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.

From your instance directory:

pipenv install invenio-subjects-mesh

This will add it to your Pipfile.

From 2025.1.15.2 onwards

This package follows the following format for versions: YYYY.mm.dd.patch where

• YYYY.mm.dd is the date of retrieval of the MeSH terms with mm and dd NOT being 0-prefixed.
• patch is the patch number (0-indexed) so that multiple releases can be done on the same day (bug/security fixes) and non-subject related releases can be done as well.

This follows calendar versioning (for year, month, and day) and adds a patch number at the end. The package is typically updated on a quarterly basis. The following are illustrative (fictitious) examples of how to understand the versioning of this distribution package:

Prior to 2025.1.15.2

This repository follows calendar versioning for year and month. It does a "best effort" attempt at tracking the MeSH updates in an up-to-and-including version date manner. The following are illustrative cases of how to understand the versioning of this distribution package:

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

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

For instance operators, 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.

Alternatively, or if you want to update your already loaded subjects to a new listing (e.g. from one year's list to another), you can update your instance's MeSH subjects as per below. Updating subjects this way takes care of everything for you: the subjects themselves and the records/drafts using those subjects. WARNING This operation can remove subjects.

# In your instance's project
# Download up-to-date listings
pipenv run invenio galter_subjects mesh download -d /path/to/downloads/storage/ -y YEAR
# Generate file containg deltas to transition your instance to the downloaded listing
pipenv run invenio galter_subjects mesh deltas -d /path/to/downloads/storage/ -y YEAR -f topic-qualifier -o deltas_mesh.csv
# Update your instance - *this operation will modify your instance*
pipenv run invenio galter_subjects update deltas_mesh.csv

Look at the help text for these commands to see additional options that can be passed. In particular, options for galter_subjects update allow you to store renamed, replaced or removed subjects on records according to a template of your choice.

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

Pre-requisite/Context

Install the distribution package for development before you do anything.

Commands

Once you have it installed, you can run the following commands in the isolated virtualenv:

# In this project
# Download up-to-date listings
(venv) invenio galter_subjects mesh download -d /path/to/downloads/storage/ -y YEAR
# Generate file containing initial listing
(venv) invenio galter_subjects mesh file -d /path/to/downloads/storage/ -y YEAR -f topic-qualifier -o invenio_subjects_mesh/vocabularies/subjects_mesh.csv

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

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

Test compatibility with the pre-release version of InvenioRDM (invenio-app-rdm):

# Step 1 - install the pre-release dependencies
(venv) pip install --pre -e .[dev_pre]
# Step 2 - Run the pre-release tests
(venv) inv test
# if using uv run:
uv run --extra dev_pre --prerelease=allow 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