Importing RIS format txt file error

soljiang

I'm trying to import RIS format txt file exported from EndNote but keep getting errors.
The error says "An error occurred while trying to import the selected file. Please ensure that the file is valid and try again.".
I'm using Zotero 3.0.3.
I really hope I can move from Endnote to Zotero coz I like this a lot.

If it's possible, I can send my text file so that some people can take a look to decide if my exported txt has problems. Thank you!

adamsmith

It would be most helpful if you could split the RIS file in smaller chunks and post a small one that still fails with that message somehwere (e.g. pastebin.com) so that multiple people can take a look.

soljiang

Sometimes it works and sometimes it doesn't, even though I have the same setting in Endnote. Also it doesn't have to do with the number of entries.

E.g. The following one does not work.


TY - JOUR
AB - A variety of recent advances in single-molecule methods are now making possible the routine measurement of the distinct catalytic trajectories of individual enzymes. Unlike their bulk counterparts, these measurements directly reveal the fluctuations inherent to enzymatic dynamics, and statistical measures of these fluctuations promise to greatly constrain possible kinetic mechanisms. In this chapter, we discuss a variety of advances, ranging from theoretical to practical, in the new and growing field of statistical kinetics. In particular, we formalize the connection between the hidden fluctuations in the kinetic states that compose a full kinetic cycle and the measured fluctuations in the time to complete this cycle. We then discuss the characterization of fluctuations in a fashion that permits kinetic constraints to be easily extracted. When there are multiple observable enzymatic outcomes, we provide the proper way to sort events so as not to bias the final statistics, and we show that these classifications provide a first level of constraint on possible kinetic mechanisms. Finally, we discuss the basic substrate dependence of an important function of the statistical moments. The new kinetic parameters of this expression, akin to the Michaelis-Menten parameters, provide model-independent constraints on the kinetic mechanism. Copyright (c) 2010 Elsevier Inc. All rights reserved.
AD - Department of Physics and Jason L. Choy Laboratory of Single-Molecule Biophysics, University of California, Berkeley, California, USA.
AN - MEDLINE:20627160
AU - Moffitt, Jeffrey R.
AU - Chemla, Yann R.
AU - Bustamante, Carlos
DA - 2010
KW - Catalysis. Kinetics. *Models, Statistical. *Molecular Motor Proteins
Index Medicus
0 / Molecular Motor Proteins
L1 - file://C:\Library\Papers\Methods\Moffitt_Bustamante_Methods in Statistical Kinetics.pdf
N1 - 20627160
PY - 2010
SN - 1557-7988
SP - 221-57
ST - Methods in statistical kinetics
T2 - Methods Enzymol
TI - Methods in statistical kinetics
UR - <Go to ISI>://MEDLINE:20627160
VL - 475
ID - 1207
ER -


TY - JOUR
AN - 1126943
AU - Strickland, S.
AU - Palmer, G.
AU - Massey, V.
C1 - 4
C2 - Enzyme Kinetics
DA - Jun 10
J2 - The Journal of biological chemistry
KW - Binding Sites
Computers, Analog
*Enzymes
*Kinetics
Ligands
Mathematics
Protein Binding
*Proteins
Time Factors
L1 - file://C:\Library\Papers\Classic Papers\Strickland & Massey - Determination of Dissociation Constants and Specific Rate Constants of Enzyme-Substrate (or Protein-Ligand) Interactions from Rapid Reaction Kinetic Data.pdf
IS - 11
N1 - Journal Article
Research Support, U.S. Gov't, P.H.S.
United states
PY - 1975
SN - 0021-9258 (Print)
SP - 4048-52
ST - Determination of dissociation constants and specific rate constants of enzyme-substrate (or protein-ligand) interactions from rapid reaction kinetic data
T2 - J Biol Chem
TI - Determination of dissociation constants and specific rate constants of enzyme-substrate (or protein-ligand) interactions from rapid reaction kinetic data
UR - http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=PubMed&dopt=Citation&list_uids=1126943
VL - 250
ID - 1273
ER -

soljiang

Actually after I further split above entry into two single entries. The first txt file works for the first one. But the second entry pop error during importing.

adamsmith

If you select them both here on the forum, press ctrl+c (cmd+c on a mac) and then do "import from clipboard" - does that work? Works for me.

adamsmith

if not, could you provide an error report ID immediately after getting the error?
http://www.zotero.org/support/reporting_bugs

soljiang

If I only copy the second one, it doesn't work and same error.
If I only copy the first one, it works.
So it's consistent with txt file. Must be something wrong with the second entry?

Submitted report
ID 552261426

adamsmith

@Dan, Simon - anything in that report?

My suspicion is that it's Windows specific, some stupid encoding hangup - Windows likes to get those.
How large is your total library, maybe we can find a workaround?

aurimas

I'll take a look at this on windows in a few hours.

@adamsmith I thought you were dual-booting

adamsmith

@aurimas - no, my wife is stubbornly sticking to Windows, so if I really need to I have Windows set-up I can use, but I rarely do. (And I really don't like Windows...).

soljiang

My export isn't too big. about ~100 entries at one time. Because I have all custom groups in Endnote and I don't know if I can just export the whole library (~2000 entries) and they show up as different groups/collections in Zotero, so I'm doing one group at time.

soljiang

I tried another txt and generated another report ID 1381614688
Seems it's the same error.

aurimas

If I only copy the second one, it doesn't work and same error.
If I only copy the first one, it works.
So it's consistent with txt file. Must be something wrong with the second entry?

Both of those records worked for me on windows. Tried it on standalone and firefox plug-in both fm clipboard and from file.

