Zotero to Bibtex to Lyx: A Problem not a baseball play.

[John Kane]

Sorry for the last part of the subject line but I am sure that there is some 
famous song (or something about a triple play. Perhaps I should have lunch.

I have been having great fun using Zotero to grab a lot of references lately 
and wanted to use the results in a LyX file.  I selected a subset of references 
that I wanted to use and exported them to Bibtex.

I do not seem to be able to get the exported Bibtex file to work.

I can load it, select a citation and insert it.  However when I compile, I get 
(?) if using Natbib and Author Year or [?] if using default and plainnat.  I've 
fooled around with a couple of other settings (forgotten now) with the same 
results.

I can remove the Bibtex file, add a new (home-grown ) file and everything works 
fine.  

The Bibtex file under Jabref looks reasonable but some of the keys look very 
strange in LyX itself.  I seem to be getting some files with  which may 
just mean that some of the pdf or web sites are not dated.

My OS is MS XP Home and I am using LyX 1.6.5 with Jabref 2.5 as my Bibtex 
editor.

I had a quick look at the Zotero forums with no luck and thought that I'd ask 
here first before learning how to navigate them.

Any suggestions?   

Thanks.






  __
Looking for the perfect gift? Give the gift of Flickr! 

http://www.flickr.com/gift/

Re: Zotero to Bibtex to Lyx: A Problem not a baseball play.

[Pierfranco Minsenti]

Hi John,

I use a lot both Zotero and LyX but my workflow consists in never using
bibtex files directly exported from Zotero. Instead (for several reasons and
not because of the problems you mention) I always export from Zotero to
BibDesk (an application similar to JabRef, but only available for Mac OS X)
and then I use from LyX the .bib file generated by BibDesk. This always
works very well.

So, I could only try to give you the following 2 different suggestions:

1) 1st suggested solution: export from Zotero to JabRef and then use the
JabRef file in conjunction with LyX
OR:
2) 2nd suggested solution: try to use the .bib file generated by Zotero but
when you export this file from Zotero don't check the UTF8 option

As to the fact that sometimes the key of some records in the .bib file
generated by Zotero has 4 ? this is due to the fact that Zotero, when
exports records in the bibtex format, automatically creates the bibtex key
for each records following this convention:
lastname1stauthor_1stwordoftitle_publication year.
When the publication year field is empty, Zotero adds 4 ? at the end of the
bibtex key created as explained above.

Hope this can be useful.

Best wishes

pierfranco



2009/12/27 John Kane jrkrid...@yahoo.ca

 Sorry for the last part of the subject line but I am sure that there is
 some famous song (or something about a triple play. Perhaps I should have
 lunch.

 I have been having great fun using Zotero to grab a lot of references
 lately and wanted to use the results in a LyX file.  I selected a subset of
 references that I wanted to use and exported them to Bibtex.

 I do not seem to be able to get the exported Bibtex file to work.

 I can load it, select a citation and insert it.  However when I compile, I
 get (?) if using Natbib and Author Year or [?] if using default and
 plainnat.  I've fooled around with a couple of other settings (forgotten
 now) with the same results.

 I can remove the Bibtex file, add a new (home-grown ) file and everything
 works fine.

 The Bibtex file under Jabref looks reasonable but some of the keys look
 very strange in LyX itself.  I seem to be getting some files with  which
 may just mean that some of the pdf or web sites are not dated.

 My OS is MS XP Home and I am using LyX 1.6.5 with Jabref 2.5 as my Bibtex
 editor.

 I had a quick look at the Zotero forums with no luck and thought that I'd
 ask here first before learning how to navigate them.

 Any suggestions?

 Thanks.






  __
 Looking for the perfect gift? Give the gift of Flickr!

 http://www.flickr.com/gift/

Re: Zotero to Bibtex to Lyx: A Problem not a baseball play.

[rgheck]

On 12/27/2009 01:29 PM, John Kane wrote:

Sorry for the last part of the subject line but I am sure that there is some 
famous song (or something about a triple play. Perhaps I should have lunch.

I have been having great fun using Zotero to grab a lot of references lately 
and wanted to use the results in a LyX file.  I selected a subset of references 
that I wanted to use and exported them to Bibtex.

I do not seem to be able to get the exported Bibtex file to work.

I can load it, select a citation and insert it.  However when I compile, I get 
(?) if using Natbib and Author Year or [?] if using default and plainnat.  I've 
fooled around with a couple of other settings (forgotten now) with the same 
results.

   

Most likely problem is some encoding error. BibTeX does not handle Unicode.

rh

Fwd: Get Footnotes to appear on the same page when exporting to HTML?

[jf7]

Update to my previous message about italics footnotes when exported to  
html with htlatex, (please see that message -- too much to  
re-quote here):


I've upgraded LyX to 1.6.5 (that's 1.6.7 to you Paul Sutton ;-) and  
TexShop to 2.29 and the problems mentioned persist.


jamie faunt
---BeginMessage---


Yes there is a way to get your html footnotes on the same page. If  
you're using htlatex / tex4ht the converter line for latex-html is:


htlatex $$i xhtml,fn-in

Took me ages to find that fn-in parameter. The documentation of  
htlatex is pretty cryptic. But it works if you don't mind...


