Translation/retrieval issues

Leon
Somehow, about 3 months ago, I got some kind of virus, and when I took it to the computer shop, they reloaded the computer to deal with the virus, which means that all my programs were newer programs, and not exactly the way I had it.
But did I obtain a disc with the zotero sqlite files on it.
after the virus issue, and the now newer version of Firefox, I just started all over again with a new library of notes and the like until today when I needed to obtain some of the information that I had stored on my old library.
I inserted the disc and transferred the old sqlite file in the zotero profiles and storage.
When I tried to access it, it did not load the library, neither the old one, nor the new one. The information is there on the profiles, but I just can't access it through the zotero application.
When it did not load the old library, I reverted to the new one, only it still does not load the new library either. It just acts as though I don't have a library and only displays the quick start guide. So, I'm at a loss as to what to do. Does anyone happen to know how I can get it to work again?
  • Tjowens
    edited September 30, 2008
    Generally these issues stem from either being in the wrong Firefox profile, or Zotero looking in the wrong place for your data.

    Here are two things to try.

    1. Make sure you are in the correct Firefox Profile: Occasionally when upgrading Firefox creates a new profile. You can use the Firefox Profile Manager to make sure that you are in fact in the correct profile.

    2. Make sure you have the correct zotero.sqlite file. Use the “Show Data Directory” button in the Advanced tab of your Zotero preferences to check exactly where Zotero is looking for your zotero.sqlite file. If you have previously used a custom data directory location, you may need to adjust the setting in the Advanced tab. You might want to look for a larger copy of zotero.sqlite elsewhere on your hard drive.
  • Leon
    Hi Tjowens,

    Thanks for the reply, I'm not exactly sure that the problem is a firefox profile issue, since the retrieval problem was encountered all at about the same time, which, I would think, would mean the same profile, but then again, I could be wrong.

    I have transferred a zotero library before on a different computer, and it worked fine, and the preferences tell me that I'm looking in the right place this time around. Now, I've tried creating a different profile and selecting a custom directory profile and that still hasn't worked.
    Now, I have a larger sqlite file, the old one, in the folder that it says it is accessing, and have tried having that one as the sole file in the folder even, among other things, and it just seems that I can't get it to access the file, it just reads me a message that it can't translate the file. I'm not exactly sure what that means but I'm guessing that it may be having some trouble reading the sqlite file, for what reason, I don't know.
  • dstillman
    it just reads me a message that it can't translate the file
    What's the message, exactly?
  • Leon
    "No translator could be found for the given file."
  • dstillman
    It sounds like you may be trying to import a Zotero database (.sqlite file) directly, which isn't possible.

    In the Advanced pane of the Zotero prefs, use either the default location or a custom location, restart Firefox, go back to the Advanced pane and click Show Data Directory, close Firefox, copy your old data directory files (zotero.sqlite, 'storage', etc.) into that directory, and restart Firefox. Don't overwrite anything without making a backup.
  • Leon
    edited October 5, 2008
    I have tried translating a database from the default location as the only one to be accessed, restarting Firefox, and rather than access it, it [zotero] just creates a new one [directory] with the quick start guide as the only thing in it. I also tried that with a custom location folder with the database. I still don't get anything. It's just strange as a result, because it has worked in the past.
  • dstillman
    Are you selecting the 'storage' directory instead of the parent directory?
  • Leon
    Just to ensure that all the relevant information is present, I'd like to recap the exact modus:

    From Local Disk, I select "Documents and Settings", then the primary user [which is the one that it says it uses], then application data, then "Mozilla", then "Firefox", then "profiles", then I select the default profile, [which is what it also uses], then "zotero". This is the folder that it says that it uses as the default.
    [D:\Documents and Settings\User\Application Data\Mozilla\Firefox\Profiles\default\zotero]

    The sqlite file is the one that it stores the data in, other than images and the like, and when it is moved, it is no longer accessed, so naturally, it does not access it, but creates a new one, of course. The zotero-written sqlite file in that folder is, according to zotero, the file that it accesses, so it should be able to access it, which means the one that it was accessing earlier that day, however, it does not appear to be doing so. That day's database is still an inaccessible sqlite file, and still sitting in the zotero application data profile folder.
    However, the insertion of a different sqlite zotero written file should enable it to access that file, and thus a different database, which has been a previously successful procedure, why it is not operating this time around is a mystery to me.
    However, at present that particular database is not my concern, retrieving the most recent library, however, is. And that is what I'm trying to do.

