MSID: 93191 Version: 1 DOI: rs.3.rs-2356429/v3

nlisgo commented 10 months ago

[PLACE MANUSCRIPT AND EDITOR DETAILS HERE WHEN AVAILABLE] See step 3

[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=93191)

Step 2. Create preview of manuscript

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

[ ] Manuscript is available for preview (https://prod--epp.elifesciences.org/preview/93191/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/10.21203/rs.3.rs-2356429/v3)
[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/93191/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/93191)
- [ ] 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/93191

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/93191

Step 7: Introduce PDF to data folder and git repo

[ ] PDF is avaliable at https://github.com/elifesciences/enhanced-preprints-data/raw/master/data/93191/v1/93191-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/93191)
- [ ] 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!

naushinthomson commented 10 months ago

@fred-atherden none of the equations are displaying

fred-atherden commented 10 months ago

Well spotted @naushinthomson. It looks like the equation images were missing from the manifest.xml file in the meca package. I've uploaded a corrected package to s3://prod-elife-epp-meca/93191-v1-meca.zip and re-run the workflow in temporal. Hopefully these will start showing shortly.

@JGilbert-eLife are you OK to feedback to Exeter? No need for them to do anything at this stage since I've corrected it.

JGilbert-eLife commented 10 months ago

Will do - it's from October last year so before they had some of their tests in place, so hopefully it won't recur.

fred-atherden commented 10 months ago

Ah OK - fine not to feedback I think then.

JGilbert-eLife commented 10 months ago

Ah, too late! I already sent an email - I wanted to double-check I'm right about there being tests for that in place now, just to be sure.

fred-atherden commented 10 months ago

No worries - sounds like that will still be worthwhile.

fred-atherden commented 9 months ago

@naushinthomson, I think this should be resolved now

naushinthomson commented 9 months ago

@fred-atherden the equations do look rather large in some places, I assume this is something we just have to proceed with?

fred-atherden commented 9 months ago

Yes unfortunately so, the size of the equations is a platform issue

elifesciences / enhanced-preprints-import