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* [WIP/RFC] Bibliography support ODT + JabRef
@ 2013-07-18 20:01 Jambunathan K
  2013-07-24 14:53 ` [ANN] " Jambunathan K
  0 siblings, 1 reply; 8+ messages in thread
From: Jambunathan K @ 2013-07-18 20:01 UTC (permalink / raw)
  To: emacs-orgmode

[-- Attachment #1: Type: text/plain, Size: 1504 bytes --]


[WIP/RFC] Bibliography support ODT + JabRef

I need some quick feedback on how this works out.  Look at the Org and
ODT file and tell me to what extent it will suffice.

I am not interested in Org syntax at the moment.  But I am willing to
exchange notes with anyone who wants to "canonicalize" some Citation
support in Org.  For now, the keys are referenced with \cite{key1, key2}

I am dumping

1. messages buffer.  Shows how JabRef can be invoked on the command
   line.

--8<---------------cut here---------------start------------->8---
Extracting Citation Reference (suzuki_studies_1998)
Running java -jar /home/kjambunathan/Downloads/JabRef-2.9.2.jar -n true -m suzuki_studies_1998,jabref-16048-fF.xml,ooxml.reference MyLibrary.bib
Extracting Citation Reference (blyth_zen_1966)
Running java -jar /home/kjambunathan/Downloads/JabRef-2.9.2.jar -n true -m blyth_zen_1966,jabref-16048LqL.xml,ooxml.reference MyLibrary.bib
Extracting Citation Reference (watts_way_1999)
Running java -jar /home/kjambunathan/Downloads/JabRef-2.9.2.jar -n true -m watts_way_1999,jabref-16048Y0R.xml,ooxml.reference MyLibrary.bib
--8<---------------cut here---------------end--------------->8---


2. JabRef's jstyle and layout files split out from the Jstyle.

   The jstyle is the one that comes with Jabref's OOplugin itself ->
   Default Style (numerical citations).

   The layout files were broken apart from the Jstyle for the purpose of
   org-odt export.  The files may not be perfect but gets the job done.





[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #2: cite.org --]
[-- Type: text/x-org, Size: 490 bytes --]


* Some section

This paragraph has some footnote references[fn:1] and cites some
bibliographic references \cite{watts_way_1999,blyth_zen_1966}.  There
are more bibliographic references. \cite{suzuki_studies_1998}.  Here I
re-cite an earlier book \cite{watts_way_1999}.  Here is another footnote.[fn:2]

#+ATTR_ODT: :style custom
#+BIBLIOGRAPHY: MyLibrary plain option:-d

* Another section

So on and so forth.

* Footnotes

[fn:1] This is a footnote.

[fn:2] This is another footnote.




[-- Attachment #3: cite.odt --]
[-- Type: application/vnd.oasis.opendocument.text, Size: 10798 bytes --]

[-- Warning: decoded text below may be mangled, UTF-8 assumed --]
[-- Attachment #4: MyLibrary.bib --]
[-- Type: text/x-bibtex, Size: 3106 bytes --]

@misc{_101_????,
	title = {101 Zen Stories},
	url = {http://www.101zenstories.com/},
	urldate = {2013-06-10},
	file = {101 Zen Stories:/home/kjambunathan/.mozilla/firefox/htr1myi9.default/zotero/storage/67EHBZZ6/www.101zenstories.com.html:text/html}
},

@book{blyth_zen_1966,
	edition = {{1St} Edition},
	title = {Zen and Zen Classics Volume 4 Mumonkan},
	publisher = {The Hokuseido Press},
	author = {Blyth, R. H.},
	year = {1966}
},

@book{watts_way_1999,
	title = {The Way of Zen},
	isbn = {0375705104},
	publisher = {Vintage},
	author = {Watts, Alan W.},
	month = jan,
	year = {1999}
},

@misc{center_for_history_and_new_media_zotero_????,
	title = {Zotero Quick Start Guide},
	url = {http://zotero.org/support/quick_start_guide},
	author = {{Center for History and New Media}},
	annote = {Welcome to {Zotero!View} the Quick Start Guide to learn how to begin collecting, managing, citing, and sharing your research {sources.Thanks} for installing Zotero.}
},