The problem with it which I haven't been able to solve is that the  
footnotes come out in italics. :-( But at least they're on the same  
page.


To get rid of the italics edit the .css file and find the  
div.footnotes line and get rid of the font-style: italic;


If you don't mind that extra hassle the results are perfect.

Oddly, when htlatex is run (from the command line rather than from  
LyX-export) on the same latex file it does not add the italics to the  
footnotes but just nicely puts them in-line where they should be.


I've searched and searched every shred of documentation I could find  
to find a parameter that would put the footnotes in normal text. But  
apparently it's not in the htlatex utility itself but in something  
that happens with the LyX export.


Since the utility itself does not have this problem, it seems like a  
bug in the exporting in LyX. But I'm not reporting it as a bug yet  
because I'm using LyX 1.6.2. (Crossing my fingers that 1.6.5 doesn't  
continue the problem.)


The other html converter I've used with LyX is tth.  It's very good.  
Does the footnotes as you'd expect. The problem with it though is it  
won't do tables of contents and will only work with encapsulated  
postscript graphic files. (.eps) -- no .png, .jpg or any others.


The other oddity which the author says is not needed is that it  
doesn't generate head and body tags unless you include a 'w1'  
parameter. But that solves it fine. The converter command line is:


tth -w1 $$i

(or omit the -w1 if you don't care about the head and body tags)

The documentation for tth is far easier. And the program is reliable  
if its short-comings don't affect you. There's a free version for  
non-commercial use.


Despite the cryptic documentation and a now deceased author, htlatex  
works great except for the italics with in-line footnotes -- which  
I've found is a LyX -- not htlatex problem.


If this has been fixed, or if there's a solution, I'd sure like to know.

I'd also need a way to add a body - margin line either in .css or the  
.html file without having to enter them manually. That may be too much  
to wish for. But if anyone knows how, I'd really appreciate knowing  
that too!  (I know the syntax for both html and css -- just need to  
know if there's a way to generate one or the other with export.)


Anyway, I hope the above is helpful.

jamie faunt


Quoting Yaron Y. Goland ya...@goland.org:
The articles I create with LyX are destined for my blog and form a  
single piece of HTML. But when I export to HTML any footnotes I have  
get generated on a separate HTML page. Is there anyway to configure  
the HTML exporter so that it will generate the footnotes at the end of  
the main HTML page and then use anchors to navigate to them?

Thanks,
Yaron
DeleteReply Forward RedirectView ThreadBlacklistWhitelistMessage  
SourceResumeSave asPrintHeaders



---End Message---

Re: Fwd: Get Footnotes to appear on the same page when exporting to HTML?

[rgheck]

On 12/27/2009 03:54 PM, j...@musicalskills.com wrote:


Update to my previous message about italics footnotes when exported to 
html with htlatex, (please see that message -- too much to 
re-quote here):


I've upgraded LyX to 1.6.5 (that's 1.6.7 to you Paul Sutton ;-) and 
TexShop to 2.29 and the problems mentioned persist.


That's likely because none of that upgraded htlatex. I don't know if 
that is a known bug or not. I've heard that htlatex is not under active 
development now, though.


rh

RE: Zotero to Bibtex to Lyx: A Problem not a baseball play

[Rob Oakes]

Hi John,

By default, Zotero produces atrocious looking BibTeX.  By far the ugliest
offenders, as you have noticed, are in the citation keys.  It uses weird
character encodings (I'm frankly not even sure what they are), that can't be
processed by LaTeX.  When these characters appear, the only way I've been
able to get things to work is by manually redefining the citation keys.  Of
course, this must be done after every export.  (A tremendous and
non-productive pain.)

The best solution I've found is to not use Zotero for BibTeX.  But since I
love using Zotero to collect citations and references from the web, this
poses a problem.

Luckily, I've managed to rig an acceptable alternative using a reference
manager called Mendeley as an intermediary.  You can configure Mendeley so
that it will sync with the Zotero database.  Any updates to Zotero will
automatically be reflected in Mendeley.  (Unfortunately, reverse sync is not
supported, so changes made in Mendeley won't appear in Zotero.)

Mendeley, unlike Zotero, can create clean BibTeX with custom citation keys.
Therefore, while Zotero BibTeX won't work with LyX, I've had no problems
with Mendeley BibTeX.  I've been using it for two papers and a book I'm
working on.

Another nice feature is the automatic creation of BibTeX database files.  If
you set this up, then the creation of your BibTeX is completely automatic.
Whenever you add a new citation to Zotero, it will show up in your BibTeX
database automatically via Mendeley.

I've been using Mendeley for a couple of months, and though it's still in
beta it's pretty stable (or it has been since the 0.9.5.2 update at least).
There were a few problems specific to Ubuntu Linux, but those appear to have
been sorted out.

Additionally Mendeley makes it very easy to organize and sync your reference
library to multiple machines.  Zotero can do something similar, but I've
found Mendeley easier to use.

