Re: [O] bibliography as part of the source document?

[John Kitchin]

You might checkout the function at the end of this org-ref issue:
https://github.com/jkitchin/org-ref/issues/176

It provides a way to extract all bibtex src blocks to a file and is a
bit different than using org-babel-tangle.

Ken Mankoff writes:

> On 2016-06-14 at 21:29, Ken Mankoff  wrote:
>> I don't know how to tell Org to tangle-on-export with an argument or a
>> setting, but it can evaluate code blocks on export, and one of those
>> can do the tangling for you. The following might work?
>>
>> #+begin_src emacs-lisp :exports none
>>   (org-babel-goto-named-src-block "bibtex")
>>   (org-babel-tangle)
>> #+end_src
>>
>> #+begin_src bibtex :tangle file.bib
>> bib contents go here
>> #+end_src
>
> Oops. Consider the above pseudo-code. The bibtex block must be named, so that 
> (org-babel-goto-NAMED...) can find it. And I'm not sure what "#+begin_src 
> bibtex" actually means to Org. It might have to be a #+BEGIN_EXAMPLE or a 
> "#+BEGIN_SRC ", but tangled to a .Bib file. If running 
> latest Git head, it might also need ":eval no-export" on the bibtex block. 
> Hopefully this is enough to help you solve it. Feel free to post an MWE if 
> you get it working.
>
>   -k.


-- 
Professor John Kitchin
Doherty Hall A207F
Department of Chemical Engineering
Carnegie Mellon University
Pittsburgh, PA 15213
412-268-7803
@johnkitchin
http://kitchingroup.cheme.cmu.edu

Re: [O] bibliography as part of the source document?

[Ken Mankoff]

On 2016-06-14 at 21:29, Ken Mankoff  wrote:
> I don't know how to tell Org to tangle-on-export with an argument or a
> setting, but it can evaluate code blocks on export, and one of those
> can do the tangling for you. The following might work?
>
> #+begin_src emacs-lisp :exports none
>   (org-babel-goto-named-src-block "bibtex")
>   (org-babel-tangle)
> #+end_src
>
> #+begin_src bibtex :tangle file.bib
> bib contents go here
> #+end_src

Oops. Consider the above pseudo-code. The bibtex block must be named, so that 
(org-babel-goto-NAMED...) can find it. And I'm not sure what "#+begin_src 
bibtex" actually means to Org. It might have to be a #+BEGIN_EXAMPLE or a 
"#+BEGIN_SRC ", but tangled to a .Bib file. If running 
latest Git head, it might also need ":eval no-export" on the bibtex block. 
Hopefully this is enough to help you solve it. Feel free to post an MWE if you 
get it working.

  -k.

Re: [O] bibliography as part of the source document?

[Ken Mankoff]

On 2016-06-13 at 13:28, Sharon Kimble  wrote:
> Ken Mankoff  writes:
>> On 2016-06-13 at 13:07, Sharon Kimble  wrote:
>>> I'm trying to have all my information for a org-mode document
>>> exported to latex contained within the source document. Specifically
>>> having the bibliography within the source document.
>>>
>>> But how do I do it? I've tried googling but haven't turned up
>>> anything useful. Can you help please?
>>
>> What about putting the BibTeX contents in the Org file. Tangle on
>> export to Bib file.
>>
>
> Yes, that's what I'm trying to do, but how do I tangle it?

I don't know how to tell Org to tangle-on-export with an argument or a setting, 
but it can evaluate code blocks on export, and one of those can do the tangling 
for you. The following might work? 

#+begin_src emacs-lisp :exports none
  (org-babel-goto-named-src-block "bibtex")
  (org-babel-tangle)
#+end_src

#+begin_src bibtex :tangle file.bib
bib contents go here
#+end_src

  -k.

Re: [O] bibliography as part of the source document?

[Sharon Kimble]

Ken Mankoff  writes:

> On 2016-06-13 at 13:07, Sharon Kimble  wrote:
>> I'm trying to have all my information for a org-mode document exported
>> to latex contained within the source document. Specifically having the
>> bibliography within the source document.
>>
>> But how do I do it? I've tried googling but haven't turned up anything
>> useful. Can you help please?
>
> What about putting the BibTeX contents in the Org file. Tangle on export to 
> Bib file.
>

Yes, that's what I'm trying to do, but how do I tangle it?

Thanks
Sharon.
-- 
A taste of linux = http://www.sharons.org.uk
TGmeds = http://www.tgmeds.org.uk
Debian 8.4, fluxbox 1.3.7, emacs 25.0.95


signature.asc
Description: PGP signature

Re: [O] bibliography as part of the source document?

[Ken Mankoff]

On 2016-06-13 at 13:07, Sharon Kimble  wrote:
> I'm trying to have all my information for a org-mode document exported
> to latex contained within the source document. Specifically having the
> bibliography within the source document.
>
> But how do I do it? I've tried googling but haven't turned up anything
> useful. Can you help please?

What about putting the BibTeX contents in the Org file. Tangle on export to Bib 
file.

  -k.

Re: [O] #+BIBLIOGRAPHY multiple entries

[Andreas Kiermeier]

Hi Johnny,

​
On 24 November 2014 at 08:08, yggdra...@gmx.co.uk wrote:

 I use
 #+BIBLIOGRAPHY mybibliographyfile plain
 which works, but
 #+BIBLIOGRAPHY myfirstbibliographyfile mysecondbibliographyfile plain
 does not.


Instead of #+BIBLIOGRAPHY I tend to use

#+LATEX: \bibliographystyle{plainnat}
#+LATEX: \bibliography{C:/Users/andreas/Dropbox/_biblio/refs}

were all my bibtex entries are in refs.bib. I keep everything in the one
place and hence need to use the full path.

You can put these where you want the bibliography placed and you can
include multiple files in LaTeX' \bibliography{} command.

In your case I imagine it would look something like this.

#+LATEX: \bibliographystyle{plainnat}
#+LATEX: \bibliography{C:/Users/andreas/Dropbox/_biblio/refs}

HTH.

Cheers,

Andreas​

Re: [O] Bibliography woes!

[Rainer M Krug]

Ken Mankoff mank...@gmail.com writes:

 On 2014-05-05 at 19:39, John Hendy wrote:
 If this works, someone can chime in regarding how to modify Org so
 that it will run the necessary biber/biblatex commands so you don't
 have to jump to a command line every time. Or perhaps that's a one
 time thing -- maybe as long as biber generates the .bbl file, you can
 refer to anything you want in that file from then on?

 I've found latexmk to be the best tool for compiling LaTeX
 documents. It runs all necessary commands as many times as needed,
 including pdflatex, bibtex, biblatex, etc.. It is fairly smart and will
 run the command to make the index if you load the index, for example. 

 It can run in daemon mode and monitor the included files (and graphics)
 so if one of those changes, the PDF is regenerated.

 I prefer daemon mode, so I bring up a terminal and run latexmk file.tex
 in the folder where I'm working on file.org. This also speeds things up,
 since exporting to latex is fast, but compiling is slow. I can export
 and still use emacs, rather than waiting for the compile to finish.

This sounds very interesting. Could you please provide some details on
how you use latexmk? Do you use any special options?

Rainer


 But if you want to run latexmk from Org, that works too. The -pvc-
 turns off the preview continuous mode (daemon).

 (setq org-latex-pdf-process (list /usr/texbin/latexmk -f -gg -pvc- %f))

   -k.


-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :   +33 - (0)9 53 10 27 44
Cell:   +33 - (0)6 85 62 59 98
Fax :   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug

PGP: 0x0F52F982


pgpO2hoF39fia.pgp
Description: PGP signature

Re: [O] Bibliography woes!

[Ken Mankoff]

On 2014-05-06 at 03:33, Rainer M Krug wrote:
 Ken Mankoff mank...@gmail.com writes:
 I've found latexmk to be the best tool for compiling LaTeX
 documents.

 This sounds very interesting. Could you please provide some details on
 how you use latexmk? Do you use any special options?

