refbase - Web Reference Database

Hi all,

I ran into a problem with the import of several formats that are
supported by bibutils. i think, i set up bibutils correctly (more or
less), because the export to e.g. bibtex works fine, the command "SELECT
* FROM depends;" gives me

1  	refbase  	true  	NULL
2 	bibutils 	true
/afs/rz.uni-jena.de/www/chemie/www.lit.uni-jena.de/bibutils/
3 	pdftotext 	true 	NULL

which appears to be correct. I even added a new $sessionTempDir that is
writable. My refbase version is the svn trunk. The error messages for
both file upload and text paste of the demos from refbase.net are:

"There were validation errors regarding the data you entered:"
"Record 1: Unrecognized data format! Required field missing: TY"

The really strange thing is, that if I copy all of the bibtex examples,
my refbase installation imports all entries correctly, except the first
one. Looks like it needs the first entry for recognition of the format?!

It would be brilliant, if we could solve my problem and I thank you very
much in advance for your answers.

Kind regards,
der Max

Programms in the bibutilspath are:
bib2xml       copac2xml  end2xml   isi2xml  modsclean  wordbib2xml
xml2bib  xml2isi  xml2wordbib  biblatex2xml  ebi2xml    endx2xml
med2xml  ris2xml    xml2ads      xml2end  xml2ris
System infos:
Linux www3.rz.uni-jena.de 2.6.18-194.3.1.el5 #1 SMP Fri May 7 01:52:57
EDT 2010 i686
PHP Version 5.1.6
Apache 2
safe_mode off
mysql Client API version 5.0.77
mysql Server Version: 5.0.77

Re: [refbase-talk] Problem with bibtex import, but not with export From: Richard Karnesky <karnesky@gm...> - 2010-06-03 17:51 > My refbase version is the svn trunk. The error messages for > both file upload and text paste of the demos from refbase.net are: > > "There were validation errors regarding the data you entered:" > "Record 1: Unrecognized data format! Required field missing: TY" Is this the same error you get for ALL file formats & ALL files in that format? > The really strange thing is, that if I copy all of the bibtex examples, > my refbase installation imports all entries correctly, except the first > one. What version of bibutils are you running? Have you tried to run it manually on the files that you are trying to import to see what it produces? --Rick

Re: [refbase-talk] Problem with bibtex import, but not with export From: Maximilian Bräutigam <max-braeu@gm...> - 2010-06-03 20:01 Attachments: test.xml      test.bib      Hi Rick, thank you for your email. Am 03.06.2010 17:55, schrieb Richard Karnesky: >> My refbase version is the svn trunk. The error messages for >> both file upload and text paste of the demos from refbase.net are: >> >> "There were validation errors regarding the data you entered:" >> "Record 1: Unrecognized data format! Required field missing: TY" > > Is this the same error you get for ALL file formats & ALL files in that > format? > RIS, RefWorks, Scifinder, PubMed MEDLINE, ISI Web of Science, CSA Illumina, are ok. In Endnote, Bibtex, PubMed XML, MODS XML the first entry needs to be skipped. Here I get the same error like above. I only tried a few bibtex-files, there I have the strange behavior all the time and for the rest I just used the examples online at refbase.net. > >> The really strange thing is, that if I copy all of the bibtex examples, >> my refbase installation imports all entries correctly, except the first >> one. > > What version of bibutils are you running? Have you tried to run it > manually on the files that you are trying to import to see what it produces? bibutils_4.9_src.tgz - C source code A test.bib file is attached, then I tried to convert it with bib2xml and the result is in file test.xml. I cannot see something unusual in the xml. Then I tried to import both bibtex and xml file to refbase and got the same error: "There were validation errors regarding the data you entered:" "Record 1: Unrecognized data format! Required field missing: TY" "Skip records with unrecognized data format" If I say yes to the last, it imports everything except the first entry. But the first entry is valid: I copied this entry twice to the file and the second will be recognized. Strange behavior ... > --Rick Thanks again. Kind regards, Max -- Maximilian Bräutigam max-braeu@... GPG key-id F9E42811 http://www.jcf.uni-jena.de

Re: [refbase-talk] Problem with bibtex import, but not with export From: Richard Karnesky <karnesky@gm...> - 2010-06-03 20:31 >> What version of bibutils are you running? Have you tried to run it >> manually on the files that you are trying to import to see what it produces? > > bibutils_4.9_src.tgz - C source code Unless there is a reason to run this version, you may try to downgrade to 3.40, available from: http://bibutils.refbase.org/ and see if this works. > A test.bib file is attached, then I tried to convert it with bib2xml and > the result is in file test.xml. I cannot see something unusual in the > xml. And what do you get when you run xml2ris ? --Rick

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