MSID: 100788 Version: 1 DOI: 10.1101/2024.06.18.599531

fred-atherden commented 3 weeks ago

MSID: 100788

Version: 1

Preprint DOI: https://doi.org/10.1101/2024.06.18.599531

Step 1. Awaiting reviews

Editorial to post reviews via hypothesis

Useful links:

DocMap: https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v2/by-publisher/elife/get-by-manuscript-id?manuscript_id=100788
New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
Reviews on sciety: https://sciety.org/articles/activity/10.1101/2024.06.18.599531

For trouble shooting (e.g. no Docmaps available):

DocMap issue addressing: https://miro.com/app/board/uXjVNCwK6EI=/
Explore DataHub DocMaps API: https://lookerstudio.google.com/reporting/4c2f0368-babb-4beb-b5b3-497e7e7b0f08/page/ejphD
Unmatched submissions and preprints: https://lookerstudio.google.com/u/0/reporting/9f86204f-3bf7-477c-9b18-5c5ef141bf69/page/p_gxi57ha93c
Unmatched manuscripts spreadsheet: https://docs.google.com/spreadsheets/d/15QcK8w-ssB7109RQEDtFpJPZ0J5HTGxoHa_2TtpMBbg/edit#gid=1336081641

Step 2. Preview reviewed preprint

Production QC content ahead of publication

Instructions:

QC preview: https://prod--epp.elifesciences.org/previews/100788v1
Update ticket with any problems (add blocked label)
When QC OK, add QC OK label to ticket and add publication date and time to https://docs.google.com/spreadsheets/d/1amAlKvdLcaDp5W8Z8g77NmkwbMF5n_u89ArSqPMO8jg
Move card to next column
(At end of the day post link in #enhanced-preprint and ask for PDF to be generated)

Useful links:

Preprint DOI : https://doi.org/10.1101/2024.06.18.599531
Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/100788/v1/reviews
To update the MECA path in the docmap: https://docs.google.com/spreadsheets/d/1mctCQuNFBjSn97Lihy7_vBO6z7-N-oqyLv4clyi6zHg

Step 3: Awaiting search reindex

This step adds the reviewed preprint to the 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.

Useful links:

Jenkins pipeline to reindex search can be triggered sooner or monitored here: https://alfred.elifesciences.org/job/process/job/process-reindex-reviewed-preprints/

Step 4: Published! PDF requested

Waiting for PDF to be generated

Useful links:

PDF tracking: https://docs.google.com/spreadsheets/d/106_XeDjmuBae7gexOTNzg60lapeqjl2aRn9DzupGyS8/

Step 5: Introduce PDF to data folder and git repo

Upload PDF to relevent folder in git repo https://github.com/elifesciences/enhanced-preprints-data/

Step 6: Done!

[ ] Kettle is on!

elife-bot commented 1 week ago

- error: [author-corresp-no-email] Author William R Thomas has the attribute corresp="yes", but they do not have a child email element or an xref with the attribute ref-type="corresp".
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/05qghxh33; https://ror.org/05wyq9e07 in 1 https://ror.org/05qghxh33 https://ror.org/05wyq9e07 Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/04ydmy275; https://ror.org/0260j1g46; https://ror.org/03hamhx47 in 2 https://ror.org/04ydmy275 https://ror.org/0260j1g46 https://ror.org/03hamhx47 Department of Psychology, Developmental and Brain Sciences Program, University of Massachusetts Boston, Boston, Massachusetts, United States
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/03vzbgh69; https://ror.org/02w6m7e50 in 6 https://ror.org/03vzbgh69 https://ror.org/02w6m7e50 Department of Radiology, University Medical Center Freiburg, Freiburg, Germany
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/04m5j1k67; https://ror.org/02jk5qe80 in 7 https://ror.org/04m5j1k67 https://ror.org/02jk5qe80 Health Science and Technology, Aalborg University, Aalborg, Denmark
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/05qghxh33; https://ror.org/05wyq9e07 in 8 https://ror.org/05qghxh33 https://ror.org/05wyq9e07 Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, United States
- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [preprint-ref-article-title] This preprint reference (id c74) has no article-title element.
- error: [sec-empty] sec element is not populated with any content. Either there's a mistake or the section should be removed.
- error: [article-no-emails] This preprint has no emails for corresponding authors, which must be incorrect.
! warning: [given-names-test-12] given-names ends with ' von' - should this be captured as the beginning of the surname instead? - 'Dominik von'.
! warning: [given-names-test-12] given-names ends with ' von' - should this be captured as the beginning of the surname instead? - 'Dominik von'.
! warning: [journal-ref-text-content] This journal reference (id c71) has untagged textual content - . O’Rourke, . Is it tagged correctly?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c179) has a publication-type='other'. Is that correct?
! warning: [title-upper-case] Content of <title> element is entirely in upper case: Is that correct? 'CCDC22'
! warning: [title-upper-case] Content of <title> element is entirely in upper case: Is that correct? 'FAM57B'
! warning: [title-upper-case] Content of <title> element is entirely in upper case: Is that correct? 'GPR3'
+ info: [article-version-flag] This is preprint version 1.1.
! warning: [article-corresp] The number of corresponding authors and distinct emails is the same, but a match between them has been unable to be made. As its stands the corresp will display on EPP: *william.thomas@stonybrook.edu.
+ info: [permissions-info] This article is licensed under a CC BY 4.0 license. http://creativecommons.org/licenses/by/4.0/ https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#permissions-info

