Importing EndNote libaray, INCLUDING PDF attachments

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  • davidinbj
    Am desperately trying to convert to zotero and seem to have the exact same problem (after 5 hours of trying!) as the above query by 'eagutt' way back in 2009: "Was trying to import my data from Endnotes...into Zotero, following the instructions above: setting output style in EN to "refman RIS", exporting to text file, then choosing import (I don't have embedded pdfs, so no complications that way.). I got the error message: "An error occurred while trying to import the selected file. Please ensure that the file is valid and try again." A number of entries got imported, but most did not. How can I ensure that the file is valid? Thanks for any help".

    I couldn't see an answer to eagutt's query...can anyone help?

    David
  • noksagt
    You can help make the Zotero translator more robust by finding the entry that failed (by dividing your RIS file into several files (each with a different subset of items)).

    Alternatively, you can try to cleanup the RIS file (by passing it through, for example, bibutils).
  • mark
    Also always do notify the makers of EndNote of these problems. It is a real issue for their paying customers. As their customer, you have the right to ask them to deliver at least the service of consistent and standard export formats. (Ask your librarians to do this for you if you have an institutional license.)
  • nprause
    Endote has placed most .pdfs within folders now, so the text replacement strategy presented for us Linux users above does not work. In other words, a path to the EndNote PDF like
    'file://Euros/bases_biblio/MyTeam/MyName/PDF/Author2007.pdf'
    used to work, but no longer will because now:
    file://Euros/bases_biblio/MyTeam/MyName/PDF/Author2007/Author2007.pdf'
    is the path. Does anyone know the syntax trick to copy the name only information as needed to use this recommended command:
    sed 's/internal-pdf:\/\/.*\//\/media\/CORSAIR\/References.Data\/PDF\/*/g' /home/user/Dropbox/TransferToZetoro.txt > /home/user/Dropbox/Author2007/Author2007.ris
    ?
  • nprause
    Excuse me, the better sample of what needs to be changed is this:
    sed 's/internal-pdf:\/\/.*\//\/media\/CORSAIR\/References.Data\/PDF\//g' /home/user/Dropbox/TransferToZetoro.txt > /home/user/Dropbox/GoingToZotero_PDF.ris

    to

    sed 's/internal-pdf:\/\/.*\//\/media\/CORSAIR\/References.Data\/PDF\/*[what-goes-here?]/g' /home/user/Dropbox/TransferToZetoro.txt > /home/user/Dropbox/GoingToZotero_PDF.ris
  • nprause
    This thread suggests that the original does a search for the .pdf that perhaps should be creating the extention automatically:
    http://forums.zotero.org/discussion/12476/duplicates-ris-pdf-endnote-file-not-found/

    A solution also was suggested in that thread (editing the EndNote RIS output style) that did not work for me.
  • nprause
    I figured out the structure of the paste command, but am still getting errors. Consistent with previous feedback I have tried:
    file:///media
    file://media
    /media

    and also moved the .pdf to the local desktop.

    Still importing only about 10 of ~4000 references then receiving error "Please ensure that the file is valid and try again."

