Re: JabRef insertion to LyX fails with accented character

[Rich Shepard]

On Wed, 3 Jan 2024, Herbert Voss wrote:


I suppose again the "mergedate=..." option problem in the setting
of biblatex.


Herbert,

That's long gone.


In general biber uses the encoding from the main document unless
you explicitely call
biber --bibencoding=latin9 


And I've not done that.


Looks to me like these two are the source of the problems.


yes and no, because the bibliography is wrong, but should have some
entries. It is only a warning not an error.


Yes, changing the citation style from `Biblatex' to `Biblatex (natbib mode)'
allowed the bibliography to be included in the PDF.

Why only with non-accented characters remains unanswered, but I doubt the
expected audience for this doc will notice any difference.

Many thanks,

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Re: JabRef insertion to LyX fails with accented character

[Herbert Voss]

Am 03.01.24 um 16:51 schrieb Rich Shepard:

On Wed, 3 Jan 2024, Herbert Voss wrote:


every problem is listed in the logfiles ...

The .log file, line 725:
LaTeX Warning: Citation 'Ant=E3o2021' on page 5 undefined on input 
line

324.



Rich,
I suppose again the "mergedate=..." option problem in the setting
of biblatex.




.blg


The biodiversity.blg:

INFO - Writing 'biodiversity.bbl' with encoding 'latin9'


In general biber uses the encoding from the main document unless
you explicitely call

biber --bibencoding=latin9 



INFO - Output to biodiversity.bbl
WARN - I didn't find a database entry for 'Ant=E3o2021' (section 0)
INFO - WARNINGS: 1

Two things:
1. Where is biber finding the latin9 encoding?
2. The string E3 is a hex color, not ã.

Looks to me like these two are the source of the problems.


yes and no, because the bibliography is wrong, but should have some
entries. It is only a warning not an error.

Herbert
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Re: JabRef insertion to LyX fails with accented character

[Rich Shepard]

On Wed, 3 Jan 2024, Herbert Voss wrote:


every problem is listed in the logfiles ...


Herbert,

Just re-exported to LaTeX (pdflatex) and ran pdflatex and biber.


.log


The .log file, line 725:
LaTeX Warning: Citation 'Ant=E3o2021' on page 5 undefined on input line
324.


.blg


The biodiversity.blg:
$ biber biodiversity 
INFO - This is Biber 2.19

INFO - Logfile is 'biodiversity.blg'
INFO - Reading 'biodiversity.bcf'
INFO - Found 12 citekeys in bib section 0
INFO - Processing section 0
INFO - Looking for bibtex file '/home/rshepard/documents/jabrefdb.bib' for 
section 0
INFO - LaTeX decoding ...
INFO - Found BibTeX data source '/home/rshepard/documents/jabrefdb.bib'
INFO - Overriding locale 'en-US' defaults 'variable = shifted' with 'variable = 
non-ignorable'
INFO - Overriding locale 'en-US' defaults 'normalization = NFD' with 
'normalization = prenormalized'
INFO - Sorting list 'nyt/global//global/global' of type 'entry' with template 
'nyt' and locale 'en-US'
INFO - No sort tailoring available for locale 'en-US'
INFO - Writing 'biodiversity.bbl' with encoding 'latin9'
INFO - Output to biodiversity.bbl
WARN - I didn't find a database entry for 'Ant=E3o2021' (section 0)
INFO - WARNINGS: 1

Two things:
1. Where is biber finding the latin9 encoding?
2. The string E3 is a hex color, not ã.

Looks to me like these two are the source of the problems.

Thanks,

Rich
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Re: JabRef insertion to LyX fails with accented character

[Herbert Voss]

Am 03.01.24 um 15:41 schrieb Rich Shepard:

Now I've learned how to insert accented characters using my keyboard I
corrected the lead author's name in JabRef from Antao to Antão. This 
morning
when I tried compiling the document with that citation it failed to 
find the

non-accented record in the .bib.

I deleted the ??.?? citation and tried to push the accented one to the
document. It keeps failing; the citation is still ??.??. I'm really
surprised that this happens.


Rich,

every problem is listed in the logfiles ...

.log
.blg

Herbert





Is this a LyX or JabRef issue?

TIA,

Rich


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Re: Jabref error

[Wolfgang Engelmann]

Am 17.05.22 um 13:00 schrieb Herbert Voss:



Am 17.05.22 um 11:24 schrieb Wolfgang Engelmann:

Slightly OT

I use jabref as a reference manager for including literature in my lyx 
documents.

I get a very annoying error >
The library has been modified by another program
 and I don't know how to handle it.

I use
JabRef 5.6--2022-04-25--5c9d898
Linux 5.10.0-14-amd64 amd64

and according to a search in the internet this error should not occur 
in version 5.6 anymore.


Has somebody a solution? I tried various changes in the preferences, 
without success so far.


Another program or instance of JabRef changed the current open file.
You could _reload_ the bib file and save it again.

Herbert
Thanks, Joel and Herbert, for the proposals. I used Herberts for the 
time being and will collect the case if I run into it again and send it 
to the JabRef maintainers.

Wolfgang
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Re: Jabref error

[Herbert Voss]

Am 17.05.22 um 11:24 schrieb Wolfgang Engelmann:

Slightly OT

I use jabref as a reference manager for including literature in my lyx 
documents.

I get a very annoying error >
The library has been modified by another program
 and I don't know how to handle it.

I use
JabRef 5.6--2022-04-25--5c9d898
Linux 5.10.0-14-amd64 amd64

and according to a search in the internet this error should not occur 
in version 5.6 anymore.


Has somebody a solution? I tried various changes in the preferences, 
without success so far.


Another program or instance of JabRef changed the current open file.
You could _reload_ the bib file and save it again.

Herbert
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Re: Jabref error

[Joel Kulesza]

On Tue, May 17, 2022 at 03:25 Wolfgang Engelmann 
wrote:

> Slightly OT
>
> I use jabref as a reference manager for including literature in my lyx
> documents.
> I get a very annoying error >
> The library has been modified by another program
>   and I don't know how to handle it.
>
> I use
> JabRef 5.6--2022-04-25--5c9d898
> Linux 5.10.0-14-amd64 amd64
>
> and according to a search in the internet this error should not occur in
> version 5.6 anymore.
>
> Has somebody a solution? I tried various changes in the preferences,
> without success so far.
>
> Wolfgang
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>
Wolfgang,

I have seen the same message and I ignore it (it has never caused me
problems). I also keep my .bib in a git repository to provide additional
assurance/monitoring regarding changes. I recommend raising this to JabRef
developers, particularly if you’re able to reliably reproduce the behavior
through some repeatable process.

Thanks,
Joel
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Re: JabRef entry warning

[Dr Eberhard Lisse]

Paul,

this is why I am getting irritated at the (ie his) persistent lack of
sending in MWEs.  Having to go through this (and every time) borders on
the rude, and frustrates people like you (and me) who want to help.

A small file such as your dummy file, producing the error with the
required files allows anyone to just run the sucker and see where the
issue comes from.  Then one can also open the BIB file with another tool
(I like BibDesk on the Mac) and see what errors this flags.

I also find, when I have such an issue myself, reducing the file to
nothing else but the error producing text often makes me find the error
:-)-O

Never mind (him) sending in stuff with typos.

el

 12/10/2021 20:56, Paul A. Rubin wrote:
[...]

I turned your entry into a .bib file, cited it in a dummy document,
and compiled with biblatex.  It specifically flagged the first entry
that ended with a comma.  I think the "name" in the error message is
because it thinks that, after that last comma, there will be another
name = value pair in the field that it never finds (due to the closing
brace).  Not the ideal error message in my opinion, but deleting the
surplus comma did fix it.

I spotted the "and and" Maria flagged, but in my test that did not
cause an error message, it just mucked up the printed citation.

[...]

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Re: JabRef entry warning

[Paul A. Rubin]

On 10/12/21 2:31 PM, Rich Shepard wrote:

On Tue, 12 Oct 2021, Paul A. Rubin wrote:


You have commas at the end of several fields (inside the closing curly
brace), including institution, which I think is triggering the error
message.


Paul,

All key:value pairs end with commas except for the last one.

You also have a few places with a funky dash separating a pair of 
numbers,
rather than a double dash ('--'). That might be the result of copying 
from

a PDF and pasting. I don't know if that will also cause any indigestion.


Yes, that's not uncommon. I try to catch and repair them when I enter the
document in JabRef, but aren't always successful. Now corrected.

The error specified the document name, not any key:value pair between the
opening and closing braces:
WARN - Name in key 'Paul2012' is empty (probably consecutive 'and'):
skipping entry 'Paul2012'

The name key has no 'and' in it.

While this is a warning, not an error, I'd still like to have biber 
accept

it as correct.

Still puzzled,

Rich

I turned your entry into a .bib file, cited it in a dummy document, and 
compiled with biblatex. It specifically flagged the first entry that 
ended with a comma. I think the "name" in the error message is because 
it thinks that, after that last comma, there will be another name = 
value pair in the field that it never finds (due to the closing brace). 
Not the ideal error message in my opinion, but deleting the surplus 
comma did fix it.


I spotted the "and and" Maria flagged, but in my test that did not cause 
an error message, it just mucked up the printed citation.


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Re: JabRef entry warning

[Rich Shepard]

On Tue, 12 Oct 2021, Maria Gouskova wrote:


Maybe it was the two "ands" in a row in the author field:


Maria,

Yep, that's the problem. It's like the reading test where the paragraph has
the word 'the' twice, once at the end of a line, the other at the beginning
of the following line.

I hadn't noticed that when I looked at each field, but your fresh eyes
caught it. Thank you very much.

Stay well,

Rich
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Re: JabRef entry warning

[Rich Shepard]

On Tue, 12 Oct 2021, Paul A. Rubin wrote:


You have commas at the end of several fields (inside the closing curly
brace), including institution, which I think is triggering the error
message.


Paul,

All key:value pairs end with commas except for the last one.


You also have a few places with a funky dash separating a pair of numbers,
rather than a double dash ('--'). That might be the result of copying from
a PDF and pasting. I don't know if that will also cause any indigestion.


Yes, that's not uncommon. I try to catch and repair them when I enter the
document in JabRef, but aren't always successful. Now corrected.

The error specified the document name, not any key:value pair between the
opening and closing braces:
WARN - Name in key 'Paul2012' is empty (probably consecutive 'and'):
skipping entry 'Paul2012'

The name key has no 'and' in it.

While this is a warning, not an error, I'd still like to have biber accept
it as correct.

Still puzzled,

Rich

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Re: JabRef entry warning

[Maria Gouskova]

On Tue, Oct 12, 2021 at 2:01 PM Paul A. Rubin  wrote:

> On 10/12/21 1:21 PM, Rich Shepard wrote:
> > On Tue, 12 Oct 2021, Paul A. Rubin wrote:
> >
> >> You mention 'Paul2012' in the warning but show the entry with key
> >> 'Paul2017'. Is one of those a typo, or did you show us the wrong entry?
> >
> > Paul2021,
> >
> > :-)
> >
> > Probably need to re-caffinate. Corrected entry just posted.
> >
> > Thanks,
> >
> > Rich
> Rich,
>
> You have commas at the end of several fields (inside the closing curly
> brace), including institution, which I think is triggering the error
> message.
>
> You also have a few places with a funky dash separating a pair of
> numbers, rather than a double dash ('--'). That might be the result of
> copying from a PDF and pasting. I don't know if that will also cause any
> indigestion.
>
> Paul
>
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Maybe it was the two "ands" in a row in the author field:

author = {Paul, A.P. and Paretti, N.V. and MacCoy, D.E. *and and* Brasher,
A.M.D.},
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Re: JabRef entry warning

[Paul A. Rubin]

On 10/12/21 1:21 PM, Rich Shepard wrote:

On Tue, 12 Oct 2021, Paul A. Rubin wrote:

You mention 'Paul2012' in the warning but show the entry with key 
'Paul2017'. Is one of those a typo, or did you show us the wrong entry?


Paul2021,

:-)

Probably need to re-caffinate. Corrected entry just posted.

Thanks,

Rich

Rich,

You have commas at the end of several fields (inside the closing curly 
brace), including institution, which I think is triggering the error 
message.


You also have a few places with a funky dash separating a pair of 
numbers, rather than a double dash ('--'). That might be the result of 
copying from a PDF and pasting. I don't know if that will also cause any 
indigestion.


Paul

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Re: JabRef entry warning

[Rich Shepard]

On Tue, 12 Oct 2021, Paul A. Rubin wrote:

You mention 'Paul2012' in the warning but show the entry with key 'Paul2017'. 
Is one of those a typo, or did you show us the wrong entry?


Paul2021,

:-)

Probably need to re-caffinate. Corrected entry just posted.

Thanks,

Rich
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Re: JabRef entry warning

[Rich Shepard]

On Tue, 12 Oct 2021, Kornel Benko wrote:


Warning from 'Paul2012', but you cite 'Paul2017' here.


Kornel,

Mea culpa! The proper entry is:
@techreport{Paul2012,
abstract = {As part of the National Water-Quality Assessment Program of 
the U.S.
Geological Survey, this study examines the occurrence of nine trace
elements in bed sediment of varying mineralogy and land use and assesses
the possible effects of these trace elements on 
aquatic-macroinvertebrate
community structure. Samples of bed sediment and macroinvertebrates
were collected from 154 streams at sites representative of undeveloped,
...
and Naididae all demonstrated resilience to trace-element exposure
and, in some cases, possible changes in physical habitat within stream
ecosystems. The taxa characteristics within the Ozark Highland ecoregion
were different than other ecoregions as evidenced by generally more
diverse mayfly populations. In addition, Baetis sp. was common and
dominated many of the mayfly populations found in the Rocky Mountain
streams within the Mountain Southern Rockies and Mountain Northern
Rockies ecoregions; however, within the Ozark Highland ecoregion,
Tricorythodes sp. appeared to be more common than Baetis sp.},
author = {Paul, A.P. and Paretti, N.V. and MacCoy, D.E. and and 
Brasher, A.M.D.},
institution = {U.S. Geological Survey Scientific Investigations Report 
2012–5272,},
keywords = {streams, rivers, benthos, macroinvertebrates, sediments, 
land use, trace elements, statistics, metals},
number = {Scientific Investigations Report 2012–5272,},
title = {{The occurrence of trace elements in bed sediment collected 
from areas of varying land use and potential effects on stream 
macroinvertebrates in the conterminous western United States, Alaska, and 
Hawaii, 1992–2000.}},
year = {2012}
}

I redacted most of the abstract to save space as the issue is with the name.

Thanks for pointing out my mistake,

Rich
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Re: JabRef entry warning

[Paul A. Rubin]

On 10/12/21 1:00 PM, Rich Shepard wrote:
Biber tells me "WARN - Name in key 'Paul2012' is empty (probably 
consecutive

'and'): skipping entry 'Paul2012'" and the entry in the jabrefdb.bib is:
@techreport{Paul2017,
abstract = {This paper summarizes the application of algae as 
indicators of nutrient

pollution in water quality management. It describes the use of algal
indicators to develop water quality diagnostics for nutrient 
pollution

in the United States (U.S.) and then reviews scientific developments
in the use and application of algal indicators across the world.
The paper is intended as a technical resource for the water quality
manager/practitioner seeking to utilize algae to detect the presence
of nutrient pollution and to estimate the risks of nutrient pollution
in adversely affecting the condition of stream ecosystems.},
author = {Paul, M.J.},
institution = {Tetra Tech, Inc./ Center for Ecological Sciences},
keywords = {streams, rivers, lakes, ponds, algae, pollution, water 
quality, indicators},

pagetotal = {44},
title = {{Algal Indicators in Streams: A Review of Their 
Application in Water Quality Management of Nutrient Pollution}},

type = {techreport},
year = {2017}
}

I'm not seeing the empty error in the name. Why does biber find it empty?

Rich


Rich,

You mention 'Paul2012' in the warning but show the entry with key 
'Paul2017'. Is one of those a typo, or did you show us the wrong entry?


Paul2021

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Re: JabRef entry warning

[Kornel Benko]

Am Tue, 12 Oct 2021 10:00:08 -0700 (PDT)
schrieb Rich Shepard :

> Biber tells me "WARN - Name in key 'Paul2012' is empty (probably consecutive
> 'and'): skipping entry 'Paul2012'" and the entry in the jabrefdb.bib is:
> @techreport{Paul2017,
>   abstract = {This paper summarizes the application of algae as 
> indicators of
> nutrient pollution in water quality management. It describes the use of algal
>   indicators to develop water quality diagnostics for nutrient pollution
>   in the United States (U.S.) and then reviews scientific developments
>   in the use and application of algal indicators across the world.
>   The paper is intended as a technical resource for the water quality
>   manager/practitioner seeking to utilize algae to detect the presence
>   of nutrient pollution and to estimate the risks of nutrient pollution
>   in adversely affecting the condition of stream ecosystems.},
>   author = {Paul, M.J.},
>   institution = {Tetra Tech, Inc./ Center for Ecological Sciences},
>   keywords = {streams, rivers, lakes, ponds, algae, pollution, water 
> quality,
> indicators}, pagetotal = {44},
>   title = {{Algal Indicators in Streams: A Review of Their Application in 
> Water
> Quality Management of Nutrient Pollution}}, type = {techreport},
>   year = {2017}
> }
> 
> I'm not seeing the empty error in the name. Why does biber find it empty?
> 
> Rich
> 

Warning from 'Paul2012', but you cite 'Paul2017' here.

Kornel


pgp0Z5TQ3ELx2.pgp
Description: Digitale Signatur von OpenPGP
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Re: Jabref 5.3.1

[Wolfgang Engelmann]

Am 23.07.21 um 17:57 schrieb Herbert Voss:



Am 23.07.21 um 17:34 schrieb Wolfgang Engelmann:



Am 22.07.21 um 20:44 schrieb Herbert Voss:


First I deleted the old JabRef. Then I downloaded the new deb file
and with doubleclick on that file it will be installed by the install 
manager.

After that I can use jabref as usual.

Herbert


 I did also delete the old JabRef.
I downloaded for Ubuntu/Debian Jabref_5.3-1_amd64.deb (155MB)
 via download.fosshub.com
opened with GDebi-Paket-Installationprogramm (Standard)
and clicked Paket installieren

I tried
jabref
./jabref



After a successful instalation it should be available by the menu. With 
an input

of "jab" the icon of jabref should be on the screen.

Herbert




tried again after 7 minutes (don't know how long the installation 
takes, there is no info on it)


to no avail

Herbert, did you use another source for the Debian package?

