Can I do a backup from my Zotero WEB library? And, is there a danger that synchronizing...

Eivy
edited March 7, 2022
Can I do a backup from my Zotero WEB library? And, is there a danger that synchronizing from an out-of-date computer may wipe out some of my library?

Hi -

Until recently, I have been using Zotero on my Macbook Air, with my library syncing apparently correctly to the web library in my account. My Macbook Air laptop recently crashed with all data on it lost. I had no backup for the Zotero Library on my laptop, but the Zotero Web Library looks completed (the silver-lining of upgrading my Zotero storage).

The crash of my laptop as my main working device brought me to using an older desktop/iMac computer on which Zotero appears to have stopped syncing around 2017. So, My Library on this iMac showed last stored references having been made in 2017. Zotero was not updated on this computer as I was not using it for work any longer, so the current version is Zotero 4.0.29.11

In the process of getting back to working on the generally out of date iMac (not only Zotero, but browsers as well, with the general OS X system left at 10.8.5 Lion), I think I may have tried to save on iMac Zotero one reference, which I do not really see now in the Zotero Web Library. I would think this is because the computer was not synchronising. I tried syncing the iMac, hoping that the web library will be downloaded on my Mac. At this point, I got the message to update Zotero to 5 for Mac. I tried to update but it did not work (because of the very old OS X system and browsers). In the process of trying to update Zotero, the Zotero library stored on the iMac (i.e. everything up to a 2017 date plus the very last reference which i tried to save when starting to re-use the iMac) disappeared from my computer. The Zotero (standalone?) window, now appears to only have one file 'Zotero quick start guide', the syncing icon does not work and by its side there is the icon of a bell with an exclamation point on which when we click it says 'Zotero 4 is no longer supported. Please upgrade to Zotero 5'.

Could you please advise how to do the safest the following:

1) Before updating Zotero on my iMac, I would like, if possible, to do a backup of my data from the Zotero Web Library in my account. Is this possible? I could not find instructions for doing the backup in this way.

2) Can I update Zotero on my iMac computer and then synchronise safely from my Zotero Web Library, without the danger that my Zotero web data is partially whipped out by the out-of-date library (2017) that I have on my iMac?

Not sure if all this makes sense; my terminology may not be all that accurate, sorry.

Any advice much appreciated. Thanks in advance.
  • dstillman
    edited March 7, 2022
    Can I do a backup from my Zotero WEB library?
    Yes, by syncing with a current version of Zotero. Zotero 4 no longer syncs.
    And, is there a danger that synchronizing from an out-of-date computer may wipe out some of my library?
    Not unless you deleted items on that computer previously. Syncing only transfers explicit deletions you make. Simply syncing a computer that hasn't yet been synced will never delete newer data — it's the same as getting a new computer and setting up syncing, which obviously wouldn't wipe out your online library.
  • Eivy
    Thank you very much for the reply. The syncing makes total sense, of course; i just did not have the courage to go ahead with it.

    Regarding the backing up, I was looking for a way to do it from the Web library on an external drive, prior to syncing. I understand from your answer that this is not possible. However, as you reassured me regarding the syncing of my computer where the library is stuck in 2017, I will do it the backing up after updating to Zotero 5 and syncing. Thanks again for the clarifications and reassurance.
  • Eivy
    edited March 13, 2022
    One more question, as i hit another stumbling block, i am afraid:

    I have now updated from Zotero 4 (on the computer that has not been syncing since 2017, as mentioned initially) to Zotero 5. All went well until i clicked on the green syncing sign. This message came up:

    "You are about to sync the ‘[name of account]’ account to an empty Zotero database. This could happen if you removed your previous database or if the location of your Zotero data directory changed.

    If your Zotero data exists elsewhere on this computer, you should move it to the current data directory or change the data directory location to point to your existing data."

    The options that come with the message are:
    -change data directory
    -cancel
    -sync

    I do not know what i should do. I have not knowingly removed the previous database nor changed the location of the data directory. As mentioned in my initial post, i have been using a different computer, where my Zotero library was up to date but that computer broke and have not backup. My Zotero library on the web account looks ok, with all items up to date in the Zotero storage space.

    On the current computer, not used since 2017, the Zotero library was initially visible till 2017 but did not want to sync, asking me to upgrade to Zotero 5. From that failed attempt, Zotero library on this computer did not appear any longer; it only showed an empty library, albeit with the correct account name appearing in the Sync/Zotero Preferences. In order to to be able to upgrade from Zotero 4 to Zotero 5, I had first to update the whole Mac OS X system from 10.8.5 to MacOS Sierra 10.12.6 (Mojave will follow at the next stage, once i get some use of my Zotero library first).

    I do not understand the message pasted above and i am afraid to proceed with syncing, fearing messing up my library or worse, deleting it. Any advice would be greatly appreciated. Thanks in advance.
    Eyvi
  • dstillman
    edited March 13, 2022
    Since you don't need any local data, you can just sync. Before you do, I would just make sure Zotero is pointing at the default data directory location in the Advanced → Files and Folders pane of the Zotero preferences.

