howto question about order of importing, moving, renaming, setup dropbox sync

gvdbroek
Edit: At the end of this post (after the ==================), you can find the steps that I am now using based on the responses here in the forum. I'll leave the original question for archiving purposes and so that you know what I wanted to achieve. It still works like a charm!


Question: I would like to start using Zotero and do several things (renaming, saving pdfs in new folder, syncing data with Zotero and sync pdfs with dropbox). I read something about each of these in the documentation but I am unsure in which order I should adjust the settings such as not to create duplicate entries etc. I have very bad experience with a similar attempt with Mendeley, so I want to make sure that I do it correctly this time.
If someone had time to look over my plan of action, that would be tremendously helpful. I will edit this post afterwards so that it can be a resource for others with a similar question.

*Goals*:
I have a (fairly large) pdf collection with terrible file names. I would like to
1) rename the files systematically (once)
2) move the pdfs to a dropbox folder that I can access from different computers
3) use Zotero to organize the files in this dropbox folder and make a bibliography/cite in Word etc. (on different computers)
4) later: add new files to the library

*My plan, which I am hoping someone could check:*
a) Define one (the same) dropbox folder as storage folder for Zotero on my two computers
howto: https://www.zotero.org/support/preferences/advanced, see “Linked Attachment Base Directory”
b) Import my old pdfs, which are still in the old folder, into Zotero as links (press shift,ctrl and drag and drop)
howto: https://zotero-manual.github.io/zotero-manual/adding-files see “File Links with Relative Paths”
c) Use the Zotero/Zotfile? function to download meta data for the imported files
howto: https://www.zotero.org/support/retrieve_pdf_metadata
d) Use Zotfile to rename all files
howto: http://superuser.com/questions/542078/how-to-use-zoterozotfile-to-rename-all-pdf-files-in-a-directory
e) Move the renamed pdfs into the storage folder that I defined in a)
??? howto: by hand ???
f) Set up automatic data sync to make sure that I have my Zotero data (lists, folders, etc) available on both computers, and turn off storage sync (because I want to use dropbox to sync pdfs between computers)
? howto: https://www.zotero.org/support/sync
g) Setup Zotfile so that new pdfs are immediately renamed and saved into my dropbox folder
howto: https://freecity.commons.gc.cuny.edu/2013/12/14/setting-up-a-portable-library-with-zotfile/

*Questions*:
I. Are the steps above correct and can I execute them in this order? Would this give me my old files copied and renamed into the storage folder on dropbox, and linked to Zotero, so that I can use Zotero on different computers with this setup?
II. Step e), moving the pdfs, should I do this earlier?
III. During the meta data retrieval, something seems to change so that the files are not just linked anymore but directly attached to the Zotero entries. The little icon that showed a link changes after meta data retrieval.
Do I have to undo this so that my links + shared dropbox folder strategy works?
If so, how can I make sure the entries only contain links?
IV. For the renaming of the files: Do I need an interim step in which I still have my old folder with pdfs and a new one with the renamed pdfs? If so, when it is safe to delete the old folder?
V. Double-check: I have read about Symbolic Links to move the Zotero storage to dropbox. I’m gonna assume that this is not necessary anymore because I am using the linked attachment base path, right?

==================
==================
Here is what I do and what has worked nicely for several weeks already!

1. Define one (the same) dropbox folder as storage folder for Zotero on my two computers
howto: https://www.zotero.org/support/preferences/advanced, see “Linked Attachment Base Directory”

2. Import my old pdfs, which are still in the old folder, into Zotero as links (press shift,ctrl and drag and drop)
howto: https://zotero-manual.github.io/zotero-manual/adding-files see “File Links with Relative Paths”

3.* Use the Zotero/Zotfile? function to download meta data for the imported files
howto: https://www.zotero.org/support/retrieve_pdf_metadata

4.* Use Zotfile to rename all files
howto: http://superuser.com/questions/542078/how-to-use-zoterozotfile-to-rename-all-pdf-files-in-a-directory
Because I have a storage folder defined in Zotfile, it will not only rename the file but also move it to the new directory (i.e., delete it from the old folder).

5. Set up automatic data sync to make sure that I have my Zotero data (lists, folders, etc) available on both computers, and turn off storage sync (because I want to use dropbox to sync pdfs between computers)
howto: https://www.zotero.org/support/sync

6. optional, but very nice: Setup Zotfile to monitor my download folder, so that new pdfs can be quickly renamed and moved into my dropbox folder
howto: https://freecity.commons.gc.cuny.edu/2013/12/14/setting-up-a-portable-library-with-zotfile/

*In my experience, it is better to do Step 3 and 4 for a few files at a time, at least in the beginning until you understand what the program does.