You can find more information on their web site:

http://www.mendeley.com/

Cheers,

Rob Oakes

Re: Zotero to Bibtex to Lyx: A Problem not a baseball play

[Pavel Sanda]

Rob Oakes wrote:
 able to get things to work is by manually redefining the citation keys.  Of
 course, this must be done after every export.  (A tremendous and
 non-productive pain.)

btw thats part of bug http://www.lyx.org/trac/ticket/6300 .
we only need somebody to actually do it ;)
pavel

LyZ: LyX plugin for Zotero

[Petr Šimon]

Hello,
I have put together a simple plugin for Zotero that does little more 
than just inserting citations to LyX documents. It's been inspired by 
Lytero, which I wanted to improve, but ended up starting from scratch 
(with some help of Lytero code). Hence the new name.


My ideal for LyX/Zotero plugin was:
1. no need to export to bibtex every time I added articles to Zotero
2. automatic updates of the bibtex database
3. no need to specify the document and bibtex file every time I close 
Zotero or LyX

4. custom keys

Hope others will find it useful.
Please see: http://www.klubko.net/?page_id=945 for details and the 
installation file.
I have tested only on Windows XP, Firefox 3.5.6. It seems to be working 
quite smoothly, but more testing and some improvement will follow. 
Please let me know about any problems you encounter and 
comments/improvement ideas.


Petr

Re: LyZ: LyX plugin for Zotero

[Steve Litt]

On Monday 28 December 2009 01:26:04 Petr Šimon wrote:
 Hello,
 I have put together a simple plugin for Zotero that does little more
 than just inserting citations to LyX documents. It's been inspired by
 Lytero, which I wanted to improve, but ended up starting from scratch
 (with some help of Lytero code). Hence the new name.
 
 My ideal for LyX/Zotero plugin was:
 1. no need to export to bibtex every time I added articles to Zotero
 2. automatic updates of the bibtex database
 3. no need to specify the document and bibtex file every time I close
 Zotero or LyX
 4. custom keys
 
 Hope others will find it useful.
 Please see: http://www.klubko.net/?page_id=945 for details and the
 installation file.
 I have tested only on Windows XP, Firefox 3.5.6. It seems to be working
 quite smoothly, but more testing and some improvement will follow.
 Please let me know about any problems you encounter and
 comments/improvement ideas.

Hi Petr,

I know nothing about citations. I've used bibliographies in a couple books, 
but that's about it. So it would be a great favor to me (and I'm probably not 
the only one) if you could explain a little about Reference Management 
Software, why you want it, what you do with it, what you look for in the 
Reference Management Software best suited to you?

What's the difference between citations, references and bibliographies?

Assuming citations are individual elements of bibliographies, could you please 
explain why Zotero makes adding and maintaining them easier than doing it with 
bibtex or whatever is normally used in LyX?

Also, your website has this line: When you try to add already existing BibTeX 
database to a new document, you will be warned that you are about to overwrite 
the file. Don’t worry and press OK. The file is not really going to be 
overwritten, that’s just standard dialog that I don’t know how to remove (lazy 
to look :) ).

Normally I don't care about errors in new software, but this is a particularly 
nasty error because it will either: 1) cause people not to use your software, 
or 2) cause people to disregard your software's overwrite warnings, even when 
it's really true. #1 is bad, #2 is disastrous. I'd suggest you find and fix 
that one bug.

Thanks

SteveT

Steve Litt
Recession Relief Package
http://www.recession-relief.US
Twitter: http://www.twitter.com/stevelitt

Zotero to Bibtex to Lyx: A Problem not a baseball play.

[John Kane]

Sorry for the last part of the subject line but I am sure that there is some 
famous song (or something about a triple play. Perhaps I should have lunch.

I have been having great fun using Zotero to grab a lot of references lately 
and wanted to use the results in a LyX file.  I selected a subset of references 
that I wanted to use and exported them to Bibtex.

I do not seem to be able to get the exported Bibtex file to work.

I can load it, select a citation and insert it.  However when I compile, I get 
(?) if using Natbib and Author Year or [?] if using default and plainnat.  I've 
fooled around with a couple of other settings (forgotten now) with the same 
results.

I can remove the Bibtex file, add a new (home-grown ) file and everything works 
fine.  

The Bibtex file under Jabref looks reasonable but some of the keys look very 
strange in LyX itself.  I seem to be getting some files with  which may 
just mean that some of the pdf or web sites are not dated.

My OS is MS XP Home and I am using LyX 1.6.5 with Jabref 2.5 as my Bibtex 
editor.

I had a quick look at the Zotero forums with no luck and thought that I'd ask 
here first before learning how to navigate them.

Any suggestions?   

Thanks.






  __
Looking for the perfect gift? Give the gift of Flickr! 

http://www.flickr.com/gift/

Re: Zotero to Bibtex to Lyx: A Problem not a baseball play.

[Pierfranco Minsenti]

Hi John,

I use a lot both Zotero and LyX but my workflow consists in never using
bibtex files directly exported from Zotero. Instead (for several reasons and
not because of the problems you mention) I always export from Zotero to
BibDesk (an application similar to JabRef, but only available for Mac OS X)
and then I use from LyX the .bib file generated by BibDesk. This always
works very well.

