From 451a3b6766a1e226deb4550b9c01b2297e5705fe Mon Sep 17 00:00:00 2001
From: Steve Jahl <636687+sjahl@users.noreply.github.com>
Date: Fri, 20 Sep 2024 10:28:06 -0400
Subject: [PATCH] Export Reads deployment (#1613)

---
 .cloudbuild/reads.cloudbuild.yaml             |  40 +++++
 deploy/deployctl/__main__.py                  |   4 -
 .../subcommands/reads_deployments.py          | 164 ------------------
 deploy/deployctl/subcommands/reads_images.py  |  71 --------
 deploy/docs/Deployment.md                     |  18 +-
 .../manifests/reads/base/kustomization.yaml   |   4 -
 .../reads/base/reads.deployment.yaml          |  83 ---------
 reads/docker-build.sh                         |  33 ++++
 8 files changed, 80 insertions(+), 337 deletions(-)
 create mode 100644 .cloudbuild/reads.cloudbuild.yaml
 delete mode 100644 deploy/deployctl/subcommands/reads_deployments.py
 delete mode 100644 deploy/deployctl/subcommands/reads_images.py
 delete mode 100644 deploy/manifests/reads/base/kustomization.yaml
 delete mode 100644 deploy/manifests/reads/base/reads.deployment.yaml
 create mode 100755 reads/docker-build.sh

diff --git a/.cloudbuild/reads.cloudbuild.yaml b/.cloudbuild/reads.cloudbuild.yaml
new file mode 100644
index 000000000..fa6040a4a
--- /dev/null
+++ b/.cloudbuild/reads.cloudbuild.yaml
@@ -0,0 +1,40 @@
+# Submitting a cloud build using this config from your local machine can be done as:
+# gcloud builds submit --config .cloudbuild/reads.cloudbuild.yaml \
+#                      --substitutions=_BRANCH_FOR_IMAGE_NAME="my-branch-name",SHORT_SHA="6f3f419" .
+
+steps:
+  - name: 'gcr.io/cloud-builders/docker'
+    args:
+      [
+        'build',
+        '-t',
+        'us-docker.pkg.dev/${PROJECT_ID}/gnomad/gnomad-reads-server:$SHORT_SHA',
+        '-t',
+        'us-docker.pkg.dev/${PROJECT_ID}/gnomad/gnomad-reads-server:${_BUILD_TAG}',
+        '-f',
+        'deploy/dockerfiles/reads/reads-server.dockerfile',
+        '.',
+      ]
+  - name: 'gcr.io/cloud-builders/docker'
+    args:
+      [
+        'build',
+        '-t',
+        'us-docker.pkg.dev/${PROJECT_ID}/gnomad/gnomad-reads-api:$SHORT_SHA',
+        '-t',
+        'us-docker.pkg.dev/${PROJECT_ID}/gnomad/gnomad-reads-api:${_BUILD_TAG}',
+        '-f',
+        'deploy/dockerfiles/reads/reads-api.dockerfile',
+        '.',
+      ]
+options:
+  dynamicSubstitutions: true
+substitutions:
+  _BUILD_TAG: '${_BRANCH_FOR_IMAGE_NAME}-${BUILD_ID}'
+
+# push tag with the short sha, and also a branch-based UUID
+images:
+  - 'us-docker.pkg.dev/${PROJECT_ID}/gnomad/gnomad-reads-server:$SHORT_SHA'
+  - 'us-docker.pkg.dev/${PROJECT_ID}/gnomad/gnomad-reads-server:${_BUILD_TAG}'
+  - 'us-docker.pkg.dev/${PROJECT_ID}/gnomad/gnomad-reads-api:$SHORT_SHA'
+  - 'us-docker.pkg.dev/${PROJECT_ID}/gnomad/gnomad-reads-api:${_BUILD_TAG}'
diff --git a/deploy/deployctl/__main__.py b/deploy/deployctl/__main__.py
index f48db9730..2b1742467 100755
--- a/deploy/deployctl/__main__.py
+++ b/deploy/deployctl/__main__.py
@@ -11,8 +11,6 @@
 from deployctl.subcommands import elasticsearch
 from deployctl.subcommands import ingress_demo
 from deployctl.subcommands import ingress_production
-from deployctl.subcommands import reads_deployments
-from deployctl.subcommands import reads_images
 
