MSID: 92493 Version: 1 DOI: 2023.07.18.549568

[nlisgo]

"msas": "Evolutionary Biology", "Microbiology and Infectious Disease" "msid": "92493" "preprintDoi": "10.1101/2023.07.18.549568" "Reviewed Preprint posted": "2023-12-28" "Sent for peer review": "2023-09-25" "Posted to bioRxiv": "2023-09-21" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2023.07.18.549568v2/")

[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/v2/by-publisher/elife/get-by-manuscript-id?manuscript_id=92493)

Step 2. Create preview of manuscript

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

• [ ] Manuscript is available for preview (https://prod--epp.elifesciences.org/preview/92493/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: [PLACE LINK TO PULL REQUEST HERE]

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

Step 3: Awaiting public reviews and QC

Who can help: Production team

• [ ] QC passed or QC not needed

Who can help: Editorial team

• [x] Public reviews available on sciety (https://sciety.org/articles/activity/10.1101/2023.07.18.549568)
• [x] Manuscript and editor details at the top of this issue (Supplied by Editorial team)
• [ ] Reviews returned by EPP - https://prod--epp.elifesciences.org/api/reviewed-preprints/92493/v1/reviews

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)

• [ ] Reviewed preprint is published to EPP (https://elifesciences.org/reviewed-preprints/92493)
  • [ ] 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: [PLACE LINK TO PULL REQUEST HERE] #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/92493

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/92493

Step 7: Introduce PDF to data folder and git repo

• [ ] PDF is avaliable at https://github.com/elifesciences/enhanced-preprints-data/raw/master/data/92493/v1/92493-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/92493)
  • [ ] 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!

[JGilbert-eLife]

Wrong version of the preprint has been imported. It should be the v2. www.biorxiv.org/content/10.1101/2023.07.18.549568v2

[fred-atherden]

v2 is imported now that automation is in place. Confirmed in this file s3://prod-elife-epp-data/automation/92493/v1/content/549568.xml having:

<article-version>1.2</article-version>

[fred-atherden]

Issues with refs 2 and 66 (duplicated info, formatting), but this is a platform issue instead of issue with the content