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[Refdb-devel] [ refdb-Bugs-2619021 ] "pickref -r" causes premature end of transmission

From: SourceForge.net <no...@so...> - 2009-02-27 09:32:47

Bugs item #2619021, was opened at 2009-02-20 07:48
Message generated for change (Comment added) made by nobody
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2619021&group_id=26091

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Category: refdbd
Group: None
Status: Open
Resolution: Works For Me
Priority: 5
Private: No
Submitted By: Torsten Bronger (bronger)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: "pickref -r" causes premature end of transmission

Initial Comment:
When sending "pickref -r -l listname" to the server, the server ends the communication immediately after the transmission of the IDs.

Despite that, the item is removed from the list.  You can see this problem even in refdbc:

refdbc: dumpref -d biblio -b wichtig 1
error


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

Comment By: Nobody/Anonymous (nobody)
Date: 2009-02-27 09:32

Message:
I installed now the SVN version but I still get

refdbc: pickref -b wichtig 1
421:'chantal-wichtig' -> REFERENCE:Bld2006
999:1 picked:0 skipped:0 failed
refdbc: dumpref -b wichtig 1
error
refdbc:


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

Comment By: Torsten Bronger (bronger)
Date: 2009-02-22 21:32

Message:
Yes, sorry, I used -b instead of -l.  I run

refdbc 0.9.9-1 built from svn revision 531
refdbd 0.9.9-1 built from svn revision 531

I have not the time to investigate this further at the moment.  Maybe in a
couple of weeks.  A quick look at the diffs revealed nothing spectacular. 
However, I don't speak C very well.

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

Comment By: Markus Hoenicka (mhoenicka)
Date: 2009-02-22 20:41

Message:
I cannot reproduce this problem here using refdbc. If you run into this
problem consistently, it may have been fixed unintentionally as there are
no hints to such a problem in the cvs logs of refdbdref.c. Which version of
RefDB are you using?

Sending "pickref -r -l listname" to the server is likely to cause problems
because "-l" is not a valid option. Use "-b" instead to pass the list name.
If you found "-l" somewhere in the docs, it's a bug and I'd like to fix it.

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2619021&group_id=26091

[Refdb-devel] [ refdb-Bugs-2619021 ] "pickref -r" causes premature end of transmission

From: SourceForge.net <no...@so...> - 2009-02-22 22:25:19

Bugs item #2619021, was opened at 2009-02-20 08:48
Message generated for change (Comment added) made by bronger
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2619021&group_id=26091

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including the initial issue submission, for this request,
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Category: refdbd
Group: None
Status: Open
Resolution: Works For Me
Priority: 5
Private: No
Submitted By: Torsten Bronger (bronger)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: "pickref -r" causes premature end of transmission

Initial Comment:
When sending "pickref -r -l listname" to the server, the server ends the communication immediately after the transmission of the IDs.

Despite that, the item is removed from the list.  You can see this problem even in refdbc:

refdbc: dumpref -d biblio -b wichtig 1
error


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

>Comment By: Torsten Bronger (bronger)
Date: 2009-02-22 22:32

Message:
Yes, sorry, I used -b instead of -l.  I run

refdbc 0.9.9-1 built from svn revision 531
refdbd 0.9.9-1 built from svn revision 531

I have not the time to investigate this further at the moment.  Maybe in a
couple of weeks.  A quick look at the diffs revealed nothing spectacular. 
However, I don't speak C very well.

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

Comment By: Markus Hoenicka (mhoenicka)
Date: 2009-02-22 21:41

Message:
I cannot reproduce this problem here using refdbc. If you run into this
problem consistently, it may have been fixed unintentionally as there are
no hints to such a problem in the cvs logs of refdbdref.c. Which version of
RefDB are you using?

Sending "pickref -r -l listname" to the server is likely to cause problems
because "-l" is not a valid option. Use "-b" instead to pass the list name.
If you found "-l" somewhere in the docs, it's a bug and I'd like to fix it.

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2619021&group_id=26091

[Refdb-devel] [ refdb-Bugs-2619021 ] "pickref -r" causes premature end of transmission

From: SourceForge.net <no...@so...> - 2009-02-22 20:41:15

Bugs item #2619021, was opened at 2009-02-20 08:48
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2619021&group_id=26091

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including the initial issue submission, for this request,
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Category: refdbd
Group: None
Status: Open
>Resolution: Works For Me
Priority: 5
Private: No
Submitted By: Torsten Bronger (bronger)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: "pickref -r" causes premature end of transmission

Initial Comment:
When sending "pickref -r -l listname" to the server, the server ends the communication immediately after the transmission of the IDs.

Despite that, the item is removed from the list.  You can see this problem even in refdbc:

refdbc: dumpref -d biblio -b wichtig 1
error


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

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2009-02-22 21:41

Message:
I cannot reproduce this problem here using refdbc. If you run into this
problem consistently, it may have been fixed unintentionally as there are
no hints to such a problem in the cvs logs of refdbdref.c. Which version of
RefDB are you using?

Sending "pickref -r -l listname" to the server is likely to cause problems
because "-l" is not a valid option. Use "-b" instead to pass the list name.
If you found "-l" somewhere in the docs, it's a bug and I'd like to fix it.

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2619021&group_id=26091

[Refdb-devel] [ refdb-Bugs-2623944 ] Docs: options for second stage in protocol wrong

From: SourceForge.net <no...@so...> - 2009-02-22 01:05:02

Bugs item #2623944, was opened at 2009-02-21 14:11
Message generated for change (Comment added) made by mhoenicka
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https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2623944&group_id=26091

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Category: unspecified
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Torsten Bronger (bronger)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Docs: options for second stage in protocol wrong

Initial Comment:
See <http://refdb.sourceforge.net/manual/ch23s02.html>.  The options don't seem to be correct.  In particular, I found out that a lowercase "-s" must be used to set the bibliography style.


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

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2009-02-22 02:05

Message:
The usage of "-s" with getbib was indeed missing from the docs. I've
updated the info in svn. Feel free to reopen this bug if you run into other
incorrect or incomplete options.

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

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[Refdb-devel] [ refdb-Bugs-2623944 ] Docs: options for second stage in protocol wrong

From: SourceForge.net <no...@so...> - 2009-02-21 13:11:28

Bugs item #2623944, was opened at 2009-02-21 14:11
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2623944&group_id=26091

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Category: unspecified
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Torsten Bronger (bronger)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Docs: options for second stage in protocol wrong

Initial Comment:
See <http://refdb.sourceforge.net/manual/ch23s02.html>.  The options don't seem to be correct.  In particular, I found out that a lowercase "-s" must be used to set the bibliography style.


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2623944&group_id=26091

[Refdb-devel] [ refdb-Bugs-2619021 ] "pickref -r" causes premature end of transmission

From: SourceForge.net <no...@so...> - 2009-02-20 07:48:36

Bugs item #2619021, was opened at 2009-02-20 08:48
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2619021&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Torsten Bronger (bronger)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: "pickref -r" causes premature end of transmission

Initial Comment:
When sending "pickref -r -l listname" to the server, the server ends the communication immediately after the transmission of the IDs.

Despite that, the item is removed from the list.  You can see this problem even in refdbc:

refdbc: dumpref -d biblio -b wichtig 1
error


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2619021&group_id=26091

[Refdb-devel] [ refdb-Bugs-2457306 ] wrapper scripts do not honor program-prefix setting

From: SourceForge.net <no...@so...> - 2009-02-08 20:07:01

Bugs item #2457306, was opened at 2008-12-22 04:20
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2457306&group_id=26091

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Category: unspecified
Group: None
>Status: Closed
Resolution: Fixed
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: wrapper scripts do not honor program-prefix setting

Initial Comment:
The shell scripts which call other refdb executables do not get rewritten to honor a prefix specified with the --program-prefix option to configure.

The affected files include (but may not be limited to):
bib2ris-utf8
refdb-init
refdbctl

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

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2009-02-08 21:06

Message:
As there were no further complaints, I'm going to close this bug.

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

Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-12-24 00:29

Message:
I've attempted to fix this problem. Please check out the latest svn
revision and see if it works for you.
regards,
Markus

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2457306&group_id=26091

[Refdb-devel] [ refdb-Bugs-2580216 ] Wrong protocol version in docs

From: SourceForge.net <no...@so...> - 2009-02-08 20:06:15

Bugs item #2580216, was opened at 2009-02-08 20:35
Message generated for change (Comment added) made by mhoenicka
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https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2580216&group_id=26091

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including the initial issue submission, for this request,
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Category: unspecified
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Torsten Bronger (bronger)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Wrong protocol version in docs

Initial Comment:
http://refdb.sourceforge.net/manual/ch23s03.html#id2655889 says that the protocol versionto be submitted is "3", however, I succeded only with some two-digit numbers.  By the way, I son't know exactly what to transmit.  At least, "30" was fine.

