docbook export skips species names that are in braces

[bernhard-kleine]

• [ ] I have tested the latest master version from http://builds.jabref.org/master/ and the problem persists

JabRef version 4.1

Steps to reproduce:

1. this is the citation:

Article (AW06) Audsley, N. & Weaver, R. J. Analysis of peptides in the brain and corpora cardiaca-corpora allata of the honey bee, {A}pis mellifera using MALDI-TOF mass spectrometry. Peptides, 2006, 27, 512-20.

2. Using a line like this java -jar C:\Programme\JabRe4.1\JabRef-4.1.jar -o cha13addBiB.xml,docbook -n true addkap13.bib

3. I get

N.Audsley R. J.Weaver Analysis of peptides in the brain and corpora cardiaca-corpora allata of the honey bee, mellifera using MALDI-TOF mass spectrometry. Peptides 27 512–20 2006

Note that the {A}pis is left out. This is valid not only for this example, but about 50% of my citations are errorneous.

[stefan-kolb]

@johannes-manner Maybe you can help here, as you just worked on some exporters.

[johannes-manner]

I tried to reproduce the bug, but I get a different xml-result. Please share the .bib and .xml files with me for a further investigation of this bug.

[bernhard-kleine]

I have tested this again and still some instances of braced e.g. Drosophila are removed.

I used the following line to start the program

java -jar C:\Programme\JabRef4.2Test\JabRef-4.2Test.jar -o testbraces.xml,docbook -n true testbraces.bib

JabRef4.2Test contains the files in the image In that period I downloaded the following jabref install files:

.bib file and .xml file are attached. Thanks for looking into this.

Bernhard Am 28.05.2018 um 17:07 schrieb Johannes Manner:

I tried to reproduce the bug, but I get a different xml-result. Please share the .bib and .xml files with me for a further investigation of this bug.

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[johannes-manner]

GitHub does not support .bib and .xml files to attach in comments. Maybe you can alter the file ending in .bib.txt and .xml.txt. Then an upload is possible here.

[bernhard-kleine]

Sorry, that I didnot take in account. The two screenshots were also omitted. I can sent them when they are neccessary. The offending lack of Drosophila is obvious in the title of paper Baggerman et al., Choi et al, Clark et al. e.g. In Dai et al. we are missing Manduca. These were obvious be checking only a small number. Not any instance of Drosophila in abstracts was removed, not even those in braces (I added braces to some instances in the .bib abstracts), but those braces in the title resulted in missing words in the xml. testbraces.bib.txt testbraces.xml.txt.

By the way most of this braces, if not all, are from using PUBMED input into jabref while searching for the PMID which is the way I add citations to jabref while looking for DOI gives fewer information. Normally I would not note these braces since they are only present in the source file, not shown in jabref.

Bernhard

[bernhard-kleine]

@tobiasdiez anything missing?

[bernhard-kleine]

Did you manage some progress?

[tobiasdiez]

@bernhard-kleine please don't post such "ping" messages because they only add unnecessary noise. Usually, you can see if there was any progress by looking at the linked pullrequests/other issues (in this case #4108 which, however, is not yet in a workable state). Please also respect that we cannot fix every bug in a timely fashion. As you know, everybody involved works on JabRef in their freetime!

[tobiasdiez]

Thanks to @johannes-manner this should be fixed in the latest development version. Could you please check the build from http://builds.jabref.org/master/. Thanks! Please remember to make a backup of your library before trying-out this version.