MSID: 88777 Version: 2 DOI: 10.48550/arXiv.2302.14157

[nlisgo]

MSID: 88777

Version: 2

Preprint DOI: https://doi.org/10.48550/arXiv.2302.14157

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=88777
• New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
• Reviews on sciety: https://sciety.org/articles/activity/10.48550/arXiv.2302.14157

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/88777v2
• 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/10.48550/arXiv.2302.14157
• Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/88777/v2/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!

[KJT08]

Hi @fred-atherden this one isn't showing on Sciety, but I understand there is an issue with preprints on arXiv showing.

[fred-atherden]

Thanks @KJT08, yes the Sciety issue is not a problem although there is a separate problem with the reviews.

@acollings we have the same issue with this one where the AR has been added to the non-versioned URL (https://arxiv.org/abs/2302.14157 instead of https://arxiv.org/abs/2302.14157v2).

Please could you take a look?

The URLS are:

• https://hypothes.is/a/tJ9UAr6rEe60al-PS186vg
• https://hypothes.is/a/sAELFr6DEe6CWmvD89KTSQ
• https://hypothes.is/a/sG27sr6DEe6QGDv4wLtxKg
• https://hypothes.is/a/r4rNFr6DEe61BIvqfkXnFg

[fred-atherden]

Just to add it looks like the reviews for the v1 made it onto the v1 link:

[acollings]

Thanks @fred-atherden I've moved the reviews etc across across

[fred-atherden]

Here's what we now have:

Unfortunately I see the AR is on the v1. I do also notice though that the docmap does not have the info on the revision here. I've added the info for the v2 to the unmatched spreadsheet. Let's see how that changes things once the information has made its way to the docmap

[fred-atherden]

@de-code - I wonder if you'd be willing to assist with updating the comments via hypothesis API here? (I'm assuming authorization is required to patch; I don't have credentials if so)

All the comments for the v2 are attached to the non-versioned link: https://arxiv.org/abs/2302.14157.

[de-code]

@de-code - I wonder if you'd be willing to assist with updating the comments via hypothesis API here? (I'm assuming authorization is required to patch; I don't have credentials if so)

Sure, I will try to get the credentials / an API key

[fred-atherden]

Sorry @de-code - I assumed you had the credentials, as a result of this comment. But re-reading it now I see that you just tested with your own account.

Maybe @acollings can help with the credentials?

[acollings]

(I'm not sure I can!! but I have a way of logging in to hypothes.is from an eLife account: let me know if that's what you need!)

[de-code]

Hi @acollings it would be good to quickly pair on it. If you have a way of logging in, then you should be able to create an API key if there isn't one already. I am not familiar with Hypothes.is permission system, whether there can be multiple people having permissions to update an annotation. In which case you could also add my account if that gave me the permissions.

[de-code]

Andy shared the API key with me...

Hi @fred-atherden just to avoid any potential confusion, we would like to move the following Hypothes.is annotations:

• 1v_CRr9wEe6l0u-LOdwdmg
• 5L75TL9wEe6mUbdQ8VZ2Ig
• z2aJNL9wEe6zqq_Q3-Gy2A
• 3WR2aL9wEe6EgLv-jzz2vw

From https://arxiv.org/abs/2302.14157 to https://arxiv.org/abs/2302.14157v2

Is that correct?

[fred-atherden]

Thanks @de-code Yes - thats right, those ones need shifting onto the v2 link.

[de-code]

Done:

DocMaps dashboard is showing the update:

I've create a Google Sheet to move Hypothes.is annotation. I don't want to share it too widely due to the embedded API key. Perhaps next week could share it with you. It would allow you to update the URIs yourself.

[fred-atherden]

Amazing - thanks Daniel.

Yeah if you could share the google sheet with Andy and I, that would be really helpful.

[fred-atherden]

This one is ready to check

[JGilbert-eLife]

Looks like the theorem sections have been interpreted as figures rather than text and equations:

Original PDF; tagging should be correct in the meca package:

Equations 4 and 7 too:

[de-code]

Amazing - thanks Daniel.

Yeah if you could share the google sheet with Andy and I, that would be really helpful.

I have shared the Google Sheet with you two. I also updated the script to store the API token in a user property instead which makes it a bit more secure. But you will have to set the API token in order to use it (I or Andy can share it with you separately).

[fred-atherden]

@JGilbert-eLife, I've resolved the above issue with a workaround