    The "storage" file is a sub-file of the "zotero" file, i.e. the "parent directory", which is what I have been telling it to access, which it had told me, and I knew, that it accessed. The "storage" file stores other relevant things like images, webpages, urls and things of that nature, which we already know, but, as far as I know, is not the main library content itself, which is what, I think, the sqlite file does, at least it's done that in the past, I think.

    Maybe you can spot something I did wrong, or tell me where I goofed.
  • noksagt
    It sounds like what you are doing is what you should be doing (assuming that Firefox is closed when you do it), so I don't know why it wouldn't work. Have you verified that the zotero.sqlite file contains your old database (and not merely the default database) using some other tool?

    If so, I suppose that you can try this:
    1. Set Zotero to use the directory that you will want it to use.
    2. Exit Firefox.
    3. Find all zotero.sqlite and zotero.sqlite.bak files on your machine.
    4. Move them all into another folder (renaming them if you have more than one of each, so that you don't overwrite any of them).
    5. Open Firefox, letting Zotero re-create zotero.sqlite.
    6. Exit Firefox.
    7. Find the new (default) zotero.sqlite and zotero.sqlite.bak files on your machine.
    8. Overwrite these with copies of your preferred database files.
    9. Restart Firefox. Report if it is using your database, has overwritten your database with the default one, or has created a new database somewhere
  • dstillman
    A new documentation page: Troubleshooting Zotero Data
  • Leon
    Hi Noksagt,

    I have verified the library using Microsoft WordPad.
    The funny thing is that I've tried doing that exact operation already, since that's really the only way to do it, I have a second file for custom directory that I labeled zotero2, yet I have not been able to get it to access the old or new data, it just creates a new one; but I can try it again and see if will work this time around.
    Thanks for the new documentation page, Dan.
    The old library is one I backed up from a disc from the loss of my old computer. Trying to re-access it, and the more recent one, is where the trouble is.
    I will play around with it and see if I can pinpoint the problem.
  • noksagt
    I have verified the library using Microsoft WordPad.
    How? A sqlite file is binary (not plain or rich text). If it was 100% readable in WordPad, you are not trying to import the correct file.

    If it merely had several strings in it, that isn't validation that sqlite can read the file.
  • Leon
    No, it was not 100% readable. It contained a whole lot of unreadable stuff.
    It just displayed the file, it did not translate it into something one could read.

    For instance, open the zotero sqlite file, which contains notes, in wordpad, and examine closely the file, or search it for the exact text you want. There is a lot of computer mumbo jumbo there, but buried in all that is all of the notes and so forth.
    There are three files in the zotero directory:
    "Storage", "zotero.sqlite SQLITE File", and "zotero.sqlite BAK File"
    The second one can be opened in Wordpad, but readability is another thing.
    But then, I could be wrong.
  • dstillman
    I have a second file for custom directory that I labeled zotero2, yet I have not been able to get it to access the old or new data, it just creates a new one
    You need to explain what you mean by "creates a new one" (which you also used above). Creates a new what, where? Please list all the paths, filenames, and file sizes of the files you're referring to.
  • Leon
    It creates a new sqlite file within the zotero directory folder, mentioned above, where the other sqlite files are also stored, and seems to have a preference for the new one, and therefore begins a new zotero library through the new sqlite file. I have not succeeded in getting it to access the old data.
    The path is the one laid out above, and the file name that it assigns the new sqlite files is the same as the other ones.
  • noksagt
    edited October 9, 2008
    If the filename is "the same as the other ones" (presumably 'zotero.sqlite'), do you mean that it is overwriting your original 'zotero.sqlite' file? Is your original file moved somewhere else? And how do you know that a new sqlite file is created? From filesize/the "wordpad check?"

    Finally: What happens to the zotero.sqlite.bak files during this process?
  • Leon
    No, it is not overwriting, it simply begins a new .sqlite file in the directory that it accesses. So, if I have one there already, I would then have another sqlite file in the directory. I don't know how to get it to preference an old one over the newer, which is why I have not been able to get it to access the old one over a newer one. This means that once a new one is created, there are two zotero.sqlite files and two BAK files in the directory for two different libraries. The original file remains where it is, the new one is simply placed right beside it, which newer one is the one accessed by zotero in Firefox.
    Another is created because there are more than one sqlite files and BAK files in the same directory, so, if this new one is not a new one, then from whence does it come? I can't verify the info in it, so whether the info is new info or not, I cannot ascertain.
    The only way I was able to verify the old data in the older ones was by searching the text of the sqlite file for a text that I knew it should contain [in this case it contains my entire coursework, so searching for a text that that coursework contains locates the course texts]. In this case, I'm not sure I know how to do that.
  • noksagt
    How can you possibly have two files with the same name in the same directory? Could their be a typo in the filename that you are missing? Do you have explorer setup to show you file extensions (e.g. could an extension have been appended that is now hidden, such as inadvertently saving the file in WordPad)?

