running zotero-standalone-4x to fix existing/broken zotero-3x

TomRoche
I've been running zotero via firefox/iceweasel on debian testing (via LMDE) for awhile, but it recently broke: when in FF I do Tools>Zotero, I get dialog=Alert "There was an error starting Zotero." (This is presumably due to FF upgrade as indicated @ https://forums.zotero.org/discussion/27989/zotero-does-not-start-in-firefox-20-beta/) However, when in FF Add-ons Manager entry for Zotero 3.0.11 I hit button=Preferences, I get the expected dialog; also, FWIW, I have

FF_PROFILE_DIR="${HOME}/.mozilla/firefox/default"
FF_ABOUT_CONFIG="${FF_PROFILE_DIR}/prefs.js"
mee@it:~$ fgrep -ie 'extensions.zotero' ${FF_ABOUT_CONFIG}
> user_pref("extensions.zotero.dataDir", "/home/mee/.zotero/zotero/20111008/zotero");
> user_pref("extensions.zotero.duplicateLibraries", "0");
> user_pref("extensions.zotero.export.bibliographySettings", "copy-to-clipboard");
> user_pref("extensions.zotero.export.displayCharsetOption", true);
> user_pref("extensions.zotero.export.lastStyle", "http://www.zotero.org/styles/ieee");
> user_pref("extensions.zotero.export.lastTranslator", "9cb70025-a888-4a29-a210-93ec52da40d4");
> user_pref("extensions.zotero.export.quickCopy.setting", "bibliography=http://www.zotero.org/styles/ieee");
> user_pref("extensions.zotero.export.translatorSettings", "{\"exportCharset\":\"UTF-8\",\"exportNotes\":false,\"exportFileData\":false,\"useJournalAbbreviation\":false}");
> user_pref("extensions.zotero.firstRun2", false);
> user_pref("extensions.zotero.firstRunGuidanceShown.authorMenu", true);
> user_pref("extensions.zotero.firstRunGuidanceShown.saveIcon", true);
> user_pref("extensions.zotero.import.charset", "UTF-8");
> user_pref("extensions.zotero.lastDataDir", "/home/mee/.zotero/zotero/20111008/zotero");
> user_pref("extensions.zotero.lastLongTagDelimiter", " ");
> user_pref("extensions.zotero.lastLongTagMode", 2);
> user_pref("extensions.zotero.newItemTypeMRU", "4,3");
> user_pref("extensions.zotero.pane.persist", [too long to list]
> user_pref("extensions.zotero.search.quicksearch-mode", "fields");
> user_pref("extensions.zotero.sync.autoSync", false);
> user_pref("extensions.zotero.unfiledLibraries", "0");
> user_pref("extensions.zotero.useDataDir", true);
> user_pref("extensions.zotero@chnm.gmu.edu.install-event-fired", true);

To get zotero working again, and since it seemed useful to decouple it from the browser (am I missing something?), I installed debian package=zotero-standalone (version=4.0.6-6--see https://forums.zotero.org/discussion/29198/package-available-in-debian/ , http://packages.debian.org/sid/zotero-standalone), uneventfully (aside from the expected sources.list-jiggling, since I don't normally run unstable). I'm wondering, how best to run zotero-standalone, given that

1. I still want to be able to run zotero from FF. Hence I intend to install the 4.x FF extension (and also to install the Chrome extension, unless that's problematic, although I don't use Chrome much).

2. (as noted above) I have already zotero preferences in an FF profile, which I would presumably like to use (unless something's obviously broken)

3. (as noted above) I have a dataDir separate from my FF profile, which I want to continue to use (and which I backup regularly, along with my FF profile, et much al).

? I'd be especially interested to have *all* my zotero preferences separate from my FF profile ... but I don't see how to do that without violating condition 1.

Should I just run `zotero &` and choose my current FF profile?

Apologies if this is a FAQ, but I didn't see anything similar in https://www.zotero.org/support/frequently_asked_questions or when googling https://www.google.com/search?q=%22zotero+standalone%22+OR+%22zotero-standalone%22
  • adamsmith
    what do you mean by "Zotero preferences"? You mean data?

    Generally:
    1. That's fine
    2. They will auto-update when you update Zotero
    3. This is a bit confusing - so you have two separate data folders for Zotero? One in a Firefox profile and one outside of it? Not sure how that makes sense. In any case, merging to libraries is possible, though a bit more involved.
    Just having one single data directory and using that for both Standalone and Zotero for Firefox is no problem, though - just point both to the same directory.

    Should I just run `zotero &` and choose my current FF profile?
    Zotero should ask you whether you want to use/share your existing Zotero profiles on first run.
  • TomRoche
    edited June 14, 2013
    TomRoche 13 Jun 2013 ~1500
    >> FF_PROFILE_DIR="${HOME}/.mozilla/firefox/default"
    >> FF_ABOUT_CONFIG="${FF_PROFILE_DIR}/prefs.js"
    >> mee@it:~$ fgrep -ie 'extensions.zotero' ${FF_ABOUT_CONFIG}
    >> > user_pref("extensions.zotero.dataDir", "/home/mee/.zotero/zotero/20111008/zotero");
    >> > user_pref("extensions.zotero.duplicateLibraries", "0");
    >> > user_pref("extensions.zotero.export.bibliographySettings", "copy-to-clipboard");
    >> > user_pref("extensions.zotero.export.displayCharsetOption", true);

    adamsmith 13 Jun 2013 ~1700
    > What do you mean by "Zotero preferences"? You mean data?