So, I could only try to give you the following 2 different suggestions:

1) 1st suggested solution: export from Zotero to JabRef and then use the
JabRef file in conjunction with LyX
OR:
2) 2nd suggested solution: try to use the .bib file generated by Zotero but
when you export this file from Zotero don't check the UTF8 option

As to the fact that sometimes the key of some records in the .bib file
generated by Zotero has 4 ? this is due to the fact that Zotero, when
exports records in the bibtex format, automatically creates the bibtex key
for each records following this convention:
lastname1stauthor_1stwordoftitle_publication year.
When the publication year field is empty, Zotero adds 4 ? at the end of the
bibtex key created as explained above.

Hope this can be useful.

Best wishes

pierfranco



2009/12/27 John Kane jrkrid...@yahoo.ca

 Sorry for the last part of the subject line but I am sure that there is
 some famous song (or something about a triple play. Perhaps I should have
 lunch.

 I have been having great fun using Zotero to grab a lot of references
 lately and wanted to use the results in a LyX file.  I selected a subset of
 references that I wanted to use and exported them to Bibtex.

 I do not seem to be able to get the exported Bibtex file to work.

 I can load it, select a citation and insert it.  However when I compile, I
 get (?) if using Natbib and Author Year or [?] if using default and
 plainnat.  I've fooled around with a couple of other settings (forgotten
 now) with the same results.

 I can remove the Bibtex file, add a new (home-grown ) file and everything
 works fine.

 The Bibtex file under Jabref looks reasonable but some of the keys look
 very strange in LyX itself.  I seem to be getting some files with  which
 may just mean that some of the pdf or web sites are not dated.

 My OS is MS XP Home and I am using LyX 1.6.5 with Jabref 2.5 as my Bibtex
 editor.

 I had a quick look at the Zotero forums with no luck and thought that I'd
 ask here first before learning how to navigate them.

 Any suggestions?

 Thanks.






  __
 Looking for the perfect gift? Give the gift of Flickr!

 http://www.flickr.com/gift/

Re: Zotero to Bibtex to Lyx: A Problem not a baseball play.

[rgheck]

On 12/27/2009 01:29 PM, John Kane wrote:

Sorry for the last part of the subject line but I am sure that there is some 
famous song (or something about a triple play. Perhaps I should have lunch.

I have been having great fun using Zotero to grab a lot of references lately 
and wanted to use the results in a LyX file.  I selected a subset of references 
that I wanted to use and exported them to Bibtex.

I do not seem to be able to get the exported Bibtex file to work.

I can load it, select a citation and insert it.  However when I compile, I get 
(?) if using Natbib and Author Year or [?] if using default and plainnat.  I've 
fooled around with a couple of other settings (forgotten now) with the same 
results.

   

Most likely problem is some encoding error. BibTeX does not handle Unicode.

rh

Fwd: Get Footnotes to appear on the same page when exporting to HTML?

[jf7]

Update to my previous message about italics footnotes when exported to  
html with htlatex, (please see that message -- too much to  
re-quote here):


I've upgraded LyX to 1.6.5 (that's 1.6.7 to you Paul Sutton ;-) and  
TexShop to 2.29 and the problems mentioned persist.


jamie faunt
---BeginMessage---


Yes there is a way to get your html footnotes on the same page. If  
you're using htlatex / tex4ht the converter line for latex-html is:


htlatex $$i xhtml,fn-in

Took me ages to find that fn-in parameter. The documentation of  
htlatex is pretty cryptic. But it works if you don't mind...


The problem with it which I haven't been able to solve is that the  
footnotes come out in italics. :-( But at least they're on the same  
page.


To get rid of the italics edit the .css file and find the  
div.footnotes line and get rid of the font-style: italic;


If you don't mind that extra hassle the results are perfect.

Oddly, when htlatex is run (from the command line rather than from  
LyX-export) on the same latex file it does not add the italics to the  
footnotes but just nicely puts them in-line where they should be.


I've searched and searched every shred of documentation I could find  
to find a parameter that would put the footnotes in normal text. But  
apparently it's not in the htlatex utility itself but in something  
that happens with the LyX export.


Since the utility itself does not have this problem, it seems like a  
bug in the exporting in LyX. But I'm not reporting it as a bug yet  
because I'm using LyX 1.6.2. (Crossing my fingers that 1.6.5 doesn't  
continue the problem.)


The other html converter I've used with LyX is tth.  It's very good.  
Does the footnotes as you'd expect. The problem with it though is it  
won't do tables of contents and will only work with encapsulated  
postscript graphic files. (.eps) -- no .png, .jpg or any others.


The other oddity which the author says is not needed is that it  
doesn't generate head and body tags unless you include a 'w1'  
parameter. But that solves it fine. The converter command line is:


tth -w1 $$i

(or omit the -w1 if you don't care about the head and body tags)

The documentation for tth is far easier. And the program is reliable  
if its short-comings don't affect you. There's a free version for  
non-commercial use.


Despite the cryptic documentation and a now deceased author, htlatex  
works great except for the italics with in-line footnotes -- which  
I've found is a LyX -- not htlatex problem.


