MSID: 102676 Version: 1 DOI: 10.1101/2024.08.21.608981

[fred-atherden]

MSID: 102676

Version: 1

Preprint DOI: https://doi.org/10.1101/2024.08.21.608981

Step 1. Awaiting reviews

Editorial to post reviews via hypothesis

Useful links:

• DocMap: https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v2/by-publisher/elife/get-by-manuscript-id?manuscript_id=102676
• New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
• Reviews on sciety: https://sciety.org/articles/activity/10.1101/2024.08.21.608981

For trouble shooting (e.g. no Docmaps available):

• DocMap issue addressing: https://miro.com/app/board/uXjVNCwK6EI=/
• Explore DataHub DocMaps API: https://lookerstudio.google.com/reporting/4c2f0368-babb-4beb-b5b3-497e7e7b0f08/page/ejphD
• Unmatched submissions and preprints: https://lookerstudio.google.com/u/0/reporting/9f86204f-3bf7-477c-9b18-5c5ef141bf69/page/p_gxi57ha93c
• Unmatched manuscripts spreadsheet: https://docs.google.com/spreadsheets/d/15QcK8w-ssB7109RQEDtFpJPZ0J5HTGxoHa_2TtpMBbg/edit#gid=1336081641

Step 2. Preview reviewed preprint

Production QC content ahead of publication

Instructions:

• QC preview: https://prod--epp.elifesciences.org/previews/102676v1
• Update ticket with any problems (add blocked label)
• When QC OK, add QC OK label to ticket and add publication date and time to https://docs.google.com/spreadsheets/d/1amAlKvdLcaDp5W8Z8g77NmkwbMF5n_u89ArSqPMO8jg
• Move card to next column
• (At end of the day post link in #enhanced-preprint and ask for PDF to be generated)

Useful links:

• Preprint DOI : https://doi.org/10.1101/2024.08.21.608981
• Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/102676/v1/reviews
• To update the MECA path in the docmap: https://docs.google.com/spreadsheets/d/1mctCQuNFBjSn97Lihy7_vBO6z7-N-oqyLv4clyi6zHg

Step 3: Awaiting search reindex

This step adds the reviewed preprint to the homepage: https://elifesciences.org

The search reindex is triggered once an hour. We need the reviewed preprint to be indexed as the search application serves the journal homepage.

Useful links:

• Jenkins pipeline to reindex search can be triggered sooner or monitored here: https://alfred.elifesciences.org/job/process/job/process-reindex-reviewed-preprints/

Step 4: Published! PDF requested

Waiting for PDF to be generated

Useful links:

• PDF tracking: https://docs.google.com/spreadsheets/d/106_XeDjmuBae7gexOTNzg60lapeqjl2aRn9DzupGyS8/

Step 5: Introduce PDF to data folder and git repo

Upload PDF to relevent folder in git repo https://github.com/elifesciences/enhanced-preprints-data/

Step 6: Done!

• [ ] Kettle is on!

[fred-atherden]

@gnott, any idea what might have gone wrong with the workflow here? I can see the reviews in the DocMap, but the package isn't present at s3://prod-elife-epp-meca/reviewed-preprints/102676-v1-meca.zip.

[gnott]

Hi @fred-atherden, the workflow reached a timed out status. The last completed step was MecaPeerReviews, next up was the MecaXslt which was attempted three times until the workflow timed out.

I don't see evidence of anything else in the worker.log, and it's hard to say exactly what was at fault. It's possible the step didn't actually start and was still trying to be scheduled, so it's not necessarily an issue with the XSLT endpoint.

I recommend we try and ingest it again to see if we get the same result.

[elife-bot]

! warning: [journal-ref-text-content] This journal reference (id c65) has untagged textual content - :eabe1707. doi:. Is it tagged correctly?
! warning: [journal-ref-text-content] This journal reference (id c67) has untagged textual content - :10.1128/mbio.02457-19. doi:. Is it tagged correctly?
! warning: [ref-year-value-2] Ref with id c57 has a year element which does not contain a digit. Is it correct? (it's acceptable for this element to contain 'no date' or equivalent non-numerical information relating to year of publication)
+ info: [article-version-flag] This is preprint version 1.1.
+ info: [permissions-info] This article is licensed under a CC BY 4.0 license. http://creativecommons.org/licenses/by/4.0/ https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#permissions-info

[gnott]

Results! Probably an AWS / bot issue. There was a CNPIEC workflow timeout around the same time, and another (AdminEmail) during the same 15 minute gap or so, it's hard to pin down the exact reason.

[fred-atherden]

Makes sense - thanks for your help Graham!

[fred-atherden]

WOS query sent

[fred-atherden]

OK to proceed