Store PDFs in logical folder structure?

albo

Hello Folks,

I'm evaluating zotero, and will probably use it in some stage of my workflow. I'm curious about its file-storing capabilities. Specifically, by default, stored files (or "snapshots" - they seem to be the same thing in zotero?) get stored in one configurable directory. However, I like to have my files stored in some sort of folder structure that makes some sense. Thus, I would like to be able to click to download a pdf, to attach to a reference, and be able to choose where to store that pdf. Is this possible with zotero?

Ideally, it'd be awesome to be able to configure it to get stored in a folder structure that mirrors the category structure, but that's probably a pipe dream...

thanks,
allie

meetewlul

Good morning,

I store my pdf-downloads/scans (journal articles) in a folder named “SurgicalJournals” – some sort of a “Library”. The subfolders take the journal name. The tertiary folder then the month issue, etc.
The whole Journal “Library” is put in my Zotero Folder – ZoteroLibrary.
For example: d:\ZoteroLibrary\SurgicalJournals\BrJSurg\Vol123\Nr02\SomethingAboutSurgery.pdf
The articles I’ve already worked with in Zotero are linked to the corresponding .pdf file in my Journal Library. So when I need the whole text, I only have to double click on the Link Symbol in Zotero. That functions excellent.
On one side you have your Zotero Reference Structure that is (or should be) thematic, but on the other side you can at any time “peruse” your journal articles in your virtual “issues” or you can add a download or a new scan to the journal issue the text belongs to.
Then, I have a synchrocopy (in a Windows suitcase) of the whole Zotero folder on my USB-stick together with a mobile variety of Firefox and Zotero.
I hope, I could help

meetewlul

albo

Thanks - that's just how i'd like to organize things myself. However, when you save a pdf "snapshot" in zotero, it only seems to be able to put them in one directory. Is there an option somewhere that allows a dialog box to pop up, asking where you want to physically store the snapshot?

It sounds to me like you're downloading the pdf's manually, placing them in the folder hierarchy, and then linking the pdfs to zotero. I'd like to not have to download the pdf's manually.

thanks,
allie

meetewlul

There are two aspects
First: Zotero stores snapshots in its “Storage”directory. In the Manual (Zotero site) there is a description of how you can change the spot of this folder on your hard disk.
You can change the snapshot file location too – say - into a folder that has the structure you want. But it means manual work – Zotero doesn’t automatically offer you an option for storing a snapshot into a particular folder. This could be a useful function, and it could be a consideration for the developers.
The second aspect: I DO store my periodicals manually but I am doing it all my life, and it’s worth investing time in it.

albo

Yeah, I store my pdf's manually as well, and then link them to my citation manager. While zotero offers an option to change the folder location, it is still tied to one particular folder, if I understand all the options correctly. If you wanted zotero to store the pdf in the exact location you want, if that location is changing everytime, you'd have to go into options each time you stored a snapshot. Please correct me if i'm wrong.

thanks,
allie

mark

No, you are right. Zotero currently offers no options to automatically make the folder structure more sensible.

albo

Nor pop up a dialog box for snapshot location, right?

mark

Not currently, unfortunately - you are right.

albo

great - thanks mark and meetewlul. Good to know.

krueschan

As for attaching pdf files to zotero entries: the "Add" button on the "Attachments" tab offers you the option to
a) Link to file
b) Store copy of file
+ c) + d)

if you use b) zotero behaves as it would when getting the 'snapshot' directly from a website which has been described in this thread (ie saving the file to a randomly named subfolder in 'storage').
However, when using a) the item can be located anywhere else, including in a location within a logically constructed folder structure.
It seems, from the discussion, that this is what albo should do with his pdf file collection since (s)he is storing the pdfs manually anyway.

albo

thanks k,

well, that *is* what i should do, but not because that's how i do it anyway. I'd *prefer* to have zotero pop up dialog boxes asking where to store my snapshot. And it'd be really nice to have zotero be able to automatically organize snapshots in a folder structure based on the categorization of the references.

but, a dialog box would be good enough, as long as it was smart about what it chose as it's default directory.

If I do have to do it manually, it would be nice if drag-and-dropping pdf's onto the refs was customizable vis-a-vis making a copy vs. linking to the original file. Right now it seems to make a copy in the default snapshot directory, with no way I can find to change that behavior.

mark

Exactly, there should just be a couple of options in the preferences for this:

1. When dragging and dropping attachments from file manager, either (A) make a copy or (B) make a link
2. if 1A = true, either (A) use a meaningless flat folder structure for all attachments (default) or (B) organize attachments in folders.

