| Name | invenio-subjects-mesh JSON |
| Version |
2024.3.5
JSON |
| download |
| home_page | None |
| Summary | MeSH subject terms with qualifiers |
| upload_time | 2024-08-12 12:54:12 |
| maintainer | None |
| docs_url | None |
| author | None |
| requires_python | >=3.9 |
| license | MIT License Copyright (C) 2021 Northwestern University. Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software. THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. |
| keywords |
invenio
inveniordm
subjects
mesh
|
| VCS |
 |
| bugtrack_url |
|
| requirements |
No requirements were recorded.
|
| Travis-CI |
No Travis.
|
| coveralls test coverage |
No coveralls.
|
# 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](https://github.com/galterlibrary/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:
```bash
pipenv install invenio-subjects-mesh
```
This will add it to your Pipfile.
## Versions
This repository follows [calendar versioning](https://calver.org/) 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 operators
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.
```bash
# 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.
### Maintainers
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](#development) before you do anything.
**Commands**
Once you have it installed, you can run the following commands in the isolated virtualenv:
```bash
# 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.
## Development
Install the project in editable mode with `dev` dependencies in an isolated virtualenv (`(venv)` denotes that going forward):
```bash
(venv) pip install -e .[dev]
# or if using pipenv
pipenv run pip install -e .[dev]
```
Run tests:
```bash
(venv) invoke test
# or shorter
(venv) inv test
# or if using pipenv
pipenv run inv test
```
Check manifest:
```bash
(venv) inv check-manifest
# or if using pipenv
pipenv run inv check-manifest
```
Clean out artefacts:
```bash
(venv) inv clean
# or if using pipenv
pipenv run inv clean
```
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"description": "# invenio-subjects-mesh\n\n*MeSH topical subject terms with qualifiers for InvenioRDM*\n\nInstall this extension to get Medical Subject Headings topics with qualifiers into your instance.\n\nIf you are looking for a smaller MeSH vocabulary without the qualifiers, use\n[invenio-subjects-mesh-lite](https://github.com/galterlibrary/invenio-subjects-mesh-lite) instead.\n\n> [!NOTE]\n> Both extensions map the `MeSH` subject id, so you can only install one of them. However, they\n> use the same pattern for subject ids, so you can switch from one to the other easily if your\n> needs change in the future.\n\n\n## Installation\n\nFrom your instance directory:\n\n```bash\npipenv install invenio-subjects-mesh\n```\n\nThis will add it to your Pipfile.\n\n## Versions\n\nThis repository follows [calendar versioning](https://calver.org/) for year and month:\n\n`2021.06.18` is both a valid semantic version and an indicator of the year-month corresponding to the loaded MeSH terms.\n`18` here is a patch number (not a day).\n\nSo far the package is compatible with InvenioRDM 9.1+'s subjects \"ABI\". If there is a breaking change, a compatibility\ntable will be provided to indicate which version is compatible with with InvenioRDM's \"ABI\".\n\n## Usage\n\nThere are 2 types of users for this package. Instance administrators and package maintainers.\n\n### Instance operators\n\nFor 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.\n\nAlternatively, 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.\n\n```bash\n# In your instance's project\n# Download up-to-date listings\npipenv run invenio galter_subjects mesh download -d /path/to/downloads/storage/ -y YEAR\n# Generate file containg deltas to transition your instance to the downloaded listing\npipenv run invenio galter_subjects mesh deltas -d /path/to/downloads/storage/ -y YEAR -f topic-qualifier -o deltas_mesh.csv\n# Update your instance - *this operation will modify your instance*\npipenv run invenio galter_subjects update deltas_mesh.csv\n```\n\nLook at the help text for these commands to see additional options that can be passed.\nIn particular, options for `galter_subjects update` allow you to store renamed, replaced or removed subjects on records according to a template of your choice.\n\n### Maintainers\n\nWhen a new list of MeSH term comes out, this package should be updated. Here we show how.\n\n**Pre-requisite/Context**\n\n[Install the distribution package for development](#development) before you do anything.\n\n**Commands**\n\nOnce you have it installed, you can run the following commands in the isolated virtualenv:\n\n```bash\n# In this project\n# Download up-to-date listings\n(venv) invenio galter_subjects mesh download -d /path/to/downloads/storage/ -y YEAR\n# Generate file containing initial listing\n(venv) invenio galter_subjects mesh file -d /path/to/downloads/storage/ -y YEAR -f topic-qualifier -o invenio_subjects_mesh/vocabularies/subjects_mesh.csv\n```\n\nWhen you are happy with the list, bump the version in `pyproject.toml` and release it.\n\n## Development\n\nInstall the project in editable mode with `dev` dependencies in an isolated virtualenv (`(venv)` denotes that going forward):\n\n```bash\n(venv) pip install -e .[dev]\n# or if using pipenv\npipenv run pip install -e .[dev]\n```\n\nRun tests:\n\n```bash\n(venv) invoke test\n# or shorter\n(venv) inv test\n# or if using pipenv\npipenv run inv test\n```\n\nCheck manifest:\n\n```bash\n(venv) inv check-manifest\n# or if using pipenv\npipenv run inv check-manifest\n```\n\nClean out artefacts:\n\n```bash\n(venv) inv clean\n# or if using pipenv\npipenv run inv clean\n```\n",
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