Wiki

This space is to provide resources for the project, such as important links, procedures, hints for other tools involved in each project stage, etc.

Links

Devin’s https://github.com/DevinBayly/vis-seive/ (MAIN)

Carolina’s https://github.com/carolinarr/vis-sieve (temporary)

PDF Storage - https://data.cyverse.org/dav-anon/iplant/home/baylyd/vis_sieve/

https://docs.openalex.org/

Label Studio - http://149.165.169.100:8080/

CSR account: c.roe email, low sec password

Project Stages

1. url gathering
2. pdf retrieval
3. (get figs?)
4. visualization

1. URL Gathering Stage

https://github.com/DevinBayly/vis-seive

2. PDF grabbing

Cyverse Datastore link https://data.cyverse.org/dav-anon/iplant/home/baylyd/vis_sieve/

Example python hear_me_ROR_script.py run:

python hear_me_ROR_script.py 2017 2018 --database ../database/publications.db --content_root ../database/content

python hear_me_ROR_script.py --help to see all the options

3. labeling

http://149.165.169.100:8080/user/login/

go ahead adn try to log in to and attempt to label a few things

4. Visualization Stage

Observable Framework

more details to come, but https://observablehq.com/framework/what-is-framework is a promising start. Note, it’s recommended to setup a code space from the vissieve repo.

https://devinbayly.observablehq.cloud/hello-duckdb/vissieve-test

Procedures

Docker Container + Reload Setup Instructions

1. Follow "Setup docker container" instructions here: https://github.com/DevinBayly/vis-sieve/tree/main/visualization BUT use this docker command instead: docker run -it --rm --mount type=bind,source="$(pwd)",target=/place -p 8080:8080 ghcr.io/devinbayly/vis_sieve_d3
   1. Notes
      1. ghcr = github-container-registry
      2. See devin's repo to view what's installed in container when you open it: https://github.com/DevinBayly/github-ci/blob/main/vis_sieve_d3
      3. If you open with docker command from vis-sieve repo (not updated command mentioned above), then you would run the following commands instead (once docker container opens):
         1. apt update
         2. apt install npm
            1. note: takes awhile
         3. npm install -g reload
            1. note: -g makes it global, so that any directory we go into we can run this reload command
2. Navigate to 'place' folder: cd place
3. Run the reload command: reload
4. Open browser and input URL: localhost:8080
5. Change index.html file, and whenever you save, page should update

6. To exit:

   1. I think 'Ctrl + C' to exit reload?
   2. I think 'exit' to exit docker container?

   Database Information

Database Information

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