Custom citation style no longer works in SA, but works fine in FF

Abstract: My difficulty is with a custom citation style that used to work just fine with both Zotero SA and the Zotero FF extension, but after a recent Zotero SA update, now works as it should only with the Zotero FF extension. For these reasons, I have posted the below to both the Citation Style and the Zotero SA forums.

You would think that in 2012 citation styles would have evolved to accommodate the fact that the line between print and online journals have blurred considerably and a source may be located in print by volume, issue, page AND online by doi and/or a URL. Oftentimes, peer-reviewed online versions of papers lay behind a pay-wall that not all can access, and in the interest of intellectual honesty one should indicate as many ways as possible for readers to locate the cited source. If there is a print version one might find at a local library, or on an online library database like EBSCO or Proquest, by a static URL, or by a doi, then any competent citation style should be flexible enough and thorough enough to indicate all of them.

As an undergraduate, one of the things I appreciated about the MLA style is the thoroughness with which it cites sources, making the process of fact-checking an author's writing easier. However, the "in text" author-date citations of the MLA style are "speed bumps" for the eyes and brain, making an MLA paper a very difficult and jarring read for anyone that was not an English major. Now out of school and an aspiring science writer/blogger, I want to thoroughly cite my sources like the MLA style, while not making my citations so obnoxious and jarring that my pieces are hard to read.

To that end, I modified the format for the journal Nature, so that within the body of the text, there is but an unobtrusive, numerical superscript with a robust, MLA-type citation in the bibliography.

Until last week, my modified style was working just fine with both Zotero Standalone and the Zotero Firefox extension and I could effortlessly drag and drop citations into both Word 2010 and LibreOfiice Writer documents. After a Zotero SA update late last week I could no longer drag and drop from Zotero SA, but my custom style still drags and drops like it always did with the Zotero Firefox extension.

And to make this highly selective bug even more annoying, my custom style still validates just fine at the Validator.nu site.

I would welcome any insight into the causes(s) and possible solutions of this issue.

PS: Might I suggest that the forum posts be sorted by date. It is not at all helpful when one finds a post that appears to be related to a user's current dilemma, only to find that the post was from 2008.
  • What version of Zotero Standalone do you have? There was a bug with certain styles in 3.0.2 that has been fixed in 3.0.3.
  • PS: Might I suggest that the forum posts be sorted by date. It is not at all helpful when one finds a post that appears to be related to a user's current dilemma, only to find that the post was from 2008.
    If you're referring to search results, the forum search available from the left-hand sidebar sorts by date descending. (I actually think we should get rid of the Google forum search and just use that one from the navbar as well.)
  • If 3.0.3 doesn't fix this, we would want to see the citation style - the easiest is to post it to a public gist at gist.github.com and post the url here
  • Thanks for the rapid response everyone.

    In answer to Simon's question, I am running Zotero SA (Z-SA) 3.0.3 which was automatically download on 2/17/2012. I am running Zotero FF extension (Z-FF) version 3.0.1. FF is my default browser and I run both LibreOffice 3.4.3 and MS Office 2010.

    Dan, thanks for pointing that out about the search, and I too agree that the built-in search should be "front and center " and the most obvious one to users as I had to go down several levels to find where is can be sorted by date. After clicking on a few search results from the "Search" at the top right of the page and seeing that the dates are all mixed up, and therefore not very helpful, a novice user would likely just give up.

    After I posted my original question, I have noted further anomalous behaviors of the stock version of the journal Nature's citation style available from the Style Repository (modified date "2012-02-07"‒a month after I got my modified version working as I wanted it). From within LibreOffice (I have not tried this using MS Word), when I insert a citation, it uses the "author" in-text citation format, like so: (Harris & Fiske)‒not the superscripted number one expects. Then, again from within LibreOffice, when I create a bibliography, it is formatted like an MLA bibliography entry (complete with hanging indent) as shown below:

    Harris, Lasana T., and Susan T. Fiske. “Dehumanized Perception.” Zeitschrift Für Psychologie / Journal of Psychology 219.3 (2011) : 175-181. 20 Dec. 2011. <http://www.sciencedaily.com/releases/2011/12/111214162103.htm>.

