Upgrade StorageHalf my PDFs gone in one click?!?!
OK... I've maybe done something dumb, and certainly something terrible. Please please help. That is years worth of stuff... just gone.
What I know:
1. I seem to have two places Zotero stores PDFs. Some strange place within Zotero's own directory (with a crazy string of letters for each subfile?), or in a directory full of PDFs (Which I named Zotero Main). I don't really understand why I had two, or whether that was dumb, or what I was supposed to do differently.
2. At some point I moved the directory "Zotero Main" and broke a whole ton of links. I never did figure out how to fix that. I would have to go re-associate each file to the new location the first time I wanted to use it. I'd love a fix for that, but now it is probably moot.
3. Just now I was redoing an association, and somehow clicked the wrong article within "Zotero Main." Now some Article X was coming up when I was trying to open Article A.
4. I didn't realize yet that I had mis-associated, so I thought maybe my original download of Article A was in error, so I reacquired Article A... and then had two entries in my library, the one that was mis-associated, and the one I had just downloaded.
5. I realize that I had somehow mis-associated, and thought I could fix it easy enough. I clicked on the mis-associated one and I think I clicked Manage Attachment>Rename Attachment, in the hopes to find the right file to change it to.
6. My "Zotero Main" directory went from having 100s of PDFs, to having exactly two - both with the same name, but one pulling up Article X. Somehow in renaming an association, I appear to have lost years worth of accumulated PDFs.
7. I have an upgraded Zotero online account. I THOUGHT that meant that all my PDFs were securely cloud-stored. That doesn't seem to be the case unless I am missing something. Only some portion are stored. And I can't see how to download the entire Library regardless.
How boned am I? Is there a way to recover my 100s of lost PDFs? What the hell?
Thanks. I'm pretty choked right now and could sure use some help...
Kevin
What I know:
1. I seem to have two places Zotero stores PDFs. Some strange place within Zotero's own directory (with a crazy string of letters for each subfile?), or in a directory full of PDFs (Which I named Zotero Main). I don't really understand why I had two, or whether that was dumb, or what I was supposed to do differently.
2. At some point I moved the directory "Zotero Main" and broke a whole ton of links. I never did figure out how to fix that. I would have to go re-associate each file to the new location the first time I wanted to use it. I'd love a fix for that, but now it is probably moot.
3. Just now I was redoing an association, and somehow clicked the wrong article within "Zotero Main." Now some Article X was coming up when I was trying to open Article A.
4. I didn't realize yet that I had mis-associated, so I thought maybe my original download of Article A was in error, so I reacquired Article A... and then had two entries in my library, the one that was mis-associated, and the one I had just downloaded.
5. I realize that I had somehow mis-associated, and thought I could fix it easy enough. I clicked on the mis-associated one and I think I clicked Manage Attachment>Rename Attachment, in the hopes to find the right file to change it to.
6. My "Zotero Main" directory went from having 100s of PDFs, to having exactly two - both with the same name, but one pulling up Article X. Somehow in renaming an association, I appear to have lost years worth of accumulated PDFs.
7. I have an upgraded Zotero online account. I THOUGHT that meant that all my PDFs were securely cloud-stored. That doesn't seem to be the case unless I am missing something. Only some portion are stored. And I can't see how to download the entire Library regardless.
How boned am I? Is there a way to recover my 100s of lost PDFs? What the hell?
Thanks. I'm pretty choked right now and could sure use some help...
Kevin
This is an old discussion that has not been active in a long time. Before commenting here, you should strongly consider starting a new discussion instead. If you think the content of this discussion is still relevant, you can link to it from your new discussion.
Are the files now actually inaccessible in Zotero? That is, do they have empty blue circles in the middle pane, and when you click on them does it say that they're missing?
Have you searched your computer for some of the filenames that are missing? ZotFile helps you use linked files. Zotero only syncs stored files. See Stored Files and Linked Files. That's the difference between the files in the Zotero data directory (in the random directories) and the ones in "Zotero Main". By default, Zotero uses stored files and manages and syncs everything for you. That's likely easily fixable if you find the files. We can also explain how to set things up correctly so that that never happens.