@book{besserman_crazy_1991,
	title = {Crazy Clouds: Zen radicals, rebels, and reformers},
	isbn = {9780877735434},
	shorttitle = {Crazy Clouds},
	language = {en},
	publisher = {Shambhala},
	author = {Besserman, Perle and Steger, Manfred},
	month = may,
	year = {1991},
	keywords = {Philosophy / General, Philosophy / Zen, Priests, Zen, Religion / Buddhism / General, Religion / Buddhism / Zen, Religion / General, Zen priests, Zen priests/ Biography}
},

@misc{_believing_????,
	title = {{ON} {BELIEVING} {IN} {MIND} ({SHINJIN-NO-MEI)} by Seng-t'san},
	url = {http://home.primusonline.com.au/peony/faith_in_mind.htm},
	urldate = {2013-06-10},
	file = {ON BELIEVING IN MIND (SHINJIN-NO-MEI) by Seng-t'san:/home/kjambunathan/.mozilla/firefox/htr1myi9.default/zotero/storage/SD4HNP5X/faith_in_mind.html:text/html}
},

@book{suzuki_studies_1998,
	title = {Studies in Zen},
	isbn = {0802216781},
	publisher = {Chartwell Books {Inc.,U.S.}},
	author = {Suzuki},
	month = dec,
	year = {1998}
},

@misc{_gateless_????,
	title = {The Gateless Gate Index},
	url = {http://www.sacred-texts.com/bud/glg/index.htm},
	urldate = {2013-06-10},
	file = {The Gateless Gate Index:/home/kjambunathan/.mozilla/firefox/htr1myi9.default/zotero/storage/WWH3MDSG/index.html:text/html}
},

@book{blyth_zen_1970,
	title = {Zen and Zen classics},
	language = {en},
	publisher = {Hokuseido Press},
	author = {Blyth, Reginald Horace},
	year = {1970},
	keywords = {Philosophy / Zen, Religion / Buddhism / General, Religion / Buddhism / Zen, Zen Buddhism}
},

@book{blofeld_zen_1994,
	edition = {First Evergreen Edition},
	title = {The Zen Teaching of Huang-Po: On the Transmission of Mind},
	isbn = {0802150926},
	shorttitle = {The Zen Teaching of Huang-Po},
	publisher = {Grove Press},
	translator = {Blofeld, John Eaton Calthorpe},
	month = jan,
	year = {1994}
},

@book{blofeld_zen_1994-1,
	edition = {First Evergreen Edition},
	title = {The Zen Teaching of Huang-Po: On the Transmission of Mind},
	isbn = {0802150926},
	shorttitle = {The Zen Teaching of Huang-Po},
	publisher = {Grove Press},
	translator = {Blofeld, John Eaton Calthorpe},
	month = jan,
	year = {1994}
}

[-- Attachment #5: ooxml.text.article.layout --]
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<text:span text:style-name="Bold">\format[Authors(LastFirst,Semicolon)]{\author}</text:span> (<text:span text:style-name="Bold">\year\uniq</text:span>). <text:span text:style-name="Emphasis">\title</text:span>, \journal \volume\begin{pages} : \format[FormatPagesForHTML]{\pages}\end{pages}.

[-- Attachment #6: ooxml.text.book.layout --]
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\format[Authors(LastFirst,Semicolon)]{\author}\begin{editor}\format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\editor} (Ed.)\end{editor}, <text:span text:style-name="Bold">\year\uniq</text:span>. <text:span text:style-name="Emphasis">\title</text:span>. \publisher, \address.

[-- Attachment #7: ooxml.text.inbook.layout --]
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\format[Authors(LastFirst,Semicolon)]{\author} (<text:span text:style-name="Bold">\year\uniq</text:span>). <text:span text:style-name="Emphasis">\chapter</text:span>. In: \format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\editor} (Ed.), <text:span text:style-name="Emphasis">\title</text:span>, \publisher.

[-- Attachment #8: ooxml.text.incollection.layout --]
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\format[Authors(LastFirst,Semicolon)]{\author} (<text:span text:style-name="Bold">\year\uniq</text:span>). <text:span text:style-name="Emphasis">\title</text:span>. In: \format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\editor} (Ed.), <text:span text:style-name="Emphasis">\booktitle</text:span>, \publisher.

