[Solved] Another RIS Import failure report

fkober
Hi there,

for completeness I would like to report that I also have trouble importing RIS text files, in my case larger than 2 (!) entries. Maybe there are some helpful observations in the following. I'm using linux and tried with both the firefox plugin (v 4.0.12) and the standalone version (4.0.10).

1) I did import several rather large files successfully only two weeks ago (up to 4500 references).
2) at some point I deleted one of the collections (with entries).
3) when re-uploading that one an interruption happend, maybe a broken network connection, the import stopped and I had to quit firefox and restart.
4) now when trying to import any (not only the deleted collection) RIS larger than 2 entries I get similar errors as those reported before ("Cannot start a DB transaction from a different wait level", forum thread 31127) in the java error console.
5) The behavior is as that reported before, the import progress bar shows up and remains frozen.
6) Yes I've done full syncs before launching the import

Any chances for a fix or workaround?

Thanks and thanks for making Zotero

Frank
  • fkober
    I solved this problem by ... emptying the trash, which had contained > 10k references. In fact I hadn't realized that "Delete collection and Items" means "Delete collection and move Items to Trash".
    Since the trash is empty I can now import RIS as expected again, so there might be a link between the total number of references in the library+trash and the RIS "DB transaction" problem.
    Btw, emptying the trash with this large number of refs was not a straight forward thing, as reported by others already. I went through the web interface at zotero.org to my library to delete packs of 25 at a time....

    I'm back to normal work with Zotero enjoying it very much.
  • ssalo
    I encounter a similar problem in trying to import an ris file. Also was able to import large files recently, but not now. (I need to replace the earlier collection with a revised one.) As above, the import bar appears but remains frozen. The same behavior occurs in both online and standalone. Restarting the computer did not help. There is nothing in trash. In my case there are no error messages. Any suggestions?
  • adamsmith
    how long have you let this run?
  • ssalo
    It ran about 2 hours without any progress along the bar.
  • dstillman
    In my case there are no error messages.
    You wouldn't see the "Cannot start a DB transaction from a different wait level" error in the UI. You'd have to view the Error Console, via Tools -> Web Developer -> Error Console (with slight variations depending on your OS). Can you check whether you're getting that?
  • ssalo
    Dan, thank you for writing. Displaying my ignorance here, but where do I find Tools?
  • ssalo
    I found what you meant -- Firefox tools. Below are errors shown. There are a lot of warnings as well. Do you need those?

    Timestamp: 8/29/2013 11:24:30 AM
    Error: TypeError: History.getState is not a function
    Source File: http://www.zotero.org/static/js/_zoterowwwAll.bugly.1366653817.js
    Line: 4466

    Timestamp: 8/29/2013 11:25:31 AM
    Error: ReferenceError: dw_locktimer is not defined
    Source File: http://www.zotero.org/support/lib/exe/js.php?tseed=1375914067
    Line: 1

    Timestamp: 8/29/2013 11:25:31 AM
    Error: TypeError: $tree.dw_tree is not a function
    Source File: http://www.zotero.org/support/lib/exe/js.php?tseed=1375914067
    Line: 1

    Thank you.
  • dstillman
    Anything that mentions zotero.org is irrelevant. No other errors show up when the import fails?
  • ssalo
    No.

    Do you think the number of items in duplicates is an issue? I am slowly merging them.
  • adamsmith
    My recommendation would be at this point to import the RIS in batches. RIS is a very simple data format, you can split the file between any two entries (i.e. between ER - and TY). There's a chance this is a memory issue or the like - in which case importing in batches would solve it - or there is a weird entry that hangs Zotero - which you'd be more likely to find when importing in smaller batches (I'm thinking a couple of hundred at a time, depending on the size of your import).
  • ssalo
    I attempted to import a group of 10 items to test the updated translator dealing with date formatting. The import did not work (the bar ran quickly to about 2/3 and then stopped).

