links and directories deleted

In the process of trying to sync my macbook and my desktop I managed to delete all the links to files in both machines and on the zotero site.
The problem started when I tried to import My Library onto my desktop manually to save time with a slow connection, ended up with duplicates of everything then manually deleted the library on my laptop. Somehow this has now messed up everything across the board. I have a "My Library" file with all the links for pdfs etc (they show as being there)but can't get Zotero to link to them.I have checked the paths via advanced preferences and everything seems to be where it should be, and I am hesitant to tinker any further for fear of messing things up even more.

The online Zotero has all my directories intact before I messed up, and I have stopped syncing so that does not mess up too, but my main computer has deleted everything from the directories.

I have a time machine backup from before I created this mess. PLEASE can anyone help me get my life back other than having to upload each and every file individually.

Anyone who can help with this will be a life saver.

[I am thinking the best bet is just to completely uninstall one machine, get the other one fixed and synced with the online files and then reinstall and sync?]
  • The first thing I'd actually try is to use "Restore from Server" under the "Reset" tab of the Sync pane in the Zotero preferences. This will overwrite the local version of the library with what's on the server and given your description that may very well do the trick.
    If it doesn't, we'll be able to help you restore from your back-up, so there's no reason to panic. Don't re-install anything, that won't make a difference.
  • Thank you so much for the quick response.

    I think in the interim I have compounded the issue. We restored from Time Machine from before I made the mess and that seemed fine - but as soon as I began syncing files began disappearing from my desktop - so somehow the "delete"exercise I performed on my laptop is still affecting everything. To compound issues, after restoring from TimeMachine I have lost older versions of TimeMachine. I still have the My Library file I made that started the problem on a separate hard drive - I just created that with "export". It has a My Library.rdf file and a folder called "files" - those files have numerical filenames (short numbers - not the long strings I see in another version of My Library when I follow the instructions I found on another forum). This file is large - around 3 GB - which is what my storage was at before the whole mess started. This is the version I trust.

    I think I had messed the server version up before the Time Machine restore because my Library usage was 0 at that point so everything had already purged.
    ANY help you can give will literally be a life-saver as all my work and my dissertation were linked to this.

    I don't mind losing my folders and subfolders - but I would like to be able to keep the entries with the linked files. Losing notes would be disastrous.
  • edited April 13, 2014
    Are you saying that your online library is not correct? You have almost 6,000 items (including child items) online, with over 800 notes and 180MB of files. (This is in your personal library, not your group libraries.)

    The first step here is really just to browse your library on zotero.org and see if it has what you want. If it does, you just need to do what adamsmith says.
  • edited April 13, 2014
    A 3GB export certainly sounds different from what you currently have, though.

    But I'm not really clear what you mean by "links to files" in your first sentence. Can you be more specific? A Zotero library has top-level items, note items, attachment items, and then the associated attachment files on disk. What are you referring to?
  • Sorry I haven't been very clear - this is the sequence of events:

    1) I needed to sync my laptop as I was going away - but that day we didn't have reliable internet so I thought by exporting My Library from my desktop and importing on my laptop I would be able to update. It copied all the files so I had duplicates of all the files that existed at the time the laptop was previously synced. I still have that restore file.(as described above).
    2) I thought that the easiest way to get rid of the duplicates was to delete everything on the laptop and restore from the exported file. I did this and everything seemed fine, but when I tried to open attached items they I got the "files not available or have been moved message" (on the laptop). The laptop then synced to the remote file. I thought what I was doing was getting the files and attachments (everything) from the server but it seems to have removed the attachments from the server.
    3) In the intervening time I worked on the laptop, adding new items - those remained. I assumed that when I got home and synced from my desktop it would fix things but
    4) when I began sync from my desktop it began to delete folders and delete the attachments.

    I hadn't done anything on the group files so those are still intact (and I assume a whole lot that I put into another group that is a separate account).

    The situation at the moment is that most of the attachments (pdfs) that are showing on my computer and on the server are not opening and are giving the error message. Only those that I have added after the deletion or manually fixed will open. (The amount showing as stored on the server is what I added in the process of trying to correct the problem or after deletion). So what I need is the simplest way to get as close as possible to what I had before my own stupidity and impatience caused this problem, and get back to work.
  • edited April 13, 2014
    So as far as Zotero is concerned, importing an RDF file creates entirely new items, which are in no way related to your old ones. Thus, they are also not linked to any items you have previously inserted into your documents. (you discovered this the hard way)
    To compound issues, after restoring from TimeMachine I have lost older versions of TimeMachine.
    Are you sure there is no way you can redo the restore to the point before you deleted all items? (on either of your computers)

    Without the above restore point, you essentially have no backup of your old library and I can't think of a way for you to be able to restore links to your documents.

    Having said that, I'm not sure why you're having issues with links to files that you have imported from the RDF file. Could you take one such item, find its entry in the RDF file (open in a text editor, search by title), copy the full entry (starting with something like <bib:JournalArticle...> and ending with </bib:JournalArticle>) and paste it to https://gist.github.com/ and link to it here.

    We'll need you to do a few more lookups like that after you post the above.

    But the point is that importing from the RDF file should not result in broken links to file attachments and we may be able to fix this part. As I said before though, without the ability to get a copy of your library before the deletions happened, we won't be able to help you restore links to references in your documents.
  • Yeah, I'm not sure how restoring from Time Machine would've cleared old backups, unless your backup drive isn't big enough and the oldest backup (as indicated in the Time Machine preferences) is very recent.
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