I can offer you a few tips:

First, a question. Why do you want to have all of your pdfs in one folder? What is the use case of this? I find that the value of using a reference manager like Zotero is that I can search for pdfs, notes, annotations, etc. without having to ever interact with a native file structure. Especially with what you are describing, I don't think I see any value of directly interacting with the pdf storage folder.

Quick Clarification: The "Data Directory" is where the database file that has all of the reference information (not the attachments) for your library is stored. Unless you have a compelling reason to store this somewhere other than the default, leave it there--you never have to interact with this outside of Zotero.

The "Attachment Base Directory" feature makes it easier to sync across multiple computers if you link to attachments, rather than storing them directly in Zotero. If you don't do this, you won't use this feature. I recommend storing them directly in Zotero (where you will see the little pdf symbol next to the attachment, rather than the chain link symbol). I will explain these a bit more below.

You also seem confused by the fact that there are multiple different tools available for using a tablet with Zotero. Zotfile "Send to Tablet" and ZotPad are separate solutions; you aren't intended to use both.

Here is what I recommend for your desired uses:
1. Store your pdfs as Attached Files in Zotero, not linked files. Sync them using Zotero storage or a WebDAV-compatible cloud storage. I recommend Zotero storage--buying extra space is very cheap and supports further development. If you need a free solution, I suggest CloudMe or Box.

2. Use the ZotPad or Papership apps on your iPad. Papership is newer and has a nicer interface and more features. However, it doesn't presently support group libraries. If you need that, use ZotPad. With either of these apps, you can search your library using the Zotero interface and find your pdfs. You can then annotate them and save the annotated files in the app, all without ever having to deal with the file storage structure. You can annotate pdfs directly in Papership. With ZotPad, you send them to Goodreader, annotate them, then select the "Send Back" command in the Share menu in Goodreader.


I don't recommend using Dropbox for storing your pdfs. While Dropbox is excellent for its intended use of syncing your working files across computers, it does not play well with other apps or services, like Zotero. It doesn't support WebDAV, which is the most stable way to deal with file syncing in Zotero besides using Zotero storage.

If you absolutely have to use Dropbox, here are the steps you follow:
1. Do not make a symbolic link to move your Zotero storage folders to Dropbox. This method bypasses the Zotero storage system.

2. In Zotero preferences, under "Advanced", "Files and Folders", revert to Absolute Paths. You will be using Zotfile to manage your storage path, not this feature.

3. In the Zotfile preference, in the general settings pane, under "Location of Files", select Custom Location, and select the folder where you will store your pdfs in Dropbox. You can tell it to create subfolders organized by year, author, journal, etc. if desired (read the instructions by hovering over the (i) button). This setup will automatically change attachments to links that direct the pdfs to the folder you select.

4. Use Zotpad on your iPad. You need to go into the Zotpad settings in the Settings app. Under "File Service", select "Dropbox". Click "Advanced Dropbox Settings". Change the "Location of files in Dropbox" to whatever you set it in Zotfile on your computer. Set the "Custom Filename Settings" to match exactly the settings in the "Renaming Rules" pane of the Zotfile preferences on your computer. If you set up any journal/author/year subfolders in Zotfile on your computer, you need to set these settings exactly the same in the "Subfolder pattern" field.

5. To annotate a pdf, search for it in Zotpad, send the pdf to Goodreader, annotate it, and use the "Send Back" command in the Share menu in Goodreader. Do not set up your Goodreader app to access the pdf storage folder directly.

If the previous section was confusing, I understand. It is rather complicated to set up. That is why I recommend using the sync systems that Zotero has built in (Zotero storage or WebDAV).

Hope this cleared some things up a bit for you.

I am also a new user of Zotero and first of all I want to say it is a wonderful tool! It has really changed my work

The only problem I have, is the issue described in this post: To find an efficient way to combine Zotero with tablets.

This is a problem which seems to be in the forums for quite a few years. However, myself, I think that it solution lies elsewhere, I would really appreciate it if bwiernik and adamsmith could help us:

---We need a plugin to save articles, automatically, in anything but the "random string"---

Why do I think this is the solution for our issues? These are my arguments:

1) In my case, I use an android tablet. I have my zotero library/data folder in dropbox. To sync my dropbox with android you can use dropsync (which provides two-way sync in tables), you can also use foldersync app for all the other cloud services. However, because all the article folders in zotero have a random name... you cannot consult them efficiently...

2) In ios devices this is even harder... because it does not have a shared folder structure... However, some apps, such as goodreader or iannotate can automatically like your dropbox folder everytime you launch... However, again, because of the random folder name, it is difficult to consult your articles...

3) In windows, linux or macos computers, this is a smaller issue because you can directly use zotero, qnotero and also the file explorers have an inbuilt search option... However, it is still far from efficient....

Plugins such as zotfile can rename the articles pdfs to anything you want but not the folders which contain them....

I could easily write a code which can rename the folders random name to the articles name or keyname, for example, but this would mess the zotero library...