    By "Zotero preferences" I mean everything in a prefs.js (or equivalent application key/value store) relating to Zotero. (Note above the prefix "user_pref" :-) *One* of those preferences is the *location* of one's Zotero data ("extensions.zotero.dataDir")--and by "Zotero data" I mean (and I believe this is standard usage--note the string "dataDir" in the preference key above) one's bibliographic payload.

    > so you have two separate data folders for Zotero?

    No. Please review the difference between

    * Zotero preferences. Their locus (at least for FF) is a *file* (prefs.js) located in an FF profile folder (${FF_PROFILE_DIR} above). Their target is Zotero itself: these preferences presumably have negligible portability beyond Zotero; i.e., they are meaningful only to Zotero and very-Zotero-like applications.

    * Zotero data. This is the bibliographic data for which the user is currently using Zotero, but which could presumably be managed by a number of similar applications, and is presumably portable between apps. The locus for Zotero data is a folder, which in XULish environments is pointed to by the preference with key="extensions.zotero.dataDir" in a file name=prefs.js in a profile folder.
  • Simon
    If you tell Zotero Standalone to share data directories with Zotero for Firefox when you first open it, it will import your preferences from Firefox, but preferences will not be shared between Zotero for Firefox and Zotero Standalone after that.
  • TomRoche
    TomRoche 13 Jun 2013 ~1500
    >> I've been running [Zotero for Firefox (ZF)] on debian testing (via LMDE) for awhile, but [my ZF-3.0.11] recently broke [...]
    >> due to FF upgrade as indicated @ https://forums.zotero.org/discussion/27989/zotero-does-not-start-in-firefox-20-beta/) [...]
    >> To get zotero working again, [and] to decouple it from the browser, I installed debian package=zotero-standalone [(ZS).]
    >> I'm wondering, how best to run zotero-standalone, given that

    >> 1. I still want to be able to run [ZF as a connector]. Hence I intend to install the 4.x FF extension[.]
    >> 2. (as noted above) I have already [ZF] preferences in an FF profile, which I [want] to use[.]
    >> 3. (as noted above) I have a dataDir separate from my FF profile, which I want to continue to use[.]

    >> ? I'd be especially interested to have *all* my zotero preferences separate from my FF profile ... but I don't see how to do that without violating condition 1.

    Simon 14 Jun 2013 ~1200
    > If you tell Zotero Standalone to share data directories with Zotero for Firefox when you first open it,
    > [ZS] will import your preferences from Firefox, but preferences will not be shared between [ZF] and [ZS] after that.

    Sounds good! but I still have 2 questions about the relationship between ZF and ZS:

    1. As noted above, I want to run ZF as a connector: particularly I want ZS to manage the datastore (pointed to by XUL key="extensions.zotero.dataDir") and ZF to get that information from ZS. Is that "how it works Out Of The Box," or must I do something to enable that? I'd particularly like to avoid a situation where ZS was using one datastore and ZF was using another.
    2. As noted above, I want to run ZF as a connector, and my current ZF-3.0.11 (which was never run with ZS) is broken. How to fix? I'm guessing the sequence is like [install ZS, run ZS, configure ZS, remove ZF-3 extension from FF/iceweasel, install ZF-4 extension in FF/iceweasel]. Is that correct?

    Your assistance is appreciated. If there's an appropriate place to add this information to the wiki, please let me know, and I will add it. (I'm not seeing anything about ZS @ http://www.zotero.org/support/start , and the only reference to ZS in the Knowledge Base is http://www.zotero.org/support/kb/linux_packaging , which I should update to point to the debian and ubuntu packages ... presuming I can remember my Docuwiki credentials :-)
  • Simon
    1. As noted above, I want to run ZF as a connector: particularly I want ZS to manage the datastore (pointed to by XUL key="extensions.zotero.dataDir") and ZF to get that information from ZS. Is that "how it works Out Of The Box," or must I do something to enable that? I'd particularly like to avoid a situation where ZS was using one datastore and ZF was using another.
    If you tell Zotero for Firefox and Zotero Standalone to share databases, this is how it works out of the box.
    2. As noted above, I want to run ZF as a connector, and my current ZF-3.0.11 (which was never run with ZS) is broken. How to fix? I'm guessing the sequence is like [install ZS, run ZS, configure ZS, remove ZF-3 extension from FF/iceweasel, install ZF-4 extension in FF/iceweasel]. Is that correct?
    Just install Zotero Standalone and the new Zotero extension (it will install over the old version). Order doesn't matter.
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