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rialto-airflow

.github/workflows/test.yml

Airflow for harvesting data for open access analysis and research intelligence. The workflow integrates data from sul_pub, rialto-orgs, OpenAlex and Dimensions APIs to provide a view of publication data for Stanford University research. The basic workflow is: fetch Stanford Research publications from SUL-Pub, OpenAlex, and Dimensions, enrich them with additional metadata from OpenAlex and Dimensions using the DOI, merge the organizational data found in [rialto_orgs], and publish the data to our JupyterHub environment.

flowchart TD
  sul_pub_harvest(SUL-Pub harvest) --> sul_pub_pubs[/SUL-Pub publications/]
  rialto_orgs_export(Manual RIALTO app export) --> org_data[/Stanford organizational data/]
  org_data --> dimensions_harvest_orcid(Dimensions harvest ORCID)
  org_data --> openalex_harvest_orcid(OpenAlex harvest ORCID)
  dimensions_harvest_orcid --> dimensions_orcid_doi_dict[/Dimensions DOI-ORCID dictionary/]
  openalex_harvest_orcid --> openalex_orcid_doi_dict[/OpenAlex DOI-ORCID dictionary/]
  dimensions_orcid_doi_dict -- DOI --> doi_set(DOI set)
  openalex_orcid_doi_dict -- DOI --> doi_set(DOI set)
  sul_pub_pubs -- DOI --> doi_set(DOI set)
  doi_set --> dois[/All unique DOIs/]
  dois --> dimensions_enrich(Dimensions harvest DOI)
  dois --> openalex_enrich(OpenAlex harvest DOI)
  dimensions_enrich --> dimensions_enriched[/Dimensions publications/]
  openalex_enrich --> openalex_enriched[/OpenAlex publications/]
  dimensions_enriched -- DOI --> merge_pubs(Merge publications)
  openalex_enriched -- DOI --> merge_pubs
  sul_pub_pubs -- DOI --> merge_pubs
  merge_pubs --> all_enriched_publications[/All publications/]
  all_enriched_publications --> join_org_data(Join organizational data)
  org_data --> join_org_data
  join_org_data --> publications_with_org[/Publication with organizational data/]
  publications_with_org -- DOI & SUNET --> contributions(Publications to contributions)
  contributions --> contributions_set[/All contributions/]
  contributions_set --> publish(Publish)
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Running Locally with Docker

Based on the documentation, Running Airflow in Docker.

  1. Clone repository git clone https://github.com/sul-dlss/rialto-airflow.git

  2. Start up docker locally.

  3. Create a .env file with the AIRFLOW_UID and AIRFLOW_GROUP values. For local development these can usually be:

AIRFLOW_UID=50000
AIRFLOW_GROUP=0
AIRFLOW_VAR_DATA_DIR="data"

(See Airflow docs for more info.)

  1. Add to the .env values for any environment variables used by DAGs. Not in place yet--they will usually applied to VMs by puppet once productionized.

Here is an script to generate content for your dev .env file:

for i in `vault kv list -format yaml puppet/application/rialto-airflow/dev | sed 's/- //'` ; do \
  val=$(echo $i| tr '[a-z]' '[A-Z]'); \
  echo AIRFLOW_VAR_$val=`vault kv get -field=content puppet/application/rialto-airflow/dev/$i`; \
done
  1. The harvest DAG requires a CSV file of authors from rialto-orgs to be available. This is not yet automatically available, so to set up locally, download the file at https://sul-rialto-dev.stanford.edu/authors?action=index&commit=Search&controller=authors&format=csv&orcid_filter=&q=. Put the authors.csv file in the data/ directory.

Development

Set-up

  1. Install uv for dependency management as described in the uv docs.
  2. Create a virtual environment:
uv venv

This will create the virtual environment at the default location of .venv/. uv automatically looks for a venv at this location when installing dependencies.

  1. Activate the virtual environment:
source .venv/bin/activate

Install dependencies

uv pip install -r requirements.txt

To add a dependency:

  1. uv pip install flask
  2. Add the dependency to pyproject.toml.
  3. To re-generate the locked dependencies in requirements.txt:
uv pip compile pyproject.toml -o requirements.txt

Unlike poetry, uv's dependency resolution is not platform-agnostic. If we find we need to generate a requirements.txt for linux, we can use uv's multi-platform resolution options.

Upgrading dependencies

To upgrade Python dependencies:

uv pip compile pyproject.toml -o requirements.txt --upgrade

Run Tests

First enable the virtual environment:

source .venv/bin/activate

Then ensure the app dependencies and dev dependencies are installed.

uv pip install -r requirements.txt -r requirements-dev.txt

Then run the tests:

pytest

Linting and formatting

  1. Run linting: ruff check
  2. Automatically fix linting: ruff check --fix
  3. Run formatting: ruff format (or ruff format --check to identify any unformatted files)

Deployment

First you'll need to build a Docker image and publish it DockerHub:

DOCKER_DEFAULT_PLATFORM="linux/amd64" docker build . -t suldlss/rialto-airflow:latest
docker push suldlss/rialto-airflow

Deployment to https://sul-rialto-airflow-dev.stanford.edu/ is handled like other SDR services using Capistrano. You'll need to have Ruby installed and then:

bundle exec cap dev deploy