    The file opens fine in a text editor and the replacement appears correct in each permutation.
  • adamsmith
    do small batches, try to narrow down the error - does it not import any files or is there maybe another problem?
  • nprause
    I deleted the files that were importing correctly and now receive the error "The selected file is not in an accepted format". The exported format was RIS as specified in the Zotero documentation. I tried with .txt and .ris extensions with the same result. The file opens in a text editor.
  • adamsmith
    post one entry that isn't working here. (i.e. copy and paste the RIS for one item from the text editor).
  • nprause
    I narrowed it down such that one file fails to import. When a handful of references are deleted, it imports successfully. However, when I attempt to import only those references that were deleted (which must be where a problem lies), they import successfully too. Thus, I am unable to determine any specific references that are not importing properly to provide an example.
  • nprause
    I just replicated this in another file. I reduced the file a citation at a time. I finally found a citation which, once removed, allowed the file to be imported. Yet, the "problem" file in isolation imports just fine.
  • adamsmith
    try running debug while importing and look at the output - maybe you can find something helpful.
    http://www.zotero.org/support/debug_output
  • nprause
    The citation prompting the fail when in the context of a larger file being imported is:
    TY - JOUR
    AB - Two studies have examined whether there exists a relationship between
    resting frontal alpha asymmetry and the Behavioral Inhibition and
    Activation Scales (C. S. Carver & T. L. White, 1994), which are based on
    Gray's Behavioral Inhibition and Behavioral Activation Systems. Findings
    suggest that greater relative left frontal activity characterizes
    individuals higher in self-reported behavioral activation sensitivity (E.
    Harmon-Jones & J. J. B. Allen, 1997; S. K. Sutton & R. J. Davidson, 1997),
    and, in one instance, lower behavioral inhibition sensitivity (S. K.
    Sutton & R. J. Davidson, 1997). In the present study, relatively greater
    left frontal activity correlated positively with behavioral activation
    scores. No significant relationship between resting frontal alpha
    asymmetry and the behavioral inhibition score emerged. These data suggest
    that relatively greater left frontal activity is indeed an index of
    approach oriented, appetitive motivational tendencies, whereas the
    relationship between relative right frontal activity and the behavioral
    inhibition system is likely to be complex and not accounted for by
    behavioral withdrawal alone.
    AU - Coan , James A.
    AU - Allen, John J. B.
    L1 - /home/nprause/Desktop/Ovaration.Data/PDF/0915289608Coan-2729962254/0915289608Coan.pdf
    M1 - 1
    N1 - Two studies disagreed on the asymmetry associated with BIS, so this study was to see which could be replicated.
    Used multiple reference schemes
    N=36
    BAS appears more clearly an approach, but BIS not necessarily (could be interrupting ongoing behavior, increasing arousal, or increasing attention that need not lead to withdrawal)
    Greater left EEG in midfrontal and lateral-frontal = more BAS
    Greater right EEG in midfrontal = trend to more BIS (agrees with Sutton and Davidson 1997)
    Suggests that BIS does not fit neatly as a "withdraw" tendency
    PY - 2003
    SP - 106
    ST - Frontal EEG asymmetry and the behavioral activation and inhibition systems
    T2 - Psychophysiology
    TI - Frontal EEG asymmetry and the behavioral activation and inhibition systems
    VL - 40
    ID - 1960
    ER -

    The debugging output when an import containing this citation fails begins:
    3)(+0000000): Translate: Searching for translators for an undisclosed location

    (3)(+0003754): Translate: Searching for translators for /home/nprause/Desktop/Reduced17.txt

    (4)(+0000000): Translate: Binding sandbox to http://www.example.com/

    (4)(+0000001): Translate: Parsing code for Bibliontology RDF

    (3)(+0000004): Translate: Checking whether file is UTF-8

    (3)(+0000217): Translate: Preparing IO for Bibliontology RDF failed:

    (3)(+0000000): 'fileName' => "chrome://zotero/content/xpcom/translation/browser_firefox.js"
    'lineNumber' => 323


    (2)(+0000000): Translate: Detect using Bibliontology RDF failed:
    thrown exception => Error loading translator into sandbox
    url => /home/nprause/Desktop/Reduced17.txt
    downloadAssociatedFiles => true
    automaticSnapshots => true

    (4)(+0000000): Translate: Parsing code for MODS

    (3)(+0000003): Translate: Checking whether file is UTF-8

    (3)(+0000210): Translate: Preparing IO for MODS failed:

    (3)(+0000000): 'fileName' => "chrome://zotero/content/xpcom/translation/browser_firefox.js"
    'lineNumber' => 323
  • adamsmith
    that is bizarre - the way the RIS translator works is that it checks whether

    TY -

    is in the first four lines of the file - if it is, it should at least try to treat this as RIS - which it doesn't. Is there any way the first entry in the file could have moved down too far?
    If you don't mind, you could post a non-working RIS as a public gist to gist.github.com and post the URL here.
  • nprause
    Public clone:
    git://gist.github.com/1236377.git

    (Will remove this after you take a look as it has notes I don't want preserved online.)
  • nprause
    May be easier direct:
    https://gist.github.com/1236377
  • adamsmith
    OK, I got it.
  • nprause
    Thanks, deleted original.