So I ask again, is there anyway to change the <randomstring> in the zotero file structure? Also, I know I can like the files to the location I want but this breaks the purpose of zotero great autodownload features.

Please any advice would be most welcome.

Hi adamsmith: Thank you very much for the reply! However, I still have these concerns:

1) With zotfile you can move the files... But you have to do it manually, no? Each time you download a new you need to select it and click on "send to tablet" to move them to knew folder... I need to go back to the zotfile manual... But so far, it has been creating a copy of each pdf and it does not move the other attachments from the article...

2) I am very happy with zotero it is an awesome app: That is why I would like to combine it with other great apps: There are awesome pdf readers in android to view your articles and modify them. I will take a look at this zotero web reader...

I hope you agree with me it is "weird" to use a randomstring to generate folder names... We would not even need zotfile if this could be changed...

Thanks again for your reply: Sorry I do not want to annoy you but I really want to learn how to do this (I make video tutorials (http://www.youtube.com/watch?v=ZsQPx5ow1JY) for science software and zotero is high on my list)

In the first reply you told me:

"that's incorrect. Zotfile can move your files wherever you want it to as bwiernik explains in step 3."

That's why I thought it was it's only functionality... I do not have zotero close by but I will check this as soon as possible...

Please just give me this confirmation:

This means that with zotfile everytime you download a reference and its article (by the normal means) It will save the files to the location you want (with the author, year structure options described by bwiernik) and then if you add notes from zotero, for example, they will also be saved there?

Thanks again

Thank you very much you made me very happy! :D

I will check this immediatly

Just to tie things up I have been trying this set-up and it works nicely. Yesterday, I formatted my pc and below I include the steps I employed to install Zotero and Zotfile in case someone needs them.

However, there are two issues I must mention:

1) Now, thanks to zotfile, zotero downloads the articles, automatically, to folders with any structure we want. However, the files already in our collection remain in the old folders... This is an issue if you have a big library... There must be an problem with my installation if anyone has and suggestion on how to solve it, I would be most welcome.

2) To solve the previous problem I found a solution which could be also the procedure to restore your library to a new computer. However, I am not sure this is right procedure to back up your library (specially if you have many plugins) so I need to investigate more (proceed carefully):

-Use the export function in the "File" menu to back up your library
-Delete your library in zotero (At this point you may want to disconnect your computer from the internet to avoid messing your internet library)
-Configure your zotfile to save your library pdf attachments to the location you want
-Use the import function in the "File" menu to bring back you library. Now, zotfile will impose its configuration in the old files...

Any advice/warning will be most welcome. Anyway this is my installation for zotero/zotfile (using ubuntu 64):


----Zotero installation: Following guide at http://anterotesis.com/wordpress/2011/11/installing-zotero-standalone-on-ubuntu-11-10/

1) Get zotero http://www.zotero.org/download/

2) Download file Zotero-4.0.16_linux-x86_64.tar.bz2

3) Extract folder Zotero_linux-x86_64

4) Move folder sudo mv Zotero_linux-x86_64/ /opt/

5) Create file-link in sudo gedit /usr/share/applications/zotero.desktop

6) Paste these lines:

#!/usr/bin/env xdg-open
[Desktop Entry]
Type=Application
Name=Zotero
GenericName=Bibliography Manager
Icon=/opt/Zotero_linux-x86_64/chrome/icons/default/default48.png
Exec= /opt/Zotero_linux-x86_64/zotero %f
Categories=Office
Terminal=false

**Note** The addresses used here (in "icon" and "Exec" should be adjusted to your operative system and its architecture (32bits, 64bits)



----Zotfile installation: http://www.jlegewie.com/zotfile.html

7) Download zotfile https://addons.mozilla.org/en-US/firefox/addon/zotfile/

8) Install xpi addon In zotero go to "Tools->Add-on" and in the corner icon go to "Install-Addon from file"

9) Now in the zotero main window click on the gear icon and go to "Zotfile Preferences"

10) On the "General Settings" in the middle lower region you have the "Location of Files" section. In here, "choose..." a "custom location". In my case, I selected a folder within dropbox. Incidentaly, you can activate the subfolder option to create subfolders for authors, years, publication... Now zotero will save new files to this location.

11) In the "Zotfile Preferences" you can also go to "Renaming Rules" to adjust file naming to your needs (the rules can be found by clicking on the link close to the subfolder option we saw at point nine)

**NOTE** If you had zotero managing your attachements location you need to go to "Zotero preferences" and in the "Advanced" menu go to the "Files and Folders" subtab and click on "Revert to Absolute Paths" as described above.

