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From: <mar...@mh...> - 2002-12-15 01:30:23
|
Michael Below writes: > Hi, > > I just installed refdb, but I can't connect to the database: > > If I call viewstat in refdba, it says: > > could not connect to database server > > In the logfile of refdbd, I find messages like this one: > > 6:pid=340:Sat Dec 14 13:18:23 2002:adding client on fd 6 > 6:pid=340:Sat Dec 14 13:18:23 2002:server waiting n_max_fd=6 > 6:pid=812:Sat Dec 14 13:18:23 2002:serving client on fd 6 with > protocol version > 0 > 4:pid=812:Sat Dec 14 13:18:23 2002:creating database connection > structure failed This error message is caused by the call: dbi_conn_new(ptr_clrequest->dbserver) in refdbda.c. There's essentially two possible causes for the failure of this call: 1) libdbi is not set up correctly. Did you run make check after building libdbi? Please also make sure that you built libdbi with the --with-mysql switch as this is required to build the MySQL driver. Please check also that the driver is in a standard location, like /usr/local/lib/dbd/libmysql.so 2) refdbd is configured incorrectly. Please check the settings in /usr/local/etc/refdb/refdbdrc and make sure that you selected mysql as the dbserver. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
|
From: Michael B. <mb...@an...> - 2002-12-14 13:47:31
|
Hi, I just installed refdb, but I can't connect to the database: If I call viewstat in refdba, it says: could not connect to database server In the logfile of refdbd, I find messages like this one: 6:pid=340:Sat Dec 14 13:18:23 2002:adding client on fd 6 6:pid=340:Sat Dec 14 13:18:23 2002:server waiting n_max_fd=6 6:pid=812:Sat Dec 14 13:18:23 2002:serving client on fd 6 with protocol version 0 4:pid=812:Sat Dec 14 13:18:23 2002:creating database connection structure failed 6:pid=812:Sat Dec 14 13:18:23 2002:child finished client on fd 6 In mysql, I am able to see the refdb1 database: ~ $mysqlshow refdb1 Database: refdb1 +-----------------+ | Tables | +-----------------+ | CITSTYLE | | POSITIONS | | REFSTYLE | | SEPARATORS | | t_journal_words | +-----------------+ The mysqld and refdbd are listening on the default ports on localhost, refdba is configured like this: refdba: set serverip 127.0.0.1 port 9734 verbose t pager less username root timeout 60 logfile /var/log/refdba.log logdest FILE loglevel INFO refdblib /var/log/refdba.log doesn't contain anything. Any ideas? Ciao Michael |
|
From: Florent I. <ing...@gr...> - 2002-12-12 15:05:43
|
Hi Markus, I'm glad to have a working refdb. The patch you sent seems to fix the problem as far as I can test it, when I use it the way you said (aka. using the ID KEY only to cite refs). I really have to thank you for giving an answer and more important a solution so rapidly (althoug it isn't the case for my present answer ;-) ). regards, Florent -- --------------------------------- Florent Ingwiller Laboratoire Louis NEEL / CNRS 25, avenue des Martyrs BP 166 38042 Genoble CEDEX 9 Tel : +33 (0)4 76 88 12 89 Fax : +33 (0)4 76 88 11 91 email : ing...@gr... --------------------------------- |
|
From: <mar...@mh...> - 2002-12-07 01:30:51
|
Hi Florent,
Florent Ingwiller writes:
> So there is a serious problem with the bibtex backend. As I don't have
> time to understand the complete implementation of this backend and of
> refdb in general, I can't track this bug further.
>
After a quick test I can unfortunately only agree with your
statement. In fact, bibtex support is utterly broken in the current
release as a result of the major changes from 0.8.x to 0.9.
I've checked in a fix which at least works in the few tests I ran. I'd
ask you to try it out. Either use the patch for backend-bibtex.c
attached to this mail, or download the current version 1.8.2.10 from
CVS (in the libdbi-pre1 branch).
In order to get this fix out in a reasonable amount of time I've made
two simplifications which hopefully won't hurt too much: first, you
can only use citation keys, not numerical IDs in your citations (but
this is what BibTeX users prefer anyway, I guess). Second, you can't
use citations from different databases at the moment. Regardless of what
the manual says you have to use something like the following:
\begin{document}
\bibliographystyle{plain}
This is a citation \cite{Nakane2002}
\bibliography{bibtest.bib}
\end{document}
Please keep me posted about your tests. And I really appreciated your
extensive bug report. This indeed helped a lot to track down the bugs.
regards,
Markus
|
|
From: Florent I. <ing...@gr...> - 2002-12-06 16:27:36
|
Hi,
I and a few persons in our lab are interested in using a bibliography
manager in conjunction with latex so refdb seems to fit our needs. I
know that your principal goal is to implement the sgml/xml part of the
system and that the bibtex support is only a sort of "collateral
effect". Anyway since version 0.9 I haven't been able to make it work
properly with bibtex formating backend.
With version 0.8.6 it worked just fine for this part, but the web
frontend didn't work at all. Now it's the inverse i can retrieve
reference in any way : through the refdbc client or through the web
frontend. But refdbib (in fact the bibtex backend) seems to have
problems with bibtex output . I get this king of error message :
/flamm@FarStar:~/temp/test$ refdbib -d xxxxxxxx -u xxxxxxxx -w xxxxxxxx
-S bibtex-full -t bibtex -V -l 7 testlatex.aux
out of memory
0 reference(s) retrieved, 1 failed
out of memory
0 reference(s) retrieved, 1 failed
/and the corresponding logs in refdbd.log :
/
6:pid=9355:Fri Dec 06 14:28:26 2002:parent removing client on fd
6
6:pid=9355:Fri Dec 06 14:28:26 2002:server waiting
n_max_fd=5
6:pid=9355:Fri Dec 06 14:28:27 2002:child exited with code
0
6:pid=9355:Fri Dec 06 14:28:27 2002:server waiting
n_max_fd=5
6:pid=9355:Fri Dec 06 14:29:39 2002:adding client on fd
6
6:pid=9355:Fri Dec 06 14:29:39 2002:server waiting
n_max_fd=6
6:pid=9491:Fri Dec 06 14:29:39 2002:serving client on fd 6 with protocol
version
0
4:pid=9491:Fri Dec 06 14:29:39 2002:no CITSTYLE
found
4:pid=9491:Fri Dec 06 14:29:39 2002:could not load style
information
6:pid=9491:Fri Dec 06 14:29:39 2002:child finished client on fd
6
6:pid=9355:Fri Dec 06 14:29:39 2002:parent removing client on fd
6
6:pid=9355:Fri Dec 06 14:29:39 2002:server waiting
n_max_fd=5
6:pid=9355:Fri Dec 06 14:29:39 2002:child exited with code
0
6:pid=9355:Fri Dec 06 14:29:39 2002:server waiting
n_max_fd=5
//
/
Even to obtain theses messages I have to correct a little mistake in the
file *backend-bibtex.c *at line 153 where refdb.CITSTYLE remains instead
of refdb1.CITSTYLE.