    And thank you for taking a closer look! So weird.
  • adamsmith
    to me this looks like the line spacing is indeed the issue.
    I downloaded the file and got the same error message as you.
    Then opened in gedit and ran search and replace
    \n\n --> \n
    saved and it imported fine.
  • nprause
    In gedit my \n\n finds none. Using \r\n\r\n it replaces the spaces between records, but that is all and it still does not import. When opened in Notepad I could replace the carriage return pairs with a single carriage and that worked, including accurately importing the affiliated pdfs.

    Hope this helps someone else!
  • adamsmith
    yay! glad I got you on the right track and it's working now.
  • jonnycrunch
    With Mac OS X, using the sed replacement script one must include the full path to the PDF folder that starts with /Users and ending in PDF ( note no trailing slash ), resulting in three forward slashes!

    sed -e 's/internal-pdf:\/\//file:\/\/ [ path to PDF folder starts with \/Users\/ ... ending .. /PDF ] \//g' [ input.txt ] > [ output.txt ]

    so in Zotero the URL field is now file:///Users/....../PDF/[file.].pdf

    for example from the folder that contains the file to be replaced using sed:

    sed -e 's/internal-pdf:\/\//file:\/\/\/Users\/jonathan\/research_project\/references\/history_project_references.Data\/PDF\//g' history_project_references_to_import.txt > history_project_reference_export_and_replaced.txt

    the three escaped forwarded slashed took me a while to figure out.
  • ellentje
    Hello,

    I'm too having problems with importing the endnote (X2) library into zotero with the pdf attachments.

    I did follow the suggestions mentioned on the forum (renaming internal-pdf etc.), importing the references works fine, but the pdf files are nowhere to be found. In the "info" section of the reference, the link to the file is given, but I cannot directly access the pdf!

    Is this normal or was a mistake made?

    Thanks!
    Ellen
  • ellentje
    Meanwhile, I found the solution. The problem was that some of the pdfs I had were sent to me by email from an endnote library, resulting in strange and long pdf names.. Changing the names of these pdfs was the solution

    Cheers
    Ellen
  • lukasl 1
    Hi all! I have kind of a strange problem when trying to get my Endnote library into Zotero, I can import the pure citations without a problem, however, there are no "internal-pdf://"-links in the file when I save it as a "text only" (of course using the RIS output style).

    When I save it as a xml I´m able to see the links (and I can replace them), but when I try to import it too Zotero it tells me that xml is not supported. Did anyone run into a similar problem and know how to solve it?

    I use a Mac OS X, Zotero version 3.0.8.1 and have an Endnote X5. Thanks for your help! Lukas
  • adamsmith
    Zotero currently doesn't import Endnote XML (though we should probably think about that/just do it). So the way would be through RIS - I can't tell you how to get the pdflinks, though, someone more familiar with Endnote would have to say.
  • giamellaro
    edited February 7, 2013
    Just want to thank the contributors here. After way too long I was finally able to import from endnote 6.0.2 to Zotero WITH the pdfs based on the three slash method. All on Mac mtn lion. Endnote is clearly designing the software to make this process difficult. Feels like I shed a parasite!
  • aurimas
    FWIW, pdf imports from EndNote should now work without any modifications to the RIS file. see www.zotero.org/support/kb/importing_records_from_endnote
  • gbucini
    Hi,

    I'm exporting my Endnote library and want to export the pdf files along.

    I replaced the Endnote default string and my RIS file now has the full path:
    L1 - "file://C:/Users/myname/Documents/EndNote/savanna_UVM.Data/PDF/AgnewADQ_etal_1993_JVegScience_vegswitch-2620602995/AgnewADQ_etal_1993_JVegScience_vegswitch.pdf"

    Zotero imports the reference but not the pdf file.

    Can anybody see where the problem is in my RIS file?

    Thank you very much!

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