Wolfgang



perhaps the up to date java is an issue? Which one is needed?
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Re: Jabref 5.3.1

[Herbert Voss]

Am 23.07.21 um 17:34 schrieb Wolfgang Engelmann:



Am 22.07.21 um 20:44 schrieb Herbert Voss:


First I deleted the old JabRef. Then I downloaded the new deb file
and with doubleclick on that file it will be installed by the install 
manager.

After that I can use jabref as usual.

Herbert


 I did also delete the old JabRef.
I downloaded for Ubuntu/Debian Jabref_5.3-1_amd64.deb (155MB)
 via download.fosshub.com
opened with GDebi-Paket-Installationprogramm (Standard)
and clicked Paket installieren

I tried
jabref
./jabref



After a successful instalation it should be available by the menu. With 
an input

of "jab" the icon of jabref should be on the screen.

Herbert




tried again after 7 minutes (don't know how long the installation 
takes, there is no info on it)


to no avail

Herbert, did you use another source for the Debian package?

Wolfgang


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Re: Jabref 5.3.1

[Wolfgang Engelmann]

Am 22.07.21 um 20:44 schrieb Herbert Voss:


First I deleted the old JabRef. Then I downloaded the new deb file
and with doubleclick on that file it will be installed by the install 
manager.

After that I can use jabref as usual.

Herbert


 I did also delete the old JabRef.
I downloaded for Ubuntu/Debian Jabref_5.3-1_amd64.deb (155MB)
 via download.fosshub.com
opened with GDebi-Paket-Installationprogramm (Standard)
and clicked Paket installieren

I tried
jabref
./jabref

tried again after 7 minutes (don't know how long the installation takes, 
there is no info on it)


to no avail

Herbert, did you use another source for the Debian package?

Wolfgang
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Re: Jabref 5.3.1

[Dr Eberhard Lisse]

Get a Mac :-)-O

el

On 22/07/2021 21:31, Paul A. Rubin wrote:

On 7/22/21 2:25 PM, Wolfgang Engelmann wrote:

Am 22.07.21 um 20:12 schrieb Wolfgang Engelmann:

Am 22.07.21 um 17:32 schrieb Paul A. Rubin:

On 7/22/21 9:31 AM, Wolfgang Engelmann wrote:

[...]


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Re: Jabref 5.3.1

[Paul A. Rubin]

On 7/22/21 2:25 PM, Wolfgang Engelmann wrote:



Am 22.07.21 um 20:12 schrieb Wolfgang Engelmann:



Am 22.07.21 um 17:32 schrieb Paul A. Rubin:

On 7/22/21 9:31 AM, Wolfgang Engelmann wrote:

There is a new Jabref (5.3.1) available under
https://www.fosshub.com/JabRef.html
There is a download for Ubuntu+Debian
and a Linux portable.
I wanted to try the latter, but don't know how to run it.
Could somebody advice me?
Wolfgang
Download the archive file and extract it, which will create a folder 
named JabRef which in turn contains bin and lib folders. Put that 
folder wherever you want it. (Since this is the portable version, I 
suspect you might want it on a thumb drive.)




Strange:
~/Downloads/JabRef/bin$ ./JabRef
Error opening "/home/wolfgang/Downloads/JabRef/lib/app/JabRef.cfg" 
file: No such file or directory

??
I am on Debian 11
Could the existing older JabRef be the cause?
Wolfgang

The JabRef contains two folders,
bin
and lib

in bin is JabRef
in lib is a folder runtime
  which contains lib, conf, bin, legal as folders

where is JabRef.cfg ? >
find -iname 'JabRef.cfg'
./lib/app/JabRef.cfg

why is it not found?

Wolfgang



Strange indeed. I do not encounter that error on my system (Linux Mint, 
which is Ubuntu-based and pretty compatible with Debian), with the 
extracted program in exactly the same folder (~/Downloads). I have 
JabRef 3.8.2 installed, and it does not interfere with launching the 
portable version.


You might try shifting the terminal to the ~/Downloads/JabRef folder and 
running "bin/JabRef", but I suspect the same error will occur.


A nonprinting control character embedded in the path might cause the 
file not found error, but it is very hard to see how one might get into 
the path.


You could also try copying the JabRef folder to /tmp and repeat the 
experiment there. If running ./JabRef in /tmp/JabRef/bin works, a stray 
character in the path becomes more plausible.


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Re: Jabref 5.3.1

[Herbert Voss]

Am 22.07.21 um 20:25 schrieb Wolfgang Engelmann:



Am 22.07.21 um 20:12 schrieb Wolfgang Engelmann:



Am 22.07.21 um 17:32 schrieb Paul A. Rubin:

On 7/22/21 9:31 AM, Wolfgang Engelmann wrote:

There is a new Jabref (5.3.1) available under
https://www.fosshub.com/JabRef.html
There is a download for Ubuntu+Debian
and a Linux portable.
I wanted to try the latter, but don't know how to run it.
Could somebody advice me?
Wolfgang
Download the archive file and extract it, which will create a folder 
named JabRef which in turn contains bin and lib folders. Put that 
folder wherever you want it. (Since this is the portable version, I 
suspect you might want it on a thumb drive.)


First I deleted the old JabRef. Then I downloaded the new deb file
and with doubleclick on that file it will be installed by the install 
manager.

After that I can use jabref as usual.

Herbert








Strange:
~/Downloads/JabRef/bin$ ./JabRef
Error opening "/home/wolfgang/Downloads/JabRef/lib/app/JabRef.cfg" 
file: No such file or directory

??
I am on Debian 11
Could the existing older JabRef be the cause?
Wolfgang

The JabRef contains two folders,
bin
and lib

in bin is JabRef
in lib is a folder runtime
  which contains lib, conf, bin, legal as folders

where is JabRef.cfg ? >
find -iname 'JabRef.cfg'
./lib/app/JabRef.cfg

why is it not found?

Wolfgang





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Re: Jabref 5.3.1

[Wolfgang Engelmann]

Am 22.07.21 um 20:12 schrieb Wolfgang Engelmann:



Am 22.07.21 um 17:32 schrieb Paul A. Rubin:

On 7/22/21 9:31 AM, Wolfgang Engelmann wrote:

There is a new Jabref (5.3.1) available under
https://www.fosshub.com/JabRef.html
There is a download for Ubuntu+Debian
and a Linux portable.
I wanted to try the latter, but don't know how to run it.
Could somebody advice me?
Wolfgang
Download the archive file and extract it, which will create a folder 
named JabRef which in turn contains bin and lib folders. Put that 
folder wherever you want it. (Since this is the portable version, I 
suspect you might want it on a thumb drive.)




Strange:
~/Downloads/JabRef/bin$ ./JabRef
Error opening "/home/wolfgang/Downloads/JabRef/lib/app/JabRef.cfg" file: 
No such file or directory

??
I am on Debian 11
Could the existing older JabRef be the cause?
Wolfgang

The JabRef contains two folders,
bin
and lib

in bin is JabRef
in lib is a folder runtime
  which contains lib, conf, bin, legal as folders

where is JabRef.cfg ? >
find -iname 'JabRef.cfg'
./lib/app/JabRef.cfg

why is it not found?

Wolfgang



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Re: Jabref 5.3.1

[Wolfgang Engelmann]

Am 22.07.21 um 17:32 schrieb Paul A. Rubin:

On 7/22/21 9:31 AM, Wolfgang Engelmann wrote:

There is a new Jabref (5.3.1) available under
https://www.fosshub.com/JabRef.html
There is a download for Ubuntu+Debian
and a Linux portable.
I wanted to try the latter, but don't know how to run it.
Could somebody advice me?
Wolfgang
Download the archive file and extract it, which will create a folder 
named JabRef which in turn contains bin and lib folders. Put that folder 
wherever you want it. (Since this is the portable version, I suspect you 
might want it on a thumb drive.)




Strange:
~/Downloads/JabRef/bin$ ./JabRef
Error opening "/home/wolfgang/Downloads/JabRef/lib/app/JabRef.cfg" file: 
No such file or directory

??
I am on Debian 11
Could the existing older JabRef be the cause?
Wolfgang
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Re: Jabref 5.3.1

[Wolfgang Engelmann]

Am 22.07.21 um 17:32 schrieb Paul A. Rubin:

On 7/22/21 9:31 AM, Wolfgang Engelmann wrote:

There is a new Jabref (5.3.1) available under
https://www.fosshub.com/JabRef.html
There is a download for Ubuntu+Debian
and a Linux portable.
I wanted to try the latter, but don't know how to run it.
Could somebody advice me?
Wolfgang
Download the archive file and extract it, which will create a folder 
named JabRef which in turn contains bin and lib folders. Put that folder 
wherever you want it. (Since this is the portable version, I suspect you 
might want it on a thumb drive.)


To run it, open a terminal and run the command "/bin/JabRef" 
(where  is the path to the extracted JabRef folder), or just open 
the terminal in the bin folder and run "./JabRef". I got a lot of error 
messages in the terminal when I tried it (Linux Mint), but it opened and 
appeared to work okay.



Thanks, Paul for your detailed advice. Will do so tomorrow.
Wolfgang
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Re: Jabref 5.3.1

[Paul A. Rubin]

On 7/22/21 9:31 AM, Wolfgang Engelmann wrote:

There is a new Jabref (5.3.1) available under
https://www.fosshub.com/JabRef.html
There is a download for Ubuntu+Debian
and a Linux portable.
I wanted to try the latter, but don't know how to run it.
Could somebody advice me?
Wolfgang
Download the archive file and extract it, which will create a folder 
named JabRef which in turn contains bin and lib folders. Put that folder 
wherever you want it. (Since this is the portable version, I suspect you 
might want it on a thumb drive.)


To run it, open a terminal and run the command "/bin/JabRef" 
(where  is the path to the extracted JabRef folder), or just open 
the terminal in the bin folder and run "./JabRef". I got a lot of error 
messages in the terminal when I tried it (Linux Mint), but it opened and 
appeared to work okay.


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SOLVED: Re: Jabref linked identifiers DOI/URL open Thunderbird instead of Firefox ESR

[Wolfgang Engelmann]

Am 24.09.20 um 10:11 schrieb Wolfgang Engelmann:
This is a bit off topic, but since some of the people in the list are 
using Jabref as a reference manager for Lyx, I might get help.
If I click in Jabref on the linked identifiers, the DOI and/or URL 
opens, however clicking on it tries to open my thunderbird (Mail) 
instead of my Firefox. I must have done some setting since it used to 
work before, but I don't know what. I could not find a clue in the 
Jabref help.

I am using Debian and Jabref 5.1
Wolfgang


The reason was, that my firefox was not set to be the standard browser.
Wolfgang
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SOLVED > Re: jabref 5 on debian

[Wolfgang Engelmann]

Am 06.01.20 um 14:35 schrieb Rich Shepard:

On Mon, 6 Jan 2020, Wolfgang Engelmann wrote:

I downloaded Jabref_5.0-1_amd64.deb from 
https://builds.jabref.org/master/

to my Download folder (Debian bullseye/sid).

How do I get now jabref to work? It says, it is distributed with 
bundled Java runtime Environment > no need for java installation.


Wolfgang,

JabRef has many unresolved issues. Some versions required not only 
specific
Java versions but would work only with Oracle's JDK and not openJDK. I 
had

extensive e-mail exchanges with one of the lead developers about these
issues and he told me that he, too, was frustrated by their (the devs)
inability to resolve them. I dropped Jabef for kbibtex (which imported my
jabrefdb.bib (which is still its name) and Riki helped me past the 
initial

hurdles of getting it to work.

While I used JabRef for years I could no longer waste time getting it to
work instead of using it when I needed to find appropriate references and
insert them in documents I was writing. I encourage you to explore
alternatives and spend your time elsewhere rather than futzing with 
JabRef.


Such a change will help you have a happy new year. :-)

Regards,

Rich

Thanks, Rich, but I could install JabRef 5 via the Debian Discover 
Installer without problems.


Wolfgang

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Re: Jabref question

[Axel Dessecker]

Wolfgang,

This rather looks like a JabRef issue. Why not post it at 
http://discourse.jabref.org/ ?

Axel


Am Freitag, 21. Juni 2019, 15:23:00 CEST schrieb Wolfgang Engelmann:
> I am using Jabref as a reference manager for my lyx documents. Lately I
> get this type of output from literature searches using Medline/PubMed
> 
>   javax.xml.bind.JAXBElement@3a508a29
> 
> instead of the name of the organism. Does somebody know how th get the
> actual names?
> 
> Wolfgang

re: Jabref

[Rich Shepard]

On Fri, 25 Jan 2019, F M Salter wrote:


    I use linux with the KDE environment.  In KDE, one can add extra
buttons to windows' frames.  One of these is "keep below" other windows. 
If this is set, the jabref entry window appears on top.


Frank et al.,

With Xfce4 the window manager can be set to obtain focus when the cursor
enters its frame or require a left click to change the focus to the window
in which the cursor is located.

Carpe weekend,

Rich

re: Jabref

[F M Salter]

 Wolfgang Enlelmann asked about window hiding with Jabref.  I think 
the only universal solution for all OS's is to use the button to hide 
the Jabref main window, which reveals the entry window below..


    I use linux with the KDE environment.  In KDE, one can add extra 
buttons to windows' frames.  One of these is "keep below" other 
windows.  If this is set, the jabref entry window appears on top.


Regards

Frank Salter

Re: jabref

[John Kane]

Those questions are far beyond my knowledge level. We need one of the gurus
to step in. Sorry.

On Wed, 23 Jan 2019 at 10:57, Wolfgang Engelmann 
wrote:

> On 22.01.19 20:37, John Kane wrote:
>
> Strange, I tossed your reference into an existing .bib file and the Umlaute
> came through just fine when I exported to text and to html.  I don't use
> jabref a lot so I may not be duplicating your actions> I simply went File >
> Export
> On Tuesday, January 22, 2019, 2:06:49 p.m. EST, Wolfgang Engelmann
>   wrote:
>
>
> Sorry, off topic,
>
> but I have two questions re Jabref
>
> 1. If I want to save or select a file, the menu opens BEHIND the Jabref.
> How can I get it in the forground?
>
> 2. I can't get Jabref (it's 4.3.1) to export Umlaute (neither in UTF8
> nor in Din1505 nor in html.
>
> Example:
> @Article{Buenning1932c,
>   author  = {Bünning, E.},
>   title   = {Über die {E}rblichkeit der {T}agesperiodizität bei den
> \emph{{P}haseolus}-{B}lättern},
>   journal = {Jb. wiss. Botanik},
>   year= {1932},
>   volume  = {77},
>   pages   = {283-320},
> }
>
> Note, that I talk just about the Jabref export itself, not via lyx.
>
> I could not find help in the net, it just says it would work. But not
> for me.
>
> Wolfgang
>
> Thanks, John. I have, by the way, tried also to use biblatex in Jabref.
> Same problem. I also tried German as the language- no cure. Could it be due
> to a general language setting on my PC? And where would I check for it? I
> am using
>
> Downloads$ cat /etc/issue Linux Mint 18.3 Sylvia \n \l and the KDE version
>
> This is the keybord input configuration:
>
> Current configuration for the input method:
>
> * Active configuration: missing (normally missing)
>
> * Normal automatic choice: none (normally ibus or fcitx or uim)
>
> * Override rule:
> zh_CN,fcitx:zh_TW,fcitx:zh_HK,fcitx:zh_SG,fcitx:ja_JP,fcitx:ko_KR,fcitx:vi_VN,fcitx
>
> * Current override choice: (de_DE)
>
> * Current automatic choice: none
>
> * Number of valid choices: 1 (normally 1)
>
> The override rule is defined in /etc/default/im-config.
>
> The configuration set by im-config is activated by re-starting X.
>
> Explicit selection is not required to enable the automatic configuration
> if the active one is default/auto/cjkv/missing.
>
> Wolfgang
>


-- 
John Kane
Kingston ON Canada

Re: jabref

[Wolfgang Engelmann]

On 23.01.19 11:30, Wolfgang Engelmann wrote:


On 22.01.19 20:37, John Kane wrote:
Strange, I tossed your reference into an existing .bib file and the 
Umlaute came through just fine when I exported to text and to html.  
I don't use jabref a lot so I may not be duplicating your actions> I 
simply went File > Export
On Tuesday, January 22, 2019, 2:06:49 p.m. EST, Wolfgang Engelmann 
 wrote:



Sorry, off topic,

but I have two questions re Jabref

1. If I want to save or select a file, the menu opens BEHIND the Jabref.
How can I get it in the forground?

2. I can't get Jabref (it's 4.3.1) to export Umlaute (neither in UTF8
nor in Din1505 nor in html.

Example:
@Article{Buenning1932c,
  author  = {Bünning, E.},
  title   = {Über die {E}rblichkeit der {T}agesperiodizität bei den
\emph{{P}haseolus}-{B}lättern},
  journal = {Jb. wiss. Botanik},
  year    = {1932},
  volume  = {77},
  pages   = {283-320},
}

Note, that I talk just about the Jabref export itself, not via lyx.

I could not find help in the net, it just says it would work. But not
for me.

Wolfgang


Thanks, John. I have, by the way, tried also to use biblatex in 
Jabref. Same problem. I also tried German as the language- no cure. 
Could it be due to a general language setting on my PC? And where 
would I check for it? I am using


Downloads$ cat /etc/issue Linux Mint 18.3 Sylvia \n \l and the KDE version

This is the keybord input configuration:

Current configuration for the input method:

* Active configuration: missing (normally missing)

* Normal automatic choice: none (normally ibus or fcitx or uim)

* Override rule: 
zh_CN,fcitx:zh_TW,fcitx:zh_HK,fcitx:zh_SG,fcitx:ja_JP,fcitx:ko_KR,fcitx:vi_VN,fcitx


* Current override choice: (de_DE)

* Current automatic choice: none

* Number of valid choices: 1 (normally 1)

The override rule is defined in /etc/default/im-config.

The configuration set by im-config is activated by re-starting X.

Explicit selection is not required to enable the automatic 
configuration if the active one is default/auto/cjkv/missing.


Wolfgang




I had started the new Jabref (4.3.1) from the folder in which I keep it 
by using


~/JABREF-4.3.1$ java -jar JabRef-4.3.1.jar

I noticed that synaptic has an old jabref, which I now removed 
completely via synaptic. Now the export of Umlaute works. No idea, what 
went wrong before.