Thanks to bwiernik and adamsmith for your detailed answers. I'd like to point out that when adamsmith says "select items and click on Manage attachments → Rename attachments", it's important to realize that's "items" in the plural. I selected all the items with attachments in my library and moved/renamed all the files at once. It doesn't get any easier.

suaracahaya, I've written up instructions--which partially have to do with switching my PDF library from calibre to Zotero--on my blog at http://freecity.commons.gc.cuny.edu/2013/12/14/setting-up-a-portable-library-with-zotfile/. Thanks for starting this thread. I've been using Zotero for a couple of years, but just today I set out to do the same thing as you, so your question couldn't have come at a better time.

Thanks adamsmith, I've added the suggested screenshot.

looks great, leehach, thanks.

Now I've got Zotero & Zotfile works with Dropbox! Thanks for all the discussion :)
(Although, Zotpad on my iPad still won't download the pdfs from dropbox eventhough I already complete the setting...)

I have a new situation: I have some lecture notes in pdf already compiled in Zotero directory, with naming format: "Lecturer_LectureName_#lecture" e.g. "Romi_DM_01.pdf" until "Romi_DM_05.pdf". I put all the 5 pdf under one parent item, "Data Mining Lecture Notes".
I want to move them from Zotero inner directory to the new Dropbox Base Directory and have them as linked attachment; but if I use Zotfile's "Rename attachment", all of them will have the same name.

Question: Is there any way to make a linked attachment without using Zotfile's "Rename attachment"?

@suaracahaya

The methods that leehach describe work well. I like to have more automated control over the file names. To do that, I create a separate Zotero item for each lecture where I add a lecture number using the Short Title field. I then create an separate Zotero item for the class as a whole that I connect to the individual lectures as Related Items. This is also how I handle entries for a book and its individual chapters. This method allows me to automate renaming of attachments, as well as to add individual tags and notes to each lecture.

I'm not sure what you mean by this:

I'm thinking of having Zotfile store the pdfs on my university's LMS by using WebDav.

ZotFile doesn't really interact with WebDAV.
It sounds like you just want to use ZotFile's Send to Tablet functionality, which works with any service that syncs folders across devices (box.com, Dropbox, spideroak etc.)

For example, imagine a lightweight app that let you search your Zotero library for items with attachments, written by "John Doe," and having tags "foo" and "bar." This might yield a relatively small number of items from which one could check selected ones and have them sent to the tablet, either by using services like box,

I'm confused now - that's exactly what ZotFile's Send to Tablet does. You use Zotero to search for the files (why do you need a lightweight app for that if you have Zotero?) Send them to your box folder, let box do the syncing and have the files available on your tablet via box. What am I missing?
Unless you want to have that app on the tablet? I think you're imagining that part a lot easier than it is, given that it'd be very hard to do these types of search operations, especially wrt tags, without a significant amount of syncing beforehand, at which point you're quite close to ZotPad again.

OK, so all I can tell you it that it doesn't currently exist, I don't think anyone is working on it--it's likely technically possible, though not trivial given that you'd have to structure this as API requests. You can ask the app developers, but I wouldn't get my hopes up.

I'm thinking of having Zotfile store the pdfs on my university's LMS by using WebDav.

I was mainly trying to answer your original question, i.e. whether that'd work.
I don't think WebDAV is a particularly easy way to set up a sync folder across computers and you obviously don't have an iPad app, which is really where my confusion with your original idea comes from.
If you're going to use ZotFile, you'll almost certainly want to do that with drobox, box, or something of the kind, which is what the developer had in mind.

Thanks for your feedback Adam.

After some investigation, I've decided to use Zotfile and a iPad pdf-annotator (TBD) for now. But since so many of my pdf files are for "deep storage" (i.e., not being used right now), I want to rearrange them.

Ideally, I'd keep the ones I'm not using right now on my university's LMS and access them via WebDAV. I'll experiment with accessing them via Zotero, but even having to move them manually would not be a big problem because they're not being used. OTOH, I would move everything I'm currently using to my Zotero File Storage (ZFS) account and sync the easy way. If the WebDAV experiment works, I think I may be able to put the ZFS stuff into a group, so my Zotero clients would be able to see both sets of files simultaneously.

If this approach will work, then the first step will be retrieving all my files currently on ZFS, going through them, deciding where to keep them, and moving some of them to the LMS. Next, I'll clear out the files that were moved to the LMS. Finally, I'll add the files I'm using for my current projects to ZFS.

This raises at least these questions:

1. To experiment with WebDAV on the LMS, can one temporarily change the settings in a Zotero client from the current ZFS setting to the WebDAV server without causing major harm?

2. I run both the Firefox & Standalone versions of Zotero. If I change one, will it affect the other?

3. How does one isolate only those items in the library that have attachments on ZFS? (E.g., as distinct from linked attachments.)

4. Is there an easy way to batch download all the attachments in #3, or does one have to do it item-by-item?

5. Is there an easier way to move attachments between two different services other than opening individual attachment from Zotero and saving them one-by-one in an attached folder on the other service? (ZFS & the LMS WebDAV in this case, but in general people might be interested in Box, Dropbox, etc.)

Thanks ahead of time to Adam or anyone else who has answers to these questions.