OBO Metadata Editor

A web based editor for modifying existing and creating new OBO Metadata configurations.

Before running the server:

1. Install the necessary python dependencies using pip by navigating to the directory in which server.py is located and running the following command:

pip install -r requirements.txt

2. Make sure that the following environment variables have been set:

• GITHUB_CLIENT_ID
• GITHUB_CLIENT_SECRET
• GITHUB_APP_STATE
• FLASK_SECRET_KEY
• FLASK_HOST

To obtain the values for the first two settings, send an email to james@overton.ca. For the values of GITHUB_APP_STATE and FLASK_SECRET_KEY, a randomly generated string may be used. FLASK_HOST should be the full server address, including the protocol and (optionally) the port, e.g., https://purl-editor.com:5000.

3. Edit the file config.py and make sure that the configuration settings are correct. Note in particular the settings for LOG_LEVEL, GITHUB_ORG, SCHEMAFILE, and ONTOLOGY_METADATA_URL.

• LOG_LEVEL should be set to one of: DEBUG, INFO, WARNING, ERROR, CRITICAL (without quotes). Note that setting logging to DEBUG will only be effective if FLASK_ENV is set to development (the default is production)
• GITHUB_ORG should be set to the organization or username that owns the repository. Normally it should be set to OBOFoundry.
• SCHEMAFILE is the location of the jsonschema file that will be used to validate YAML code.
• ONTOLOGY_METADATA_URL is the URL from which descriptive information about various ontologies can be found.

Running the server

• Navigate to the directory in which server.py is located, and then run the following commands:

export FLASK_APP=server.py
export FLASK_DEBUG=1 (optional)
export FLASK_ENV=development (optional)
python3 -m flask run