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elifesciences / enhanced-preprints-import

Enhanced Preprints import system
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MSID: 88900 Version: 1 DOI: 2023.06.15.545144 #543

Open nlisgo opened 1 year ago

nlisgo commented 1 year ago

"msas": "Neuroscience", "Structural Biology and Molecular Biophysics" "msid": "88900" "preprintDoi": "10.1101/2023.06.15.545144"

"Reviewed Preprint posted": "2023-07-05" "Sent for peer review": "2023-05-04" "Posted to bioRxiv": "2023-06-16" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2023.06.15.545144v1")

[PLACE PDF URL HERE WHEN AVAILABLE] See step 7

Step 1. Inform bioRxiv

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

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

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

Hi Ted,

Please can you prepare the preprint MECA for 10.1101/2023.06.15.545144

Thanks

Step 2. Create preview of manuscript

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

Pull request: https://github.com/elifesciences/enhanced-preprints-data/pull/119

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

Step 3: Awaiting public reviews

Who can help: 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)

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/88900

Step 5: Awaiting search reindex

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

#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/88900

Step 7: Introduce PDF to data folder and git repo

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

Step 8: Add PDF url to manuscripts.json

[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!

fred-atherden commented 1 year ago

Full text on bioRxiv, but no packages returned by their API:

curl 'https://api.biorxiv.org/meca_index/elife/all/2023.06.15.545144' | jq

{
  "status": [
    {
      "count": 0,
      "messages": "none found"
    }
  ]
}

@QueenKraken, can you reach out to Ted please?

QueenKraken commented 1 year ago

I've emailed Ted.

fred-atherden commented 1 year ago

Potentially fixed:

{
  "status": [
    {
      "count": 1,
      "messages": "ok"
    }
  ],
  "results": [
    {
      "msid": "545144",
      "tdm_doi": "10.1101/2023.06.15.545144",
      "ms_version": "1",
      "filedate": "2023-04-27",
      "tdm_path": "s3://transfers-elife/biorxiv_Current_Content/June_2023/17_Jun_23_Batch_1645/f2b1ee77-6c31-1014-9dbc-93632d7a9bbe.meca",
      "transfer_type": "api"
    }
  ]
}
QueenKraken commented 1 year ago

Yeah, received a message from Ted advising this had gone through.