elife-bot commented 2 days ago

- error: [author-corresp-no-email] Author William R Thomas has the attribute corresp="yes", but they do not have a child email element or an xref with the attribute ref-type="corresp".
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/05qghxh33; https://ror.org/05wyq9e07 in 1 https://ror.org/05qghxh33 https://ror.org/05wyq9e07 Department of Ecology and Evolution, Stony Brook University, Stony Brook, New York, United States
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/04ydmy275; https://ror.org/0260j1g46; https://ror.org/03hamhx47 in 2 https://ror.org/04ydmy275 https://ror.org/0260j1g46 https://ror.org/03hamhx47 Department of Psychology, Developmental and Brain Sciences Program, University of Massachusetts Boston, Boston, Massachusetts, United States
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/03vzbgh69; https://ror.org/02w6m7e50 in 6 https://ror.org/03vzbgh69 https://ror.org/02w6m7e50 Department of Radiology, University Medical Center Freiburg, Freiburg, Germany
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/04m5j1k67; https://ror.org/02jk5qe80 in 7 https://ror.org/04m5j1k67 https://ror.org/02jk5qe80 Health Science and Technology, Aalborg University, Aalborg, Denmark
- error: [aff-multiple-ids] Affiliation contains more than one institution-id element: https://ror.org/05qghxh33; https://ror.org/05wyq9e07 in 8 https://ror.org/05qghxh33 https://ror.org/05wyq9e07 Consortium for Inter-Disciplinary Environmental Research, Stony Brook University, Stony Brook, New York, United States
- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [aff-institution-wrap-test-3] institution-wrap cannot contain text. It can only contain elements.
- error: [preprint-ref-article-title] This preprint reference (id c74) has no article-title element.
- error: [sec-empty] sec element is not populated with any content. Either there's a mistake or the section should be removed.
- error: [article-no-emails] This preprint has no emails for corresponding authors, which must be incorrect.
! warning: [given-names-test-12] given-names ends with ' von' - should this be captured as the beginning of the surname instead? - 'Dominik von'.
! warning: [given-names-test-12] given-names ends with ' von' - should this be captured as the beginning of the surname instead? - 'Dominik von'.
! warning: [journal-ref-text-content] This journal reference (id c71) has untagged textual content - . O’Rourke, . Is it tagged correctly?
! warning: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c179) has a publication-type='other'. Is that correct?
! warning: [title-upper-case] Content of <title> element is entirely in upper case: Is that correct? 'CCDC22'
! warning: [title-upper-case] Content of <title> element is entirely in upper case: Is that correct? 'FAM57B'
! warning: [title-upper-case] Content of <title> element is entirely in upper case: Is that correct? 'GPR3'
+ info: [article-version-flag] This is preprint version 1.1.
! warning: [article-corresp] The number of corresponding authors and distinct emails is the same, but a match between them has been unable to be made. As its stands the corresp will display on EPP: *william.thomas@stonybrook.edu.
+ info: [permissions-info] This article is licensed under a CC BY 4.0 license. http://creativecommons.org/licenses/by/4.0/ https://elifeproduction.slab.com/posts/licensing-and-copyright-rqdavyty#permissions-info

rkcook312 commented 2 days ago

@fred-atherden bit concerning the workflow for this has just rerun, not sure why?

fred-atherden commented 2 days ago

@rkcook312, thanks. I don't see any update to the reviews (although could be wrong), so something to discuss with @gnott perhaps. Could be something to do with how the eLife bot recognises newly posted reviews - this one has had reviews posted for a long time (7 days), perhaps the timeframe for checking has elapsed and this is now considered a 'new' preprint by the bot.

I think we still have access to the package you changed at s3://prod-elife-epp-data/automation/100788/v1/content.meca. I will replace the package at s3://prod-elife-epp-meca/reviewed-preprints/100788-v1-meca.zip with that one now.

rkcook312 commented 2 days ago

Many thanks @fred-atherden!

gnott commented 2 days ago

Correcting my early statement on our call @fred-atherden, I was able to find the difference in the docmaps to account for why it was ingested again.

The docmap for 100788 at about 2024-11-19 10:30 UTC had extra steps, probably duplicate values for the existing steps. The higher peer review count would have caused it to run again. It might be possible for me to improve this, to avoid counting duplicate steps if they are present, however I think it was caused by something in data hub I haven't accounted for (yet).

