MSID: 86324 DOI: rs.3.rs-2197876/v1

nlisgo commented 1 year ago

"msas": "Evolutionary Biology", "Genetics and Genomics" "msid": "86324" "version": "1" "preprintDoi": "10.21203/rs.3.rs-2197876/v1" "articleType": "Reviewed Preprint" "status": "Published from the original preprint after peer review and assessment by eLife."

"Reviewed Preprint posted": "2023-04-28" "Sent for peer review": "2023-02-20" "Posted to Research Square": "2022-10-25" (link: "Go to Research Square": "https://www.researchsquare.com/article/rs-2197876/v1")

[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/get-by-doi?preprint_doi=10.21203/rs.3.rs-2197876/v1)

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

[ ] Confirmed with Ted at bioRxiv that MECA archive is available

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

Hi Ted,

Please can you prepare the preprint MECA for 10.21203/rs.3.rs-2197876/v1

Thanks

Step 2. Create preview of manuscript

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

[x] Manuscript is available for preview (https://prod--epp.elifesciences.org/preview/10.21203/rs.3.rs-2197876/v1)
- [x] Pull request created to enhanced-preprint-data
- [x] Post link to pull request below

Pull request: https://github.com/elifesciences/enhanced-preprints-data/pull/59

Instructions

``` $ git clone git@github.com:elifesciences/enhanced-preprints-data.git $ cd enhanced-preprints-data $ git checkout -b import-rs.3.rs-2197876 origin/master $ ./scripts/fetch_meca_archive.sh rs.3.rs-2197876 incoming/ $ ./scripts/extract_mecas.sh incoming/ data/ $ rm -rf incoming/ $ git add . $ git commit -m 'import-rs.3.rs-2197876' $ git push -u origin import-rs.3.rs-2197876 ``` Create pull request: https://github.com/elifesciences/enhance/compare/master...import-rs.3.rs-2197876 Merge in after CI passes and reviewing changes. Manuscript should be available for preview shortly afterwards. an example with multiple: ``` $ for doi in 2022.06.17.496451 2022.10.29.514266; do ./scripts/fetch_meca_archive.sh $doi incoming/; done $ ./scripts/extract_mecas.sh incoming/ data/ $ rm -rf incoming/ $ for doi in 2022.06.17.496451 2022.10.29.514266; do git checkout --no-track -b "import-$doi" origin/master; git add data/10.1101/$doi/.; git commit -m "import-$doi"; git push origin "import-$doi"; done; git checkout master; ```

Step 3: Awaiting public reviews

Who can help: Editorial team

[x] Public reviews available on sciety (https://sciety.org/articles/activity/10.21203/rs.3.rs-2197876/v1)
[x] Manuscript and editor details at the top of this issue (Supplied by 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)

[ ] Reviewed preprint is published to EPP (https://elifesciences.org/reviewed-preprints/86324)
- [ ] Pull request created to enhanced-preprint-client
- [ ] Post link to pull request below
[ ] Request that a doi be registered
- [ ] Post link to #enhanced-preprint comment below

Pull request: https://github.com/elifesciences/enhanced-preprints-client/pull/667 #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 workflow at https://github.com/elifesciences/enhanced-preprints-client/pulls 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/86324

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/86324

Step 7: Upload PDF to git repo

[ ] PDF is avaliable at https://github.com/elifesciences/enhanced-preprints-data/raw/master/data/10.21203/rs.3.rs-2197876/rs.3.rs-2197876.pdf

Instructions to upload pdf to git repo

Download the PDF and rename to `rs.3.rs-2197876.pdf` Goto: https://github.com/elifesciences/enhanced-preprints-data/upload/master/data/10.21203/rs.3.rs-2197876 Upload the file `rs.3.rs-2197876.pdf` and commit directly to the master branch

Step 8: Add PDF url to manuscripts.json

[ ] Reviewed preprint PDF is available for download (https://prod--epp.elifesciences.org/reviewed-preprints/86324)
- [ ] Pull request created to enhanced-preprint-client
- [ ] 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 workflow at https://github.com/elifesciences/enhanced-preprints-client/pulls 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!

nlisgo commented 1 year ago

Ticket created to address issue with non-biorxiv manuscripts not displaying: https://github.com/elifesciences/enhanced-preprints-issues/issues/581

fred-atherden commented 1 year ago

Blocked by issues which will be solved in https://github.com/elifesciences/enhanced-preprints-biorxiv-xslt/pull/18

fred-atherden commented 1 year ago

Fix for above issues in https://github.com/elifesciences/enhanced-preprints-data/pull/65

fred-atherden commented 1 year ago

Blocked because the DocMaps do not contain the reviews.

elifesciences / enhanced-preprints-import