 
 def main():
@@ -22,8 +20,6 @@ def main():
         "config": config,
         "deployments": browser_deployments,
         "images": browser_images,
-        "reads-deployments": reads_deployments,
-        "reads-images": reads_images,
         "production": ingress_production,
         "demo": ingress_demo,
         "data-pipeline": data_pipeline,
diff --git a/deploy/deployctl/subcommands/reads_deployments.py b/deploy/deployctl/subcommands/reads_deployments.py
deleted file mode 100644
index 36eda3527..000000000
--- a/deploy/deployctl/subcommands/reads_deployments.py
+++ /dev/null
@@ -1,164 +0,0 @@
-import argparse
-import datetime
-import glob
-import os
-import string
-import sys
-import typing
-
-from deployctl.config import config
-from deployctl.shell import kubectl, get_most_recent_tag, image_exists, get_k8s_deployments
-
-
-KUSTOMIZATION_TEMPLATE = """---
-apiVersion: kustomize.config.k8s.io/v1beta1
-kind: Kustomization
-resources:
-  - ../../base
-commonLabels:
-  deployment: '{deployment_name}'
-nameSuffix: '-{deployment_name}'
-images:
-  - name: gnomad-reads-server
-    newName: {reads_server_image_repository}
-    newTag: '{reads_server_tag}'
-  - name: gnomad-reads-api
-    newName: {reads_api_image_repository}
-    newTag: '{reads_api_tag}'
-"""
-
-
-def deployments_directory() -> str:
-    path = os.path.realpath(os.path.join(os.path.dirname(__file__), "../../manifests/reads/deployments"))
-    if not os.path.exists(path):
-        os.makedirs(path)
-    return path
-
-
-def list_deployments() -> None:
-    print("Local configurations")
-    print("====================")
-    paths = reversed(sorted(glob.iglob(f"{deployments_directory()}/*/kustomization.yaml"), key=os.path.getmtime))
-    for path in paths:
-        print(os.path.basename(os.path.dirname(path)))
-
-    print()
-
-    print("Cluster deployments")
-    print("===================")
-    for deployment in get_k8s_deployments("component=gnomad-reads"):
-        print(deployment[len("gnomad-reads-") :])
-
-
-def create_deployment(name: str, reads_server_tag: str = None, reads_api_tag: str = None) -> None:
-    if not name:
-        name = datetime.datetime.now().strftime("%Y%m%d-%H%M")
-    else:
-        allowed_characters = set(string.ascii_lowercase) | set(string.digits) | {"-"}
-        if set(name).difference(allowed_characters):
-            raise ValueError(f"invalid deployment name '{name}'")
-
-        if name == "latest":
-            raise ValueError("'latest' cannot be used for a deployment name")
-
-    deployment_directory = os.path.join(deployments_directory(), name)
-
-    if os.path.exists(deployment_directory):
-        raise RuntimeError(f"deployment '{name}' already exists")
-
-    if reads_server_tag:
-        if not image_exists(config.reads_server_image_repository, reads_server_tag):
-            raise RuntimeError(f"could not find image {config.reads_server_image_repository}:{reads_server_tag}")
-    else:
-        reads_server_tag = get_most_recent_tag(config.reads_server_image_repository)
-        print(f"No server tag provided, using most recent ({reads_server_tag})")
-
-    if reads_api_tag:
-        if not image_exists(config.reads_api_image_repository, reads_api_tag):
-            raise RuntimeError(f"could not find image {config.reads_api_image_repository}:{reads_api_tag}")
-    else:
-        reads_api_tag = get_most_recent_tag(config.reads_api_image_repository)
-        print(f"No API tag provided, using most recent ({reads_api_tag})")
-
-    os.makedirs(deployment_directory)
-
-    with open(os.path.join(deployment_directory, "kustomization.yaml"), "w") as kustomization_file:
-        kustomization = KUSTOMIZATION_TEMPLATE.format(
-            deployment_name=name,
-            reads_server_image_repository=config.reads_server_image_repository,
-            reads_server_tag=reads_server_tag,
-            reads_api_image_repository=config.reads_api_image_repository,
-            reads_api_tag=reads_api_tag,
-        )
-
-        kustomization_file.write(kustomization)
-
-    print(f"configured deployment '{name}'")
-
-
-def apply_deployment(name: str) -> None:
-    deployment_directory = os.path.join(deployments_directory(), name)
-
-    if not os.path.exists(deployment_directory):
-        raise RuntimeError(f"no configuration for deployment '{name}'")
-
-    kubectl(["apply", "-k", deployment_directory])
-
-
-def delete_deployment(name: str, clean: bool = False) -> None:
-    deployment_directory = os.path.join(deployments_directory(), name)
-