My ~/.latexmkrc file is below. It appears I have extra functions for
making glossaries and working with PythonTeX. There is plenty of support
for latexmk on TeX.SE
https://tex.stackexchange.com/questions/tagged/latexmk

Since I turn on preview_continuous_mode in my ~/.latexmkrc, I need to
explicitly turn it off if I am calling latexmk from Org, hence the
-pvc- option here:

(setq org-latex-pdf-process (list /usr/texbin/latexmk -f -gg -pvc- %f))

But as I said, I find I prefer to bring up a terminal in the directory
where I am working, and dedicate it to running 'latexmk' in continuous
monitoring mode. When I want to clean up a project I'll run latexmk -c
file.tex to discard all of the temporary files. I have Skim.app or
Preview.app (OS X PDF viewers) open the PDF file. I edit Org files,
export to LaTeX (C-c C-e l l), and then keep working while the PDF
regenerates. 

  -k.



# BEGIN ~/.latexmkrc

$pdf_mode = 1;
$preview_continuous_mode = 1;
$new_viewer_always = 1;
$silent = 1; # don't stop on errors
$verbose = 0;
#$halt_on_error = 1;

$clean_ext = 'bbl run.xml %R-blx.bib acn glo xdy synctex.gz';

# continue past errors
$force_mode = 1; 
$shell_escape = 1;

# shell escape
$pdflatex = 'pdflatex --shell-escape -file-line-error -synctex=1 %O %S';

# $pdf_previewer = 'open -a /Applications/Preview.app';
$pdf_previewer = 'open -a /Users/mankoff/local/Applications/Skim.app';

# Sage:
# http://permalink.gmane.org/gmane.comp.mathematics.sage.support/17166

# glossaries 
http://tex.stackexchange.com/questions/1226/how-to-make-latexmk-use-makeglossaries
add_cus_dep('glo', 'gls', 0, 'makeglo2gls');
sub makeglo2gls {
system(makeindex -s '$_[0]'.ist -t '$_[0]'.glg -o '$_[0]'.gls 
'$_[0]'.glo);
}

# PythonTeX
add_cus_dep('pytxcode', 'pyg', 0, 'pythontexcompile');
sub pythontexcompile {
system(pythontex.py $_[0]);
}

Re: [O] Bibliography woes!

[Rainer M Krug]

Ken Mankoff mank...@gmail.com writes:

 On 2014-05-06 at 03:33, Rainer M Krug wrote:
 Ken Mankoff mank...@gmail.com writes:
 I've found latexmk to be the best tool for compiling LaTeX
 documents.

 This sounds very interesting. Could you please provide some details on
 how you use latexmk? Do you use any special options?

 My ~/.latexmkrc file is below. It appears I have extra functions for
 making glossaries and working with PythonTeX. There is plenty of support
 for latexmk on TeX.SE
 https://tex.stackexchange.com/questions/tagged/latexmk

 Since I turn on preview_continuous_mode in my ~/.latexmkrc, I need to
 explicitly turn it off if I am calling latexmk from Org, hence the
 -pvc- option here:

 (setq org-latex-pdf-process (list /usr/texbin/latexmk -f -gg -pvc- %f))

 But as I said, I find I prefer to bring up a terminal in the directory
 where I am working, and dedicate it to running 'latexmk' in continuous
 monitoring mode. When I want to clean up a project I'll run latexmk -c
 file.tex to discard all of the temporary files. I have Skim.app or
 Preview.app (OS X PDF viewers) open the PDF file. I edit Org files,
 export to LaTeX (C-c C-e l l), and then keep working while the PDF
 regenerates. 

Thanks a lot - this gives me some ideas on how to use it. I also prefer
the terminal approach, and I am using it at the moment, but with no
additional parameters.

Cheers,

Rainer


   -k.



 # BEGIN ~/.latexmkrc

 $pdf_mode = 1;
 $preview_continuous_mode = 1;
 $new_viewer_always = 1;
 $silent = 1;   # don't stop on errors
 $verbose = 0;
 #$halt_on_error = 1;

 $clean_ext = 'bbl run.xml %R-blx.bib acn glo xdy synctex.gz';

 # continue past errors
 $force_mode = 1; 
 $shell_escape = 1;

 # shell escape
 $pdflatex = 'pdflatex --shell-escape -file-line-error -synctex=1 %O %S';

 # $pdf_previewer = 'open -a /Applications/Preview.app';
 $pdf_previewer = 'open -a /Users/mankoff/local/Applications/Skim.app';

 # Sage:
 # http://permalink.gmane.org/gmane.comp.mathematics.sage.support/17166

 # glossaries 
 http://tex.stackexchange.com/questions/1226/how-to-make-latexmk-use-makeglossaries
 add_cus_dep('glo', 'gls', 0, 'makeglo2gls');
 sub makeglo2gls {
 system(makeindex -s '$_[0]'.ist -t '$_[0]'.glg -o '$_[0]'.gls 
 '$_[0]'.glo);
 }

 # PythonTeX
 add_cus_dep('pytxcode', 'pyg', 0, 'pythontexcompile');
 sub pythontexcompile {
 system(pythontex.py $_[0]);
 }



-- 
Rainer M. Krug, PhD (Conservation Ecology, SUN), MSc (Conservation Biology, 
UCT), Dipl. Phys. (Germany)

Centre of Excellence for Invasion Biology
Stellenbosch University
South Africa

Tel :   +33 - (0)9 53 10 27 44
Cell:   +33 - (0)6 85 62 59 98
Fax :   +33 - (0)9 58 10 27 44

Fax (D):+49 - (0)3 21 21 25 22 44

email:  rai...@krugs.de

Skype:  RMkrug

PGP: 0x0F52F982


pgp7ZOH9UdIFy.pgp
Description: PGP signature

Re: [O] Bibliography woes! SOLVED.

[Sharon Kimble]

John.
Thank you for a most informative and useful post. Using your method
I've just created the cat.org with 14 bibliographic records! I've
amended it slightly, which I'll document in line. 

John Hendy jw.he...@gmail.com writes:

 On Mon, May 5, 2014 at 5:23 PM, Sharon Kimble
 boudic...@skimble.plus.com wrote:
 Eric S Fraga e.fr...@ucl.ac.uk writes:


 [...]


 and this is the bibliography file
 @Article{,

 change this line to

   @Article{1,

 although I would recommend a more description label personally...

 I've set it up with the articles author and year, but it is still
 failing. I'm attaching the original org file, the generated tex and
 pdf, and the bib file. Hopefully this will help find a solution?

 I've been following this from a distance, as I'm interested in
 eventually getting into this. I would kindly ask that you slow down
 your pace, check things over, and proceed *simply* to solve your
 problem. Eric advocated using @Article{1, ...

 Without ever having used biblatex, I immediately wondered whether a
 comma delimited bibliography would tolerate:

 @Article{MacRae K, et al;2002, ...

 The answer is that it will not. You also have multiple lines loading
 the same package:

 #+LaTeX_HEADER: \usepackage{biblatex}
 #+LATEX_HEADER:
 \usepackage[citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex}
 # #+LaTeX_HEADER: \usepackage[backend=bibtex,style=verbose]{biblatex}

 Lastly, I would highly suggest limiting your requests for help to
 extremely simple examples. For example, remove packages that do not
 affect the behavior of the problem, such as bussproofs, babel,
 fancyhdr, etc.

