[Refdb-devel] [ refdb-Bugs-1951049 ] bibtex + ELEC

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Bugs item #1951049, was opened at 2008-04-24 20:07
Message generated for change (Comment added) made by mhoenicka
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https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951049&group_id=26091

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Category: refdbd
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Damien Jade Duff (damienjadeduff)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: bibtex + ELEC

Initial Comment:

Hi again!

Now I think I've got a history with this citation type. However, this report should be unrelated to that old stuff (hope so).

Now bibtex generation of ELEC entries into MISC bibtex types is dropping the AUTHOR part. This is new to 1.0.0-pre1 (and in svn). In 0.9.9-1 this generation was adding an extra comma instead (or this change may have occured because I have updated some other software on which refdb depends while I did the upgrade to svn).

See the example below.

Thanks again!
Damien

mycomp% refdbc -u djd -w 123 -d djdphd -C getref -t bibtex -N 1 :TY:=ELEC > bib1.bib
999:1 retrieved:0 failed

mycomp% cat bib1.bib
@MISC{ ZIEMKE2001,
  YEAR = {2005},
  TITLE = {Are Robots Embodied?},
  URL = { http://www.ida.his.se/\~tom/EpiRob.web.pdf}
}

mycomp% refdbc -u djd -w 123 -d djdphd -C getref -t risx -N 1 :TY:=ELEC > bib1.risx
999:1 retrieved:0 failed

mycomp% cat bib1.risx
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.2.0//EN" "http://refdb.sourceforge.net/dtd/risx-1.2.0/risx.dtd" [
<!ENTITY lt "&#38;#60;">
<!ENTITY gt "&#62;">
<!ENTITY amp "&#38;#38;">
<!ENTITY mdash "&#x2014;">
<!ENTITY lsquo "&#x2018;">
<!ENTITY rsquo "&#x2019;">
]>
<ris>

  <entry type="ELEC" id="2" citekey="ZIEMKE2001">
    <publication>
      <title type="full">Are Robots Embodied?</title>
      <author>
        <lastname>Ziemke</lastname>
        <firstname>Tom</firstname>
      </author>
      <pubinfo>
        <pubdate type="primary">
          <date><year>2005</year></date>
        </pubdate>
        <link type="url">http://www.ida.his.se/~tom/EpiRob.web.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>Entered For/PhD</notes>
      <reprint status="INFILE"/>
      <availability type="useroot">Embodied Robots/Ziemke2001.pdf</availability>
    </libinfo>
    <contents>
      <keyword>embodied</keyword>
      <keyword>embodied robotics</keyword>
      <keyword>robotics</keyword>
    </contents>
  </entry>
</ris>
acws-0175%

My system configuration now is:
refdb-1.0.0-pre1 (also happening on the svn as of this morning)
libdbi-cvs-20080421
libdbi-drivers-cvs-20080421
sqlite-3.5.8
Linux acws-0175 2.6.9-67.0.7.ELsmp #1 SMP Sat Mar 15 06:54:55 EDT 2008 i686 i686 i386 GNU/Linux

Cheerios!
Damien

----------------------------------------------------------------------

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-05-01 00:53

Message:
Logged In: YES 
user_id=85809
Originator: NO

Hi,

you caught me red-handed! I thought I'd get away with testing the bibtex
output of a couple of existing entries, but these tests went ok. Now I ran
the test just as you outlined, using your original data, and voila - the
author is gone. Turns out it was a problem of the risx import. refdbd is
supposed to assign default author roles unless roles are specifically
requested in a risx dataset. This works ok with RIS data, but a stupid bug
in the risx import would assign roles only if they were explicitly taken
from the risx dataset, leaving the field empty otherwise. The bibtex output
is the only one that strictly relies on author roles (to distinguish
authors from editors), so this is where the problem finally haunted me.

I've checked in a new version of risxhandler.c which should fix this
problem.

regards,
Markus

----------------------------------------------------------------------

Comment By: Damien Jade Duff (damienjadeduff)
Date: 2008-04-30 16:09

Message:
Logged In: YES 
user_id=2066694
Originator: YES

Hiya

Thanks lots Markus for your fixes! Works fine for the other bug [ 1951835
] now.

I've had an opportunity to take a look at this other problem [ 1951049 ]
(bibtex + ELEC) from the latest SVN version and unfortunately the problem
persists, the publication author is still lost when generating bibtex. 
Again, I'm creating a blank DB as per previous script - using
refdb.3.dump.sqlite (when using refdbd -a, which is working now - yay! -
the issue is also produced) then starting refdbd then using createdb in
refdba to create a reference DB then uploading my test reference from risx
- same config files as in previous script too.

I've also attached the refdbd output for the getref -t bibtex command at
the bottom.

Let us map out these little-trodden hills so that others who come after
may wonder at the weird little patterns of stones.

