Release v0.11.0

.dockerignore

@@ -20,4 +20,5 @@ node_modules/
 pephub/data
 postgres/
 .idea
-qdrant_storage/
+qdrant_storage/
+local_cache/

.github/workflows/deploy-api.yml

@@ -0,0 +1,83 @@
+# This workflow will build and push a new container image to Amazon ECR,
+# and then will deploy a new task definition to Amazon ECS, when a release is created
+#
+# To use this workflow, you will need to complete the following set-up steps:
+#
+# 1. Create an ECR repository to store your images.
+#    For example: `aws ecr create-repository --repository-name my-ecr-repo --region us-east-2`.
+#    Replace the value of `ECR_REPOSITORY` in the workflow below with your repository's name.
+#    Replace the value of `aws-region` in the workflow below with your repository's region.
+#
+# 2. Create an ECS task definition, an ECS cluster, and an ECS service.
+#    For example, follow the Getting Started guide on the ECS console:
+#      https://us-east-2.console.aws.amazon.com/ecs/home?region=us-east-2#/firstRun
+#    Replace the values for `service` and `cluster` in the workflow below with your service and cluster names.
+#
+# 3. Store your ECS task definition as a JSON file in your repository.
+#    The format should follow the output of `aws ecs register-task-definition --generate-cli-skeleton`.
+#    Replace the value of `task-definition` in the workflow below with your JSON file's name.
+#    Replace the value of `container-name` in the workflow below with the name of the container
+#    in the `containerDefinitions` section of the task definition.
+#
+# 4. Store an IAM user access key in GitHub Actions secrets named `AWS_ACCESS_KEY_ID` and `AWS_SECRET_ACCESS_KEY`.
+#    See the documentation for each action used below for the recommended IAM policies for this IAM user,
+#    and best practices on handling the access key credentials.
+
+on:
+  push:
+    branches:
+      - master
+  workflow_dispatch:
+    inputs: null
+
+name: Deploy pephub.databio.org API to AWS - primary
+
+jobs:
+  deploy:
+    env:
+      server: primary
+    name: Deploy
+    runs-on: ubuntu-latest
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v2
+      - name: Configure AWS credentials
+        uses: aws-actions/configure-aws-credentials@v1
+        with:
+          aws-access-key-id: ${{ secrets.AWS_ACCESS_KEY_ID }}
+          aws-secret-access-key: ${{ secrets.AWS_SECRET_ACCESS_KEY }}
+          aws-region: us-east-1
+
+      - name: Login to Amazon ECR
+        id: login-ecr
+        uses: aws-actions/amazon-ecr-login@v1
+
+      - name: Build, tag, and push image to Amazon ECR
+        id: build-image
+        env:
+          ECR_REGISTRY: ${{ steps.login-ecr.outputs.registry }}
+          ECR_REPOSITORY: pephub
+          IMAGE_TAG: ${{ github.sha }}
+        run: |
+          # Build a docker container and
+          # push it to ECR so that it can
+          # be deployed to ECS.
+          docker build -t $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG deployment/pephub.databio.org/.
+          docker push $ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG
+          echo "::set-output name=image::$ECR_REGISTRY/$ECR_REPOSITORY:$IMAGE_TAG"
+
+      - name: Fill in the new image ID in the Amazon ECS task definition
+        id: task-def
+        uses: aws-actions/amazon-ecs-render-task-definition@v1
+        with:
+          task-definition: deployment/task_defs/primary.json
+          container-name: pephub-container
+          image: ${{ steps.build-image.outputs.image }}
+
+      - name: Deploy Amazon ECS task definition
+        uses: aws-actions/amazon-ecs-deploy-task-definition@v1
+        with:
+          task-definition: ${{ steps.task-def.outputs.task-definition }}
+          service: pephub-service-primary
+          cluster: yeti
+          wait-for-service-stability: true

.github/workflows/deploy-dockerhub.yml

@@ -4,22 +4,26 @@ on:
       - created
   workflow_dispatch:
     inputs: null
-    
+
 name: Deploy to Dockerhub on release
 
 jobs:
   deploy:
     name: Deploy
     runs-on: ubuntu-latest
     steps:
-    - name: Checkout
-      uses: actions/checkout@v2
+      - name: Checkout
+        uses: actions/checkout@v2
+
+      - name: Log in to Docker Hub
+        uses: docker/login-action@v3
+        with:
+          username: ${{ secrets.DOCKERHUB_USERNAME }}
+          password: ${{ secrets.DOCKER_PASSWORD }}
 
