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BRAVO Deployment with Ansible

Three roles:

  • Install components & configure.
  • Download, unpack, and load backing data.
  • Run applications as systemd services.

Dependencies

  • AWS Credentials configured locally.
  • Ansible installed
  • Requires Ansible collection community.mongodb 
    ansible-galaxy collection install -r requirements.yml
  • ssh keys to use to access the EC2 instances: key-pair docs

Optional S3 Dependency for Data Loading

Data for staging deployment may be downloaded from an S3 bucket to disk. It can then be subsequently loaded into mongo.

This is a convenience for smaller data sets like the staging data. It is not suitable for large data sets such as the production data.

Optional S3 Runtime Dependency

Subsets of the coverage and crams data can be retrieved from S3 at runtime to save on disk space. This requires a build of HTSLIB that supports the libcurl and s3 plugins.

In order to use S3 as the backing data for crams or coverage, the corresponding variable needs to be defined for the application host or group variables. E.g. in group_vars/bravo_staging/dirs.yml:

---
coverage_url: "s3://example-bucket/runtime/coverage"
sequences_url: "s3://example-bucket/runtime/crams"

Data Loading

The data loading step is time consuming. The role creates lock files to indicate that it's already been run. This facilitates a hack to avoid trying to figure out if data needs to be reloaded. If data loading needs to be re-done, the lock files on the app server must be removed.

The download task is time consuming, but does not produce a lock file nor check if files are already present.

Auth Configuration

To enable OAuth using Google as the identity provider, the client id and secrent must be given. The following configuration is expected to be in group_vars/app/auth.yml

---
gauth_client_id: "yourcliendid"
gauth_client_secret: "yourclientsecret"

When absent, the generated application config will set DISABLE_LOGIN to true.

Run deployment

Prior to running ansible, an ssh config and inventory needs to be written. The make_ansible_support_files.sh script creates these. The script is meant to be run from the directory in which it's located. By default it reads the terraform cloud project 'bravo-staging'. To get the production configs, export WORKSPACE_NAME=bravo-production before running the script.

The following sub-sections provide the commands for different deployment situations.

Full deployment including download & data loading

Data will be downloaded from s3 and processes to load data into mongodb will be run. Need to provide three variables data_bucket and load_data do_download. Data download, unpacking, and loading can take a long time and should only need to be done once.

  • load_data: (default false) Load basis data from disk into mongo instance.
  • do_download: (default false) Download the data from bucket prior to loading.
  • data_bucket: name of your s3 bucket without leading protocol (s3://).
ansible-playbook --ssh-common-args='-F inv/ssh-config' \
  -i 'inv/servers' playbook.yml \
  -e ' load_data=true do_download=true data_bucket=your_bucket_name'

Full deployment with data loading (no bucket download)

To load the data only for the cases where it's already in place on disk, only load_data=true should be specified since do_download is false by default.

ansible-playbook --ssh-common-args='-F inv/ssh-config' \
  -i 'inv/servers' playbook.yml -e 'load_data=true'

Deploy from specific git branch

To deploy from a specific reference on github, specify the bravo_ref variable (default value is "main").

ansible-playbook --ssh-common-args='-F inv/ssh-config' \
  -i 'inv/servers' playbook.yml -e 'bravo_ref=example'

Only redeploy the python application:

Only update the API and restart the systemd service running it.

ansible-playbook --ssh-common-args='-F inv/ssh-config'\
  -i 'inv/servers' --tags instance playbook.yml

Deployment including dependencies:

This is the default run. Updates the machine, installs dependencies, installs application.

ansible-playbook --ssh-common-args='-F inv/ssh-config' -i 'inv/servers' playbook.yml