MY FIRST QUESTION REMAINS:

1. If I want to save or select a file, the menu opens BEHIND the Jabref.
How can I get it in the forground?
Thanks for help,
Wolfgang

Re: jabref

[Wolfgang Engelmann]

On 22.01.19 20:37, John Kane wrote:
Strange, I tossed your reference into an existing .bib file and the 
Umlaute came through just fine when I exported to text and to html.  I 
don't use jabref a lot so I may not be duplicating your actions> I 
simply went File > Export
On Tuesday, January 22, 2019, 2:06:49 p.m. EST, Wolfgang Engelmann 
 wrote:



Sorry, off topic,

but I have two questions re Jabref

1. If I want to save or select a file, the menu opens BEHIND the Jabref.
How can I get it in the forground?

2. I can't get Jabref (it's 4.3.1) to export Umlaute (neither in UTF8
nor in Din1505 nor in html.

Example:
@Article{Buenning1932c,
  author  = {Bünning, E.},
  title   = {Über die {E}rblichkeit der {T}agesperiodizität bei den
\emph{{P}haseolus}-{B}lättern},
  journal = {Jb. wiss. Botanik},
  year    = {1932},
  volume  = {77},
  pages   = {283-320},
}

Note, that I talk just about the Jabref export itself, not via lyx.

I could not find help in the net, it just says it would work. But not
for me.

Wolfgang


Thanks, John. I have, by the way, tried also to use biblatex in Jabref. 
Same problem. I also tried German as the language- no cure. Could it be 
due to a general language setting on my PC? And where would I check for 
it? I am using


Downloads$ cat /etc/issue Linux Mint 18.3 Sylvia \n \l and the KDE version

This is the keybord input configuration:

Current configuration for the input method:

* Active configuration: missing (normally missing)

* Normal automatic choice: none (normally ibus or fcitx or uim)

* Override rule: 
zh_CN,fcitx:zh_TW,fcitx:zh_HK,fcitx:zh_SG,fcitx:ja_JP,fcitx:ko_KR,fcitx:vi_VN,fcitx


* Current override choice: (de_DE)

* Current automatic choice: none

* Number of valid choices: 1 (normally 1)

The override rule is defined in /etc/default/im-config.

The configuration set by im-config is activated by re-starting X.

Explicit selection is not required to enable the automatic configuration 
if the active one is default/auto/cjkv/missing.


Wolfgang

Re: jabref

[John Kane]

 Strange, I tossed your reference into an existing .bib file and the Umlaute 
came through just fine when I exported to text and to html.  I don't use jabref 
a lot so I may not be duplicating your actions> I simply went File > Export
   On Tuesday, January 22, 2019, 2:06:49 p.m. EST, Wolfgang Engelmann 
 wrote:  
 
 Sorry, off topic,

but I have two questions re Jabref

1. If I want to save or select a file, the menu opens BEHIND the Jabref. 
How can I get it in the forground?

2. I can't get Jabref (it's 4.3.1) to export Umlaute (neither in UTF8 
nor in Din1505 nor in html.

Example:
@Article{Buenning1932c,
   author  = {Bünning, E.},
   title   = {Über die {E}rblichkeit der {T}agesperiodizität bei den 
\emph{{P}haseolus}-{B}lättern},
   journal = {Jb. wiss. Botanik},
   year    = {1932},
   volume  = {77},
   pages   = {283-320},
}

Note, that I talk just about the Jabref export itself, not via lyx.

I could not find help in the net, it just says it would work. But not 
for me.

Wolfgang

  

Re: Jabref Journal abbreviations

[Wolfgang Engelmann]

I think, what I did wrong was not to select all the references with ctr 
a and use afterward the abbreviation step.


What I haven't solved yet is this:

if I select in JabRef e.g. options, it opens *behind* the JabRef main 
window. How do I get it to open in such a way that it is visible right 
away without having to move the main window aside?


Wolfgang



On 04.09.2018 09:00, Wolfgang Engelmann wrote:


I am trying to use the built in journal abbreviation list of JabRef-4.3.1

With Options>manage Journal abbreviations I select

JabRef built in list

but it does not seem to work for the references. If I check again 
Options>manage Journal abbreviations


the list is not selected any more. I looked in the Internet but could 
not find a remedy. Does somebody know how to do it?


By the way, if I select in JabRef e.g. options, it opens *behind* the 
JabRef main window. How do I get it to open in such a way that it is 
visible right away without having to move the main window aside?


Sorry for the OT question, but the JabRef FAQs are difficult to search 
through.


BTW, I am using Linux Mint

Wolfgang

Re: Jabref under linux-mint

[Rich Shepard]

On Thu, 30 Aug 2018, Paul A. Rubin wrote:


In any case, I downloaded the 4.3.1 jar file just now and ran it
successfully with exactly the same command line you used. I opened the
terminal in the folder where the jar file was located. Is it possible that
you are in a different directory and just need to supply the path to the
jar file?


  This is one reason to use shell scripts. For example, my jabref.sh* (chmod
a+x) contains:

#!/bin/bash

cd /opt/JabRef/
java -jar JabRef-3.8.2.jar
cd

  This lets me open it from any virtual desktop (Xfce4 panel).

HTH,

Rich

Re: Jabref under linux-mint > semi - solved

[Wolfgang Engelmann]

On 30.08.2018 17:26, Paul A. Rubin wrote:

On 08/29/2018 07:13 AM, Wolfgang Engelmann wrote:

Slightly OT:

Is there somebody who uses Jabref as a reference manager under 
Linux-Mint successfully and could give me a hint how he/she 
succeeded? I am always getting


java -jar Jabref-4.3.1.jar

Error: Unable to access jarfile Jabref-4.3.1.jar

I tried under Linux-mint 18.3 Sylvia openjdk version "1.8.0_181", 
and  Java SE Runtime environment of Oracle, and have set the Path in 
/etc/profile to


export JAVA_HOME=/home/wolfgang/java/jre-10.0.2
export PATH=$JAVA_HOME/bin:$PATH

Cheers,

Wolfgang


Wolfgang,

I use JabRef on the same setup (Mint 18.3, Oracle runtime) with no 
problems. I installed JabRef from the repositories (using Software 
Manager), which means I've got version 2.10. I don't know why the 
repos are so far behind.


In any case, I downloaded the 4.3.1 jar file just now and ran it 
successfully with exactly the same command line you used. I opened the 
terminal in the folder where the jar file was located. Is it possible 
that you are in a different directory and just need to supply the path 
to the jar file?


Paul


Thanks, Paul.
I have my JabRef-4.3.1.jar file in my home under /JABREF
If I mouseclick on it, it opens alright. If I open it in a terminal, I 
am told:


wolfgang@wolfgang-Mr-Whisper-Ultra-SSD-II:/mnt/sdb/we/JABREF-4.3.1$ java 
-jar JabRef-4.3.1.jar
17:58:43.101 [AWT-EventQueue-0] ERROR org.jabref.logic.l10n.Localization 
- Messages are not initialized before accessing Your current Java 
version (%0) is not supported. Please install version %1 or higher.


So I can work with it, but I do not understand the terminal message. 
Perhaps somebody had an idea, what's going wrong here.


Wolfgang

Re: Jabref under linux-mint

[Paul A. Rubin]

On 08/29/2018 07:13 AM, Wolfgang Engelmann wrote:

Slightly OT:

Is there somebody who uses Jabref as a reference manager under 
Linux-Mint successfully and could give me a hint how he/she succeeded? 
I am always getting


java -jar Jabref-4.3.1.jar

Error: Unable to access jarfile Jabref-4.3.1.jar

I tried under Linux-mint 18.3 Sylvia openjdk version "1.8.0_181", and  
Java SE Runtime environment of Oracle, and have set the Path in 
/etc/profile to


export JAVA_HOME=/home/wolfgang/java/jre-10.0.2
export PATH=$JAVA_HOME/bin:$PATH

Cheers,

Wolfgang


Wolfgang,

I use JabRef on the same setup (Mint 18.3, Oracle runtime) with no 
problems. I installed JabRef from the repositories (using Software 
Manager), which means I've got version 2.10. I don't know why the repos 
are so far behind.


In any case, I downloaded the 4.3.1 jar file just now and ran it 
successfully with exactly the same command line you used. I opened the 
terminal in the folder where the jar file was located. Is it possible 
that you are in a different directory and just need to supply the path 
to the jar file?


Paul

Re: Jabref under linux-mint > solved

[Wolfgang Engelmann]

On 29.08.2018 13:13, Wolfgang Engelmann wrote:

Slightly OT:

Is there somebody who uses Jabref as a reference manager under 
Linux-Mint successfully and could give me a hint how he/she succeeded? 
I am always getting


java -jar Jabref-4.3.1.jar

Error: Unable to access jarfile Jabref-4.3.1.jar

I tried under Linux-mint 18.3 Sylvia openjdk version "1.8.0_181", and  
Java SE Runtime environment of Oracle, and have set the Path in 
/etc/profile to


export JAVA_HOME=/home/wolfgang/java/jre-10.0.2
export PATH=$JAVA_HOME/bin:$PATH

Cheers,

Wolfgang


Sorry for the noice, I used instead of JabRef-4.3.1.jar > Jabref-4.3.1.jar
r instead of R! I wonder how often this happens.
Wolfgang

Re: Jabref-3.7 > solved

[Wolfgang Engelmann]

I would like to thank Paul A. Rubin and Richard Shepard for their 
suggestions and help re Jabref-3.7 installation (which I use as a 
reference manager under Lyx).


The problem was, that my Jabref 2.10 did recently not give any results 
under WEB search for references, e.g. by using medline (I am using 
debian jessie)


It turned out that the solution was quite simple:

Since Jabref 3.8 needs Java 8, I installed this first by using synaptic. 
In /search /I asked for java8 (not java 8 -this gives you more offers) 
and got


1- oracle-java8-installer

2- oracle-java8-set-default

3- oracle-java8-iunlimited-jce-policy

out of which I selected /1 and 2/, but NOT yet 3, for installing.

/3/ was installed AFTER 1 and 2 installation was finished

Since jabref of debian offers only version 2.10 as the newest version, I 
downloaded it from

 https://sourceforge.net/projects/jabref/
as JabRef-3.7.jar (35MiB) and put it as a starter on my desktop. Now I 
can start it by clicking at the icon and I am able to use the medline 
data bank again.

Wolfgang

Re: Jabref-3.7

[Paul A. Rubin]

On 11/29/2016 12:07 PM, Wolfgang Engelmann wrote:




On 29.11.2016 17:10, Paul A. Rubin wrote:

On 11/29/2016 10:41 AM, Wolfgang Engelmann wrote:




On 29.11.2016 15:49, Wolfgang Engelmann wrote:



On 29.11.2016 15:05, Rich Shepard wrote:

On Tue, 29 Nov 2016, Wolfgang Engelmann wrote:

I am using Jabref for my lyx work (debian). The version I use 
(2.10) does not support the medline any more.


Wolfgang,

  I, too, use JabRef with LyX; it's great! I'm using JabRef-3.7 
and ...

Thanks, Rich,
but Jabref-3.7 is the trouble. I have it installed already and used 
it all the time, but it is not supporting medline any more, which I 
used to use and need for fetching references from the web.

Wolfgang


I apparently need Java 8 for it -JRE or JDK are offered, which 
should go
in /opt. Which one is recommendable? None is given in synaptic. 
And how do
I > unpack the JRE or JDK into /opt? Do I extract it first on my 
home/download and copy the folder as root into it?


  I'm using openjdk-8u91_b14 on Slackware. I recommend it (or 
Oracle's Java
JDK) over the limited JRE version as it gives you more 
capabilities and

storage space is generally not an issue.

How do I install jabref-3.7? Unpacking it gives me a lot of 
folders/files,

but I can't find a help||


  I don't know Debian or its derivatives, so I suggest that you go 
to the
download Web page , select 
the second
option, "Download JabRef Platform independent runnable JAR," and 
deposit the

download in /opt/. You'll have /opt/JabRef-3.7.jar.

  To run it, I have a simple shell script (called jabref.sh):

#!/bin/bash

cd /opt/JabRef/
java -jar JabRef-3.7.jar
cd

  No muss, no bother.

HTH,

Rich



I guess the problem I encounter has to do with these first lines 
from the script Paul pointed out. I checked the /etc/apt/sources.list
echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial 
main" | tee /etc/apt/sources.list.d/webupd8team-java.list
echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu 
xenial main" | tee -a /etc/apt/sources.list.d/webupd8team-java.list


but there is listed also sources.list.d (see NOTE below) which 
contains the files

lyx-devel-release-jessie.list
with:
deb http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main
# deb-src http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main

and
webupd8team-java.list
with
deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main
deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main

NOTE:
The function of the |/etc/apt/sources.list.d| directory is as follows:

Using the directory you can easily add new repositories w/o the need 
to edit the central |/etc/apt/sources.list| file. I.e. you can just 
put a file with a unique name and the same format as 
|/etc/apt/sources.list| into this folder and it is used by apt. In 
order to remove this source again you can just remove that specific 
file w/o the need for handling side effects, parsing or mangling 
with |/etc/apt/sources.list|. It's mainly for scripts or other 
packages to put their repositories there automatically - if you 
manually add repositories you could add them to 
|/etc/apt/sources.list| manually.


My QUESTION: should the script work with the infos in the two files in
sources.list.d?

Wolfgang

Wolfgang,

The webupd8team-java.list looks okay provided that you are either 
running Ubuntu Xenial (or a distribution built on that) or Debian 
Stretch (which is apparently the Debian version upon which Xenial is 
based). If, as the LyX list suggests, you're running Debian Jessie, 
then I think you need a webupd8team archive based on one of the 
following Ubuntu versions: Trusty; Utopic; Vivid; or Wily.


Paul


I am running Debian Jessie. So I should have used
lyx-devel-release-jessie.list
with:
deb http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main
# deb-src http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main

and not
webupd8team-java.list
with
deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main
deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main

??
Wolfgang
I'm not sure about the LyX PPA. If you got a version of LyX that works, 
I guess I would leave it alone. I would have thought you would need to 
specify an Ubuntu version, such as


 deb http://ppa.launchpad.net/lyx-devel/release/ubuntu/ trusty main

or one of the other Ubuntu versions derived from Jessie.

For the webupd8team-java.list entry, I would change "xenial" to "wily" 
in both lines and see if that helps. If any of the webupd8-java packages 
installed before you got the abort, you probably should uninstall them 
through Synaptic or apt, then (after fixing the .list file) update and 
try installing the two packages from the webupd8team PPA.


Paul

Re: Jabref-3.7

[Wolfgang Engelmann]

On 29.11.2016 17:10, Paul A. Rubin wrote:

On 11/29/2016 10:41 AM, Wolfgang Engelmann wrote:




On 29.11.2016 15:49, Wolfgang Engelmann wrote:



On 29.11.2016 15:05, Rich Shepard wrote:

On Tue, 29 Nov 2016, Wolfgang Engelmann wrote:

I am using Jabref for my lyx work (debian). The version I use 
(2.10) does not support the medline any more.


Wolfgang,

  I, too, use JabRef with LyX; it's great! I'm using JabRef-3.7 and 
...

Thanks, Rich,
but Jabref-3.7 is the trouble. I have it installed already and used 
it all the time, but it is not supporting medline any more, which I 
used to use and need for fetching references from the web.

Wolfgang


I apparently need Java 8 for it -JRE or JDK are offered, which 
should go
in /opt. Which one is recommendable? None is given in synaptic. 
And how do
I > unpack the JRE or JDK into /opt? Do I extract it first on my 
home/download and copy the folder as root into it?


  I'm using openjdk-8u91_b14 on Slackware. I recommend it (or 
Oracle's Java
JDK) over the limited JRE version as it gives you more capabilities 
and

storage space is generally not an issue.

How do I install jabref-3.7? Unpacking it gives me a lot of 
folders/files,

but I can't find a help||


  I don't know Debian or its derivatives, so I suggest that you go 
to the
download Web page , select the 
second
option, "Download JabRef Platform independent runnable JAR," and 
deposit the

download in /opt/. You'll have /opt/JabRef-3.7.jar.

  To run it, I have a simple shell script (called jabref.sh):

#!/bin/bash

cd /opt/JabRef/
java -jar JabRef-3.7.jar
cd

  No muss, no bother.

HTH,

Rich



I guess the problem I encounter has to do with these first lines from 
the script Paul pointed out. I checked the /etc/apt/sources.list
echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial 
main" | tee /etc/apt/sources.list.d/webupd8team-java.list
echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial 
main" | tee -a /etc/apt/sources.list.d/webupd8team-java.list


but there is listed also sources.list.d (see NOTE below) which 
contains the files

lyx-devel-release-jessie.list
with:
deb http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main
# deb-src http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main

and
webupd8team-java.list
with
deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main
deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main

NOTE:
The function of the |/etc/apt/sources.list.d| directory is as follows:

Using the directory you can easily add new repositories w/o the need 
to edit the central |/etc/apt/sources.list| file. I.e. you can just 
put a file with a unique name and the same format as 
|/etc/apt/sources.list| into this folder and it is used by apt. In 
order to remove this source again you can just remove that specific 
file w/o the need for handling side effects, parsing or mangling with 
|/etc/apt/sources.list|. It's mainly for scripts or other packages to 
put their repositories there automatically - if you manually add 
repositories you could add them to |/etc/apt/sources.list| manually.


My QUESTION: should the script work with the infos in the two files in
sources.list.d?

Wolfgang

Wolfgang,

The webupd8team-java.list looks okay provided that you are either 
running Ubuntu Xenial (or a distribution built on that) or Debian 
Stretch (which is apparently the Debian version upon which Xenial is 
based). If, as the LyX list suggests, you're running Debian Jessie, 
then I think you need a webupd8team archive based on one of the 
following Ubuntu versions: Trusty; Utopic; Vivid; or Wily.


Paul


I am running Debian Jessie. So I should have used
lyx-devel-release-jessie.list
with:
deb http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main
# deb-src http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main

and not
webupd8team-java.list
with
deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main
deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main

??
Wolfgang

Re: Jabref-3.7

[Wolfgang Engelmann]

On 29.11.2016 16:51, Paul A. Rubin wrote:

On 11/29/2016 10:06 AM, Wolfgang Engelmann wrote:




On 29.11.2016 14:57, Paul A. Rubin wrote:

On 11/29/2016 04:34 AM, Wolfgang Engelmann wrote:


Slightly off topic:

I am using Jabref for my lyx work (debian). The version I use 
(2.10) does not support the medline any more.