 I was able to get your file working via the following method:

 - Modified cat.bib:

 @Article{1,
   author = {MacRae K. Pattison J.},
   title = {Home chemotherapy.},
   journaltitle = {Nursing Times},
   year = {2002},
   key = {1},
   volume = {98},
   number = {35},
   pages = {34-35},
 }

 - Modified/shortened/simplified cat.org:

 # -*- mode:org; mode:reftex; indent-tabs-mode:nil; tab-width:2 -*-
 #+OPTIONS: toc:nil num:nil ^:{}
 #+TITLE: Cat on the mat - 2014
 #+AUTHOR: Sharon Kimble  Sarah ?
 #+LATEX_CLASS: article
 #+LATEX_CLASS_OPTIONS: [a4paper]
 #+LaTeX_HEADER: 
 \usepackage[backend=biber,style=verbose,style=numeric]{biblatex}
 #+LaTeX_HEADER: \bibliography{/home/jwhendy/Downloads/cat.bib} %%% -
 change this path
 #+LaTeX_HEADER: \bibliography{cat


 * Chapter 1
 Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy
 nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat.\cite{1}

 * Bibliography
 \printbibliography

 Note that you needed to load biblatex before your bibliography (which
 you sort of did, but then re-loaded it with a bunch of options and
 then perhaps again at the end depending on how Org deals with the #
 symbol before #+ lines. You can tweak the options to biblatex however
 you'd like; I just simplified a bit to single down to one line loading
 it.

 \bibliography needed to call the file cat, not bibliography.

 In addition, I had to run C-c C-e l p to export to latex, then check
 the buffer *Org PDF LaTeX Output* for messages regarding the failed
 citation. It suggested to run biber on the file cat, which I did from
 the command line.

When you add references to cat.bib you have to run C-c C-e l p
again to generate cat.blg.

 # note that I saved all your stuff in my download folder
 $ cd ~/Downloads
 $ biber cat

 Make sure you have the biber executable installed. I didn't know
 anything about it and thought biblatex might provide it. I had to
 explicitly install biber. You should be a path as the response to the
 following if you have it:

 $ which biber

 Running biber generated .bbl.

Then run biber cat on the command line to generate cat.bbl. Then
you can run C-c C-e l p on cat.org which generates cat.pdf
which includes the bibliography! Yahay! Success! 

 Then, re-running C-c C-e l p from Org works for me (at least I think;
 see attached to verify).

 Lastly, when I encountered an error, I googled to find out what to do:
 - Using biber: http://tex.stackexchange.com/questions/26516/how-to-use-biber
 - Why \bibliography was giving me an error:
 http://kb.mit.edu/confluence/pages/viewpage.action?pageId=3907111

 If this works, someone can chime in regarding how to modify Org so
 that it will run the necessary biber/biblatex commands so you don't
 have to jump to a command line every time. Or perhaps that's a one
 time thing -- maybe as long as biber generates the .bbl file, you can
 refer to anything you want in that file from then on?

If you have this in your .emacs
--8---cut here---start-8---
;; org to latex customisations, -shell-escape needed for minted
(setq org-export-dispatch-use-expert-ui t ; non-intrusive export dispatch
  org-latex-pdf-process ; for regular export
  '(xelatex -shell-escape 

Re: [O] Bibliography woes!

[Vikas Rawal]

 I'm having no success in getting the bibliography to display in my
 document, so these are my relevant settings -
 ╭
 │#+LaTeX_HEADER: \usepackage{biblatex}
 │#+LaTeX_HEADER: 
 \bibliography{/home/boudiccas/.emacs.d/research/references.bib}
 │#+LaTeX_HEADER: \bibliography{references}
 ╰


Although I cannot be sure, it seems to me that the problem may be that biblatex 
is not looking for references.bib in the right place.

I had similar trouble when I started using citations (then with bibtex).  I 
then solved it by create a link to the bib file in the working directory, and 
continue to use that solution for everything I write.

In your working directory, where you org file is, just create a symbolic link:

ln -s /home/boudiccas/.emacs.d/research/references.bib references.bib

If my diagnosis is correct, that should solve the problem.

Vikas

Re: [O] Bibliography woes!

[Leonard Avery Randall]

Hi,

Sharon Kimble wrote:



But page 3 of what? input line 139 of what?



Page 3 of the PDF and input line 139 of the .tex file.



It all looks okay to me, except I cant see what the latex warnings
relate to. Any ideas folks please?



The most likely problem is that you have you have not called bibtex (or 
biber) the appropriate number of times and so your references have not 
been processed correctly. The way to check this is to run bibtex or 
biber (whichever you use, your setup looks like it was designed for 
bibtex so bibtex is probably the one you want) on your .tex file and 
then call xelatex again, and see if the errors go away. If that is the 
problem. You should look at how you have set up org-latex-pdf-process to 
make sure that it calls xelatex and bibtex the appropriate number of 
times. (another option is to use latexmk, it is really convenient, but 
it takes a bit of work to configure it properly).


All best,
Leonard

Re: [O] Bibliography woes!

[Sharon Kimble]

Leonard Avery Randall leonard.a.rand...@gmail.com writes:

 Hi,

 Sharon Kimble wrote:

 But page 3 of what? input line 139 of what? 
 

 Page 3 of the PDF and input line 139 of the .tex file. 

 It all looks okay to me, except I cant see what the latex warnings
 relate to. Any ideas folks please?
 

 The most likely problem is that you have you have not called bibtex
 (or biber) the appropriate number of times and so your references have
 not been processed correctly. The way to check this is to run bibtex
 or biber (whichever you use, your setup looks like it was designed for
 bibtex so bibtex is probably the one you want) on your .tex file and
 then call xelatex again, and see if the errors go away. If that is the
 problem. You should look at how you have set up org-latex-pdf-process
 to make sure that it calls xelatex and bibtex the appropriate number
 of times. (another option is to use latexmk, it is really convenient,
 but it takes a bit of work to configure it properly).

Still not getting it right. This is in my setup-testbed.el
--8---cut here---start-8---
;; org to latex customisations, -shell-escape needed for minted
(setq org-export-dispatch-use-expert-ui t ; non-intrusive export dispatch
  org-latex-pdf-process ; for regular export
  '(xelatex -shell-escape -interaction nonstopmode -output-directory %o %f
bibtex %b
xelatex -shell-escape -interaction nonstopmode 
-output-directory %o %f
xelatex -shell-escape -interaction nonstopmode -output-directory %o %f
xelatex -shell-escape -interaction nonstopmode -output-directory %o %f
xelatex -shell-escape -interaction nonstopmode -output-directory %o 
%f))
--8---cut here---end---8---
and the partial transcript of the output log
--8---cut here---start-8---
LaTeX Warning: Citation '4' on page 3 undefined on input line 135.

LaTeX Warning: Citation '5' on page 3 undefined on input line 137.

LaTeX Warning: Citation '4' on page 3 undefined on input line 145.

LaTeX Warning: Citation '6' on page 3 undefined on input line 154.

LaTeX Warning: Citation '7' on page 4 undefined on input line 167.

LaTeX Warning: Citation '8' on page 4 undefined on input line 175.

LaTeX Warning: Citation '12' on page 4 undefined on input line 204.

LaTeX Warning: Citation '7' on page 4 undefined on input line 209.

LaTeX Warning: Citation '9' on page 4 undefined on input line 222.

LaTeX Warning: Citation '1' on page 5 undefined on input line 259.

LaTeX Warning: Citation '3' on page 6 undefined on input line 285.

LaTeX Warning: Citation '10' on page 7 undefined on input line 349.

LaTeX Warning: Citation '10' on page 7 undefined on input line 400.

LaTeX Warning: Citation '13' on page 9 undefined on input line 458.

LaTeX Warning: Citation '11' on page 9 undefined on input line 475.

LaTeX Warning: Citation '14' on page 9 undefined on input line 495.

LaTeX Warning: Citation '14' on page 10 undefined on input line 527.

LaTeX Warning: Citation '2' on page 11 undefined on input line 569.

LaTeX Warning: Empty bibliography on input line 576.

[11] (./uh2014.aux)

LaTeX Warning: There were undefined references.

Package biblatex Warning: Please (re)run Biber on the file:
(biblatex)uh2014
(biblatex)and rerun LaTeX afterwards.
--8---cut here---end---8---

and in my org-mode file I have these headers
--8---cut here---start-8---
#+LaTeX_HEADER: \usepackage{biblatex}
#+LaTeX_HEADER: \usepackage[backend=biber,style=verbose]{biblatex}
#+LaTeX_HEADER: \bibliography{/home/boudiccas/.emacs.d/research/references.bib}
#+LaTeX_HEADER: \bibliography{references}
--8---cut here---end---8---

I have created the link to the reference file in my
$USER/.emacs.d/org/ directory using this command
╭
│ln -s /home/boudiccas/.emacs.d/research/references.bib references.bib
╰

Any ideas please folks, or some code to try please?

