invenio-subjects-mesh

MeSH topical subject terms with qualifiers for InvenioRDM

Install this extension to get Medical Subject Headings topics with qualifiers into your instance.

If you are looking for a smaller MeSH vocabulary without the qualifiers, use invenio-subjects-mesh-lite instead.

Note

Both extensions map the MeSH subject id, so you can only install one of them. However, they use the same pattern for subject ids, so you can switch from one to the other easily if your needs change in the future.

Installation

From your instance directory:

pipenv install invenio-subjects-mesh

This will add it to your Pipfile.

Versions

This repository follows calendar versioning for year and month:

2021.06.18 is both a valid semantic version and an indicator of the year-month corresponding to the loaded MeSH terms. 18 here is a patch number (not a day).

So far the package is compatible with InvenioRDM 9.1+'s subjects "ABI". If there is a breaking change, a compatibility table will be provided to indicate which version is compatible with with InvenioRDM's "ABI".

Usage

There are 2 types of users for this package. Instance administrators and package maintainers.

Instance administrators

For instance administrators, after you have installed the extension as per the steps above, you will want to reload your instance's fixtures: pipenv run invenio rdm-records fixtures. This will install the new terms in your instance.

Updating existing terms currently requires manual replacement.

Maintainers

When a new list of MeSH term comes out, this package should be updated. Here we show how.

Install this package locally with the dev extra:

pipenv run pip install -e .[dev]

Use the installed galter-subjects-utils tool to get the new list:

pipenv run galter-subjects-utils mesh --filter topic-qualifier --output-file invenio_subjects_mesh/vocabularies/subjects_mesh.jsonl

This will

Download the new list(s)
Read it filtering for topics
Convert terms to InvenioRDM subjects format
Write those to the specified file
Check the manifest (it should typically be all good)

pipenv run inv check-manifest

When you are happy with the list, bump the version and release it.

Development

Install the project in editable mode with dev dependencies in an isolated virtualenv ((venv) denotes that going forward):

(venv) pip install -e .[dev]
# or if using pipenv
pipenv run pip install -e .[dev]

Run tests:

(venv) invoke test
# or shorter
(venv) inv test
# or if using pipenv
pipenv run inv test

Check manifest:

(venv) inv check-manifest
# or if using pipenv
pipenv run inv check-manifest

Clean out artefacts:

(venv) inv clean
# or if using pipenv
pipenv run inv clean