The result of this work will create a normal AGU article with a new submission type for "Notebooks". This will have a link back to Curvenote, which adds computational capabilities. Curvenote is creating JATS XML from the notebook source as well as LaTeX to be used in production typesetting.
Notebook Submission Workflow¶
- Author will submit a GitHub, MECA or Zip file directly to Curvenote
- Validation will be completed on the notebook for computational reproducibility and other checks
- A MECA file will be generated see MECA examples
- This includes the
manifest.xml,transfer.xml, notebooks (and other sources), PDF andarticle.xml - A link to Curvenote documents will be added to the header of the
article.xml - MECA file is deposited using SFTP in EJP, which triggers additional steps
- This includes the
- Peer review happens as usual in EJP/GEMS
- The link provided is an authenticated magic-link that provides access for peer-reviewers and editors
- Revisions are requested
- Author resubmits notebooks and manuscript in Curvenote
- An updated MECA bundle is sent to EJP (using an SFTP deposit)
- Manuscript is accepted and moved to production
- Curvenote updates the MECA file for production (including production links)
- Curvenote provides an archived version of the notebooks and maintains the executable environment
- Curvenote deposits MECA with Wiley production team (how?!)
- Typesetting is completed on the LaTeX bundle, only for the main article (not the notebooks)
- Wiley creates the final JATS, and has a link to the notebooks in the
<front>and in a callout in the article PDF and online
- Curvenote updates the MECA file for production (including production links)
- Article goes live on Wiley digital library
- A signal to Curvenote to make the notebooks live?
Questions¶
- After we deposit the MECA bundle with EJP, what action is taken? Does the author have to take action?
- How do we associate a resubmission in EJP with a new MECA bundle?
Next Steps¶
- Ensure we can parse the LaTeX and it can go through the system
- Practice an SFTP upload in the test system
Outstanding Items¶
- Get setup with SFTP on EJP [in progress, Oct 12 - have SFTP access]
- We also saw a "trigger submission" xml. Action: confirm this is not needed
- Final production links back to Curvenote in the published manuscript
- Process of how to turn notebooks to public
Next year goals¶
- Aim for high-enough quality JATS that we can use this for production directly