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

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2009-02-08 21:06

Message:
This information is outdated, unfortunately. The current svn revision uses
protocol number 6. This is a constant which is set in src/connect.h. That
is, all you need to transmit initially to talk to a current refdbd server
is the string '6\0\0\0\0'. The four consecutive null bytes are the message
terminator which should be safe with any multibyte character set. I've
updated the version number in the docs. If this does not help, feel free to
reopen this tracker item.

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2580216&group_id=26091

[Refdb-devel] [ refdb-Bugs-2580216 ] Wrong protocol version in docs

From: SourceForge.net <no...@so...> - 2009-02-08 19:35:36

Bugs item #2580216, was opened at 2009-02-08 20:35
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2580216&group_id=26091

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including the initial issue submission, for this request,
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Category: unspecified
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Torsten Bronger (bronger)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Wrong protocol version in docs

Initial Comment:
http://refdb.sourceforge.net/manual/ch23s03.html#id2655889 says that the protocol versionto be submitted is "3", however, I succeded only with some two-digit numbers.  By the way, I son't know exactly what to transmit.  At least, "30" was fine.

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2580216&group_id=26091

[Refdb-devel] [ refdb-Bugs-2457306 ] wrapper scripts do not honor program-prefix setting

From: SourceForge.net <no...@so...> - 2008-12-23 23:30:01

Bugs item #2457306, was opened at 2008-12-22 04:20
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2457306&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
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Category: unspecified
Group: None
Status: Open
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: wrapper scripts do not honor program-prefix setting

Initial Comment:
The shell scripts which call other refdb executables do not get rewritten to honor a prefix specified with the --program-prefix option to configure.

The affected files include (but may not be limited to):
bib2ris-utf8
refdb-init
refdbctl

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

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-12-24 00:29

Message:
I've attempted to fix this problem. Please check out the latest svn
revision and see if it works for you.
regards,
Markus

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2457306&group_id=26091

[Refdb-devel] [ refdb-Bugs-2457306 ] wrapper scripts do not honor program-prefix setting

From: SourceForge.net <no...@so...> - 2008-12-22 03:20:20

Bugs item #2457306, was opened at 2008-12-22 03:20
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2457306&group_id=26091

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including the initial issue submission, for this request,
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Category: unspecified
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Nobody/Anonymous (nobody)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: wrapper scripts do not honor program-prefix setting

Initial Comment:
The shell scripts which call other refdb executables do not get rewritten to honor a prefix specified with the --program-prefix option to configure.

The affected files include (but may not be limited to):
bib2ris-utf8
refdb-init
refdbctl

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=2457306&group_id=26091

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

From: SourceForge.net <no...@so...> - 2008-05-01 09:47:10

Bugs item #1951049, was opened at 2008-04-24 19:07
Message generated for change (Comment added) made by damienjadeduff
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951049&group_id=26091

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Category: refdbd
Group: None
>Status: Closed
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: Damien Jade Duff (damienjadeduff)
Date: 2008-05-01 10:47

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

'Allo!
Seems to have done the job! Full speed ahead!
Cheerios
Damien

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

Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-30 23:53

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 15:09

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 21:47

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 17:05

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

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

From: SourceForge.net <no...@so...> - 2008-04-30 22:53:23

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

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
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

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

From: SourceForge.net <no...@so...> - 2008-04-30 14:09:35

Bugs item #1951049, was opened at 2008-04-24 19:07
Message generated for change (Comment added) made by damienjadeduff
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951049&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
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: Damien Jade Duff (damienjadeduff)
Date: 2008-04-30 15:09

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 21:47

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 17:05

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

[Refdb-devel] [ refdb-Bugs-1951835 ] risx url multiplying

From: SourceForge.net <no...@so...> - 2008-04-29 22:12:01

Bugs item #1951835, was opened at 2008-04-25 20:32
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Private: No
Submitted By: Damien Jade Duff (damienjadeduff)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: risx url multiplying

Initial Comment:
Hiya!

Sorry but got another one here for the pile!

Now I'm using sqlite here and the issue seems similar to a previous one in which it wasn't refdb but libdbi. 

If I UPDATE a reference using refdbc that already has a LINK TYPE="url" but I have changed the url (i.e. the update is one in which the url changes), the url tag multiplies - I get another tag, one with the old url, one with the new. I presume I can get any number of them but I haven't checked. The way I judge the intended behaviour of updateref, an update should swap the reference with everything in the RIS tag and drop the old information. Whaddya reckon? Details below.

Cheerios!
Damien

SETUP:

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

EXAMPLE:

mycomp% cat thisisatest2.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="CONF" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes></notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C addref -A risx < thisisatest2.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout1.risx
999:1 retrieved:0 failed
mycomp% cat testout1.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat thisisatest.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="CONF" id="196" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C updateref -A risx < thisisatest.risx
999:1 updated:0 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout2.risx
999:1 retrieved:0 failed
mycomp% cat testout2.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>


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

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-30 00:11

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

Hi again,

I've checked in a fix which resolves the URL duplication (and hopefully
doesn't break anything else), as well as an updated installation chapter
which avoids naming the dump file versions explicitly. I'm going to close
this bug, but feel free to reopen it if updating references should still
fail on your box.

regards,
Markus

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

Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-29 21:55

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

Hi,

lets go through your tests one by one:

Part 1: URL duplication
I'm afraid I made an error when checking the URL duplication stuff.
Apparently I updated an existing entry with the original dataset - this
reproducibly does not duplicate the URL. However, if I follow your
instructions step by step, I do see the duplicate. I'll provide a fix
asap.

Part 2: refdb main database file creation
If the manual still mentions refdb.2.dump.sqlite, the information is
outdated. I'll try and rewrite the sections so I don't have to update them
with each new version of the dump files. Indeed, refdb.3.dump.sqlite is the
current version which should work ok.

Part 3: refdbd -a
As for upgrading from a main database version 2 to version 3, there was
indeed a bug caused by an incomplete migration to the latest libdbi
version. I've fixed that in svn, and I can successfully update a sqlite3
main database.

Other stuff:
I had forgotten to check in refdbrtfrc.  It should pop up next time you
upgrade your svn version.

regards,
Markus



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

Comment By: Damien Jade Duff (damienjadeduff)
Date: 2008-04-29 18:51

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

Oh, hi
Incidentally, I should mention that the same stuff also happens if I don't
ever add the ~/simplerisx.risx file, which only is an older version of risx
because I used an older xml skeleton and haven't updated. I just was using
it to check that the system was working.
Peace
Damien

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

Comment By: Damien Jade Duff (damienjadeduff)
Date: 2008-04-29 18:43

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

Hi there!

Thanks very much for your reply! I appreciate you taking a look!

I was, it is true, using 0.9.9-1 when I first started using refdb again
recently, but I'm now using the svn. But the thing is I put the refs into
the DB by adding an old dumped RISX file into an empty DB (I give an
example below).

I was thinking that it may be my route to installation that is specific?
Since 'refdbd -a' segfaults (not sure why, but details below - part *3) and
refdb complains that a DB created with refdb.2.dump.sqlite is an out of
date DB (again below, part *2 - though I think the manual still refers to
refdb.2.dump.sqlite), I was creating a basic refdb DB using the provided
sql file refdb.3.dump.sqlite (full details below, part *1, including a
replication of bug 1951835 after creating a new DB from scratch) - which
*seemed* to produce the desired results, except for the bugs I mentioned
which made themselves apparent later, so I had (perhaps foolishingly)
assumed it was the way to go.

The other two things that are unique about my install is that I'm using my
own database file directory for the embedded DB, and the whole install was
done onto a user owned file system (i.e. nothing from root). I'm not sure
if that would make any difference. ALSO, in the source directory I needed
to go to /etc and type "touch refdbrtfrc" as the make script seemed to need
it but it wasn't there, and I renamed the man and doc directories (and put
in dummy Makefiles) so that it would compile without the docs (again, I
don't think any of that should make a difference?).

Anyway, I'll just put the logs of my journey, from DB creation to
insertion, below, and hope the tale will amuse...