    Note that the above is with the unmodified version of the Nature style. Before I installed the unmodified version of the Nature style from the Style Repository, I made triple-dog damned certain that I removed all prior versions of the Nature style from the three locations on my machine shown below...

    Location 1: "C:\Documents and Settings\Mark\Application Data\Zotero\Zotero\Profiles\3s9pw29w.default\zotero\styles"

    Location 2: "C:\Documents and Settings\Mark\Application Data\Mozilla\Firefox\Profiles\z9luvl44.default\zotero\styles"

    Location 3: "C:\Program Files\Zotero Standalone\Zotero Data and Libraries\styles"

    No matter what instance of Zotero is running (i.e. Z-SA on and Z-FF off, or Z-FF on and Z-SA off), it spits out a "no superscript" and "author" in-text citation with an MLA-type "hanging indent" bibliography.

    However, as I noted in my original post, if I am "drag-n-dropping" a citation into an appropriate document (i.e. word processing, email, etc.) AND using Z-FF (with or without Z-SA running) with the unmodified Nature style as the default output format, it looks like the below:

    1. Kruger, J. & Dunning, D. Unskilled and Unaware of It: How Difficulties in Recognizing One’s Own Incompetence Lead to Inflated Self-Assessments. Journal of Personality & Social Psychology 77, 1121-1134 (1999).

    The above is just as one would expect for the "stock" Nature citation format. Using my customized Nature format, a "dragged n-dropped" citation with Z-FF looks like the below:

    1. Kruger, J. & Dunning, D. ‘Unskilled and Unaware of It: How Difficulties in Recognizing One’s Own Incompetence Lead to Inflated Self-Assessments’. Journal of Personality & Social Psychology 77, 1121-1134 (1999). at <http://search.ebscohost.com/login.aspx?direct=true&db=keh&AN=2622629&site=ehost-live>; accessed on: 14 Mar. 2011

    The above bibliography entry is just how I wanted it to look. I was even able to get my customized Nature style to handle films, as shown below:

    1. Reiner, R. The Princess Bride. Film. (1987). at <http://www.imdb.com/title/tt0093779/>; accessed on: 8 Jan. 2012

    Looking at the code in the most current version of the Nature style from the Style Repository, there is a line which was not, as near as I can tell, in the prior Nature styles, nor is it in the styles for the specialized Nature journals that I took an unscientific random sample of. The line of code I am referring to is the fourth line shown below:

    <title>Nature</title>
    <id>http://www.zotero.org/styles/nature</id>;
    <link href="http://www.zotero.org/styles/nature" rel="self"/>
    <link href="http://www.nature.com/nature/authors/gta/index.html#a5.4" rel="documentation"/>

    What initially drew my eye was the "index.html#a5.4" bit. I have posted my customized Nature style here: https://gist.github.com/1861616

    If there is not a simple (and quick) fix to this, is there anywhere I can download pre-3.0.2 version of Z-SA?

    Thanks for the help.
  • The line in the nature style is just a link to the documentation.
    This is not a problem with a style. It sounds like something is wrong with your installation. I'd save your custom style somewhere else and then reset styles from the advanced tab of the Zotero preferences.
  • As I noted in my original question/post my goal is for my in-text citations to have the subtle unobtrusiveness of a style like that of Nature. For my bibliographic entries, I want to provide for a reader the robust, thorough, and maximally useful information found in MLA-type styles.

    The bibliographic entries below were copied straight from the Zotero Reference Test pane at: chrome://zotero/content/tools/csledit.xul and used my modified Nature CSL style:

    1. Nakamura, K. & Particle Data Group. ‘Review of Particle Physics’. Journal of Physics G: Nuclear and Particle Physics 37, 075021 (2010). doi:10.1088/0954-3899/37/7A/075021 at http://adsabs.harvard.edu/abs/2010JPhG...37g5021N accessed on: 20 Nov. 2011

    And...

