Locutus Utilities

Overview

The locutus_utilities repository includes scripts and tools that facilitate the development and maintenance of Locutus. These utilities may include automation tools, and other resources that support the application's lifecycle.

Prerequisites

1. Google Cloud SDK: Installed and authenticated to use Google Cloud services.
2. Firestore enabled in your Google Cloud project.
3. Install setuptools
4. If running the 'update_ontology_api' option, You'll need a UMLS api key. If you don't already have one, log in and request an API key from UMLS. When you have this you can create a environment variable with the code below.

export UMLS_API_KEY=your_actual_umls_api_key

Installation

Installation

1. Create and activate a virtual environment (recommended):
   [Click here] for more on virtual environments.

   # Step 1: cd into the directory to store the venv
   
   # Step 2: run this code. It will create the virtual env named utils_venv in the current directory.
   python3 -m venv utils_venv
   
   # Step 3: run this code. It will activate the utils_venv environment
   source utils_venv/bin/activate # On Windows: venv\Scripts\activate
   
   # You are ready for installations! 
   # If you want to deactivate the venv run:
   deactivate

2. Install the package and dependencies:

   pip install git+https://github.com/NIH-NCPI/locutus_utilities.git

3. Run a command/action

   Available actions:

   • utils_run
     

Commands

utils_run

usage

utils_run -p <project_id> -o <option> -a <action>

• -p, --project

  • Description: GCP Project to edit.
  • Required: Yes

• -o, --option

  • Description: Choose the operation to perform.
  • Choices:
    • update_ontology_api: Updates the ontology API in Firestore.
    • update_seed_data: Updates seed data in Firestore.
    • delete_project_data: Deletes all data from the Firestore database.
    • reset_database: Deletes all data, then reseeds the Firestore database.
  • Required: Yes

• -a, --action

  • Description: Specify the action to take. Only used when running update_ontology_api, or reset_database
  • Choices:
    • upload_from_csv: Upload data from an existing CSV file to Firestore.
    • update_csv: Fetch data from APIs and update the CSV file only.
    • fetch_and_upload: Fetch data from APIs and upload it to Firestore.
  • Default: upload_from_csv
  • Required: No

• -u, --which_ontologies

  • Description: Choose to include all ontologies or only a selection. Only used when running update_ontology_api, or reset_database
  • Choices:
    • curated_ontologies_only: Use the selected default ontologies.
    • all_ontologies: Use all ontologies.
  • Default: all_ontologies

Working on a branch?

If working on a new feature it is possible to install a package version within
the remote or local branch
  ```
# remote
pip install git+https://github.com/NIH-NCPI/locutus_utilities.git@{branch_name}

# If using the command above, you may need to force a reinstallation to ensure the latest version.
pip install --force-reinstall --no-cache-dir git+https://github.com/NIH-NCPI/locutus_utilities.git

# local - if working on the package the installation will automatically update
pip install -e .

```