    To avoid future confusion, you should also look for a 'zotero' folder within your Zotero profile directory or Firefox profile directory that contains a zotero.sqlite file larger than 1 MB or 5 MB and a 'storage' folder with folders corresponding to your previous usage of Zotero and move the 'zotero' folder to the trash. You can delete it permanently once you're sure all your data is syncing.

    (Basically, if you followed the Data Missing After Zotero 5 Upgrade steps, you would see your pre-2017 data, but you don't need it here and should just get rid of it to avoid confusion.)
  • Eivy
    edited March 13, 2022
    Thank you very much for the prompt reply.

    1) "...make sure Zotero is pointing at the default data directory location in the Advanced → Files and Folders pane of the Zotero preferences." - I checked and the default data directory is selected as option, so this step is fine.

    2) "... also look for a 'zotero' folder within your Zotero profile directory or Firefox profile directory that contains a zotero.sqlite file larger than 1 MB or 5 MB and a 'storage' folder with folders corresponding to your previous usage of Zotero and move the 'zotero' folder to the trash." - i don't seem to find the file you mention. The pathway I took is the following, as indicated in the link you sent:

    users//Library/Application Support/Zotero/Profiles/[randomstring]/

    in the [randomstring] folder, there are a good number of various files but there is no zotero.sqlite file of any size (also, not sure what you meant by 'larger than 1MB or 5MB'; is it a typo or i am missing a nuance here?). In the [randomstring] folder, there is however a 'storage.sqlite' file of only 512 bytes.

    I would like to tidy up the data as you suggest, but not sure how to proceed in the absence of the files you mentioned, that should be moved to trash. Sorry if i may have misunderstood the instructions :(.
    Thanks in advance for clarifications.
  • dstillman
    Look in both the Zotero profile directory and, if you've used Firefox, the Firefox profile directory for the 'zotero' folder. Other .sqlite files in the profile directory itself aren't relevant.
  • dstillman
    (also, not sure what you meant by 'larger than 1MB or 5MB'; is it a typo or i am missing a nuance here?)
    An empty zotero.sqlite file will be either 1 MB or 5 MB.
  • Eivy
    edited March 14, 2022
    Thank you very much for the reply. I realise that the information I offer is not always complete as I am not always sure what may be of relevance. In this particular case, I should have maybe mentioned that, during my search for using my obsolete Mac, I also installed Waterfox. Please see below the outline of the three Profile directory details, for Zotero, Firefox and Waterfox. I hope these help in identifying what files i should put in trash:


    ZOTERO Profile directory

    users//Library/Application Support/Zotero/Profiles/[randomstring]/ - inside this:
    -no zotero.sqlite file
    -no storage folder

    FIREFOX Profile directory

    users//Library/Application Support/Firefox/Profiles/[randomstring]/ - inside this:
    -no zotero folder and thus
    ---no zotero.sqlite file
    ---no 'storage' file in a Zotero folder; (there is however a 'storage' folder in the [randomstring] folder above, with three sub-folders inside: 'default', 'permanent' and 'temporary' and a file 'ls-archive.sqlite'. I suspect these do not relate to Zotero though)

    WATERFOX Profile directory
    (NB: Waterfox was installed about a month ago, when I started re-using the at-the-time obsolete Mac, before updating the MacOS system, as Firefox was not updating any longer and I found advice that the Waterfox was the Firefox surrogate that would still work with my Mac OS X 10.8.5 at the time).

    users//Library/Application Support/Waterfox/Profiles/[randomstring]/ and inside this folder:
    -zotero folder with four sub-folders named 'locate', 'pipes', 'styles' and 'translators'; and three files named: 'zotero.sqlite' of 1MB, 'zotero.sqlite-journal' of 91KB and 'zotero.sqlite.bak' of 1MB (all three files show having been created 30 Jan 2022, i.e. around the time I installed Waterfox and tried to get back using Zotero on my obsolete Mac.)
    -there is no 'storage' sub-folder in this Zotero folder though.
    (NB: there is a 'storage' folder stemming from the [randomstring] folder with three sub-folders in it: 'default', 'permanent' and 'temporary' but I guess this relates to Waterfox storage generally, as no mention of Zotero)

    Is the folder you are recommending putting in trash the one in Waterfox, i.e. sub-folder of [randomestring]? Even if it contains no 'storage' folder as you initially mentioned in the instructions? If so, should I just drag whole 'zotero' folder (with the four sub-folders and three files) to the trash, keep it there until the syncing is finished and if all ok, then empty trash?

    Or should I move to trash something else /or something else as well (i.e. from Zotero profile directory and/or Firefox profile directory) in order to finish the tidying up?

    Thanks in advance for your help and apologies for possibly missing information (to give or understand).
  • dstillman
    You can move the Waterfox 'zotero' folder to the trash, though that isn't the one that contained your data previously. I'm not sure where that would be — you can try searching your computer for other zotero.sqlite files, in case you were using some custom data directory with Zotero 4. It doesn't really matter, though, as long as you're now using the default location with Zotero 5.
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