Linked attachments: Two requests

I'd like make a couple of feature requests, please, with regard to linked attachments. (Please forgive me if these issues have been raised before. I've done a quick search, but I may have missed something.)

1) I link to my pdf files, rather than storing copies of them in zotero. I'd like to use the store function, so I could back them up my files and sync them between computers, but I'm put off by the way zotero stores files, using a complex hierarchy which makes them next to impossible to access outside the program. (And I have too many pdfs to keep duplicates.) So, Request 1: Please could we have an option for zotero to treat linked attachments like internally stored files and include them in syncs?

2) At present, if one moves a linked file to a different folder, the link is broken and the moved file has to be relocated manually. Obviously, this makes housekeeping difficult, and transferring files between computers becomes a nightmare. So, Request #2: Please could zotero track changes in the locations of attachments? Or, if that would be too complex to implement, please could a bulk re-addressing function be added, so that a user could instruct the program that all attachments previously in folder X are now in folder Y?

Thanks for reading and congratulations on a great program.
  • 2) seems really hard to do. Even the "simpler" option you suggest. To the best of my knowledge "moved" files don't leave traces. Or are there programs that are able to do this? That's the main reason, btw., I don't use attachments. As for the alternative request, how exactly would that work? If one link gets lost, Zotero looks for all files that share part of its path and then allow you to rename that path? That seems more feasible, but still not simple.

    1) also seems hard to do from what I understand about syncing.

    Maybe you could give the method suggested here a try:

    1) could also be solved I guess, if you store a link and a copy of each file, though that seems a bit redundant...
  • Please could we have an option for zotero to treat linked attachments like internally stored files and include them in syncs?
    Well, the main problem currently is that links quite often aren't portable between computers, and never across platforms. See below for a relevant feature request. But even if the links were portable, I'm not sure Zotero should touch files outside its own data directory.
    Please could zotero track changes in the locations of attachments?
    No. There's not really any way to do that.

    But directory-relative storage might be a feature you would want.

    A question, though: if Zotero had a different folder naming scheme (or if you used the method adamsmith links to), would you still use linked files?
  • adamsmith: Thanks for your comments. On (2) I can see that the tracking option might be difficult to implement. But (naively perhaps -- I'm not a programmer) the alternative seems fairly easy. Couldn't it be done simply with a bulk find-and-replace command along the lines of: For any attached file currently stored in directory c:\a\b\c\, change directory to d:\x\y\z\ ? This would still be pretty basic, and it would leave a lot of scope for the user to mess things up (with multiple locations, etc), but it would be a vast improvement over the present situation, which has no functionality at all in this respect.

    On 1: I'll try the method you suggest and see how I get on. I wish I could sync my files, but I don't want to bury them away out of reach, and duplication is messy and wasteful.

    It would be great if at least 2 could be done. At present, the user has an unattractive choice: unwieldy attachments or inaccessible storage.

    But zotero is still the best citation manager I've tried!
  • Dan: Thanks for your reply.

    Yes, directory-relative storage looks like a *very* desirable feature.

    Would I still use linked files if zotero had a different naming structure? It depends what the new structure was. I'd like to have my files in zotero, but I also want them to be easily accessible outside it, from my file manager. Partly it's that I don't like to be hostage to a particular program, no matter how good it is; partly it's that I want to do stuff with my files without loading my citation manager (e.g. attaching them to emails).

    At present, as I said to adamsmith, I feel that both available options are unattractive. Linking is clumsy, and storing is inconvenient. Perhaps a more transparent storage format would solve both problems.

    But in the short term, directory-relative storage for linked files would help a lot.
  • Hi

    Albeit discussion is idle since July, I'm eager (and I supposed several other Zotero's evangelists like me) to know how the different folder naming scheme (a lot better solution than relative storage for links) is advancing (supposing it is)?
    Every week I have somebody from my research group trying to scape Zotero due to the clumsy links (as said well by Keith).

    I did a similar request (asking for feedback) in another thread dealing with link's relative storage without succes and I would be very happy to receive some info.

    I second Keith, a more transparent storage format would solve these problems.

    Thanks a lot

  • ewandro: This thread is primarily about linked attachments, not folder naming. There are many other threads on folder naming.
  • Hi,

    I just stumbled over this thread while looking for something completely different and found Keith’s second request quite interesting. I don’t see why it would be so hard to implement. As long as the file has only been moved to another location within the same filesystem, which will true in the vast majority of cases, it should be easy to locate it via its inode number, which could be stored along with its name when it’s added. Of course, locating the file this way might take some time, depending on where we start looking, but it would not require manual intervention by the user. I assume I’m missing something, but what?

  • I assume I’m missing something, but what?
    That way we have no way of doing this in Firefox.
  • Could I suggest something as a bit of a compromise? Couldn't one select a collection or a few files, and have copies of those attachments put into a folder?