Here's the JSON from that hour for reference (taken from s3://elife-poa-packaging/docmaps/run_2024_11_19_0011/docmap_index/docmap_index.json):

{
    "@context": "https://w3id.org/docmaps/context.jsonld",
    "type": "docmap",
    "id": "https://data-hub-api.elifesciences.org/enhanced-preprints/docmaps/v2/by-publisher/elife/get-by-manuscript-id?manuscript_id=100788",
    "created": "2024-06-21T14:50:31+00:00",
    "updated": "2024-06-21T14:50:31+00:00",
    "publisher": {
        "account": {
            "id": "https://sciety.org/groups/elife",
            "service": "https://sciety.org"
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        "id": "https://elifesciences.org/",
        "logo": "https://sciety.org/static/groups/elife--b560187e-f2fb-4ff9-a861-a204f3fc0fb0.png",
        "name": "eLife"
    },
    "first-step": "_:b0",
    "steps": {
        "_:b0": {
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                    "outputs": [
                        {
                            "type": "preprint",
                            "identifier": "100788",
                            "doi": "10.7554/eLife.100788.1",
                            "versionIdentifier": "1",
                            "license": "http://creativecommons.org/licenses/by/4.0/"
                        }
                    ]
                }
            ],
            "assertions": [
                {
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                        "type": "preprint",
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                    "happened": "2024-06-26T18:16:44+00:00"
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            "inputs": [
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                        }
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                            "doi": "10.7554/eLife.100788.1.sa0",
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                            "actor": {
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                    "outputs": [
                        {
                            "type": "review-article",
                            "published": "2024-11-11T13:14:06.722996+00:00",
                            "doi": "10.7554/eLife.100788.1.sa1",
                            "license": "http://creativecommons.org/licenses/by/4.0/",
                            "url": "https://doi.org/10.7554/eLife.100788.1.sa1",
                            "content": [
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                                {
                                    "type": "web-page",
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                        {
                            "actor": {
                                "name": "anonymous",
                                "type": "person"
                            },
                            "role": "peer-reviewer"
                        }
                    ],
                    "outputs": [
                        {
                            "type": "review-article",
                            "published": "2024-11-11T13:14:07.540804+00:00",
                            "doi": "10.7554/eLife.100788.1.sa2",
                            "license": "http://creativecommons.org/licenses/by/4.0/",
                            "url": "https://doi.org/10.7554/eLife.100788.1.sa2",
                            "content": [
                                {
                                    "type": "web-page",
                                    "url": "https://hypothes.is/a/1RN3WKAuEe-jvIe9ARUAkg"
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                                {
                                    "type": "web-page",
                                    "url": "https://sciety.org/articles/activity/10.1101/2024.06.18.599531#hypothesis:1RN3WKAuEe-jvIe9ARUAkg"
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                        {
                            "actor": {
                                "name": "anonymous",
                                "type": "person"
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                            "role": "peer-reviewer"
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                    ],
                    "outputs": [
                        {
                            "type": "review-article",
                            "published": "2024-11-11T13:14:08.338039+00:00",
                            "doi": "10.7554/eLife.100788.1.sa3",
                            "license": "http://creativecommons.org/licenses/by/4.0/",
                            "url": "https://doi.org/10.7554/eLife.100788.1.sa3",
                            "content": [
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                                    "type": "web-page",
                                    "url": "https://hypothes.is/a/1Y1zPKAuEe-xyUMQqViEtQ"
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                                    "type": "web-page",
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                                "type": "person",
                                "name": "Vincent Lynch",
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                                    "location": "Buffalo, United States of America"
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                                "affiliation": {
                                    "type": "organization",
                                    "name": "Pennsylvania State University",
                                    "location": "University Park, United States of America"
                                }
                            },
                            "role": "senior-editor"
                        }
                    ],
                    "outputs": [
                        {
                            "type": "evaluation-summary",
                            "published": "2024-11-11T13:14:09.095356+00:00",
                            "doi": "10.7554/eLife.100788.1.sa4",
                            "license": "http://creativecommons.org/licenses/by/4.0/",
                            "url": "https://doi.org/10.7554/eLife.100788.1.sa4",
                            "content": [
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                                    "type": "web-page",
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                                    "type": "web-page",
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                                }
                            ]
                        }
                    ]
                },
                {
                    "participants": [],
                    "outputs": [
                        {
                            "type": "preprint",
                            "identifier": "100788",
                            "doi": "10.7554/eLife.100788.1",
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                            "license": "http://creativecommons.org/licenses/by/4.0/",
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                            "doi": "10.7554/eLife.100788.1",
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                            "license": "http://creativecommons.org/licenses/by/4.0/",
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                                "electronicArticleIdentifier": "RP100788",
                                "complement": []
                            }
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fred-atherden commented 1 day ago

Interesting - thanks Graham!

elifesciences / publish-reviewed-preprints-issues