MedCATtrainer Client

A Python client for interacting with a MedCATTrainer web application instance. This package allows you to manage datasets, concept databases, vocabularies, model packs, users, projects, and more via Python code or the command line.

Features

  • Manage datasets, concept databases, vocabularies, and model packs

  • Create and manage users and projects

  • Retrieve and upload project annotations

  • Command-line interface (CLI) for automation

Installation

pip install mctclient

Or, if installing from source:

cd client
python -m build
pip install dist/*.whl

Python Usage

export MCTRAINER_USERNAME=<username>
export MCTRAINER_PASSWORD=<password>

from mctclient import MedCATTrainerSession, MCTDataset, MCTConceptDB, MCTVocab, MCTModelPack, MCTMetaTask, MCTRelTask, MCTUser, MCTProject

# Connect to your MedCATTrainer instance
session = MedCATTrainerSession(server="http://localhost:8001")

# List all projects
projects = session.get_projects()
for project in projects:
    print(project)

# Create a new dataset
dataset = session.create_dataset(name="My Dataset", dataset_file="path/to/data.csv")

# Create a new user
user = session.create_user(username="newuser", password="password123")

# Create a new project
project = session.create_project(
    name="My Project",
    description="A new annotation project",
    members=[user],
    dataset=dataset
)

MedCATTrainerSession Methods

  • create_project(name, description, members, dataset, cuis=[], cuis_file=None, concept_db=None, vocab=None, cdb_search_filter=None, modelpack=None, meta_tasks=[], rel_tasks=[])

  • create_dataset(name, dataset_file)

  • create_user(username, password)

  • create_medcat_model(cdb, vocab)

  • create_medcat_model_pack(model_pack)

  • get_users()

  • get_models()

  • get_model_packs()

  • get_meta_tasks()

  • get_rel_tasks()

  • get_projects()

  • get_datasets()

  • get_project_annos(projects)

Each method returns the corresponding object or a list of objects.

License

This project is licensed under the Apache 2.0 License.

Contributing

Pull requests are welcome! For major changes, please open an issue first to discuss what you would like to change.