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chore(migration): copy all missing users from mongo to postgres #3288

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chore(migration): copy all missing users from mongo to postgres

chore(migration): copy all missing users from mongo to postgres #3288

Workflow file for this run

.github/workflows/ci.yml at f07d06e
name: ci
on:
pull_request:
branches:
- "main"
push:
branches:
- "main"
workflow_dispatch:
env:
IMAGE_NAME: virtool/virtool
REGISTRY: ghcr.io
jobs:
# Build the Docker image so we now it is successful before we create a release and try
# to push a production image to the registry.
build:
runs-on: ubuntu-22.04
steps:
- name: Checkout
uses: actions/checkout@v4
with:
fetch-depth: 0
- name: Build
uses: docker/build-push-action@v5
with:
context: .
# Generate the OpenAPI specification and upload it as an artifact.
oas:
runs-on: ubuntu-22.04
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Setup Python
uses: actions/setup-python@v5
with:
python-version: '3.12'
- name: Setup Poetry
id: setup-poetry
uses: snok/install-poetry@v1
with:
virtualenvs-create: true
virtualenvs-in-project: true
installer-parallel: true
- name: Load Cached Packages
id: cached-poetry-dependencies
uses: actions/cache@v4
with:
path: .venv
key: venv-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
- name: Install Packages
if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
run: poetry install --no-interaction
- name: Write OAS
run: |
mkdir -p virtool/spec
poetry run virtool oas > virtool/spec/openapi.json
- name: Upload OAS
uses: actions/upload-artifact@v4
with:
name: openapi.json
path: virtool/spec/openapi.json
# Run our test suite.
test:
runs-on: ubuntu-22.04
services:
redis:
image: redis:6.0
ports:
- 6379:6379
postgres:
image: postgres:13.1
env:
POSTGRES_USER: virtool
POSTGRES_PASSWORD: virtool
POSTGRES_DB: virtool
options: >-
--health-cmd pg_isready
--health-interval 10s
--health-timeout 5s
--health-retries 5
ports:
- 5432:5432
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Start OpenFGA
run: |
bash .github/workflows/scripts/setup_postgres.sh
docker run --network ${{ job.services.postgres.network }} --rm openfga/openfga:v0.2.5 migrate --datastore-engine postgres --datastore-uri 'postgres://virtool:virtool@postgres:5432/openfga?sslmode=disable'
docker run -d --name openfga --network=${{ job.services.postgres.network }} -p 8080:8080 openfga/openfga:v0.2.5 run --datastore-engine postgres --datastore-uri 'postgres://virtool:virtool@postgres:5432/openfga?sslmode=disable' --playground-enabled=false
- name: Start MongoDB
uses: supercharge/mongodb-github-action@1.11.0
with:
mongodb-version: 6.0
mongodb-replica-set: rs
- name: Setup Python
id: setup-python
uses: actions/setup-python@v5
with:
python-version: '3.12'
- name: Install Poetry
uses: snok/install-poetry@v1
with:
virtualenvs-create: true
virtualenvs-in-project: true
installer-parallel: true
- name: Load Cached Packages
id: cached-poetry-dependencies
uses: actions/cache@v4
with:
path: .venv
key: venv-${{ steps.setup-python.outputs.python-version }}-${{ hashFiles('**/poetry.lock') }}
- name: Install Packages
if: steps.cached-poetry-dependencies.outputs.cache-hit != 'true'
run: poetry install --no-interaction
- name: Install bowtie
run: |
wget https://github.com/BenLangmead/bowtie2/releases/download/v2.5.3/bowtie2-2.5.3-linux-x86_64.zip
unzip bowtie2-2.5.3-linux-x86_64.zip
cp -rv bowtie2-2.5.3-linux-x86_64 /opt/bowtie2
ln -s /opt/bowtie2/bowtie* /usr/local/bin
- name: Run
run: >-
poetry run
pytest
--db-connection-string mongodb://localhost:27017
-n 3
--openfga-host localhost:8080
--postgres-connection-string postgresql+asyncpg://virtool:virtool@localhost
--redis-connection-string redis://localhost:6379
--snapshot-details
--snapshot-warn-unused
release:
runs-on: ubuntu-22.04
if: github.repository_owner == 'Virtool' && github.event_name == 'push'
needs: [build, oas, test]
outputs:
git-tag: ${{ steps.semantic.outputs.git-tag }}
permissions:
contents: write
steps:
- name: Checkout
uses: actions/checkout@v4
- name: Download OAS
uses: actions/download-artifact@v4
with:
name: openapi.json
path: virtool/spec/openapi.json
- name: Setup Node.js
uses: actions/setup-node@v4
with:
node-version: 20
- name: Install semantic-release
run: npm i semantic-release@v23.0.8 @semantic-release/exec@v6.0.3 conventional-changelog-conventionalcommits@7.0.2
- name: Run semantic-release
id: semantic
env:
GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}
run: npx semantic-release
ghcr:
runs-on: ubuntu-22.04
if: github.repository_owner == 'Virtool' && github.event_name == 'push' && needs.release.outputs.git-tag != ''
needs: [release]
steps:
- name: Checkout
uses: actions/checkout@v4
with:
ref: ${{ needs.release.outputs.git-tag }}
- name: Login to Registry
uses: docker/login-action@v3
with:
registry: ${{ env.REGISTRY }}
username: ${{ github.actor }}
password: ${{ secrets.GITHUB_TOKEN }}
- name: Extract Docker Metadata
id: meta
uses: docker/metadata-action@v5
with:
context: git
images: ${{ env.REGISTRY }}/${{ env.IMAGE_NAME}}
- name: Build and Push
id: push
uses: docker/build-push-action@v5
with:
context: .
push: true
tags: ${{ steps.meta.outputs.tags }}
labels: ${{ steps.meta.outputs.labels }}
- name: Trigger Cloudflare Hook
if: steps.semantic.outputs.git-tag != ''
run: curl -X POST ${{ secrets.CLOUDFLARE_HOOK }}