MSID: 100706 Version: 1 DOI: 10.1101/2024.07.09.602713

[fred-atherden]

MSID: 100706

Version: 1

Preprint DOI: https://doi.org/10.1101/2024.07.09.602713

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=100706
• New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
• Reviews on sciety: https://sciety.org/articles/activity/10.1101/2024.07.09.602713

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/100706v1
• 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/10.1101/2024.07.09.602713
• Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/100706/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]

- error: [sec-empty] sec element is not populated with any content. Either there's a mistake or the section should be removed.
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! warning: [mixed-citation-person-group-flag-2] mixed-citation in reference (id=c54) does not have an author person-group. Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c55) has a publication-type='other'. Is that correct?
+ info: [article-version-flag] This is preprint version 1.1.

[JGilbert-eLife]

Authors need to update preprint with new text. Asking WoS question at same time.

[JGilbert-eLife]

Chased

[JGilbert-eLife]

Authors have updated bioRxiv, need to wait for it to process: https://www.biorxiv.org/content/10.1101/2024.07.09.602713v2

[JGilbert-eLife]

@fred-atherden The V2 has processed at bioRxiv; please can we pull over the new versions?

[fred-atherden]

The bioRxiv API is still not showing the v2 MECA:

https://api.biorxiv.org/meca_index/elife/all/2024.07.09.602713

{
  "status": [
    {
      "count": 1,
      "messages": "ok"
    }
  ],
  "results": [
    {
      "msid": "602713",
      "tdm_doi": "10.1101/2024.07.09.602713",
      "ms_version": "1",
      "filedate": "2024-06-26",
      "tdm_path": "s3://transfers-elife/biorxiv_Current_Content/July_2024/14_Jul_24_Batch_2038/0c637946-72cc-1014-875a-a73c88ae1a5a.meca",
      "transfer_type": "api"
    }
  ]
}

However, the new API, only recently shared, does have a MECA package at a separate location:

https://api.biorxiv.org/meca_index_v2/elife/2024.07.09.602713v2

{
  "status": [
    {
      "messages": "ok",
      "count": 1,
      "request": "2024.07.09.602713v2"
    }
  ],
  "results": [
    {
      "msid": "602713",
      "tdm_doi": "10.1101/2024.07.09.602713",
      "ms_version": "2",
      "filedate": "2024-11-06",
      "tdm_path": "s3://biorxiv-src-daily/Current_Content/November_2024/06_Nov_24_Batch_2153/ca33ef89-7e41-1014-861e-b5822e93e9b1.meca",
      "transfer_type": "api"
    }
  ]
}

I'm not sure if the bot has access to biorxiv-src-daily, but it seems that I do. So I've copied the package over to s3://prod-elife-epp-meca/100706-v1-meca.zip for good measure (the bot definitely has access to that), and update the spreadsheet to include that as the meca path in the DocMap.

I've also moved the Reviews over to the v2. Let's see if this all works...

[JGilbert-eLife]

@gnott Please could you take a look at this in Fred's absence? The new package for this article doesn't appear to have been reprocessed yet and I'm not sure why, since the steps Fred took seem like they should have resulted in it being rerun based on s3://prod-elife-epp-meca/100706-v1-meca.zip.

[elife-bot]

- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [sec-empty] sec element is not populated with any content. Either there's a mistake or the section should be removed.
! warning: [aff-no-country] Affiliation does not contain a country element: 2 https://ror.org/03gnh5541 Institute of Science and Technology Austria
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! warning: [journal-ref-text-content] This journal reference (id c74) has untagged textual content - , no. . Is it tagged correctly?
! warning: [journal-ref-text-content] This journal reference (id c77) has untagged textual content - , no. . Is it tagged correctly?
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! warning: [journal-ref-text-content] This journal reference (id c85) has untagged textual content - , no. . Is it tagged correctly?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c2) has a publication-type='other'. Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c7) has a publication-type='other'. Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c9) has a publication-type='other'. Is that correct?
! warning: [mixed-citation-person-group-flag-2] mixed-citation in reference (id=c54) does not have an author person-group. Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c55) has a publication-type='other'. Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c72) has a publication-type='other'. Is that correct?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c76) has a publication-type='other'. Is that correct?
+ info: [article-version-flag] This is preprint version 1.2.
+ 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]

Hi @JGilbert-eLife, it's possible this would not run again automatically so I started an ingestion workflow again manually. It has produced some results above and the output zip will be on its way.

[JGilbert-eLife]

Brilliant, thanks @gnott - I'll check this tomorrow.