Zotero Syncing

MJ94
Good evening!

I started using Zotero earlier this year by collecting sources mainly via the Zotero Chrome extension. I add the publications to my Library and then can conveniently double click them to open the PDF of the paper and additional details, etc.

I often right-click an item, click "Add Attachment," and attach a stored copy of a file. Then, I navigate to a file that I have on my local machine, such as a paper I just downloaded (or, if I am more organized, a paper in my research folder on my desktop).

I mistakenly assumed that my local client was set up to sync to the web and wiped my SSD. Now, Zotero is complaining (and rightfully so) that "The attached file could not be found at the following path [...] It may have been moved or deleted outside of Zotero, or a Linked Attachment Base Directory may be set incorrectly on one of your computers."

Totally my mistake—and yes, I have a backup. I have now enabled automatic syncing and "sync attachment files..." in both options. However, my online storage says I have 0 MB of content stored.

1. How can I sync what I currently have in Zotero to the web? What I am hoping to accomplish is the ability to sync Zotero so that if I switch computers or wipe my SSD in some "I'm-so-desperate-to-procrastinate-on-my-capstone-that-I'll-clean-out-my-years-of-storage-on-my-computer" situation, I'll still have the PDFs and source details handy (always).
2. Am I making the correct choice in uploading the files via a stored copy of a file? I have the PDFs on my computer or in my backup, so I'll re-add what I lost, but I want to make sure I don't lose it again.

I will also accept any "dude, do it this way, not that way" workflow tips. I'm always open to admit I'm doing it wrong and learn something new.

Thank you for the great tool!

Michael
  • dstillman
    edited October 7, 2020
    I mistakenly assumed that my local client was set up to sync to the web and wiped my SSD. Now, Zotero is complaining (and rightfully so) that "The attached file could not be found at the following path [...] It may have been moved or deleted outside of Zotero, or a Linked Attachment Base Directory may be set incorrectly on one of your computers."
    I'm actually a bit confused as to the situation you're in. Stored files are stored in the 'storage' folder of your Zotero data directory, along with your Zotero database (zotero.sqlite). If you wiped your disk, you'd have an empty library when you started Zotero, not a library with warnings about missing attachment files. So what did you do to get your Zotero library back?

    Or had you set up Zotero syncing but disabled file syncing, so that when you synced your empty library it pulled down your data from the online library but no files were available to download?

    Using stored files (which you can also do just by dragging PDFs into Zotero) is the default approach. If you set up syncing, everything will just sync between all your computers and the online library and you shouldn't have to think about it. But I'm not really sure of the state of your library and data directory now.
    I often right-click an item, click "Add Attachment," and attach a stored copy of a file. Then, I navigate to a file that I have on my local machine, such as a paper I just downloaded (or, if I am more organized, a paper in my research folder on my desktop).
    Unrelated, but this isn't really the standard Zotero workflow. See Adding Items to Zotero. Normally you would just save items from the web, and PDFs would be automatically attached and organized within Zotero's data directory. You generally wouldn't save PDFs separately on your computer or have to worry about manually attaching them.
  • MJ94
    I'm actually a bit confused as to the situation you're in. Stored files are stored in the 'storage' folder of your Zotero data directory, along with your Zotero database (zotero.sqlite). If you wiped your disk, you'd have an empty library when you started Zotero, not a library with warnings about missing attachment files. So what did you do to get your Zotero library back?"

    Yeah, I wiped my drive but did carry over some files/folders that I thought were important. I can't remember exactly what, but I believe I carried over some Zotero files. My library is completely in-tact, my attached PDFs just say they can't be found.

    "Using stored files (which you can also do just by dragging PDFs into Zotero) is the default approach. If you set up syncing, everything will just sync between all your computers and the online library and you shouldn't have to think about it. But I'm not really sure of the state of your library and data directory now."

    Yes. I unfortunately had syncing off until tonight, though. What I'm asking is if Zotero will now sync from my local client to the web? Because nothing is stored in the online library even though syncing is now on.

    "Unrelated, but this isn't really the standard Zotero workflow. See Adding Items to Zotero. Normally you would just save items from the web, and PDFs would be automatically attached and organized within Zotero's data directory. You generally wouldn't save PDFs separately on your computer or have to worry about manually attaching them."

    Thanks for letting me know. This is how several of my articles were added to Zotero, but I also had interlibrary loans (ILL) that were emailed to me and not hosted anywhere online. So, in those cases, I had to download the files. Once they were in my downloads folder (or I moved them to my desktop, I then attached them to Zotero. It looks like the files that I saved from the web and automatically attached are in my "Zotero" folder that contains the sqlite database, but the files I downloaded from my email from interlibrary loan (I couldn't save them because they weren't found on an open database) aren't in the sqlite database and are instead referenced elsewhere. For example, "Open Data, Grey Data, and Stewardship" is in /Users//Zotero/storage/K7ALTGAD whereas one of my downloaded ILL files says, "he attached file could not be found at the following path: /Users/michaeljackson/Downloads/01MNPALSCSS0010550.pdf It may have been moved or deleted outside of Zotero, or a Linked Attachment Base Directory may be set incorrectly on one of your computers." This makes sense because I downloaded it and attached it as a file since it wasn't available online and I had to request it.

    Sorry for the confusion. Does this make more sense? I am happy to provide more clarity as needed.

    Sidenote: How do I quote sections of text in a discussion as you did? Regular Markdown didn't work.

    Thanks again for your help.

  • dstillman
    Oh, I didn't look closely enough at the actual message you were getting. It's not a question of where the files come from. These are just linked files rather than stored files. You didn't actually use Add Attachment → "Attach Stored Copy of File" for these — you added them as linked files, either manually (by using "Attach Link to File") or by configuring the ZotFile plugin to create linked files. If you don't want linked files, don't add them that way, and everything will just be stored in your Zotero data directory and sync properly. Linked files don't sync.
    What I'm asking is if Zotero will now sync from my local client to the web? Because nothing is stored in the online library even though syncing is now on.
    Yes, if you have syncing on then data and stored files will sync. Linked files won't. Note that you have dozens of items and 65 MB of (stored) files in your online library.
    Sidenote: How do I quote sections of text in a discussion as you did?
    Use <blockquote></blockquote> tags.
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