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snf2ye merged 2 commits into from
Oct 1, 2024
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DC-1227 - Reduce costs by shutting down personal deployments when not in use #1822

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5bbc25b
reduce cost by shutting down personal deployments when not in use
snf2ye Sep 25, 2024
592d927
Move datarepo-helm-definitions instructions to other repo
snf2ye Sep 30, 2024
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111 changes: 12 additions & 99 deletions docs/jade-getting-started.md
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Original file line number Diff line number Diff line change
Expand Up @@ -272,10 +272,10 @@ First, make sure you have run through the following steps:
* Auth as your broadinstitute.org to pull from Google Secrets Manager `gcloud auth login <you>@broadinstitute.org`
* Run `./scripts/run-db start` to start the DB in a docker container

** Run test in the Command Line **
**Run test in the Command Line**
* Run `GRADLE_ARGS='--tests *<specific test name>' ./scripts/run connected` to run a specific connected test

** Run or Debug test in Intellij **
**Run or Debug test in Intellij**
* Run
`./scripts/render-configs.sh -i` which will put all the environment variables into your clipboard
and then you can paste them into the Intellij test setup.
Expand All @@ -289,10 +289,10 @@ First, make sure you have run through the following steps:
* Auth as your broadinstitute.org to pull from Google Secrets Manager `gcloud auth login <you>@broadinstitute.org`
* Run `./scripts/run-db start` to start the DB in a docker container

** Run test in the Command Line **
**Run test in the Command Line**
* Run `GRADLE_ARGS='--tests *<specific test name>' ./scripts/run integration` to run a specific integration test

** Run or Debug test in Intellij **
**Run or Debug test in Intellij**
* Run
`./scripts/render-configs.sh -i -a integration` which will put all the environment variables into your clipboard and then you
can paste them into the Intellij test setup.
Expand Down Expand Up @@ -326,6 +326,14 @@ export PROXY_URL=http://localhost:8080
```
You need to have data repo running with `./gradlew bootRun` and the UI running with `npm start`.

### 6. Testing in a deployed environment
**Testing in a BEE (Branch Engineering Environment)**
* You can test your changes in a BEE by following the instructions [here](https://docs.google.com/document/d/1kyjrOKzUthwKu-m38Da2niNEh-IkbUzxtfT29EWw8ag/edit?usp=sharing)
* You can point the [python setup script](https://github.com/DataBiosphere/jade-data-repo/blob/develop/tools/setupResourceScripts/setup_tdr_resources.py) to your BEE by setting the --host flag to the BEE url.

**Testing Helm Chart Changes (holdover until datarepo-helm moves to terra-helmfile)**
* Helm chart changes in datarepo-helm can be tested by spinning up a personal dev environment. See [instructions in datarepo-helm-definitions](https://github.com/broadinstitute/datarepo-helm-definitions) for more information.

## 11. Set up TDR resources

After running bootRun, you may want to create some datasets locally for use in testing.
Expand All @@ -336,12 +344,6 @@ See the [README](https://github.com/DataBiosphere/jade-data-repo/blob/develop/to
You can also run some of the notebooks from [the Jade Client examples](https://github.com/broadinstitute/jade-data-repo-client-example/tree/master/src/main/python),
such as `AzureY1Demo.ipynb`

## 12. Set up TDR on BEEs

You can follow [these instructions](https://docs.google.com/document/d/1kyjrOKzUthwKu-m38Da2niNEh-IkbUzxtfT29EWw8ag/edit?usp=sharing) to get a BEE setup to work with TDR.

Additionally, you can point the [python setup script](https://github.com/DataBiosphere/jade-data-repo/blob/develop/tools/setupResourceScripts/setup_tdr_resources.py) to your BEE by setting the --host flag to the BEE url.

## 13. Running locally with other locally running services
1. Sam - set environment variable `SAM_BASEPATH` to `https://local.broadinstitute.org:50443`

Expand All @@ -367,92 +369,3 @@ Ensure that:
## Resources
* [Stairway Flight Developer Guide](https://github.com/DataBiosphere/stairway/blob/develop/FLIGHT_DEVELOPER_GUIDE.md) - Data Repo utilizes Stairway to run asynchronous operations throughout the code base.
* [Data Repo Service](https://ga4gh.github.io/data-repository-service-schemas/docs/) - The Data Repo implements parts of the The Data Repository Service (DRS) specification.

## Appendix

### Personal Dev Environment Setup
We're moving away from setting up personal dev environments for every developer. Instead, we are moving
towards using BEEs ([BEE url](https://beehive.dsp-devops.broadinstitute.org/environments/new), [TDR on BEEs](https://docs.google.com/document/d/1kyjrOKzUthwKu-m38Da2niNEh-IkbUzxtfT29EWw8ag/edit#heading=h.5gsyp5q4qds5))
However, there are still some use cases for personal dev environments.

Throughout these instructions, replace all instances of `ZZ` with your initials.

> There is a video of us walking through
these steps in our [Jade Google Drive Folder](https://drive.google.com/drive/folders/1JM-_M0qsX6eXocyPc9TB7ivCKJTji3dX?usp=sharing).

1. Follow the
[instructions in our terraform-jade repository](https://github.com/broadinstitute/terraform-jade/tree/master/old#new-team-member-process)
to add your initials to the terraform templates and generate the static resources needed
to deploy your personal development environment.
Apply the changes and create a pull request to merge your additions to `terraform-jade`.

2. Create your datarepo helm definition:
- In `datarepo-helm-definitions/dev` directory,
copy an existing developer definition and change all initials to your own.
Double-check with the team if you're not sure what to use, but the most recently added
is probably the best choice.
- By default, leave release chart versions unspecified in your `helmfile.yaml` so that
latest versions are automatically picked up when running helmfile commands.
Otherwise, verify that specified versions match the
[latest dependency versions](https://github.com/broadinstitute/datarepo-helm/blob/master/charts/datarepo/Chart.lock).
- Create a pull request with these changes in
[datarepo-helm-definitions](https://github.com/broadinstitute/datarepo-helm-definitions).


3. Log in to [Google Cloud Platform](https://console.cloud.google.com).
In the top-left corner, select the **BROADINSTITUTE.ORG** organization.
Select **broad-jade-dev** from the list of projects.

4. From the left hand sidebar, select **Kubernetes Engine -> Clusters** under
**COMPUTE**.

5. Click **Connect** on the **dev-master** cluster.
(You can also navigate here via
[direct link](https://console.cloud.google.com/kubernetes/clusters/details/us-central1/dev-master/details?project=broad-jade-dev).)
This gives you a `kubectl` command to copy and paste into the terminal:

```
gcloud container clusters get-credentials dev-master --region us-central1 --project broad-jade-dev
```

6. Starting from your [project directory](#6-code-checkout) in `datarepo-helm-definitions`,
bring up Helm services (note it will take up to 10-15 minutes for ingress and cert creation):

Note: Make sure you are on the VPN, otherwise the helmfile apply will fail.

```
cd datarepo-helm-definitions/dev/ZZ
helmfile apply

# check that the deployments were created
helm list --namespace ZZ
```

7. Update the following authorized domains within the
[Jade Data Repository OAuth2 Client configuration](https://console.cloud.google.com/apis/credentials/oauthclient/970791974390-1581mjhtp2b3jmg4avhor1vabs13b7ur.apps.googleusercontent.com?authuser=0&project=broad-jade-dev):

- Under Authorized JavaScript origins, add `https://jade-ZZ.datarepo-dev.broadinstitute.org`
- Under Authorized redirect URIs, add `https://jade-ZZ.datarepo-dev.broadinstitute.org/login/google` and
`https://jade-ZZ.datarepo-dev.broadinstitute.org/webjars/springfox-swagger-ui/oauth2-redirect.html`

8. Connect to your new dev postgres database instance:
Note that this is a different instance than the local one you will configure in [step 10](#10-install-postgres-11).
The following command connects to the database via a proxy.

```
cd jade-data-repo/ops
DB=datarepo-ZZ SUFFIX=ZZ ENVIRONMENT=dev ./db-connect.sh
```

9. Now that you're connected to your dev database, run the following command
(Once [DR-1156](https://broadworkbench.atlassian.net/browse/DR-1156) is done, this will no longer be needed):

```
create extension pgcrypto;
```

10. Create a pull request to `terraform-ap-deployments` to add
`https://jade-ZZ.datarepo-dev.broadinstitute.org` under the
['personal deployments'](https://github.com/broadinstitute/terraform-ap-deployments/blob/e9ecc7a637fe4a7743011b568f76a296a4e85ed2/azure/b2c/tfvars/dev.tfvars#L20)
section of `dev.tfvars/b2c_tdr_hosts`. This allows B2C as a means of authentication, which is
the default across environments.