    At least, you can do "start->run->'cmd'", cd to your zotero directory & run 'dir' to get the canonical names. You can verify the integrity of your database file with some other sqlite client (the command line client, OO.o Base (?), the database repair service, whatever). The former two should be able to tell you what data is contained in the file.
  • Leon
    1. Set Zotero to use the directory that you will want it to use.
    2. Exit Firefox.
    3. Find all zotero.sqlite and zotero.sqlite.bak files on your machine.
    4. Move them all into another folder (renaming them if you have more than one of each, so that you don't overwrite any of them).
    5. Open Firefox, letting Zotero re-create zotero.sqlite.
    6. Exit Firefox.
    7. Find the new (default) zotero.sqlite and zotero.sqlite.bak files on your machine.
    8. Overwrite these with copies of your preferred database files.
    9. Restart Firefox. Report if it is using your database, has overwritten your database with the default one, or has created a new database somewhere
    An accurate explanation of the situation I believe can ensue by utilizing a characterization of this process:

    I created a secondary folder, mentioned above, moved the files.
    Upon restarting firefox, zotero re-created, as it is supposed to do, the sqlite files.
    I then moved files back to the original directory, attempting to allow it to access them, which it has not done. I believe the problem is that I don't know how to overwrite one sqlite file with another. Could you elaborate on that please?
  • Leon
    In the Advanced pane of the Zotero prefs, use either the default location or a custom location, restart Firefox, go back to the Advanced pane and click Show Data Directory, close Firefox, copy your old data directory files (zotero.sqlite, 'storage', etc.) into that directory, and restart Firefox.
    This is what I attempted to do, if that helps.
  • Leon
    I have just repeated the process up to stage 5. Exactly what do I do to overwrite the new file with an older one?
  • noksagt
    edited October 10, 2008
    When you launch zotero pointing at a source that does not have a zotero.sqlite file, it will create a new zotero.sqlite file in that place--that's the expected reaction for step 5.
    I then moved files back to the original directory, attempting to allow it to access them, which it has not done. I believe the problem is that I don't know how to overwrite one sqlite file with another. Could you elaborate on that please?
    I don't know how to elaborate much more--you're probably missing something very simple.

    WITH FIREFOX CLOSED, again search your computer for zotero.sqlite files, You should only find some that are in the directory you moved all of your older files to & ONE that isn't in that folder. That one file must, by definition, be in the folder that zotero is using.

    Now copy your older/larger/hopefully-info-containing 'zotero.sqlite' and 'zotero.sqlite.bak' files into that directory as you would any other file on your system (e.g. what you did in step 4: in windows explorer (or whatever file manager that you use), ctrl-drag or copy/paste your files into the folder that you've determined zotero is using). Explorer should ask you if you really want to replace the newly-created smaller default files with your backup. If it doesn't ask you this, you're either trying to copy the wrong files or are trying to copy them to the wrong place. Confirm that you want to really replace the files.

    At this point, you can even run the same 'find' command that you ran in steps 3 and 7. You should still see that files are only in one of two locations (your backup & your zotero directories).

    Restart Firefox. Hopefully, you will see your old data. If you don't, you need to determine precisely what has happened: search your computer for sqlite files again and manually inspect the zotero directory. What has changed?
  • Leon
    I don't know how to elaborate much more--you're probably missing something very simple.
    That is very probable.