I did some debugging, and found out that this error message (/out of
memory/) happens at line 973 in *backend-bibtex.c* so the procedure
/render_bibtex(&rendinfo)/ doesn't produce a correct output (it is
void). Indeed, as I traced the corresponding mySQL queries in the log
file I found this 2 ones :
18 Query SELECT ID, QSTYLE, XSTYLE, YSTYLE,
ZSTYLE, QABBREVIATEFIRST, XABBREVIATEFIRST, YABBREVIATEFIRST,
ZABBREVIATEFIRST, QABBREVIATESUBSEQ, XABBREVIATESUBSEQ,
YABBREVIATESUBSEQ, ZABBREVIATESUBSEQ,QABBREVIATEFIRSTMAXAUTHOR,
XABBREVIATEFIRSTMAXAUTHOR, YABBREVIATEFIRSTMAXAUTHOR,
ZABBREVIATEFIRSTMAXAUTHOR, QABBREVIATESUBSEQMAXAUTHOR,
XABBREVIATESUBSEQMAXAUTHOR, YABBREVIATESUBSEQMAXAUTHOR,
ZABBREVIATESUBSEQMAXAUTHOR, QABBREVIATEFIRSTDISPLAYAUTHOR,
XABBREVIATEFIRSTDISPLAYAUTHOR, YABBREVIATEFIRSTDISPLAYAUTHOR,
ZABBREVIATEFIRSTDISPLAYAUTHOR, QABBREVIATESUBSEQDISPLAYAUTHOR,
XABBREVIATESUBSEQDISPLAYAUTHOR, YABBREVIATESUBSEQDISPLAYAUTHOR,
ZABBREVIATESUBSEQDISPLAYAUTHOR, QAEMPTY, XAEMPTY, YAEMPTY, ZAEMPTY,
QASAME, XASAME, YASAME, ZASAME, QPRECEEDING, XPRECEEDING, YPRECEEDING,
ZPRECEEDING, QFOLLOWING, XFOLLOWING, YFOLLOWING, ZFOLLOWING,
QAUTHORSEPSTWOSEPS, XAUTHORSEPSTWOSEPS, YAUTHORSEPSTWOSEPS,
ZAUTHORSEPSTWOSEPS, QAUTHORSEPSTHREESEPSTHREESEPSEACH,
XAUTHORSEPSTHREESEPSTHREESEPSEACH, YAUTHORSEPSTHREESEPSTHREESEPSEACH,
ZAUTHORSEPSTHREESEPSTHREESEPSEACH, QAUTHORSEPSTHREESEPSTHREESEPSLAST,
XAUTHORSEPSTHREESEPSTHREESEPSLAST, YAUTHORSEPSTHREESEPSTHREESEPSLAST,
ZAUTHORSEPSTHREESEPSTHREESEPSLAST, QAUTHORNAMESNAMEFIRSTNAMEORDER,
XAUTHORNAMESNAMEFIRSTNAMEORDER, YAUTHORNAMESNAMEFIRSTNAMEORDER,
ZAUTHORNAMESNAMEFIRSTNAMEORDER, QAUTHORNAMESNAMEFIRSTINITIALSTYLE,
XAUTHORNAMESNAMEFIRSTINITIALSTYLE, YAUTHORNAMESNAMEFIRSTINITIALSTYLE,
ZAUTHORNAMESNAMEFIRSTINITIALSTYLE, QAUTHORNAMESNAMEFIRSTUPPERCASE,
XAUTHORNAMESNAMEFIRSTUPPERCASE, YAUTHORNAMESNAMEFIRSTUPPERCASE,
ZAUTHORNAMESNAMEFIRSTUPPERCASE, QAUTHORNAMESNAMEOTHERNAMEORDER,
XAUTHORNAMESNAMEOTHERNAMEORDER, YAUTHORNAMESNAMEOTHERNAMEORDER,
ZAUTHORNAMESNAMEOTHERNAMEORDER, QAUTHORNAMESNAMEOTHERINITIALSTYLE,
XAUTHORNAMESNAMEOTHERINITIALSTYLE, YAUTHORNAMESNAMEOTHERINITIALSTYLE,
ZAUTHORNAMESNAMEOTHERINITIALSTYLE, QAUTHORNAMESNAMEOTHERUPPERCASE,
XAUTHORNAMESNAMEOTHERUPPERCASE, YAUTHORNAMESNAMEOTHERUPPERCASE,
ZAUTHORNAMESNAMEOTHERUPPERCASE, QTEXTTEXTSINGLEPRECEEDING,
XTEXTTEXTSINGLEPRECEEDING, YTEXTTEXTSINGLEPRECEEDING,
ZTEXTTEXTSINGLEPRECEEDING, QTEXTTEXTSINGLEFOLLOWING,
XTEXTTEXTSINGLEFOLLOWING, YTEXTTEXTSINGLEFOLLOWING,
ZTEXTTEXTSINGLEFOLLOWING, QTEXTTEXTMULTIPLEPRECEEDING,
XTEXTTEXTMULTIPLEPRECEEDING, YTEXTTEXTMULTIPLEPRECEEDING,
ZTEXTTEXTMULTIPLEPRECEEDING, QTEXTTEXTMULTIPLEFOLLOWING,
XTEXTTEXTMULTIPLEFOLLOWING, YTEXTTEXTMULTIPLEFOLLOWING,
ZTEXTTEXTMULTIPLEFOLLOWING, PUBDATEPRECEEDING, PUBDATEFOLLOWING,
PUBDATEFORMAT, PUBDATESEQUENCE, PUBDATEMONTHFORMAT, PUBDATEDAYFORMAT,
PUBDATEYEARFORMAT, PUBDATEPADLEADINGZERO, PUBDATESTYLE,
PUBDATESECPRECEEDING, PUBDATESECFOLLOWING, PUBDATESECFORMAT,
PUBDATESECSEQUENCE, PUBDATESECMONTHFORMAT, PUBDATESECDAYFORMAT,
PUBDATESECYEARFORMAT, PUBDATESECPADLEADINGZERO, PUBDATESECSTYLE,
PUBDATEALLPRECEEDING, PUBDATEALLFOLLOWING, PUBDATEALLFORMAT,
PUBDATEALLSEQUENCE, PUBDATEALLMONTHFORMAT, PUBDATEALLDAYFORMAT,
PUBDATEALLYEARFORMAT, PUBDATEALLPADLEADINGZERO, PUBDATEALLSTYLE,
TITLEPRECEEDING, TITLEFOLLOWING, TITLECASE, TITLESTYLE,
BOOKTITLEPRECEEDING, BOOKTITLEFOLLOWING, BOOKTITLECASE, BOOKTITLESTYLE,
SERIESTITLEPRECEEDING, SERIESTITLEFOLLOWING, SERIESTITLECASE,
SERIESTITLESTYLE, ALLTITLEPRECEEDING, ALLTITLEFOLLOWING, ALLTITLECASE,
ALLTITLESTYLE, JOURNALNAMEPRECEEDING, JOURNALNAMEFOLLOWING,
JOURNALNAMECASE, JOURNALNAMEDEFAULTTEXT, JOURNALNAMEALTERNATETEXT,
JOURNALNAMEPUNCTUATION, JOURNALNAMESTYLE, VOLUMEPRECEEDING,
VOLUMEFOLLOWING, VOLUMESTYLE, ISSUEPRECEEDING, ISSUEFOLLOWING,
ISSUESTYLE, PAGESSTYLE, PAGESSINGLEPAGEPRECEEDING,
PAGESSINGLEPAGEFOLLOWING, PAGESPAGERANGEPRECEEDING,
PAGESPAGERANGEFOLLOWING, PAGESPAGERANGETYPE, PUBLISHERPRECEEDING,
PUBLISHERFOLLOWING, PUBLISHERSTYLE, PUBPLACEPRECEEDING,
PUBPLACEFOLLOWING, PUBPLACESTYLE,
PAGESPRECEEDING, PAGESFOLLOWING, REFNUMBERPRECEEDING,
REFNUMBERFOLLOWING, REFNUMBERSTYLE, PUBDATEFIRSTSEP, PUBDATESECONDSEP,
PUBDATESECFIRSTSEP, PUBDATESECSECONDSEP, PUBDATEALLFIRSTSEP,
PUBDATEALLSECONDSEP, PAGESPAGERANGERANGESEPARATOR from refdb1.REFSTYLE
where PUBTYPE='JOUR' and CITSTYLEID=0
18 Query SELECT ID, QSTYLE, XSTYLE, YSTYLE,
ZSTYLE, QABBREVIATEFIRST, XABBREVIATEFIRST, YABBREVIATEFIRST,
ZABBREVIATEFIRST, QABBREVIATESUBSEQ, XABBREVIATESUBSEQ,
YABBREVIATESUBSEQ, ZABBREVIATESUBSEQ, QABBREVIATEFIRSTMAXAUTHOR,
XABBREVIATEFIRSTMAXAUTHOR, YABBREVIATEFIRSTMAXAUTHOR,
ZABBREVIATEFIRSTMAXAUTHOR, QABBREVIATESUBSEQMAXAUTHOR,
XABBREVIATESUBSEQMAXAUTHOR, YABBREVIATESUBSEQMAXAUTHOR,
ZABBREVIATESUBSEQMAXAUTHOR, QABBREVIATEFIRSTDISPLAYAUTHOR,
XABBREVIATEFIRSTDISPLAYAUTHOR, YABBREVIATEFIRSTDISPLAYAUTHOR,
ZABBREVIATEFIRSTDISPLAYAUTHOR, QABBREVIATESUBSEQDISPLAYAUTHOR,
XABBREVIATESUBSEQDISPLAYAUTHOR, YABBREVIATESUBSEQDISPLAYAUTHOR,
ZABBREVIATESUBSEQDISPLAYAUTHOR, QAEMPTY, XAEMPTY, YAEMPTY, ZAEMPTY,
QASAME, XASAME, YASAME, ZASAME, QPRECEEDING, XPRECEEDING, YPRECEEDING,
ZPRECEEDING, QFOLLOWING, XFOLLOWING, YFOLLOWING, ZFOLLOWING,
QAUTHORSEPSTWOSEPS, XAUTHORSEPSTWOSEPS, YAUTHORSEPSTWOSEPS,
ZAUTHORSEPSTWOSEPS, QAUTHORSEPSTHREESEPSTHREESEPSEACH,
XAUTHORSEPSTHREESEPSTHREESEPSEACH, YAUTHORSEPSTHREESEPSTHREESEPSEACH,
ZAUTHORSEPSTHREESEPSTHREESEPSEACH, QAUTHORSEPSTHREESEPSTHREESEPSLAST,
XAUTHORSEPSTHREESEPSTHREESEPSLAST, YAUTHORSEPSTHREESEPSTHREESEPSLAST,
ZAUTHORSEPSTHREESEPSTHREESEPSLAST, QAUTHORNAMESNAMEFIRSTNAMEORDER,
XAUTHORNAMESNAMEFIRSTNAMEORDER, YAUTHORNAMESNAMEFIRSTNAMEORDER,
ZAUTHORNAMESNAMEFIRSTNAMEORDER, QAUTHORNAMESNAMEFIRSTINITIALSTYLE,
XAUTHORNAMESNAMEFIRSTINITIALSTYLE, YAUTHORNAMESNAMEFIRSTINITIALSTYLE,
ZAUTHORNAMESNAMEFIRSTINITIALSTYLE, QAUTHORNAMESNAMEFIRSTUPPERCASE,
XAUTHORNAMESNAMEFIRSTUPPERCASE, YAUTHORNAMESNAMEFIRSTUPPERCASE,
ZAUTHORNAMESNAMEFIRSTUPPERCASE, QAUTHORNAMESNAMEOTHERNAMEORDER,
XAUTHORNAMESNAMEOTHERNAMEORDER, YAUTHORNAMESNAMEOTHERNAMEORDER,
ZAUTHORNAMESNAMEOTHERNAMEORDER, QAUTHORNAMESNAMEOTHERINITIALSTYLE,
XAUTHORNAMESNAMEOTHERINITIALSTYLE, YAUTHORNAMESNAMEOTHERINITIALSTYLE,
ZAUTHORNAMESNAMEOTHERINITIALSTYLE, QAUTHORNAMESNAMEOTHERUPPERCASE,
XAUTHORNAMESNAMEOTHERUPPERCASE, YAUTHORNAMESNAMEOTHERUPPERCASE,
ZAUTHORNAMESNAMEOTHERUPPERCASE, QTEXTTEXTSINGLEPRECEEDING,
XTEXTTEXTSINGLEPRECEEDING, YTEXTTEXTSINGLEPRECEEDING,
ZTEXTTEXTSINGLEPRECEEDING, QTEXTTEXTSINGLEFOLLOWING,
XTEXTTEXTSINGLEFOLLOWING, YTEXTTEXTSINGLEFOLLOWING,