Cheerios!
Damien

**** FIRST PART *1 - REFDB.3.DUMP.SQLITE + DUPLICATED URLS ****

mycomp% ls

mycomp% sqlite3 refdb < ~/HD/binary/share/refdb/sql/refdb.3.dump.sqlite

mycomp% ls
refdb

** (start refdbd in another window) **

mycomp% refdbd -s -l 7 -e 0
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
application server started
share extended notes by default
use /tmp/refdbd_fifo8917 as fifo
server waiting n_max_fd=4

** (back to original window) **

mycomp% refdba
refdba: createdb djdphd
999:1 created:0 failed
refdba: quit

mycomp% ls
DB_VERSION  djdphd  refdb

mycomp% refdbc -u 132 -w 123 -C addref -A risx < ~/simplerisx.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C addref -A risx < ~/thisisatest2.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C updateref -A risx < ~/thisisatest.risx
999:1 updated:0 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C getref -t risx :ID:\>0 >
~/aftertesting.risx
999:2 retrieved:0 failed
mycomp% cat ~/aftertesting.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="GEN" id="1" citekey="TESTY">
    <part>
      <title type="full"/>
    </part>
    <publication>
      <title type="full">test1</title>
      <author>
        <name>testa testb</name>
      </author>
      <pubinfo>
        <pubdate type="primary">
          <date><year>2008</year><month>00</month><day>00</day></date>
        </pubdate>
      </pubinfo>
    </publication>
  </entry>


  <entry type="CONF" id="2" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
        <link
type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb
puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/thisisatest2.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="CONF" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link
type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes></notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/thisisatest.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="CONF" id="196" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb
puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/simplerisx.risx

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.0.2//EN"
"/data/private/djd/binary/share/refdb/dtd/risx.dtd"
[
<!ENTITY lt "&#38;#60;">
<!ENTITY gt "&#62;">
<!ENTITY amp "&#38;#38;">
]>
<ris>
        <entry type="GEN" citekey="TESTY">
                <publication>
                        <title type="full">test1</title>
                        <author>
                                <name>testa testb</name>
                        </author>
                        <pubinfo>
                                <pubdate>
                                        <date>
                                                <year>2008</year>
                                                <month></month>
                                                <day></day>
                                        </date>
                                </pubdate>

                        </pubinfo>
                </publication>

        </entry>
</ris>

mycomp%

**** SECOND PART *2 - REFDB.2.DUMP.SQLITE ****

(go to other window and close refdbd)
(then come back)

mycomp% pwd
/data/private/djd/Library/ReferenceDatabaseSqlite3
mycomp% rm *
mycomp% sqlite3 refdb < ~/HD/binary/share/refdb/sql/refdb.2.dump.sqlite

** (go back now and restart refdbd) **

mycomp% refdbd -s -l 7 -e 0
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
application server started
share extended notes by default
use /tmp/refdbd_fifo9031 as fifo
server waiting n_max_fd=4

** (and now back to original window) **

mycomp% refdba
refdba: createdb djdphd
main database version is not supported
refdba: quit

**** THIRD PART *3 - REFDBD -A ****

** (go to other window and close refdbd)** 
** (then come back) **

mycomp% pwd
/data/private/djd/Library/ReferenceDatabaseSqlite3

mycomp% rm *

mycomp% refdbd -a -e 0 -l 7
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
check main database version
localhost
djd



sqlite3
/data/private/djd/Library/ReferenceDatabaseSqlite3/
UTF-8
Segmentation fault
mycomp%

**** SYSTEM INFO ****

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.
mycomp% refdbc -v
refdbc 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.
mycomp% refdba -v
refdba 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.
mycomp% uname -a
Linux mycomp 2.6.9-67.0.7.ELsmp #1 SMP Sat Mar 15 06:54:55 EDT 2008 i686
i686 i386 GNU/Linux
mycomp%

LIBDBI:
libdbi-cvs-20080421
libdbi-drivers-cvs-20080421

mycomp% cat ~/HD/binary/etc/refdb/refdbdrc | sed s/^#.\*\$// | grep '.'
refdblib /data/private/djd/binary/share/refdb
main_db refdb
serverip        localhost
dbsport
dbserver        sqlite3
dbpath          /data/private/djd/Library/ReferenceDatabaseSqlite3/
port    9734
logfile /data/private/djd/binary/var/log/refdbd.log
logdest file
loglevel info
pidfile         /data/private/djd/binary/var/run/refdbd.pid
remoteadmin f
remoteconnect f
keep_pnames t
keyword_scan f
db_encoding     UTF-8
in_encoding     UTF-8

mycomp% cat ~/.refdbarc | sed s/^#.\*\$// | grep '.'
serverip        127.0.0.1
port    9734
pager   less
username  root
passwd
logdest file
loglevel info
logfile /data/private/djd/binary/var/log/refdba.log

mycomp% cat ~/.refdbcrc | sed s/^#.\*\$// | grep '.'
serverip        127.0.0.1
port    9734
pager   less
passwd *
defaultdb       djdphd
pdfroot /data/private/djd/Library
logdest file
loglevel info
logfile /data/private/djd/binary/var/log/refdbc.log
cssurl /data/private/djd/binary/share/refdb/css/refdb.css
fromencoding UTF-8
toencoding UTF-8



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

Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-27 22:48

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

I guess this is sort of a duplicate of #1951049. If you missed the upgrade
notice from 0.9.8 or earlier to 0.9.9 or later, I reckon you'd see this
kind of problem. Please see the comments to bug #1951049 for further
instructions.

regards,
Markus

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

[Refdb-devel] [ refdb-Bugs-1951835 ] risx url multiplying

From: SourceForge.net <no...@so...> - 2008-04-29 19:55:22

Bugs item #1951835, was opened at 2008-04-25 20:32
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Damien Jade Duff (damienjadeduff)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: risx url multiplying

Initial Comment:
Hiya!

Sorry but got another one here for the pile!

Now I'm using sqlite here and the issue seems similar to a previous one in which it wasn't refdb but libdbi. 

If I UPDATE a reference using refdbc that already has a LINK TYPE="url" but I have changed the url (i.e. the update is one in which the url changes), the url tag multiplies - I get another tag, one with the old url, one with the new. I presume I can get any number of them but I haven't checked. The way I judge the intended behaviour of updateref, an update should swap the reference with everything in the RIS tag and drop the old information. Whaddya reckon? Details below.

Cheerios!
Damien

SETUP:

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

EXAMPLE:

mycomp% cat thisisatest2.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="CONF" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes></notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C addref -A risx < thisisatest2.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout1.risx
999:1 retrieved:0 failed
mycomp% cat testout1.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat thisisatest.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="CONF" id="196" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C updateref -A risx < thisisatest.risx
999:1 updated:0 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout2.risx
999:1 retrieved:0 failed
mycomp% cat testout2.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>


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

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-29 21:55

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

Hi,

lets go through your tests one by one:

Part 1: URL duplication
I'm afraid I made an error when checking the URL duplication stuff.
Apparently I updated an existing entry with the original dataset - this
reproducibly does not duplicate the URL. However, if I follow your
instructions step by step, I do see the duplicate. I'll provide a fix
asap.

Part 2: refdb main database file creation
If the manual still mentions refdb.2.dump.sqlite, the information is
outdated. I'll try and rewrite the sections so I don't have to update them
with each new version of the dump files. Indeed, refdb.3.dump.sqlite is the
current version which should work ok.

Part 3: refdbd -a
As for upgrading from a main database version 2 to version 3, there was
indeed a bug caused by an incomplete migration to the latest libdbi
version. I've fixed that in svn, and I can successfully update a sqlite3
main database.

Other stuff:
I had forgotten to check in refdbrtfrc.  It should pop up next time you
upgrade your svn version.

regards,
Markus



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

Comment By: Damien Jade Duff (damienjadeduff)
Date: 2008-04-29 18:51

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

Oh, hi
Incidentally, I should mention that the same stuff also happens if I don't
ever add the ~/simplerisx.risx file, which only is an older version of risx
because I used an older xml skeleton and haven't updated. I just was using
it to check that the system was working.
Peace
Damien

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

Comment By: Damien Jade Duff (damienjadeduff)
Date: 2008-04-29 18:43

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

Hi there!

Thanks very much for your reply! I appreciate you taking a look!

I was, it is true, using 0.9.9-1 when I first started using refdb again
recently, but I'm now using the svn. But the thing is I put the refs into
the DB by adding an old dumped RISX file into an empty DB (I give an
example below).