    2. Ehrlinger, J., Johnson, K., Banner, M., Dunning, D. & Kruger, J. ‘Why the Unskilled Are Unaware: Further Explorations of (absent) Self-insight Among the Incompetent. Organizational Behavior and Human Decision Processes 105, 98 (2008). at http://proquest.umi.com/pqdweb?did=1411198641&Fmt=7&clientId=44573&RQT=309&VName=PQD

    As you can see, the bibliographic entries above provide a reader multiple options for locating the cited material. The first has the necessary information to locate the cited papers in the print holdings of a library, by a doi, and a URL. The second does not have a doi associated with it, but through the URL, one knows that the cited journal is indexed by ProQuest. Far too often I have been in the situation of having to search lists of journals indexed by on-line databases like Ebsco and ProQuest to see if they covered the one I needed-a citation that included that little snippet would have been welcomed indeed. All-in-all, far more information than is provided by the average journal's citation style. That is my target.

    Following my post of nearly 24 hours ago I took the following steps, which resulted in, at best, a slight improvement:

    After backing up my Z-SA data (both locally and to the Zotero servers online) I completely uninstalled Z-SA 3.0.3, checking the box that instructs the uninstall program to completely remove all settings and preferences. I then downloaded and saved (without installing) a fresh copy of the Z-SA 3.0.3 setup from Zotero.org. I then shut down my system, allowing it to sit for several minutes before starting it back up.

    I then scrubbed my Windows Registry, removing anything pertaining to Z-SA. I also rooted out the MS Word and LibreOffice plug-ins from the Windows Registry, the FireFox extensions/add-ins, Z-FF, and from the MS Word/LibreOffice side. If it looked like removing a bit of something might affect Z-FF, I left it alone. I then shut down my system again, waited for several more minutes, bought it back up and confirmed through Z-FF and by bringing up MS Word/LibreOffice, that the word processor plug-ins were no longer installed.

    Only then, after doing all the above, did I reinstall Z-SA 3.0.3 and update my locally-stored library, and re-install the word processor plug-ins. There was some slight improvement.

    The below citation and bibliographic entry was made with Z-FF off and Z-SA running (using LibreOffice 3.4.3).

    "Sometimes, people really are as stupid as they appear.1"

    1. Ehrlinger, J., Johnson, K., Banner, M., Dunning, D. & Kruger, J. ‘Why the Unskilled Are Unaware: Further Explorations of (absent) Self-insight Among the Incompetent’. Organizational Behavior and Human Decision Processes 105, 98 (2008).

    Note that the in-text citation is indeed an unobtrusive superscript and the bibliographic entry does not have a hanging indent-an improvement from what was happening before, but the url is missing.

    The below citation with bibliographic entry was made with Z-SA off and Z-FF running.

    "Self-awareness is the best prophylactic against self-delusion.1"

    1. Ehrlinger, J., Johnson, K., Banner, M., Dunning, D. & Kruger, J. ‘Why the Unskilled Are Unaware: Further Explorations of (absent) Self-insight Among the Incompetent’. Organizational Behavior and Human Decision Processes 105, 98 (2008). at http://proquest.umi.com/pqdweb?did=1411198641&Fmt=7&clientId=44573&RQT=309&VName=PQD

    As you can see, the above citation and bibliographic entry are exactly as I want them to be using my modified citation style.

    The facts are these:

    1. My custom style validates using the http://validator.nu site and as of less than an hour ago and returned the following results:

    "1. Warning: Being lax about non-RNC Content-Type:
    text/plain-https://raw.github.com/citation-style-language/schema/v1.0/csl.rnc

    2. Warning: Being lax about non-RNC Content-Type:
    text/plain-https://raw.github.com/citation-style-language/schema/v1.0/csl-terms.rnc

    3. Warning: Being lax about non-RNC Content-Type:
    text/plain-https://raw.github.com/citation-style-language/schema/v1.0/csl-types.rnc

    4. Warning: Being lax about non-RNC Content-Type:
    text/plain-https://raw.github.com/citation-style-language/schema/v1.0/csl-variables.rnc

    5. Warning: Being lax about non-RNC Content-Type:
    text/plain-https://raw.github.com/citation-style-language/schema/v1.0/csl-categories.rnc

    The document validates according to the specified schema(s) and to additional constraints checked by the validator."

