MSID: 92311 Version: 2 DOI: 10.48550/arXiv.2305.04587

[nlisgo]

MSID: 92311

Version: 2

Preprint DOI: https://doi.org/10.48550/arXiv.2305.04587

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=92311
• New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
• Reviews on sciety: https://sciety.org/articles/activity/10.48550/arXiv.2305.04587

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/92311v2
• 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/10.48550/arXiv.2305.04587
• Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/92311/v2/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!

[naushinthomson]

@fred-atherden code formatting isn't displaying on EPP

[fred-atherden]

Thanks for flagging @naushinthomson.

I notice in the meca file provided by Exeter, these are captured as code elements:

<p>The code and data to reproduce our analyses is openly available at <ext-link ext-link-type="uri" xlink:href="https://gitlab.uzh.ch/samuel.pawel/rsAbsence">https://gitlab.uzh.ch/samuel.pawel/rsAbsence</ext-link>. A snapshot of the repository at the time of writing is available at <ext-link ext-link-type="uri" xlink:href="https://doi.org/10.5281/zenodo.7906792">https://doi.org/10.5281/zenodo.7906792</ext-link>. We used the statistical programming language R version 4.3.2 (<xref ref-type="bibr" rid="c54">R Core Team, 2022</xref>) for analyses. The R packages <code>ggplot2</code> (<xref ref-type="bibr" rid="c66">Wickham, 2016</xref>), <code>dplyr</code> (<xref ref-type="bibr" rid="c67">Wickham et al., 2022</xref>), <code>knitr</code> (<xref ref-type="bibr" rid="c68">Xie, 2022</xref>), and <code>reporttools</code> (<xref ref-type="bibr" rid="c57">Rufibach, 2009</xref>) were used for plotting, data preparation, dynamic reporting, and formatting, respectively. The data from the RPCB were obtained by downloading the files from <ext-link ext-link-type="uri" xlink:href="https://github.com/mayamathur/rpcb">https://github.com/mayamathur/rpcb</ext-link> (commit a1e0c63) and extracting the relevant variables as indicated in the R script <code>preprocess-rpcb-data.R</code> which is available in our git repository. The RPP and EPRP data were obtained from the <code>RProjects</code> data set available in the R package <code>ReplicationSuccess</code> (<xref ref-type="bibr" rid="c25">Held, 2020</xref>), see the package documentation (<ext-link ext-link-type="uri" xlink:href="https://CRAN.R-project.org/package=ReplicationSuccess">https://CRAN.R-project.org/package=ReplicationSuccess</ext-link>) for details on data extraction.</p>

These have been converted to codeBlocks in the JSON (appropriate conversion), but EPP does not support code blocks. In any case, monospace would be more appropriate here.

I have fixed the package at s3://prod-elife-epp-meca/92311-v2-meca.zip, and triggered the temporal workflow. I think this should be resolved now (but LMK if not).