Thanks
Sharon.
-- 
A taste of linux = http://www.sharons.org.uk
my git repo = https://bitbucket.org/boudiccas/dots
TGmeds = http://www.tgmeds.org.uk
Debian testing, Fluxbox 1.3.5, emacs 24.4.50.19


signature.asc
Description: PGP signature

Re: [O] Bibliography woes!

[Vikas Rawal]

 
 Any ideas please folks, or some code to try please?
 


I use

#+LATEX_HEADER: 
\usepackage[citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex}

Can you try this, and if it works, modify as you prefer.

Also, as Leonard suggested, I would create a tex file, and work on it from the 
terminal to see what is wrong.

Compile the tex file, run biber and then compile the tex file again. This would 
help identify what is wrong.

Vikas

Re: [O] Bibliography woes!

[Leonard Avery Randall]

Hi Sharon,
Your setup seems to only call bibtex once. I find that with biblatex 
this is usually not enough to resolve references. I would call bibtex a 
second time after the second run of biblatex.

All best,
Leonard

Re: [O] Bibliography woes!

[Sharon Kimble]

Vikas Rawal vikasli...@agrarianresearch.org writes:

 
 Any ideas please folks, or some code to try please?
 
 

 I use

 #+LATEX_HEADER: \usepackage
 [citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex}

 Can you try this, and if it works, modify as you prefer.

 Also, as Leonard suggested, I would create a tex file, and work on it
 from the terminal to see what is wrong.

 Compile the tex file, run biber and then compile the tex file again.
 This would help identify what is wrong.

How do I do it from the command-line please? Using what commands? I
can do it from inside org-mode, and I've created a test file and bib
references, details now. 

This is the test file
--8---cut here---start-8---
# -*- mode:org; mode:reftex; indent-tabs-mode:nil; tab-width:2 -*-
#+OPTIONS: toc:nil num:nil
#+OPTIONS: ^:{}
#+TITLE: Cat on the mat - 2014
#+AUTHOR: Sharon Kimble  Sarah ?
#+LATEX_CLASS: article
#+LATEX_CLASS_OPTIONS: [a4paper]
#+LATEX_HEADER: \usepackage 
[citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex}
# #+LATEX_HEADER: \usepackage[hyperref,x11names]{xcolor}
# #+LATEX_HEADER: \usepackage[colorlinks=true]{hyperref}
#+LaTeX_HEADER: \usepackage{bussproofs}
#+LaTeX_HEADER: \usepackage{amsmath,amssymb,amsopn}
#+LaTeX_HEADER: \usepackage{graphicx}
#+LaTeX_HEADER: \usepackage{makeidx} %robustindex % Indexing
#+LaTeX_HEADER: \usepackage[british]{babel} % For british english hyphenation 
patterns
#+LaTeX_HEADER: \usepackage{fancyhdr} % Change caption style; changes headers 
and page styles
# #+LaTeX_HEADER: \usepackage{biblatex}
# #+LaTeX_HEADER: \usepackage[backend=bibtex,style=verbose]{biblatex}
#+LaTeX_HEADER: \bibliography{/home/boudiccas/.emacs.d/research/cat.bib}
#+LaTeX_HEADER: \bibliography{references}


\pagebreak

* Chapter 1
Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy nibh
euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi enim ad
minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut
aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in
vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla
facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent
luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber
tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod
mazim placerat facer possim assum. Typi non habent claritatem insitam; est usus
legentis in iis qui facit eorum claritatem. Investigationes demonstraverunt
lectores legere me lius quod ii legunt saepius \cite{1}. Claritas est etiam 
processus
dynamicus, qui sequitur mutationem consuetudium lectorum. Mirum est notare quam
littera gothica, quam nunc putamus parum claram, anteposuerit litterarum formas
humanitatis per seacula quarta decima et quinta decima. Eodem modo typi, qui
nunc nobis videntur parum clari, fiant sollemnes in futurum.

* Chapter 2
Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy nibh
euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi enim ad
minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut
aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in
vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla
facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent
luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber
tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod
mazim placerat facer possim assum. Typi non habent claritatem insitam; est usus
legentis in iis qui facit eorum claritatem. Investigationes demonstraverunt
lectores legere me lius quod ii legunt saepius. Claritas est etiam processus
dynamicus, qui sequitur mutationem consuetudium lectorum. Mirum est notare quam
littera gothica, quam nunc putamus parum claram, anteposuerit litterarum formas
humanitatis per seacula quarta decima et quinta decima. Eodem modo typi, qui
nunc nobis videntur parum clari, fiant sollemnes in futurum.

* Bibliography
\printbibliography

* Index

--8---cut here---end---8---

and this is the bibliography file
--8---cut here---start-8---
@Article{,
  author =   {MacRae K. Pattison J.},
  title ={Home chemotherapy.},
  journaltitle = {Nursing Times},
  year = {2002},
  key =  {1},
  volume =   {98},
  number =   {35},
  pages ={34-35},
}
--8---cut here---end---8---

and this is the pdf output file
--8---cut here---start-8---
This is XeTeX, Version 

Re: [O] Bibliography woes!

[Eric S Fraga]

On Monday,  5 May 2014 at 18:08, Sharon Kimble wrote:

[...]

 How do I do it from the command-line please? Using what commands? I
 can do it from inside org-mode, and I've created a test file and bib
 references, details now. 

Sharon, have you not seen my other email?  Your problem is the actual
bibtex entry is wrong, missing the label that is needed to be able to
cite it in LaTeX.


[...]

 lectores legere me lius quod ii legunt saepius \cite{1}. Claritas est etiam 
 processus

[...]

 and this is the bibliography file
 @Article{,

change this line to

  @Article{1,
  
although I would recommend a more description label personally...

-- 
: Eric S Fraga (0xFFFCF67D), Emacs 24.4.50.2, Org release_8.2.6-923-g233c11

Re: [O] Bibliography woes!

[Sharon Kimble]

Eric S Fraga e.fr...@ucl.ac.uk writes:

 On Monday,  5 May 2014 at 18:08, Sharon Kimble wrote:

 [...]

 How do I do it from the command-line please? Using what commands? I
 can do it from inside org-mode, and I've created a test file and bib
 references, details now. 

 Sharon, have you not seen my other email?  Your problem is the actual
 bibtex entry is wrong, missing the label that is needed to be able to
 cite it in LaTeX.

I'd sent my reply before getting and reading your email, sorry Eric.

 [...]

 lectores legere me lius quod ii legunt saepius \cite{1}. Claritas est etiam 
 processus

 [...]

 and this is the bibliography file
 @Article{,

 change this line to

   @Article{1,
   
 although I would recommend a more description label personally...

I've set it up with the articles author and year, but it is still
failing. I'm attaching the original org file, the generated tex and
pdf, and the bib file. Hopefully this will help find a solution?

Thanks
Sharon.