I was thinking that it may be my route to installation that is specific?
Since 'refdbd -a' segfaults (not sure why, but details below - part *3) and
refdb complains that a DB created with refdb.2.dump.sqlite is an out of
date DB (again below, part *2 - though I think the manual still refers to
refdb.2.dump.sqlite), I was creating a basic refdb DB using the provided
sql file refdb.3.dump.sqlite (full details below, part *1, including a
replication of bug 1951835 after creating a new DB from scratch) - which
*seemed* to produce the desired results, except for the bugs I mentioned
which made themselves apparent later, so I had (perhaps foolishingly)
assumed it was the way to go.

The other two things that are unique about my install is that I'm using my
own database file directory for the embedded DB, and the whole install was
done onto a user owned file system (i.e. nothing from root). I'm not sure
if that would make any difference. ALSO, in the source directory I needed
to go to /etc and type "touch refdbrtfrc" as the make script seemed to need
it but it wasn't there, and I renamed the man and doc directories (and put
in dummy Makefiles) so that it would compile without the docs (again, I
don't think any of that should make a difference?).

Anyway, I'll just put the logs of my journey, from DB creation to
insertion, below, and hope the tale will amuse...

Cheerios!
Damien

**** FIRST PART *1 - REFDB.3.DUMP.SQLITE + DUPLICATED URLS ****

mycomp% ls

mycomp% sqlite3 refdb < ~/HD/binary/share/refdb/sql/refdb.3.dump.sqlite

mycomp% ls
refdb

** (start refdbd in another window) **

mycomp% refdbd -s -l 7 -e 0
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
application server started
share extended notes by default
use /tmp/refdbd_fifo8917 as fifo
server waiting n_max_fd=4

** (back to original window) **

mycomp% refdba
refdba: createdb djdphd
999:1 created:0 failed
refdba: quit

mycomp% ls
DB_VERSION  djdphd  refdb

mycomp% refdbc -u 132 -w 123 -C addref -A risx < ~/simplerisx.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C addref -A risx < ~/thisisatest2.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C updateref -A risx < ~/thisisatest.risx
999:1 updated:0 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C getref -t risx :ID:\>0 >
~/aftertesting.risx
999:2 retrieved:0 failed
mycomp% cat ~/aftertesting.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="GEN" id="1" citekey="TESTY">
    <part>
      <title type="full"/>
    </part>
    <publication>
      <title type="full">test1</title>
      <author>
        <name>testa testb</name>
      </author>
      <pubinfo>
        <pubdate type="primary">
          <date><year>2008</year><month>00</month><day>00</day></date>
        </pubdate>
      </pubinfo>
    </publication>
  </entry>


  <entry type="CONF" id="2" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
        <link
type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb
puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/thisisatest2.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="CONF" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link
type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes></notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/thisisatest.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="CONF" id="196" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb
puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/simplerisx.risx

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.0.2//EN"
"/data/private/djd/binary/share/refdb/dtd/risx.dtd"
[
<!ENTITY lt "&#38;#60;">
<!ENTITY gt "&#62;">
<!ENTITY amp "&#38;#38;">
]>
<ris>
        <entry type="GEN" citekey="TESTY">
                <publication>
                        <title type="full">test1</title>
                        <author>
                                <name>testa testb</name>
                        </author>
                        <pubinfo>
                                <pubdate>
                                        <date>
                                                <year>2008</year>
                                                <month></month>
                                                <day></day>
                                        </date>
                                </pubdate>

                        </pubinfo>
                </publication>

        </entry>
</ris>

mycomp%

**** SECOND PART *2 - REFDB.2.DUMP.SQLITE ****

(go to other window and close refdbd)
(then come back)

mycomp% pwd
/data/private/djd/Library/ReferenceDatabaseSqlite3
mycomp% rm *
mycomp% sqlite3 refdb < ~/HD/binary/share/refdb/sql/refdb.2.dump.sqlite

** (go back now and restart refdbd) **

mycomp% refdbd -s -l 7 -e 0
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
application server started
share extended notes by default
use /tmp/refdbd_fifo9031 as fifo
server waiting n_max_fd=4

** (and now back to original window) **

mycomp% refdba
refdba: createdb djdphd
main database version is not supported
refdba: quit

**** THIRD PART *3 - REFDBD -A ****

** (go to other window and close refdbd)** 
** (then come back) **

mycomp% pwd
/data/private/djd/Library/ReferenceDatabaseSqlite3

mycomp% rm *

mycomp% refdbd -a -e 0 -l 7
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
check main database version
localhost
djd



sqlite3
/data/private/djd/Library/ReferenceDatabaseSqlite3/
UTF-8
Segmentation fault
mycomp%

**** SYSTEM INFO ****

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.
mycomp% refdbc -v
refdbc 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.
mycomp% refdba -v
refdba 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.
mycomp% uname -a
Linux mycomp 2.6.9-67.0.7.ELsmp #1 SMP Sat Mar 15 06:54:55 EDT 2008 i686
i686 i386 GNU/Linux
mycomp%

LIBDBI:
libdbi-cvs-20080421
libdbi-drivers-cvs-20080421

mycomp% cat ~/HD/binary/etc/refdb/refdbdrc | sed s/^#.\*\$// | grep '.'
refdblib /data/private/djd/binary/share/refdb
main_db refdb
serverip        localhost
dbsport
dbserver        sqlite3
dbpath          /data/private/djd/Library/ReferenceDatabaseSqlite3/
port    9734
logfile /data/private/djd/binary/var/log/refdbd.log
logdest file
loglevel info
pidfile         /data/private/djd/binary/var/run/refdbd.pid
remoteadmin f
remoteconnect f
keep_pnames t
keyword_scan f
db_encoding     UTF-8
in_encoding     UTF-8

mycomp% cat ~/.refdbarc | sed s/^#.\*\$// | grep '.'
serverip        127.0.0.1
port    9734
pager   less
username  root
passwd
logdest file
loglevel info
logfile /data/private/djd/binary/var/log/refdba.log

mycomp% cat ~/.refdbcrc | sed s/^#.\*\$// | grep '.'
serverip        127.0.0.1
port    9734
pager   less
passwd *
defaultdb       djdphd
pdfroot /data/private/djd/Library
logdest file
loglevel info
logfile /data/private/djd/binary/var/log/refdbc.log
cssurl /data/private/djd/binary/share/refdb/css/refdb.css
fromencoding UTF-8
toencoding UTF-8



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

Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-27 22:48

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

I guess this is sort of a duplicate of #1951049. If you missed the upgrade
notice from 0.9.8 or earlier to 0.9.9 or later, I reckon you'd see this
kind of problem. Please see the comments to bug #1951049 for further
instructions.

regards,
Markus

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

[Refdb-devel] [ refdb-Bugs-1951835 ] risx url multiplying

From: SourceForge.net <no...@so...> - 2008-04-29 16:51:44

Bugs item #1951835, was opened at 2008-04-25 19:32
Message generated for change (Comment added) made by damienjadeduff
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Damien Jade Duff (damienjadeduff)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: risx url multiplying

Initial Comment:
Hiya!

Sorry but got another one here for the pile!

Now I'm using sqlite here and the issue seems similar to a previous one in which it wasn't refdb but libdbi. 

If I UPDATE a reference using refdbc that already has a LINK TYPE="url" but I have changed the url (i.e. the update is one in which the url changes), the url tag multiplies - I get another tag, one with the old url, one with the new. I presume I can get any number of them but I haven't checked. The way I judge the intended behaviour of updateref, an update should swap the reference with everything in the RIS tag and drop the old information. Whaddya reckon? Details below.

Cheerios!
Damien

SETUP:

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

EXAMPLE:

mycomp% cat thisisatest2.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="CONF" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes></notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C addref -A risx < thisisatest2.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout1.risx
999:1 retrieved:0 failed
mycomp% cat testout1.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat thisisatest.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="CONF" id="196" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C updateref -A risx < thisisatest.risx
999:1 updated:0 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout2.risx
999:1 retrieved:0 failed
mycomp% cat testout2.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>


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

>Comment By: Damien Jade Duff (damienjadeduff)
Date: 2008-04-29 17:51

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

Oh, hi
Incidentally, I should mention that the same stuff also happens if I don't
ever add the ~/simplerisx.risx file, which only is an older version of risx
because I used an older xml skeleton and haven't updated. I just was using
it to check that the system was working.
Peace
Damien

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

Comment By: Damien Jade Duff (damienjadeduff)
Date: 2008-04-29 17:43

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

Hi there!