-    if os.path.exists(deployment_directory):
-        kubectl(["delete", "-k", deployment_directory])
-        if clean:
-            clean_deployment(name)
-    else:
-        create_deployment(name)
-        delete_deployment(name, clean=True)
-
-
-def clean_deployment(name: str) -> None:
-    deployment_directory = os.path.join(deployments_directory(), name)
-    os.remove(os.path.join(deployment_directory, "kustomization.yaml"))
-    os.rmdir(deployment_directory)
-
-
-def main(argv: typing.List[str]) -> None:
-    parser = argparse.ArgumentParser(prog="deployctl")
-    subparsers = parser.add_subparsers()
-
-    list_parser = subparsers.add_parser("list")
-    list_parser.set_defaults(action=list_deployments)
-
-    create_parser = subparsers.add_parser("create")
-    create_parser.set_defaults(action=create_deployment)
-    create_parser.add_argument("--name")
-    create_parser.add_argument("--server-tag", dest="reads_server_tag")
-    create_parser.add_argument("--api-tag", dest="reads_api_tag")
-
-    apply_parser = subparsers.add_parser("apply")
-    apply_parser.set_defaults(action=apply_deployment)
-    apply_parser.add_argument("name")
-
-    delete_parser = subparsers.add_parser("delete")
-    delete_parser.set_defaults(action=delete_deployment)
-    delete_parser.add_argument("name")
-    delete_parser.add_argument("--clean", action="store_true")
-
-    clean_parser = subparsers.add_parser("clean")
-    clean_parser.set_defaults(action=clean_deployment)
-    clean_parser.add_argument("name")
-
-    args = parser.parse_args(argv)
-
-    if "action" not in args:
-        parser.print_usage()
-        sys.exit(1)
-
-    action = args.action
-    del args.action
-    try:
-        action(**vars(args))
-    except Exception as err:  # pylint: disable=broad-except
-        print(f"Error: {err}", file=sys.stderr)
-        sys.exit(1)
diff --git a/deploy/deployctl/subcommands/reads_images.py b/deploy/deployctl/subcommands/reads_images.py
deleted file mode 100644
index ebb2f8c2e..000000000
--- a/deploy/deployctl/subcommands/reads_images.py
+++ /dev/null
@@ -1,71 +0,0 @@
-import argparse
-import os
-import subprocess
-import sys
-import typing
-
-from deployctl.config import config
-from deployctl.tag import get_tag_from_git_revision
-
-
-def build_images(tag: str = None, push: bool = False) -> None:
-    repository_root = os.path.realpath(os.path.join(os.path.dirname(__file__), "../../.."))
-
-    if not tag:
-        tag = get_tag_from_git_revision()
-
-    images = [
-        ("deploy/dockerfiles/reads/reads-server.dockerfile", config.reads_server_image_repository),
-        ("deploy/dockerfiles/reads/reads-api.dockerfile", config.reads_api_image_repository),
-    ]
-
-    for dockerfile_path, image_repository in images:
-        subprocess.check_call(
-            [
-                "docker",
-                "build",
-                "--pull",
-                f"--file={dockerfile_path}",
-                f"--tag={image_repository}:{tag}",
-                f"--tag={image_repository}:latest",
-                ".",
-            ],
-            cwd=repository_root,
-            env=dict(os.environ, DOCKER_BUILDKIT="1"),
-        )
-
-    if push:
-        for dockerfile_path, image_repository in images:
-            subprocess.check_call(["docker", "push", f"{image_repository}:{tag}"])
-
-    for _, image_repository in images:
-        print(f"Tagged {image_repository}:{tag}")
-        print(f"Tagged {image_repository}:latest")
-
-    if push:
-        for _, image_repository in images:
-            print(f"Pushed {image_repository}:{tag}")
-
-
-def main(argv: typing.List[str]) -> None:
-    parser = argparse.ArgumentParser(prog="deployctl")
-    subparsers = parser.add_subparsers()
-
-    build_parser = subparsers.add_parser("build")
-    build_parser.set_defaults(action=build_images)
-    build_parser.add_argument("--tag")
-    build_parser.add_argument("--push", action="store_true")
-
-    args = parser.parse_args(argv)
-
-    if "action" not in args:
-        parser.print_usage()
-        sys.exit(1)
-
-    action = args.action
-    del args.action
-    try:
-        action(**vars(args))
-    except Exception as err:  # pylint: disable=broad-except
-        print(f"Error: {err}", file=sys.stderr)
-        sys.exit(1)
diff --git a/deploy/docs/Deployment.md b/deploy/docs/Deployment.md
index 3aaa35f7a..3d5523d78 100644
--- a/deploy/docs/Deployment.md
+++ b/deploy/docs/Deployment.md
@@ -335,25 +335,21 @@ The production gnomad browser uses a [blue/green deployment](https://martinfowle
 