I apparently need Java 8 for it -JRE or JDK are offered, which 
should go in /opt. Which one is recommendable?  None is given in 
synaptic. And how do I unpack the JRE or JDK into /opt? Do I 
extract it first on my home/download and copy the folder as root 
into it?


How do I install jabref-3.7? Unpacking it gives me a lot of 
folders/files, but I can't find a help.

||

A long discussion is in the following, but it is beyond me:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=814901

Wolfgang


||

Wolfgang,

You might want to look at 
https://launchpad.net/~webupd8team/+archive/ubuntu/java 
. If you 
add their PPA to Synaptic and install their package (which is an 
updater, not Java itself), it will install Java 8. Moreover, as new 
versions of Java appear, their package will show up in your usual 
updates and, when you update it, will automatically install the 
latest Java. It also takes care of various configuration nonsense, 
such as setting the latest Java as the preferred version, that 
otherwise can be a PITA.


Cheers,
Paul

Thanks, Paul, for the pointer. I have run the script but at the end I 
was asked whether I would like to continue: [J/n] y
I tried j (ja in German), J, y and just return > in all cases I get 
an abortion:

Es müssen 39,7 kB an Archiven heruntergeladen werden.
Nach dieser Operation werden 180 kB Plattenplatz zusätzlich benutzt.
Möchten Sie fortfahren? [J/n] y
Abbruch.
root@wolfgang-Mr-Whisper-Ultra-SSD-II:~#
any idea what I could do to get it to continue?
Wolfgang

Wolfgang,

First, what operating system do you have (and what architecture -- 
i86, amd64, ...)? Second, which script did you run?


Paul


Its Debian Jessie and amd64
Wolfgang

Re: Jabref-3.7

[Paul A. Rubin]

On 11/29/2016 10:41 AM, Wolfgang Engelmann wrote:




On 29.11.2016 15:49, Wolfgang Engelmann wrote:



On 29.11.2016 15:05, Rich Shepard wrote:

On Tue, 29 Nov 2016, Wolfgang Engelmann wrote:

I am using Jabref for my lyx work (debian). The version I use 
(2.10) does not support the medline any more.


Wolfgang,

  I, too, use JabRef with LyX; it's great! I'm using JabRef-3.7 and ...

Thanks, Rich,
but Jabref-3.7 is the trouble. I have it installed already and used 
it all the time, but it is not supporting medline any more, which I 
used to use and need for fetching references from the web.

Wolfgang


I apparently need Java 8 for it -JRE or JDK are offered, which 
should go
in /opt. Which one is recommendable? None is given in synaptic. And 
how do
I > unpack the JRE or JDK into /opt? Do I extract it first on my 
home/download and copy the folder as root into it?


  I'm using openjdk-8u91_b14 on Slackware. I recommend it (or 
Oracle's Java

JDK) over the limited JRE version as it gives you more capabilities and
storage space is generally not an issue.

How do I install jabref-3.7? Unpacking it gives me a lot of 
folders/files,

but I can't find a help||


  I don't know Debian or its derivatives, so I suggest that you go 
to the
download Web page , select the 
second
option, "Download JabRef Platform independent runnable JAR," and 
deposit the

download in /opt/. You'll have /opt/JabRef-3.7.jar.

  To run it, I have a simple shell script (called jabref.sh):

#!/bin/bash

cd /opt/JabRef/
java -jar JabRef-3.7.jar
cd

  No muss, no bother.

HTH,

Rich



I guess the problem I encounter has to do with these first lines from 
the script Paul pointed out. I checked the /etc/apt/sources.list
echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial 
main" | tee /etc/apt/sources.list.d/webupd8team-java.list
echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial 
main" | tee -a /etc/apt/sources.list.d/webupd8team-java.list


but there is listed also sources.list.d (see NOTE below) which 
contains the files

lyx-devel-release-jessie.list
with:
deb http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main
# deb-src http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main

and
webupd8team-java.list
with
deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main
deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main

NOTE:
The function of the |/etc/apt/sources.list.d| directory is as follows:

Using the directory you can easily add new repositories w/o the need 
to edit the central |/etc/apt/sources.list| file. I.e. you can just 
put a file with a unique name and the same format as 
|/etc/apt/sources.list| into this folder and it is used by apt. In 
order to remove this source again you can just remove that specific 
file w/o the need for handling side effects, parsing or mangling with 
|/etc/apt/sources.list|. It's mainly for scripts or other packages to 
put their repositories there automatically - if you manually add 
repositories you could add them to |/etc/apt/sources.list| manually.


My QUESTION: should the script work with the infos in the two files in
sources.list.d?

Wolfgang

Wolfgang,

The webupd8team-java.list looks okay provided that you are either 
running Ubuntu Xenial (or a distribution built on that) or Debian 
Stretch (which is apparently the Debian version upon which Xenial is 
based). If, as the LyX list suggests, you're running Debian Jessie, then 
I think you need a webupd8team archive based on one of the following 
Ubuntu versions: Trusty; Utopic; Vivid; or Wily.


Paul

Re: Jabref-3.7

[Paul A. Rubin]

On 11/29/2016 10:06 AM, Wolfgang Engelmann wrote:




On 29.11.2016 14:57, Paul A. Rubin wrote:

On 11/29/2016 04:34 AM, Wolfgang Engelmann wrote:


Slightly off topic:

I am using Jabref for my lyx work (debian). The version I use (2.10) 
does not support the medline any more.


I apparently need Java 8 for it -JRE or JDK are offered, which 
should go in /opt. Which one is recommendable?  None is given in 
synaptic. And how do I unpack the JRE or JDK into /opt? Do I extract 
it first on my home/download and copy the folder as root into it?


How do I install jabref-3.7? Unpacking it gives me a lot of 
folders/files, but I can't find a help.

||

A long discussion is in the following, but it is beyond me:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=814901

Wolfgang


||

Wolfgang,

You might want to look at 
https://launchpad.net/~webupd8team/+archive/ubuntu/java 
. If you 
add their PPA to Synaptic and install their package (which is an 
updater, not Java itself), it will install Java 8. Moreover, as new 
versions of Java appear, their package will show up in your usual 
updates and, when you update it, will automatically install the 
latest Java. It also takes care of various configuration nonsense, 
such as setting the latest Java as the preferred version, that 
otherwise can be a PITA.


Cheers,
Paul

Thanks, Paul, for the pointer. I have run the script but at the end I 
was asked whether I would like to continue: [J/n] y
I tried j (ja in German), J, y and just return > in all cases I get an 
abortion:

Es müssen 39,7 kB an Archiven heruntergeladen werden.
Nach dieser Operation werden 180 kB Plattenplatz zusätzlich benutzt.
Möchten Sie fortfahren? [J/n] y
Abbruch.
root@wolfgang-Mr-Whisper-Ultra-SSD-II:~#
any idea what I could do to get it to continue?
Wolfgang

Wolfgang,

First, what operating system do you have (and what architecture -- i86, 
amd64, ...)? Second, which script did you run?


Paul

Re: Jabref-3.7

[Wolfgang Engelmann]

On 29.11.2016 15:49, Wolfgang Engelmann wrote:



On 29.11.2016 15:05, Rich Shepard wrote:

On Tue, 29 Nov 2016, Wolfgang Engelmann wrote:

I am using Jabref for my lyx work (debian). The version I use (2.10) 
does not support the medline any more.


Wolfgang,

  I, too, use JabRef with LyX; it's great! I'm using JabRef-3.7 and ...

Thanks, Rich,
but Jabref-3.7 is the trouble. I have it installed already and used it 
all the time, but it is not supporting medline any more, which I used 
to use and need for fetching references from the web.

Wolfgang


I apparently need Java 8 for it -JRE or JDK are offered, which 
should go
in /opt. Which one is recommendable? None is given in synaptic. And 
how do
I > unpack the JRE or JDK into /opt? Do I extract it first on my 
home/download and copy the folder as root into it?


  I'm using openjdk-8u91_b14 on Slackware. I recommend it (or 
Oracle's Java

JDK) over the limited JRE version as it gives you more capabilities and
storage space is generally not an issue.

How do I install jabref-3.7? Unpacking it gives me a lot of 
folders/files,

but I can't find a help||


  I don't know Debian or its derivatives, so I suggest that you go to 
the
download Web page , select the 
second
option, "Download JabRef Platform independent runnable JAR," and 
deposit the

download in /opt/. You'll have /opt/JabRef-3.7.jar.

  To run it, I have a simple shell script (called jabref.sh):

#!/bin/bash

cd /opt/JabRef/
java -jar JabRef-3.7.jar
cd

  No muss, no bother.

HTH,

Rich



I guess the problem I encounter has to do with these first lines from 
the script Paul pointed out. I checked the /etc/apt/sources.list
echo "deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main" 
| tee /etc/apt/sources.list.d/webupd8team-java.list
echo "deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial 
main" | tee -a /etc/apt/sources.list.d/webupd8team-java.list


but there is listed also sources.list.d (see NOTE below) which contains 
the files

lyx-devel-release-jessie.list
with:
deb http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main
# deb-src http://ppa.launchpad.net/lyx-devel/release/ubuntu/ jessie main

and
webupd8team-java.list
with
deb http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main
deb-src http://ppa.launchpad.net/webupd8team/java/ubuntu xenial main

NOTE:
The function of the |/etc/apt/sources.list.d| directory is as follows:

Using the directory you can easily add new repositories w/o the need to 
edit the central |/etc/apt/sources.list| file. I.e. you can just put a 
file with a unique name and the same format as |/etc/apt/sources.list| 
into this folder and it is used by apt. In order to remove this source 
again you can just remove that specific file w/o the need for handling 
side effects, parsing or mangling with |/etc/apt/sources.list|. It's 
mainly for scripts or other packages to put their repositories there 
automatically - if you manually add repositories you could add them to 
|/etc/apt/sources.list| manually.


My QUESTION: should the script work with the infos in the two files in
sources.list.d?

Wolfgang

Re: Jabref-3.7

[Wolfgang Engelmann]

On 29.11.2016 14:57, Paul A. Rubin wrote:

On 11/29/2016 04:34 AM, Wolfgang Engelmann wrote:


Slightly off topic:

I am using Jabref for my lyx work (debian). The version I use (2.10) 
does not support the medline any more.


I apparently need Java 8 for it -JRE or JDK are offered, which should 
go in /opt. Which one is recommendable?  None is given in synaptic. 
And how do I unpack the JRE or JDK into /opt? Do I extract it first 
on my home/download and copy the folder as root into it?


How do I install jabref-3.7? Unpacking it gives me a lot of 
folders/files, but I can't find a help.

||

A long discussion is in the following, but it is beyond me:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=814901

Wolfgang


||

Wolfgang,

You might want to look at 
https://launchpad.net/~webupd8team/+archive/ubuntu/java 
. If you 
add their PPA to Synaptic and install their package (which is an 
updater, not Java itself), it will install Java 8. Moreover, as new 
versions of Java appear, their package will show up in your usual 
updates and, when you update it, will automatically install the latest 
Java. It also takes care of various configuration nonsense, such as 
setting the latest Java as the preferred version, that otherwise can 
be a PITA.


Cheers,
Paul

Thanks, Paul, for the pointer. I have run the script but at the end I 
was asked whether I would like to continue: [J/n] y
I tried j (ja in German), J, y and just return > in all cases I get an 
abortion:

Es müssen 39,7 kB an Archiven heruntergeladen werden.
Nach dieser Operation werden 180 kB Plattenplatz zusätzlich benutzt.
Möchten Sie fortfahren? [J/n] y
Abbruch.
root@wolfgang-Mr-Whisper-Ultra-SSD-II:~#
any idea what I could do to get it to continue?
Wolfgang

Re: Jabref-3.7

[Wolfgang Engelmann]

On 29.11.2016 15:05, Rich Shepard wrote:

On Tue, 29 Nov 2016, Wolfgang Engelmann wrote:

I am using Jabref for my lyx work (debian). The version I use (2.10) 
does not support the medline any more.


Wolfgang,

  I, too, use JabRef with LyX; it's great! I'm using JabRef-3.7 and ...

Thanks, Rich,
but Jabref-3.7 is the trouble. I have it installed already and used it 
all the time, but it is not supporting medline any more, which I used to 
use and need for fetching references from the web.

Wolfgang



I apparently need Java 8 for it -JRE or JDK are offered, which should go
in /opt. Which one is recommendable? None is given in synaptic. And 
how do
I > unpack the JRE or JDK into /opt? Do I extract it first on my 
home/download and copy the folder as root into it?


  I'm using openjdk-8u91_b14 on Slackware. I recommend it (or Oracle's 
Java

JDK) over the limited JRE version as it gives you more capabilities and
storage space is generally not an issue.

How do I install jabref-3.7? Unpacking it gives me a lot of 
folders/files,

but I can't find a help||


  I don't know Debian or its derivatives, so I suggest that you go to the
download Web page , select the 
second
option, "Download JabRef Platform independent runnable JAR," and 
deposit the

download in /opt/. You'll have /opt/JabRef-3.7.jar.

  To run it, I have a simple shell script (called jabref.sh):

#!/bin/bash

cd /opt/JabRef/
java -jar JabRef-3.7.jar
cd

  No muss, no bother.

HTH,

Rich

Re: Jabref-3.7

[Rich Shepard]

On Tue, 29 Nov 2016, Wolfgang Engelmann wrote:


Usually, when you only care about running Java programs on your browser or
computer you will only install *JRE*. It's all you need. On the other
hand, if you are planning to do some Java programming, you will also need
*JDK*.


Wolfgang,

  There may be tools and applications you use that need to be locally built
so installing the JDK prevents a build failing because part of it is in Java
and you can't compile that portion. A rare event, but the JDK covers you.

Rich

Re: Jabref-3.7

[Rich Shepard]

On Tue, 29 Nov 2016, Wolfgang Engelmann wrote:

I am using Jabref for my lyx work (debian). The version I use (2.10) does not 
support the medline any more.


Wolfgang,

  I, too, use JabRef with LyX; it's great! I'm using JabRef-3.7 and ...


I apparently need Java 8 for it -JRE or JDK are offered, which should go
in /opt. Which one is recommendable? None is given in synaptic. And how do
I > unpack the JRE or JDK into /opt? Do I extract it first on my home/download 
and copy the folder as root into it?


  I'm using openjdk-8u91_b14 on Slackware. I recommend it (or Oracle's Java
JDK) over the limited JRE version as it gives you more capabilities and
storage space is generally not an issue.


How do I install jabref-3.7? Unpacking it gives me a lot of folders/files,
but I can't find a help||


  I don't know Debian or its derivatives, so I suggest that you go to the
download Web page , select the second
option, "Download JabRef Platform independent runnable JAR," and deposit the
download in /opt/. You'll have /opt/JabRef-3.7.jar.

  To run it, I have a simple shell script (called jabref.sh):

#!/bin/bash

cd /opt/JabRef/
java -jar JabRef-3.7.jar
cd

  No muss, no bother.

HTH,

Rich

Re: Jabref-3.7

[Paul A. Rubin]

On 11/29/2016 04:34 AM, Wolfgang Engelmann wrote:


Slightly off topic:

I am using Jabref for my lyx work (debian). The version I use (2.10) 
does not support the medline any more.


I apparently need Java 8 for it -JRE or JDK are offered, which should 
go in /opt. Which one is recommendable?  None is given in synaptic. 
And how do I unpack the JRE or JDK into /opt? Do I extract it first on 
my home/download and copy the folder as root into it?


How do I install jabref-3.7? Unpacking it gives me a lot of 
folders/files, but I can't find a help.

||

A long discussion is in the following, but it is beyond me:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=814901

Wolfgang


||

Wolfgang,

You might want to look at 
https://launchpad.net/~webupd8team/+archive/ubuntu/java 
. If you add 
their PPA to Synaptic and install their package (which is an updater, 
not Java itself), it will install Java 8. Moreover, as new versions of 
Java appear, their package will show up in your usual updates and, when 
you update it, will automatically install the latest Java. It also takes 
care of various configuration nonsense, such as setting the latest Java 
as the preferred version, that otherwise can be a PITA.


Cheers,
Paul

Re: Jabref-3.7

[Wolfgang Engelmann]

On 29.11.2016 10:34, Wolfgang Engelmann wrote:


Slightly off topic:

I am using Jabref for my lyx work (debian). The version I use (2.10) 
does not support the medline any more.


I apparently need Java 8 for it -JRE or JDK are offered, which should 
go in /opt. Which one is recommendable?  None is given in synaptic. 
And how do I unpack the JRE or JDK into /opt? Do I extract it first on 
my home/download and copy the folder as root into it?


How do I install jabref-3.7? Unpacking it gives me a lot of 
folders/files, but I can't find a help.

||

A long discussion is in the following, but it is beyond me:

https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=814901

Wolfgang


To answer my first question:
http://stackoverflow.com/questions/1906445/what-is-the-difference-between-jdk-and-jre

*JRE*: Java Runtime Environment. It is basically the Java Virtual 
Machine where your Java programs run on. It also includes browser 
plugins for Applet execution.


*JDK*: It's the full featured Software Development Kit for Java, 
including *JRE*, and the compilers and tools (like JavaDoc, and Java 
Debugger) to create and compile programs.


Usually, when you only care about running Java programs on your browser 
or computer you will only install *JRE*. It's all you need. On the other 
hand, if you are planning to do some Java programming, you will also 
need *JDK*.

Re: JabRef reference in brackets, compiles to '?' [RESOLVED]

[Rich Shepard]

On Wed, 24 Jun 2015, Rich Shepard wrote:


 I'm not seeing what is different in this new document compared with other
docs. Running lyx-2.1.3 and JabRef-2.10 on Slackware-14.1.


  Saw the light: I had not insertec the bibliography at the end of the
document and pointed it to jabref.bib. Sigh.

Rich

Re: JabRef reference in brackets, compiles to '?' [RESOLVED]

[Rich Shepard]

On Wed, 24 Jun 2015, Rich Shepard wrote:


 I'm not seeing what is different in this new document compared with other
docs. Running lyx-2.1.3 and JabRef-2.10 on Slackware-14.1.


  Saw the light: I had not insertec the bibliography at the end of the
document and pointed it to jabref.bib. Sigh.

Rich

Re: JabRef reference in brackets, compiles to '?' [RESOLVED]

[Rich Shepard]

On Wed, 24 Jun 2015, Rich Shepard wrote:


 I'm not seeing what is different in this new document compared with other
docs. Running lyx-2.1.3 and JabRef-2.10 on Slackware-14.1.