Thanks very much for your reply! I appreciate you taking a look!

I was, it is true, using 0.9.9-1 when I first started using refdb again
recently, but I'm now using the svn. But the thing is I put the refs into
the DB by adding an old dumped RISX file into an empty DB (I give an
example below).

I was thinking that it may be my route to installation that is specific?
Since 'refdbd -a' segfaults (not sure why, but details below - part *3) and
refdb complains that a DB created with refdb.2.dump.sqlite is an out of
date DB (again below, part *2 - though I think the manual still refers to
refdb.2.dump.sqlite), I was creating a basic refdb DB using the provided
sql file refdb.3.dump.sqlite (full details below, part *1, including a
replication of bug 1951835 after creating a new DB from scratch) - which
*seemed* to produce the desired results, except for the bugs I mentioned
which made themselves apparent later, so I had (perhaps foolishingly)
assumed it was the way to go.

The other two things that are unique about my install is that I'm using my
own database file directory for the embedded DB, and the whole install was
done onto a user owned file system (i.e. nothing from root). I'm not sure
if that would make any difference. ALSO, in the source directory I needed
to go to /etc and type "touch refdbrtfrc" as the make script seemed to need
it but it wasn't there, and I renamed the man and doc directories (and put
in dummy Makefiles) so that it would compile without the docs (again, I
don't think any of that should make a difference?).

Anyway, I'll just put the logs of my journey, from DB creation to
insertion, below, and hope the tale will amuse...

Cheerios!
Damien

**** FIRST PART *1 - REFDB.3.DUMP.SQLITE + DUPLICATED URLS ****

mycomp% ls

mycomp% sqlite3 refdb < ~/HD/binary/share/refdb/sql/refdb.3.dump.sqlite

mycomp% ls
refdb

** (start refdbd in another window) **

mycomp% refdbd -s -l 7 -e 0
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
application server started
share extended notes by default
use /tmp/refdbd_fifo8917 as fifo
server waiting n_max_fd=4

** (back to original window) **

mycomp% refdba
refdba: createdb djdphd
999:1 created:0 failed
refdba: quit

mycomp% ls
DB_VERSION  djdphd  refdb

mycomp% refdbc -u 132 -w 123 -C addref -A risx < ~/simplerisx.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C addref -A risx < ~/thisisatest2.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C updateref -A risx < ~/thisisatest.risx
999:1 updated:0 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C getref -t risx :ID:\>0 >
~/aftertesting.risx
999:2 retrieved:0 failed
mycomp% cat ~/aftertesting.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="GEN" id="1" citekey="TESTY">
    <part>
      <title type="full"/>
    </part>
    <publication>
      <title type="full">test1</title>
      <author>
        <name>testa testb</name>
      </author>
      <pubinfo>
        <pubdate type="primary">
          <date><year>2008</year><month>00</month><day>00</day></date>
        </pubdate>
      </pubinfo>
    </publication>
  </entry>


  <entry type="CONF" id="2" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
        <link
type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb
puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/thisisatest2.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="CONF" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link
type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes></notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/thisisatest.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="CONF" id="196" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb
puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/simplerisx.risx

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.0.2//EN"
"/data/private/djd/binary/share/refdb/dtd/risx.dtd"
[
<!ENTITY lt "&#38;#60;">
<!ENTITY gt "&#62;">
<!ENTITY amp "&#38;#38;">
]>
<ris>
        <entry type="GEN" citekey="TESTY">
                <publication>
                        <title type="full">test1</title>
                        <author>
                                <name>testa testb</name>
                        </author>
                        <pubinfo>
                                <pubdate>
                                        <date>
                                                <year>2008</year>
                                                <month></month>
                                                <day></day>
                                        </date>
                                </pubdate>

                        </pubinfo>
                </publication>

        </entry>
</ris>

mycomp%

**** SECOND PART *2 - REFDB.2.DUMP.SQLITE ****

(go to other window and close refdbd)
(then come back)

mycomp% pwd
/data/private/djd/Library/ReferenceDatabaseSqlite3
mycomp% rm *
mycomp% sqlite3 refdb < ~/HD/binary/share/refdb/sql/refdb.2.dump.sqlite

** (go back now and restart refdbd) **

mycomp% refdbd -s -l 7 -e 0
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
application server started
share extended notes by default
use /tmp/refdbd_fifo9031 as fifo
server waiting n_max_fd=4

** (and now back to original window) **

mycomp% refdba
refdba: createdb djdphd
main database version is not supported
refdba: quit

**** THIRD PART *3 - REFDBD -A ****

** (go to other window and close refdbd)** 
** (then come back) **

mycomp% pwd
/data/private/djd/Library/ReferenceDatabaseSqlite3

mycomp% rm *

mycomp% refdbd -a -e 0 -l 7
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
check main database version
localhost
djd



sqlite3
/data/private/djd/Library/ReferenceDatabaseSqlite3/
UTF-8
Segmentation fault
mycomp%

**** SYSTEM INFO ****

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.
mycomp% refdbc -v
refdbc 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.
mycomp% refdba -v
refdba 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.
mycomp% uname -a
Linux mycomp 2.6.9-67.0.7.ELsmp #1 SMP Sat Mar 15 06:54:55 EDT 2008 i686
i686 i386 GNU/Linux
mycomp%

LIBDBI:
libdbi-cvs-20080421
libdbi-drivers-cvs-20080421

mycomp% cat ~/HD/binary/etc/refdb/refdbdrc | sed s/^#.\*\$// | grep '.'
refdblib /data/private/djd/binary/share/refdb
main_db refdb
serverip        localhost
dbsport
dbserver        sqlite3
dbpath          /data/private/djd/Library/ReferenceDatabaseSqlite3/
port    9734
logfile /data/private/djd/binary/var/log/refdbd.log
logdest file
loglevel info
pidfile         /data/private/djd/binary/var/run/refdbd.pid
remoteadmin f
remoteconnect f
keep_pnames t
keyword_scan f
db_encoding     UTF-8
in_encoding     UTF-8

mycomp% cat ~/.refdbarc | sed s/^#.\*\$// | grep '.'
serverip        127.0.0.1
port    9734
pager   less
username  root
passwd
logdest file
loglevel info
logfile /data/private/djd/binary/var/log/refdba.log

mycomp% cat ~/.refdbcrc | sed s/^#.\*\$// | grep '.'
serverip        127.0.0.1
port    9734
pager   less
passwd *
defaultdb       djdphd
pdfroot /data/private/djd/Library
logdest file
loglevel info
logfile /data/private/djd/binary/var/log/refdbc.log
cssurl /data/private/djd/binary/share/refdb/css/refdb.css
fromencoding UTF-8
toencoding UTF-8



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

Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-27 21:48

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

I guess this is sort of a duplicate of #1951049. If you missed the upgrade
notice from 0.9.8 or earlier to 0.9.9 or later, I reckon you'd see this
kind of problem. Please see the comments to bug #1951049 for further
instructions.

regards,
Markus

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

[Refdb-devel] [ refdb-Bugs-1951835 ] risx url multiplying

From: SourceForge.net <no...@so...> - 2008-04-29 16:43:08

Bugs item #1951835, was opened at 2008-04-25 19:32
Message generated for change (Comment added) made by damienjadeduff
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Damien Jade Duff (damienjadeduff)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: risx url multiplying

Initial Comment:
Hiya!

Sorry but got another one here for the pile!

Now I'm using sqlite here and the issue seems similar to a previous one in which it wasn't refdb but libdbi. 

If I UPDATE a reference using refdbc that already has a LINK TYPE="url" but I have changed the url (i.e. the update is one in which the url changes), the url tag multiplies - I get another tag, one with the old url, one with the new. I presume I can get any number of them but I haven't checked. The way I judge the intended behaviour of updateref, an update should swap the reference with everything in the RIS tag and drop the old information. Whaddya reckon? Details below.

Cheerios!
Damien

SETUP:

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

EXAMPLE:

mycomp% cat thisisatest2.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="CONF" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes></notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C addref -A risx < thisisatest2.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout1.risx
999:1 retrieved:0 failed
mycomp% cat testout1.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat thisisatest.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="CONF" id="196" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C updateref -A risx < thisisatest.risx
999:1 updated:0 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout2.risx
999:1 retrieved:0 failed
mycomp% cat testout2.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>


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

>Comment By: Damien Jade Duff (damienjadeduff)
Date: 2008-04-29 17:43

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

Hi there!

