NIMH-8 - Section 2.2 PDF to XML, Setup custom docker file to bake in ScienceBeam Parser

[gitstart-app[bot]]

This PR was created by GitStart to address the requirements from this ticket: NIMH-8. This ticket was imported from: NIMH-8

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Loom Video\

https://www.loom.com/share/19d7d6e77d1049f891852e513e076226?sid=786b2381-ce9a-45b5-8361-7f0fe87b4713

How to build the image and run the container:

• Navigate to the project's root directory in your terminal
• Run docker build -t osm-image .to build the image
• When the build is complete, run docker run -it osm-image bashto run the Docker container

[leej3]

Running docker run -it osm-image runs the command directive of the docker file (python osm/cli.py --help), and fails to import from commands.

[gitstart-nimhdsst]

Running docker run -it osm-image runs the command directive of the docker file (python osm/cli.py --help), and fails to import from commands.

Just a heads up, we've managed to replicate this issue and are actively working on resolving it, in conjunction with the science-beam parser PR.

[gitstart-nimhdsst]

Can you rebase this if you chose to move forward with a dockerfile that uses elifescience/sciencebeam-parser as it's base. Otherwise use debian/neurodebian as a base image.

Understood, we will rebase. We had made updates to use a debian image in the current Dockerfile. We are yet to push this update though since it is still in progress.

[agt24]

Superseded by #25