Peace
Damien

mycomp% refdbc -u 123 -w 123 -C countref :ID:\>0
999:0 counted

mycomp% cat ~/testauthorloss.risx
<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.2.0//EN"
"http://refdb.sourceforge.net/dtd/risx-1.2.0/risx.dtd" [
<!ENTITY lt "&#38;#60;">
<!ENTITY gt "&#62;">
<!ENTITY amp "&#38;#38;">
<!ENTITY mdash "&#x2014;">
<!ENTITY lsquo "&#x2018;">
<!ENTITY rsquo "&#x2019;">
]>
<ris>

  <entry type="BOOK" id="8" citekey="CORBALLIS2003">
    <publication>
      <title type="full">From Hand to Mouth: The Origins of
Language</title>
      <author>
        <lastname>Michael C. Corballis</lastname>
      </author>
      <pubinfo>
        <pubdate type="primary">
          <date><year>2003</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Princeton</city>
        <publisher>Princeton University Press</publisher>
        <serial>ISBN0691116733</serial>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>Entered For/Peripheral:Entered For/PhD</notes>
      <reprint status="NOTINFILE"/>
    </libinfo>
    <contents>
      <keyword>evolution</keyword>
      <keyword>hemisphericity</keyword>
      <keyword>language</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -u 123 -w 123 -C addref -A risx < ~/testauthorloss.risx
999:1 added:0 skipped:0 failed

mycomp% refdbc -u 123 -w 123 -C getref -t bibtex :ID:\>0 >
~/testauthorloss.bib
999:1 retrieved:0 failed

mycomp% cat ~/testauthorloss.bib
@BOOK{ CORBALLIS2003,
  YEAR = {2003},
  TITLE = {From Hand to Mouth: The Origins of Language},
  PUBLISHER = {Princeton University Press}
}

**** REFDBD OUTPUT FROM GETREF -T BIBTEX COMMAND: ****

adding client 127.0.0.1 on fd 5
server waiting n_max_fd=5
try to read from client
parent removing client on fd 5
server waiting n_max_fd=4
serving client on fd 5 with protocol version 6
012-47-22-83
send pseudo-random string to client
getref  -u 123 -w 102037101 -d djdphd -t "bibtex" -R
/data/private/djd/Library -E UTF-8 -G
/data/private/djd/binary/share/refdb/css/refdb.css 10
dbi is up
localhost
123
123
djdphd

sqlite3
/data/private/djd/Library/ReferenceDatabaseSqlite3/
UTF-8
refdb
connected to database server using database:
refdb
Main database looks ok:
refdb
localhost
123
123
djdphd