  Saw the light: I had not insertec the bibliography at the end of the
document and pointed it to jabref.bib. Sigh.

Rich

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 10:17 AM, Wolfgang Engelmann wrote:

Sorry, this is slightly off topic, but if sombody is using jabref as a data
base program for the bib-files of Lyx,

could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.

I tired finding out from the handbook, but must have overlooked the part
describing it.



I don't use custom filters myself, but JabRef allows you to define a 
custom export filter (Help  Custom Export Filters).  They're usually 
intended for a format change (output to RTF, HTML etc.), but there is 
nothing stopping you from writing a filter that outputs a .bib file with 
some fields stripped out.


If you'd rather not write your own filter, you might look on the project 
resources page (http://jabref.sourceforge.net/resources.php) and 
particularly at the Chicago style export filters 
(http://jabref.sourceforge.net/plugins/Chicago_export_filters.pdf). 
Again, I've never used them, but one of them might accomplish what you 
want.  I think they export to RTF, but you could easily import that into 
a new JabRef file.


/Paul

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 11:17 AM, Paul A. Rubin wrote:



could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.



I think I just found an arguably easier (or at least less technical) 
method.  Load your database, go to Tools  Set/clear/rename fields, put 
'Abstract' in the field name and click the 'All entries' and 'Clear 
fields' buttons and click Ok.  Repeat for other fields. Save with a new 
name.


If you are going to do it regularly, I think the export filter is worth 
investigating, but if you are only going to do it occasionally, this 
might be the path of least resistance.


/Paul

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

I've had this problem myself because of a lot of german and french
references in my work. My solution is as follows:


   1. Use a RegExp tool like RegexBuddy (http://www.regexbuddy.com) that has
   a full-featured regular-expression engine and search and replace features
   (grep + sed + find can do this under *NIX).
   2. Search in all .bib files for characters in the range \x80-\xFF (all
   extended ASCII characters)
   3. Now you have a list of matches and you can visually identify the
   offending characters.
   4. For each offending character, simply craft a single search-and-replace
   that replaces an extended caracter to its LaTeX accented equivalent. For
   instance, I would search for all 'ü' and replace with '\u', 'é' is replaced
   with '\'e', 'À' is replaced with '\`a', etc.

I found that to replace these in about 500 references took about 20 minutes.
Then, for every new reference you add manually or download from a database,
just make sure to replace extended characters with LaTeX versions with
escaped diacritics and you should be fine.

Hope this helps.

Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)


On 21 August 2010 10:17, Wolfgang Engelmann engelm...@uni-tuebingen.dewrote:

 Sorry, this is slightly off topic, but if sombody is using jabref as a data
 base program for the bib-files of Lyx,

 could he/she tell me how to avoid the export of abstract, school,
 institutions? Those contain apparently sometimes wrong encodings, which
 bibtex/biblatex/biber doesn't like.

 I tired finding out from the handbook, but must have overlooked the part
 describing it.

 Wolfgang

Re: jabref-how to get rid of abstract

[Wolfgang Engelmann]

Am Saturday 21 August 2010 18:36:25 schrieb Paul A. Rubin:
 On 8/21/2010 11:17 AM, Paul A. Rubin wrote:
  could he/she tell me how to avoid the export of abstract, school,
  institutions? Those contain apparently sometimes wrong encodings, which
  bibtex/biblatex/biber doesn't like.

 I think I just found an arguably easier (or at least less technical)
 method.  Load your database, go to Tools  Set/clear/rename fields, put
 'Abstract' in the field name and click the 'All entries' and 'Clear
 fields' buttons and click Ok.  Repeat for other fields. Save with a new
 name.

 If you are going to do it regularly, I think the export filter is worth
 investigating, but if you are only going to do it occasionally, this
 might be the path of least resistance.

 /Paul

Thanks, Paul and Tennessee,

using Pauls proposal I got rid of the Abstract field, but not the school  and 
institution, which is shown in the preview, e.g.

Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
I would like to have
Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, 2006, 16, 547-549
only.

It does not seem to be a field. 
In preferencesentry preview it is shown as 
begin{school}...end{school}
begin{institution}...end{institution}

The log file of my pdf output refers to errors occurring in these items. Thats 
the reason I would like to get them out.

Wolfgang 

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

On 21 August 2010 16:51, Wolfgang Engelmann engelm...@uni-tuebingen.dewrote:

 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends
 Cell
 Biol, Department of Molecular Biology, Sciences III, University of Geneva,
 30
 Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
 I would like to have
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends
 Cell
 Biol, 2006, 16, 547-549
 only.

 It does not seem to be a field.
 In preferencesentry preview it is shown as
 begin{school}...end{school}
 begin{institution}...end{institution}


I'm not sure I understand what you want, but maybe what could cause the
error is the - sign. There are several extended-size (long, short, medium)
dashes that are in extended character sets. They are often impossible to
tell from the regular dashes unless they are next one to another.


Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)

Re: jabref-how to get rid of abstract

[Paul Rubin]

Wolfgang Engelmann engelmann at uni-tuebingen.de writes:

 
 using Pauls proposal I got rid of the Abstract field, but not the school  and 
 institution, which is shown in the preview, e.g.
 
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
 Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
 Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
 I would like to have
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
 Biol, 2006, 16, 547-549
 only.
 
 It does not seem to be a field. 
 In preferencesentry preview it is shown as 
 begin{school}...end{school}
 begin{institution}...end{institution}

School and Institution are both fields and can be deleted the same way you got
rid of Abstract (at least in JabRef 2.5, which is what I have available as I
type this).

Of course, you could also edit individual records and just delete the field
(from a copy of the database, so as not to lose the information).

/Paul

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 10:17 AM, Wolfgang Engelmann wrote:

Sorry, this is slightly off topic, but if sombody is using jabref as a data
base program for the bib-files of Lyx,

could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.

I tired finding out from the handbook, but must have overlooked the part
describing it.



I don't use custom filters myself, but JabRef allows you to define a 
custom export filter (Help  Custom Export Filters).  They're usually 
intended for a format change (output to RTF, HTML etc.), but there is 
nothing stopping you from writing a filter that outputs a .bib file with 
some fields stripped out.


If you'd rather not write your own filter, you might look on the project 
resources page (http://jabref.sourceforge.net/resources.php) and 
particularly at the Chicago style export filters 
(http://jabref.sourceforge.net/plugins/Chicago_export_filters.pdf). 
Again, I've never used them, but one of them might accomplish what you 
want.  I think they export to RTF, but you could easily import that into 
a new JabRef file.


/Paul

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 11:17 AM, Paul A. Rubin wrote:



could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.



I think I just found an arguably easier (or at least less technical) 
method.  Load your database, go to Tools  Set/clear/rename fields, put 
'Abstract' in the field name and click the 'All entries' and 'Clear 
fields' buttons and click Ok.  Repeat for other fields. Save with a new 
name.


If you are going to do it regularly, I think the export filter is worth 
investigating, but if you are only going to do it occasionally, this 
might be the path of least resistance.


/Paul

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

I've had this problem myself because of a lot of german and french
references in my work. My solution is as follows:


   1. Use a RegExp tool like RegexBuddy (http://www.regexbuddy.com) that has
   a full-featured regular-expression engine and search and replace features
   (grep + sed + find can do this under *NIX).
   2. Search in all .bib files for characters in the range \x80-\xFF (all
   extended ASCII characters)
   3. Now you have a list of matches and you can visually identify the
   offending characters.
   4. For each offending character, simply craft a single search-and-replace
   that replaces an extended caracter to its LaTeX accented equivalent. For
   instance, I would search for all 'ü' and replace with '\u', 'é' is replaced
   with '\'e', 'À' is replaced with '\`a', etc.

I found that to replace these in about 500 references took about 20 minutes.
Then, for every new reference you add manually or download from a database,
just make sure to replace extended characters with LaTeX versions with
escaped diacritics and you should be fine.

Hope this helps.

Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)


On 21 August 2010 10:17, Wolfgang Engelmann engelm...@uni-tuebingen.dewrote:

 Sorry, this is slightly off topic, but if sombody is using jabref as a data
 base program for the bib-files of Lyx,

 could he/she tell me how to avoid the export of abstract, school,
 institutions? Those contain apparently sometimes wrong encodings, which
 bibtex/biblatex/biber doesn't like.

 I tired finding out from the handbook, but must have overlooked the part
 describing it.

 Wolfgang

Re: jabref-how to get rid of abstract

[Wolfgang Engelmann]

Am Saturday 21 August 2010 18:36:25 schrieb Paul A. Rubin:
 On 8/21/2010 11:17 AM, Paul A. Rubin wrote:
  could he/she tell me how to avoid the export of abstract, school,
  institutions? Those contain apparently sometimes wrong encodings, which
  bibtex/biblatex/biber doesn't like.

 I think I just found an arguably easier (or at least less technical)
 method.  Load your database, go to Tools  Set/clear/rename fields, put
 'Abstract' in the field name and click the 'All entries' and 'Clear
 fields' buttons and click Ok.  Repeat for other fields. Save with a new
 name.

 If you are going to do it regularly, I think the export filter is worth
 investigating, but if you are only going to do it occasionally, this
 might be the path of least resistance.

 /Paul

Thanks, Paul and Tennessee,

using Pauls proposal I got rid of the Abstract field, but not the school  and 
institution, which is shown in the preview, e.g.

Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
I would like to have
Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, 2006, 16, 547-549
only.

It does not seem to be a field. 
In preferencesentry preview it is shown as 
begin{school}...end{school}
begin{institution}...end{institution}

The log file of my pdf output refers to errors occurring in these items. Thats 
the reason I would like to get them out.

Wolfgang 

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

On 21 August 2010 16:51, Wolfgang Engelmann engelm...@uni-tuebingen.dewrote:

 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends
 Cell
 Biol, Department of Molecular Biology, Sciences III, University of Geneva,
 30
 Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
 I would like to have
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends
 Cell
 Biol, 2006, 16, 547-549
 only.

 It does not seem to be a field.
 In preferencesentry preview it is shown as
 begin{school}...end{school}
 begin{institution}...end{institution}


I'm not sure I understand what you want, but maybe what could cause the
error is the - sign. There are several extended-size (long, short, medium)
dashes that are in extended character sets. They are often impossible to
tell from the regular dashes unless they are next one to another.


Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)

Re: jabref-how to get rid of abstract

[Paul Rubin]

Wolfgang Engelmann engelmann at uni-tuebingen.de writes:

 
 using Pauls proposal I got rid of the Abstract field, but not the school  and 
 institution, which is shown in the preview, e.g.
 
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
 Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
 Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
 I would like to have
 Article (Asher2006) Asher, G.  Schibler, U. A CLOCK-less clock. Trends Cell 
 Biol, 2006, 16, 547-549
 only.
 
 It does not seem to be a field. 
 In preferencesentry preview it is shown as 
 begin{school}...end{school}
 begin{institution}...end{institution}

School and Institution are both fields and can be deleted the same way you got
rid of Abstract (at least in JabRef 2.5, which is what I have available as I
type this).

Of course, you could also edit individual records and just delete the field
(from a copy of the database, so as not to lose the information).

/Paul

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 10:17 AM, Wolfgang Engelmann wrote:

Sorry, this is slightly off topic, but if sombody is using jabref as a data
base program for the bib-files of Lyx,

could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.

I tired finding out from the handbook, but must have overlooked the part
describing it.



I don't use custom filters myself, but JabRef allows you to define a 
custom export filter (Help > Custom Export Filters).  They're usually 
intended for a format change (output to RTF, HTML etc.), but there is 
nothing stopping you from writing a filter that outputs a .bib file with 
some fields stripped out.


If you'd rather not write your own filter, you might look on the project 
resources page (http://jabref.sourceforge.net/resources.php) and 
particularly at the Chicago style export filters 
(http://jabref.sourceforge.net/plugins/Chicago_export_filters.pdf). 
Again, I've never used them, but one of them might accomplish what you 
want.  I think they export to RTF, but you could easily import that into 
a new JabRef file.


/Paul

Re: jabref-how to get rid of abstract

[Paul A. Rubin]

On 8/21/2010 11:17 AM, Paul A. Rubin wrote:



could he/she tell me how to avoid the export of abstract, school,
institutions? Those contain apparently sometimes wrong encodings, which
bibtex/biblatex/biber doesn't like.



I think I just found an arguably easier (or at least less technical) 
method.  Load your database, go to Tools > Set/clear/rename fields, put 
'Abstract' in the field name and click the 'All entries' and 'Clear 
fields' buttons and click Ok.  Repeat for other fields. Save with a new 
name.


If you are going to do it regularly, I think the export filter is worth 
investigating, but if you are only going to do it occasionally, this 
might be the path of least resistance.


/Paul

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

I've had this problem myself because of a lot of german and french
references in my work. My solution is as follows:


   1. Use a RegExp tool like RegexBuddy (http://www.regexbuddy.com) that has
   a full-featured regular-expression engine and search and replace features
   (grep + sed + find can do this under *NIX).
   2. Search in all .bib files for characters in the range \x80-\xFF (all
   extended ASCII characters)
   3. Now you have a list of matches and you can visually identify the
   offending characters.
   4. For each offending character, simply craft a single search-and-replace
   that replaces an extended caracter to its LaTeX accented equivalent. For
   instance, I would search for all 'ü' and replace with '\"u', 'é' is replaced
   with '\'e', 'À' is replaced with '\`a', etc.

I found that to replace these in about 500 references took about 20 minutes.
Then, for every new reference you add manually or download from a database,
just make sure to replace extended characters with LaTeX versions with
escaped diacritics and you should be fine.

Hope this helps.

Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)


On 21 August 2010 10:17, Wolfgang Engelmann wrote:

> Sorry, this is slightly off topic, but if sombody is using jabref as a data
> base program for the bib-files of Lyx,
>
> could he/she tell me how to avoid the export of abstract, school,
> institutions? Those contain apparently sometimes wrong encodings, which
> bibtex/biblatex/biber doesn't like.
>
> I tired finding out from the handbook, but must have overlooked the part
> describing it.
>
> Wolfgang
>

Re: jabref-how to get rid of abstract

[Wolfgang Engelmann]

Am Saturday 21 August 2010 18:36:25 schrieb Paul A. Rubin:
> On 8/21/2010 11:17 AM, Paul A. Rubin wrote:
> >> could he/she tell me how to avoid the export of abstract, school,
> >> institutions? Those contain apparently sometimes wrong encodings, which
> >> bibtex/biblatex/biber doesn't like.
>
> I think I just found an arguably easier (or at least less technical)
> method.  Load your database, go to Tools > Set/clear/rename fields, put
> 'Abstract' in the field name and click the 'All entries' and 'Clear
> fields' buttons and click Ok.  Repeat for other fields. Save with a new
> name.
>
> If you are going to do it regularly, I think the export filter is worth
> investigating, but if you are only going to do it occasionally, this
> might be the path of least resistance.
>
> /Paul

Thanks, Paul and Tennessee,

using Pauls proposal I got rid of the Abstract field, but not the school  and 
institution, which is shown in the preview, e.g.

Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
I would like to have
Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends Cell 
Biol, 2006, 16, 547-549
only.

It does not seem to be a field. 
In preferences>entry preview it is shown as 
begin{school}...end{school}
begin{institution}...end{institution}

The log file of my pdf output refers to errors occurring in these items. Thats 
the reason I would like to get them out.

Wolfgang 

Re: jabref-how to get rid of abstract

[Tennessee Carmel-Veilleux]

On 21 August 2010 16:51, Wolfgang Engelmann wrote:

> Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends
> Cell
> Biol, Department of Molecular Biology, Sciences III, University of Geneva,
> 30
> Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
> I would like to have
> Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends
> Cell
> Biol, 2006, 16, 547-549
> only.
>
> It does not seem to be a field.
> In preferences>entry preview it is shown as
> begin{school}...end{school}
> begin{institution}...end{institution}
>
>
I'm not sure I understand what you want, but maybe what could cause the
error is the "-" sign. There are several extended-size (long, short, medium)
dashes that are in extended character sets. They are often impossible to
tell from the regular dashes unless they are next one to another.


Best regards,

Tennessee Carmel-Veilleux, ing. jr (OIQ)
Electrical engineering masters student, ETS (http://www.etsmtl.ca)
Project AREXIMAS (http://areximas.etsmtl.ca)

Re: jabref-how to get rid of abstract

[Paul Rubin]

Wolfgang Engelmann  uni-tuebingen.de> writes:

> 
> using Pauls proposal I got rid of the Abstract field, but not the school  and 
> institution, which is shown in the preview, e.g.
> 
> Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends Cell 
> Biol, Department of Molecular Biology, Sciences III, University of Geneva, 30 
> Quai Ernest Ansermet, CH-1211 Geneva-4, Switzerland., 2006, 16, 547-549
> I would like to have
> Article (Asher2006) Asher, G. & Schibler, U. A CLOCK-less clock. Trends Cell 
> Biol, 2006, 16, 547-549
> only.
> 
> It does not seem to be a field. 
> In preferences>entry preview it is shown as 
> begin{school}...end{school}
> begin{institution}...end{institution}

School and Institution are both fields and can be deleted the same way you got
rid of Abstract (at least in JabRef 2.5, which is what I have available as I
type this).

Of course, you could also edit individual records and just delete the field
(from a copy of the database, so as not to lose the information).

/Paul

Re: JabRef and Lyx on Mac

[Julio Rojas]

Have you inserted the bibliography through Insert-List/ToC-BibTeX
Bibliography?
-
Julio Rojas
jcredbe...@gmail.com


On Tue, Nov 17, 2009 at 3:27 PM, Phil Underwood philjunderw...@gmail.comwrote:

 Hi there,

 I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
 MacTex-2009
 on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
 haven't
 ruled out the possibility that I am doing something wrong. Are you able to
 tell
 from the explanation of my problem below whether I have a technical or user
 fault:

 I have configured my LyXServer path in LyX and Path to LyX pipe in
 JabRef
 both to: /Applications/LyX.app/Contents/Resources/lyxpipe

 I then start a new *.lyx file in LyX.

 I then highlight the references I would like to push to LyX and click the
 Push selection to LyX/Kile button in JabRef.

 At this point it is confirmed that the two are communicating with each
 other as
 the predefined 'Bibtexkey' appears in square brackets on the new *.lyx
 document, i.e.  [Author2009] . However, when I view the file in any
 format
 (PDF or PostScript) the reference appears on the document to be simply a
 question mark in square brackets -  [?] , and not the full reference as
 expected.

 Any thoughts?

