ontoma 0.0.2

Ontology mapping for Open Targets

This software was developed as part of the Open Targets project. For more information please see:

http://www.opentargets.org
Target Validation platform

Licensed under the Apache License, Version 2.0 (the "License");
you may not use this file except in compliance with the License.
You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software
distributed under the License is distributed on an "AS IS" BASIS,
WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.

See the License for the specific language governing permissions and
limitations under the License.
Description: OnToma is a python module that helps you map your disease/phenotype terms to the
ontology we use in the Open Targets platform.

# Usage

## Installing

`pip install ontoma`

## Quickstart

Basic usage should be simple:

```python
from ontoma import OnToma

otmap = OnToma()
print(otmap.find_efo('asthma'))

#outputs:
'EFO_000270'
```

or the command line version

```sh
ontoma -i <input_file> -o <output_dir>
```

where input file is a file of diseases/traits in either codes or text

```
ICD9:720
asthma
alzheimer's
DO:124125
```

More detailed documentation is at [](http://ontoma.readthedocs.io/en/latest/?badge=latest)
http://ontoma.readthedocs.io/en/stable/

# Developing

## set up your environment
First clone this repo

```
git clone https://github.com/opentargets/OnToma.git
```

[Install pipenv](https://pipenv.readthedocs.io/en/latest/install/#homebrew-installation-of-pipenv) and then run
```sh
pipenv install --dev
```
to get all development dependencies installed.

Test everything is working:
```sh
pipenv run pytest
```

**if you don't like pipenv** you can stick with the more traditional
setuptools/virtualenv setup:

```sh
git clone https://github.com/opentargets/OnToma.git
virtualenv -p python3 venv
source venv/bin/activate
pip install --editable .
```

## How to add a dependency

**Add to both pipenv AND setup.py**

To add a dep for a library, add it by hand to `setup.py`, then add it separately
to `Pipfile`, so that it shows up both as a transitive dependency and in your
locked dev environment

## Release to PyPi

Simply run `./bumpversion.sh`

The script will tag, push and trigger a new CI run.
The package will be automatically uploaded to pypi.

## TODO:

- [ ] memoize/lru_cache the OBO/__init__ file requests

see one of :
https://docs.python.org/3/library/functools.html
https://stackoverflow.com/questions/3012421/python-memoising-deferred-lookup-property-decorator
https://stackoverflow.com/questions/17486104/python-lazy-loading-of-class-attributes
https://stackoverflow.com/questions/14946264/python-lru-cache-decorator-per-instance
singleton implementation at module level - defer loading

- [ ] command line interface
Keywords: opentargets ontology efo mapper
Platform: UNKNOWN
Classifier: Intended Audience :: Developers
Classifier: Operating System :: OS Independent
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.6
Classifier: Programming Language :: Python :: 3 :: Only
Requires-Python: >=3.2