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elifesciences / enhanced-preprints-import

Enhanced Preprints import system
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MSID: 93405 Version: 1 DOI: 2023.10.24.563872 #2226

Open nlisgo opened 10 months ago

nlisgo commented 10 months ago

"msas": "Stem Cells and Regenerative Medicine" "msid": "93405" "preprintDoi": "10.1101/2023.10.24.563872" "Reviewed Preprint posted": "2024-01-10" "Sent for peer review": "2023-10-24" "Posted to bioRxiv": "2023-12-23" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2023.10.24.563872v2/")

[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/93405

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/93405

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!

acollings commented 10 months ago

@naushinthomson the authors needed to tweak something in the preprint, so we should now be using https://www.biorxiv.org/content/10.1101/2023.10.24.563872v2.

Is there anything we need to do to ensure we use V2 for the first version of the RP?? Thanks!

naushinthomson commented 10 months ago

I'm actually not sure whether things change here under automation. Usually we'd reload the preprint but that might be different now @nlisgo do you happen to know?

fred-atherden commented 10 months ago

Looks like the docmap already currently has v2 in it:

 "inputs": [
                {
                    "type": "preprint",
                    "doi": "10.1101/2023.10.24.563872",
                    "url": "https://www.biorxiv.org/content/10.1101/2023.10.24.563872v2",
                    "versionIdentifier": "2",
                    "published": "2023-12-23",
                    "content": [
                        {
                            "type": "computer-file",
                            "url": "s3://transfers-elife/biorxiv_Current_Content/December_2023/25_Dec_23_Batch_1836/b689ce6b-6c55-1014-a475-f1612352b28e.meca"
                        }
                    ]
                }
            ]

@acollings If my understanding is right, the version being pulled in via automation should be the version that has been commented on in hypothesis by default. So (regardless of the above) as long as the reviews are added to the v2, then the v2 should be loaded (unless we deliberately are loading a different package for some reason).

acollings commented 10 months ago

Super, thanks @fred-atherden!