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Re: [O] zotero plain, org-odt, and citations in general


From: Thomas S. Dye
Subject: Re: [O] zotero plain, org-odt, and citations in general
Date: Thu, 10 Nov 2011 05:50:00 -1000

Jambunathan K <address@hidden> writes:

>>    1. org-zotero.el
>>
>>       This permits insertion of zotero reference links *only* and
>>       opening them with a browser. 
>>
>>       Specifically I don't see the translator of these links to
>>       individual backends like latex, html or more importantly ODT.
>>
>>       #+begin_src emacs-lisp
>>         (org-add-link-type TYPE &optional FOLLOW EXPORT)
>>       #+end_src
>>
>>    2. zotero.el
>>
>>       This (apparently) permits download of data from firefox and
>>       importing it within Emacs.
>
>
> I think I now have some understanding of what Erik's library does[1]. 
>
> It creates a bibliographic entry (as in Footnotes) using Quick Copy.  It
> doesn not create a footnote reference. One can use the Firefox Zotero
> and see how Quick Copy works with both RTF and HTML formats[2].
>
> [Question to Erik: Can one not use "Copy from Clipboard" from elisp
> instead of going the mozrepl route to create a biblio.text]
>
> Instead of working with JS libraries, I think the right starting point
> would be to work with the underlying zotero.sqlite database itself. It
> is not difficult to get a key of the selected item in Zotero
> pane[3]. Once this is done the underlying zotero.sqlite database could
> be queried for the item properties[4].
>
> Fortunately there is already a GUI/Command line tool - Gnotero[5] -for
> accessing the sqlite database.
>
> As for exploiting the power of using zotero within libreoffice - which
> is to have the same citation presented in different citation styles -
> one need to look at how the reference marks are produced within
> OpenDocument XML.
>
> Here is a typical reference mark for an item with local zotero URL[6]:
> zotero://report/items/579241_E7232HE2/html/report.html
>
> LIBRARY=>579241
> KEY=>E7232HE2
>
>
> #+begin_src nxml
>   <text:p text:style-name="Footnote">
>     <text:reference-mark-start text:name="ZOTERO_ITEM 
> {&quot;citationID&quot;:&quot;2lhcdnkups&quot;,&quot;citationItems&quot;:[{&quot;uri&quot;:[&quot;http://zotero.org/groups/51961/items/E7232HE2&quot;]}]}
>  RNDB7mi3QiueI"/>Crew, “Alltagsgeschichte.”
>     <text:reference-mark-end text:name="ZOTERO_ITEM 
> {&quot;citationID&quot;:&quot;2lhcdnkups&quot;,&quot;citationItems&quot;:[{&quot;uri&quot;:[&quot;http://zotero.org/groups/51961/items/E7232HE2&quot;]}]}
>  RNDB7mi3QiueI"/>
>   </text:p>
> #+end_src nxml
>
> One can see the following components:
> 1. ZOTERO_ITEM 
> 2. citationID and citationItems
>    - The citationItem has the following Zotero URI:
>      http://zotero.org/groups/51961/items/E7232HE2
>      
>      GROUP=>51961
>      KEY=>E7232HE2
>
>      Note that the keys for the entry are the same on both the local
>      zotero store and the global zotero URI.
> 3. RNDB7mi3QiueI
>    - This is a cookie entered by Zotero which maps the citation entry to
>      an entry in the zotero database. Note that it starts with RND.
>
>      This is what is called as a "FieldCode" in zotero parlance.
>
>      Note: Have you seen the "Remove Field Codes" in Zotero menu within
>      ODT document. Once you remove the field codes the document becomes
>      a simple ODT document and one would no longer be able to move
>      between different citation styles.
>
>      In essence, "Field Code" is the MAGIC WAND that zotero uses.
>
> From my little research, I can say with confidence that global zotero
> URIs and the above mentioned reference marks are *very* recent
> developments.
>
> Exercising the MAGIC WAND within ODT exporter requires diving in to
> zotero server inner workings - which is non-trivial as Erik notes - but
> would also be futile (as in chasing a shifting sand)
>
> I believe the best course would be to do convention/static footnoting
> with the simplest of Chicago styles using a choice of entry types like
> Article, Journal, Book or a Website.
>
> Proposal for Org+Zotero integration
> ===================================
>
> An org document like this
>
> #+begin_src org
> * Headline
>   This is a footnote reference[1]
>
> Footnotes:
> [1] zotero://report/items/579241_E7232HE2/html/report.html
> #+end_src org
>
> will be transformed to this on ODT export
>
> #+begin_odt
> * Headline
>   This is a footnote reference[1]     
>
> Bibliography:
>
> 1. David F. Crew, “Alltagsgeschichte: A New Social History ‘From
> below’?,” Central European History 22, no. 3/4 (1989): 394-407.
> #+end_odt
>
> Note that the footnote link is an org stlye link captured with
> org-protocol and has both a LIBRARY_ID and KEY_ID. The bibliography
> entry will be generated by "exporting" zotero link to the required
> format using a variation of gnotero. The "following/opening" of zotero
> link will be done by mapping the local zotero link to
> http://zotero.org-based URI (again) using gnotero.
>
>
> I see that there is a need for bib2odt in much the same way as there is
> a bib2html. Can someone post an example of Org file which would use
> BibTex for post-processing (either to HTML or LaTeX) The ODT exporter
> can also emulate what other backend does.
>
> ps: This mail is more of a note to self or a note to any future
> hackers. I am not certain I will be able to hack gnotero and have it
> integrate with Emacs - but for a whimsical and a bored hacker like
> nothing can be said with certainty.
>
> Btw, gnotero is good. Not sure how usable it is though ...
>
> Jambunathan K.
>
> Footnotes: 
>
> [1]  With Mozrepl 1.1 beta2 on Firefox 3.6.23, I am unable to make
> org-zotero.el work. It hangs and I have to C-g out (Christian! you are
> not alone). I am able to get as far as creating the LIBRARY_KEY for the
> selected item in the zotero pane and not further.
>
> [2] Quick Copy: http://www.zotero.org/support/creating_bibliographies
>
> [3] For producing ITEM keys: One could use zotero.el or simply "Right
> Click" on an item and do a "Generate Report from Selected Item". The
> resulting url in firefox could be captured using org-protocol and
> imported in to the org buffer. A typical URL looks like this:
>
> zotero://report/items/0_6EETTDBE/html/report.html
> 0 => My Library
> 6EETTDBE => Key of the selected item
>
> or 
> zotero://report/items/579241_E7232HE2/html/report.html
> 579241 => The local library key for "Digital Humanities UofT group"
> E7232HE2 => Key of the selected item.
>
> [4]  For locating zotero.sqlite and querying it with Sqlite Manager see
> - https://www.zotero.org/utils/dbfix/
> - http://kimmonsdesign.com/node/24
>
> [5]  http://cogsci.nl/software/qnotero
> http://www.cogsci.nl/blog/tutorials/97-writing-a-command-line-zotero-client-in-9-lines-of-code
> http://files.cogsci.nl/software/gnotero/extras/gnotero_cmdline.py
>
> [6]  See the attached zotero-libreoffice.odt

Aloha Jambunathan,

For examples of Org-mode files that use bibtex, the following might be
helpful.

A tutorial of sorts:

http://orgmode.org/worg/org-tutorials/org-latex-export.html#sec-17

A piece of reproducible research:

https://github.com/tsdye/LKFS

hth,
Tom

-- 
Thomas S. Dye
http://www.tsdye.com



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