sqlite3
/data/private/djd/Library/ReferenceDatabaseSqlite3/
UTF-8
djdphd
SELECT meta_app,meta_type,meta_dbversion FROM t_meta WHERE
meta_type='risx'
connected to database server using database:
djdphd
no character encoding conversion required
output encoding is:
UTF-8
SELECT DISTINCT t_refdb.refdb_id, t_refdb.refdb_type,
t_refdb.refdb_pubyear, t_refdb.refdb_startpage, t_refdb.refdb_endpage,
t_refdb.refdb_abstract, t_refdb.refdb_title, t_refdb.refdb_volume,
t_refdb.refdb_issue, t_refdb.refdb_booktitle, t_refdb.refdb_city,
t_refdb.refdb_publisher, t_refdb.refdb_title_series, t_refdb.refdb_address,
t_refdb.refdb_issn, t_refdb.refdb_periodical_id,
t_refdb.refdb_pyother_info, t_refdb.refdb_secyear,
t_refdb.refdb_secother_info, t_refdb.refdb_user1, t_refdb.refdb_user2,
t_refdb.refdb_user3, t_refdb.refdb_user4, t_refdb.refdb_user5,
t_refdb.refdb_typeofwork, t_refdb.refdb_area, t_refdb.refdb_ostype,
t_refdb.refdb_degree, t_refdb.refdb_runningtime,
t_refdb.refdb_classcodeintl, t_refdb.refdb_classcodeus,
t_refdb.refdb_senderemail, t_refdb.refdb_recipientemail,
t_refdb.refdb_mediatype, t_refdb.refdb_numvolumes, t_refdb.refdb_edition,
t_refdb.refdb_computer, t_refdb.refdb_conferencelocation,
t_refdb.refdb_registrynum, t_refdb.refdb_classification,
t_refdb.refdb_section, t_refdb.refdb_pamphletnum, t_refdb.refdb_chapternum,
t_refdb.refdb_citekey FROM t_refdb WHERE refdb_type!='DUMMY' AND
t_refdb.refdb_id>'0' ORDER BY t_refdb.refdb_id
SELECT
t_author.author_name,t_author.author_lastname,t_author.author_firstname,t_author.author_middlename,t_author.author_suffix,t_xauthor.xauthor_role,
t_xauthor.author_id FROM t_author INNER JOIN t_xauthor ON
t_author.author_id=t_xauthor.author_id WHERE  t_xauthor.xauthor_type=2 AND 
 t_xauthor.xauthor_role='author' AND  t_xauthor.refdb_id=1 ORDER BY
t_xauthor.xauthor_position
SELECT
t_author.author_name,t_author.author_lastname,t_author.author_firstname,t_author.author_middlename,t_author.author_suffix,t_xauthor.xauthor_role,
t_xauthor.author_id FROM t_author INNER JOIN t_xauthor ON
t_author.author_id=t_xauthor.author_id WHERE  t_xauthor.xauthor_type=2 AND 
 t_xauthor.xauthor_role='editor' AND  t_xauthor.refdb_id=1 ORDER BY
t_xauthor.xauthor_position
SELECT
t_author.author_name,t_author.author_lastname,t_author.author_firstname,t_author.author_middlename,t_author.author_suffix,t_xauthor.xauthor_role,
t_xauthor.author_id FROM t_author INNER JOIN t_xauthor ON
t_author.author_id=t_xauthor.author_id WHERE  t_xauthor.xauthor_type=3 AND 
 t_xauthor.refdb_id=1 ORDER BY t_xauthor.xauthor_position
SELECT DISTINCT t_link.link_url FROM t_user,t_link INNER JOIN t_xlink ON
t_link.link_id=t_xlink.link_id WHERE t_xlink.xlink_type='URL' AND
t_xlink.xlink_source='REFERENCE' AND t_xlink.xref_id=1 AND
((t_xlink.user_id=t_user.user_id AND t_user.user_name='123') OR
t_xlink.user_id=0)
SELECT DISTINCT t_link.link_url FROM t_user,t_link INNER JOIN t_xlink ON
t_link.link_id=t_xlink.link_id WHERE t_xlink.xlink_type='PDF' AND
t_xlink.xlink_source='REFERENCE' AND t_xlink.xref_id=1 AND
((t_xlink.user_id=t_user.user_id AND t_user.user_name='123') OR
t_xlink.user_id=0)
SELECT DISTINCT t_link.link_url FROM t_user,t_link INNER JOIN t_xlink ON
t_link.link_id=t_xlink.link_id WHERE t_xlink.xlink_type='FULLTEXT' AND
t_xlink.xlink_source='REFERENCE' AND t_xlink.xref_id=1 AND
((t_xlink.user_id=t_user.user_id AND t_user.user_name='123') OR
t_xlink.user_id=0)
SELECT DISTINCT t_link.link_url FROM t_user,t_link INNER JOIN t_xlink ON
t_link.link_id=t_xlink.link_id WHERE t_xlink.xlink_type='RELATED' AND
t_xlink.xlink_source='REFERENCE' AND t_xlink.xref_id=1 AND
((t_xlink.user_id=t_user.user_id AND t_user.user_name='123') OR
t_xlink.user_id=0)
SELECT DISTINCT t_link.link_url FROM t_user,t_link INNER JOIN t_xlink ON
t_link.link_id=t_xlink.link_id WHERE t_xlink.xlink_type='IMAGE' AND
t_xlink.xlink_source='REFERENCE' AND t_xlink.xref_id=1 AND
((t_xlink.user_id=t_user.user_id AND t_user.user_name='123') OR
t_xlink.user_id=0)
SELECT DISTINCT t_link.link_url FROM t_user,t_link INNER JOIN t_xlink ON
t_link.link_id=t_xlink.link_id WHERE t_xlink.xlink_type='DOI' AND
t_xlink.xlink_source='REFERENCE' AND t_xlink.xref_id=1 AND
((t_xlink.user_id=t_user.user_id AND t_user.user_name='123') OR
t_xlink.user_id=0)
command processing done, finish dialog now
child finished client on fd 5
child exited with code 0
server waiting n_max_fd=4

----------------------------------------------------------------------

Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-27 22:47

Message:
Logged In: YES 
user_id=85809
Originator: NO

Are you still using reference databases created with RefDB 0.9.8 or
earlier? As I cannot reproduce this problem here, I suspect your reference
database was not properly upgraded when moving from 0.9.8 to the current
version. The internal data representation has changed somewhat, and this
would nicely explain the problems you see. Please check carefully the
UPGRADING file which explains the background and the proper procedure to
upgrade. Let me know if the problem persists, or if you can reproduce it
with a fresh database created with 0.9.9 or later.

regards,
Markus

----------------------------------------------------------------------

Comment By: Damien Jade Duff (damienjadeduff)
Date: 2008-04-25 18:05

Message:
Logged In: YES 
user_id=2066694
Originator: YES

Hi

I just noticed that this applies also to BOOK ris types (always) and GEN
ris types (when the author is inside the risx publication tag) - bibtex
generation is not giving back the author. Hope this is useful..

Peace
Damien

mycomp% refdbd -v
refdbd 1.0.0-pre1 built from svn revision 613 ma...@mh...
You may redistribute and modify this software under the terms of the GNU
General Public License.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951049&group_id=26091