[-- Attachment #9: ooxml.text.layout --]
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\format[Authors(LastFirst,Semicolon)]{\author} (<text:span text:style-name="Bold">\year\uniq</text:span>). <text:span text:style-name="Emphasis">\title</text:span>, \journal \volume\begin{pages} : \format[FormatPagesForHTML]{\pages}\end{pages}.

[-- Attachment #10: ooxml.text.phdthesis.layout --]
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\format[Authors(LastFirst,Semicolon)]{\author} (<text:span text:style-name="Bold">\year\uniq</text:span>). <text:span text:style-name="Emphasis">\title</text:span>, \school.

[-- Attachment #11: ooxml.numbered.jstyle --]
[-- Type: text/plain, Size: 1707 bytes --]

# Written by Morten O. Alver.
# This file is licensed under the terms of the GPL version 2 (or later).

NAME
Example style file for JabRef-oo plugin.

JOURNALS
Journal name 1
Journal name 2

PROPERTIES
Title="References"
IsSortByPosition="true"
IsNumberEntries="true"
ReferenceParagraphFormat="Text body"
ReferenceHeaderParagraphFormat="Heading 2"

CITATION
BracketBefore="["
BracketAfter="]"
BracketBeforeInList="["
BracketAfterInList="] "
CitationSeparator="; "
UniquefierSeparator=","
GroupedNumbersSeparator="-"
MinimumGroupingCount="3"
FormatCitations="false"
CitationCharacterFormat="Default"
PageInfoSeparator="; "

LAYOUT
article=<b>\format[Authors(LastFirst,Semicolon)]{\author}</b> (<b>\year\uniq</b>). <i>\title</i>, \journal \volume\begin{pages} : \format[FormatPagesForHTML]{\pages}\end{pages}.

book=\format[Authors(LastFirst,Semicolon)]{\author}\begin{editor}\format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\editor} (Ed.)\end{editor}, <b>\year\uniq</b>. <i>\title</i>. \publisher, \address.

incollection=\format[Authors(LastFirst,Semicolon)]{\author} (<b>\year\uniq</b>). <i>\title</i>. In: \format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\editor} (Ed.), <i>\booktitle</i>, \publisher.

inbook=\format[Authors(LastFirst,Semicolon)]{\author} (<b>\year\uniq</b>). <i>\chapter</i>. In: \format[AuthorLastFirst,AuthorAbbreviator,AuthorAndsReplacer]{\editor} (Ed.), <i>\title</i>, \publisher.

phdthesis=\format[Authors(LastFirst,Semicolon)]{\author} (<b>\year\uniq</b>). <i>\title</i>, \school.

default=\format[Authors(LastFirst,Semicolon)]{\author} (<b>\year\uniq</b>). <i>\title</i>, \journal \volume\begin{pages} : \format[FormatPagesForHTML]{\pages}\end{pages}.

^ permalink raw reply	[flat|nested] 8+ messages in thread
* Re: [ANN] Bibliography support ODT + JabRef
@ 2013-07-29  4:31 Jambunathan K
  0 siblings, 0 replies; 8+ messages in thread
From: Jambunathan K @ 2013-07-29  4:31 UTC (permalink / raw)
  To: emacs-orgmode; +Cc: Nicolas Goaziou


> It can work with Chinese characters now. thanks!

Thanks for confirming this.

> 2. Word "References" should be added to `org-export-dictionary'

I am CCing Ngz.  

Currently Bibliography support in Org is EXPERIMENTAL.  Things will be
in a state of flux until it gets standardized.

I also think the spaces preceding the \cite{ } element should be gobbled
up by the exporter.  In actuality, this is something that ox.el has to
take care as part of standardization effort (I think).

(Ngz can ignore the rest of the message)

> 1. the current issue is that the exported references like: 
>
> References
>
> * .............
> * ..............
> * ..............
>
> instead of :
>
> References
>
> [1] .......
> [2] .......
> [3] ........ 
>
> Is it default setting or a bug?

Do you see numbered list in the ODT file that I sent you.  If yes, then
it is likely that you don't have the new styles file
(etc/styles/OrgOdtStyles.xml) or that the exporter is picking up the old
styles file.

