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checking in progress of gene-search component #926

checking in progress of gene-search component

checking in progress of gene-search component #926

name: Schematic API CI
on:
pull_request:
branches:
- main
env:
NX_BRANCH: ${{ github.event.number }}
NX_RUN_GROUP: ${{ github.run_id }}
NX_CLOUD_AUTH_TOKEN: ${{ secrets.NX_CLOUD_AUTH_TOKEN }}
NX_CLOUD_ENCRYPTION_KEY: ${{ secrets.NX_CLOUD_ENCRYPTION_KEY }}
NX_CLOUD_ENV_NAME: 'linux'
SONAR_TOKEN: ${{ secrets.SONAR_TOKEN }}
DOCKER_USERNAME: ${{ github.actor }}
DOCKER_PASSWORD: ${{ secrets.GITHUB_TOKEN }}
jobs:
pr:
runs-on: ubuntu-22.04-4core-16GBRAM-150GBSSD
# Runs this job if:
# 1. Triggered by a PR
# 2. The PR originate from the Schematic-API-Staging branch
# 3. Targets the main branch
if: |
github.event_name == 'pull_request' &&
github.event.pull_request.base.ref == 'main' &&
github.event.pull_request.head.ref == 'Schematic-API-Staging'
steps:
- uses: actions/checkout@v3
with:
ref: ${{ github.event.pull_request.head.ref }}
repository: ${{ github.event.pull_request.head.repo.full_name }}
fetch-depth: 0
- name: Derive appropriate SHAs for base and head for `nx affected` commands
uses: nrwl/nx-set-shas@v3
- name: Set up pnpm cache
uses: actions/cache@v3
with:
path: '/tmp/.pnpm-store'
key: ${{ runner.os }}-pnpm-store-${{ hashFiles('**/pnpm-lock.yaml') }}
restore-keys: |
${{ runner.os }}-pnpm-store-
- name: Set up Poetry cache
uses: actions/cache@v3
with:
path: '/tmp/.cache/pypoetry'
key: ${{ runner.os }}-poetry-${{ hashFiles('**/poetry.lock') }}
- name: Set up venv cache
uses: actions/cache@v3
with:
path: |
/tmp/.local/share/virtualenv
**/.venv
key: ${{ runner.os }}-venv-${{ hashFiles('**/poetry.lock') }}
- name: Set up Gradle cache
uses: actions/cache@v3
with:
path: |
/tmp/.gradle/caches
/tmp/.gradle/wrapper
key: ${{ runner.os }}-gradle-${{ hashFiles('**/*.gradle*', '**/gradle-wrapper.properties') }}
restore-keys: |
${{ runner.os }}-gradle-
- name: Install the Dev Container CLI
run: npm install -g @devcontainers/[email protected]
- name: Start the dev container
run: |
mkdir -p \
/tmp/.pnpm-store \
/tmp/.cache/R/renv/cache \
/tmp/.cache/pypoetry \
/tmp/.local/share/virtualenv \
/tmp/.gradle/caches \
/tmp/.gradle/wrapper
devcontainer up \
--mount type=bind,source=/tmp/.pnpm-store,target=/workspaces/sage-monorepo/.pnpm-store \
--mount type=bind,source=/tmp/.cache/R/renv/cache,target=/home/vscode/.cache/R/renv/cache \
--mount type=bind,source=/tmp/.cache/pypoetry,target=/home/vscode/.cache/pypoetry \
--mount type=bind,source=/tmp/.local/share/virtualenv,target=/home/vscode/.local/share/virtualenv \
--mount type=bind,source=/tmp/.gradle/caches,target=/home/vscode/.gradle/caches \
--mount type=bind,source=/tmp/.gradle/wrapper,target=/home/vscode/.gradle/wrapper \
--workspace-folder ../sage-monorepo
- name: Prepare the workspace
run: |
devcontainer exec --workspace-folder ../sage-monorepo bash -c "
sudo chown -R vscode:vscode \
/workspaces/sage-monorepo \
/home/vscode/.cache \
/home/vscode/.local \
/home/vscode/.gradle \
&& . ./dev-env.sh \
&& workspace-install"
- name: Set up synapse config
run: |
import yaml
secrets = {
"synapse_token": "${{ secrets.SCHEMATIC_SYNAPSE_TOKEN }}",
"test_project": "${{ secrets.SCHEMATIC_TEST_PROJECT }}",
"test_dataset": "${{ secrets.SCHEMATIC_TEST_DATASET }}",
"test_manifest": "${{ secrets.SCHEMATIC_TEST_MANIFEST }}",
"test_asset_view": "${{ secrets.SCHEMATIC_TEST_ASSET_VIEW }}"
}
for key, secret in secrets.items():
assert secret is not None
assert isinstance(secret, str)
assert len(secret) > 0
with open('apps/schematic/api/schematic_api/test/data/synapse_config.yaml', 'w') as file:
yaml.dump(secrets, file)
shell: python
- name: Set up google credentials
env:
SERVICE_ACCOUNT_CREDS: ${{ secrets.SCHEMATIC_SERVICE_ACCT_CREDS }}
run: |
import json
import os
credentials_dict = json.loads(os.environ["SERVICE_ACCOUNT_CREDS"])
credentials_file_name = "apps/schematic/api/schematic_service_account_creds.json"
with open(credentials_file_name, 'w', encoding='utf-8') as f:
json.dump(credentials_dict, f, ensure_ascii=False, indent=4)
shell: python
- name: Test the affected projects (all)
run: |
devcontainer exec --workspace-folder ../sage-monorepo bash -c ". ./dev-env.sh \
&& nx affected --target=test-all"
- name: Remove the dev container
run: docker rm -f sage_devcontainer