How to batch convert Link to file attachments into copy of file attachment?

Is there a way to batch convert attachments on items that are "Link to file" into "Store Copy of file"?

I migrated from Mendeley, so all my existing items have attachments as "Link to file". I have 500+ items, and I would like Zotero to no longer have a "Link to file", but store a copy that is Zotero internally manages.

I looked into ZotFile, however, I still have not figured out a way to batch convert existing item "Link to file" attachment into copy of file.
  • ZotFile at least _should_ do this when you have it set to "Attach stored copy of file" and then use Manage Attachment --> Rename attachments and I know this used to work. I have a vague recollection that someone was having problems with this some time ago, but definitely worth trying.
  • edited September 24, 2018
    @adamsmith I tested out your suggestion, however, it ZotFile did try to rename/move the files, but it only does it to one item even though I selected multiple items. ZotFile does recognize that I am trying to move/rename multiple items and it even gives me a dialog saying it, but in the end, it will only move/rename one item. In addition, ZotFile actually renamed and moved my "original" PDF files instead of creating copy of it. Not is not good. I created a bug report on GitHub regarding this issue for ZotFile: https://github.com/jlegewie/zotfile/issues/368

    One down side of this method requires to "force" rename the files. What if I don't want to rename the files?

    Just out of curiosity, is it a complex task to implement the conversion of links to copies natively in Zotero?

  • One down side of this method requires to "force" rename the files. What if I don't want to rename the files?
    Zotero also force renames files it attaches, so that's in line with that.

    I don't think this would be crazy _complicated_ to implement in Zotero itself, but since there's currently nothing along those lines at all, it would probably a good amount of work, yes.
  • edited September 24, 2018
    @adamsmith Thanks you for response.

    1) Zotero does not force user to rename the files. Under Edit >> Preferences >> General >> File Handling, I have the ability to disable "Automatically rename attachment files using parent metadata".

    2) Can we have the native support in Zotero for converting existing "Link to file" attachment into "Store Copy of file" attachment be put on a wish list or feature request for Zotero?

    After migrating from Mendeley, I have over 500+ items with attachments as "link to file". All my future additions to Zotero will be copy of files, but the initial items are still stuck with "link to file" thus I can't take advantage of syncing.

    Below are examples of people needing the feature of converting "link to file" into "store copy of file":

    https://forums.zotero.org/discussion/34463/convert-linked-file-attachments-to-stored-attachments
    https://forums.zotero.org/discussion/9043/automatic-conversion-from-linked-files-to-copied-files


    Although ZotFile is a possible temporary work around, it still doesn't properly work due to bugs. Below are some examples of issues:

    https://github.com/jlegewie/zotfile/issues/368
    https://forums.zotero.org/discussion/comment/316079

  • @adamsmith Any chance my previous comment can be considered? Thanks :)
  • Not a part of the code I touch, but the devs that do read every thread, so yes, this is being considered.
  • @adamsmith Thank you for letting me know. You guys are doing a great job! I love Zotero! Thank you for all your efforts.
  • @dstillman @adamsmith In retrospect I realized that feature I am requesting is a very niche case to be considered as a core feature of Zotero. However, it be possible to incorporate this feature in the Mendeley import feature (https://forums.zotero.org/discussion/72260/available-for-beta-testing-mendeley-import)? When a user uses the Mendeley import feature to migrate from Mendeley to Zotero, all the attachment are set as "Link to file" by default. Would it be possible to allow the user to select if they want to migrate the attachments as "Link to file" vs. "Store Copy of file"?
  • When a user uses the Mendeley import feature to migrate from Mendeley to Zotero, all the attachment are set as "Link to file" by default.
    That's actually not the case. In Mendeley files can be stored either in a "Downloaded" folder in the profile folder or elsewhere on the computer in a folder specified in the preferences. When importing from Mendeley, files in Downloaded are copied and stored, whereas files in the designated folder are linked.

    We could add an option to store all files, but it would mean losing the folder hierarchy that Mendeley optionally creates. The alternative for someone who wanted to keep that would generally be to install the ZotFile plugin and set it to use that same folder structure. Of course, linked files in Zotero don't sync, so if syncing is more important than the folder structure — which it sounds like is the case for you — you might choose to store files instead.
  • edited 21 days ago
    @dstillman Thanks for the clarification.

    Yes, I think giving an option to 'store all files' would be helpful so that users can decide if their priority is syncing or maintaining a folder hierarchy of attachments locally. This would benefit first time migrators on how they plan their future use of Zotero, and they don't have to get stuck with portion of their library being 'linked' and a portion being 'stored'.

    I understand one can use ZotFile to convert linked attachments to stored attachments. However, based on my experience, ZotFile has an issue with batch conversions. Therefore, after a test migration from Mendeley, I wasn't able to convert all my linked attachments as stored copies.

    Previously I preferred to maintain linked attachments so I can have control over my organization and structure. I now prefer to let Zotero store the file so I can use the syncing feature. With zotero-file-hierarchy (thanks to @emilianoheyns ), I can always recovery the attachment folder hierarchy if I ever stop using Zotero.
  • @dstillman Sorry, don't mean to bump this thread. I was just wondering if the feature to have an option to 'store all files' during Mendeley migration will considered for implementation. If your team agrees, do you know if it will be happening in near term? I am just asking so I can plan for migration from Mendeley accordingly.
  • Just a couple day ago I switched on my Linux machine from Mendeley to Zotero. The switch was totally worth it, enjoy working with your software.
    Everything seemed to have worked out nicely. I set up syncing using my Nextcloud account.

    Now on my windows machine I have noticed, that all files werejust linked and not really synced or copied ,because i cannot open any here. I will have to see if I do a completely new import or if one of the suggested workaround works for me.

    I just wanted to add, that it would be helpful to give the option to actually import/copy all files using the mendeley import tool, or at least make the user aware, that files are just linked.
  • I think we'll be able to do something here soon, but we have to figure out a few things first.
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