    I am told in Zotero's Support and Documentation area that the warnings above are nothing to worry about.

    2. As demonstrated previously, pasting my modified style into the Zotero Reference Test pane gives exactly the formatting results I am aiming for.

    3. Using Zotero for FireFox, in-text citations, bibliographic entries, and "drag-n-drop" citations work as they should using my customized style.

    I confess that I am not a coder, neither by training or by avocation, and it may be that the custom style I kludged together may be at fault. However, I am a natural autodidact and am not afraid to take on a new challenge by jumping into something and poking around until I figure out how to do whatever it is I set out to do.

    It seems VERY fishy indeed that my custom style worked just fine in both Z-FF and Z-SA, passing the criteria set by the debugging and troubleshooting tools available online until two Z-SA updates, the second coming out right on the heels of the one prior, starting about two weeks ago. It was only then, following the installation of Z-SA 3.0.2 that my custom style ceased working. After the release of, and my installation of, Z-SA 3.0.3-intended to fix style-related issues with Z-SA 3.0.2-the formatting issues with my custom style continued, BUT ONLY in Z-SA, AND NOT in Z-FF.

    If it is my custom style, then the CSL validator and the Zotero Reference Test pane are not catching the error(s), and that implies that they too are somehow broken and so who knows what other errors/bugs they are not catching. The implication of the foregoing is that the on-line de-bugging tools cannot be trusted, and therefore no one can, with any certainty, ever know where errors or bugs in the coding of novel citation styles might lie. In line with Occam's razor, the most parsimonious conclusion is that the "fixes" in Z-SA 3.0.3 for the style-related problems in Z-SA 3.0.2, did not, in fact, catch all of them.
  • Do you have "Include URLs of paper articles in references" enabled under Zotero Preferences->Cite->Styles in Zotero for Firefox but not Zotero Standalone?
  • This looks like you want the "Include URLs" checkbox checked in the cite/styles tab of the Z-SA preferences. Unless that box is checked, Zotero will never include URLs for items that have a page-range. I would be very surprised if that box isn't already checked in Zotero-FF.
  • 19 February, 2012, 2330 GMT -7:00
    Thanks, that seemed to fix the part where the URL is not included when inserting citations/bibliographies in MS Word/LibreOffice. As Darwin's Bulldog T.H. Huxley is reputed to have exclaimed upon reading The Origin of Species, "Of course, how stupid of me not to have thought of that myself!" I feel stupid about not seeing that.

    A question...when installing the word processor plug-ins, do Z-SA and Z-FF install them to different places? I ask because I am still unable to "drag-n-drop" quick citations into Word or LibreOffice through Z-SA. When I attempt to do so, in both MS Word 2010 and in LibreOffice, my cursor changes to a circle with a diagonal line through it from upper left to lower right. In Word 2010, I get a message in the status bar that says "Cannot drop at current location" but I do not get such a message from LibreOffice. This happens only when I am trying to drag-n-drop a "quick citation" from Z-SA.

    I went through the material at: http://www.zotero.org/support/word_processor_plugin_troubleshooting and I located the MS Word and LibreOffice plug-ins in my FF profile and in the startup folders for Word and LibreOffice. All that it says about the Z-SA word processor plug-ins is that they are bundled with Z-SA. Is the behavior of Z-SA with regard to word processors determined by the plug-ins in the start-up directory for the individual word processor programs? Should the plug-ins for Z-SA and Z-FF be identical and/or are they interchangeable between Z-FF and Z-SA? What might the symptoms be if they are supposed to be identical but are in fact different? I am running WinXP SP 3.

    Another, but unrelated question, is there any reason why Z-FF and Z-SA ought not share the same data (storage) directory?

    (Cue elevator music while I monkey around with stuff for about 20 minutes...)

    Okay now...I started fooling with the de-bugging outputs, comparing the information in the error reports from Z-SA with that from Z-FF, looking for I don't know what exactly. I cleared the contents of the error files, then by turns restarted them and looked at them again. I wanted to see what errors might be generated when I attempted the now-notorious (at least to me) "drag-n-drop" from Z-SA and see what happened when I did it from within Z-FF...and much to my astonishment the "drag-n-drop" from Z-SA worked!!!!! I closed Z-SA, brought up both Word and LibreOffice, restarted Z-SA, and again the "drag-n-drop" worked!

