Zotero(& plugins): Seeking a Complete Reference Manager

Hello everybody,

Firstly, I'd just like to start off by saying what an excellent piece of software Zotero is. It's a wonderful tool and I'm in indebted at the efforts and dedication of those who've spent their time developing it.

Myself and a group of six of my peers in grad school studying a range of social sciences have been using Zotero for over a semester now. Collectively, we've compiled a list of things that we feel are somewhat lacking or need refined for Zotero to become the ultimate, go-to reference manager for those that it is not for already. All the items numbered below (for convenience) have been experienced by more than one user within the peer group utilising Zotero to exclude machine/user-dependent errors. We certainly do not expect these to be resolved overnight and perhaps some shall never be, but we thought we should nonetheless highlight what we felt needs addressing so that Zotero can become a complete reference manager - in our humble opinion at least. Hopefully this post can serve as a one-stop shop in that respect. All testing was done on windows machines from win 8-10 and the items below (keys etc.) reflect this; they've been divided into broad categories.

File-folder exploration / collections & sub-collections

1. Back and forward buttons: synonymous with file explorers which allow users to navigate back to the last folder they were in (and forward to folders), it would be great to see this implemented into Zotero so that the user can simply navigate to the previous collection or sub-collection that they were in.

2. Selecting multiple folders: again, like typical file explorers which allows users to select multiple folders at once (using the Ctrl button), it'd be a great addition to be able to select multiple sub-collections at once, for example, to make moving them to other collections a less tedious process.

3. Shortcut for making new collections/sub-collections: not sure whether this would come under the domain of the Zutilo add-in, but Zotero needs a keyboard shortcut for creating a collection (e.g Ctrl + N) or a new sub-collection (e.g Ctrl + S). A built-in feature for the Zotero program itself for making multiple collections/sub-collections at once would also be ideal - for example, pressing the new collection button, in the pop-up box that appears, separating words with $ signs or another symbol would indicate this to be a new collection ('Alcohol and Substance abuse$ Drug habits$' - would create two separate collections') and so multiple collections would be made upon pressing 'OK'. A radio button, 'Collection' 'Sub-collection' would allow the user to select which they wanted.

Browser-addins

4. The chrome extension is buggy. i) Sometimes the pdf download symbol will come up immediately, other times it wants to 'Save to Zotero (Embedded Metadata)' and multiple refreshes of the page is needed until the pdf can option appears in the extension and can works properly. ii) Sometimes the pdf option appears right away but pressing it does nothing. Double, even triple presses, fails to download the file to Zotero. iii) Sometimes double-clicking the save pdf option will download the file to Zotero when the single click does not, but then two saves are made to Zotero. It was experienced across multiple machines that lots of single clicks of the extension won't download the pdf but a double-click will and doing so ends up in two copies being downloaded and the user having to go delete one.

5. An add-in for Edge is needed. Several users used Microsoft Edge solely but had to download other browsers i.e. Chrome to utilise Zotero effectively. An Edge extension would be immensely beneficial.

Tags

6. The colours assigned to tags (#1s-#9) i.e. the coloured tags keyboard shortcuts are buggy. Several users had various issues with the numbered keyboard shortcuts not working, with several only working i.e. pressing '2' and '3' on the keyboard would assign the designated colour to the selected item but no other number would despite all numbers have colours assigned to them. Tags (and their colours) would have to be deleted and re-added to correct this issue. This was sporadic across users with no clear pattern emerging, with everyone having assigned their coloured tags numbers from 1-9, some users would have numbers 2,3,5 working others 1-5, 8, and another 6 and 9 but no others.

Miscellaneous

7. Generating reports from items. A popular request among those of us testing Zotero was the ability to be able to export reports direct from Zotero to word for ex. If there was a little right arrow (>) next to the 'generate report from items' option obtained when right-clicking several items in a collection, that simply exported the content in the generated Zotero Report window straight to a word doc. for instance that'd be super helpful as I'd save a great amount of time than manually copying and pasting from the window to a word doc each time a report is generated (which is a lot if using Zotfile to extract annotations from your pdfs).

ZotFile

8. When grabbing metadata for a file, it'd be great if the pdf under the parent item was automatically renamed based upon the rules established by the user using Zotfile rather than having to manually select the pdfs and 'manage attachments > rename attachments'.

9. Renaming pdfs without moving them: at times users simply wanted to use ZotFile to rename files and keep them in their original locations in their file manager without Zotero moving them to it's own internal storage in the user's internal file management i.e. moving pdf form my docs into Zotero via drag and drop and right clicking pdf to rename according to ZotFile rules (in both Zotero and the file in the my docs) after metadata is grabbed and having the file stay in my docs rather than moving it to Zotero storage file folder JFKGJDN, for ex. ZotFile seems incapable of doing this however - I believe this issue has been raised in the past but it's not yet been resolved (https://forums.zotero.org/discussion/68517/zotfile-renaming-linked-files-but-not-moving-them)

I believe that's everything we've come across. If there's any additional I've missed I'll be sure to add them. If nothing else, we hope this can serve to answer those who are asking what can Zotero do to improve. The above points in no way detract from the excellent overall quality of Zotero and its plugins like ZotFile and Zutilo and we're beyond grateful for the work that's been put in to developing the software.

