MSID: 89936 Version: 2 DOI: 10.1101/2023.06.29.547009

fred-atherden commented 3 weeks ago

MSID: 89936

Version: 2

Preprint DOI: https://doi.org/10.1101/2023.06.29.547009

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=89936
New model tracking: https://docs.google.com/spreadsheets/d/1_fHaoOy7hjyocptKtVJRijeNpUY4hBS7Ck_aVmx6ZJk/
Reviews on sciety: https://sciety.org/articles/activity/10.1101/2023.06.29.547009

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/89936v2
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/10.1101/2023.06.29.547009
Confirm reviews returned by EPP: https://prod--epp.elifesciences.org/api/reviewed-preprints/89936/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!

fred-atherden commented 1 week ago

warn: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c15) has a publication-type='other'. Is that correct? warn: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c25) has a publication-type='other'. Is that correct? warn: [mixed-citation-other-publication-flag] mixed-citation in reference (id=c39) has a publication-type='other'. Is that correct?

rkcook312 commented 1 week ago

Hi @fred-atherden, not sure why temporal is taking ages running this one (extract Meca)?

fred-atherden commented 1 week ago

Hi @rkcook312, looks like there's lots of files in the zip named oddly/placed inside a hidden __MACOSX folder:

I can find these in terminal via the following command:

unzip -l 89936-v2-meca.zip

Archive:  89936-v2-meca.zip
  Length      Date    Time    Name
---------  ---------- -----   ----
        0  06-17-2024 08:12   content/
      215  06-17-2024 08:12   __MACOSX/._content
  5012672  04-12-2024 15:40   content/547009v2_fig1.tif
      215  04-12-2024 15:40   __MACOSX/content/._547009v2_fig1.tif
        0  04-12-2024 18:00   content/supplements/
      215  04-12-2024 18:00   __MACOSX/content/._supplements
  4759944  04-12-2024 15:40   content/547009v2_fig2.tif
      215  04-12-2024 15:40   __MACOSX/content/._547009v2_fig2.tif
  7139288  04-12-2024 15:40   content/547009v2_fig3.tif
      215  04-12-2024 15:40   __MACOSX/content/._547009v2_fig3.tif
  2852896  04-12-2024 15:41   content/547009v2_fig4.tif
      215  04-12-2024 15:41   __MACOSX/content/._547009v2_fig4.tif
  6017940  04-12-2024 15:41   content/547009v2_fig5.tif
      215  04-12-2024 15:41   __MACOSX/content/._547009v2_fig5.tif
     5952  04-12-2024 15:42   content/547009v2_ueqn7.gif
      215  04-12-2024 15:42   __MACOSX/content/._547009v2_ueqn7.gif
    11813  04-12-2024 15:42   content/547009v2_ueqn6.gif
      215  04-12-2024 15:42   __MACOSX/content/._547009v2_ueqn6.gif
    11443  04-12-2024 15:41   content/547009v2_ueqn4.gif
      215  04-12-2024 15:41   __MACOSX/content/._547009v2_ueqn4.gif
    11620  04-12-2024 15:42   content/547009v2_ueqn5.gif
      215  04-12-2024 15:42   __MACOSX/content/._547009v2_ueqn5.gif
     3258  04-12-2024 15:43   content/547009v2_ueqn10.gif
      215  04-12-2024 15:43   __MACOSX/content/._547009v2_ueqn10.gif
     2606  04-12-2024 16:25   content/547009v2_ueqn1.gif
      215  04-12-2024 16:25   __MACOSX/content/._547009v2_ueqn1.gif
     5054  04-12-2024 16:46   content/547009v2_ueqn2.gif
      215  04-12-2024 16:46   __MACOSX/content/._547009v2_ueqn2.gif
     2424  04-12-2024 16:46   content/547009v2_ueqn3.gif
      215  04-12-2024 16:46   __MACOSX/content/._547009v2_ueqn3.gif
     6409  04-12-2024 15:42   content/547009v2_ueqn8.gif
      215  04-12-2024 15:42   __MACOSX/content/._547009v2_ueqn8.gif
     2941  04-12-2024 15:43   content/547009v2_ueqn9.gif
      215  04-12-2024 15:43   __MACOSX/content/._547009v2_ueqn9.gif
  1475332  04-10-2024 09:25   content/547009.pdf
      215  04-10-2024 09:25   __MACOSX/content/._547009.pdf
   111629  06-17-2024 15:28   content/547009.xml
      314  06-17-2024 15:28   __MACOSX/content/._547009.xml
  3779952  04-10-2024 09:22   content/supplements/547009_file02.pdf
      215  04-10-2024 09:22   __MACOSX/content/supplements/._547009_file02.pdf
      280  04-12-2024 18:32   directives.xml
      215  04-12-2024 18:32   __MACOSX/._directives.xml
     2815  04-12-2024 18:32   manifest.xml
      215  04-12-2024 18:32   __MACOSX/._manifest.xml
       20  04-12-2024 18:32   mimetype
      215  04-12-2024 18:32   __MACOSX/._mimetype
     1099  04-12-2024 18:32   transfer.xml
      215  04-12-2024 18:32   __MACOSX/._transfer.xml
---------                     -------
 31222646                     48 files

I've deleted these files via terminal, e.g.: zip -d 89936-v2-meca.zip __MACOSX/\*

And re-uploaded the file/re-run the workflow in temporal.

I have no idea how those hidden files are introduced tbh.

rkcook312 commented 1 week ago

many thanks @fred-atherden!

elifesciences / publish-reviewed-preprints-issues