ZTEXTTEXTSINGLEFOLLOWING, QTEXTTEXTMULTIPLEPRECEEDING,
XTEXTTEXTMULTIPLEPRECEEDING, YTEXTTEXTMULTIPLEPRECEEDING,
ZTEXTTEXTMULTIPLEPRECEEDING, QTEXTTEXTMULTIPLEFOLLOWING,
XTEXTTEXTMULTIPLEFOLLOWING, YTEXTTEXTMULTIPLEFOLLOWING,
ZTEXTTEXTMULTIPLEFOLLOWING, PUBDATEPRECEEDING, PUBDATEFOLLOWING,
PUBDATEFORMAT, PUBDATESEQUENCE, PUBDATEMONTHFORMAT, PUBDATEDAYFORMAT,
PUBDATEYEARFORMAT, PUBDATEPADLEADINGZERO, PUBDATESTYLE,
PUBDATESECPRECEEDING, PUBDATESECFOLLOWING, PUBDATESECFORMAT,
PUBDATESECSEQUENCE, PUBDATESECMONTHFORMAT, PUBDATESECDAYFORMAT,
PUBDATESECYEARFORMAT, PUBDATESECPADLEADINGZERO, PUBDATESECSTYLE,
PUBDATEALLPRECEEDING, PUBDATEALLFOLLOWING, PUBDATEALLFORMAT,
PUBDATEALLSEQUENCE, PUBDATEALLMONTHFORMAT, PUBDATEALLDAYFORMAT,
PUBDATEALLYEARFORMAT, PUBDATEALLPADLEADINGZERO, PUBDATEALLSTYLE,
TITLEPRECEEDING, TITLEFOLLOWING, TITLECASE, TITLESTYLE,
BOOKTITLEPRECEEDING, BOOKTITLEFOLLOWING, BOOKTITLECASE, BOOKTITLESTYLE,
SERIESTITLEPRECEEDING, SERIESTITLEFOLLOWING, SERIESTITLECASE,
SERIESTITLESTYLE, ALLTITLEPRECEEDING, ALLTITLEFOLLOWING, ALLTITLECASE,
ALLTITLESTYLE, JOURNALNAMEPRECEEDING, JOURNALNAMEFOLLOWING,
JOURNALNAMECASE, JOURNALNAMEDEFAULTTEXT, JOURNALNAMEALTERNATETEXT,
JOURNALNAMEPUNCTUATION, JOURNALNAMESTYLE, VOLUMEPRECEEDING,
VOLUMEFOLLOWING, VOLUMESTYLE, ISSUEPRECEEDING, ISSUEFOLLOWING,
ISSUESTYLE, PAGESSTYLE, PAGESSINGLEPAGEPRECEEDING,
PAGESSINGLEPAGEFOLLOWING, PAGESPAGERANGEPRECEEDING,
PAGESPAGERANGEFOLLOWING, PAGESPAGERANGETYPE, PUBLISHERPRECEEDING,
PUBLISHERFOLLOWING, PUBLISHERSTYLE, PUBPLACEPRECEEDING,
PUBPLACEFOLLOWING, PUBPLACESTYLE,
PAGESPRECEEDING, PAGESFOLLOWING, REFNUMBERPRECEEDING,
REFNUMBERFOLLOWING, REFNUMBERSTYLE, PUBDATEFIRSTSEP, PUBDATESECONDSEP,
PUBDATESECFIRSTSEP, PUBDATESECSECONDSEP, PUBDATEALLFIRSTSEP,
PUBDATEALLSECONDSEP, PAGESPAGERANGERANGESEPARATOR from refdb1.REFSTYLE
where PUBTYPE='GEN' and CITSTYLEID=0
18 Quit
Sorry it isn't easy to read. But first as you can see, the condition
CITSTYLEID=0 can't be satisfied since in refdb1.REFSTYLE, CITSTYLEID
begins with a value equal to 1, there is no 0. On the other hand, if I
force this value to be 1 (which exists in the database) I get the same
error.
So there is a serious problem with the bibtex backend. As I don't have
time to understand the complete implementation of this backend and of
refdb in general, I can't track this bug further.
I hope that this report will be helpfull to give you any clues to
correct these imperfections.
sincerely,
Florent.
ps :
my configuration : Linux Slackware 8.1 kernel 2.4.20, mySQL 2.23.53,
TeTeX 1.0.7
--
---------------------------------
Florent Ingwiller
Laboratoire Louis NEEL / CNRS
25, avenue des Martyrs
BP 166
38042 Genoble CEDEX 9
Tel : +33 (0)4 76 88 12 89
Fax : +33 (0)4 76 88 11 91
email : ing...@gr...
---------------------------------
|
|
From: <mar...@mh...> - 2002-12-05 19:25:51
|
Hi all, RefDB 0.9.1 is out. This is mainly a bugfix release but it also adds a couple of nice new features. Bugfixes: - printf() conversion specifier incompatibility on Solaris was fixed. - refdbctl was fixed to run on Solaris out of the box - nmed2ris now handles datasets w/o end page or w/o page information or w/o volume/issue information properly. - selecting character encodings with PostgreSQL now works properly. - creating bibliographies with PostgreSQL should now work properly - citations.dsl was fixed - import of RIS data with non-tagged lines now works properly - runbib now creates the proper .bib file for DocBook XML - example documents were fixed and extended - refdbxp now treats strings containing "%" properly Improvements: - A new interactive shell script refdbnd (like "new document") creates a new skeleton document with a SGML or XML prolog and an entity declaration for your bibliography. It also creates a Makefile that controls all of the subsequent processing steps. - A new Perl script med2ris.pl converts Pubmed XML datasets to RIS. This script is intended to replace nmed2ris, although the latter will remain in the distribution for a while. - The marc2ris.pl Perl script was extended to handle UKMARC and UNIMARC data. - A new tutorial is available online at http://refdb.sourceforge.net/doc.html. This is targeted at new users (not administrators) and explains the basics with a lot of examples. Comments, suggestions, bug reports are welcome. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
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From: <mar...@mh...> - 2002-11-28 11:19:05
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Hi Massimo, at first sight this looks to me like the Solaris implementation of printf doesn't understand the %qu conversion specification which RefDB uses to convert unsigned long long values to a string. I've dug up a man page saying that it uses 'll' (ell-ell) instead. I'm afraid I'll have to check for this behaviour during configure and modify the program accordingly. regards, Markus Massimo Baleani writes: > Hi all, > I installed refdb-0.9 on a Solaris2.6system with mysql and I tested the > installation as suggested in the "testing your installation" manual page. I > was able to create and delete DBs, and add users as well using the refdba > client, but finally, when I come to run > > refdbc: addref -d foo examples/testrefs.ris > > I get the following error(s): > > Processing set 0 failed > try to add set as reference qu > insert into t_xuser failed > Processing set 1 failed > try to add set as reference qu > insert into t_xuser failed > ...... > > Do you have any idea on where the problem is? > Any help will be highly appreciate. > TIA, > Massimo. -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
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From: Massimo B. <mba...@pa...> - 2002-11-28 08:51:31
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Hi all, I installed refdb-0.9 on a Solaris2.6system with mysql and I tested the installation as suggested in the "testing your installation" manual page. I was able to create and delete DBs, and add users as well using the refdba client, but finally, when I come to run refdbc: addref -d foo examples/testrefs.ris I get the following error(s): Processing set 0 failed try to add set as reference qu insert into t_xuser failed Processing set 1 failed try to add set as reference qu insert into t_xuser failed ...... Do you have any idea on where the problem is? Any help will be highly appreciate. TIA, Massimo. |
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From: <mar...@mh...> - 2002-11-27 00:20:08
