OpenSciMetrics (OSM) applies NLP and LLM-based metrics and indicators related to transparency, data sharing, rigor, and open science on biomedical publications.
How to build the Docker image and run the Docker container
Navigate to the project's root directory and run docker-compose up --build
When the image is built and the containers are running, open another terminal and start the osm container in interactive mode using the command docker-compose run osm bash
You can do file conversions in the container using this command osm pdf-xml-json "path_to_file_name.pdf" output_file_path
Or use the command docker-compose run --rm osm osm pdf-xml-json "path_to_file_name.pdf" output_file_path to convert files in non-interactive mode
supercedes #20.
Rebased version of previous PR
Loom video
https://www.loom.com/share/2b2dfbd8ef334f8280ed676dbde66b4b?sid=f5e951bb-2362-434c-baae-b02fdee8bd17
How to test
pip install -e .docker run --rm -p 8070:8070 elifesciences/sciencebeam-parserand keep it running for the rest of the testing periodosm pdf-xml-json "example_pdf_inputs/test_sample.pdf" {the output file}Loom Video https://www.loom.com/share/d4d3819fce9c439d9799eee4c4a9cc22?sid=f8fc9515-dbd9-4ebb-89d1-b2e0ba1abffd
How to build the Docker image and run the Docker container
Navigate to the project's root directory and run docker-compose up --build
When the image is built and the containers are running, open another terminal and start the osm container in interactive mode using the command docker-compose run osm bash
You can do file conversions in the container using this command osm pdf-xml-json "path_to_file_name.pdf" output_file_path
Or use the command docker-compose run --rm osm osm pdf-xml-json "path_to_file_name.pdf" output_file_path to convert files in non-interactive mode