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Merge pull request #3 from bioimage-io/add_publish
Add publish workflow
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name: backup | ||
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on: | ||
schedule: | ||
- cron: "0 0 * * 0" # every sunday at midnight | ||
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concurrency: ${{vars.ZENODO_URL}} | ||
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env: | ||
S3_HOST: ${{vars.S3_HOST}} | ||
S3_BUCKET: ${{vars.S3_BUCKET}} | ||
S3_FOLDER: ${{vars.S3_FOLDER}} | ||
ZENODO_URL: ${{vars.ZENODO_URL}} | ||
S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}} | ||
S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}} | ||
ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}} | ||
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jobs: | ||
call: | ||
uses: ./.github/workflows/backup_call.yaml | ||
with: | ||
S3_HOST: ${{vars.S3_HOST}} | ||
S3_BUCKET: ${{vars.S3_BUCKET}} | ||
S3_FOLDER: ${{vars.S3_FOLDER}} | ||
ZENODO_URL: ${{vars.ZENODO_URL}} | ||
secrets: inherit |
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name: backup | ||
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on: | ||
workflow_call: | ||
inputs: | ||
S3_HOST: | ||
required: true | ||
type: string | ||
S3_BUCKET: | ||
required: true | ||
type: string | ||
S3_FOLDER: | ||
required: true | ||
type: string | ||
ZENODO_URL: | ||
required: true | ||
type: string | ||
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concurrency: ${{ZENODO_URL}}-call | ||
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env: | ||
S3_HOST: ${{inputs.S3_HOST}} | ||
S3_BUCKET: ${{inputs.S3_BUCKET}} | ||
S3_FOLDER: ${{inputs.S3_FOLDER}} | ||
ZENODO_URL: ${{inputs.ZENODO_URL}} | ||
S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}} | ||
S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}} | ||
ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}} | ||
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jobs: | ||
publish: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v4 | ||
- uses: actions/setup-python@v5 | ||
with: | ||
python-version: "3.12" | ||
cache: "pip" # caching pip dependencies | ||
- run: pip install -r requirements.txt | ||
- run: | | ||
python scripts/backup.py |
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name: publish | ||
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on: | ||
workflow_dispatch: | ||
inputs: | ||
resource_id: | ||
description: "Bioimageio ID of the resource - to be used to access the resource on S3" | ||
required: true | ||
type: string | ||
stage_nr: | ||
description: stage nr to publish | ||
required: true | ||
type: number | ||
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concurrency: ${{inputs.resource_id}} | ||
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env: | ||
S3_HOST: ${{vars.S3_HOST}} | ||
S3_BUCKET: ${{vars.S3_BUCKET}} | ||
S3_FOLDER: ${{vars.S3_FOLDER}} | ||
S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}} | ||
S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}} | ||
ZENODO_URL: ${{vars.ZENODO_URL}} | ||
ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}} | ||
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jobs: | ||
call: | ||
uses: ./.github/workflows/publish_call.yaml | ||
with: | ||
resource_id: ${{inputs.resource_id}} | ||
stage_nr: ${{inputs.stage_nr}} | ||
S3_HOST: ${{vars.S3_HOST}} | ||
S3_BUCKET: ${{vars.S3_BUCKET}} | ||
S3_FOLDER: ${{vars.S3_FOLDER}} | ||
ZENODO_URL: ${{vars.ZENODO_URL}} | ||
secrets: inherit |
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name: publish | ||
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on: | ||
workflow_call: | ||
inputs: | ||
resource_id: | ||
description: "Bioimageio ID of the resource - to be used to access the resource on S3" | ||
required: true | ||
type: string | ||
stage_nr: | ||
description: stage nr to publish | ||
required: true | ||
type: number | ||
S3_HOST: | ||
required: true | ||
type: string | ||
S3_BUCKET: | ||
required: true | ||
type: string | ||
S3_FOLDER: | ||
required: true | ||
type: string | ||
ZENODO_URL: | ||
required: true | ||
type: string | ||
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concurrency: ${{inputs.resource_id}}-call | ||
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env: | ||
S3_HOST: ${{inputs.S3_HOST}} | ||
S3_BUCKET: ${{inputs.S3_BUCKET}} | ||
S3_FOLDER: ${{inputs.S3_FOLDER}} | ||
ZENODO_URL: ${{inputs.ZENODO_URL}} | ||
S3_ACCESS_KEY_ID: ${{secrets.S3_ACCESS_KEY_ID}} | ||
S3_SECRET_ACCESS_KEY: ${{secrets.S3_SECRET_ACCESS_KEY}} | ||
ZENODO_API_ACCESS_TOKEN: ${{secrets.ZENODO_API_ACCESS_TOKEN}} | ||
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jobs: | ||
publish: | ||
runs-on: ubuntu-latest | ||
steps: | ||
- uses: actions/checkout@v4 | ||
- uses: actions/setup-python@v5 | ||
with: | ||
python-version: "3.12" | ||
cache: "pip" # caching pip dependencies | ||
- run: pip install -r requirements.txt | ||
- run: | | ||
python scripts/publish.py "${{ inputs.resource_id }}" "${{ inputs.stage_nr }}" | ||
# - name: Publish to Zenodo | ||
# run: | | ||
# python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Publishing to Zenodo" "5" | ||
# python .github/scripts/upload_model_to_zenodo.py --resource_path "${{inputs.resource_path}}" | ||
# python .github/scripts/update_status.py "${{ inputs.resource_path }}" "Publishing complete" "6" |
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import os | ||
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import typer | ||
from dotenv import load_dotenv | ||
from loguru import logger | ||
from utils.s3_client import Client | ||
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_ = load_dotenv() | ||
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def backup(): | ||
"""backup collection | ||
Returns: | ||
list of folders and file names backed up | ||
""" | ||
client = Client() | ||
content_to_backup = list(client.ls("")) | ||
destination = os.environ["ZENODO_URL"] | ||
logger.error("Backup to '{}': {}", destination, content_to_backup) | ||
return content_to_backup | ||
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if __name__ == "__main__": | ||
typer.run(backup) |
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import typer | ||
from utils.remote_resource import PublishedVersion, StagedVersion | ||
from utils.s3_client import Client | ||
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def publish(resource_id: str, stage_nr: int): | ||
staged = StagedVersion(client=Client(), id=resource_id, version=stage_nr) | ||
published = staged.publish() | ||
assert isinstance(published, PublishedVersion) | ||
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if __name__ == "__main__": | ||
typer.run(publish) |
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