 ## Create and Update Reads Deployment
 
-Create Reads Deployment
+### Production
 
-- Build Docker images and push to GCR.
+Docker images are built after merging to main. Once the build succeeds, and you have a new tag, update the reads deployment in [gnomad-deployments/reads](https://github.com/broadinstitute/gnomad-deployments/tree/main/reads). See the instructions in the deployment repo to create a new blue/green version, and deploy it to the cluster.
 
-  ```
-  ./deployctl reads-images build --push
-  ```
+### Development / Demo
 
-- Create deployment manifests.
+- Build Docker images and push to GCR.
 
   ```
-  ./deployctl reads-deployments create
+  ./reads/docker-build.sh
   ```
 
-- Apply deployment.
+- Create deployment manifests.
 
-  ```
-  ./deployctl reads-deployments apply <deployment-name>
-  ```
+  Follow the instructions in the [gnomad-deployments/reads](https://github.com/broadinstitute/gnomad-deployments/tree/main/reads) repo to create and apply a new demo deployment.
 
 Update Reads Deployment
 
diff --git a/deploy/manifests/reads/base/kustomization.yaml b/deploy/manifests/reads/base/kustomization.yaml
deleted file mode 100644
index 91c508d59..000000000
--- a/deploy/manifests/reads/base/kustomization.yaml
+++ /dev/null
@@ -1,4 +0,0 @@
-apiVersion: kustomize.config.k8s.io/v1beta1
-kind: Kustomization
-resources:
-  - ./reads.deployment.yaml
diff --git a/deploy/manifests/reads/base/reads.deployment.yaml b/deploy/manifests/reads/base/reads.deployment.yaml
deleted file mode 100644
index f533e08a6..000000000
--- a/deploy/manifests/reads/base/reads.deployment.yaml
+++ /dev/null
@@ -1,83 +0,0 @@
----
-kind: Deployment
-apiVersion: apps/v1
-metadata:
-  name: gnomad-reads
-  labels:
-    component: gnomad-reads
-spec:
-  replicas: 1
-  selector:
-    matchLabels:
-      name: gnomad-reads
-  template:
-    metadata:
-      labels:
-        name: gnomad-reads
-    spec:
-      containers:
-        - name: web
-          image: gnomad-reads-server
-          env:
-            - name: PROXY_IPS
-              valueFrom:
-                configMapKeyRef:
-                  name: proxy-ips
-                  key: ips
-          imagePullPolicy: Always
-          ports:
-            - name: http
-              containerPort: 80
-          resources:
-            requests:
-              cpu: '50m'
-              memory: '4Gi'
-            limits:
-              cpu: '100m'
-              memory: '4Gi'
-          readinessProbe:
-            httpGet:
-              path: /health/ready
-              port: http
