Advice for indexing and syncing files

Hello,
I apologise for an seemingly obvious topic, but I would like some advice to help me get something "right" the first time I use it (to save me from getting lost half way through a massive project). I would like some information on how to work out my Zotero library, but I would also appreciate some suggestions or insight as to how academics maintain their own system.

About me:
I'm a 5th year phd student, having gone through multiple organisation strategies over the years. I am now thinking of settling with a setup of Scrivener, zotero, and Evernote. I study Japanese politics, so half of my resources are English, half are Japanese. I have so many subfolders of topics, such as Politics>Public Policy>Policymaking>NetworkTheory... etc. So I've deciced to move away from the folder hierarchy and try a single directory using tags for sorting.
Files names are a joke for me. Initially I had no system, but after a while I decided to go with "Title (Surname, Date)". I thought this was fine, but felt that it was prisoner to the folder hierarchy system. So now I am shifting to single folders (Politics, History, etc with no subfolders), and using "Name (date) Title".

What I want to do with my files:
I would like to index my pdfs to Zotero, but I would like some advice on how to move files. I do not want to use zotero storage (I would prefer the free version, and my files add up to more than 300 mb, so indexing is the only option right now).

My set up is Mac OSX, and I will be keeping my pdfs (and other documents) in a single location on my hard drive. At the moment, I have hundreds of pdfs across numerous folders, but I would like to centralise them to make them easy to find.

I want to index these files from one folder to Zotero, but I notice that when I move one file to another location, the link breaks. So, what happens if I ever want to move the entire folder to another location? Is there a way to move entire folders of linked items without the link breaking?

I am wondering if this is what the database file is for? If I have all the information for a pdf in the database (such as notes, tags, etc), even if I break the link by moving the folder, can I recover this data when I re-link the files? (eg., the linked item will restore the "parent directory" with all the bibliographical data and notes etc)

Another question then, is what should I be taking into consideration here? A follow up question is, what kind of issues would I be running into in the future.

For the time being, I would like to keep the files on my local hard drive. Should I keep them in my Macbook's "My document" folder, or should I put them in my own desired location?


Any advice and or suggestions would be greatly appreciated.

Cheers!
  • edited July 5, 2019
    I do not want to use zotero storage (I would prefer the free version, and my files add up to more than 300 mb, so indexing is the only option right now).
    I'm not sure what you mean by "indexing" — do you mean "linking"? — but this may be a misunderstanding. Zotero Storage is only required for syncing files between computers, not just for storing them in Zotero. Unless you're trying to use Zotero on multiple computers, you can still use stored files without a storage subscription. You can use linked files (generally with the ZotFile plugin), but they're more complicated and error-prone.
    Is there a way to move entire folders of linked items without the link breaking?
    Yes. You can use the Linked Attachment Base Directory setting. (That discusses multiple computers, but the same would apply if you moved your PDF folder on the same computer. You'd just need to update the base directory, and since the attachments would be stored with relative paths from the base they'd continue to work.)
  • Hi,
    Thanks for the quick reply. Yes, I meant "linking" when I said indexing (I was mixing up terminology from another program).

    I guess I wanted to enter the files as links because I dont like the arbitrary folder naming system that Zotero uses. I may have seen it somewhere, but is there an option to change that?

    But having read some other users' tips, I guess it doesnt really matter where the files are kept on my hard drive, because Zotero has the option to "Show File" in its folder location.
    I guess my concerns stems from an attachment to file hierarchy style organisation, and being able to easily access the files from a finder window.
    If I use zotero as THE base directory for my pdfs, then I guess it doesnt matter if they are split up into different subfolders, as long as I can access them through Zotero then it should be ok.

    Just to double check:
    the base directory is where is all the actual files like pdfs are stored, and the data directory is where the file information, links, and metadata for my files are stored? And that I should always leave the data directory on my hard drive, not in a cloud storage system.
  • Also, sorry for the simple questions, but I'm not really sure what relative and absolute paths are, which is why I didnt want to fiddle the settings.
  • the base directory is where is all the actual files like pdfs are stored, and the data directory is where the file information, links, and metadata for my files are stored?
    Not quite.

    The Zotero data directory is where Zotero stores its database and stored attachment files (which are the default).

    The Linked Attachment Base Directory is specifically for linked files, and it determines whether Zotero stores absolute paths (/Users/:user/Documents/PDFs/Thesis/foo.pdf) or relative paths (Thesis/foo.pdf). It doesn't apply to stored files, and it doesn't control where your files are stored. (Generally you'd set ZotFile to move files to that directory when linking them.)
    And that I should always leave the data directory on my hard drive, not in a cloud storage system.
    Yes.
    I guess my concerns stems from an attachment to file hierarchy style organisation, and being able to easily access the files from a finder window.
    Zotero provides many more options for organization and searching — items can exist in multiple collections (unlike folders), you can search on full metadata and content, you can use the tag selector to quickly filter things, etc. You can open files just by double-clicking the item in Zotero. You can use Show File to access the file itself, or you can even just drag the attachment item to a folder on your desktop or (depending on what you use) your email client to copy the file without even going to the Finder. There are various ways to export all your files later if you want to leave Zotero or use them in some other way.

    If you do want to search for PDFs via the Finder, that's fine too — you can search via Spotlight or set up saved searches that look for all PDFs within the data directory (though I've found advanced searches in the Finder to be extremely buggy in recent macOS releases).
Sign In or Register to comment.