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Hi all, I've found an important request in the list archive. I was switching my email provider at the time this was posted so I didn't receive it back then. The author is apparently no subscriber, and his email address is protected in the archive. If you have the message (reprinted at the bottom) still in your inbox, please let me know as I'd like to contact that person. Now I'll address the problems listed below: - refdbib had a bug in the 0.8.x series so it wouldn't read the configuration file properly (or crash right away). This is fixed in 0.9 and in 0.8.6. - the 0.8.x version of the citations.dsl stylesheet indeed has a bug that shows up only with DocBook XML whereas DocBook SGML and TEI XML work properly. This bug was fixed in 0.9, but at the same time I couldn't resist introducing another stupid bug which makes the script utterly useless. Please use the current CVS version or wait for the upcoming 0.9.1 bugfix release - Jade and the fixed citations.dsl do work for XML files. I'll try to hack a XSL stylesheet that creates the same output in the long run, to free XML authors from having to install Jade just for this one purpose. - The closing tag issue for empty elements is a matter of using the correct syntax, if I understand this correctly. With DocBook SGML, just writing the start tag is ok for the xref element. With DocBook XML, use the <xref/> syntax instead. - I'll try and fix the documentation if it indeed leaves the impression that RefDB works only for DocBook 3.1. In fact, it works with all DocBook SGML releases since 3.1 (and maybe earlier ones also but I've never tried), all DocBook XML versions, and TEI P4. regards, Markus The original post follows: Hello, I have been looking at RefDB for a few weeks, and I've been able to get it running on a couple different machines in a couple different configurations. However, I have gotten stuck using it the way I was hoping to. I am stuck in the creation of a bibliography from a DocBook XML file. I followed through the documentation with an example document that I created. If I stick strictly to DocBook SGML V3.1 then things seem to work; however, if I move to XML things don't quite work so well. As I am relatively new to XML please don't discount ignorance on my part. I've attached two sample files, one SGML and one XML that I've been using. Note that there are some minor difference in these files as the <artheader> tag was superceded by the <articleinfo> tag. This tag, the PUBLICID/SYSTEMID, and the <xref> closing tag--more explanation below--should be the only differences between the two files. Let's start with the DocBook V3.1 SGML file. The documentation states to run "runbib;" however, there is a problem with this because I need to enter my password when the "rundbib" step is run and "runbib" doesn't forward the password. So, I chose to go through the steps manually--besides I learn more this way. The first step is to run Jade to transform the original document into the CitationList XML file. The documentation says: jade -t sgml -d citations.dsl /usr/lib/sgml/declaration/docbook-3.1.dcl foo.sgml > foo.id.xml It is interesting to note that the "citations.dsl" file gives a slightly different version of this command line. Which is correct? For me the following works: jade -t sgml -c /etc/sgml/catalog -d /usr/local/share/refdb/dsssl/citations.dsl /usr/share/sgml/docbook/sgml-dtd-3.1-1.0-8/docbook.dcl pa-ref.sgml > pa-ref.id.xml The documentation also shows the <xref> tag without a close tag or trailing "/". While this is apparently correct for SGML, I should still be able to use a closing tag if I choose. this doesn't work and produces an error: "end tag for element \"XREF\" which is not open." I didn't take it any further than successfully creating the CitationList (pa-ref.id.xml) file--I assume RefDB will do what it is supposed to. But, I want to create my documents in XML, and RefDB allegedly supports DocBook XML documents. Since there is "no official" version of DocBook XML before 4.0, I have been using what was installed on my RedHat 7.3 system: DocBook XML V4.1.2. I would expect that the Jade command only needs to change to select XML as the type and point to the XML declarations instead of the SGML declarations. However, this does not work; when I run OpenJade I get errors: jade -t xml -d /usr/local/share/refdb/dsssl/citations.dsl -c /etc/sgml/catalog /usr/share/sgml/xml.dcl pa-ref.xml > pa-ref.xml.id.xml This gives the following error for each XREF tag I have: jade:/usr/local/share/refdb/dsssl/citations.dsl:156:16:E: 1st argument for primitive "string-length" of wrong type: "#f" not a string If I change the type back to SGML, then I get different errors--something about entities in the entity files not being functions. It appears that any line with a "#" in it causes an error. I'm guessing this is because I really want to use an XSL stylesheet instead of a DSSSL stylesheet for the transformation to the CitationList. If this is true, shouldn't RefDB supply one if it claims to support XML? If not, what am I doing wrong? For clarity I am using a stock RedHat 7.3 installation with "everything" installed. As such I use OpenJade 1.3.1. I have RefDB 0.8.4a installed on two machines and 0.8.6 installed on a third machine, and the problem exists in all cases. FYI, I have validated the docs using onsgmls and xmllint, and I can process the xml files normally, i.e. create HTML and PDF from the source using xsltproc and pdflatex. I hope I have described the problem sufficiently. If you need anything else from me, I'd be happy to provide it. One last question, the documentation states in several places that RefDB can handle DocBook V3.1; does this mean that any version above this would not be supported yet? If so, how soon with newer DocBook versions be supported? If not, what are the implications of using V4.1 or V4.2 instead of V3.1? Thanks for the effort in making RefDB and helping me with this problem. Al -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
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From: <mar...@mh...> - 2002-11-19 20:05:49