What is the value of 

  (custom-set-variables
   '(org-odt-citation-transcoders
     (quote
      (org-odt-citation-reference/numbered
      . org-jabref-odt-bibliography/numbered))))

You need the above setting for creating numbered entries.  Yes, there
are multiple transcoders that you can use.  One of the transcoders will
NOT use the numbered list.  See custom buffer for details.

If you do

  M-x load-library RET ox-odt.el RET

and subsequently look at *Messages* buffer what styles file is it
using.  It should use the updated styles file.  In my case, I see

  Debug (ox-odt): Using styles under
  /home/kjambunathan/src/org-mode/etc/styles/

If you have "merged" from my git repo, you will have the updated styles
file.  But for some reason it may not be picked up.  In that case,
update your .emacs with this line.  The path below should point to the
parent of the "styles" sub-directory.

  (setq org-odt-data-dir "~/src/org-mode/etc/")

The ODT style that is newly introduced is called "OrgBibliographyList".
If everything is alright, it should be visible as a List Style in
LibreOffice's Stylist.

feng shu <tumashu@gmail.com> writes:

> On Mon, Jul 29, 2013 at 3:48 AM, Jambunathan K
> <kjambunathan@gmail.com> wrote:
>
>     Sorry about spamming you.
>     
>     > s/RTFChars/XMLChars/ is what was needed.
>     
>     If I use XMLChars, then the Chinese characters in content.xml are
>     actually numerically encoded. This would make reading of
>     content.xml
>     and hence debugging of corruption issues very difficult.
>     
>     So, I have used s/XMLChars/FormatChars/ and pushed one more update
>     to
>     the JabRef plugin.
>     
>     The download link below is still the same. It always points to the
>     latest plugin jar.
>     
>     
>
> 2. Word "References" should be added to `org-export-dictionary'
>
>     Jambunathan K <kjambunathan@gmail.com> writes:
>     
>     > OK. I have pushed a fix.
>     >
>     > Here is the direct link to updated JabRef Plugin:
>     >
>     >
>     http://repo.or.cz/w/JabRefChicagoForOrgmode.git/blob_plain/master:/net.
>     sf.jabref.export.Chicago.ODF(English)-1.2.jar
>     >
>     > Git repository (Home Page):
>     > http://repo.or.cz/w/JabRefChicagoForOrgmode.git
>     >
>     > Pull URL:
>     > git://repo.or.cz/JabRefChicagoForOrgmode.git
>     > http://repo.or.cz/r/JabRefChicagoForOrgmode.git
>     >
>     > s/RTFChars/XMLChars/ is what was needed. With export preferences
>     set to
>     > utf-8, I am able to export you *.bib entry. I am attaching the
>     test
>     > case file. They seem OK to my non-chinese eye.
>     >
>     >
>     >
>     >
>     >
>     > Jambunathan K <kjambunathan@gmail.com> writes:
>     >
>     >> Thanks for trying out.
>     >>
>     >> I don't understand JabRef. So both of us are proceeding blindly
>     here.
>     >>
>     >> Possibility 1:
>     >> =============
>     >>
>     >> The original JabRef plugin is actually a RTF exporter.
>     >>
>     >> 1. Identify the type of the Bib entry you are exporting. Looks
>     like the
>     >> entry below is a masterthesis (It could be book, article
>     >> etc). Identify the correspoding layout file. For example,
>     >>
>     >> Chicago.text.mastersthesis.layout
>     >> Chicago.reference.mastersthesis.layout
>     >>
>     >> ,----
>     >> | \begin{author}
>     >> | \format[RTFChars,AuthorLastFirstCommas]{\author}. \end
>     {author}
>     >> | \begin{year}\format[RTFChars]{\year}. \end{year}
>     >> | \begin{title}\format[RTFChars]{\title}. \end{title}Masters
>     thesis,
>     >> | \format[RTFChars]{\school}. \\par\\par
