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docker-importer

Import data from external data sources into the portal.

The docker-importer is a docker container which has functionalities for metadata import. Currently the following sources are supported:

  • Wikidata
  • zbMATH
  • CRAN
  • arXiv
  • polyDB
  • crossref
  • Zenodo
  • ORCID

Documentation

The importer functionality is encapsulated within the python package mardi_importer. This package is installed in a docker environment to run cronjobs that schedule the import tasks.

The documentation for the package mardi_importer is available at:
mardi4nfdi.github.io/docker-importer

The importer interacts with the wikibase instance deployed at portal.mardi4nfdi.de using the mardiclient package.

Basic requirements

  • Imports should run at least once a day and import only new data
  • The importer shall be extendable, i.e. imports from different sources should be possible
  • Ideally, import operations should be switchable by configuration, i.e. without editing the program
  • If an import doesn't succeeed, a rollback should be possible

Configuring the import

Copy config/import_config.config.template to config/import_config.config and edit.

Setup for local development

Create a local image:

docker build -t ghcr.io/mardi4nfdi/docker-importer:main .

Update portal-compose-dev.yml or portal-compose.override.yml in the portal-compose folder with the appropriate volume route to link to the mardi_importer folder, e.g.

importer:
    restart: ${RESTART}
    volumes:
    - ../docker-importer/mardi_importer:/mardi_importer:ro

Sphinx documentation

The documentation for the mardi_importer package is updated for every push to main by running make html in docs/ and deploying to the gh-pages branch.
The result is directly available at mardi4nfdi.github.io/docker-importer

Local testing of python modules

First install the requirements from requirements.txt,

pip install -r requirements.txt

Then install the python package bundle ("mardi-importer") via

pip install -U -e .

-U enforces reinstalling the package, with -e modifications in the source files are automatically taken into account.

Note: it is recommended (when not using docker) for local installations to use virtual environments.

To run the tests, do:

docker exec -ti mardi-importer /bin/bash /tests/run_tests.sh