--8---cut here---start-8---
Attachments
% Created 2014-05-05 Mon 23:14
\documentclass[a4paper]{article}
\usepackage[T1]{fontenc}
\usepackage{fixltx2e}
\usepackage{graphicx}
\usepackage{longtable}
\usepackage{float}
\usepackage{wrapfig}
\usepackage{rotating}
\usepackage[normalem]{ulem}
\usepackage{amsmath}
\usepackage{textcomp}
\usepackage{marvosym}
\usepackage[nointegrals]{wasysym}
\usepackage{amssymb}
\usepackage{hyperref}
\tolerance=1000
\usepackage{libertine}
\usepackage{xltxtra}
\usepackage{amsmath}
\usepackage{bussproofs}
\usepackage{amsmath,amssymb,amsopn}
\usepackage{graphicx}
\usepackage{makeidx} %robustindex % Indexing
\usepackage[british, english]{babel} % For british english hyphenation patterns
\usepackage{fancyhdr} % Change caption style; changes headers and page styles
\usepackage{biblatex}
\bibliography{/home/boudiccas/.emacs.d/research/cat.bib}
\usepackage[citestyle=authoryear-icomp,bibstyle=authoryear,hyperref=true,backref=true,maxcitenames=3,url=true,backend=biber,natbib=true]{biblatex}
\bibliography{references}
\author{Sharon Kimble \ Sarah ?}
\date{\today}
\title{Cat on the mat - 2014}
\hypersetup{
  pdfkeywords={},
  pdfsubject={},
  pdfcreator={Emacs 24.4.50.19 (Org mode 8.2.6)}}
\begin{document}

\maketitle


\pagebreak

\section*{Chapter 1}
\label{sec-1}
Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy
nibh euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi
enim ad minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis
nisl ut aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in
hendrerit in vulputate velit esse molestie consequat, vel illum dolore eu
feugiat nulla facilisis at vero eros et accumsan et iusto odio dignissim qui
blandit praesent luptatum zzril delenit augue duis dolore te feugait nulla
facilisi. Nam liber tempor cum soluta nobis eleifend option congue nihil
imperdiet doming id quod mazim placerat facer possim assum. Typi non habent
claritatem insitam; est usus legentis in iis qui facit eorum
claritatem. Investigationes demonstraverunt lectores legere me lius quod ii
legunt saepius \cite{MacRae K, et al;2002}. Claritas est etiam processus
dynamicus, qui sequitur mutationem consuetudium lectorum. Mirum est notare
quam littera gothica, quam nunc putamus parum claram, anteposuerit litterarum
formas humanitatis per seacula quarta decima et quinta decima. Eodem modo
typi, qui nunc nobis videntur parum clari, fiant sollemnes in futurum.

\section*{Chapter 2}
\label{sec-2}
Lorem ipsum dolor sit amet, consectetuer adipiscing elit, sed diam nonummy nibh
euismod tincidunt ut laoreet dolore magna aliquam erat volutpat. Ut wisi enim ad
minim veniam, quis nostrud exerci tation ullamcorper suscipit lobortis nisl ut
aliquip ex ea commodo consequat. Duis autem vel eum iriure dolor in hendrerit in
vulputate velit esse molestie consequat, vel illum dolore eu feugiat nulla
facilisis at vero eros et accumsan et iusto odio dignissim qui blandit praesent
luptatum zzril delenit augue duis dolore te feugait nulla facilisi. Nam liber
tempor cum soluta nobis eleifend option congue nihil imperdiet doming id quod
mazim placerat facer possim assum. Typi non habent claritatem insitam; est usus
legentis in iis qui facit eorum claritatem. Investigationes demonstraverunt
lectores legere me lius quod ii legunt saepius. Claritas est etiam processus
dynamicus, qui sequitur mutationem consuetudium lectorum. Mirum est notare quam
littera gothica, quam nunc putamus parum claram, anteposuerit litterarum formas
humanitatis per seacula quarta decima et quinta decima. Eodem modo typi, qui
nunc nobis videntur parum clari, fiant sollemnes in futurum.

\section*{Bibliography}
\label{sec-3}
\printbibliography

\section*{Index}
\label{sec-4}
% Emacs 24.4.50.19 (Org mode 8.2.6)
\end{document}


cat.pdf
Description: Adobe PDF document
@Article{MacRae K, et al;2002,
  author = 		 {MacRae K. Pattison J.},
  title = 		 {Home chemotherapy.},
  

Re: [O] Bibliography woes!

[Leonard Avery Randall]

Hi,
As Henry just noted, one of your main problem is your bibtex key. It 
should not contain spaces, commas, backslashes, semicolons, or other 
special characters that might mess up the syntax of the bibtex file. A 
common convention is to use author:year or if you have many articles by 
the same authors in the same year you can use author:yeara, author:yearb 
etc.

All best,
Leonard

Re: [O] Bibliography woes!

[Ken Mankoff]

On 2014-05-05 at 19:39, John Hendy wrote:
 If this works, someone can chime in regarding how to modify Org so
 that it will run the necessary biber/biblatex commands so you don't
 have to jump to a command line every time. Or perhaps that's a one
 time thing -- maybe as long as biber generates the .bbl file, you can
 refer to anything you want in that file from then on?

I've found latexmk to be the best tool for compiling LaTeX
documents. It runs all necessary commands as many times as needed,
including pdflatex, bibtex, biblatex, etc.. It is fairly smart and will
run the command to make the index if you load the index, for example. 

It can run in daemon mode and monitor the included files (and graphics)
so if one of those changes, the PDF is regenerated.

I prefer daemon mode, so I bring up a terminal and run latexmk file.tex
in the folder where I'm working on file.org. This also speeds things up,
since exporting to latex is fast, but compiling is slow. I can export
and still use emacs, rather than waiting for the compile to finish.

But if you want to run latexmk from Org, that works too. The -pvc-
turns off the preview continuous mode (daemon).

(setq org-latex-pdf-process (list /usr/texbin/latexmk -f -gg -pvc- %f))

  -k.

Re: [O] Bibliography and ODT

[Christian Moe]

Hi,

What seems to work for most people is exporting to latex, running
bibtex, and using one of these tools to convert to ODT:

- TeX4ht (the usual recommendation)
- Pandoc

or to convert to a format that ODT imports reasonably well:

- LaTeX2RTF (and import RTF into LibreOffice)
- LaTeX2HTML (and copy-paste or import HTML into LibreOffice)

If you're feeling adventurous, you may want to try a half-baked solution
of mine:
http://lists.gnu.org/archive/html/emacs-orgmode/2012-01/msg00128.html
Feedback is appreciated.

Yours,
Christian



Roger Mason writes:

 Hello,

 I'm finishing a paper that will need to be submitted to the publisher as 
 MS Word. I use neither Word nor Libre/OpenOffice. I need to have a 
 bibliography with cross-references from the text and intended to export 
 from org to ODT then Word.  My bibliography file is in bibtex format.  
 After a search I see various messages discussing bibliographies but I'm 
 unsure what the current situation is with respect to exporting to 
 ODT.Can someone enlighten me? If direct export to ODT of a document 
 with a bibliography is not currently implemented, can someone suggest a 
 workflow to get from org - ODT?

 Thanks,
 Roger

 This electronic communication is governed by the terms and conditions at
 http://www.mun.ca/cc/policies/electronic_communications_disclaimer_2012.php

Re: [O] Bibliography and ODT

[Roger Mason]

hello Christian,

On 07/14/2013 05:07 PM, Christian Moe wrote:

Hi,

What seems to work for most people is exporting to latex, running
bibtex, and using one of these tools to convert to ODT:

- TeX4ht (the usual recommendation)
- Pandoc

or to convert to a format that ODT imports reasonably well:

- LaTeX2RTF (and import RTF into LibreOffice)
- LaTeX2HTML (and copy-paste or import HTML into LibreOffice)

If you're feeling adventurous, you may want to try a half-baked solution
of mine:
http://lists.gnu.org/archive/html/emacs-orgmode/2012-01/msg00128.html
Feedback is appreciated.

Yours,
Christian


Thanks.  I'll try one (or more) of those.

Cheers,
Roger

This electronic communication is governed by the terms and conditions at
http://www.mun.ca/cc/policies/electronic_communications_disclaimer_2012.php

Re: [O] Bibliography

[Vikas Rawal]

  at the keyword please.
 
 Here's a new take on the problem. You need to use latest maint (or
 master) revision. What do you think?


I have been trying ox-bibtex.el. One problem I have is that the
\cite{key} does not put a number with a link to the citation, but puts
[key] in place of the number.

I have tried different styles, but nothing seems to work.

See, for example, http://www.indianstatistics.org/education.html.
\cite{vikaseducation2011} shows up as [vikaseducation2011] instead of
[1].

Any idea why this is happening?

Vikas

Re: [O] Bibliography

[Nicolas Goaziou]

Hello,

Vikas Rawal vikasli...@agrarianresearch.org writes:

 I have been trying ox-bibtex.el. One problem I have is that the
 \cite{key} does not put a number with a link to the citation, but puts
 [key] in place of the number.

