Metadata-Version: 2.1
Name: disease-normalizer
Version: 0.2.11
Summary: VICC normalization routine for diseases
Home-page: https://github.com/cancervariants/disease-normalization
Author: VICC
Author-email: help@cancervariants.org
License: MIT
Description: # Disease Normalization
        Services and guidelines for normalizing disease terms
        
        ## Developer instructions
        Following are sections include instructions specifically for developers.
        
        ### Installation
        For a development install, we recommend using Pipenv. See the
        [pipenv docs](https://pipenv-fork.readthedocs.io/en/latest/#install-pipenv-today)
        for direction on installing pipenv in your compute environment.
        
        Once installed, from the project root dir, just run:
        
        ```commandline
        pipenv sync
        ```
        
        ### Deploying DynamoDB Locally
        
        We use Amazon DynamoDB for our database. To deploy locally, follow [these instructions](https://docs.aws.amazon.com/amazondynamodb/latest/developerguide/DynamoDBLocal.DownloadingAndRunning.html).
        
        ### Init coding style tests
        
        Code style is managed by [flake8](https://github.com/PyCQA/flake8) and checked prior to commit.
        
        We use [pre-commit](https://pre-commit.com/#usage) to run conformance tests.
        
        This ensures:
        
        * Check code style
        * Check for added large files
        * Detect AWS Credentials
        * Detect Private Key
        
        Before first commit run:
        
        ```commandline
        pre-commit install
        ```
        
        
        ### Running unit tests
        
        Running unit tests is as easy as pytest.
        
        ```commandline
        pipenv run pytest
        ```
        
        ### Updating the disease normalization database
        
        Before you use the CLI to update the database, run the following in a separate terminal to start DynamoDB on `port 8000`:
        
        ```
        java -Djava.library.path=./DynamoDBLocal_lib -jar DynamoDBLocal.jar -sharedDb
        ```
        
        To change the port, simply add `-port value`.
        
        #### Update source(s)
        
        The sources we currently use are: OncoTree, OMIM, Disease Ontology, and Mondo.
        
        The application will automatically retrieve input data for all sources but OMIM, for which a source file must be manually acquired and placed in the `disease/data/omim` folder within the library root. In order to access OMIM data, users must submit a request [here](https://www.omim.org/downloads). Once approved, the relevant OMIM file (`mimTitles.txt`) should be renamed according to the convention `omim_YYYYMMDD.tsv`, where `YYYYMMDD` indicates the date that the file was generated, and placed in the appropriate location.
        
        To update one source, simply set `--normalizer` to the source you wish to update. Accepted source names are `DO` (for Disease Ontology), `Mondo`, `OncoTree`, and `OMIM`.
        
        From the project root, run the following to update the Mondo source:
        
        ```commandline
        python3 -m disease.cli --normalizer="Mondo"
        ```
        
        To update multiple sources, you can use the `normalizer` flag with the source names separated by spaces.
        
        ```commandline
        python3 -m disease.cli --normalizer="Mondo OMIM DO"
        ```
        
        #### Update all sources
        
        To update all sources, use the `--update_all` flag.
        
        From the project root, run the following to update all sources:
        
        ```commandline
        python3 -m disease.cli --update_all
        ```
        
        ### Create Merged Concept Groups
        The `normalize` endpoint relies on merged concept groups.
        
        To create merged concept groups, use the `--update_merged` flag with the `--update_all` flag.
        
        ```commandline
        python3 -m disease.cli --update_all --update_merged
        ```
        
        #### Specifying the database URL endpoint
        
        The default URL endpoint is `http://localhost:8000`.
        
        There are two different ways to specify the database URL endpoint.
        
        The first way is to set the `--db_url` flag to the URL endpoint.
        
        ```commandline
        python3 -m disease.cli --update_all --db_url="http://localhost:8001"
        ```
        
        The second way is to set the `DISEASE_NORM_DB_URL` to the URL endpoint.
        ```commandline
        export DISEASE_NORM_DB_URL="http://localhost:8001"
        python3 -m disease.cli --update_all
        ```
        
        ### Starting the disease normalization service
        
        From the project root, run the following:
        
        ```commandline
        uvicorn disease.main:app --reload
        ```
        
        Next, view the OpenAPI docs on your local machine:
        
        http://127.0.0.1:8000/disease
        
Platform: UNKNOWN
Classifier: Development Status :: 3 - Alpha
Classifier: Intended Audience :: Science/Research
Classifier: Intended Audience :: Developers
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: License :: OSI Approved :: MIT License
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3.8
Requires-Python: >=3.8
Description-Content-Type: text/markdown