>     >> `----
>     >>
>     >> You can open the Jar file right within Emacs with C-x C-f
>     >> whatever.jar.
>     >>
>     >> 2. Fix up the layout files.
>     >>
>     >> i.e, Replace \format[RTFChars] with \format[XMLChars]. The
>     >> documentation in
>     http://jabref.sourceforge.net/help/CustomExports.php
>     >> is not very clear.
>     >>
>     >> 3. Zip up the Jarfile.
>     >>
>     >> 4. Uninstall the old plugin
>     >>
>     >> 5. Install the new plugin
>     >>
>     >> 6. Re-export.
>     >>
>     >> 7. See whether the output now makes sense.
>     >>
>     >> Possibility 2:
>     >> ==============
>     >>
>     >> ,---- See http://jabref.sourceforge.net/faq.php
>     >> |
>     >> | Q: Does JabRef support Chinese characters?
>     >> |
>     >> | A: Yes. Go to Options->Preferences->General->Default
>     Encoding. Set it to
>     >> | UTF8. At “Appearance” set table font as simsun (or any other
>     Chinese
>     >> | font). At “General”, you can change the UI language to
>     Chinese. More
>     >> | information was available at
>     >> |
>     http://yenlung.math.nccu.edu.tw/~yenlung/notes/latex_in_Windows.pdf,
>     but
>     >> | the link is currently broken.
>     >> |
>     >> `----
>     >>
>     >> See whether this setting makes a differnce.
>     >>
>     >>
>     >> Possibility 3:
>     >> =============
>     >>
>     >> If both 1 and 2, doesn't work, choose some other already
>     existng XML
>     >> based export format. (I see docbook as supported export
>     format). See
>     >> whether you can export entries using GUI.
>     >>
>     >> See *Messages* buffer for how you can export a key via command
>     line or
>     >> use the GUI to check results directly.
>     >>
>     >> ,----
>     >> | kjambunathan@debian-6:~/Downloads$ java -jar JabRef-2.9.2.jar
>     -n true -help
>     >> | Found 5 plugin(s):
>     >> | - net.sf.jabref.core
>     (jar:file:/home/kjambunathan/Downloads/JabRef-2.9.2.jar!/plugins/net.
>     sf.jabref.core/plugin.xml)
>     >> | - net.sf.jabref.export.chicago.ODF
>     (jar:file:/home/kjambunathan/.jabref/plugins/net.sf.jabref.export.Chicago.
>     ODF(English)-1.2.jar!/plugin.xml)
>     >> | - net.sf.jabref.export.chicago
>     (jar:file:/home/kjambunathan/.jabref/plugins/net.sf.jabref.export.Chicago
>     (English)-1.2.jar!/plugin.xml)
>     >> | - net.sf.jabref.oo.ooplugin
>     (jar:file:/home/kjambunathan/.jabref/plugins/net.sf.jabref.oo.ooplugin-
>     0.9.jar!/plugin.xml)
>     >> | - net.sf.jabref.export.misq
>     (jar:file:/home/kjambunathan/Downloads/JabRef-2.9.2.jar!/plugins/net.
>     sf.jabref.export.misq/plugin.xml)
>     >> |
>     >> | jabref [options] [bibtex-file]
>     >> |
>     >> | Option Name Type Description
>     >> |
>     >> | -f, --fetch <STRING> Run Fetcher, e.g.
>     "--fetch=Medline:cancer"
>     >> | -o, --output <STRING> Output or export file: filename[,export
>     format]
>     >> | -p, --primp <STRING> Import preferences from file
>     >> | -n, --nogui <BOOLEAN> No GUI. Only process command line
>     options.
>     >> | -a, --aux <STRING> Subdatabase from aux: file[.aux],new[.bib]
>     >> | -h, --help <BOOLEAN> Display help on command line options
>     >> | -b, --blank <BOOLEAN> Do not open any files at startup
>     >> | --importToOpen <STRING> Import to open tab
>     >> | -i, --import <STRING> Import file: filename[,import format]
>     >> | -s, --nosplash <BOOLEAN> Do not show splash window at startup
>     >> | -x, --prexp <STRING> Export preferences to file
>     >> | -d, --prdef <STRING> Reset preferences (key1,key2,... or '