 I have tried different styles, but nothing seems to work.

 See, for example, http://www.indianstatistics.org/education.html.
 \cite{vikaseducation2011} shows up as [vikaseducation2011] instead of
 [1].

 Any idea why this is happening?

Yes: code typo. Here's an update.


Regards,

-- 
Nicolas Goaziou


ox-bibtex.el
Description: application/emacs-lisp

Re: [O] Bibliography

[Nicolas Goaziou]

Hello,

Fabrice Popineau fabrice.popin...@supelec.fr writes:

 It defnitely helps a lot with Org-LaTeX files (scientific papers).
 There is one thing that is not taken into account  and I wonder if there
 is an Org solution for it.
 In laTeX you can use \cite{foo1999, foo2002} . I don't think that
 current links in Org allow this and I don't see an easy way for it.
 In Org, you would have [[bibtex:foo1999]][[bibtex:foo2002]] .
 May be the exporter for bibtex links should look around and merge
 other links found.

 Fabrice


 Could it be possible to allow [[bibtex:foo1999, foo2002]]

No, it's not possible (what would be the destination of such link
anyway?). Though, the current implementation of ox-bibtex.el (latest
posted in this thread) should split

  \cite{foo1999, foo2002} 

into:

  [a name=#foo1999foo1999/a][a name=#foo2002foo1999/a]

Isn't it the correct behaviour?


Regards,

-- 
Nicolas Goaziou

Re: [O] Bibliography

[Vikas Rawal]

  See, for example, http://www.indianstatistics.org/education.html.
  \cite{vikaseducation2011} shows up as [vikaseducation2011] instead of
  [1].
 
  Any idea why this is happening?
 
 Yes: code typo. Here's an update.
Thanks.

Vikas

Re: [O] Bibliography

[Fabrice Popineau]

It defnitely helps a lot with Org-LaTeX files (scientific papers).
There is one thing that is not taken into account  and I wonder if there
is an Org solution for it.
In laTeX you can use \cite{foo1999, foo2002} . I don't think that
current links in Org allow this and I don't see an easy way for it.
In Org, you would have [[bibtex:foo1999]][[bibtex:foo2002]] .
May be the exporter for bibtex links should look around and merge
other links found.

Fabrice


Could it be possible to allow [[bibtex:foo1999, foo2002]]


2013/5/13 Vikas Rawal vikasli...@agrarianresearch.org

  This works fine except that I can't place it at the keyword. How does
  one do it? I thought having a line say [BIBLIOGRAPHY] would work but
  it does not.
 

 Figured it myself.

 Placing the line '#+BIBLIOGRAPHY: blah blah...' at the right place did
 it.

 Thanks again,

 Vikas




-- 
Fabrice Popineau
-
SUPELEC
Département Informatique
3, rue Joliot Curie
91192 Gif/Yvette Cedex
Tel direct : +33 (0) 169851950
Standard : +33 (0) 169851212
--

Re: [O] Bibliography

[Nicolas Goaziou]

Hello,

Vikas Rawal vikasli...@agrarianresearch.org writes:

 Actually, ox-html.el also tries to do something with bibliographies,
 which introduces the duplication.
 
 We should decide if the code handling them should be in contrib/ or in
 the various export back-ends. Since HTML handling requires external
 programs, I lean towards the former.

 I agree. Better to keep it separately in contrib/

 If we agree, I'll remove the faulty code from ox-html.el and prepare
 a new version for ox-bibtex.el.

 +1 from me.

 By the way, where should the bibliography be inserted: at the keyword or
 at the end of the document (in both HTML and LaTeX)?

 at the keyword please.

Here's a new take on the problem. You need to use latest maint (or
master) revision. What do you think?

I'm Cc'ing Taru Karttunen, the org-exp-bibtex.el author, to know if he
agrees with the changes.


Regards,

-- 
Nicolas Goaziou


ox-bibtex.el
Description: application/emacs-lisp

Re: [O] Bibliography

[Vikas Rawal]

  By the way, where should the bibliography be inserted: at the keyword or
  at the end of the document (in both HTML and LaTeX)?
 
  at the keyword please.
 
 Here's a new take on the problem. You need to use latest maint (or
 master) revision. What do you think?


This works fine except that I can't place it at the keyword. How does
one do it? I thought having a line say [BIBLIOGRAPHY] would work but
it does not.

Vikas

Re: [O] Bibliography

[Vikas Rawal]

 This works fine except that I can't place it at the keyword. How does
 one do it? I thought having a line say [BIBLIOGRAPHY] would work but
 it does not.
 

Figured it myself.

Placing the line '#+BIBLIOGRAPHY: blah blah...' at the right place did
it.

Thanks again,

Vikas

Re: [O] Bibliography

[Rafael]

Vikas Rawal vikasli...@agrarianresearch.org writes:

 Note for Mac OSX users:. I am using Ubuntu Precise, not OSX, and
 TeXlive 2012, not 2010, and I got the Executing bibtex2html failed
 when testing this also (even without limit:t). The only way I can
 imagine to work around was to first run the recommended 'export
 TMPDIR=.' in a terminal, and then 'emacs' in the same terminal. I wish I
 knew a cleaner way to do that, since I imagine it would not be wise to
 put 'export TMPDIR=.' in .bashrc.

 This may be the cleaner solution:
 http://lists.gnu.org/archive/html/emacs-orgmode/2012-11/msg00164.html

Thanks for your followup! In my case, though, Emacs can find the
executable of bibtex2html. However, another message in the thread you
mentioned together with some googling led me to adding 'TEXMFOUTPUT =
/tmp' to /usr/local/texlive/2012/texmf.cnf, and now I can reproduce your
results, namely, without limit:t, the bibliography in the html export
appears twice and with it, I get Executing bibtex2html failed.

Re: [O] Bibliography

[Vikas Rawal]

 Note for Mac OSX users:. I am using Ubuntu Precise, not OSX, and
 TeXlive 2012, not 2010, and I got the Executing bibtex2html failed
 when testing this also (even without limit:t). The only way I can
 imagine to work around was to first run the recommended 'export
 TMPDIR=.' in a terminal, and then 'emacs' in the same terminal. I wish I
 knew a cleaner way to do that, since I imagine it would not be wise to
 put 'export TMPDIR=.' in .bashrc.

This may be the cleaner solution:
http://lists.gnu.org/archive/html/emacs-orgmode/2012-11/msg00164.html

Vikas

Re: [O] Bibliography

[Vikas Rawal]

 
  Yes please. I am waiting for something that will export bibtex to
  html. With the old exporter, org-exp-bibtex used bibtex2html to
  achieve it. But nothing similar is possible with the new exporter.
 
 I attach a port of org-exp-bibtex.el (renamed ox-bibtex.el) for the new
 export framework. Would you mind testing it?

A big thank you!

Here is a quick comment. More to follow.

If an org file, say temp.org, refers to a bibtex file called foo.bib,
ox-bibtex creates two files: foo.html and foo_bib.html. I suggest that
these be named foo_temp.html and foo_temp_bib.html. Since there may be
multiple org files in a project linking to the same bibtex file, the
present implementation would cause a problem.

Vikas

Re: [O] Bibliography

[Vikas Rawal]

 
 I attach a port of org-exp-bibtex.el (renamed ox-bibtex.el) for the new
 export framework. Would you mind testing it?
 


I am attaching my test files. I have following problems.

1. When I use limit:t, I get an error: if: Executing bibtex2html failed

2. The bibliography is inserted in the exported html file above
the main body of org file as well as below the main body of the org
file. Am I doing something silly?

Vikas

Re: [O] Bibliography

[Vikas Rawal]

  I attach a port of org-exp-bibtex.el (renamed ox-bibtex.el) for the new
  export framework. Would you mind testing it?
 
 A big thank you!
 
 Here is a quick comment. More to follow.
 