Thanks very much for your reply! I appreciate you taking a look!

I was, it is true, using 0.9.9-1 when I first started using refdb again
recently, but I'm now using the svn. But the thing is I put the refs into
the DB by adding an old dumped RISX file into an empty DB (I give an
example below).

I was thinking that it may be my route to installation that is specific?
Since 'refdbd -a' segfaults (not sure why, but details below - part *3) and
refdb complains that a DB created with refdb.2.dump.sqlite is an out of
date DB (again below, part *2 - though I think the manual still refers to
refdb.2.dump.sqlite), I was creating a basic refdb DB using the provided
sql file refdb.3.dump.sqlite (full details below, part *1, including a
replication of bug 1951835 after creating a new DB from scratch) - which
*seemed* to produce the desired results, except for the bugs I mentioned
which made themselves apparent later, so I had (perhaps foolishingly)
assumed it was the way to go.

The other two things that are unique about my install is that I'm using my
own database file directory for the embedded DB, and the whole install was
done onto a user owned file system (i.e. nothing from root). I'm not sure
if that would make any difference. ALSO, in the source directory I needed
to go to /etc and type "touch refdbrtfrc" as the make script seemed to need
it but it wasn't there, and I renamed the man and doc directories (and put
in dummy Makefiles) so that it would compile without the docs (again, I
don't think any of that should make a difference?).

Anyway, I'll just put the logs of my journey, from DB creation to
insertion, below, and hope the tale will amuse...

Cheerios!
Damien

**** FIRST PART *1 - REFDB.3.DUMP.SQLITE + DUPLICATED URLS ****

mycomp% ls

mycomp% sqlite3 refdb < ~/HD/binary/share/refdb/sql/refdb.3.dump.sqlite

mycomp% ls
refdb

** (start refdbd in another window) **

mycomp% refdbd -s -l 7 -e 0
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
application server started
share extended notes by default
use /tmp/refdbd_fifo8917 as fifo
server waiting n_max_fd=4

** (back to original window) **

mycomp% refdba
refdba: createdb djdphd
999:1 created:0 failed
refdba: quit

mycomp% ls
DB_VERSION  djdphd  refdb

mycomp% refdbc -u 132 -w 123 -C addref -A risx < ~/simplerisx.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C addref -A risx < ~/thisisatest2.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C updateref -A risx < ~/thisisatest.risx
999:1 updated:0 added:0 skipped:0 failed
mycomp% refdbc -u 132 -w 123 -C getref -t risx :ID:\>0 >
~/aftertesting.risx
999:2 retrieved:0 failed
mycomp% cat ~/aftertesting.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="GEN" id="1" citekey="TESTY">
    <part>
      <title type="full"/>
    </part>
    <publication>
      <title type="full">test1</title>
      <author>
        <name>testa testb</name>
      </author>
      <pubinfo>
        <pubdate type="primary">
          <date><year>2008</year><month>00</month><day>00</day></date>
        </pubdate>
      </pubinfo>
    </publication>
  </entry>


  <entry type="CONF" id="2" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
        <link
type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb
puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/thisisatest2.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="CONF" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link
type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes></notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/thisisatest.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="CONF" id="196" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear
Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and
Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb
puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat ~/simplerisx.risx

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.0.2//EN"
"/data/private/djd/binary/share/refdb/dtd/risx.dtd"
[
<!ENTITY lt "&#38;#60;">
<!ENTITY gt "&#62;">
<!ENTITY amp "&#38;#38;">
]>
<ris>
        <entry type="GEN" citekey="TESTY">
                <publication>
                        <title type="full">test1</title>
                        <author>
                                <name>testa testb</name>
                        </author>
                        <pubinfo>
                                <pubdate>
                                        <date>
                                                <year>2008</year>
                                                <month></month>
                                                <day></day>
                                        </date>
                                </pubdate>

                        </pubinfo>
                </publication>

        </entry>
</ris>

mycomp%

**** SECOND PART *2 - REFDB.2.DUMP.SQLITE ****

(go to other window and close refdbd)
(then come back)

mycomp% pwd
/data/private/djd/Library/ReferenceDatabaseSqlite3
mycomp% rm *
mycomp% sqlite3 refdb < ~/HD/binary/share/refdb/sql/refdb.2.dump.sqlite

** (go back now and restart refdbd) **

mycomp% refdbd -s -l 7 -e 0
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
application server started
share extended notes by default
use /tmp/refdbd_fifo9031 as fifo
server waiting n_max_fd=4

** (and now back to original window) **

mycomp% refdba
refdba: createdb djdphd
main database version is not supported
refdba: quit

**** THIRD PART *3 - REFDBD -A ****

** (go to other window and close refdbd)** 
** (then come back) **

mycomp% pwd
/data/private/djd/Library/ReferenceDatabaseSqlite3

mycomp% rm *

mycomp% refdbd -a -e 0 -l 7
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
pgsql
sqlite3
Requested libdbi driver found:
sqlite3
Database directory:
/data/private/djd/Library/ReferenceDatabaseSqlite3/
check main database version
localhost
djd



sqlite3
/data/private/djd/Library/ReferenceDatabaseSqlite3/
UTF-8
Segmentation fault
mycomp%

**** SYSTEM INFO ****

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.
mycomp% refdbc -v
refdbc 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.
mycomp% refdba -v
refdba 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.
mycomp% uname -a
Linux mycomp 2.6.9-67.0.7.ELsmp #1 SMP Sat Mar 15 06:54:55 EDT 2008 i686
i686 i386 GNU/Linux
mycomp%

LIBDBI:
libdbi-cvs-20080421
libdbi-drivers-cvs-20080421

mycomp% cat ~/HD/binary/etc/refdb/refdbdrc | sed s/^#.\*\$// | grep '.'
refdblib /data/private/djd/binary/share/refdb
main_db refdb
serverip        localhost
dbsport
dbserver        sqlite3
dbpath          /data/private/djd/Library/ReferenceDatabaseSqlite3/
port    9734
logfile /data/private/djd/binary/var/log/refdbd.log
logdest file
loglevel info
pidfile         /data/private/djd/binary/var/run/refdbd.pid
remoteadmin f
remoteconnect f
keep_pnames t
keyword_scan f
db_encoding     UTF-8
in_encoding     UTF-8

mycomp% cat ~/.refdbarc | sed s/^#.\*\$// | grep '.'
serverip        127.0.0.1
port    9734
pager   less
username  root
passwd
logdest file
loglevel info
logfile /data/private/djd/binary/var/log/refdba.log

mycomp% cat ~/.refdbcrc | sed s/^#.\*\$// | grep '.'
serverip        127.0.0.1
port    9734
pager   less
passwd *
defaultdb       djdphd
pdfroot /data/private/djd/Library
logdest file
loglevel info
logfile /data/private/djd/binary/var/log/refdbc.log
cssurl /data/private/djd/binary/share/refdb/css/refdb.css
fromencoding UTF-8
toencoding UTF-8



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

Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-27 21:48

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

I guess this is sort of a duplicate of #1951049. If you missed the upgrade
notice from 0.9.8 or earlier to 0.9.9 or later, I reckon you'd see this
kind of problem. Please see the comments to bug #1951049 for further
instructions.

regards,
Markus

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

[Refdb-devel] [ refdb-Bugs-1951835 ] risx url multiplying

From: SourceForge.net <no...@so...> - 2008-04-27 20:48:14

Bugs item #1951835, was opened at 2008-04-25 20:32
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Damien Jade Duff (damienjadeduff)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: risx url multiplying

Initial Comment:
Hiya!

Sorry but got another one here for the pile!

Now I'm using sqlite here and the issue seems similar to a previous one in which it wasn't refdb but libdbi. 

If I UPDATE a reference using refdbc that already has a LINK TYPE="url" but I have changed the url (i.e. the update is one in which the url changes), the url tag multiplies - I get another tag, one with the old url, one with the new. I presume I can get any number of them but I haven't checked. The way I judge the intended behaviour of updateref, an update should swap the reference with everything in the RIS tag and drop the old information. Whaddya reckon? Details below.

