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elifesciences / enhanced-preprints-import

Enhanced Preprints import system
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MSID 85786 DOI 2022.12.06.519376 #59

Open nlisgo opened 1 year ago

nlisgo commented 1 year ago

"msas": "Neuroscience" "msid": "85786" "version": "1" "preprintDoi": "10.1101/2022.12.06.519376" "articleType": "Reviewed Preprint" "status": "Published from the original preprint after peer review and assessment by eLife."

"Reviewed Preprint posted": "2023-05-16" "Sent for peer review": "2023-01-20" "Posted to bioRxiv": "2022-12-07" (link: "Go to bioRxiv": "https://www.biorxiv.org/content/10.1101/2022.12.06.519376v1")

[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: https://github.com/elifesciences/enhanced-preprints-data/pull/30

Instructions ``` $ git clone git@github.com:elifesciences/enhanced-preprints-data.git $ cd enhanced-preprints-data $ git checkout -b import-2022.12.06.519376 origin/master $ ./scripts/fetch_meca_archive.sh 2022.12.06.519376 incoming/ $ ./scripts/extract_mecas.sh incoming/ data/ $ rm -rf incoming/ $ git add . $ git commit -m 'import-2022.12.06.519376' $ git push -u origin import-2022.12.06.519376 ``` Create pull request: https://github.com/elifesciences/enhance/compare/master...import-2022.12.06.519376 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

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: Deprecated (no longer necessary)

Step 5: Modify manuscripts.json (no PDF)

Pull request: https://github.com/elifesciences/enhanced-preprints-client/pull/713 #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/85786

Step 6: 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 7: Published! Request PDF generation

#sciety-general 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/85786

Step 8: Add PDF to git repo

Instructions Download the PDF and rename to `2022.12.06.519376.pdf` Goto: https://github.com/elifesciences/enhanced-preprints-data/upload/master/data/10.1101/2022.12.06.519376 Upload the file `2022.12.06.519376.pdf` and commit directly to the master branch

Step 9: Add PDF url to manuscripts.json

[PLACE LINK TO PULL REQUEST HERE]

Instructions - 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 10: Done!

QueenKraken commented 1 year ago

No public reviews yet

fred-atherden commented 1 year ago

@hazalCiplak, @elifesciences/epp-tech-team It looks like this one has 7 public reviews in the DocMap, but at Sciety there are only 4 - with 3 being deleted.

Some of the links will return a 404 as a result of being deleted - https://sciety.org/evaluations/hypothesis:N37ACOm8Ee2rVhuprzKVeg/content. Are we able to proceed as is, or does this need updating in the DocMap (so that only reviews that aren't deleted are included)?

scottaubrey commented 1 year ago

@HazalCiplak, @elifesciences/epp-tech-team It looks like this one has 7 public reviews in the DocMap, but at Sciety there are only 4 - with 3 being deleted.

Some of the links will return a 404 as a result of being deleted - https://sciety.org/evaluations/hypothesis:N37ACOm8Ee2rVhuprzKVeg/content. Are we able to proceed as is, or does this need updating in the DocMap (so that only reviews that aren't deleted are included)?

From an EPP perspective, it is failing to retrieve the reviews as you would expect, and so I think we need a clean set of reviews in the docmap before publishing. Unless it's problematic in some way @HazalCiplak, I think we should remain blocked on this one until the docmap is fixed.

FYI @nlisgo @QueenKraken

fred-atherden commented 1 year ago

Good to know - thanks Scott.

HazalCiplak commented 1 year ago

Have these review been deleted in hypothesis too? If yes we need to delete them from data hub manually other wise it will reappear in data hub again.

fred-atherden commented 1 year ago

Sorry Hazal, I'm not sure. @acollings do you know?

acollings commented 1 year ago

Hi @HazalCiplak, @fred-atherden, yes, they've been deleted in hypothesis.

fred-atherden commented 1 year ago

@acollings, how often do you foresee needing to delete the public reviews?

@HazalCiplak is there anything we can do long term to make the removal of deleted Sciety/hypothesis reviews from DocMaps automated?

In the meantime, I happened to see this by chance when minting the DOIs prior to publishing this one. It sounds like, as a protocol, prior to publication we should check whatever the equivalent of https://prod--epp.elifesciences.org/api/reviewed-preprints/85786/reviews is for a RP, to make sure that the reviews aren't causing issues in EPP.

acollings commented 1 year ago

Thanks @fred-atherden It should be rare. This was caused by human error, as a result of the authors asking to provide an author response very late on (after the reviews had been added but before publication of the RP).

HazalCiplak commented 1 year ago

@HazalCiplak is there anything we can do long term to make the removal of deleted Sciety/hypothesis reviews from DocMaps automated?

@de-code, do you know how do sciety update?

de-code commented 1 year ago

@HazalCiplak, @elifesciences/epp-tech-team It looks like this one has 7 public reviews in the DocMap, but at Sciety there are only 4 - with 3 being deleted.

It looks like Sciety also includes the three deleted annotations:

https://sciety.org/articles/activity/10.1101/2022.12.06.519376

image

i.e. the issue exists there too (and there are some past papers with the same issue)

The problem is that Hypthesis doesn't seem to provide an API that would tell us something was deleted. The only way to find out seem to be to query those hypothesis annotations again and get a 404.

As this happens rarely, are we happy to proceed on the basis that we manually notice it?

I suppose having more than four annotations could also be a good indicator.

fred-atherden commented 1 year ago

As this happens rarely, are we happy to proceed on the basis that we manually notice it?

Sounds good to me - thanks

HazalCiplak commented 1 year ago

Hello,

I have created a Google Spreadsheet (https://docs.google.com/spreadsheets/d/1naXfcCxvTC8fLPhR8K1znC9B5DMxGP7HMpp-2CcO_sY/edit#gid=0) to track deleted hypothesis_ids. We will import this data to Data Hub and utilize this document to filter out these annotations from our Docmap API input. We need to make sure to add the corresponding IDs to the spreadsheet whenever any deletions are made from hypothes.is.

HazalCiplak commented 1 year ago

The docmap has been updated.

Hi @acollings, And in the deleting process of any review is it possible to be sure to add the corresponding deleted ids in this spreadsheet (https://docs.google.com/spreadsheets/d/1naXfcCxvTC8fLPhR8K1znC9B5DMxGP7HMpp-2CcO_sY/edit#gid=0) If there is a documentation for deletion protocol, it would be beneficial to include this step.

acollings commented 1 year ago

Will do, thanks!