 If an org file, say temp.org, refers to a bibtex file called foo.bib,
 ox-bibtex creates two files: foo.html and foo_bib.html. I suggest that
 these be named foo_temp.html and foo_temp_bib.html. Since there may be
 multiple org files in a project linking to the same bibtex file, the
 present implementation would cause a problem.
 
Sorry, this problem will perhaps be relevant only when ox-bibtex is
being used with limit:t, so that only cited references would show up
on each page. Since limit:t is not yet working for me, I am unable to
test it.

Vikas

Re: [O] Bibliography

[Vikas Rawal]

 
 I am attaching my test files. I have following problems.
 
Sorry, forgot to attach my files. Here they are.

Vikas
#+TITLE: Statistics on Indian Economy and Society
#+LINK_UP: data.html
#+LINK_HOME: index.html
#+OPTIONS: num:nil toc:nil
#+HTML_HEAD:link rel=stylesheet type=text/css href=css/worg.css /
#+BIBLIOGRAPHY: bibliobase plain 

* Introductory notes on sources of data

Data on banking are primarily available from the Reserve Bank of
India. There are three major sources of data:

1. Basic Statistical Returns of Scheduled Commercial Banks in India
2. Statistical Tables Relating to Banks in India
3. Trend and Progress of Banking in India. \cite{ramakumar2011}




% This file was created with JabRef 2.7b.
% Encoding: UTF-8

@BOOK{acharyawages1988,
  title = {Agricultural wages in India: A disaggregated analysis},
  publisher = {Center for Asian Development Studies, Boston University},
  year = {1988},
  author = {Acharya, S.}
}

@TECHREPORT{RePEc:iim:iimawp:wp01456,
  author = {Bhattacharjee, Sourindra and Desai, B M and Naik, Gopal},
  title = {Viability of Rural Banking by The Nationalized Commercial Banks in
India},
  institution = {Indian Institute of Management Ahmedabad, Research and 
Publication
Department},
  type = {IIMA Working Papers},
  number = {WP1997-07-01_01456},
  abstract = {This paper examines the viability of rural banking by the 
Nationalized
Commercial Banks and the factors influencing it. The viability was
examined using both cost and profitability analyses. Theory of costs
is used for the former, while multi-variate econometric model is
formulated for the latter. Factors influencing viability in both
the analysis are classified into innovative and non-innovative based
on unique characteristics of rural banking in India. The results
show that rural banking is viable and it could be further improved
by reaping scale economies rather than raising interest rate. But
this would require more decentralized, autonomous and accountable
form of rural banking.},
  url = {http://ideas.repec.org/p/iim/iimawp/wp01456.html}
}

@ARTICLE{chavangender2008,
  author = {Chavan, P.},
  title = {Gender Inequality in Banking Services},
  journal = {Economic and Political Weekly},
  year = {2008},
  pages = {18--21},
  publisher = {JSTOR}
}

@ARTICLE{chavancredit2007,
  author = {Chavan, P.},
  title = {Access to Bank Credit: Implications for Dalit Rural Households},
  journal = {Economic and Political Weekly},
  year = {2007},
  pages = {3219--3224},
}

@ARTICLE{chavanbanking2005,
  author = {Chavan, P.},
  title = {How'Inclusive'Are Banks under Financial Liberalisation?},
  journal = {Economic and Political Weekly},
  year = {2005},
  pages = {4647--4649},
}

@ARTICLE{chavanwages2006,
  author = {Chavan, P. and Bedamatta, R.},
  title = {Trends in agricultural wages in India 1964-65 to 1999-2000},
  journal = {Economic and Political Weekly},
  year = {2006},
  pages = {4041-4051},
}

@ARTICLE{chavanmicrocredit2009,
  author = {Chavan, P. and Birajdar, B.},
  title = {Micro finance and financial inclusion of women: An evaluation},
  journal = {Reserve Bank of India Occasional Papers},
  year = {2009},
  volume = {30},
  pages = {109-129},
  number = {2},
}

@ARTICLE{chavanmicrocredit2002,
  author = {Chavan, P. and Ramakumar, R.},
  title = {Micro-credit and rural poverty: An analysis of empirical evidence},
  journal = {Economic and Political Weekly},
  year = {2002},
  pages = {955-965},
}

@ARTICLE{gaihawages1997,
  author = {Gaiha, R.},
  title = {Do rural public works influence agricultural wages? The case of the
employment guarantee scheme in India},
  journal = {Oxford Development Studies},
  year = {1997},
  volume = {25},
  pages = {301--314},
  number = {3},
  publisher = {Taylor \ Francis}
}

@ARTICLE{josewages1988,
  author = {Jose, AV},
  title = {Agricultural wages in India},
  journal = {Economic and Political Weekly},
  year = {1988},
  pages = {46--58},
  publisher = {JSTOR}
}

@ARTICLE{lalwages1976,
  author = {Lal, D.},
  title = {Agricultural growth, real wages, and the rural poor in India},
  journal = {Economic and Political Weekly},
  year = {1976},
  pages = {47--61},
  publisher = {JSTOR}
}

@BOOK{vkr_wagelabour_1995,
  title = {Wage Labour and Unfreedom in Agriculture: An Indian Case Study},
  publisher = {Clarendon Press},
  author = {Ramachandran, V. K.},
  altauthor = {Ramachandran, V. K.}
}

@ARTICLE{ramachandranbanking2002,
  author = {Ramachandran, V. K. and Swaminathan, Madhura},
  title = {Rural banking and landless labour households: institutional reform
and rural credit markets in India},
  journal = {Journal of Agrarian Change},
  year = {2002},
  volume = {2},
  pages = {502--544},
  number = {4},
  publisher = {Wiley Online Library}
}

@BOOK{vkrvrms_andhra_2010,
  title = {Socio-economic Surveys of Three Villages in Andhra Pradesh: A Study

Re: [O] Bibliography

[Vikas Rawal]

 
 I attach a port of org-exp-bibtex.el (renamed ox-bibtex.el) for the new
 export framework. Would you mind testing it?
 
In the latex export, the bibliography is added before the main content
of the org file. The tex file shows following lines inserted before
the main content rather than after.

***

\bibliographystyle{plain}
\bibliography{foo}

***

Vikas

Re: [O] Bibliography

[Rafael]

Vikas Rawal vikasli...@agrarianresearch.org writes:

 
 I attach a port of org-exp-bibtex.el (renamed ox-bibtex.el) for the new
 export framework. Would you mind testing it?
 


 I am attaching my test files. I have following problems.

 1. When I use limit:t, I get an error: if: Executing bibtex2html failed


For this, maybe you are getting the error mentioned in the page
https://www.lri.fr/~filliatr/bibtex2html/, in the paragraph starting
Note for Mac OSX users:. I am using Ubuntu Precise, not OSX, and
TeXlive 2012, not 2010, and I got the Executing bibtex2html failed
when testing this also (even without limit:t). The only way I can
imagine to work around was to first run the recommended 'export
TMPDIR=.' in a terminal, and then 'emacs' in the same terminal. I wish I
knew a cleaner way to do that, since I imagine it would not be wise to
put 'export TMPDIR=.' in .bashrc.

However, the exported html file does not include any bibliograpy at
all. :(



 2. The bibliography is inserted in the exported html file above
 the main body of org file as well as below the main body of the org
 file. Am I doing something silly?

 Vikas

Re: [O] Bibliography

[Nicolas Goaziou]

Hello,

Vikas Rawal vikasli...@agrarianresearch.org writes:

 I am attaching my test files. I have following problems.

 1. When I use limit:t, I get an error: if: Executing bibtex2html
 failed

OK, I'll have a look at it.

 2. The bibliography is inserted in the exported html file above
 the main body of org file as well as below the main body of the org
 file. Am I doing something silly?

Actually, ox-html.el also tries to do something with bibliographies,
which introduces the duplication.

We should decide if the code handling them should be in contrib/ or in
the various export back-ends. Since HTML handling requires external
programs, I lean towards the former.

If we agree, I'll remove the faulty code from ox-html.el and prepare
a new version for ox-bibtex.el.

