Ingest and Natural Language Processing of Research Outputs

The package is not yet deployed to PyPI. Only an editable (development) install is possible.

1. Provide a list of DOIs in a CSV file format list_of_dois.csv

2. Clone the repository git clonehttps://github.com/ClimateCompatibleGrowth/research_index_backend.git

3. Change directory cd research_index_backend

4. Install the package pip install -e . as an editable package (development install)

5. Obtain an OpenAIRE Graph refresh token and create a .env file with the following parameters:

      MG_PORT=
      MG_PORT_ALT=
      ORCID_NAME_SIMILARITY_THRESHOLD=
      NAME_SIMILARITY_THRESHOLD=
      OPENAIRE_API="https://api.openaire.eu"
      OPENAIRE_SERVICE="https://services.openaire.eu"
      REFRESH_TOKEN=
   

6. Provision Memgraph graph database and set up environment variables

   Once the VM is up and running, SSH into the VM, download and install memgraph

    $ curl -O https://download.memgraph.com/memgraph/v2.14.1/ubuntu-20.04/memgraph_2.14.1-1_amd64.deb
    $ sudo dpkg -i /memgraph_2.14.1-1_amd64.deb
   

7. Run the backend:

    $ research_index --help
    usage: research_index [-h] [--initialise INITIALISE] list_of_dois
   
    positional arguments:
    list_of_dois          Provide the path to CSV file containing a list of dois
   
    options:
    -h, --help            show this help message and exit
    --initialise INITIALISE
                          Deletes any existing data and creates a new database
   
    $ research_index list_of_dois.csv --initalise
   

Development

The package is maintained using hatch.

To run the tests run:

    hatch test