    Here are the error reports generated:

    Timestamp: 8/29/2013 4:52:00 PM
    Error: syntax error
    Source File: moz-nullprincipal:{31f2196a-85ad-4ff4-b69d-75ad12c5fd6d}
    Line: 1, Column: 1
    Source Code:
    TY - JOUR

    Timestamp: 8/29/2013 4:52:00 PM
    Error: syntax error
    Source File: moz-nullprincipal:{cf298cd4-d2db-4b52-a4fc-44db76e0a6f4}
    Line: 1, Column: 1
    Source Code:
    TY - JOUR

    Timestamp: 8/29/2013 4:52:00 PM
    Error: syntax error
    Source File: http://www.example.com/
    Line: 1, Column: 1
    Source Code:
    TY - JOURA1 - Traverso, Georgina JillT1 - A Bear-Leader in Mexico CityJF - Journal of the Gypsy Lore SocietyPY - 1966/07-1966/10/31VL - 3, 45IS - 3-4SP - 149-150N1 - Notes: NoteKW - Notes and QueriesER -

    Timestamp: 8/29/2013 4:52:00 PM
    Error: syntax error
    Source File: moz-nullprincipal:{24fbf25e-c61b-41b8-b960-88a2d8df8d9c}
    Line: 1, Column: 1
    Source Code:
    TY - JOUR
    Timestamp: 8/29/2013 4:52:01 PM
    Error: Cannot start a DB transaction from a different wait level

    The last error was repeated 4 times.

    Here is the RIS file in question:

    TY - JOUR
    A1 - Traverso, Georgina Jill
    T1 - A Bear-Leader in Mexico City
    JF - Journal of the Gypsy Lore Society
    PY - 1966/07-1966/10/31
    VL - 3, 45
    IS - 3-4
    SP - 149-150
    N1 - Notes: Note
    KW - Notes and Queries
    ER -

    TY - JOUR
    A1 - Fraser, Angus M.
    T1 - F. H. Groome
    JF - Journal of the Gypsy Lore Society
    PY - 1968/01-1968/04/30
    VL - 3, 47
    IS - 1-2
    SP - 79
    N1 - Notes: Note
    KW - Notes and Queries
    ER -

    TY - JOUR
    A1 - Fraser, Angus M.
    T1 - Fielding, Bampfylde-Moore Carew, and the Gypsies
    JF - Journal of the Gypsy Lore Society
    PY - 1968/01-1968/04/30
    VL - 3, 47
    IS - 1-2
    SP - 79-80
    N1 - Notes: Note
    KW - Notes and Queries
    ER -

    TY - JOUR
    A1 - Breay, J.
    T1 - Appendix to Tilly's Carol
    JF - Journal of the Gypsy Lore Society
    PY - 1968/07-1968/10/31
    VL - 3, 47
    IS - 3-4
    SP - 149-150
    N1 - Notes: Note
    KW - Notes and Queries
    ER -

    TY - JOUR
    A1 - Dawson, Robert M.
    T1 - The Gypsy Fashion
    JF - Journal of the Gypsy Lore Society
    PY - 1968/07-1968/10/31
    VL - 3, 47
    IS - 3-4
    SP - 150
    N1 - Notes: Note
    KW - Notes and Queries
    ER -

    TY - JOUR
    A1 - Drukker, Richard
    A1 - Drukker, Barbara
    T1 - Turkish Gypsy Bear-Leaders
    JF - Journal of the Gypsy Lore Society
    PY - 1968/07-1968/10/31
    VL - 3, 47
    IS - 3-4
    SP - 150-151
    N1 - Notes: Note
    KW - Notes and Queries
    ER -

    TY - JOUR
    A1 - McDowell, Hobart
    T1 - An Encounter with a Turkish Gypsy Fortune Teller
    JF - Journal of the Gypsy Lore Society
    PY - 1969/01-1969/04/30
    VL - 3, 48
    IS - 1-2
    SP - 73
    N1 - Notes: Note
    KW - Notes and Queries
    ER -

    TY - JOUR
    A1 - Newman, W. L.
    T1 - Gypsies in Albania
    JF - Journal of the Gypsy Lore Society
    PY - 1969/01-1969/04/30
    VL - 3, 48
    IS - 1-2
    SP - 74
    N1 - Notes: Note
    KW - Notes and Queries
    ER -

    TY - JOUR
    A1 - Paltineanu, V.
    A1 - Kenrick, Donald S., translator
    T1 - Gypsies in Albania
    JF - Journal of the Gypsy Lore Society
    PY - 1969/01-1969/04/30
    VL - 3, 48
    IS - 1-2
    SP - 74
    N1 - Notes: Note
    KW - Notes and Queries
    ER -