7. Now that all is set up, I just add new entries every now and then to Zotero. I do this as follows (just in case, took me a while to figure out so maybe you find this helpful):
When I add a new file, I download the meta data from the journal website using the Zotero button in firefox, and download the pdf into my default Firefox download folder. I have Zotfile setup to monitor that folder, so Zotero will show a small popup and ask me if I want to attach the new pdf in my Firefox download folder to the highlighted entry in Zotero (which should be the one I just added). I click yes, and Zotero will then automatically rename the file, move it into the dropbox folder, and keep the link (synced) in Zotero. Done. So easy and convenient!
This video here helped me understand this work flow (skipped the early parts): https://www.youtube.com/watch?v=3wIFxkotviU
  • adamsmith
    I - yes
    II - no, there is fine. You can use ZotFile to do this, too (the "Rename attachment" function in ZotFile also moves files)
    III - it shouldn't, unless you mean that they get attached to a Zotero item, i.e. you'd see an article icon, but then you see the same link icon as an attachment to that. If the actual attachment icon turns into a pdf-style icon, something isn't right (ZotFile setup?)
    IV - I don't think so, no, they're not going anywhere
    V - correct
  • gvdbroek
    Thank you for the very quick response.
    Regarding the rename function from ZotFile, I read here that it does not move the files: http://superuser.com/questions/542078/how-to-use-zoterozotfile-to-rename-all-pdf-files-in-a-directory
    But elsewhere (and in your post) that it does move the files. Is the post incorrect or does moving depend on the settings?
  • adamsmith
    The post is correct and it depends on the settings. If you have a custom location specified, Zotfile does move files; if you don't, it doesn't.
  • gvdbroek
    Excellent, so I can combine step d) and e) if I first set the custom location in Zotfile(I actually already set that location, so it is good to know this will happen).

    Off-topic: I can't believe zotero has this functionality and compatibility with Dropbox - people are shouting for these features on the Mendeley forums.. I just didn't switch earlier because I read repeatedly that zotero has only paid cloud space above 300mb - not realizing that unlike mendeley it doesn't force you to use that cloud because it is compatible with Dropbox + co.. I'll give it a try now and then start making pr for it ;)
  • adamsmith
    There are some limitations to this, most importantly that files in Dropbox aren't accessible through the Zotero webpage (and thus also not really on any mobile applications -- ZotPad has some support, but isn't otherwise maintained) and that this won't work for groups at this time, but yes, otherwise this works nicely.
  • gvdbroek
    edited June 20, 2016
    Adam, do you mean the Zotero firefox plugin when you say "Zotero webpage"?
    I installed both the browser plugin and the Standalone version but the Zotfile options only appeared in the browser plugin, so I was planning to rely on that one. Are you saying that the browser version does not work with the linked attachments though?
    (And no need for mobile applications in my case but thanks for the information)
  • bwiernik
    No, he meant browsing your library on Zotero.org.

    Zotfile works with both Zotero for Firefox and Standalone, but you have to install the plugin separately into each program.
  • gvdbroek
    Just a brief update: So far, the steps work fine but I would recommend to import large libraries in groups of 20 pdfs or so. Because the meta data retrieval does not work for every document, Zotfile renaming and moving of files doesn't always work without further clicking on each file separately, and that means that some files are left in the original folder. If you are not aware of that, you can end up creating duplicates when you try to import the files again.

    (The steps seem to work fine but I haven't completed the transfer yet and therefore haven't updated this post.)
  • ctomasin
    Folks, I don't see this question answered anywhere so far, and it kind of fits this thread...
    If a person has started with Dropbox, and has put numerous article .pdfs into dropbox, AND THEN wants to start using Zotero... i.e. create the set-up where the .pdfs continue to live in Dropbox, but the citations are in Zotero.... how do you get the citations into Zotero?

    Do you have to start from scratch, and refind (online) the citation for each article you have as a .pdf inside Dropbox?

    And then, having kind of manually re-found each citation, create the link from the Zotero citation to the Dropbox .pdf?


    Thanks very much.
  • bwiernik
    edited July 26, 2016
    Easiest way is to drag all the PDFs into Zotero, select them all, right-click, and choose "Retrieve Metadata for PDF". Depending on the quality of the PDFs, this should find metadata for most of the items. To store the PDFs in Dropbox, use the Zotfile plugin (instructions and download here: http://zotfile.com).
  • adamsmith
    You could also use "Link to File" (under the green plus) or shift+drag (cmd+drag on Mac) to create links to files already existing and the use retrieve metadata. You can still use Zotfile to move new files into the same folder.
  • ChelseaBW
    Hello,

    I am trying to discover the best way to transfer file citations of hundreds of Dropbox files into Zotero. There is a research project that I am working on that has a large collection of files in varying formats (PDFs, HTMLs, etc) in an online Dropbox account. Those working on the project do not need the actual files in Zotero, but rather would like to use Zotero as a searchable citation and keyword database. Does this make the transfer of information any easier?

    Some of the files are original scans of archival material and are not able to be located as digital online files, these I assume must be entered manually, but I had thought others should be able to be transferred more easily.

    I very much look forward to any advice anyone can offer on tackling this task.

    Thank you kindly.
  • bwiernik
    The responses adamsmith and I made above should both work in your case.
  • gvdbroek
    Chelsea, I think you could follow the steps that I am using, with storage sync. The meta data retrieval works better with newer than older references, in my experience.
    It takes a bit of figuring out but works well.
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