    I moved all my zotero files into a zotero3 folder. All of the transitioned files are still present in the folder.
    Following Step I, zotero is set to use a "zotero" folder.
    The folder was empty until it was preferenced for use.
    That folder now contains one file, a new sqlite file, which zotero has just created.
    All the other older files are contained in the "zotero3" folder.
    WITH FIREFOX CLOSED, again search your computer for zotero.sqlite files, You should only find some that are in the directory you moved all of your older files to & ONE that isn't in that folder. That one file must, by definition, be in the folder that zotero is using.
    I don't exactly notice any of the transitioned files being absent from the new folder.
    Now copy your older/larger/hopefully-info-containing 'zotero.sqlite' and 'zotero.sqlite.bak' files into that directory
    You mean the mainly empty directory zotero now accesses?
    as you would any other file on your system (e.g. what you did in step 4: in windows explorer (or whatever file manager that you use), ctrl-drag or copy/paste your files into the folder that you've determined zotero is using).
    I think I understand the process now. Copying the older files into the [primarily] empty directory zotero now uses.
    Will have feedback info probably sometime in the morning.
  • Leon
    So far, it hasn't worked.
    Now copy your older/larger/hopefully-info-containing 'zotero.sqlite' and 'zotero.sqlite.bak' files into that directory as you would any other file on your system (e.g. what you did in step 4: in windows explorer (or whatever file manager that you use), ctrl-drag or copy/paste your files into the folder that you've determined zotero is using). Explorer should ask you if you really want to replace the newly-created smaller default files with your backup. If it doesn't ask you this, you're either trying to copy the wrong files or are trying to copy them to the wrong place.
    So, that copying process consists of deleting the current zotero files, and then inserting the old ones?
    It doesn't seem to restore my access to the data.
  • noksagt
    You are not providing enough information. What do you mean by "it hasn't worked?" What is it doing? If you are seeing the default database in the Zotero pane & no new database file has been created, you are either not properly replacing the file or the file you are moving is, itself, the default database. If you are not seeing the default database, you need to say exactly what you do see.

    Please try following the instructions again, but this time write down EXACTLY what you do as you do it. Be very specific (e.g. how you found all zotero.sqlite files, their full paths and expected contents (list filesizes and datestamps, as appropriate); when did you open/close firefox; how did you move the files (and again to which specific path, etc.)
  • Leon
    Hi again,

    The following was the process:

    1. Firefox is set to access folder "zotero".
    2. All zotero files were translated to a folder titled "zotero3", some of them renamed.
    3. Firefox is opened.
    4. Firefox is closed.
    5. newly zotero-created files located.
    6. Files deleted.
    7. old zotero files are moved into their places.
    8. zotero does not access the older files, but, instead, re-creates itself anew.
    9. Back to square 1.

    Zotero folder location:
    D:\Documents and Settings\User\Application Data\Mozilla\Firefox\Profiles\default\zotero

    location of older info before being translated to "zotero" folder:
    D:\Documents and Settings\User\Application Data\Mozilla\Firefox\Profiles\default\zotero3
  • noksagt
    After your step 7 (when you've moved zotero.sqlite and zotero.sqlite.bak to "D:\Documents and Settings\User\Application Data\Mozilla\Firefox\Profiles\default\zotero"), what are all of the files in "D:\Documents and Settings\User\Application Data\Mozilla\Firefox\Profiles\default\zotero" & what are their sizes & time stamps?

    Same question after your step 8: when Zotero seemingly creates a new set of files, what are all of the files in "D:\Documents and Settings\User\Application Data\Mozilla\Firefox\Profiles\default\zotero" & what are their sizes & time stamps?
  • Leon
    "zotero" file:

    zotero
    SQLITE File
    1,511 KB

    zotero.sqlite
    BAK File
    1,511 KB

    TIME:
    Oct. 10, 2008
    ______________________

    "Zotero3" File:

    zotero.sqlite
    SQLITE File
    2,798 KB
    July 3, 2008

    zotero.sqlite.BAK
    BAK File
    2,798 KB
    July 3, 2008
  • noksagt
    edited October 19, 2008
    This is obviously before you copy the needed files into the zotero directory.

    Again: double-check sizes/dates in your zotero directory
    1. immediately after you have copied your files over (before you launch firefox)
    2. after you have launched firefox.
    Please also list ALL files in the zotero directory (names of subdirectories, any journal files, etc.).
  • Leon
    I deleted the new files which zotero creates in startup from the last attempt back on Oct. 11, while firefox was closed.
    Following this, I replaced them with the slightly older files, including the most recent directory.
    I then closed all open windows and then opened Firefox.
    I accessed zotero.
    zotero displays the proper index, giving me back access to my information and the directory created since July 3--a great relief.
    However, I'm still trying to access my pre-July zotero library--what prompted all of this.
    1. Firefox is set to access folder "zotero".
    2. All zotero files were translated to a folder titled "zotero3", some of them renamed.
    3. Firefox is opened.
    4. Firefox is closed.
    5. newly zotero-created files located.
    6. Files deleted.
    7. old zotero files are moved into their places.
    8. zotero does not access the older files, but, instead, re-creates itself anew.
    This is pretty much the same thing I've been doing and have just done; think this time, my renaming the files to the default name is what allowed it to access them.
    I'll back-up the current library and make one last attempt to access the older library.

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