 Cheers,
 Phil

RE: JabRef and Lyx on Mac

[Rob Oakes]

Hi Phil,

I've long had similar problems.  I was never able to figure out the problem,
though I believe it had something to do with the Java VM on Mac.  (Which is
a strange creature.)  I finally had to move to another program.

I understand that Change Programs is a poor solution, but nevertheless,
you might want to take a look at BibDesk or at Mendeley (which can sync
references to a BibTeX reference file).

http://bibdesk.sourceforge.net/
http://www.mendeley.com/

I use both programs and I've been very happy with them.  They also instantly
solved by JabRef problems.

Cheers,

Rob Oakes

-Original Message-
From: news [mailto:n...@ger.gmane.org] On Behalf Of Phil Underwood
Sent: Tuesday, November 17, 2009 7:27 AM
To: lyx-users@lists.lyx.org
Subject: JabRef and Lyx on Mac

Hi there,

I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
MacTex-2009
on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
haven't 
ruled out the possibility that I am doing something wrong. Are you able to
tell
from the explanation of my problem below whether I have a technical or user 
fault:

I have configured my LyXServer path in LyX and Path to LyX pipe in
JabRef 
both to: /Applications/LyX.app/Contents/Resources/lyxpipe

I then start a new *.lyx file in LyX.

I then highlight the references I would like to push to LyX and click the 
Push selection to LyX/Kile button in JabRef.

At this point it is confirmed that the two are communicating with each other
as 
the predefined 'Bibtexkey' appears in square brackets on the new *.lyx 
document, i.e.  [Author2009] . However, when I view the file in any format
(PDF or PostScript) the reference appears on the document to be simply a
question mark in square brackets -  [?] , and not the full reference as 
expected.

Any thoughts?

Cheers,
Phil

Re: JabRef and Lyx on Mac

[Phil Underwood]

Hi Rob,

I'm still having the same issue, even after Julio's suggestion and so am now 
entertaining your suggestion.

BibDesk is the same one that came with MacTex? Do you have a preferred tool? 
The screenshots of Mendeley look nice. Is it a native Mac application?

Also, do you know if there's an easy way to import my existing JabRef *.bib 
database with either tool?

Cheers,
Phil

On 17 Nov 2009, at 15:31, Rob Oakes wrote:

 Hi Phil,
 
 I've long had similar problems.  I was never able to figure out the problem,
 though I believe it had something to do with the Java VM on Mac.  (Which is
 a strange creature.)  I finally had to move to another program.
 
 I understand that Change Programs is a poor solution, but nevertheless,
 you might want to take a look at BibDesk or at Mendeley (which can sync
 references to a BibTeX reference file).
 
 http://bibdesk.sourceforge.net/
 http://www.mendeley.com/
 
 I use both programs and I've been very happy with them.  They also instantly
 solved by JabRef problems.
 
 Cheers,
 
 Rob Oakes
 
 -Original Message-
 From: news [mailto:n...@ger.gmane.org] On Behalf Of Phil Underwood
 Sent: Tuesday, November 17, 2009 7:27 AM
 To: lyx-users@lists.lyx.org
 Subject: JabRef and Lyx on Mac
 
 Hi there,
 
 I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
 MacTex-2009
 on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
 haven't 
 ruled out the possibility that I am doing something wrong. Are you able to
 tell
 from the explanation of my problem below whether I have a technical or user 
 fault:
 
 I have configured my LyXServer path in LyX and Path to LyX pipe in
 JabRef 
 both to: /Applications/LyX.app/Contents/Resources/lyxpipe
 
 I then start a new *.lyx file in LyX.
 
 I then highlight the references I would like to push to LyX and click the 
 Push selection to LyX/Kile button in JabRef.
 
 At this point it is confirmed that the two are communicating with each other
 as 
 the predefined 'Bibtexkey' appears in square brackets on the new *.lyx 
 document, i.e.  [Author2009] . However, when I view the file in any format
 (PDF or PostScript) the reference appears on the document to be simply a
 question mark in square brackets -  [?] , and not the full reference as 
 expected.
 
 Any thoughts?
 
 Cheers,
 Phil
 
 

RE: JabRef and Lyx on Mac

[Rob Oakes]

Hi Phil,

I honestly can't remember if BibDesk comes with MacTek, but I wouldn't be
surprised if it did.  The native file format for BibDesk is .bib, as a
result, you'll just be able to open it and work with it in the same way that
you did in JabRef.  This is one of the wonderful things of using standards,
your data is imminently portable.  Moreover, there isn't any messiness or
energy lost in the dance of export and import.

In regards to Mendeley.  It is a native Mac application (though based on the
Qt framework, so cross platform).  To import .bib references into the BibTeX
database, just click on the add references button and select your .bib
file. You can set up the .bib sync options in the preferences pane.

I actually use them for very different reasons.  Mendeley is my main
reference management tool since it can also work with Zotero (for references
and citations things off the web) and Microsoft Word/OpenOffice for writing.
(Which, unfortunately, is a necessity when working with technically
incompetent medical doctors.)  I also use it to organize/sync my pdf library
amongst different computers and share papers with collaborators.  It's a
very cool program.

I use BibDesk when doing literature searches.  It's far easier to download
the references to a separate .bib file and then go about deleting those that
aren't pertinent.  I then can then tag all of them with a project
description and import my working file into Mendeley for citation.  Mendeley
has a really nice feature called Collections that can be used for
organizing the citations and creating project specific .bib files.  More
importantly, though, the BibTeX files are readable.  I've had big problems
with EndNote and Zotero creating unreadable BibTeX.  (And a few of the
people I work with are real hard-asses about it.  One of them actually codes
all of his BibTeX by hand, which just seems painful to me.)

Hope this is of some help.  Welcome to the Mac.  It is a very nice
ecosystem, but getting moved in can be painful.  Even after two years, I'm
still trying to get all of the boxes unpacked.

Cheers,

Rob 

-Original Message-
From: Phil Underwood [mailto:philjunderw...@gmail.com] 
Sent: Tuesday, November 17, 2009 9:26 AM
To: Rob Oakes
Cc: lyx-users@lists.lyx.org
Subject: Re: JabRef and Lyx on Mac

Hi Rob,

I'm still having the same issue, even after Julio's suggestion and so am now
entertaining your suggestion.

BibDesk is the same one that came with MacTex? Do you have a preferred tool?
The screenshots of Mendeley look nice. Is it a native Mac application?

Also, do you know if there's an easy way to import my existing JabRef *.bib
database with either tool?

Cheers,
Phil

On 17 Nov 2009, at 15:31, Rob Oakes wrote:

 Hi Phil,
 
 I've long had similar problems.  I was never able to figure out the
problem,
 though I believe it had something to do with the Java VM on Mac.  (Which
is
 a strange creature.)  I finally had to move to another program.
 
 I understand that Change Programs is a poor solution, but nevertheless,
 you might want to take a look at BibDesk or at Mendeley (which can sync
 references to a BibTeX reference file).
 
 http://bibdesk.sourceforge.net/
 http://www.mendeley.com/
 
 I use both programs and I've been very happy with them.  They also
instantly
 solved by JabRef problems.
 
 Cheers,
 
 Rob Oakes
 
 -Original Message-
 From: news [mailto:n...@ger.gmane.org] On Behalf Of Phil Underwood
 Sent: Tuesday, November 17, 2009 7:27 AM
 To: lyx-users@lists.lyx.org
 Subject: JabRef and Lyx on Mac
 
 Hi there,
 
 I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
 MacTex-2009
 on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
 haven't 
 ruled out the possibility that I am doing something wrong. Are you able to
 tell
 from the explanation of my problem below whether I have a technical or
user 
 fault:
 
 I have configured my LyXServer path in LyX and Path to LyX pipe in
 JabRef 
 both to: /Applications/LyX.app/Contents/Resources/lyxpipe
 
 I then start a new *.lyx file in LyX.
 
 I then highlight the references I would like to push to LyX and click the 
 Push selection to LyX/Kile button in JabRef.
 
 At this point it is confirmed that the two are communicating with each
other
 as 
 the predefined 'Bibtexkey' appears in square brackets on the new *.lyx 
 document, i.e.  [Author2009] . However, when I view the file in any
format
 (PDF or PostScript) the reference appears on the document to be simply a
 question mark in square brackets -  [?] , and not the full reference as 
 expected.
 
 Any thoughts?
 
 Cheers,
 Phil
 
 

Re: JabRef and Lyx on Mac

[Julio Rojas]

Have you inserted the bibliography through Insert-List/ToC-BibTeX
Bibliography?
-
Julio Rojas
jcredbe...@gmail.com


On Tue, Nov 17, 2009 at 3:27 PM, Phil Underwood philjunderw...@gmail.comwrote:

 Hi there,

 I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
 MacTex-2009
 on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
 haven't
 ruled out the possibility that I am doing something wrong. Are you able to
 tell
 from the explanation of my problem below whether I have a technical or user
 fault:

 I have configured my LyXServer path in LyX and Path to LyX pipe in
 JabRef
 both to: /Applications/LyX.app/Contents/Resources/lyxpipe

 I then start a new *.lyx file in LyX.

 I then highlight the references I would like to push to LyX and click the
 Push selection to LyX/Kile button in JabRef.

 At this point it is confirmed that the two are communicating with each
 other as
 the predefined 'Bibtexkey' appears in square brackets on the new *.lyx
 document, i.e.  [Author2009] . However, when I view the file in any
 format
 (PDF or PostScript) the reference appears on the document to be simply a
 question mark in square brackets -  [?] , and not the full reference as
 expected.

 Any thoughts?

 Cheers,
 Phil

RE: JabRef and Lyx on Mac

[Rob Oakes]

Hi Phil,

I've long had similar problems.  I was never able to figure out the problem,
though I believe it had something to do with the Java VM on Mac.  (Which is
a strange creature.)  I finally had to move to another program.

I understand that Change Programs is a poor solution, but nevertheless,
you might want to take a look at BibDesk or at Mendeley (which can sync
references to a BibTeX reference file).

http://bibdesk.sourceforge.net/
http://www.mendeley.com/

I use both programs and I've been very happy with them.  They also instantly
solved by JabRef problems.

Cheers,

Rob Oakes

-Original Message-
From: news [mailto:n...@ger.gmane.org] On Behalf Of Phil Underwood
Sent: Tuesday, November 17, 2009 7:27 AM
To: lyx-users@lists.lyx.org
Subject: JabRef and Lyx on Mac

Hi there,

I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
MacTex-2009
on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
haven't 
ruled out the possibility that I am doing something wrong. Are you able to
tell
from the explanation of my problem below whether I have a technical or user 
fault:

I have configured my LyXServer path in LyX and Path to LyX pipe in
JabRef 
both to: /Applications/LyX.app/Contents/Resources/lyxpipe

I then start a new *.lyx file in LyX.

I then highlight the references I would like to push to LyX and click the 
Push selection to LyX/Kile button in JabRef.

At this point it is confirmed that the two are communicating with each other
as 
the predefined 'Bibtexkey' appears in square brackets on the new *.lyx 
document, i.e.  [Author2009] . However, when I view the file in any format
(PDF or PostScript) the reference appears on the document to be simply a
question mark in square brackets -  [?] , and not the full reference as 
expected.

Any thoughts?

Cheers,
Phil

Re: JabRef and Lyx on Mac

[Phil Underwood]

Hi Rob,

I'm still having the same issue, even after Julio's suggestion and so am now 
entertaining your suggestion.

BibDesk is the same one that came with MacTex? Do you have a preferred tool? 
The screenshots of Mendeley look nice. Is it a native Mac application?

Also, do you know if there's an easy way to import my existing JabRef *.bib 
database with either tool?

Cheers,
Phil

On 17 Nov 2009, at 15:31, Rob Oakes wrote:

 Hi Phil,
 
 I've long had similar problems.  I was never able to figure out the problem,
 though I believe it had something to do with the Java VM on Mac.  (Which is
 a strange creature.)  I finally had to move to another program.
 
 I understand that Change Programs is a poor solution, but nevertheless,
 you might want to take a look at BibDesk or at Mendeley (which can sync
 references to a BibTeX reference file).
 
 http://bibdesk.sourceforge.net/
 http://www.mendeley.com/
 
 I use both programs and I've been very happy with them.  They also instantly
 solved by JabRef problems.
 
 Cheers,
 
 Rob Oakes
 
 -Original Message-
 From: news [mailto:n...@ger.gmane.org] On Behalf Of Phil Underwood
 Sent: Tuesday, November 17, 2009 7:27 AM
 To: lyx-users@lists.lyx.org
 Subject: JabRef and Lyx on Mac
 
 Hi there,
 
 I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
 MacTex-2009
 on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
 haven't 
 ruled out the possibility that I am doing something wrong. Are you able to
 tell
 from the explanation of my problem below whether I have a technical or user 
 fault:
 
 I have configured my LyXServer path in LyX and Path to LyX pipe in
 JabRef 
 both to: /Applications/LyX.app/Contents/Resources/lyxpipe
 
 I then start a new *.lyx file in LyX.
 
 I then highlight the references I would like to push to LyX and click the 
 Push selection to LyX/Kile button in JabRef.
 
 At this point it is confirmed that the two are communicating with each other
 as 
 the predefined 'Bibtexkey' appears in square brackets on the new *.lyx 
 document, i.e.  [Author2009] . However, when I view the file in any format
 (PDF or PostScript) the reference appears on the document to be simply a
 question mark in square brackets -  [?] , and not the full reference as 
 expected.
 
 Any thoughts?
 
 Cheers,
 Phil
 
 

RE: JabRef and Lyx on Mac

[Rob Oakes]

Hi Phil,

I honestly can't remember if BibDesk comes with MacTek, but I wouldn't be
surprised if it did.  The native file format for BibDesk is .bib, as a
result, you'll just be able to open it and work with it in the same way that
you did in JabRef.  This is one of the wonderful things of using standards,
your data is imminently portable.  Moreover, there isn't any messiness or
energy lost in the dance of export and import.

In regards to Mendeley.  It is a native Mac application (though based on the
Qt framework, so cross platform).  To import .bib references into the BibTeX
database, just click on the add references button and select your .bib
file. You can set up the .bib sync options in the preferences pane.

I actually use them for very different reasons.  Mendeley is my main
reference management tool since it can also work with Zotero (for references
and citations things off the web) and Microsoft Word/OpenOffice for writing.
(Which, unfortunately, is a necessity when working with technically
incompetent medical doctors.)  I also use it to organize/sync my pdf library
amongst different computers and share papers with collaborators.  It's a
very cool program.

I use BibDesk when doing literature searches.  It's far easier to download
the references to a separate .bib file and then go about deleting those that
aren't pertinent.  I then can then tag all of them with a project
description and import my working file into Mendeley for citation.  Mendeley
has a really nice feature called Collections that can be used for
organizing the citations and creating project specific .bib files.  More
importantly, though, the BibTeX files are readable.  I've had big problems
with EndNote and Zotero creating unreadable BibTeX.  (And a few of the
people I work with are real hard-asses about it.  One of them actually codes
all of his BibTeX by hand, which just seems painful to me.)

Hope this is of some help.  Welcome to the Mac.  It is a very nice
ecosystem, but getting moved in can be painful.  Even after two years, I'm
still trying to get all of the boxes unpacked.

Cheers,

Rob 

-Original Message-
From: Phil Underwood [mailto:philjunderw...@gmail.com] 
Sent: Tuesday, November 17, 2009 9:26 AM
To: Rob Oakes
Cc: lyx-users@lists.lyx.org
Subject: Re: JabRef and Lyx on Mac

Hi Rob,

I'm still having the same issue, even after Julio's suggestion and so am now
entertaining your suggestion.

BibDesk is the same one that came with MacTex? Do you have a preferred tool?
The screenshots of Mendeley look nice. Is it a native Mac application?

Also, do you know if there's an easy way to import my existing JabRef *.bib
database with either tool?

Cheers,
Phil

On 17 Nov 2009, at 15:31, Rob Oakes wrote:

 Hi Phil,
 
 I've long had similar problems.  I was never able to figure out the
problem,
 though I believe it had something to do with the Java VM on Mac.  (Which
is
 a strange creature.)  I finally had to move to another program.
 
 I understand that Change Programs is a poor solution, but nevertheless,
 you might want to take a look at BibDesk or at Mendeley (which can sync
 references to a BibTeX reference file).
 
 http://bibdesk.sourceforge.net/
 http://www.mendeley.com/
 
 I use both programs and I've been very happy with them.  They also
instantly
 solved by JabRef problems.
 
 Cheers,
 
 Rob Oakes
 
 -Original Message-
 From: news [mailto:n...@ger.gmane.org] On Behalf Of Phil Underwood
 Sent: Tuesday, November 17, 2009 7:27 AM
 To: lyx-users@lists.lyx.org
 Subject: JabRef and Lyx on Mac
 
 Hi there,
 
 I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
 MacTex-2009
 on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
 haven't 
 ruled out the possibility that I am doing something wrong. Are you able to
 tell
 from the explanation of my problem below whether I have a technical or
user 
 fault:
 
 I have configured my LyXServer path in LyX and Path to LyX pipe in
 JabRef 
 both to: /Applications/LyX.app/Contents/Resources/lyxpipe
 
 I then start a new *.lyx file in LyX.
 
 I then highlight the references I would like to push to LyX and click the 
 Push selection to LyX/Kile button in JabRef.
 
 At this point it is confirmed that the two are communicating with each
other
 as 
 the predefined 'Bibtexkey' appears in square brackets on the new *.lyx 
 document, i.e.  [Author2009] . However, when I view the file in any
format
 (PDF or PostScript) the reference appears on the document to be simply a
 question mark in square brackets -  [?] , and not the full reference as 
 expected.
 
 Any thoughts?
 