For 2B, one could think of a template tag-like approach as used in WordPress for permalinks or Winamp for CD ripping prefs, with available tags like %author%, %publication%, %year%, %volume%, %issue% so that the user themselves can specify their folder structure.

meetewlul would then probably use something like %journal%\%issue%\filename.pdf

P.S. I generally dislike popup boxes for this type of preference-based actions which will not change that often. However, one that allows me to set the preference, offers a checkbox 'don't ask this again', and tells me where I can change the preference later would be fine.

albo

i agree, mark. nice thinking - i really like the idea of being able to customize the folder structure that way. I tend to want to organize under topic though, and that might get complicated when references can have multiple tags attached to them. in that case, i'm not quite sure how the template system would work. Perhaps one could designate a main tag, or category, and that would get encoded in the %category% template field. Something like that.

I thought a dialog box might be quicker and easier for the developers to implement, but i fully agree with your suggestion!

I would also add this behavior not just for dragging and dropping, but for when snapshots get sucked in from the web too.

mark

Agreed about the snapshots.

These issues are related to the more general problem that the attachment system could use a little revamping. I've pointed out another use case related to this: Multiple records, one (physical) attachment.

apple

Hello all,

I just want to contribute my voice to the calls for a more logical folder structure & file naming convention.

It may be a lot of coding, but it can be very easily described: just mimic iTunes' "Let iTunes Manage My Library" option.

It seems Zotero was partially inspired by iTunes in the first place, so the coders might not be so averse to argument that this is part-and-parcel of the simple/easy/powerful paradigm! :-)

mronkko

This could be implemented as a zotero plugin (see for example zotfile-plugin)

What the plugin would do is
-Register an event handler to monitor when attachments are added
-When an attachment is added the plugin would do three things
1) copy the file to a path that is configured by the user
(e.g. ~/Documents/Articles/{journal}/{year}/{author} {year} {title})
2) link this file to the zotero item
3) delete the original attachment

For any decent programmer with some experience on developing firefox extensions this should not take more than a day for the first working version.

Mikko

mark

Sounds like you should take a day off to do just that :)

asplundj

But, would the pdf be synced then?

mronkko

As far as I know, you would need to use an external tool to sync the linked files.

I would use a tool called Unison for that or just store the PDFs in a folder that is located on a server.

Mikko

mark

On Windows XP, I use SyncToy 2.0 for syncing as long as Zotero's built-in storage sync is a little wonky.

kiselev

Gents,

I have been trying to have "links to files" which are located not in Zotero repository to be indexed.
After I create a link there it appears that it is "Indexed: No".

Do I understand correctly that there is no way to index files for links that lead not to Zotero repository? So indexing links only work for links maintained in Zotero repository ?

It is really hard to properly organize files in Zotero repository since it contains other things as well. It would be a VERY nice feature to have the ability to select which folders can be indexed by Zotero so one could maintain files in different folders.

PS Indexing "Store Copy Of File" works fine.

Thanks !

encdpnew

Just to echo the desire for configurability in where Zoterro stores PDFs. I currently save all my PDFs (manually) in a single folder called "Literature", by the filename format "AuthorYear". For me personally, this avoids the need to link. If I identify something of interest in zotero it is very quick to find it in my folder by looking up Author then year (I have these two columns adjacent in Zoterro).

This also meant I didnt have to bother with linking when I migrated from Jabref. Personally Id be happy with the option to save all PDFs in a single folder. Then I would bother linking all the existing pdfs. This would be easy though, by dragging all the pdfs in the literature folder into zotero, then highlighting all and selecting "retrieve metadata from pdf".

Thanks,

Paul

timolsen

I would the the capability to choose exactly where I store my PDFs as well!

adamsmith

there are a whole bunch of other threads out there - Dan's most recent reply is that it might happen eventually, but isn't high priority, since you can use a virtual folder/saved search to the same effect.

nutsy.ben

Also agree,


There is two majors things Zotero lacks:
1- Storing pdfs in a logical way (i.e. the folders structure of your zotero library)
2- Scanning efficiently a folder for pdfs. Too many times the database gets corrupted, especially if you want to use several computer for the same database). When it happens, you may appreciate to scan your old storage (even the repair tool does not get back all the entries !).

bwiernik

1) The Zotfile plugin can be used to organize PDFs according to a variety of customizable structures, including your collections in Zotero

2) Corruption should almost never happen. If you are experiencing frequent corruption, there is almost certainly something wrong with your setup. You mention using the same database on several computers. Do you mean you have the database on a network drive or in Dropbox? That isn't going to work. The correct way to use the same library on multiple computers is to use Zotero's built-in sync function.

In any event, if you continue to have corruption problems, you should start a new thread (this one is 4 years old).