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Hi all, RefDB version 0.9 is available for download at: http://sourceforge.net/projects/refdb This is a new major release with a number of significant changes. Please make sure to read the documentation. The manual has a few hints about upgrading, and the source archive has a file called "UPGRADING" which explains how to upgrade without losing your data. If you fail to follow these instructions, the new version will not work with your existing data and configuration files. I'd also like to point out that there is a new build dependency. You must have libdbi 0.6.7 (released just yesterday, available at http://sourceforge.net/projects/libdbi) installed on your system. Earlier versions of this library will not work. Bugfixes: - Fixed another segfault in refdbib - Changing databases in the web interface now actually works - All list* client commands now list everything if no regexp is given as an argument. Improvements: - RefDB now uses a database abstraction library (libdbi). Both MySQL and PostgreSQL are supported as SQL database servers. Support for additional servers is in preparation. - PostgreSQL users can choose between several character encodings including Unicode for each database. They also enjoy transaction support. - Reference databases now store a unique citation key in addition to the automatically assigned ID for each reference. This is a mnemonic string supplied by the user or auto-generated from the first author and the publication year. - The getref command uses a new tag :CK: to query the new citation key field. - SGML and XML documents can now use a greatly simplified short notation for citations. All you need to do is create a citation element and list the IDs or citation keys. A new tool refdbxp automatically expands the short to the full notation. - All configuration files are now installed in a subdirectory "refdb" of sysconfdir to unclutter the latter. - A new import filter for MARC data was added. - RefDB now offers an optional automatic keyword scan. The title and abstract fields of new references are scanned for existing keywords and all matches are added to the database. - A new teix backend allows export of reference data as TEI XML datasets. - The output of the db31 backend is improved. - All RefDB backends now treat non-abbreviated first and middle names correctly. - Deleted references are replaced by invisible skeleton entries. This greatly simplifies restoring a database with the same ID sequence from either a RIS or a SQL dump. - Bibliography styles can now be exported as XML files. - A set of example files: reference data in various formats, test documents with RefDB citations. As always, feedback is greatly appreciated. If you have problems with this version, with upgrading, or with the documentation, please complain on this list. It can be fixed. I'd greatly appreciate comments about the MARC import filter, as this certainly needs further development. If you use USMARC data, please let me know about data the script can't handle properly. Maybe this can be fixed too. Best regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
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From: Alan A. <al...@ru...> - 2002-11-09 07:26:21
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Hello, I have been looking at RefDB for a few weeks, and I've been able to get it running on a couple different machines in a couple different configurations. However, I have gotten stuck using it the way I was hoping to. I am stuck in the creation of a bibliography from a DocBook XML file. I followed through the documentation with an example document that I created. If I stick strictly to DocBook SGML V3.1 then things seem to work; however, if I move to XML things don't quite work so well. As I am relatively new to XML please don't discount ignorance on my part. I've attached two sample files, one SGML and one XML that I've been using. Note that there are some minor difference in these files as the <artheader> tag was superceded by the <articleinfo> tag. This tag, the PUBLICID/SYSTEMID, and the <xref> closing tag--more explanation below--should be the only differences between the two files. Let's start with the DocBook V3.1 SGML file. The documentation states to run "runbib;" however, there is a problem with this because I need to enter my password when the "rundbib" step is run and "runbib" doesn't forward the password. So, I chose to go through the steps manually--besides I learn more this way. The first step is to run Jade to transform the original document into the CitationList XML file. The documentation says: jade -t sgml -d citations.dsl /usr/lib/sgml/declaration/docbook-3.1.dcl foo.sgml > foo.id.xml It is interesting to note that the "citations.dsl" file gives a slightly different version of this command line. Which is correct? For me the following works: jade -t sgml -c /etc/sgml/catalog -d /usr/local/share/refdb/dsssl/citations.dsl /usr/share/sgml/docbook/sgml-dtd-3.1-1.0-8/docbook.dcl pa-ref.sgml > pa-ref.id.xml The documentation also shows the <xref> tag without a close tag or trailing "/". While this is apparently correct for SGML, I should still be able to use a closing tag if I choose. this doesn't work and produces an error: "end tag for element \"XREF\" which is not open." I didn't take it any further than successfully creating the CitationList (pa-ref.id.xml) file--I assume RefDB will do what it is supposed to. But, I want to create my documents in XML, and RefDB allegedly supports DocBook XML documents. Since there is "no official" version of DocBook XML before 4.0, I have been using what was installed on my RedHat 7.3 system: DocBook XML V4.1.2. I would expect that the Jade command only needs to change to select XML as the type and point to the XML declarations instead of the SGML declarations. However, this does not work; when I run OpenJade I get errors: jade -t xml -d /usr/local/share/refdb/dsssl/citations.dsl -c /etc/sgml/catalog /usr/share/sgml/xml.dcl pa-ref.xml > pa-ref.xml.id.xml This gives the following error for each XREF tag I have: jade:/usr/local/share/refdb/dsssl/citations.dsl:156:16:E: 1st argument for primitive "string-length" of wrong type: "#f" not a string If I change the type back to SGML, then I get different errors--something about entities in the entity files not being functions. It appears that any line with a "#" in it causes an error. I'm guessing this is because I really want to use an XSL stylesheet instead of a DSSSL stylesheet for the transformation to the CitationList. If this is true, shouldn't RefDB supply one if it claims to support XML? If not, what am I doing wrong? For clarity I am using a stock RedHat 7.3 installation with "everything" installed. As such I use OpenJade 1.3.1. I have RefDB 0.8.4a installed on two machines and 0.8.6 installed on a third machine, and the problem exists in all cases. FYI, I have validated the docs using onsgmls and xmllint, and I can process the xml files normally, i.e. create HTML and PDF from the source using xsltproc and pdflatex. I hope I have described the problem sufficiently. If you need anything else from me, I'd be happy to provide it. One last question, the documentation states in several places that RefDB can handle DocBook V3.1; does this mean that any version above this would not be supported yet? If so, how soon with newer DocBook versions be supported? If not, what are the implications of using V4.1 or V4.2 instead of V3.1? Thanks for the effort in making RefDB and helping me with this problem. Al |