 Cheers,
 Phil
 
 

Re: JabRef and Lyx on Mac

[Julio Rojas]

Have you inserted the bibliography through "Insert->List/ToC->BibTeX
Bibliography"?
-
Julio Rojas
jcredbe...@gmail.com


On Tue, Nov 17, 2009 at 3:27 PM, Phil Underwood wrote:

> Hi there,
>
> I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
> MacTex-2009
> on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
> haven't
> ruled out the possibility that I am doing something wrong. Are you able to
> tell
> from the explanation of my problem below whether I have a technical or user
> fault:
>
> I have configured my "LyXServer path" in LyX and "Path to LyX pipe" in
> JabRef
> both to: /Applications/LyX.app/Contents/Resources/lyxpipe
>
> I then start a new *.lyx file in LyX.
>
> I then highlight the references I would like to push to LyX and click the
> "Push selection to LyX/Kile" button in JabRef.
>
> At this point it is confirmed that the two are communicating with each
> other as
> the predefined 'Bibtexkey' appears in square brackets on the new *.lyx
> document, i.e. " [Author2009] ". However, when I view the file in any
> format
> (PDF or PostScript) the reference appears on the document to be simply a
> question mark in square brackets - " [?] ", and not the full reference as
> expected.
>
> Any thoughts?
>
> Cheers,
> Phil
>
>

RE: JabRef and Lyx on Mac

[Rob Oakes]

Hi Phil,

I've long had similar problems.  I was never able to figure out the problem,
though I believe it had something to do with the Java VM on Mac.  (Which is
a strange creature.)  I finally had to move to another program.

I understand that "Change Programs" is a poor solution, but nevertheless,
you might want to take a look at BibDesk or at Mendeley (which can sync
references to a BibTeX reference file).

http://bibdesk.sourceforge.net/
http://www.mendeley.com/

I use both programs and I've been very happy with them.  They also instantly
solved by JabRef problems.

Cheers,

Rob Oakes

-Original Message-
From: news [mailto:n...@ger.gmane.org] On Behalf Of Phil Underwood
Sent: Tuesday, November 17, 2009 7:27 AM
To: lyx-users@lists.lyx.org
Subject: JabRef and Lyx on Mac

Hi there,

I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
MacTex-2009
on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
haven't 
ruled out the possibility that I am doing something wrong. Are you able to
tell
from the explanation of my problem below whether I have a technical or user 
fault:

I have configured my "LyXServer path" in LyX and "Path to LyX pipe" in
JabRef 
both to: /Applications/LyX.app/Contents/Resources/lyxpipe

I then start a new *.lyx file in LyX.

I then highlight the references I would like to push to LyX and click the 
"Push selection to LyX/Kile" button in JabRef.

At this point it is confirmed that the two are communicating with each other
as 
the predefined 'Bibtexkey' appears in square brackets on the new *.lyx 
document, i.e. " [Author2009] ". However, when I view the file in any format
(PDF or PostScript) the reference appears on the document to be simply a
question mark in square brackets - " [?] ", and not the full reference as 
expected.

Any thoughts?

Cheers,
Phil

Re: JabRef and Lyx on Mac

[Phil Underwood]

Hi Rob,

I'm still having the same issue, even after Julio's suggestion and so am now 
entertaining your suggestion.

BibDesk is the same one that came with MacTex? Do you have a preferred tool? 
The screenshots of Mendeley look nice. Is it a native Mac application?

Also, do you know if there's an easy way to import my existing JabRef *.bib 
database with either tool?

Cheers,
Phil

On 17 Nov 2009, at 15:31, Rob Oakes wrote:

> Hi Phil,
> 
> I've long had similar problems.  I was never able to figure out the problem,
> though I believe it had something to do with the Java VM on Mac.  (Which is
> a strange creature.)  I finally had to move to another program.
> 
> I understand that "Change Programs" is a poor solution, but nevertheless,
> you might want to take a look at BibDesk or at Mendeley (which can sync
> references to a BibTeX reference file).
> 
> http://bibdesk.sourceforge.net/
> http://www.mendeley.com/
> 
> I use both programs and I've been very happy with them.  They also instantly
> solved by JabRef problems.
> 
> Cheers,
> 
> Rob Oakes
> 
> -Original Message-
> From: news [mailto:n...@ger.gmane.org] On Behalf Of Phil Underwood
> Sent: Tuesday, November 17, 2009 7:27 AM
> To: lyx-users@lists.lyx.org
> Subject: JabRef and Lyx on Mac
> 
> Hi there,
> 
> I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
> MacTex-2009
> on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
> haven't 
> ruled out the possibility that I am doing something wrong. Are you able to
> tell
> from the explanation of my problem below whether I have a technical or user 
> fault:
> 
> I have configured my "LyXServer path" in LyX and "Path to LyX pipe" in
> JabRef 
> both to: /Applications/LyX.app/Contents/Resources/lyxpipe
> 
> I then start a new *.lyx file in LyX.
> 
> I then highlight the references I would like to push to LyX and click the 
> "Push selection to LyX/Kile" button in JabRef.
> 
> At this point it is confirmed that the two are communicating with each other
> as 
> the predefined 'Bibtexkey' appears in square brackets on the new *.lyx 
> document, i.e. " [Author2009] ". However, when I view the file in any format
> (PDF or PostScript) the reference appears on the document to be simply a
> question mark in square brackets - " [?] ", and not the full reference as 
> expected.
> 
> Any thoughts?
> 
> Cheers,
> Phil
> 
> 

RE: JabRef and Lyx on Mac

[Rob Oakes]

Hi Phil,

I honestly can't remember if BibDesk comes with MacTek, but I wouldn't be
surprised if it did.  The native file format for BibDesk is .bib, as a
result, you'll just be able to open it and work with it in the same way that
you did in JabRef.  This is one of the wonderful things of using standards,
your data is imminently portable.  Moreover, there isn't any messiness or
energy lost in the dance of export and import.

In regards to Mendeley.  It is a native Mac application (though based on the
Qt framework, so cross platform).  To import .bib references into the BibTeX
database, just click on the "add references button" and select your .bib
file. You can set up the .bib sync options in the preferences pane.

I actually use them for very different reasons.  Mendeley is my main
reference management tool since it can also work with Zotero (for references
and citations things off the web) and Microsoft Word/OpenOffice for writing.
(Which, unfortunately, is a necessity when working with technically
incompetent medical doctors.)  I also use it to organize/sync my pdf library
amongst different computers and share papers with collaborators.  It's a
very cool program.

I use BibDesk when doing literature searches.  It's far easier to download
the references to a separate .bib file and then go about deleting those that
aren't pertinent.  I then can then tag all of them with a project
description and import my working file into Mendeley for citation.  Mendeley
has a really nice feature called "Collections" that can be used for
organizing the citations and creating project specific .bib files.  More
importantly, though, the BibTeX files are readable.  I've had big problems
with EndNote and Zotero creating unreadable BibTeX.  (And a few of the
people I work with are real hard-asses about it.  One of them actually codes
all of his BibTeX by hand, which just seems painful to me.)

Hope this is of some help.  Welcome to the Mac.  It is a very nice
ecosystem, but getting moved in can be painful.  Even after two years, I'm
still trying to get all of the boxes unpacked.

Cheers,

Rob 

-Original Message-
From: Phil Underwood [mailto:philjunderw...@gmail.com] 
Sent: Tuesday, November 17, 2009 9:26 AM
To: Rob Oakes
Cc: lyx-users@lists.lyx.org
Subject: Re: JabRef and Lyx on Mac

Hi Rob,

I'm still having the same issue, even after Julio's suggestion and so am now
entertaining your suggestion.

BibDesk is the same one that came with MacTex? Do you have a preferred tool?
The screenshots of Mendeley look nice. Is it a native Mac application?

Also, do you know if there's an easy way to import my existing JabRef *.bib
database with either tool?

Cheers,
Phil

On 17 Nov 2009, at 15:31, Rob Oakes wrote:

> Hi Phil,
> 
> I've long had similar problems.  I was never able to figure out the
problem,
> though I believe it had something to do with the Java VM on Mac.  (Which
is
> a strange creature.)  I finally had to move to another program.
> 
> I understand that "Change Programs" is a poor solution, but nevertheless,
> you might want to take a look at BibDesk or at Mendeley (which can sync
> references to a BibTeX reference file).
> 
> http://bibdesk.sourceforge.net/
> http://www.mendeley.com/
> 
> I use both programs and I've been very happy with them.  They also
instantly
> solved by JabRef problems.
> 
> Cheers,
> 
> Rob Oakes
> 
> -Original Message-
> From: news [mailto:n...@ger.gmane.org] On Behalf Of Phil Underwood
> Sent: Tuesday, November 17, 2009 7:27 AM
> To: lyx-users@lists.lyx.org
> Subject: JabRef and Lyx on Mac
> 
> Hi there,
> 
> I am having troubles with JabRef 2.5 and LyX 1.6.4.1 running with
> MacTex-2009
> on Mac OS X 10.6.2. I am new to these tools and the Mac platform, so I
> haven't 
> ruled out the possibility that I am doing something wrong. Are you able to
> tell
> from the explanation of my problem below whether I have a technical or
user 
> fault:
> 
> I have configured my "LyXServer path" in LyX and "Path to LyX pipe" in
> JabRef 
> both to: /Applications/LyX.app/Contents/Resources/lyxpipe
> 
> I then start a new *.lyx file in LyX.
> 
> I then highlight the references I would like to push to LyX and click the 
> "Push selection to LyX/Kile" button in JabRef.
> 
> At this point it is confirmed that the two are communicating with each
other
> as 
> the predefined 'Bibtexkey' appears in square brackets on the new *.lyx 
> document, i.e. " [Author2009] ". However, when I view the file in any
format
> (PDF or PostScript) the reference appears on the document to be simply a
> question mark in square brackets - " [?] ", and not the full reference as 
> expected.
> 
> Any thoughts?
> 
> Cheers,
> Phil
> 
> 

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[Erez Yerushalmi]

Hi Cas,

Sorry for not answering sooner, I'm away from computer for a week.

Zotero is great for collecting and managing my bibliography, but it is
really not made for bibtex export. I heard that others have the problem you
and I have.

I think Zotero is amazing, though!!

What I do is quite primitive, I must admit. I export zotero to bibtex, and
then import to Jabref, and clean up. But many times, it works without any
problem. You probably know that in Zotero, you can build a folder with all
the bibliography you want, and export that specific folder. So sometimes it
works. If LyX crashes, I import to Jabref and fix it until LyX works.
Primitive - I know.

Specifically, Zotero doesn't like the symbol ':'  in a title. If you have :
in a title, LyX's bibtex goes crazy and crashes. I don't know why.

There is also a plugin for Zotero and LyX called Lytero, but I think it
works only on Linux.
http://forums.zotero.org/discussion/6333/lytero-for-windows/

Best, Erez



On Mon, May 18, 2009 at 4:23 PM, castelol...@aim.com wrote:

  Hi Erez

 You said I use also zotero to collect the citations, and export it as
 bibtex file.

 The exported bibtex file does not appear to be fully compatible. A LyX (or
 MikTex?) dialogue with a host of errors is blocking me from either viewing
 or pdf-ing the document: 'missing $ inserted, extra } or forgotten $'

 What did I miss?

 /Cas

  -Original Message-
 From: Erez Yerushalmi erezyerusha...@gmail.com
 To: castelol...@aim.com
  Cc: lyx-users@lists.lyx.org
 Sent: Sun, 17 May 2009 2:57 pm
 Subject: Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

  Maybe this will help.

 A bib file is just a certain type of format, which can be saved in notepad.
 Jabref opens it up an shows it to you in an easiser way.  So,

 1. In Jabref, you create bib file called mylib.bib. You can save it
 anywhere. So lets say you created a folder where your current lyx project is
 located. Save this bib file there.

 2.Go to the place in your lyx document where you want the references to be
 presented (presumably, the end). Click Insert/ Lists  TOC/ BibT E X
 Bibliography. Point the LyX document to that specific file, by browsing for
 the mylib.bib file.

 3. Click Lyx's Layout/Document setting, choose Bibliography. Here you
 specify the style of citations you want.
 4. Now, suppose you are writing a document and you want to cite something.
 Click LyX insert/ Citation button. A menu should open and you should
 see the list of reference ,

 I use also zotero to collect the citations, and export it as bibtex file.

 Erez

 On Sun, May 17, 2009 at 2:31 AM, castelol...@aim.com wrote:

 I just started using LyX 1.6 and JabRef 2.4 and I read here that you
 cannot push refs from Jab into Lyx in windows xp.

 Here's the strange thing (coming from a beginner's perspective), I can
 create a bibliography because there are .bib files already in the
 appropriate MiKTeX 2.7 folder that appears to be supplying Lyx with its
 database. I can also manually put my JabRef .bib into that same subdirectory
 (C:\Program Files\MiKTeX 2.7\bibtex\bib\bibtopic) and it appears in the
 dialogue box along with the others (examples that installed with Lyx).

 But, insertcitation does not show any references in my .bib, though the
 others do appear and can be inserted as citations and appear in the
 references at the end of the doc.

 There must be, at the very least,  a way to put the .bib files in the
 right directory manually?

 thnx,
 Casper de Tello




 --
 Erez Yerushalmi
 PhD Student
 Warwick University, UK
 homepage:
 http://www2.warwick.ac.uk/fac/soc/economics/research/phds/3rd_year/yerushalmi

 --
 We found the real 'Hotel California' and the 'Seinfeld' diner. What will
 you find? Explore 
 *WhereItsAt.com*http://www.whereitsat.com/?ncid=emlwenew0001
 .




-- 
Erez Yerushalmi
PhD Student
Warwick University, UK
homepage:
http://www2.warwick.ac.uk/fac/soc/economics/research/phds/3rd_year/yerushalmi

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[Erez Yerushalmi]

Hi Cas,

Sorry for not answering sooner, I'm away from computer for a week.

Zotero is great for collecting and managing my bibliography, but it is
really not made for bibtex export. I heard that others have the problem you
and I have.

I think Zotero is amazing, though!!

What I do is quite primitive, I must admit. I export zotero to bibtex, and
then import to Jabref, and clean up. But many times, it works without any
problem. You probably know that in Zotero, you can build a folder with all
the bibliography you want, and export that specific folder. So sometimes it
works. If LyX crashes, I import to Jabref and fix it until LyX works.
Primitive - I know.

Specifically, Zotero doesn't like the symbol ':'  in a title. If you have :
in a title, LyX's bibtex goes crazy and crashes. I don't know why.

There is also a plugin for Zotero and LyX called Lytero, but I think it
works only on Linux.
http://forums.zotero.org/discussion/6333/lytero-for-windows/

Best, Erez



On Mon, May 18, 2009 at 4:23 PM, castelol...@aim.com wrote:

  Hi Erez

 You said I use also zotero to collect the citations, and export it as
 bibtex file.

 The exported bibtex file does not appear to be fully compatible. A LyX (or
 MikTex?) dialogue with a host of errors is blocking me from either viewing
 or pdf-ing the document: 'missing $ inserted, extra } or forgotten $'

 What did I miss?

 /Cas

  -Original Message-
 From: Erez Yerushalmi erezyerusha...@gmail.com
 To: castelol...@aim.com
  Cc: lyx-users@lists.lyx.org
 Sent: Sun, 17 May 2009 2:57 pm
 Subject: Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

  Maybe this will help.

 A bib file is just a certain type of format, which can be saved in notepad.
 Jabref opens it up an shows it to you in an easiser way.  So,

 1. In Jabref, you create bib file called mylib.bib. You can save it
 anywhere. So lets say you created a folder where your current lyx project is
 located. Save this bib file there.

 2.Go to the place in your lyx document where you want the references to be
 presented (presumably, the end). Click Insert/ Lists  TOC/ BibT E X
 Bibliography. Point the LyX document to that specific file, by browsing for
 the mylib.bib file.

 3. Click Lyx's Layout/Document setting, choose Bibliography. Here you
 specify the style of citations you want.
 4. Now, suppose you are writing a document and you want to cite something.
 Click LyX insert/ Citation button. A menu should open and you should
 see the list of reference ,

 I use also zotero to collect the citations, and export it as bibtex file.

 Erez

 On Sun, May 17, 2009 at 2:31 AM, castelol...@aim.com wrote:

 I just started using LyX 1.6 and JabRef 2.4 and I read here that you
 cannot push refs from Jab into Lyx in windows xp.

 Here's the strange thing (coming from a beginner's perspective), I can
 create a bibliography because there are .bib files already in the
 appropriate MiKTeX 2.7 folder that appears to be supplying Lyx with its
 database. I can also manually put my JabRef .bib into that same subdirectory
 (C:\Program Files\MiKTeX 2.7\bibtex\bib\bibtopic) and it appears in the
 dialogue box along with the others (examples that installed with Lyx).

 But, insertcitation does not show any references in my .bib, though the
 others do appear and can be inserted as citations and appear in the
 references at the end of the doc.

 There must be, at the very least,  a way to put the .bib files in the
 right directory manually?

 thnx,
 Casper de Tello




 --
 Erez Yerushalmi
 PhD Student
 Warwick University, UK
 homepage:
 http://www2.warwick.ac.uk/fac/soc/economics/research/phds/3rd_year/yerushalmi

 --
 We found the real 'Hotel California' and the 'Seinfeld' diner. What will
 you find? Explore 
 *WhereItsAt.com*http://www.whereitsat.com/?ncid=emlwenew0001
 .




-- 
Erez Yerushalmi
PhD Student
Warwick University, UK
homepage:
http://www2.warwick.ac.uk/fac/soc/economics/research/phds/3rd_year/yerushalmi

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[Erez Yerushalmi]

Hi Cas,

Sorry for not answering sooner, I'm away from computer for a week.

Zotero is great for collecting and managing my bibliography, but it is
really not made for bibtex export. I heard that others have the problem you
and I have.

I think Zotero is amazing, though!!

What I do is quite primitive, I must admit. I export zotero to bibtex, and
then import to Jabref, and clean up. But many times, it works without any
problem. You probably know that in Zotero, you can build a folder with all
the bibliography you want, and export that specific folder. So sometimes it
works. If LyX crashes, I import to Jabref and fix it until LyX works.
Primitive - I know.

Specifically, Zotero doesn't like the symbol ':'  in a title. If you have :
in a title, LyX's bibtex goes crazy and crashes. I don't know why.