-            initialDelaySeconds: 3
-            periodSeconds: 10
-          volumeMounts:
-            - name: readviz
-              mountPath: /readviz
-        - name: app
-          image: gnomad-reads-api
-          env:
-            - name: PORT
-              value: '8000'
-            - name: TRUST_PROXY
-              valueFrom:
-                configMapKeyRef:
-                  name: proxy-ips
-                  key: ips
-          ports:
-            - name: http
-              containerPort: 8000
-          resources:
-            requests:
-              cpu: '50m'
-              memory: '128Mi'
-            limits:
-              cpu: '100m'
-              memory: '256Mi'
-          readinessProbe:
-            httpGet:
-              path: /health/ready
-              port: http
-            initialDelaySeconds: 3
-            periodSeconds: 10
-          volumeMounts:
-            - name: readviz
-              mountPath: /readviz
-      nodeSelector:
-        cloud.google.com/gke-nodepool: 'main-pool'
-      volumes:
-        - name: readviz
-          gcePersistentDisk:
-            fsType: ext4
-            pdName: readviz-data-v4-2023-10-28  
-            readOnly: true
diff --git a/reads/docker-build.sh b/reads/docker-build.sh
new file mode 100755
index 000000000..1984aef21
--- /dev/null
+++ b/reads/docker-build.sh
@@ -0,0 +1,33 @@
+#!/bin/sh -euo pipefail
+
+# This is kind of strange, but we do this to ensure the script runs with the right
+# working directory without you having to worry about where you run the script from.
+SCRIPT_DIR="$(dirname "$0")"
+cd "$SCRIPT_DIR/.."
+
+# Tag image with git revision
+COMMIT_HASH=$(git rev-parse --short HEAD)
+IMAGE_TAG=${COMMIT_HASH}
+
+# Add current branch name to tag if not on main branch
+BRANCH=$(git symbolic-ref --short -q HEAD)
+if [ "$BRANCH" != "main" ]; then
+  TAG_BRANCH=$(echo "$BRANCH" | sed 's/[^A-Za-z0-9_\-\.]/_/g')
+  IMAGE_TAG="${IMAGE_TAG}-${TAG_BRANCH}"
+fi
+
+# Add "-modified" to tag if there are uncommitted local changes
+GIT_STATUS=$(git status --porcelain 2> /dev/null | tail -n1)
+if [ -n "$GIT_STATUS" ]; then
+  IMAGE_TAG="${IMAGE_TAG}-modified"
+fi
+
+AR_REPO="us-docker.pkg.dev/exac-gnomad/gnomad/gnomad-reads"
+docker build -f deploy/dockerfiles/reads/reads-server.dockerfile . \
+  --tag "${AR_REPO}-server:dev-${IMAGE_TAG}"
+
+docker build -f deploy/dockerfiles/reads/reads-api.dockerfile . \
+  --tag "${AR_REPO}-api:dev-${IMAGE_TAG}"
+
+echo "${AR_REPO}-server:dev-${IMAGE_TAG}"
+echo "${AR_REPO}-api:dev-${IMAGE_TAG}"