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From: Paul B. <pbo...@sc...> - 2002-09-20 15:10:15
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Hi Markus Markus Hoenicka wrote: > Hi Paul, > > Paul Borgermans writes: > > 1) To reach this goal there are is one major issue: > > We need both import and export from/to *existing* reference systems and > > databases ( these range from personal "databases" to groups who are > > using a common database/system.). To maintain backwards compatibility, > > the existing keys should be preserved in order not to break references > > in existing documents. I read in previous posts and the manual that user > > defined ID's are not supported or retained when importing. > > > > Do you plan to integrate this in some way? Perhaps as an additional > > database field other than the default one and optionally coupled to the > > user? Of course this should be also an export option to select the key > > to use with a fall back to the refdb ID if no such key exists > > > > I don't plan to add this feature to the 0.8.x series, but it is > actually implemented in the libdbi-pre1 CVS branch that will > eventually be released as 0.9. I checked in the changes just today. > > The current implementation will try to use existing citation keys > (supplied as an alphanumeric string in the ID field of the RIS > dataset) and generate an error if the citation key already exists (it > has to be unique to make sense). If no citation key is supplied by the > user, RefDB will automatically generate one using the first author and > the publication year, followed by a sequential suffix to make it > unique if necessary. The only restriction is that the citation keys > must not be entirely numeric, i.e. "44" would not be allowed but > "Miller1999" would be. Please let me know whether this implementation > would match your needs. Great! That comes close. I see some users here using reference manager and not caring about ID's, so they end up with an entirely numeric key. I'll write pre/post processing filters for it if necessary. It is going to be in some automated scripts for upload / download from the refdb repository after all. > > 2) We will also develop a refdb SOAP service (in php, calling the refdb > > client utilities) which can be called by various applications (like the > > portals we plan to develop). Initially this will be a read-only service. > > I think other people may be interested in this as well (and we'll > > release the code of course). > > I thought about SOAP myself, but I'd be more than happy if someone > beats me at it. Let me know if you need any changes on the RefDB side > to make this work. I don't think there need to be changes made for now. Let me stress it will be a read-only service to start with. It will be used in say a department portal for listing all their relevant publications, extracted from the refdb driven (central) repository. > BTW, what organization are you working for? Is that some University > project or something similar? > Similar I guess: a nuclear (no military) research organisation. More about our project (a multi-year thingie): we try to integrate and put on-line a lot of our documents and research data, transforming most to XML in the next years. On top of that, we are implementing an open source portal system (multiple actually) based on eZ publish <http://developer.ez.no> and later maybe also apache cocoon in the backend to do some special XSLT. The portal systems should make it easier to find information and will also be used to capture as much knowledge as we can (300 scientists, 300 staff personnel). This is an increasing problem for universities and large organisations: a lot gets lost over time. It may be there somewhere on paper, but if one does not know it's there, then nobody will find it. The basis to choose XML formats as storage formats, beside its intrinsic advantages of structuring data and meta-data, is also to let it remain useful over many years. Our hypothesis is that if it is in XML and we need other formats, just transform it. If they (XML variants) are clear and well thought, this process should be relatively painless and feasible. Returning to refdb: we'll integrate it with the SOAP services and clients into the portal system as an ez publish module (client part that is). This means it will also need to be linked to the ez publish document (object) repository itself. The URL (location) field in the database propbably is OK for this. I hope this clarifies a little bit Regards Paul |
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From: Markus H. <hoe...@co...> - 2002-09-19 23:10:24
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Hi Nicolas, Nicolas Brouard writes: > char verbose[PREFS_VUFS_LEN] = "f"; /* should be true (t) or false (f) */ > Ok, I missed that one too. I've fixed all this stuff a while ago in the libdbi-pre1 CVS branch that I mainly develop currently, but I hope that I'll get it done for the 0.8.x series as well. > Refdbib has always worked with a call read_prefs(,,1)" > but you setup it with (,,0). Now the latter works if you supply arguments > (-S foo -t bibtex etc.) but if you only > type ./refdbib without arguments there is still a > segmentation fault. It is probably while reading the refdbibrc file. But > what is the difference between 0 and 1 and way some clients use 1 and > refdbib should use 0. It is not clear for me. Only bib2ris uses read_prefs(,,1). This is a special case as bib2ris uses a linked list to read a theoretically unlimited number of BibTeX field to RIS field mappings from a configuration file. All other bib2ris configuration data as well as the configuration data of all other RefDB applications end up in arrays of fixed size as all variable names to look for are known at compile time. Using read_prefs(,,1) with refdbib in your experiments just so happended to not crash. It is not supposed to work, as you can see if you take a look at the implementation of read_prefs(). If running ./refdbib without arguments causes a segfault it has to be fixed. This doesn't mean that calling refdbib without arguments would make any sense, but it is still a bug. Unfortunately it doesn't crash on FreeBSD, so I'll have to wait until I can access my Linux box again to verify that this problem is fixed. regards, Markus -- Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Markus H. <hoe...@co...> - 2002-09-19 23:08:22