>     all')
>     >> | -v, --version <BOOLEAN> Display version
>     >> | -m, --exportMatches <STRING> [field]searchTerm,outputFile:
>     file[,exportFormat
>     >> | -l, --loads <BOOLEAN> Load session
>     >> |
>     >> | Available import formats:
>     >> | BibTeXML : bibtexml
>     >> | Biblioscape : biblioscape
>     >> | Biomail : biomail
>     >> | CSA : csa
>     >> | Copac : cpc
>     >> | INSPEC : inspec
>     >> | ISI : isi
>     >> | JStor (tab delimited) : jstor
>     >> | MSBib : msbib
>     >> | Medline : medline
>     >> | Ovid : ovid
>     >> | REPEC New Economic Papers (NEP) : repecnep
>     >> | RIS : ris
>     >> | Refer/Endnote : refer
>     >> | Scifinder : scifinder
>     >> | SilverPlatter : silverplatter
>     >> | Sixpack : sixpack
>     >> | XMP-annotated PDF : xmpannotatedpdf
>     >> |
>     >> | Available export formats: MSBib, bibordf, bibtexml,
>     chicago.ODF.abstract,
>     >> | chicago.ODF.biblio, chicago.ODF.footend,
>     chicago.ODF.footend.short,
>     >> | chicago.ODF.note, chicago.ODF.reference, chicago.ODF.text,
>     >> | chicago.abstract, chicago.biblio, chicago.footend,
>     >> | chicago.footend.short, chicago.note, chicago.reference,
>     chicago.text,
>     >> | din1505, docbook, endnote, harvard, html, listrefs, misq,
>     mods, mysql,
>     >> | ods, oocalc, oocsv, ooxml.reference, postgresql, ris,
>     simplehtml,
>     >> | tablerefs, tablerefsabsbib.
>     >> | kjambunathan@debian-6:~/Downloads$
>     >> `----
>     >>
>     >>
>     >> Possibility 4:
>     >> ==============
>     >>
>     >> May be I have to setup coding-system for read and write within
>     the
>     >> ox-jabref.el.
>     >>
>     >> Possibility 5: Last resort :-)
>     >> ==============
>     >>
>     >> Send me the Chinese *.bib file. I will try my best where the
>     issue
>     >> could be.
>     >>
>     >>
>     >>
>     >> Feng Shu <tumashu@gmail.com> writes:
>     >>
>     >>> I tested this patch and found that it can't work well with
>     Chinese
>     >>> character:
>     >>>
>     >>> the output xml file like this:
>     >>> #+begin_example
>     >>> <!-- BEGIN JABREF - CHICAGO ODF REFERENCE -->
>     >>>
>     >>> <text:p text:style-name="Bibliography">
>     >>> <text:bookmark text:name="zhubajie"/>
>     >>> <text:bookmark-start text:name="cite-zhubajie"/>
>     >>>
>     >>>
>     >>> \u29482?\u20843?\u25106?.
>     >>> 2005.
>     >>>
>     \u35770?\u27969?\u20307?\u39135?\u29289?\u30340?\u25345?\u20037?\u20445?
>     \u23384?. Masters
>     >>> thesis, \u24191?\u23506?\u23467?\u22823?\u23398?.
>     >>>
>     >>> <text:bookmark-end text:name="cite-zhubajie"/>
>     >>> </text:p><!-- END JABREF - CHICAGO ODF REFERENCE -->
>     >>>
>     >>> #+end_example
>     

^ permalink raw reply	[flat|nested] 8+ messages in thread
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2013-07-18 20:01 [WIP/RFC] Bibliography support ODT + JabRef Jambunathan K
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     [not found]           ` <CAJpRBmekaaeV58KoHet=HpmHJD3Ua8THw5bpACVfWngYKTQCQg@mail.gmail.com>
     [not found]             ` <87li4q9dt6.fsf@gmail.com>
     [not found]               ` <CAJpRBmewo+q8Dc-AeTQ0F=u-6_nFbRTWW_9gOF9Dn9SB8fXCnw@mail.gmail.com>
2013-07-30  5:07                 ` Jambunathan K
2013-07-30  9:39                   ` Rasmus
2013-07-30  9:56                   ` feng shu
2013-07-30 13:25                     ` Feng Shu
  -- strict thread matches above, loose matches on Subject: below --
2013-07-29  4:31 Jambunathan K

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