Best wishes,

Bill
  • 1. Back and forward buttons
    There was a plugin that did that — Zotero Item History — but it's a 404 now and I don't think it's available anymore. We might do something like this in the future.
    2. Selecting multiple folders
    Generally planned.
    4. Sometimes double-clicking the save pdf option will download the file to Zotero when the single click does not
    That's a misunderstanding. Double-clicking the save button isn't a thing — you should never do that. It's just a normal browser toolbar icon, which never takes a double-click. If your computer or the webpage is busy, there could be a slight delay before the popup appears — or there could be something that's causing some clicks not to register — but all you're doing by double-clicking is starting two individual actions, which explains why you're sometimes getting two saves by doing that (and when you don't, it's because Zotero won't save a second time on the same page, but it needs to actually begin the save process before it can detect further clicks).
    5. An add-in for Edge is needed
    The Edge extension framework has been too limited/buggy for us to create an Edge extension, but Microsoft is completely rewriting Edge to be based on the open-source project behind Chrome, which hopefully will also mean that they'll properly support Chrome/Firefox-style extensions. In the meantime, the Zotero Bookmarklet can be used to save to Zotero locally, similar to running the Zotero Connector.
    9. Renaming pdfs without moving them: at times users simply wanted to use ZotFile to rename files and keep them in their original locations in their file manager without Zotero moving them to it's own internal storage in the user's internal file management
    I can't help with ZotFile, but as noted in the linked thread, Zotero can natively rename files you link to, though the renaming options are more limited (though we're planning to extend the built-in renaming to do much of what ZotFile can do).
  • Regarding (9), if you either choose the option in Zotfile to let Zotero store the files or you leave the location field blank, Zotfile should rename your files in place when renaming them? Are you using linked files or stored files (i.e., letting Zotero manage the file locations)?
  • There's an open ticket in ZotFile for 8 (https://github.com/jlegewie/zotfile/issues/363), but the developer hasn't found a way for Zotero to signal to ZotFile when it's attaching a file after retrieving metadata (which would then trigger the rename)
  • Regarding 7, you can open the HTML file you save after generating a report directly from Word.
  • There was a plugin that did that — Zotero Item History — but it's a 404 now and I don't think it's available anymore.
    I can't find it on GitHub, but there is a Bitbucket repo: https://bitbucket.org/fbennett/zotero-item-history

    Not sure that's the latest version. Frank indicated that he updated the installer somewhere in 2014 (https://forums.zotero.org/discussion/comment/191683/#Comment_191683), whereas the last commit is from 2013.
  • Item History no longer worked for several 4.0 versions and not for 5.0.
  • Thanks for the responses everybody. I imagined there were already efforts to correct some of the points highlighted. I've listed responses to the points raised below:

    "There was a plugin that did that — Zotero Item History — but it's a 404 now and I don't think it's available anymore. We might do something like this in the future."

    I never realised there was previously something like this. Would be great to have it back.

    "Generally planned."

    Look forward to it.

    "That's a misunderstanding. ... before it can detect further clicks).

    If that's the case, the fact remains that the extension is buggy i.e. inconsistent. Some times the pdf icon will appear but clicking it does nothing and refreshes are required. You could wait five minutes after a page has loaded with the pdf icon appearing and clicking it still won't work until refresh is hit and the extension works (assuming it does so on the first refresh).

    "The Edge extension framework... similar to running the Zotero Connector."

    I was unaware of the Zotero Bookmarklet. I've given it a test with Edge and I see it can work. However, it interfers with the AdBlocker Ultimate extension. Unless a specific site is whitelisted, running the bookmarklet results in the adblocker detecting it as an ad and thus stops it from running. I've tried whitelisting the bookmarklet url itself to no avail; the adblocker oesn't allow the whitelisting of specific elements, only certain domains so an extension would be handy.

    "(though we're planning to extend the built-in renaming to do much of what ZotFile can do)."

    Can't wait to see it.

    "Regarding (9), if you either choose the option in Zotfile to let Zotero store the files or you leave the location field blank, Zotfile should rename your files in place when renaming them"

    Sorry, that doesn't work unfortunately.

    "There's an open ticket in ZotFile for 8 (https://github.com/jlegewie/zotfile/issues/363), but the developer hasn't found a way for Zotero to signal to ZotFile when it's attaching a file after retrieving metadata (which would then trigger the rename)"

    Will keep the fingers crossed that someway around this can be devised!

    "Regarding 7, you can open the HTML file you save after generating a report directly from Word."

    That works actually, thank you. Little bit of a pain in that you have to go into the generated report window to save the file rather than having an option to be able to just select it from the right-click menu i.e click 'Generate report from item...' [arrow] > 'Save report as...' for ex.


    An additional point that I should've added to the original post, the ability to copy and paste file structures. Say when I'm designing a classwork folder I have 'Sociology 1A' and in Sociology 1A I have a sub-collection of 'Readings' within which there's a sub-collection for each week's readings (and sub-collections within each week separating reading into core and further reading materials), it'd be nice to be able to copy the Readings sub-collection containing the reading folder structure for weeks 1-10, for instance, to another collection. I.e. after copying the folder structure, creating a new collection called Sociology 1B, clicking on that folder, and pressing Ctrl+v to paste that sub-collection hierarchy of Sociology 1A into Sociology 1B. Obviously if those initial sub-collections from Sociology 1A had files in them they'd also be copied over but then it'd be down to the user to go through each week within Sociology 1B and move the copied files to trash. Again, just like a typical file management system.

    Oh, and if someone could tell me how to properly quote within these forum posts like Rintze and dstillman have done in their replies that'd be swell.

    Many thanks,
  • You can quote useing <blockquote></blockquote> HTML tags (the text in between those appears as quoted)
  • You can quote useing
    HTML tags (the text in between those appears as quoted)
    Thank you!
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