How can I automatically attach .skim file into the zotero repository

yijisoo
I use Skim to add notes while reading pdf files archived in my zotero repository. Whenever I have the note, it generates .skim file in the folder that the pdf file resides, which is not automatically archived into the zotero repository. Then, if I use another computer, the .skim file is not available to me because it is not synced. Are there any easy solution to this problem?
  • dstillman
    No. Zotero syncs full directory contents (by zipping the directory) only if the main file is an HTML file.
  • yijisoo
    Are there any way to cheat zotero to do full-directory-sync for non-HTML files?
  • dstillman
    Without modifying the code, no.
  • dstillman
    Well, I suppose you could do something like create an HTML file with the PDF embedded. If Skim works as a plugin, you could then use it that way. But you'd be adding a lot of friction to the process, which would sort of defeat the purpose of using Zotero for this to begin with.
  • yijisoo
    I see. I am thinking of creating a script file to 1) scan through zotero/storage folder; 2) identify all .skim files; and 3) add unattached skim files to the zotero database. I quickly review zotero.sqlite file to see if how it should be done. What kinds of tables should I updated? If I change items and itemAttachments, will it be fine? Or, I should do much more than that?
  • dstillman
    Sorry, you're on your own here. But there's only one attachment file in the database per attachment item/folder.
  • fgiorlando
    any progress on this, would be good to have this somewhat automated...
  • lfriedla
    I also have this problem. I annotate my PDFs in Skim. Maybe enough zotero users don't use Skim, but I am guessing that many annotate files some way or another. Losing all annotations makes it necessary to create two sets of files, obviously not a good solution. So any thoughts on this would be helpful.
  • mronkko
    You should save the annotations and notes in the PDF file. This is what people do with annotations. (And I think that this is the workflow regardless of the citation management software, with the exception of Mendeley that provides built-in annotation features)

    http://skim-app.sourceforge.net/manual/SkimHelp_47.html#SEC124

    (I a have never used Skim myself, but that link came up with google.)

    Also, you can use Dropbox or some other synchronization tool to synchronize the Zotero storage folder between computers.

    As Dan explains, it is very unlikely that the .skim files will be synced because this would require large changes to Zotero due to the way the files are stored.
  • oshd
    The .skim file is only used when exporting annotations. For normal use, Skim stores annotations in extended attributes of the HFS+ filesystem (this is why you lose annotations when emailing a Skim annotated PDF to someone).

    See http://sourceforge.net/apps/mediawiki/skim-app/index.php?title=FAQ#Where_are_the_notes_and_highlights_stored.3F
  • Stuarth
    edited September 21, 2020
    I'm also struggling with this as a Zotero and Skim user. Here is a crude way to force Zotero to merge Skim notes with PDFs that have had their notes/hilights stripped (say by emailing, or syncing with another computer).

    1. In Skim, export notes as as a .skim file (Export > File Format: Skim Notes)
    2. In Zotero, command-click / right-click the PDF lacking notes, click "Show File"
    3. Copy the .skim notes to this folder with the PDF and open the .skim file.
    4. In Zotero, click "Open PDF"
    5. Zotero will ask if you want to open it with the PDF with the same name in that folder. Click yes.
    6. Save your PDF in Skim. Your notes should now be merged and will remain when you reopen the PDF through Zotero.

    Hope this helps!
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