Metadata-Version: 2.1
Name: thera-py
Version: 0.5.0.dev3
Summary: VICC normalization routines for therapeutics
Author: Alex Wagner, Kori Kuzma, James Stevenson
License: MIT License
        
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Classifier: Development Status :: 3 - Alpha
Classifier: Framework :: FastAPI
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# Thera-Py

[![DOI: 10.1093/jamiaopen/ooad093](https://img.shields.io/badge/DOI-10.1093%2Fjamiaopen%2Fooad093-blue)](https://doi.org/10.1093/jamiaopen/ooad093)

Services and guidelines for normalizing drug (and non-drug therapy) terms.

If you use Thera-Py in scientific works, please cite the following article:

> Matthew Cannon, James Stevenson, Kori Kuzma, Susanna Kiwala, Jeremy L Warner, Obi L Griffith, Malachi Griffith, Alex H Wagner, Normalization of drug and therapeutic concepts with Thera-Py, JAMIA Open, Volume 6, Issue 4, December 2023, ooad093, https://doi.org/10.1093/jamiaopen/ooad093

## Developer instructions
The following 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 data storage. To deploy locally, follow [these instructions](https://docs.aws.amazon.com/amazondynamodb/latest/developerguide/DynamoDBLocal.DownloadingAndRunning.html).

### Initialize development environment

Code style is managed by [Ruff](https://docs.astral.sh/ruff/) and checked prior to commit.

We use [pre-commit](https://pre-commit.com/#usage) to run conformance tests.

This ensures:

* Style correctness
* No large files
* AWS credentials are present
* Private key is present

Pre-commit *must* be installed before your first commit. Use the following command:

```commandline
pre-commit install
```

### Running tests

Unit tests are provided via pytest.

```commandline
pipenv run pytest
```

By default, tests will employ an existing DynamoDB database. For test environments where this is unavailable (e.g. in CI), the `THERAPY_TEST` environment variable can be set to initialize a local DynamoDB instance with miniature versions of input data files before tests are executed.

```commandline
export THERAPY_TEST=true
```

Sometimes, sources will update their data, and our test fixtures and data will become incorrect. The `tests/scripts/` subdirectory includes scripts to rebuild data files, although most fixtures will need to be updated manually.

### Updating the 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`.

### Setting Environment Variables
RxNorm requires a UMLS license, which you can register for one [here](https://www.nlm.nih.gov/research/umls/index.html).
You must set the `UMLS_API_KEY` environment variable to your API key. This can be found in the [UTS 'My Profile' area](https://uts.nlm.nih.gov/uts/profile) after singing in.

```shell script
export UMLS_API_KEY=12345-6789-abcdefg-hijklmnop  # make sure to replace with your key!
```

HemOnc.org data requires a Harvard Dataverse API token. You must create a user account on the [Harvard Dataverse website](https://dataverse.harvard.edu/), you can follow [these instructions](https://guides.dataverse.org/en/latest/user/account.html) to create an account and generate an API token. Once you have an API token, set the following environment variable:

```shell script
export HARVARD_DATAVERSE_API_KEY=12345-6789-abcdefgh-hijklmnop  # make sure to replace with your key!
```

#### Update source(s)

The Therapy Normalizer currently aggregates therapy data from:
* [ChEMBL](https://www.ebi.ac.uk/chembl/)
* [ChemIDPlus](https://chem.nlm.nih.gov/chemidplus/)
* [DrugBank](https://go.drugbank.com/) (using CC0 data only)
* [Drugs@FDA](https://www.accessdata.fda.gov/scripts/cder/daf/)
* [The IUPHAR/BPS Guide to PHARMACOLOGY](https://www.guidetopharmacology.org/)
* [HemOnc.org](https://hemonc.org/wiki/Main_Page) (using CC-BY data only).
* [The National Cancer Institute Thesaurus](https://ncithesaurus.nci.nih.gov/ncitbrowser/)
* [RxNorm](https://www.nlm.nih.gov/research/umls/rxnorm/index.html)
* [Wikidata](https://www.wikidata.org/wiki/Wikidata:Main_Page)

To update source(s), simply set `--sources` to the source(s) you wish to update separated by spaces. For example, the following command updates ChEMBL and Wikidata:

```commandline
python3 -m therapy.cli --sources="chembl wikidata"
```

You can update all sources at once with the `--update_all` flag:

```commandline
python3 -m therapy.cli --update_all
```

Thera-Py can retrieve all required data itself, using the [wags-tails](https://github.com/GenomicMedLab/wags-tails) library. By default, data will be housed under `~/.local/share/wags_tails/` in a format like the following:

```
~/.local/share/wags_tails
├── chembl
│   └── chembl_27.db
├── chemidplus
│   └── chemidplus_20200327.xml
├── drugbank
│   └── drugbank_5.1.8.csv
├── guidetopharmacology
│   ├── guidetopharmacology_ligand_id_mapping_2021.3.tsv
│   └── guidetopharmacology_ligands_2021.3.tsv
├── hemonc
│   ├── hemonc_concepts_20210225.csv
│   ├── hemonc_rels_20210225.csv
│   └── hemonc_synonyms_20210225.csv
├── ncit
│   └── ncit_20.09d.owl
├── rxnorm
│   ├── rxnorm_drug_forms_20210104.yaml
│   └── rxnorm_20210104.RRF
└── wikidata
    └── wikidata_20210425.json
```

Updates to the HemOnc source depend on the [Disease Normalizer](https://github.com/cancervariants/disease-normalization) service. If the Disease Normalizer database appears to be empty or incomplete, updates to HemOnc will also trigger a refresh of the Disease Normalizer database. See its README for additional data requirements.

### Create Merged Concept Groups
The `/normalize` endpoint relies on merged concept groups.  The `--update_merged` flag generates these groups:

```commandline
python3 -m therapy.cli --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 therapy.cli --update_all --db_url="http://localhost:8001"
```

The second way is to set the environment variable `THERAPY_NORM_DB_URL` to the URL endpoint.
```commandline
export THERAPY_NORM_DB_URL="http://localhost:8001"
python3 -m therapy.cli --update_all
```

### Starting the therapy normalization service

From the project root, run the following:

```commandline
uvicorn therapy.main:app --reload
```

Next, view the OpenAPI docs on your local machine:

http://127.0.0.1:8000/therapy


### FAQ

**A data import method raised a SourceFormatError instance. How do I proceed?**

TheraPy will automatically try to acquire the latest version of data for each source, but sometimes, sources alter the structure of their data (e.g. adding or removing CSV columns). If you encounter a SourceFormatException while importing data, please notify us by creating a new [issue](https://github.com/cancervariants/therapy-normalization/issues) if one doesn't already exist, and we will attempt to resolve it.

In the meantime, you can force TheraPy to use an older data release by removing the incompatible version from the source data folder, manually downloading and replacing it with an older version of the data per the structure described above, and calling the CLI with the `--use_existing` argument.