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Hi Paul, Paul Borgermans writes: > 1) To reach this goal there are is one major issue: > We need both import and export from/to *existing* reference systems and > databases ( these range from personal "databases" to groups who are > using a common database/system.). To maintain backwards compatibility, > the existing keys should be preserved in order not to break references > in existing documents. I read in previous posts and the manual that user > defined ID's are not supported or retained when importing. > > Do you plan to integrate this in some way? Perhaps as an additional > database field other than the default one and optionally coupled to the > user? Of course this should be also an export option to select the key > to use with a fall back to the refdb ID if no such key exists > I don't plan to add this feature to the 0.8.x series, but it is actually implemented in the libdbi-pre1 CVS branch that will eventually be released as 0.9. I checked in the changes just today. The current implementation will try to use existing citation keys (supplied as an alphanumeric string in the ID field of the RIS dataset) and generate an error if the citation key already exists (it has to be unique to make sense). If no citation key is supplied by the user, RefDB will automatically generate one using the first author and the publication year, followed by a sequential suffix to make it unique if necessary. The only restriction is that the citation keys must not be entirely numeric, i.e. "44" would not be allowed but "Miller1999" would be. Please let me know whether this implementation would match your needs. > 2) We will also develop a refdb SOAP service (in php, calling the refdb > client utilities) which can be called by various applications (like the > portals we plan to develop). Initially this will be a read-only service. > I think other people may be interested in this as well (and we'll > release the code of course). I thought about SOAP myself, but I'd be more than happy if someone beats me at it. Let me know if you need any changes on the RefDB side to make this work. BTW, what organization are you working for? Is that some University project or something similar? regards, Markus -- Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Paul B. <pbo...@sc...> - 2002-09-18 18:43:53
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Hi Markus & other developers, Thanks for your refdb open source project, it appears to get most of the basic features we may need :-) We want to implement a "distributed" system on top of a central repository (implemented with refdb) with the following properties: - store all our organisations references centrally in refdb with a unique persistent ID - provide a service to end-users to keep there existing reference applications (reference manager, endnote and bibtex) and word processors - use the central repository of references also in a library portal and in the future also use them inside xml documents which will reside in different portals. 1) To reach this goal there are is one major issue: We need both import and export from/to *existing* reference systems and databases ( these range from personal "databases" to groups who are using a common database/system.). To maintain backwards compatibility, the existing keys should be preserved in order not to break references in existing documents. I read in previous posts and the manual that user defined ID's are not supported or retained when importing. Do you plan to integrate this in some way? Perhaps as an additional database field other than the default one and optionally coupled to the user? Of course this should be also an export option to select the key to use with a fall back to the refdb ID if no such key exists A workaround for us could be to import/export them from refdb and use these databases only for new documents, but this is rather confusing and some users tend to define keys which hint to the contents of a certain reference (mainly latex users). Or do you think the use of U1..U5 and /or M1..M3 could already serve this purpose (in both directions) with additional filter stages / config options (for bibtex this seems to be the case, but what about the others)? 2) We will also develop a refdb SOAP service (in php, calling the refdb client utilities) which can be called by various applications (like the portals we plan to develop). Initially this will be a read-only service. I think other people may be interested in this as well (and we'll release the code of course). I would welcome feedback, especially on the ID/key issues Best regards Paul |
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From: Markus H. <hoe...@co...> - 2002-09-13 04:34:55
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Hi, thanks for reporting this bug. It is unfortunately silent on FreeBSD, so I did not realize that the first fix (see the archives) did not fully fix the problem. The (hopefully) correct fix for the second part of this problem is to replace the corresponding section of refdbib.c with the following chunk: -------------------------- /* initialize the array of preference values */ prefs[0].varvalue = server_ip; prefs[1].varvalue = port_address; prefs[2].varvalue = verbose; prefs[3].varvalue = the_pager; prefs[4].varvalue = username; prefs[5].varvalue = passwd; prefs[6].varvalue = current_db; prefs[7].varvalue = refdb_timeout; prefs[8].varvalue = output_type; prefs[9].varvalue = output_format; prefs[10].varvalue = log_file; prefs[11].varvalue = log_dest; prefs[12].varvalue = log_level; prefs[13].varvalue = stylespec_dir; prefs[14].varvalue = refdblib; -------------------------- Nicolas, could you please verify whether this code runs ok on Linux? regards, Markus Nicolas Brouard writes: > > Hi, > > I got again a segmentation fault in refdbib on a Linux box (Mandrake 8.2) > just at starting when it tries to read the 'rc' files. > > I changed, in line 213, of refdbib.c a 0 with a 1 (as it is on some other > clients): > read_prefs (prefs, "refdbibrc",1); > -- Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Markus H. <hoe...@co...> - 2002-09-13 04:26:56