If this has been fixed, or if there's a solution, I'd sure like to know.

I'd also need a way to add a body - margin line either in .css or the  
.html file without having to enter them manually. That may be too much  
to wish for. But if anyone knows how, I'd really appreciate knowing  
that too!  (I know the syntax for both html and css -- just need to  
know if there's a way to generate one or the other with export.)


Anyway, I hope the above is helpful.

jamie faunt


Quoting Yaron Y. Goland ya...@goland.org:
The articles I create with LyX are destined for my blog and form a  
single piece of HTML. But when I export to HTML any footnotes I have  
get generated on a separate HTML page. Is there anyway to configure  
the HTML exporter so that it will generate the footnotes at the end of  
the main HTML page and then use anchors to navigate to them?

Thanks,
Yaron
DeleteReply Forward RedirectView ThreadBlacklistWhitelistMessage  
SourceResumeSave asPrintHeaders



---End Message---

Re: Fwd: Get Footnotes to appear on the same page when exporting to HTML?

[rgheck]

On 12/27/2009 03:54 PM, j...@musicalskills.com wrote:


Update to my previous message about italics footnotes when exported to 
html with htlatex, (please see that message -- too much to 
re-quote here):


I've upgraded LyX to 1.6.5 (that's 1.6.7 to you Paul Sutton ;-) and 
TexShop to 2.29 and the problems mentioned persist.


That's likely because none of that upgraded htlatex. I don't know if 
that is a known bug or not. I've heard that htlatex is not under active 
development now, though.


rh

RE: Zotero to Bibtex to Lyx: A Problem not a baseball play

[Rob Oakes]

Hi John,

By default, Zotero produces atrocious looking BibTeX.  By far the ugliest
offenders, as you have noticed, are in the citation keys.  It uses weird
character encodings (I'm frankly not even sure what they are), that can't be
processed by LaTeX.  When these characters appear, the only way I've been
able to get things to work is by manually redefining the citation keys.  Of
course, this must be done after every export.  (A tremendous and
non-productive pain.)

The best solution I've found is to not use Zotero for BibTeX.  But since I
love using Zotero to collect citations and references from the web, this
poses a problem.

Luckily, I've managed to rig an acceptable alternative using a reference
manager called Mendeley as an intermediary.  You can configure Mendeley so
that it will sync with the Zotero database.  Any updates to Zotero will
automatically be reflected in Mendeley.  (Unfortunately, reverse sync is not
supported, so changes made in Mendeley won't appear in Zotero.)

Mendeley, unlike Zotero, can create clean BibTeX with custom citation keys.
Therefore, while Zotero BibTeX won't work with LyX, I've had no problems
with Mendeley BibTeX.  I've been using it for two papers and a book I'm
working on.

Another nice feature is the automatic creation of BibTeX database files.  If
you set this up, then the creation of your BibTeX is completely automatic.
Whenever you add a new citation to Zotero, it will show up in your BibTeX
database automatically via Mendeley.

I've been using Mendeley for a couple of months, and though it's still in
beta it's pretty stable (or it has been since the 0.9.5.2 update at least).
There were a few problems specific to Ubuntu Linux, but those appear to have
been sorted out.

Additionally Mendeley makes it very easy to organize and sync your reference
library to multiple machines.  Zotero can do something similar, but I've
found Mendeley easier to use.

You can find more information on their web site:

http://www.mendeley.com/

Cheers,

Rob Oakes

Re: Zotero to Bibtex to Lyx: A Problem not a baseball play

[Pavel Sanda]

Rob Oakes wrote:
 able to get things to work is by manually redefining the citation keys.  Of
 course, this must be done after every export.  (A tremendous and
 non-productive pain.)

btw thats part of bug http://www.lyx.org/trac/ticket/6300 .
we only need somebody to actually do it ;)
pavel

LyZ: LyX plugin for Zotero

[Petr Šimon]

Hello,
I have put together a simple plugin for Zotero that does little more 
than just inserting citations to LyX documents. It's been inspired by 
Lytero, which I wanted to improve, but ended up starting from scratch 
(with some help of Lytero code). Hence the new name.


My ideal for LyX/Zotero plugin was:
1. no need to export to bibtex every time I added articles to Zotero
2. automatic updates of the bibtex database
3. no need to specify the document and bibtex file every time I close 
Zotero or LyX

4. custom keys

Hope others will find it useful.
Please see: http://www.klubko.net/?page_id=945 for details and the 
installation file.
I have tested only on Windows XP, Firefox 3.5.6. It seems to be working 
quite smoothly, but more testing and some improvement will follow. 
Please let me know about any problems you encounter and 
comments/improvement ideas.


Petr

Re: LyZ: LyX plugin for Zotero

[Steve Litt]

On Monday 28 December 2009 01:26:04 Petr Šimon wrote:
 Hello,
 I have put together a simple plugin for Zotero that does little more
 than just inserting citations to LyX documents. It's been inspired by
 Lytero, which I wanted to improve, but ended up starting from scratch
 (with some help of Lytero code). Hence the new name.
 