    TY - JOUR
    A1 - Editor
    T1 - The Education of Gypsy Children
    JF - Journal of the Gypsy Lore Society
    PY - 1969/01-1969/04/30
    VL - 3, 48
    IS - 1-2
    SP - 75-76
    N1 - Notes: Note
    KW - Notes and Queries
    ER -

    TY - JOUR
    A1 - Wade, Richard A. R.
    T1 - Gypsies on Television
    JF - Journal of the Gypsy Lore Society
    PY - 1969/01-1969/04/30
    VL - 3, 48
    IS - 1-2
    SP - 76-77
    N1 - Notes: Note
    KW - Notes and Queries
    ER -
  • adamsmith
    right so Error: Cannot start a DB transaction from a different wait level
    is at least the same error we've seen before, which I guess is good.
    If you copy the 10 items above to your clipboard and then do "import from clipboard" - does that work? (it will import into the currently selected collection, so you may want to create a new one for that purpose).
  • ssalo
    Yes, the import does work this way. Thank you for this tip, although importing this way will be time-consuming.

    However, the publication dates now show, for example, as "1969/01-1969/04/30." As that is exactly as they are shown in the RIS (using the updated translator), it looks like I will have to rework the dates within ProCite as I mentioned earlier.
  • adamsmith
    You should be able to select large batches using shift+click, or even ctrl+a and import themthis way, so it shouldn't take that long.

    As I say above, date ranges don't work great in Zotero currently - so while it can import the date as provided in the RIS, it won't show up as a date range in citations, so you may want to consider using the issue field if those are important.
  • ssalo
    Thank you for your help.
  • algeriemunozlarroa
    Hi there,

    I have a similar problem. When I want to import an RIS list of references (around 250) the import bar appears 1/4 full but it remains frozen. An error pops behind the import bar so it is difficult to read. However when I asked for an error report it gave me this number 1608084466.

    I also tried copying from the clipboard but didn't work.

    Thanks a lot.
  • adamsmith
    @Dan - what does the error report say?
  • algeriemunozlarroa
    Hi there, In case it helps this is what my error report says. Seems to be realted with my Antivirus or Java Script?
    Thanks


    Avast Log: Running SC, 2,

    Avast Log: Avast Message, {"properties_":{"type":{"options":{},"multiplicity":"optional","id":1},"params":{"options":{},"multiplicity":"repeated","id":2},"browser":{"options":{},"multiplicity":"optional","id":3}},"values_":{"params":{"0":[104,116,116,112,115,58,47,47,119,119,119,46,103,111,111,103,108,101,46,99,111,46,110,122,47],"datatype_":{"wiretype":2},"length":1},"type":4,"browser":2},"message_type_":"wrc_gpb.All.Command.Request"},

    Avast Log: Running SC, 3,

    Avast Log: Avast Message, {"properties_":{"type":{"options":{},"multiplicity":"optional","id":1},"params":{"options":{},"multiplicity":"repeated","id":2},"browser":{"options":{},"multiplicity":"optional","id":3}},"values_":{"params":{"0":[104,116,116,112,115,58,47,47,119,119,119,46,103,111,111,103,108,101,46,99,111,46,110,122,47],"datatype_":{"wiretype":2},"length":1},"type":4,"browser":2},"message_type_":"wrc_gpb.All.Command.Request"},

    Avast Log: undefined,

    [JavaScript Error: "no se encuentra elemento" {file: "http://prod4.rest-notify.msg.yahoo.com/v1/pushchannel/atys_mx?seq=5&format=json&idle=110&imtoken=2UEcSfxHrVvlcCnWrGwNEfDkfRtovFdTmI4sV7wHq1W4._PASi5cu881bbSEdR4xrxqcNj01IryNgQokAjwyi%7CmJs21jIfSJZ8KvQ1sq1m7Q--&c=BUZFq5W2TpS&sid=BCGGW.zs3BJ5E5gRXFY4QlYF6jlVbRDxAQYYKQ--&msgrAppId=mim&cache=1380155120361" line: 1}]
  • adamsmith
    none of these are relevant. Is that from an error report right after you got the import error?
  • algeriemunozlarroa
    Hi,
    I was trying to import again to copy paste to you the error report right after I import, but this time there was no error message behind the import bar and the import was successfull!

    I am sorry I don't understand what was going on before, I tried so many times and failed and now it is quite embarrasing that it fixed itself.

    Thanks a lot for yout help anyway :)
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