help to fix a messy library

lucianf
Hello all,

I have been using zotero to keep my bibliography and it is a relatively large collection. A few years ago I started using zotfile because I liked how it was renaming the files nicely according to my preffered pattern (authorYEAR.pdf)

I have followed some tutorials on how to use zotfile and I have ended up with a weird situation. I now have some files which zotfile could not move over from the original storage location of zotero and also the folder where zotfile has moved the files in the new organizational scheme (year->journal->authorYEAR.pdf)

Jump to today and zotero 7 and zotfile is not available anymore and I am now left with this mess of two locations with my pdf files.

I have organized some of my bibliography in different colections in zotero and I would like to keep that organization if possible but revert to a single location where all the pdfs are stored.

The reason why I used zotfile in the first place was to send files to an android tablet but that was wonky at best. I have solved this with syncthing but that's another subject.

Cheers
  • tim820
    Zotmoov or attanger replace Zotfile in Zotero v7.

    As long as Zotero can still locate your PDFs when you try to open them (either from local storage under Zotero\storage, or as linked PDFs elsewhere on your computer), Zotmoov should be able to move them as linked files to wherever you want them.

    Your collection structure in Zotero will not be not affected. You can move all your linked PDFs to a single folder if that is what you want (it is the simplest way to organize linked PDFs). Disable the subdirectory options in Zotmoov. Note that Zotero's new attachment file renaming scheme is used by Zotmoov and attanger, so you will need to set that up to ensure that PDFs are named as you prefer.

    If I have misunderstood, and the "single location" you want to store your PDFs is actually as "stored" files under Zotero\storage, then you want Tools\Manage Attachments\Convert Linked Files to Stored Files, to move your remaining linked files back there. If you need online syncing of those files, you will need to remain under your online file storage quota (300mb free).

    You can test these procedures on a small number of files first to see that they are doing what you want.
  • lucianf
    thank you for your answer. I have installed zotmoov but to be honest I don't see the benefit for it now.

    what I would like to achieve is to have all my pdfs organized by zotero in a single location like storage. Actually I have symlinked storage to a folder in my nextcloud instance but for all intents and purposed zotero should just put them in storage.

    At the moment what I have is as follows:

    I have storage as a symlink to a folder in nextcloud. there I have this folder structure created by zotero way back when. When I installed zotfile a few years ago, the tutorial said to chose a different location for the folder where zotfile will move the pdfs from the regular zotero storage. So I chose a location in my google drive folder (don't ask why I have nextcloud and google drive).

    Fast forward now my settings are as follows:

    Base directory: location where zotfile dumped the pdfs in google drive

    Data directory: default i.e. /home/lucian/Zotero

    Because I have zotmoov installed I set it up with the location in google drive.

    What I would like is get all the pdfs back to a single location in nextcloud without destroying the organization in zotero and get rid of zotmoov. I just don't see what it brings to the table now and if I get too locked in to it I might end up in another zotfile situation down the line.

    Cheers!
  • tim820
    edited 14 days ago
    Firstly, for clarity, by "Base directory" I assume you mean Zotero's "Linked Attachment Base Directory" (LABD). Don't confuse the meaning of that. While it might have been set to the same folder as the Zotfile "Custom Location" (Zotmoov "move to") folder setting, the LABD has a very different meaning. It only affects where Zotero *looks* for linked files, for example when you try to open them. It has no effect on where new linked files get stored - that was determined by the Zotfile Custom Location folder (Zotmoov "move to" folder). And if you have no more linked PDFs at the end of all this, the LABD setting will become irrelevant.

    Having the Zotero\storage folder symlinked elsewhere is an unsupported configuration. But it should work if you know what you're doing. Whereas having its parent folder (...\Zotero) - where the Zotero sqlite database is - symlinked to the cloud can cause problems ...
    https://www.zotero.org/support/kb/data_directory_in_cloud_storage_folder

    Presumably you're not syncing PDF files online to Zotero servers (ie file syncing is turned OFF). In that case you would not be using your Zotero online file storage quota, and so the total size of all your PDFs wouldn't matter, except to you.

    As you want to move your linked files back under Zotero\storage as "stored" files, that would be done with Zotero's Tools\Manage Attachments\Convert Linked Files to Stored Files. You first need to select the items which will have their linked PDFs. If you're not sure which items have linked PDFs, you should just be able to select a bunch of items, and Zotero will figure out which ones have linked PDFs that need to be moved back.

    Zotero must be able to find the linked PDF in order to move it. So it must be at the location baked into the Zotero database when it was originally added (or last moved by Zotfile). Zotero does not need Zotfile/Zotmoov to find it now. The LABD can affect that too, but presumably Zotero has been able to find your linked PDFs all long to open them, so it should be fine.

    Note that Zotero will indeed *move* the linked PDFs back under Zotero\storage. There will no longer be a copy of the PDF in its original linked-file location.

    It sounds like you have no use for Zotmoov in your new scheme.
  • lucianf
    Thank you for the detailed clarification.

    I will attempt to move the files over the weekend.

    A few clarifications:

    1) I am not using the zotero cloud just as you inferred. I cannot justify that for myself.
    2) I know that officially linking the storage folder is not supported but it has been working for years and it allows me to use my own "cloud" to keep the files. I am not syncing the entire zotero folder with the database because I read that it could cause issues.

    A question:

    what is the purpose of extensions like zotmoov (and the like) now? It seems to me that zotero has integrated most of the features they provide. I must be wrong because I am not that much of a power user.

    Thanks again for your help, I'll write back after I finish with the move!
  • tim820
    edited 13 days ago
    Re your question, Zotmoov does most of what Zotfile did (including recently adding Send/Get from Tablet). Zotero doesn't do much of that same work. Zotmoov (or attanger) is thus still very useful to automate a linked file strategy. So you're effectively asking why do people use linked files. There are lots of different reasons why some people use them, despite their limitations. You're not considering Zotero syncing so alternatives to that aren't relevant to you. Your symlink of all your Zotero\storage folders to Nextcloud presumably even avoids the need for local disk PDF space (not an option accessible to most users).
    https://www.zotero.org/support/attaching_files#stored_files_and_linked_files
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