 My ideal for LyX/Zotero plugin was:
 1. no need to export to bibtex every time I added articles to Zotero
 2. automatic updates of the bibtex database
 3. no need to specify the document and bibtex file every time I close
 Zotero or LyX
 4. custom keys
 
 Hope others will find it useful.
 Please see: http://www.klubko.net/?page_id=945 for details and the
 installation file.
 I have tested only on Windows XP, Firefox 3.5.6. It seems to be working
 quite smoothly, but more testing and some improvement will follow.
 Please let me know about any problems you encounter and
 comments/improvement ideas.

Hi Petr,

I know nothing about citations. I've used bibliographies in a couple books, 
but that's about it. So it would be a great favor to me (and I'm probably not 
the only one) if you could explain a little about Reference Management 
Software, why you want it, what you do with it, what you look for in the 
Reference Management Software best suited to you?

What's the difference between citations, references and bibliographies?

Assuming citations are individual elements of bibliographies, could you please 
explain why Zotero makes adding and maintaining them easier than doing it with 
bibtex or whatever is normally used in LyX?

Also, your website has this line: When you try to add already existing BibTeX 
database to a new document, you will be warned that you are about to overwrite 
the file. Don’t worry and press OK. The file is not really going to be 
overwritten, that’s just standard dialog that I don’t know how to remove (lazy 
to look :) ).

Normally I don't care about errors in new software, but this is a particularly 
nasty error because it will either: 1) cause people not to use your software, 
or 2) cause people to disregard your software's overwrite warnings, even when 
it's really true. #1 is bad, #2 is disastrous. I'd suggest you find and fix 
that one bug.

Thanks

SteveT

Steve Litt
Recession Relief Package
http://www.recession-relief.US
Twitter: http://www.twitter.com/stevelitt

Zotero to Bibtex to Lyx: A Problem not a baseball play.

[John Kane]

Sorry for the last part of the subject line but I am sure that there is some 
famous song (or something about a triple play. Perhaps I should have lunch.

I have been having great fun using Zotero to grab a lot of references lately 
and wanted to use the results in a LyX file.  I selected a subset of references 
that I wanted to use and exported them to Bibtex.

I do not seem to be able to get the exported Bibtex file to work.

I can load it, select a citation and insert it.  However when I compile, I get 
(?) if using Natbib and Author Year or [?] if using default and plainnat.  I've 
fooled around with a couple of other settings (forgotten now) with the same 
results.

I can remove the Bibtex file, add a new (home-grown ) file and everything works 
fine.  

The Bibtex file under Jabref looks reasonable but some of the keys look very 
strange in LyX itself.  I seem to be getting some files with  which may 
just mean that some of the pdf or web sites are not dated.

My OS is MS XP Home and I am using LyX 1.6.5 with Jabref 2.5 as my Bibtex 
editor.

I had a quick look at the Zotero forums with no luck and thought that I'd ask 
here first before learning how to navigate them.

Any suggestions?   

Thanks.






  __
Looking for the perfect gift? Give the gift of Flickr! 

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Re: Zotero to Bibtex to Lyx: A Problem not a baseball play.

[Pierfranco Minsenti]

Hi John,

I use a lot both Zotero and LyX but my workflow consists in never using
bibtex files directly exported from Zotero. Instead (for several reasons and
not because of the problems you mention) I always export from Zotero to
BibDesk (an application similar to JabRef, but only available for Mac OS X)
and then I use from LyX the .bib file generated by BibDesk. This always
works very well.

So, I could only try to give you the following 2 different suggestions:

1) 1st suggested solution: export from Zotero to JabRef and then use the
JabRef file in conjunction with LyX
OR:
2) 2nd suggested solution: try to use the .bib file generated by Zotero but
when you export this file from Zotero don't check the UTF8 option

As to the fact that sometimes the key of some records in the .bib file
generated by Zotero has 4 ? this is due to the fact that Zotero, when
exports records in the bibtex format, automatically creates the bibtex key
for each records following this convention:
lastname1stauthor_1stwordoftitle_publication year.
When the publication year field is empty, Zotero adds 4 ? at the end of the
bibtex key created as explained above.

Hope this can be useful.

Best wishes

pierfranco



2009/12/27 John Kane 

> Sorry for the last part of the subject line but I am sure that there is
> some famous song (or something about a triple play. Perhaps I should have
> lunch.
>
> I have been having great fun using Zotero to grab a lot of references
> lately and wanted to use the results in a LyX file.  I selected a subset of
> references that I wanted to use and exported them to Bibtex.
>
> I do not seem to be able to get the exported Bibtex file to work.
>
> I can load it, select a citation and insert it.  However when I compile, I
> get (?) if using Natbib and Author Year or [?] if using default and
> plainnat.  I've fooled around with a couple of other settings (forgotten
> now) with the same results.
>
> I can remove the Bibtex file, add a new (home-grown ) file and everything
> works fine.
>
> The Bibtex file under Jabref looks reasonable but some of the keys look
> very strange in LyX itself.  I seem to be getting some files with  which
> may just mean that some of the pdf or web sites are not dated.
>
> My OS is MS XP Home and I am using LyX 1.6.5 with Jabref 2.5 as my Bibtex
> editor.
>
> I had a quick look at the Zotero forums with no luck and thought that I'd
> ask here first before learning how to navigate them.
>
> Any suggestions?
>
> Thanks.
>
>
>
>
>
>
>  __
> Looking for the perfect gift? Give the gift of Flickr!
>
> http://www.flickr.com/gift/
>

Re: Zotero to Bibtex to Lyx: A Problem not a baseball play.