Unless Dan can see something useful in the bug reports, it would be great if you could upload the file that is not working somewhere (not copy-paste it). E.g. dropbox or fileswap or whatever you prefer. If you don't want to upload it anywhere, Dan may tell you to email it to Zotero.

adamsmith

@soljang - before you do that, make sure to update your translators (advanced tab of the zotero preferences), restart Zotero/Firefox and try again - the update should have happened automatically, but maybe it didn't.
Aurimas did some work on the translator recently and maybe that makes a difference.

Simon

There's nothing in those reports besides an XML syntax error, which should be benign. A debug ID could be more informative.

soljiang

The Debug ID is D173530153

I tried another txt file but I think they all share the same problem.

soljiang

@aurimas, to which email address should I send the file?
@adamsmith, I'm using 3.0.3, which button should I click in order to update the translator? Reset translators?

adamsmith

"update now" (next to the "automatically update option) in the general tab of the preferences

soljiang

@adamsmith, it's already up to date.
Does Debug ID is D173530153 offer any further information?

It says:


Failed to load native module at path 'C:\Program Files (x86)\Zotero Standalone\extensions\zoteroWinWordIntegration@zotero.org\components-9.0\zoteroWinWordIntegration.dll': (80520012) <unknown; can't get error from NSPR>

Failed to load native module at path 'C:\Program Files (x86)\Zotero Standalone\extensions\zoteroWinWordIntegration@zotero.org\components-8.0\zoteroWinWordIntegration.dll': (80520012) <unknown; can't get error from NSPR>

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{6957994c-fc0e-4c66-a451-6a76a819bcc2}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{3e514f9e-65e0-4cfa-adca-0aad58f4305a}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{3e514f9e-65e0-4cfa-adca-0aad58f4305a}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{d53039ca-b819-46d9-991c-00cd18a86ab8}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{3ade2972-5b77-4df1-b69b-f9dba1af098f}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{3ade2972-5b77-4df1-b69b-f9dba1af098f}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{d352ae70-82c8-4c89-8ead-ebe3b7cbac27}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{7daf41ce-64b0-4dcb-b51e-8ad6aa18ee35}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{7daf41ce-64b0-4dcb-b51e-8ad6aa18ee35}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{60666ef0-a86b-4179-8f59-bab760009517}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{1941a5c7-423e-4f10-9635-6d5f16b9aa50}" line: 1 column: 1 source: "TY - JOUR"}]

[JavaScript Error: "syntax error" {file: "moz-nullprincipal:{1941a5c7-423e-4f10-9635-6d5f16b9aa50}" line: 1 column: 1 source: "TY - JOUR"}]


Seems tY - JOUR is a syntax error?

adamsmith

this is a wild guess, but could you try re-naming the file as .ris instead of .txt (you might have to show file extensions in Windows http://windows.microsoft.com/en-US/windows-vista/Show-or-hide-file-name-extensions ) and try again? I'm thinking that maybe Zotero is failing trying out one of the other translators first.

Maybe Dan or Simon know more about that syntax error - I have nothing.

I'm not sure if sending your file somewhere is going to be worth it since if I understood you correctly you get the same problem using copy & import from clipboard, right? Or Aurimas, what did you have in mind?

soljiang

I got the same error after renamed to ris. Why does the file work on all your computers? Do you all use Macs?

adamsmith

I use linux, but Aurimas tried this on Windows and said it worked, that's what's so confusing - which Windows version? Are you using Zotero Standalone or for Firefox? If you're using it on FF - which FF version? Would you be willing to try installing Standalone (use the standard settings and share the data directory) and see if it works there?

soljiang

I'm using standalone and I'm using Windows 7, 64-bit. I assume Zotero is 32-bit.

soljiang

I submitted another debug output logging file Debug ID is D2021244061. May I get some help on that? Thank you!!

dstillman

Translate: Translation using RIS failed:
message => (NS_ERROR_FILE_NOT_FOUND) [nsIFile.copyTo]
filename => chrome://zotero/content/xpcom/attachments.js
lineNumber => 84

I'm guessing it works if you remove the L1 line from the second entry? Does the file at that path exist on your system?

soljiang

Yes, the file of that path exists and I can open it also in endnote.

soljiang

@Dan, it does work after delete L1 line. But the file exists for that path. All my entries have a file paths associated. It's not practical for me to fish out the links that Zotero doesn't recognize and then add path only in zotero after import. Any other way to get around it?

soljiang

@Dan, may I send you an email including two files, one work and one doesn't work? I really can't tell the difference between the two files and all the paths are connected to the right files in endnote. Maybe you can help me figure out the difference that causes the problem? They are exported using the same format and method in endnote.

Thank you.

DWL-SDCA

Could this be an issue with an anti-virus intervention that questions the file reference? Might explain why some Windows machines will import the record and another does not.

dstillman

The problem is probably that, when Zotero tries to move that path into the Zotero data directory, the resulting path is too long for Windows.

I've created a ticket to shorten too-long filenames automatically on import. In the meantime you'll have to either shorten the filenames manually or move your Zotero data directory to a shorter path.

soljiang

I see, Dan. Thank you!!! It finally makes sense to me. Thanks to this information it finally makes sense. Unfortunately I find I've been doing something I didn't intend to do. I didn't mean to create internal pdf files in the storage folder. All I wanted to do is to create a link to the pdf files I had already on my computer. I didn't know Zotero has been copying pdf through the link into its storage folder...
Is there a way just to copy the file paths through which I can open the original pdf file in Zotero?

Thank you, Dan! You are awesome.