    What I'm thinking of is when I want to send a few pdfs as an attachment in an email, it'd be nice to select them have them put in a folder on the desktop, and then attach, then drop the export folder in the trash when done. In this way, one could also select the ENTIRE library, and export all attachments to a folder.

    You can pretty quickly move between your zotero library and the desired file in your exported items folder by looking at the filename. Not 100% what people are asking for in this thread, but I *think* it's doable (zotero would have it's own internal copies still, and not care about what happens in the export folder) and you would get most of the same functionality as what is being discussed above.

    Maybe I should make this a new feature request?
  • people use links for other things (e.g. they keep their entire collection with links to keep their old file structure), so no, this doesn't do the same.

    It's already pretty easy to have all attachments in a single folder by using a saved search/virtual folder - if you search the forum there are instructions for doing this in Mac and Linux, I'm pretty sure it's somehow possible in Windows, too.

    The option to export a group of files might be nice, though considering that drag&drop isn't so bad probably not a top priority.
  • Well, there are two different things here. For LINKS export wouldn't make sense, but presumably those linked files themselves would be in a folder with a human friendly organization system. Another issue in this thread is if you have Zotero save the files *IN* Zotero, you effectively lose accesses to them directly, which is an issue I have, they are buried in random folders with nonsense names. Since I don't need to directly access those files very often, it's not a big deal, but it is a huge pain if I do want to ever get more than one file at a time. Endnote is also bad this way, but let's face it, that's not a standard Zotero should aspire to.

    I will freely admit that I am no expert here, I did try dragging and dropping an item from zotero to Thunderbird, I can drag and drop the citation (neat!) but it seems not the actual file. Also, tried exporting, again, can't export the actual pdf file in any sort of clear way.

    I suppose it's worth noting the way I use my library, I have mostly papers as pdfs, and I often make reading notes to the pdf directly in my pdf viewer. So the actual file itself is important to me, but for the most part I use just zotero as the librarian to find and open that file, and I don't care where it lives. Well, until I want to back everything up that is.
  • BGarms - sure but that question has been discussed at length in other places.
    Drag&drop is broken on linux so I can't test if dragging to Thunderbird works - dragging to the Desktop should definitely work.
    And note again the saved search solution I point to if you want easy access to files - this will give you a single folder will all your pdfs.
  • I had a try with this saved search, and spent some time looking in the forums for ways to do what I'm talking about. I'm not sure if I'm being clear about what I'm trying to do, and wrote a rather long post, but decided to edit it so as not to hijack this thread.

    Basically, saved search does NOT create a folder with all pdfs in it in a easy way, it requires multiple clicks and a drag a drop for each individual file.

    In short, Zotero needs to consider that the actual pdf files are an integral part of the library. Imagine if you had a music player that could take an mp3 and find the artist, album, lyrics, etc etc, but only be able to put mp3 files on a player one by one and only with great effort could you get an album of songs into a folder on a thumbdrive. (actually the way Zotero RDF exports files reminds me very much of the way iTunes puts files on an ipod, and that feels like a system designed to be as obtuse as possible)

    This I believe is what this thread is about, some people want zotero to be the equivalent of a music manager for other files like pdfs.

    In fact, now that I think about it, this is probably why so many people think one should be able to link files and move them around outside of Zotero, most music players can manage to rescan a folder and get music back into your library even if you move them yourself outside of the player.

    Thinking about it this way, couldn't Zotero put a long alphanumeric "stamp" on the file metadata (as a keyword) and then say - this file is associated with this library item, if it's not found where it's supposed to be, then ask if you want to remove the library entry, OR what folder to scan for the file, and when the file is found, link it back where it belongs?
  • edited July 20, 2010
    Basically, saved search does NOT create a folder with all pdfs in it in a easy way, it requires multiple clicks and a drag a drop for each individual file.
    that's simply not an accurate statement. I think it's due to a misunderstanding of what I refer to with saved search. I'm not talking about the Zotero feature, but about a saved search in the operating system.
    This thread describes this for linux:
    This threads describes this for Mac:

    This does not involve dragging and dropping, nor does it involve several clicks and most certainly no attention to individual files. And it really is quite easy to do.

    Maybe someone can post a guide on how to do this on Windows, the relevant feature is called a "Virtual Folder" under XP and Vista and "Library" under Windows 7.

    Edit: As for getting the pdfs of an individual collection, that would still involve drag and drop, but not clicking on individual files - this thread outlines two options:
    although for some reason the one I suggest there doesn't work if one of the things you search for is collection. No idea why, I think that might be a bug.
  • You could do this with small modification to ZoteroQuickLook plugin. That opens the selected PDF files into QuickLook viewer. It would be quite straightforward to change the software so that it shows the PDFs in Finder instead.
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