[rgheck]

On 12/27/2009 01:29 PM, John Kane wrote:

Sorry for the last part of the subject line but I am sure that there is some 
famous song (or something about a triple play. Perhaps I should have lunch.

I have been having great fun using Zotero to grab a lot of references lately 
and wanted to use the results in a LyX file.  I selected a subset of references 
that I wanted to use and exported them to Bibtex.

I do not seem to be able to get the exported Bibtex file to work.

I can load it, select a citation and insert it.  However when I compile, I get 
(?) if using Natbib and Author Year or [?] if using default and plainnat.  I've 
fooled around with a couple of other settings (forgotten now) with the same 
results.

   

Most likely problem is some encoding error. BibTeX does not handle Unicode.

rh

Fwd: Get Footnotes to appear on the same page when exporting to HTML?

[jf7]

Update to my previous message about italics footnotes when exported to  
html with htlatex, (please see that message -- too much to  
re-quote here):


I've upgraded LyX to 1.6.5 (that's 1.6.7 to you Paul Sutton ;-) and  
TexShop to 2.29 and the problems mentioned persist.


jamie faunt
--- Begin Message ---


Yes there is a way to get your html footnotes on the same page. If  
you're using htlatex / tex4ht the converter line for latex->html is:


htlatex $$i "xhtml,fn-in"

Took me ages to find that "fn-in" parameter. The documentation of  
htlatex is pretty cryptic. But it works if you don't mind...


The problem with it which I haven't been able to solve is that the  
footnotes come out in italics. :-( But at least they're on the same  
page.


To get rid of the italics edit the .css file and find the  
div.footnotes line and get rid of the "font-style: italic;"


If you don't mind that extra hassle the results are perfect.

Oddly, when htlatex is run (from the command line rather than from  
LyX-export) on the same latex file it does not add the italics to the  
footnotes but just nicely puts them in-line where they should be.


I've searched and searched every shred of documentation I could find  
to find a parameter that would put the footnotes in normal text. But  
apparently it's not in the htlatex utility itself but in something  
that happens with the LyX export.


Since the utility itself does not have this problem, it seems like a  
bug in the exporting in LyX. But I'm not reporting it as a bug yet  
because I'm using LyX 1.6.2. (Crossing my fingers that 1.6.5 doesn't  
continue the problem.)


The other html converter I've used with LyX is tth.  It's very good.  
Does the footnotes as you'd expect. The problem with it though is it  
won't do tables of contents and will only work with encapsulated  
postscript graphic files. (.eps) -- no .png, .jpg or any others.


The other oddity which the author says is not needed is that it  
doesn't generate head and body tags unless you include a 'w1'  
parameter. But that solves it fine. The converter command line is:


tth -w1 $$i

(or omit the -w1 if you don't care about the head and body tags)

The documentation for tth is far easier. And the program is reliable  
if its short-comings don't affect you. There's a free version for  
non-commercial use.


Despite the cryptic documentation and a now deceased author, htlatex  
works great except for the italics with in-line footnotes -- which  
I've found is a LyX -- not htlatex problem.


If this has been fixed, or if there's a solution, I'd sure like to know.

I'd also need a way to add a body - margin line either in .css or the  
.html file without having to enter them manually. That may be too much  
to wish for. But if anyone knows how, I'd really appreciate knowing  
that too!  (I know the syntax for both html and css -- just need to  
know if there's a way to generate one or the other with export.)


Anyway, I hope the above is helpful.

jamie faunt


Quoting "Yaron Y. Goland" :
The articles I create with LyX are destined for my blog and form a  
single piece of HTML. But when I export to HTML any footnotes I have  
get generated on a separate HTML page. Is there anyway to configure  
the HTML exporter so that it will generate the footnotes at the end of  
the main HTML page and then use anchors to navigate to them?

Thanks,
Yaron
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--- End Message ---

Re: Fwd: Get Footnotes to appear on the same page when exporting to HTML?

[rgheck]

On 12/27/2009 03:54 PM, j...@musicalskills.com wrote:


Update to my previous message about italics footnotes when exported to 
html with htlatex, (please see that message -- too much to 
re-quote here):


I've upgraded LyX to 1.6.5 (that's 1.6.7 to you Paul Sutton ;-) and 
TexShop to 2.29 and the problems mentioned persist.


That's likely because none of that upgraded htlatex. I don't know if 
that is a known bug or not. I've heard that htlatex is not under active 
development now, though.


rh

RE: Zotero to Bibtex to Lyx: A Problem not a baseball play

[Rob Oakes]

Hi John,

By default, Zotero produces atrocious looking BibTeX.  By far the ugliest
offenders, as you have noticed, are in the citation keys.  It uses weird
character encodings (I'm frankly not even sure what they are), that can't be
processed by LaTeX.  When these characters appear, the only way I've been
able to get things to work is by manually redefining the citation keys.  Of
course, this must be done after every export.  (A tremendous and
non-productive pain.)

