Switching from linked PDFs to Zoteros own database

Swinkels
Hi,

I switched from Mendeley to Zotero a few months ago, and the switch went fine, all my were retained, etc., and all entries were added with links to PDFs in what used to be my Mendeley database.
However, I now want to be able to view these files on my personal laptop as well. Since linked files are not synced, I need to copy the linked PDFs to Zoteros own database somehow.
Unfortunately I cannot seem to find an option to do that easily.

Does anyone know a way to do this? I have about 900 entries in the database, so it needs to be a batch option of some sort.

Thanks in advance!
Piet
  • adamsmith
    I'm pretty sure Zotfile (www.zotfile.com) should allow you to do that:
    Install, set preferences to store as Zotero attachments, then select all items --> manage attachments --> Rename attachments

    That should convert linked items to Zotero stored files.
  • Swinkels
    Thanks! The method you mention *should* work, but it seems there is an issue in Zotfile which does not allow me to do this to more than 1 file at once:
    https://github.com/jlegewie/zotfile/issues/368

    Any other suggestions? Otherwise I just have to wait for Zotfile to fix the problem...
  • adamsmith
    Right, I had a vague recollection of a problem with that in ZotFile. I'm afraid that is (or rather, would be) the only way to do this in batch currently.
  • somainer
    Can other users confirm or deny if batch conversion of linked attached files to Zotero storage via Zotfile is broken?

    @Swinkels Did you find a workaround yet? If so, please share it.

    @dstillman If Zotfile batch conversion is broken, would this work: 1) export entire Zotero database including attachments as an RIS file; 2) completely erase ones database (how would you do that?); 3) Disable Zotfile management of attachments (how would you do that?) 4) import the RIS file into Zotero? I just this week switched to linked attachments managed by Zotfile, but if it’s not possible to easily get back to Zotero storage in the future (particularly now that an iOS app is likely in the pipeline), I would still have time to revert to a back up I made a couple days ago
  • somainer
    Would a developer or a very experienced user please weigh in on whether or not exporting Zotero database and attachments in RIS format (from a linked attachment file system based on Zotfile), then importing into a new database (specifying Zotero managing attachments), would be the appropriate workaround if Zotfile batch conversion is indeed broken?
  • dstillman
    You don't want to export to RIS. You could export to Zotero RDF, which will preserve your collections structure, but you'd lose item date added/modified times and links to items from word processor documents.

    I'm not sure when this will be fixed in ZotFile, but it probably makes sense for us to implement this in Zotero itself, probably with an option (unselected by default) to remove the original linked file after storing it. If you can wait a little while, I can let you know when that's available in a beta build.
  • somainer
    Thanks for your reply @dstillman and your willingness to consider implementing this feature! Zotfile has been such an excellent and well-supported add-in for so long that I have taken for granted that it would always work... but now see in the forum that the developer is stepping back, so I just wanted to be sure that I had an exit strategy in the future to preserve my data. It sounds like exporting to RDF Zotero would suffice (I care most about collections structure and attachments), so I will continue to use Zotfile to manage attachments until other Zotfile features stop working - but obviously a more complete solution for reverting to Zotero handling of attachments like you describe would be appreciated in the future. BTW, very slick job with the iPhone shortcut to add a book via scan of ISBN - I mostly work with journal articles, but love the ease of use with the occasional book. And many thanks for initiating the search for an iOS developer, as an iOS companion app which would support annotating would be awesome.
  • somainer
    Many props to the Zotero developers for implementing a former Zotfile feature!

    ChangeLog for version 5.0.75 (October 8, 2019) includes:
    Added “Convert Linked Files to Stored Files…” menu option. Available via File → Manage Attachments
  • annematthew
    Fantastic. Thanks Zotero. Many thanks Somainer for the heads up!
  • dstillman
    Just to note that I submitted a patch to ZotFile for various errors that could break batch renaming, and those fixes are now in ZotFile 5.0.13, so the ZotFile version of this probably now works again as well.
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