MSID: 101125 Version: 1 DOI: 10.1101/2024.07.24.605002

[fred-atherden]

MSID: 101125

Version: 1

Preprint DOI: https://doi.org/10.1101/2024.07.24.605002

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=101125
• New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
• Reviews on sciety: https://sciety.org/articles/activity/10.1101/2024.07.24.605002

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/101125v1
• 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/10.1101/2024.07.24.605002
• Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/101125/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!

[elife-bot]

! warning: [journal-ref-text-content] This journal reference (id c2) has untagged textual content - ). Available at: . Is it tagged correctly?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c54) has a publication-type='other'. Is that correct?
+ info: [article-version-flag] This is preprint version 1.2.

[rkcook312]

Hi @fred-atherden, is this OK, i.e. bioRxiv not cropping the figures, they only seem to have cropped the last two figures properly, or should I reach out to the authors to ask bioRxiv to update the figures?

[fred-atherden]

Nice spot @rkcook312, I wonder if the page number at the bottom was causing issues?

In any case, I think we could just crop them ourselves (if we reach out to biorxiv there'll be a long delay I expect). Are you OK to do so?

[rkcook312]

Thanks @fred-atherden, I'll give that a try now.

[rkcook312]

Hi @fred-atherden, I changed the figure files in the package but the preview has not changed, are you still seeing the page numbers?

[fred-atherden]

@rkcook312, I reckon it'll probably be a caching issue at IIIF (where the images are hosted). If I visit (for example) https://prod--epp.elifesciences.org/iiif/2/101125%2Fv1%2Fcontent%2F605002v2_fig1.tif/full/max/0/default.jpg and then append ? followed by a random string of characters to the URL then I see the updated image.

I think the easiest way to get around this would be to simply rename the figure files in the package (you'd also need to update the article XML and manifest XML file with the new filenames). Are you OK to have a go at doing so? (I'm happy to help if you'd prefer)

[rkcook312]

Thanks @fred-atherden, that did it!