MSID: 89076 Version: 1 DOI: 2023.06.09.544290

nlisgo commented 1 year ago

"msas": "Neuroscience" "msid": "89076" "preprintDoi": "10.1101/2023.06.09.544290" "Reviewed Preprint posted": "2023-08-04" "Sent for peer review": "2023-05-30" "Posted to bioRxiv": "2023-06-09" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2023.06.09.544290v1/")

[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=89076)

Step 2. Create preview of manuscript

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

[ ] Manuscript is available for preview (https://prod--epp.elifesciences.org/preview/89076/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/10.1101/2023.06.09.544290)
[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/89076/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/89076)
- [ ] 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/89076

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/89076

Step 7: Introduce PDF to data folder and git repo

[ ] PDF is avaliable at https://github.com/elifesciences/enhanced-preprints-data/raw/master/data/89076/v1/89076-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/89076)
- [ ] 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 commented 1 year ago

Author names slightly weird and corresponding authors all have same email address - result of bioRxiv input; elocations missing from reference list.

fred-atherden commented 1 year ago

Author names slightly weird and corresponding authors all have same email address

Hi @JGilbert-eLife, since I'm around today shall we block this one, and aim to get this corrected so it can be published with correct names/emails tomorrow?

JGilbert-eLife commented 1 year ago

Sounds good!

fred-atherden commented 1 year ago

Fix in https://github.com/elifesciences/enhanced-preprints-biorxiv-xslt/pull/74.

Note that since the only one of corresponding authors has an email address, only that author will be noted as corresponding after this fix.

fred-atherden commented 1 year ago

Should be fixed as indicated in the comment above now.

acollings commented 1 year ago

Hi @JGilbert-eLife and @fred-atherden. Thanks for looking after this! Definitely good to get this published, although the authors very much would like the three corresponding authors listed on the Reviewed Preprint. Is that possible? They've updated the preprint (to correct the issue with all three having the same email address), https://www.biorxiv.org/content/10.1101/2023.06.09.544290v3, but bioRxiv said it'll take 48 hours before all three display (as it'll be added when they add the full text).

The corresponding authors are:

Hu-lin Zhao (zhaohulin_90@sohu.com) Xin Xu (xuxinmm@hotmail.com) Ming-sha Zhang (mingsha.zhang@bnu.edu.cn)

Let me know what's possible (when you can)! Thanks!

fred-atherden commented 1 year ago

Thanks Andy - it's certainly possible. I'll replace the current version (1) with v3 once bioRxiv have made it available.

fred-atherden commented 1 year ago

(Full text still not available at bioRxiv)

acollings commented 1 year ago

Looks like it went up about ten minutes after @fred-atherden checked! (Authors emailed in to say it's up) https://www.biorxiv.org/content/10.1101/2023.06.09.544290v2.full

fred-atherden commented 1 year ago

Thanks Andy, good to know! bioRxiv's API is still only returning the MECA package for the v1 currently:

curl 'https://api.biorxiv.org/meca_index/elife/all/2023.06.09.544290' | jq

{
  "status": [
    {
      "count": 1,
      "messages": "ok"
    }
  ],
  "results": [
    {
      "msid": "544290",
      "tdm_doi": "10.1101/2023.06.09.544290",
      "ms_version": "1",
      "filedate": "2023-05-03",
      "tdm_path": "s3://transfers-elife/biorxiv_Current_Content/June_2023/12_Jun_23_Batch_1640/4d63c083-6cdc-1014-b9b2-fd2b4b4cd418.meca",
      "transfer_type": "api"
    }
  ]
}

Hopefully that will change soon.

Should we use the v2 or the v3 here? Looks like the latter is not yet available in full on the site.

acollings commented 1 year ago

Fine to use V2, @fred-atherden

fred-atherden commented 1 year ago

Ok thanks I'll check later to see if the mECA package is available.

fred-atherden commented 1 year ago

For some reason the MECA package for version 2 is still not available, so I've loaded v3 which is (based on the revision comments on bioRxiv, the only difference between the two versions is that v3 has the correct email address for the authors): curl 'https://api.biorxiv.org/meca_index/elife/all/2023.06.09.544290' | jq

{
  "status": [
    {
      "count": 2,
      "messages": "ok"
    }
  ],
  "results": [
    {
      "msid": "544290",
      "tdm_doi": "10.1101/2023.06.09.544290",
      "ms_version": "1",
      "filedate": "2023-05-03",
      "tdm_path": "s3://transfers-elife/biorxiv_Current_Content/June_2023/12_Jun_23_Batch_1640/4d63c083-6cdc-1014-b9b2-fd2b4b4cd418.meca",
      "transfer_type": "api"
    },
    {
      "msid": "544290",
      "tdm_doi": "10.1101/2023.06.09.544290",
      "ms_version": "3",
      "filedate": "2023-05-03",
      "tdm_path": "s3://transfers-elife/biorxiv_Current_Content/August_2023/16_Aug_23_Batch_1705/b9c4f9ee-6c00-1014-b2e4-a72c75d49daa.meca",
      "transfer_type": "api"
    }
  ]
}

Looking like this is resolved now, but let me know if I've misunderstood: Screenshot 2023-08-21 at 15 07 10

elifesciences / enhanced-preprints-import