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elifesciences / enhanced-preprints-import

Enhanced Preprints import system
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MSID: 88686 Version: 1 DOI: 2020.03.29.013649 #799

Open nlisgo opened 12 months ago

nlisgo commented 12 months ago

"msas": "Cell Biology", "Immunology and Inflammation" "msid": "88686" "preprintDoi": "10.1101/2020.03.29.013649" "Reviewed Preprint posted": "2023-08-16" "Sent for peer review": "2023-04-25" "Posted to bioRxiv": "2023-05-11" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2020.03.29.013649v2/")

[PLACE PDF URL HERE WHEN AVAILABLE] See step 7

Step 1. Inform bioRxiv

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

Step 2. Create preview of manuscript

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

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

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/88686

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/88686

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!

naushinthomson commented 11 months ago

Last author's affiliation is incorrect and different between biorxiv, the PDF, and EPP

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fred-atherden commented 11 months ago

Superscript plus is missing on EPP.

This is in the XML:

<aff id="a8"><label>8</label>NAD<sup>&#x002B;</sup> Immunology Laboratory, Huntington Medical Research Institutes, Pasadena, CA, USA</aff>

But not in the JSON:

{
      "type": "Person",
      "affiliations": [
        {
          "type": "Organization",
          "name": "NAD, Immunology Laboratory, Huntington Medical Research Institutes, Pasadena, CA, USA"
        }
      ],
      "emails": ["Abdala.elkhal@hmri.org"],
      "familyNames": ["Elkhal"],
      "givenNames": ["Abdallah"],
      "identifiers": [
        { "type": "orcid", "value": "http://orcid.org/0000-0002-4160-9416" }
      ]
    }

So we need a change in Encoda to support formatting type elements in affiliations.

@naushinthomson I'd be happy to proceed with this one if the only issue I can see is the missing superscript plus. WDYT? Is there anything else blocking this one?

fred-atherden commented 11 months ago

Sent request to get Encoda bug fixed

naushinthomson commented 11 months ago

@naushinthomson I'd be happy to proceed with this one if the only issue I can see is the missing superscript plus. WDYT? Is there anything else blocking this one?

Happy to proceed!