    I ought not be too surprised by this in retrospect. I spent 20 years in the military working on avionics systems and if I had a dollar (or ₤, or €) for every time it seemed that simply resetting power, or disconnecting and re-connecting a "black box," eliminated a fault or error code that defied conventional troubleshooting techniques, I might be able make a bit of a dent in Greece's debt.

    Thanks for putting up with me. I am still curious about the shared storage for Z-FF and Z-SA as I am the sole user of my tablet PC.
  • there is no reason for Z-FF and Z-SA not to share the a data directory - it is, in fact, the default setting for people installing Z-SA after Z-FF. It is also the recommended setting for almost all users.

    Drag&drop behavior for citations, btw. is completely unrelated to the word processor plugin. You can drag&drop citations anywhere - including e.g. to a post here. Since it works for you now, there's no need (and no way) to troubleshoot what didn't work initially.
    (in case you're interested - yes, the plugin is exactly the same for Z-FF and Z-SA).
  • Problem Fixed and a Partial Clue to a potential Z-SA Issue.

    Starting after I installed Z-SA 3.0.2 earlier in this month, my custom citation style, which had been working great in both Z-SA and Z-FF, would only allow me to drag-n-drop quick citations from Z-FF. When Z-SA 3.0.3, intended to fix citation style/formatting bugs in Z-SA 3.0.2, was released a week later, I installed it in the hope that the issue would go away.

    Unfortunately, it did not. If anything, it got worse. The drag-n-drop was still broken, and now, the formatting of my custom citations inserted through MS Word 2010 and LibreOffice 3.4.3 from Z-SA came out as an "author" style (as opposed to a subtle superscript number) for in-text citations and the bibliography was like the MLA style‒complete with hanging indent. With Z-SA closed and only Z-FF running, everything worked as it should, and the *.csl style files in Z-SA and Z-FF were identical copies, and each one worked in the Zotero Reference Test pane online and passed the validation tests at the validator.nu site. I completely deleted Z-SA from my machine, including the stuff my Windows Registry and then reinstalled Z-SA 3.0.3 from scratch. Despite this, I got the same result.

    As I investigated this, I learned that most users running Z-SA and Z-FF use the same "Zotero Data and Libraries" folder, usually the one stored in their FireFox profile. Without reflecting on it too deeply at the time, from the Advanced tab in the Z-SA Preferences, I redirected Z-SA to use the Z-FF data and libraries in my FireFox profile. The next time I tried to drag-n-drop from Z-SA into a document...IT WORKED!!!! I did not know what I did, but it was working.

    My library is probably small compared to some, especially because I usually store pdfs of papers elsewhere. Nonetheless, as I share this computer with no one else, a 1 GB+ file buried deep in my FireFox profile just seemed messy and inelegant. Part of the reason I felt this way was because when I tried to back-up my Zotero libraries to a CD before I scrubbed my system of Z-SA, the file names and the paths to them were too long for my CD burning software. So I redirected Z-SA and Z-FF to the Zotero Data and Libraries folder in my C:\Program Files\Zotero Standalone directory. Now, both Z-SA and Z-FF had the problems that were once limited to Z-SA! The problem definitely lay somewhere in the "Zotero Data and Libraries" in the Z-SA Program Files folder. Luckily for my neighbors, and unlike Archimedes, I wasn't in the bathtub when it hit me and I did not run around naked exclaiming Eureka! Doing stuff like that was never a big deal with the ancient Greeks it seems.

    I immediately copied the contents of the Zotero folder in my FF profile (locate, storage, styles, translators, and the sqlite files) to a new directory in the root of my hard drive. I then pointed Z-SA and Z-FF to use that directory. At that point, I was not too surprised to find that both Z-SA and Z-FF were working just fine.
    What I discovered quite by accident, may be a useful diagnostic tool when other users are confronted with unwanted behavior between Z-SA and Z-FF.
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