-    - name: Build and Push to DockerHub
-      uses: docker/build-push-action@v1
-      with:
-        username: ${{ secrets.DOCKER_USERNAME }}
-        password: ${{ secrets.DOCKER_PASSWORD }}
-        repository: databio/pephub
-        tags: latest
-        tag_with_ref: true
+      - name: Build and Push to DockerHub
+        uses: docker/build-push-action@v5
+        with:
+          push: true
+          context: '{{defaultContext}}:mysubdir'
+          tags: databio/pephub:latest

deployment/.gitignore

@@ -0,0 +1,2 @@
+.DS_Store
+.env

deployment/README.md

@@ -0,0 +1,48 @@
+# pephub.databio.org
+This is the publically available instance of [PEPhub](https://github.com/pepkit/pephub) provided by the Sheffield lab. You can view the deployed instance at https://pephub.databio.org
+
+## Development
+### Build the container
+```
+docker build -t pephub.databio.org .
+```
+
+
+### Run
+
+PEPhub requires many parameters to run. You can read more about those [here](https://github.com/pepkit/pephub/blob/master/docs/server-settings.md). These must be injected as environment variables. You can manually do this and inject one-by-one. There is an example script in this repo called [launch_docker.sh](launch_docker.sh).
+
+```
+launch_docker.sh
+```
+
+The basic steps are:
+
+1. Initialize env vars
+
+```
+source /home/nsheff/code/pephub/environment/production.env
+```
+
+2. Run with docker: 
+
+```
+docker run --rm -p 80:80 \
+    --env POSTGRES_HOST=$POSTGRES_HOST \
+    --env POSTGRES_DB=$POSTGRES_DB \
+    --env POSTGRES_USER=$POSTGRES_USER \
+    --env POSTGRES_PASSWORD=$POSTGRES_PASSWORD \
+    --env QDRANT_HOST=$QDRANT_HOST \
+    --env QDRANT_PORT=$QDRANT_PORT \
+    --env QDRANT_ENABLED=$QDRANT_ENABLED \
+    --env QDRANT_API_KEY=$QDRANT_API_KEY \
+    --env HF_MODEL=$HF_MODEL \
+    --env GH_CLIENT_ID=$GH_CLIENT_ID \
+    --env GH_CLIENT_SECRET=$GH_CLIENT_SECRET \
+    --env REDIRECT_URI=$REDIRECT_URI \
+    --env SERVER_ENV=$SERVER_ENV \
+    --name pephub pephub
+```
+
+3. Visit http://localhost:80 to view the server.
+

deployment/dockerhub/Dockerfile

@@ -0,0 +1,22 @@
+# -------------
+# BUILD BACKEND
+# -------------
+FROM python:3.10-slim
+LABEL authors="Nathan LeRoy, Nathan Sheffield"
+
+RUN apt-get update
+RUN apt-get install -y gcc
+RUN apt-get install -y libpq-dev
+RUN apt-get install -y --no-install-recommends git
+
+EXPOSE 5432
+EXPOSE 6333
+EXPOSE 80
+
+WORKDIR /app
+COPY . /app
+
+RUN python -m pip install --upgrade pip
+RUN pip install -r requirements/requirements-all.txt --no-cache-dir
+
+CMD ["uvicorn", "pephub.main:app", "--host", "0.0.0.0", "--port", "80"]

deployment/launch_docker.sh

@@ -0,0 +1,16 @@
+#!/bin/bash
+
+docker run -p 80:80 \
+    --env POSTGRES_HOST=$POSTGRES_HOST \
+    --env POSTGRES_DB=$POSTGRES_DB \
+    --env POSTGRES_USER=$POSTGRES_USER \
+    --env POSTGRES_PASSWORD=$POSTGRES_PASSWORD \
+    --env QDRANT_HOST=$QDRANT_HOST \
+    --env QDRANT_PORT=$QDRANT_PORT \
+    --env QDRANT_ENABLED=$QDRANT_ENABLED \
+    --env QDRANT_API_KEY=$QDRANT_API_KEY \
+    --env HF_MODEL=$HF_MODEL \
+    --env GH_CLIENT_ID=$GH_CLIENT_ID \
+    --env GH_CLIENT_SECRET=$GH_CLIENT_SECRET \
+    --env BASE_URI=$BASE_URI \
+    databio.pephub.org

deployment/pephub.databio.org/Dockerfile

@@ -0,0 +1,2 @@
+FROM databio/pephub:latest
+# pass - nothing else is needed

deployment/schemas.yaml

@@ -0,0 +1,20 @@
+pipelines/ProseqPEP:
+  name: "PEPPRO"
+  docs: "http://peppro.databio.org"
+  schema: "http://schema.databio.org/pipelines/ProseqPEP.yaml"
+pep/2.0.0:
+  name: "PEP v2.0.0"
+  docs: "http://pep.databio.org"
+  schema: "http://schema.databio.org/pep/2.0.0.yaml"
+pipelines/pepatac:
+  name: "PEPATAC"
+  docs: "http://pepatac.databio.org"
+  schema: "http://schema.databio.org/pipelines/pepatac.yaml"
+pipelines/bedmaker:
+  name: "bedmaker"
+  docs: "http://bedbase.org"
+  schema: "http://schema.databio.org/pipelines/bedmaker.yaml"
+bulker/manifest:
+  name: "bulker"
+  docs: "http://bulker.io"
+  schema: "http://schema.databio.org/bulker/manifest.yaml"