to archive
Refgenieserver can also archive your assets, creating the directory for asset archives needed to serve.
First, make sure the config has a genome_archive_folder key that points to the directory where you want to store the servable archives (genome_archive_folder is not added automatically by refgenie init). Your first time you will need to manually add this to tell refgenieserver where to store the archives.
Secondly, if you wish to store the refgenieserver configuration file separately from the genome_archive_folder, specify a genome_archive_config key. The path that this key points to will be considered relative to the refgenie configuration file, unless it's absolute.
Then run:
refgenieserver archive -c CONFIG
````
It just requires a `-c` argument or `$REFGENIE` environment variable.
This command will:
- create the `genome_archive` directory and structure that can be used to serve the assets
- create a server config file in that directory, which includes a couple of extra asset attributes, like `archive_digest` and `archive_size`.
In case you already have some of the assets archived and just want to add a new one, use:
In case you want to remove an unwanted archive, add an `-r` flag:
## How to test the `refgenie` suite of software
The `refgenie` universe includes [`refgenie`](http://refgenie.databio.org/en/latest/), [`refgenconf`](http://refgenie.databio.org/en/latest/overview/#3-the-refgenconf-python-package), and [`refgenieserver`](https://github.com/databio/refgenieserver/).
The [`test_refgenie.sh`](https://github.com/databio/refgenieserver/blob/staging/test_refgenie.sh) script will test the integration of all three tools to ensure everything is functioning, particularly following any changes or updates to one, two, or all three tools.
Use it simply as follows:
The script also requires Python's virtual environment module, Docker, and Bulker to successfully test all components.