The best solution I've found is to not use Zotero for BibTeX.  But since I
love using Zotero to collect citations and references from the web, this
poses a problem.

Luckily, I've managed to rig an acceptable alternative using a reference
manager called Mendeley as an intermediary.  You can configure Mendeley so
that it will sync with the Zotero database.  Any updates to Zotero will
automatically be reflected in Mendeley.  (Unfortunately, reverse sync is not
supported, so changes made in Mendeley won't appear in Zotero.)

Mendeley, unlike Zotero, can create clean BibTeX with custom citation keys.
Therefore, while Zotero BibTeX won't work with LyX, I've had no problems
with Mendeley BibTeX.  I've been using it for two papers and a book I'm
working on.

Another nice feature is the automatic creation of BibTeX database files.  If
you set this up, then the creation of your BibTeX is completely automatic.
Whenever you add a new citation to Zotero, it will show up in your BibTeX
database automatically via Mendeley.

I've been using Mendeley for a couple of months, and though it's still in
beta it's pretty stable (or it has been since the 0.9.5.2 update at least).
There were a few problems specific to Ubuntu Linux, but those appear to have
been sorted out.

Additionally Mendeley makes it very easy to organize and sync your reference
library to multiple machines.  Zotero can do something similar, but I've
found Mendeley easier to use.

You can find more information on their web site:

http://www.mendeley.com/

Cheers,

Rob Oakes

Re: Zotero to Bibtex to Lyx: A Problem not a baseball play

[Pavel Sanda]

Rob Oakes wrote:
> able to get things to work is by manually redefining the citation keys.  Of
> course, this must be done after every export.  (A tremendous and
> non-productive pain.)

btw thats part of bug http://www.lyx.org/trac/ticket/6300 .
we only need somebody to actually do it ;)
pavel

LyZ: LyX plugin for Zotero

[Petr Šimon]

Hello,
I have put together a simple plugin for Zotero that does little more 
than just inserting citations to LyX documents. It's been inspired by 
Lytero, which I wanted to improve, but ended up starting from scratch 
(with some help of Lytero code). Hence the new name.


My ideal for LyX/Zotero plugin was:
1. no need to export to bibtex every time I added articles to Zotero
2. automatic updates of the bibtex database
3. no need to specify the document and bibtex file every time I close 
Zotero or LyX

4. custom keys

Hope others will find it useful.
Please see: http://www.klubko.net/?page_id=945 for details and the 
installation file.
I have tested only on Windows XP, Firefox 3.5.6. It seems to be working 
quite smoothly, but more testing and some improvement will follow. 
Please let me know about any problems you encounter and 
comments/improvement ideas.


Petr

Re: LyZ: LyX plugin for Zotero

[Steve Litt]

On Monday 28 December 2009 01:26:04 Petr Šimon wrote:
> Hello,
> I have put together a simple plugin for Zotero that does little more
> than just inserting citations to LyX documents. It's been inspired by
> Lytero, which I wanted to improve, but ended up starting from scratch
> (with some help of Lytero code). Hence the new name.
> 
> My ideal for LyX/Zotero plugin was:
> 1. no need to export to bibtex every time I added articles to Zotero
> 2. automatic updates of the bibtex database
> 3. no need to specify the document and bibtex file every time I close
> Zotero or LyX
> 4. custom keys
> 
> Hope others will find it useful.
> Please see: http://www.klubko.net/?page_id=945 for details and the
> installation file.
> I have tested only on Windows XP, Firefox 3.5.6. It seems to be working
> quite smoothly, but more testing and some improvement will follow.
> Please let me know about any problems you encounter and
> comments/improvement ideas.

Hi Petr,

I know nothing about citations. I've used bibliographies in a couple books, 
but that's about it. So it would be a great favor to me (and I'm probably not 
the only one) if you could explain a little about Reference Management 
Software, why you want it, what you do with it, what you look for in the 
Reference Management Software best suited to you?

What's the difference between citations, references and bibliographies?

Assuming citations are individual elements of bibliographies, could you please 
explain why Zotero makes adding and maintaining them easier than doing it with 
bibtex or whatever is normally used in LyX?

Also, your website has this line: "When you try to add already existing BibTeX 
database to a new document, you will be warned that you are about to overwrite 
the file. Don’t worry and press OK. The file is not really going to be 
overwritten, that’s just standard dialog that I don’t know how to remove (lazy 
to look :) )."

Normally I don't care about errors in new software, but this is a particularly 
nasty error because it will either: 1) cause people not to use your software, 
or 2) cause people to disregard your software's overwrite warnings, even when 
it's really true. #1 is bad, #2 is disastrous. I'd suggest you find and fix 
that one bug.

Thanks

SteveT

Steve Litt
Recession Relief Package
http://www.recession-relief.US
Twitter: http://www.twitter.com/stevelitt