MSID: 87292 Version: 1 DOI: 2023.04.03.535399

[nlisgo]

"msas": "Cancer Biology" "msid": "87292" "version": "1" "preprintDoi": "10.1101/2023.04.03.535399" "articleType": "Reviewed Preprint" "status": "Published from the original preprint after peer review and assessment by eLife."

"Reviewed Preprint posted": "2023-05-23" "Sent for peer review": "2023-04-03" "Posted to bioRxiv": "2023-04-05" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2023.04.03.535399v1")

[PLACE PDF URL HERE WHEN AVAILABLE] See step 7

Step 1. Inform bioRxiv

Who can help: @QueenKraken, @nlisgo, @scottaubrey

• [x] Manuscript is in data hub index (https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v1/by-publisher/elife/get-by-manuscript-id?manuscript_id=87292)

or (only one should be ticked. remove other from description.)

• [ ] Confirmed with Ted at bioRxiv that MECA archive is available

Send the following email to Ted and wait for his reply.

Hi Ted,

Please can you prepare the preprint MECA for 10.1101/2023.04.03.535399

Thanks

Step 2. Create preview of manuscript

Who can help: @fred-atherden, @nlisgo, @scottaubrey

• [ ] Manuscript is available for preview (https://prod--epp.elifesciences.org/preview/87292/v1)
  • [ ] Trigger import for staging: https://prod--epp.elifesciences.org/import
  • [ ] Sync data folder with s3://prod-elife-epp-data/data
  • [ ] Trigger import for staging: https://staging--epp.elifesciences.org/import
  • [ ] Sync data folder with s3://staging-elife-epp-data/data
  • [ ] Pull request created to enhanced-preprint-data
  • [ ] Post link to pull request below

Pull request: https://github.com/elifesciences/enhanced-preprints-data/pull/92

Detailed instructions: https://github.com/elifesciences/enhanced-preprints-data#add-a-manuscript

Step 3: Awaiting public reviews

Who can help: Editorial team

• [x] Public reviews available on sciety (https://sciety.org/articles/activity/10.1101/2023.04.03.535399)
• [x] Manuscript and editor details at the top of this issue (Supplied by Editorial team)

Example

``` "msas": "Genetics and Genomics", "Neuroscience" "msid": "84628" "version": "1" "preprintDoi": "10.1101/2022.10.28.514241" "articleType": "Reviewed Preprint" "status": "Published from the original preprint after peer review and assessment by eLife." "Reviewed Preprint posted": "2023-01-02" "Sent for peer review": "2022-10-28" "Posted to bioRxiv": "2022-11-21" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2022.10.28.514241v1") Editors: Reviewing Editor Michael B Eisen University of California, Berkeley, United States Senior Editor Michael B Eisen University of California, Berkeley, United States ```

Step 4: Modify manuscripts.json (no PDF)

• [x] Reviewed preprint is published to EPP (https://elifesciences.org/reviewed-preprints/87292)
  • [ ] Pull request created to enhanced-preprint-client
  • [ ] Pull request switched to "Ready for review"
  • [ ] Post link to pull request below
• [ ] Request that a doi be registered
  • [ ] Post link to #enhanced-preprint comment below

Pull request: https://github.com/elifesciences/enhanced-preprints-client/pull/739 #enhanced-preprint comment thread: [PLACE LINK TO COMMENT HERE]

Instructions to modify manuscripts.json

- Visit: https://github.com/elifesciences/enhanced-preprints-client/actions/workflows/publish-manuscript.yaml - Click: Run workflow - Complete the form and click "Run workflow" - A successful run should result in a new pull request at https://github.com/elifesciences/enhanced-preprints-client/pulls - Open the pull request and click the "Ready for review" button to trigger tests - Once the tests pass and you are happy with the changes the PR can be merged Example pull request: https://github.com/elifesciences/enhanced-preprints-client/pull/334/files Once the pull request is merged in it should be available a few minutes later.

Request that a doi

Post the following in #enhanced-preprint:

@Fred can you register a doi for https://elifesciences.org/reviewed-preprints/87292

Step 5: Awaiting search reindex

• [ ] Reviewed preprint is avaliable on journal 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.

Additional info

If needed, the jenkins pipeline to reindex search can be triggered sooner. https://alfred.elifesciences.org/job/process/job/process-reindex-reviewed-preprints/

Step 6: Published! Request PDF generation

• [ ] Post the link to the PDF url at the top of the issue
  • [ ] Post link to #enhanced-preprint comment below

#enhanced-preprint comment thread: [PLACE LINK TO COMMENT HERE]

Post the following to the #enhanced-preprint on slack:

@Ryan Dix-Peek please can you generate a PDF for https://elifesciences.org/reviewed-preprints/87292

Step 7: Introduce PDF to data folder and git repo

• [ ] PDF is avaliable at https://github.com/elifesciences/enhanced-preprints-data/raw/master/data/87292/v1/87292-v1.pdf

Detailed instructions: https://github.com/elifesciences/enhanced-preprints-data#add-a-pdf

Step 8: Add PDF url to manuscripts.json

• [ ] Reviewed preprint PDF is available for download (https://prod--epp.elifesciences.org/reviewed-preprints/87292)
  • [ ] Pull request created to enhanced-preprint-client
  • [ ] Pull request switched to "Ready for review"
  • [ ] Post link to pull request below

[PLACE LINK TO PULL REQUEST HERE]

Instructions to add PDF url to manuscripts.json

- Visit: https://github.com/elifesciences/enhanced-preprints-client/actions/workflows/add-pdf-url-to-manuscript.yaml - Click: Run workflow - Complete the form and click "Run workflow" - A successful run should result in a new pull request at https://github.com/elifesciences/enhanced-preprints-client/pulls - Open the pull request and click the "Ready for review" button to trigger tests - Once the tests pass and you are happy with the changes the PR can be merged Example pull request: https://github.com/elifesciences/enhanced-preprints-client/pull/397/files Once the pull request is merged in it should be available a few minutes later.

Step 9: Done!

• [ ] Kettle is on!

[fred-atherden]

Hi @HazalCiplak,

I'm getting a 404 response from the DataHub API for this one:

{"detail":"No Docmaps available for requested manuscript from the publisher eLife"}

Do you know why that is? Looks like the decision for this one was original Decline to Review, but then that changed following an appeal (eLife-RP-RA-2023-87292R1-Appeal). Could that be at play here?

Thanks in advance for looking into it.

[HazalCiplak]

Hi Fred,

You are right, the reason of it is definitely that! Thanks for raising this issue now we have an example to handle appeals for docmaps. I have created a ticket to include this manuscript in the docmaps.

https://github.com/elifesciences/data-hub-issues/issues/675

[fred-atherden]

Thanks Hazal!

[HazalCiplak]

Just wanted to update you from here to too, this docmap is available now: https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v1/by-publisher/elife/get-by-manuscript-id?manuscript_id=87292

[fred-atherden]

Nice one - thanks Hazal!