There is also a plugin for Zotero and LyX called Lytero, but I think it
works only on Linux.
http://forums.zotero.org/discussion/6333/lytero-for-windows/

Best, Erez



On Mon, May 18, 2009 at 4:23 PM, <castelol...@aim.com> wrote:

>  Hi Erez
>
> You said "I use also zotero to collect the citations, and export it as
> bibtex file."
>
> The exported bibtex file does not appear to be fully compatible. A LyX (or
> MikTex?) dialogue with a host of errors is blocking me from either viewing
> or pdf-ing the document: 'missing $ inserted, extra } or forgotten $'
>
> What did I miss?
>
> /Cas
>
>  -Original Message-
> From: Erez Yerushalmi <erezyerusha...@gmail.com>
> To: castelol...@aim.com
>  Cc: lyx-users@lists.lyx.org
> Sent: Sun, 17 May 2009 2:57 pm
> Subject: Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7
>
>  Maybe this will help.
>
> A bib file is just a certain type of format, which can be saved in notepad.
> Jabref opens it up an shows it to you in an easiser way.  So,
>
> 1. In Jabref, you create bib file called mylib.bib. You can save it
> anywhere. So lets say you created a folder where your current lyx project is
> located. Save this bib file there.
>
> 2.Go to the place in your lyx document where you want the references to be
> presented (presumably, the end). Click Insert/ Lists & TOC/ BibT E X
> Bibliography. Point the LyX document to that specific file, by browsing for
> the mylib.bib file.
>
> 3. Click Lyx's Layout/Document setting, choose Bibliography. Here you
> specify the style of citations you want.
> 4. Now, suppose you are writing a document and you want to cite something.
> Click LyX insert/ Citation button. A menu should open and you should
> see the list of reference ,
>
> I use also zotero to collect the citations, and export it as bibtex file.
>
> Erez
>
> On Sun, May 17, 2009 at 2:31 AM, <castelol...@aim.com> wrote:
>
>> I just started using LyX 1.6 and JabRef 2.4 and I read here that you
>> cannot push refs from Jab into Lyx in windows xp.
>>
>> Here's the strange thing (coming from a beginner's perspective), I can
>> create a bibliography because there are .bib files already in the
>> appropriate MiKTeX 2.7 folder that appears to be supplying Lyx with its
>> database. I can also manually put my JabRef .bib into that same subdirectory
>> (C:\Program Files\MiKTeX 2.7\bibtex\bib\bibtopic) and it appears in the
>> dialogue box along with the others (examples that installed with Lyx).
>>
>> But, insert>citation does not show any references in my .bib, though the
>> others do appear and can be inserted as citations and appear in the
>> references at the end of the doc.
>>
>> There must be, at the very least,  a way to put the .bib files in the
>> right directory manually?
>>
>> thnx,
>> Casper de Tello
>>
>>
>
>
> --
> Erez Yerushalmi
> PhD Student
> Warwick University, UK
> homepage:
> http://www2.warwick.ac.uk/fac/soc/economics/research/phds/3rd_year/yerushalmi
>
> --
> We found the real 'Hotel California' and the 'Seinfeld' diner. What will
> you find? Explore 
> *WhereItsAt.com*<http://www.whereitsat.com/?ncid=emlwenew0001>
> .
>



-- 
Erez Yerushalmi
PhD Student
Warwick University, UK
homepage:
http://www2.warwick.ac.uk/fac/soc/economics/research/phds/3rd_year/yerushalmi

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[castelolxlx]

 Hi Erez 





You said I use also zotero to collect the citations, and export it as bibtex 
file.











The exported bibtex file does not appear to be fully compatible. A LyX (or 
MikTex?) dialogue with a host of errors is blocking me from either viewing or 
pdf-ing the document: 'missing $ inserted, extra } or forgotten $' 



What did I miss? 








 


/Cas








-Original Message-


From: Erez Yerushalmi erezyerusha...@gmail.com


To: castelol...@aim.com


Cc: lyx-users@lists.lyx.org


Sent: Sun, 17 May 2009 2:57 pm


Subject: Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7















Maybe this will help.


?


A bib file is just a certain type of format, which can be saved in notepad. 
Jabref opens it up an shows it to you in an easiser way.? So,


?


1. In Jabref, you create bib file called mylib.bib. You can save it anywhere. 
So lets say you created a folder where your current lyx project is located. 
Save this bib file there.



?


2.Go to the place in your lyx document where you want the references to be


presented (presumably, the end). Click Insert/ Lists  TOC/ BibT E X


Bibliography. Point the LyX document to that specific file, by browsing for the 
mylib.bib file.



?


3. Click Lyx's Layout/Document setting, choose Bibliography. Here you


specify the style of citations you want. 


4. Now, suppose you are writing a document and you want to cite something.


Click LyX insert/ Citation button. A menu should open and you should



see the list of reference , 


?


I use also zotero to collect the citations, and export it as bibtex file.? 


?


Erez









On Sun, May 17, 2009 at 2:31 AM, castelol...@aim.com wrote:




I just started using LyX 1.6 and JabRef 2.4 and I read here that you cannot 
push refs from Jab into Lyx in windows xp.






Here's the strange thing (coming from a beginner's perspective), I can create a 
bibliography because there are .bib files already in the appropriate MiKTeX 2.7 
folder that appears to be supplying Lyx with its database. I can also manually 
put my JabRef .bib into that same subdirectory (C:\Program Files\MiKTeX 
2.7\bibtex\bib\bibtopic) and it appears in the dialogue box along with the 
others (examples that installed with Lyx).






But, insertcitation does not show any references in my .bib, though the others 
do appear and can be inserted as citations and appear in the references at the 
end of the doc.





There must be, at the very least, ?a way to put the .bib files in the right 
directory manually?






thnx,


Casper de Tello























-- 


Erez Yerushalmi


PhD Student


Warwick University, UK


homepage: 
http://www2.warwick.ac.uk/fac/soc/economics/research/phds/3rd_year/yerushalmi







 

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[Paul A. Rubin]

castelol...@aim.com wrote:


The exported bibtex file does not appear to be fully compatible. A
LyX (or MikTex?) dialogue with a host of errors is blocking me from
either viewing or pdf-ing the document: 'missing $ inserted, extra }
or forgotten $'



Keep an eye out for underscores (_) in BibTeX entries -- I think it's 
possible for LaTeX to see them and think you're trying to enter a 
subscript, which makes it try to put you in math mode, which in turn 
causes assorted evils.  (Other symbols, such as carets (^), might also 
do this, but in my experience the culprit is usually an underscore.)


/Paul

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[castelolxlx]

 Hi Erez 





You said I use also zotero to collect the citations, and export it as bibtex 
file.











The exported bibtex file does not appear to be fully compatible. A LyX (or 
MikTex?) dialogue with a host of errors is blocking me from either viewing or 
pdf-ing the document: 'missing $ inserted, extra } or forgotten $' 



What did I miss? 








 


/Cas








-Original Message-


From: Erez Yerushalmi erezyerusha...@gmail.com


To: castelol...@aim.com


Cc: lyx-users@lists.lyx.org


Sent: Sun, 17 May 2009 2:57 pm


Subject: Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7















Maybe this will help.


?


A bib file is just a certain type of format, which can be saved in notepad. 
Jabref opens it up an shows it to you in an easiser way.? So,


?


1. In Jabref, you create bib file called mylib.bib. You can save it anywhere. 
So lets say you created a folder where your current lyx project is located. 
Save this bib file there.



?


2.Go to the place in your lyx document where you want the references to be


presented (presumably, the end). Click Insert/ Lists  TOC/ BibT E X


Bibliography. Point the LyX document to that specific file, by browsing for the 
mylib.bib file.



?


3. Click Lyx's Layout/Document setting, choose Bibliography. Here you


specify the style of citations you want. 


4. Now, suppose you are writing a document and you want to cite something.


Click LyX insert/ Citation button. A menu should open and you should



see the list of reference , 


?


I use also zotero to collect the citations, and export it as bibtex file.? 


?


Erez









On Sun, May 17, 2009 at 2:31 AM, castelol...@aim.com wrote:




I just started using LyX 1.6 and JabRef 2.4 and I read here that you cannot 
push refs from Jab into Lyx in windows xp.






Here's the strange thing (coming from a beginner's perspective), I can create a 
bibliography because there are .bib files already in the appropriate MiKTeX 2.7 
folder that appears to be supplying Lyx with its database. I can also manually 
put my JabRef .bib into that same subdirectory (C:\Program Files\MiKTeX 
2.7\bibtex\bib\bibtopic) and it appears in the dialogue box along with the 
others (examples that installed with Lyx).






But, insertcitation does not show any references in my .bib, though the others 
do appear and can be inserted as citations and appear in the references at the 
end of the doc.





There must be, at the very least, ?a way to put the .bib files in the right 
directory manually?






thnx,


Casper de Tello























-- 


Erez Yerushalmi


PhD Student


Warwick University, UK


homepage: 
http://www2.warwick.ac.uk/fac/soc/economics/research/phds/3rd_year/yerushalmi







 

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[Paul A. Rubin]

castelol...@aim.com wrote:


The exported bibtex file does not appear to be fully compatible. A
LyX (or MikTex?) dialogue with a host of errors is blocking me from
either viewing or pdf-ing the document: 'missing $ inserted, extra }
or forgotten $'



Keep an eye out for underscores (_) in BibTeX entries -- I think it's 
possible for LaTeX to see them and think you're trying to enter a 
subscript, which makes it try to put you in math mode, which in turn 
causes assorted evils.  (Other symbols, such as carets (^), might also 
do this, but in my experience the culprit is usually an underscore.)


/Paul

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[castelolxlx]

 Hi Erez 





You said "I use also zotero to collect the citations, and export it as bibtex 
file."











The exported bibtex file does not appear to be fully compatible. A LyX (or 
MikTex?) dialogue with a host of errors is blocking me from either viewing or 
pdf-ing the document: 'missing $ inserted, extra } or forgotten $' 



What did I miss? 








 


/Cas








-Original Message-


From: Erez Yerushalmi <erezyerusha...@gmail.com>


To: castelol...@aim.com


Cc: lyx-users@lists.lyx.org


Sent: Sun, 17 May 2009 2:57 pm


Subject: Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7















Maybe this will help.


?


A bib file is just a certain type of format, which can be saved in notepad. 
Jabref opens it up an shows it to you in an easiser way.? So,


?


1. In Jabref, you create bib file called mylib.bib. You can save it anywhere. 
So lets say you created a folder where your current lyx project is located. 
Save this bib file there.



?


2.Go to the place in your lyx document where you want the references to be


presented (presumably, the end). Click Insert/ Lists & TOC/ BibT E X


Bibliography. Point the LyX document to that specific file, by browsing for the 
mylib.bib file.



?


3. Click Lyx's Layout/Document setting, choose Bibliography. Here you


specify the style of citations you want. 


4. Now, suppose you are writing a document and you want to cite something.


Click LyX insert/ Citation button. A menu should open and you should



see the list of reference , 


?


I use also zotero to collect the citations, and export it as bibtex file.? 


?


Erez









On Sun, May 17, 2009 at 2:31 AM, <castelol...@aim.com> wrote:




I just started using LyX 1.6 and JabRef 2.4 and I read here that you cannot 
push refs from Jab into Lyx in windows xp.






Here's the strange thing (coming from a beginner's perspective), I can create a 
bibliography because there are .bib files already in the appropriate MiKTeX 2.7 
folder that appears to be supplying Lyx with its database. I can also manually 
put my JabRef .bib into that same subdirectory (C:\Program Files\MiKTeX 
2.7\bibtex\bib\bibtopic) and it appears in the dialogue box along with the 
others (examples that installed with Lyx).






But, insert>citation does not show any references in my .bib, though the others 
do appear and can be inserted as citations and appear in the references at the 
end of the doc.





There must be, at the very least, ?a way to put the .bib files in the right 
directory manually?






thnx,


Casper de Tello























-- 


Erez Yerushalmi


PhD Student


Warwick University, UK


homepage: 
http://www2.warwick.ac.uk/fac/soc/economics/research/phds/3rd_year/yerushalmi







 

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[Paul A. Rubin]

castelol...@aim.com wrote:


The exported bibtex file does not appear to be fully compatible. A
LyX (or MikTex?) dialogue with a host of errors is blocking me from
either viewing or pdf-ing the document: 'missing $ inserted, extra }
or forgotten $'



Keep an eye out for underscores (_) in BibTeX entries -- I think it's 
possible for LaTeX to see them and think you're trying to enter a 
subscript, which makes it try to put you in math mode, which in turn 
causes assorted evils.  (Other symbols, such as carets (^), might also 
do this, but in my experience the culprit is usually an underscore.)


/Paul

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[Erez Yerushalmi]

Maybe this will help.

A bib file is just a certain type of format, which can be saved in notepad.
Jabref opens it up an shows it to you in an easiser way.  So,

1. In Jabref, you create bib file called mylib.bib. You can save it
anywhere. So lets say you created a folder where your current lyx project is
located. Save this bib file there.

2.Go to the place in your lyx document where you want the references to be
presented (presumably, the end). Click Insert/ Lists  TOC/ BibT E X
Bibliography. Point the LyX document to that specific file, by browsing for
the mylib.bib file.

3. Click Lyx's Layout/Document setting, choose Bibliography. Here you
specify the style of citations you want.
4. Now, suppose you are writing a document and you want to cite something.
Click LyX insert/ Citation button. A menu should open and you should
see the list of reference ,

I use also zotero to collect the citations, and export it as bibtex file.

Erez

On Sun, May 17, 2009 at 2:31 AM, castelol...@aim.com wrote:

 I just started using LyX 1.6 and JabRef 2.4 and I read here that you cannot
 push refs from Jab into Lyx in windows xp.

 Here's the strange thing (coming from a beginner's perspective), I can
 create a bibliography because there are .bib files already in the
 appropriate MiKTeX 2.7 folder that appears to be supplying Lyx with its
 database. I can also manually put my JabRef .bib into that same subdirectory
 (C:\Program Files\MiKTeX 2.7\bibtex\bib\bibtopic) and it appears in the
 dialogue box along with the others (examples that installed with Lyx).

 But, insertcitation does not show any references in my .bib, though the
 others do appear and can be inserted as citations and appear in the
 references at the end of the doc.

 There must be, at the very least,  a way to put the .bib files in the right
 directory manually?

 thnx,
 Casper de Tello




-- 
Erez Yerushalmi
PhD Student
Warwick University, UK
homepage:
http://www2.warwick.ac.uk/fac/soc/economics/research/phds/3rd_year/yerushalmi

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[Paul A. Rubin]

castelol...@aim.com wrote:

I just started using LyX 1.6 and JabRef 2.4 and I read here that you
cannot push refs from Jab into Lyx in windows xp.


Correct.


Here's the strange thing (coming from a beginner's perspective), I
can create a bibliography because there are .bib files already in the
appropriate MiKTeX 2.7 folder that appears to be supplying Lyx with
its database. I can also manually put my JabRef .bib into that same
subdirectory (C:\Program Files\MiKTeX 2.7\bibtex\bib\bibtopic) and it
appears in the dialogue box along with the others (examples that
installed with Lyx).


pick nitTechnically, they installed with MiKTeX; LyX is not 
responsible for them./pick nit


But, insertcitation does not show any references in my .bib, though
the others do appear and can be inserted as citations and appear in
the references at the end of the doc.


Confirmed.  To fix this, you have to run the MiKTeX Settings 
application, click the Refresh FNDB button (FNDB = file name 
database), then restart LyX.  In general, dropping a file somewhere in 
MiKTeX's directory does not make MiKTeX aware of it; you have to refresh 
the file name database to let MiKTeX know it's there.  (The same is true 
for all LaTeX distributions, by the way.)  The curious thing here is 
that LyX apparently relies on MiKTeX to find the .bib file when looking 
for its contents, but not when listing it in the bibliography insertion 
dialog.  Quoting Emerson: A foolish consistency is the hobgoblin of 
little minds ...


In any event, this is not the preferred way to access your own BibTeX 
files (see below).


There must be, at the very least,  a way to put the .bib files in the
right directory manually?


The right directory is wherever your .bib files would normally live 
(typically but not necessarily somewhere in the vast morass of My 
Documents).  In the bibliography insertion dialog, click Add...  
Browse..., drill down to your .bib file (which can be anywhere), then 
click Add.


/Paul

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[Uwe Stöhr]

castelol...@aim.com schrieb:


I just started using LyX 1.6 and JabRef 2.4 and I read here that you cannot 
push refs from Jab into Lyx in windows xp.


Yes and there's also no need to.


Here's the strange thing (coming from a beginner's perspective), I can create a 
bibliography

 because there are .bib files already in the appropriate MiKTeX 2.7
 folder that appears to be supplying Lyx with its database.
LyX just takes this folder as default folder to look for BibTeX files, but you can store your BibTeX 
file wherever you want.


 I can also manually put my JabRef .bib into that same subdirectory
 (C:\Program Files\MiKTeX 2.7\bibtex\bib\bibtopic)

I recommend not to do this, to keep your MiKTeX installation unchanged and to 
avoid possible problems.


But, insertcitation does not show any references in my .bib, though the others 
do appear and can be inserted as citations and appear in the references at the end 
of the doc.

There must be, at the very least,  a way to put the .bib files in the right 
directory manually?


I guess you haven't loaded your BibTeX file in your LyX document. How this is done is explained in 
LyX's User's Guide that you find in LyX's Help menu. If you still have problems, look for example at 
the file achemso.lyx that you find in LyX's examples folder to see how there the BibTeX file 
biblioExample.bib is loaded.


regards Uwe

Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7

[castelolxlx]

 Thx to you and Erez, for your comments.

Great to know there's support for newbies when needed : )



 /Cas




-Original Message-
From: Uwe Stöhr uwesto...@web.de
To: castelol...@aim.com
Cc: lyx-users@lists.lyx.org
Sent: Sun, 17 May 2009 5:32 pm
Subject: Re: JabRef and LyX, manually putting .bib files into MiKTeX 2.7









castelol...@aim.com schrieb: 
 

 I just started using LyX 1.6 and JabRef 2.4 and I read here that you cannot 
 push refs from Jab into Lyx in windows xp. 
 

Yes and there's also no need to. 
 

 Here's the strange thing (coming from a beginner's perspective), I can create 
 a bibliography 

  because there are .bib files already in the appropriate MiKTeX 2.7 

  folder that appears to be supplying Lyx with its database. 

LyX just takes this folder as default folder to look for BibTeX files, but you 
can store your BibTeX
file wherever you want. 
 

  I can also manually put my JabRef .bib into that same subdirectory 

  (C:\Program Files\MiKTeX 2.7\bibtex\bib\bibtopic) 
 

I recommend not to do this, to keep your MiKTeX installation unchanged and to 
avoid possible problems. 
 

 But, insertcitation does not show any references in my .bib, though the 
 others do appear and can be inserted as citations and appear in the 
 references at the end of the doc. 


 There must be, at the very least,  a way to put the .bib files in the right 
 directory
 manually? 
 

I guess you haven't loaded your BibTeX file in your LyX document. How this is 
done is explained in
LyX's User's Guide that you find in LyX's Help menu. If you still have 
problems, look for example at
the file achemso.lyx that you find in LyX's examples folder to see how there 
the BibTeX file
biblioExample.bib is loaded. 
 

regards Uwe