Cheerios!
Damien

SETUP:

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

EXAMPLE:

mycomp% cat thisisatest2.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="CONF" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes></notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C addref -A risx < thisisatest2.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout1.risx
999:1 retrieved:0 failed
mycomp% cat testout1.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat thisisatest.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="CONF" id="196" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C updateref -A risx < thisisatest.risx
999:1 updated:0 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout2.risx
999:1 retrieved:0 failed
mycomp% cat testout2.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>


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

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-27 22:48

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

I guess this is sort of a duplicate of #1951049. If you missed the upgrade
notice from 0.9.8 or earlier to 0.9.9 or later, I reckon you'd see this
kind of problem. Please see the comments to bug #1951049 for further
instructions.

regards,
Markus

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

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

From: SourceForge.net <no...@so...> - 2008-04-27 20:47:55

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

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
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: 2008-04-27 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

[Refdb-devel] [ refdb-Bugs-1951835 ] risx url multiplying

From: SourceForge.net <no...@so...> - 2008-04-25 18:32:24

Bugs item #1951835, was opened at 2008-04-25 19:32
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Damien Jade Duff (damienjadeduff)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: risx url multiplying

Initial Comment:
Hiya!

Sorry but got another one here for the pile!

Now I'm using sqlite here and the issue seems similar to a previous one in which it wasn't refdb but libdbi. 

If I UPDATE a reference using refdbc that already has a LINK TYPE="url" but I have changed the url (i.e. the update is one in which the url changes), the url tag multiplies - I get another tag, one with the old url, one with the new. I presume I can get any number of them but I haven't checked. The way I judge the intended behaviour of updateref, an update should swap the reference with everything in the RIS tag and drop the old information. Whaddya reckon? Details below.

Cheerios!
Damien

SETUP:

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

EXAMPLE:

mycomp% cat thisisatest2.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="CONF" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes></notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C addref -A risx < thisisatest2.risx
999:1 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout1.risx
999:1 retrieved:0 failed
mycomp% cat testout1.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% cat thisisatest.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="CONF" id="196" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>

mycomp% refdbc -d djdphd -u djd -w abc -C updateref -A risx < thisisatest.risx
999:1 updated:0 added:0 skipped:0 failed
mycomp% refdbc -d djdphd -u djd -w abc -C getref -t risx :CK:=THISISATEST > testout2.risx
999:1 retrieved:0 failed
mycomp% cat testout2.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="CONF" id="209" citekey="THISISATEST">
    <part>
      <title type="full">A New Extension of the Kalman Filter to Nonlinear Systems</title>
      <author role="author">
        <name>Simon J. Julier</name>
      </author>
      <author role="author">
        <name>Jeffrey K. Uhlmann</name>
      </author>
    </part>
    <publication>
      <title type="full">Int. Symp. Aerospace/Defense Sensing, Simul. and Controls</title>
      <pubinfo>
        <pubdate type="primary">
          <date><year>1997</year><month>00</month><day>00</day></date>
        </pubdate>
        <city>Orlando, Florida</city>
        <link type="url">http://tinyurl.com/4dqojq</link>
        <link type="url">http://www.cs.unc.edu/~welch/kalman/media/pdf/Julier1997_SPIE_KF.pdf</link>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <notes>bibtex doesn't seem to like all the escape characters refdb puts in the original URL so we switch to tinurl for now...</notes>
      <reprint status="INFILE"/>
      <availability type="useroot"/>
    </libinfo>
    <contents>
      <keyword>bayesian</keyword>
      <keyword>kalman</keyword>
      <keyword>non-linear</keyword>
      <keyword>nonlinear</keyword>
      <keyword>probability</keyword>
      <keyword>recursive estimation</keyword>
      <keyword>tracking</keyword>
      <keyword>unscented</keyword>
    </contents>
  </entry>
</ris>


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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951835&group_id=26091

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

From: SourceForge.net <no...@so...> - 2008-04-25 16:05:29

Bugs item #1951049, was opened at 2008-04-24 19:07
Message generated for change (Comment added) made by damienjadeduff
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951049&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
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: Damien Jade Duff (damienjadeduff)
Date: 2008-04-25 17:05

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

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

From: SourceForge.net <no...@so...> - 2008-04-24 18:07:19

Bugs item #1951049, was opened at 2008-04-24 19:07
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1951049&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
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

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

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

[Refdb-devel] [ refdb-Bugs-1945901 ] risx tag multiplication & deletion

From: SourceForge.net <no...@so...> - 2008-04-24 17:44:09

Bugs item #1945901, was opened at 2008-04-18 16:36
Message generated for change (Comment added) made by damienjadeduff
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1945901&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
>Status: Closed
Resolution: None
Priority: 5
Private: No
Submitted By: Damien Jade Duff (damienjadeduff)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: risx tag multiplication & deletion

Initial Comment:
Gidday!

My reunion with refdb after some absence brings with it some possible opportunities for me to help again! I hope my feedback is helpful.

Here are two things that may be a bug or maybe some logic I'm not getting. Also it is from refdb-0.9.9-1.tar.gz, since, for reasons probably of my own making I'm not getting at the svn version now. (other system info at bottom of message)

Note that I tried case 1 and case 2 (below) with the GEN type as well as the MISC. While case 1 applies to both GEN & MISC, case 2 applies to MISC only.

This should be findable without the log file but if it ends up being a bit difficult, give me a yell and I'll do it again.

Best wishes
Damien Jade Duff 

Case 1:

By repeatedly adding and then deleting a ref using risx I was able to make the libinfo tag multiply:

First I add the following ref:

***(A)***

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.1.0//EN" "http://refdb.sourceforge.net/dtd/risx-1.1.0/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="MISC" citekey="STEEDMANBALDRIDGE2003">
		<part>
			<title type="full">Combinatory Categorial Grammar</title>
			<author>
				<name>Mark Steedman</name>
			</author>
			<author>
				<name>Jason Baldridge</name>
			</author>
	</part>
		<publication>

			<pubinfo>
				<pubdate type="primary">
					<date>
						<month>00</month>
						<day>00</day>
					</date>
				</pubdate>
			</pubinfo>
		</publication>
		<libinfo user="djd">
			<reprint status="INFILE"/>
			<availability type="useroot">Combinatorial Categorial Grammar/SteedmanBaldridge2003.pdf</availability>
		</libinfo>
	</entry>

</ris>

***

Then I retrieve it:

***(B)***

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.1.0//EN" "http://refdb.sourceforge.net/dtd/risx-1.1.0/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="MISC" id="1" citekey="STEEDMANBALDRIDGE2003">
    <publication>
      <title type="full">Combinatory Categorial Grammar</title>
      <author>
        <name>Mark Steedman</name>
      </author>
      <author>
        <name>Jason Baldridge</name>
      </author>
      <pubinfo>
        <pubdate type="primary">
          <date><month>00</month><day>00</day></date>
        </pubdate>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot">Combinatorial Categorial Grammar/SteedmanBaldridge2003.pdf</availability>
    </libinfo>
  </entry>
</ris>

***

Then I delete it:

***(C)***

refdbc: deleteref 1
999:1 deleted:0 skipped:0 failed

***

Then I add it again in the original form (as in (A) above). 

And retrieve it. Retrived reference looks like this (note the multiplication of the libinfo tag):

***(D)***

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.1.0//EN" "http://refdb.sourceforge.net/dtd/risx-1.1.0/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="MISC" id="1" citekey="STEEDMANBALDRIDGE2003">
    <publication>
      <title type="full">Combinatory Categorial Grammar</title>
      <author>
        <name>Mark Steedman</name>
      </author>
      <author>
        <name>Jason Baldridge</name>
      </author>
      <pubinfo>
        <pubdate type="primary">
          <date><month>00</month><day>00</day></date>
        </pubdate>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot">Combinatorial Categorial Grammar/SteedmanBaldridge2003.pdf</availability>
    </libinfo>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot">Combinatorial Categorial Grammar/SteedmanBaldridge2003.pdf</availability>
    </libinfo>
  </entry>
</ris>

***

If I keep doing this it keeps acquiring libinfo tags (this is from a clean database, just created using refdbd -a and createdb, using standalone sqlite3, after deleting the previous database files)

Case 2:

I can lose the author tag on MISC references, even when adding refdb generated xml.