Oh! So I'm also wrestling with a modpack issue. My MineCraft troubles follow me into my research pursuits!
Ok... I did find the lost files, so that emergency is, I think, over.
I seem to now have:
1) a Zotero directory, where Zotero lives, with all its super confusing individual random directories
2) a "Zotero Main" that is a subdirectory of X
3) a "Zotero Main" that is a subdirectory of Y, and looks brand new, and only has the two strange articles that caused this upset. The one I mis-associated, and the one I correctly associated... but now in their own directory, named the same thing, but attached elsewhere in the directory tree.
I am 100% I've caused this nonsense, and would appreciate help fixing it. I must have pointed the default to the wrong place and so it is now saving outside the "Zotero Main" directory I intended.
Regarding your question:
(Huh... I can't find formatting options, for bold or inserting quotes! I'll just try standard... which seem to not work. Sorry.)
> Are the files now actually inaccessible in Zotero? That is, do they have empty blue circles in the middle pane, and when you click on them does it say that they're missing?
* When I click on a particular item, it expands to show pdfs, notes, etc. About 50% of my pfds are nice and tidy, the other half have a "link" symbol showing on them. Those say the association is lost when I click them. Nothing I've seen anywhere is an empty blue circle. - Oh, and I'm working on a Linux system, if that changes anything.
I'll review those links and see if I can make sense of what I've done, how it should work, and how to fix it.
Thanks for your answer. I get that I might be on my own since this is tied up with ZotFile also.
When you double-click a linked file that's missing, it tells you the full path where it's looking. The easiest thing to do is just to temporarily move the directory of those files back to that location so that the files can be opened, and then set the Linked Attachment Base Directory in the Advanced → Files and Folders pane of the Zotero preferences, which will convert all attachment files under the path you set to use relative paths (e.g., 'foo/Smith 2009.pdf' instead of 'C:\Users\Username\Research\Zotero Main\foo\Smith 2009.pdf'). You can then move that directory elsewhere (e.g., 'C:\Users\Username\Research\Zotero Files') and adjust the Linked Attachment Base Directory setting to point to the new location, so that when it looks for 'foo\Smith 2009.pdf' from that directory it finds the files. You can do this a couple times to consolidate all files under a single directory.
(You can also manually update paths of linked files using the Zutilo plugin, but it's not really necessary if you understand how to use the Linked Attachment Base Directory setting.)
1) Do I understand correctly that all those files Zotfile is managing (the linked ones that I have stored in a single main directory) are therefore outside of Zotero's responsibility (essentially) and that they therefore are not part of the sync?
2) Is there a way to get all files into Zotero's domain, so that they are synced and yet I can easily see, review and backup the directory?
3) Is there a way to get all files into a sensibly named directory, instead of the random string directories, and still maintain Zotero control? According to (https://www.zotero.org/support/zotero_data) the Zotero 5 standalone should have it in some base directory and Zotero 4 does the random strings. But I'm using 5.0.85 and still seem to have the random string directories. Is there a way to get all my stuff in one place, and under Zotero control?
2) if by "review" you mean that the folder structure is human-readable, then no (though see below). Any particular reason you need that? You can easily back-up Zotero's data folder, though, so that's unrelated.
3) No -- you're misreading the documentation. All files are in folders with random strings in 5.0.x and while I think this is likely to change in the future, it won't super soon. What you _can_ do, though, is to set up a virtual folder/saved search for PDF files in zotero/storage in your operating system. That would give you a view of all PDFs in a single folder.
OK... so I understand better, I think. Thank you.
It seems to me I still need an answer to the first part of #2. Then I'll maybe know how to move forward. To wit:
Is there a way to get all the files that are currently not within the Zotero structure to be transferred into Zotero? I'm not fond of having half my files in two different places, and only half of them syncing. (Am I understanding correctly that is currently the case? I believe that is what I've learned.)