By the way, where should the bibliography be inserted: at the keyword or
at the end of the document (in both HTML and LaTeX)?


Regards,

-- 
Nicolas Goaziou

Re: [O] Bibliography

[Fabrice Popineau]

Hi Nicolas,

Thanks a lot for taking quickly of this bib issue.




2013/5/9 Nicolas Goaziou n.goaz...@gmail.com

 Hello,

 Vikas Rawal vikasli...@agrarianresearch.org writes:


  2. The bibliography is inserted in the exported html file above
  the main body of org file as well as below the main body of the org
  file. Am I doing something silly?

 Actually, ox-html.el also tries to do something with bibliographies,
 which introduces the duplication.

 We should decide if the code handling them should be in contrib/ or in
 the various export back-ends. Since HTML handling requires external
 programs, I lean towards the former.


I would tend to agree.


 If we agree, I'll remove the faulty code from ox-html.el and prepare
 a new version for ox-bibtex.el.

 By the way, where should the bibliography be inserted: at the keyword or
 at the end of the document (in both HTML and LaTeX)?


At the keyword IMHO.

 Fabrice

Re: [O] Bibliography

[Vikas Rawal]

 Actually, ox-html.el also tries to do something with bibliographies,
 which introduces the duplication.
 
 We should decide if the code handling them should be in contrib/ or in
 the various export back-ends. Since HTML handling requires external
 programs, I lean towards the former.

I agree. Better to keep it separately in contrib/

 If we agree, I'll remove the faulty code from ox-html.el and prepare
 a new version for ox-bibtex.el.

+1 from me.

 By the way, where should the bibliography be inserted: at the keyword or
 at the end of the document (in both HTML and LaTeX)?

at the keyword please.

Thanks again,

Vikas

Re: [O] Bibliography

[Nicolas Goaziou]

Hello,

Vikas Rawal vikasli...@agrarianresearch.org writes:

 My only concern is about users expecting the keyword to be
 recognized in other back-ends.

 Yes please. I am waiting for something that will export bibtex to
 html. With the old exporter, org-exp-bibtex used bibtex2html to
 achieve it. But nothing similar is possible with the new exporter.

I attach a port of org-exp-bibtex.el (renamed ox-bibtex.el) for the new
export framework. Would you mind testing it?

Thank you.


Regards,

-- 
Nicolas Goaziou


ox-bibtex.el
Description: application/emacs-lisp

Re: [O] Bibliography

[Suvayu Ali]

On Mon, May 06, 2013 at 04:26:16PM +0200, Fabrice Popineau wrote:
 Is it me or is it normal that the:
 
 #+Bibliography: foo plain
 
 line is not exported by the LaTeX backend?
 
 I assume that:
 \bibliography{foo}
 \bibliographystyle{plain}
 is a decent way to handle it.

Sometime back there was talk about integrating bibliography in the Org
syntax.  That would make it backend agnostic (always a goal with most
Org features).  If you are interested, take a look at the following
thread.

  http://thread.gmane.org/gmane.emacs.orgmode/67488/focus=67521

-- 
Suvayu

Open source is the future. It sets us free.

Re: [O] Bibliography

[Fabrice Popineau]

Sure, I remember this thread and it is clear that the problem is very
different when it is for LaTeX of for and HTML backend.
However, Reftex is provided with Emacs, and it is also integrated to Org
mode.

So I was trying to solve my simple problem about the bibliography keyword
this way:

(defadvice org-latex-keyword (around org-latex-keyword-bibliography)
  Exports `bibliography' keyword with LaTeX backend.
  (let ((key (org-element-property :key (ad-get-arg 0)))
(value (org-element-property :value (ad-get-arg 0
(if (and (string= key BIBLIOGRAPHY)
 (string-match \\(\\S-+\\)[ \t]+\\(\\S-+\\)\\([^\r\n]*\\)
value))
(let ((bibfile (match-string 1 value))
  (bibstyle (match-string 2 value)))
  (format \\bibliography{%s}\n\\bibliographystyle{%s} bibfile
bibstyle))
ad-do-it)))

(ad-activate 'org-latex-keyword)

in my personal Org mode setup. However, it does not work. The advice is
called and returns the string,
but somehow it is not inserted in the buffer. If I do the same thing in
ox-latex.el:org-latex-keyword function,
it does work. Any idea why ?

Fabrice


2013/5/6 Suvayu Ali fatkasuvayu+li...@gmail.com

 On Mon, May 06, 2013 at 04:26:16PM +0200, Fabrice Popineau wrote:
  Is it me or is it normal that the:
 
  #+Bibliography: foo plain
 
  line is not exported by the LaTeX backend?
 
  I assume that:
  \bibliography{foo}
  \bibliographystyle{plain}
  is a decent way to handle it.

 Sometime back there was talk about integrating bibliography in the Org
 syntax.  That would make it backend agnostic (always a goal with most
 Org features).  If you are interested, take a look at the following
 thread.

   http://thread.gmane.org/gmane.emacs.orgmode/67488/focus=67521

 --
 Suvayu

 Open source is the future. It sets us free.




-- 
Fabrice Popineau
-
SUPELEC
Département Informatique
3, rue Joliot Curie
91192 Gif/Yvette Cedex
Tel direct : +33 (0) 169851950
Standard : +33 (0) 169851212
--

Re: [O] Bibliography

[Nicolas Goaziou]

Hello,

Fabrice Popineau fabrice.popin...@supelec.fr writes:

 Sure, I remember this thread and it is clear that the problem is very
 different when it is for LaTeX of for and HTML backend.
 However, Reftex is provided with Emacs, and it is also integrated to Org
 mode.

Since it is back-end dependent, why don't you use:

  #+latex: \bibliography{...}\bibilographystyle{...}

instead?

 So I was trying to solve my simple problem about the bibliography keyword
 this way:

 (defadvice org-latex-keyword (around org-latex-keyword-bibliography)
   Exports `bibliography' keyword with LaTeX backend.
   (let ((key (org-element-property :key (ad-get-arg 0)))
 (value (org-element-property :value (ad-get-arg 0
 (if (and (string= key BIBLIOGRAPHY)
  (string-match \\(\\S-+\\)[ \t]+\\(\\S-+\\)\\([^\r\n]*\\)
 value))
 (let ((bibfile (match-string 1 value))
   (bibstyle (match-string 2 value)))
   (format \\bibliography{%s}\n\\bibliographystyle{%s} bibfile
 bibstyle))
 ad-do-it)))

 (ad-activate 'org-latex-keyword)

 in my personal Org mode setup. However, it does not work. The advice is
 called and returns the string,
 but somehow it is not inserted in the buffer. If I do the same thing in
 ox-latex.el:org-latex-keyword function,
 it does work. Any idea why ?

You need to set `ad-return-value' somewhere, don't you?


Regards,

-- 
Nicolas Goaziou

Re: [O] Bibliography

[Fabrice Popineau]

 Since it is back-end dependent, why don't you use:

   #+latex: \bibliography{...}\bibilographystyle{...}

 instead?


To avoid duplication.

Org-bibtex/reftex need the line:

#+bibliography: foo plain


 You need to set `ad-return-value' somewhere, don't you?


:-) This is what I was looking for.

Thanks a lot!

Fabrice

Re: [O] Bibliography

[Nicolas Goaziou]

Fabrice Popineau fabrice.popin...@supelec.fr writes:

 Since it is back-end dependent, why don't you use:

   #+latex: \bibliography{...}\bibilographystyle{...}

 instead?


 To avoid duplication.

 Org-bibtex/reftex need the line:


 #+bibliography: foo plain

OK. Then, it may indeed be wise to support #+bibliography in latex
back-end. My only concern is about users expecting the keyword to be
recognized in other back-ends.


Regards,

-- 
Nicolas Goaziou

Re: [O] Bibliography

[Vikas Rawal]

 My only concern is about users expecting the keyword to be
 recognized in other back-ends.

Yes please. I am waiting for something that will export bibtex to
html. With the old exporter, org-exp-bibtex used bibtex2html to
achieve it. But nothing similar is possible with the new exporter.

Vikas