OpenSciMetrics

OpenSciMetrics (OSM) applies NLP and LLM-based metrics and indicators related to transparency, data sharing, rigor, and open science on biomedical publications.

Running the app

N.B. pdf parsing does not work on Apple silicon...

• With docker-compose and python >=3.11 installed, run the following from the project's root directory:

pip install .
osm -f path/to/pdf-or-xml -u uuid

If you have many files to upload you may with to start up the docker-compose dependencies in a separate terminal window:

docker compose up # docker-compose on some systems

And then tell the osm tool that this has been handled:

osm -f path/to/pdf-or-xml -u uuid --user-managed-compose
osm -f path/to/pdf-or-xml2 -u uuid2 --user-managed-compose

Contributing

N.B. On Apple silicon you must use emulation and download the mongo container in advance:

export DOCKER_DEFAULT_PLATFORM=linux/amd64
docker pull mongo:4.4.6

To contribute to the project please run the following commands to set up a development environment:

pip install -e .
docker compose -f compose.yaml -f compose.development.override.yaml up --build

And in another terminal:

export OSM_API="http://localhost:80"
osm -f path/to/pdf-or-xml -u uuid --user-managed-compose

Using pre-commit for commit checks

Pre-commit will run all of its hooks on every commit you make. To install pre-commit and its hooks, run the following commands:

pip install pre-commit
pre-commit install