Again, from a clean install (as per the above)
If, rather than adding the citation in (A) above, I add the citation in (B) (i.e. the one generated by refdb itself)

Then retrieve it using getref. In the retrieval the retrieved citation has lost the author info inside the publication tag:

***(E)***

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.1.0//EN" "http://refdb.sourceforge.net/dtd/risx-1.1.0/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="MISC" id="1" citekey="STEEDMANBALDRIDGE2003">
    <publication>
      <title type="full">Combinatory Categorial Grammar</title>
      <pubinfo>
        <pubdate type="primary">
          <date><month>00</month><day>00</day></date>
        </pubdate>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot">Combinatorial Categorial Grammar/SteedmanBaldridge2003.pdf</availability>
    </libinfo>
  </entry>
</ris>

***

However, if I retrieve it in RIS rather than RISX I get:

***(F)***

TY  - MISC
ID  - STEEDMANBALDRIDGE2003
A2  - Mark Steedman
A2  - Jason Baldridge
TI  - Combinatory Categorial Grammar
PY  - /00/00/
ER  - 

***

i.e. the author information is still in the DB somewhere, just not being pulled out: suggestive that the problem is with the generation of the MISC risx.

System info:

sqlite-3.5.8
libdbi-0.8.3
libdbi-drivers-0.8.3-1
refdb-0.9.9-1
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
All installations are local non-root installations.

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

>Comment By: Damien Jade Duff (damienjadeduff)
Date: 2008-04-24 18:43

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

Thanks Marcus!
There is indeed no MISC, silly me, that's a bibtex type. 
Thanks for the fix to that, working fine!
I think if I'm to submit another bug I shall open a new job and set this
one to closed.. (?)
Thanks again for all of your efforts.
Damien

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

Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-20 00:34

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

Thanks for the complete bug information. The first problem (libinfo
duplication) turned out to be a problem of the sqlite/sqlite3 drivers. If
you have a chance to run the same test on PostgreSQL or MySQL, you can
verify that RefDB does not have a problem of its own here. I've checked in
a fix for the drivers, but you'll have to upgrade to the CVS versions of
both libdbi and libdbi-drivers to enjoy the fix.
The second problem is caused by the fact that there is no MISC type in
RIS. I haven't verified this, but you may have more luck with the GEN type.
If that still causes problems, I'll be happy to have a closer look.
BTW if you have problems accessing the svn repository, you may have an
outdated working copy. The repository URL has changed at some point in the
past. If this is what keeps you from updating your copy, toss it and check
out a fresh copy using the instructions on the web page which has the
current URLs.

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1945901&group_id=26091

[Refdb-devel] [ refdb-Bugs-1945901 ] risx tag multiplication & deletion

From: SourceForge.net <no...@so...> - 2008-04-19 23:34:06

Bugs item #1945901, was opened at 2008-04-18 17:36
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1945901&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
Status: Open
Resolution: None
Priority: 5
Private: No
Submitted By: Damien Jade Duff (damienjadeduff)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: risx tag multiplication & deletion

Initial Comment:
Gidday!

My reunion with refdb after some absence brings with it some possible opportunities for me to help again! I hope my feedback is helpful.

Here are two things that may be a bug or maybe some logic I'm not getting. Also it is from refdb-0.9.9-1.tar.gz, since, for reasons probably of my own making I'm not getting at the svn version now. (other system info at bottom of message)

Note that I tried case 1 and case 2 (below) with the GEN type as well as the MISC. While case 1 applies to both GEN & MISC, case 2 applies to MISC only.

This should be findable without the log file but if it ends up being a bit difficult, give me a yell and I'll do it again.

Best wishes
Damien Jade Duff 

Case 1:

By repeatedly adding and then deleting a ref using risx I was able to make the libinfo tag multiply:

First I add the following ref:

***(A)***

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.1.0//EN" "http://refdb.sourceforge.net/dtd/risx-1.1.0/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="MISC" citekey="STEEDMANBALDRIDGE2003">
		<part>
			<title type="full">Combinatory Categorial Grammar</title>
			<author>
				<name>Mark Steedman</name>
			</author>
			<author>
				<name>Jason Baldridge</name>
			</author>
	</part>
		<publication>

			<pubinfo>
				<pubdate type="primary">
					<date>
						<month>00</month>
						<day>00</day>
					</date>
				</pubdate>
			</pubinfo>
		</publication>
		<libinfo user="djd">
			<reprint status="INFILE"/>
			<availability type="useroot">Combinatorial Categorial Grammar/SteedmanBaldridge2003.pdf</availability>
		</libinfo>
	</entry>

</ris>

***

Then I retrieve it:

***(B)***

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.1.0//EN" "http://refdb.sourceforge.net/dtd/risx-1.1.0/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="MISC" id="1" citekey="STEEDMANBALDRIDGE2003">
    <publication>
      <title type="full">Combinatory Categorial Grammar</title>
      <author>
        <name>Mark Steedman</name>
      </author>
      <author>
        <name>Jason Baldridge</name>
      </author>
      <pubinfo>
        <pubdate type="primary">
          <date><month>00</month><day>00</day></date>
        </pubdate>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot">Combinatorial Categorial Grammar/SteedmanBaldridge2003.pdf</availability>
    </libinfo>
  </entry>
</ris>

***

Then I delete it:

***(C)***

refdbc: deleteref 1
999:1 deleted:0 skipped:0 failed

***

Then I add it again in the original form (as in (A) above). 

And retrieve it. Retrived reference looks like this (note the multiplication of the libinfo tag):

***(D)***

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.1.0//EN" "http://refdb.sourceforge.net/dtd/risx-1.1.0/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="MISC" id="1" citekey="STEEDMANBALDRIDGE2003">
    <publication>
      <title type="full">Combinatory Categorial Grammar</title>
      <author>
        <name>Mark Steedman</name>
      </author>
      <author>
        <name>Jason Baldridge</name>
      </author>
      <pubinfo>
        <pubdate type="primary">
          <date><month>00</month><day>00</day></date>
        </pubdate>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot">Combinatorial Categorial Grammar/SteedmanBaldridge2003.pdf</availability>
    </libinfo>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot">Combinatorial Categorial Grammar/SteedmanBaldridge2003.pdf</availability>
    </libinfo>
  </entry>
</ris>

***

If I keep doing this it keeps acquiring libinfo tags (this is from a clean database, just created using refdbd -a and createdb, using standalone sqlite3, after deleting the previous database files)

Case 2:

I can lose the author tag on MISC references, even when adding refdb generated xml.

Again, from a clean install (as per the above)
If, rather than adding the citation in (A) above, I add the citation in (B) (i.e. the one generated by refdb itself)

Then retrieve it using getref. In the retrieval the retrieved citation has lost the author info inside the publication tag:

***(E)***

<?xml version="1.0" encoding="UTF-8"?>
<!DOCTYPE ris PUBLIC "-//Markus Hoenicka//DTD Ris V1.1.0//EN" "http://refdb.sourceforge.net/dtd/risx-1.1.0/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="MISC" id="1" citekey="STEEDMANBALDRIDGE2003">
    <publication>
      <title type="full">Combinatory Categorial Grammar</title>
      <pubinfo>
        <pubdate type="primary">
          <date><month>00</month><day>00</day></date>
        </pubdate>
      </pubinfo>
    </publication>
    <libinfo user="djd">
      <reprint status="INFILE"/>
      <availability type="useroot">Combinatorial Categorial Grammar/SteedmanBaldridge2003.pdf</availability>
    </libinfo>
  </entry>
</ris>

***

However, if I retrieve it in RIS rather than RISX I get:

***(F)***

TY  - MISC
ID  - STEEDMANBALDRIDGE2003
A2  - Mark Steedman
A2  - Jason Baldridge
TI  - Combinatory Categorial Grammar
PY  - /00/00/
ER  - 

***

i.e. the author information is still in the DB somewhere, just not being pulled out: suggestive that the problem is with the generation of the MISC risx.

System info:

sqlite-3.5.8
libdbi-0.8.3
libdbi-drivers-0.8.3-1
refdb-0.9.9-1
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
All installations are local non-root installations.

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

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2008-04-20 01:34

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

Thanks for the complete bug information. The first problem (libinfo
duplication) turned out to be a problem of the sqlite/sqlite3 drivers. If
you have a chance to run the same test on PostgreSQL or MySQL, you can
verify that RefDB does not have a problem of its own here. I've checked in
a fix for the drivers, but you'll have to upgrade to the CVS versions of
both libdbi and libdbi-drivers to enjoy the fix.
The second problem is caused by the fact that there is no MISC type in
RIS. I haven't verified this, but you may have more luck with the GEN type.
If that still causes problems, I'll be happy to have a closer look.
BTW if you have problems accessing the svn repository, you may have an
outdated working copy. The repository URL has changed at some point in the
past. If this is what keeps you from updating your copy, toss it and check
out a fresh copy using the instructions on the web page which has the
current URLs.

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

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1945901&group_id=26091

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