SciNoBo Field of Science classification

This repository contains the code and the dockerfile for building the image and container responsible for the Field of Science classification of scientific publications.

Contents of repository

• input_files: Directory which contains test files for a demo. If you want to test the docker, then use this folder as the input volume to the docker when you run it. E.g. -v path/to/input_files:
• Dockerfile: Contains the commands for building the docker
• inference.py: Contains the code responsible for the inference procedure. This is the main script.
• input_schema.json: Example schema for how the input should be.
• L2_to_L1.json: Mapping from the L2 FoS fields to L1
• L3_to_L2.json: Mapping from the L3 FoS fields to L2
• L3_to_L4.json: Mapping from the L3 FoS fields to L4
• L4_to_L3.json: Mapping from the L4 FoS fields to L3
• multigraph.py: Contains the code for managing the inference graph of SciNoBo
• output_schema.json: Contains the output schema of the predictions
• requirements.txt: The python packages required.
• scinobo_inference_graph.p: The SciNoBo inference graph
• utils.py: Contains code for utilities
• venue_parser.py: Contains code for parsing the venue names
• venue_maps.p: Contains the abbreviations of the venues

Commands to build and run the docker

Create docker image

Use the following command to create a docker image. The flag -t specifies the name of the image that will be created with an optional tag (for example its version). docker build <-t NAME:tag> <Dockerfile location>

Example

docker build --tag intelcomp_fos .

• The name of the image in this case is intelcomp_fos, with no specific version.
• The location of the Dockerfile is the current directory.

Run image container

To run a container with the previous configuration, the following command is needed:

docker run <--rm> -i <--name CONTAINER-NAME> -v path/to/input/local/data:/input_files -v path/to/output/local/data:/output_files IMAGE-NAME python inference.py <args>

Flags:

• --rm: remove the container when execution ends. (optional)
• -i: set interactive mode. (optional)
• --name: a name for the container. (optional)
• v: volume binding. It maps a local directory to a directory inside the container so that local files can be accessed from it. The format is: /absolute/path/to/local/dir:/absolute/path/to/container/dir. You need to also specify a local directory where the docker will save the output

Reminder: If you want to test the docker, you need to use the following path as an input path --> -v path/to/input_files

Example

docker run --rm -i --name fos_inference_docker -v path/to/input/local/data/:/input_files -v path/to/output/local/data:/output_files intelcomp_fos python inference.py --file_type="parquet"

• path/to/input/local/data/ --> where the input files exist in the host
• path/to/output/local/data --> a directory in the host where you want the container to save the output

Test example

docker run --rm -i --name fos_inference_docker -v /path/to/input_files/demo_parquet:/input_files -v path/to/output/local/data:/output_files intelcomp_fos python inference.py --file_type="parquet"

Miscellaneous

• If you want to connect to the docker --> docker exec -it fos_inference_docker /bin/bash
• If you want to see the logs of the docker --> docker logs fos_inference_docker
• Copy the results of the docker to the host destination folder --> docker cp fos_inference_docker: ./output_test_files ./