RDMO MeSH plugin

The dynamic MeSH optionset will query internal database tables for descriptors matching the user input. The plugin is meant to be used with RDMO's autocomplete field and its server-side search capabilities.

Please visit the RDMO documentation for detailed information on plugin.

Setup

Install the plugin in your RDMO virtual environment using pip (directly from GitHub):

pip install git+https://github.com/rdmorganiser/rdmo-plugins-mesh

Add the rdmo_mesh app to your INSTALLED_APPS in config/settings/local.py:

from . import INSTALLED_APPS
INSTALLED_APPS = ['rdmo_mesh'] + INSTALLED_APPS

Add the plugin to the OPTIONSET_PROVIDERS in config/settings/local.py:

OPTIONSET_PROVIDERS = [
    ...
    ('mesh', _('Medical Subject Headings (MeSH)'), 'rdmo_mesh.providers.MeSHProvider'),
]

Optionally, a REST API for the MeSH data can be activated by adding the following to config/urls.py:

urlpatterns = [
    ...
    path('api/v1/mesh/', include('rdmo_mesh.urls')),  # before the regular RDMO API!
    path('api/v1/', include('rdmo.core.urls.v1')),
    ...
]

Add the locaton of the source xml files to config/settings/local.py as well:

MESH_DESCRIPTOR_URL = 'ftp://nlmpubs.nlm.nih.gov/online/mesh/MESH_FILES/xmlmesh/desc2021.xml'
MESH_QUALIFIER_URL = 'ftp://nlmpubs.nlm.nih.gov/online/mesh/MESH_FILES/xmlmesh/qual2021.xml'
MESH_PATH = '/path/to/where/the/xml/files/are/store/locally'

Since the plugin uses its own models, run the migrations:

python manage.py migrate

Import the MeSH data:

python manage.py import_mesh

After restarting RDMO, the MeSHProvider should be selectable as a provider option for option sets. Those optionsets should be used with a question using the autocomplete widget.