17 thoughts on “An organized folder is a sign of a… file organizer

  1. Hi,

    it would be even neater if there was not only an option to copy all the files to a designated folder but to rename them in-place. I’ve got already a farily thought-through folder system which I would very much like to keep, but would nevertheless appreciate Mendeley to rename some files within these folders in a more meaningful way.

    That feature would make Mendeley the most useful program to me ever!
    Cheers, T.

  2. The file organizer is indeed a very nice feature if it would just be a bit more flexible… 😉

  3. This is probably as good an opportunity as any to note that although the screenshots above show you are organizing files on OS X, there is still (I think) an outstanding bug that prevents folder watching and file reorganizing from working on external volumes under OS X (though the features do work on a local volume, as shown in the above examples). I find this particularly unfortunate, as it is precisely because my OS X machine at home has a very large number of PDFs (such that they are happier living on an external volume) that would definitely benefit from folder watching/file reorganizing — but (at this time) can’t.

    However, the features seem to work happily on the Windows machine in my university office. I would only add that, for file reorganization, being able to define custom subfolder types (perhaps based on tags or collections or something?) would be very handy indeed; more so, I think, than creating subfolders based on author, journal (though what happens to files that aren’t journal articles in this case?), or year (and does anyone really want subfolder hierarchies based on title?). I realize that subfolder hierarchies based on tags or collections would quickly run into trouble in cases where documents had multiple tags or belonged to multiple collections, but perhaps Mendeley desktop could actually simply store the file in one place and automatically generate aliases/shortcuts to that “master file” that could be stashed elsewhere in the folder hierarchy? Such feature tweaks might really make these capacities start to fly … 🙂

  4. Ricardo,
    An essential missing feature is when you delete an entry inside Mendeley the corresponding file should also be deleted from the organized folder.
    Until this happens, the folder can quickly become disorganized unless you manually delete all these files.

    Nevertheless, this folder organization feature is what converted me from EndNote.

  5. Now if only Mendeley could search for duplicates… and move entire libraries from one computer to another it would be perfect.

  6. Yes it’s a very nice feature, but it lacks something very simple: The organized files in the specified directory should be changed/deleted whenever its library entry changed/deleted. There is no way you can track manually those files and it should be no problem to delete since they are originally copies from another directory outside Mendeley’s control. So unless you leave that folder grow infinitely and have duplicates or old no longer needed files, you have to manually check each file to see if it still exists in the library!

  7. Really liked the new mendeley desktop software, recognized 100% of my newly added papers with correct meta tags like doi, authors, journals etc., big improvement to the previous version!

  8. This feature is a great addition to Mendeley, and I’ve been using it since I started using the program. However there does seem to be a problem with the way it handles renaming of papers within Mendeley and the subsequent organization of the files in the Mendeley papers folder. If you rename a paper within the program it seems that Mendeley will save a new copy of the file alongside the original. It even seems to do this in the course of typing the new title. The result is a folder full of several copies of the same file; each with an ever-more truncated version of the file name. i.e. Author-Year-Title.pdf , Author-Year-Titl.pdf , Author-Year-Ti.pdf

    I’m not sure if I can post a link in these comments, but here’s a screenshot of part of my Papers folder

    You can see what I mean from that snapshot

    I’ve posted about this in the feedback forums (currently ranked 18th) but it doesn’t seem to be getting picked up

  9. This is great and can save lots of time but I have two concerns.
    1. does this mean that you have duplicates of every file? Or can you simply delete all of the original files?
    2. I work on many different projects and prefer to make sub-folders linked to a topic or project, so that they are easily retrievable when I want to attach them in an email etc. Does Mendeley ‘File Organizer’ allow this?

  10. Hi Ricardo,
    I’ve started using Mendeley at home. We have a server where we drop our files (they are indexed by a full text browser). We use macfusion to map the directory to our mac (it’s an ftp server on a hosting company). I asked mendeley to monitor it, but when I drop files there, they are not added to the library.. any idea why a macfuse mounted library wouldn’t be monitored?


  11. Hi All,

    I am in a fix after using this feature of renaming the files.
    I accidentally renamed all my files (probably very dumb). Now I want to restore their names. Is it possible ?
    Another side effect of the above action is that none of the hyperlinks to the files are working anymore.

    please advice


  12. Hi,

    I am a bit confused by the organizer’s folder and downloaded folder. I am working with different computer, synchronizing files via Mendeley. However, The files are stored in separated folders. I cannot manage to change the ‘downloaded’ folder from the system. It is always loaded in ‘.local/share/data/Mendeley Ltd./Mendeley Desktop/Downloaded’ (Ubuntu) or ‘/application/…/Mendeley Desktop/Downloaded’. In addition, the file names can not be changed.

    On the other hand, if you add PDF files locally, they will be stored in the specified folder in ‘File Organizer’. However, if you sync in another computer, they will go to ‘Downloaded’ folder.

    Any solutions to this?

  13. This is a great feature, but it would be even better if articles could be sorted by last author instead of the first few. It’s rare for me to have multiple papers that get sorted together with the way Mendeley currently organizes with “Author”, but I’d love to be able to have all the work coming out of a single lab put together.

  14. Yes, sort by last author does make sense for some disciplines, particularly scientific research. Until we get this implemented, you may want to try tagging all the papers from a given lab. This wouldn’t work automatically for all papers, but it would include papers from the lab where the PI may not have been the last author (for example, collaborations with other labs).

  15. How about an option that takes away commas and dots from the file name? Is there really the need to keep all the coauthor names in the name of the file? I think only the first coauthor is enough to distinguish between files.

  16. What we really need is volume and page numbers available as options to be added to the file name e.g. author_year_journal_vol_page. That’s probably the optimum for a coherent archiving system with a short file character name.

  17. This is a good feature. However, a great addition will be if we can organize the files into subfolders based on the folders in Mendeley – I usually sort them according to context after importing, and it would be good if that structure could be maintained with the file system as well.

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