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Hi,
first of all, thank you very much for your detailed comments on
RefDB. I appreciate your efforts to make clear what RefDB lacks from a
user's point of view.
Please find the specific comments below.
Nicolas Brouard writes:
[...]
> working on my linux box and I want to make some comments on the
> documentation and on the product itself which could be easily improved by a
> better documentation (the implementation of Postgresql is a secondary
> priority).
This is not correct. Previous user comments pointed out two major
groups of people who don't use RefDB: those who prefer PostgreSQL over
MySQL (e.g. because everything else in their offices runs on
PostgreSQL) and those who don't want to run an external database
server at all. The switch to a database abstraction layer is therefore
essential. PostgreSQL is only the first additional database server to
be supported by RefDB. A sqlite dbi driver which doesn't need any
external database server is in preparation.
A third group is those who require support for additional character
encodings, especially Unicode. The current stable MySQL versions do
not support Unicode, and the development versions support only one
encoding per server instance. PostgreSQL supports Unicode and a bunch
of other encodings right now, selectable per database. Unicode is
essential for the planned support of MARC/UNIMARC records.
>
> - At first, there is no sample files in order to test the local
> installation. This is a pity.
Granted. RefDB should include a bunch of sample files.
> For example, my BibTeX file could not be input from the refdb WEB interface
> for an unknown reason (with a javascript warning saying that it was not a
> BibTeX file!); and I had liked to see how is a standard BibTeX/refdb input
> (is it with { or ( etc.?). Also there is no documentation on what refdb does
> with the "\citekey" field.
bib2ris (the app that does the BibTeX-to-RIS conversion behind the web
interface) uses the btparse library, so anything that this widely used
library can grok will work with RefDB. I personally ran tests with
files according to the Kopka/Daly guide and with random files pulled
from the web.
> I name citekey the text as in: @article(citekey,
>
> The citekey appears as the ID field of the RIS file after a bib2ris
> conversion but it disappears in the database and is replaced by a numbered
> ID
> @article(db-1,
>
> It is a severe limitation and truncation of your bibtex file which has to be
> documented.
Support for user-defined IDs is not yet implemented.
>
> - The first description and advertisement of RefDB on sourceforge.net
> compares RefDB with Reference Manager and EndNote; it is far from real. The
> main two advantages of these commercial products (and Procite too) consist
> in my view in: (1-import) on the "rapid" selection and "automatic" inclusion
> in an temporary database of references obtained from a search on Medline (or
> whatever bibliographic server), (2-export) on the "cite while you type"
> facility which you can use from Word or Word perfect by querying your
> reference manager.
>
> As far as I understand refdb today in order to simulate the first feature
> (1-import) you have to search your Medline with your own browser, copy and
> paste the different parts of the text of interest into your refdb browser
> (same browser but another and appropriate window). You can do it also from
> the command line but it doesn't seem to be more simple.
>
> Feature (2-export) can only be done with LaTeX/BibTeX (I am happy because
> LaTeX was what I wanted but most of the people here would like to use the
> refdb database with Word!). In most of these commercial products you can
> enter some "citekeys" into your text and if you don't remember the exact ID
> of your reference you can enter an author and/or a keyword and/or a date
> (which have to be enclosed by braces or something like that) and then by
> clicking from Word on the "Scan document" button you can select from your
> reference database one or more exact references to be inserted. Also refdb
> is not a Z39.50 server and can't be used with such, commercial or not,
> reference seekers. It has to be documented.
>
You should keep in mind is that RefDB was designed for use with
SGML/XML documents. LaTeX support is a pleasant side effect with some
still unresolved issues. So the main goal of development is not to
create a free Reference Manager lookalike but to develop a Unix-style
tool that allows you to arrive at the same result (a printable or HTML
document with a correctly formatted bibliography), but you can use
markup languages instead of proprietary word processors. What you talk
about here are usability issues from the point of view of a Windows
user (I assume). For a Windows user, there is one window that you
interact with, and this one window must have all the capabilities that
you need for a particular job. Unix has a different philosophy. A job
is done by concatenating a bunch of tools that you feel are suited
best for your needs. When I write a DocBook document, I have a few
Emacs windows on one virtual screen and half a dozen xterms on another
virtual screen, and I can do whatever I need in these windows. And if
someone wants to use vi that's ok too. Keep in mind that you basically
don't have a choice with commercial products. You have this close
integration of the bibliography stuff because one commercial product
is tighly tied to another commercial product on one particular
commercial platform. Try clicking on "Scan document" in OpenOffice on
FreeBSD and you see what I mean (there is no such thing). With RefDB
you have the choice to use whatever you like, at the price of
requiring some work to integrate it into your personal environment.
This approach offers the benefit of "scriptability". As an example,
you could subscribe to an email service that runs your favourite
Medline query once a week, mark the references you're interested in,
and hand the data to a script that adds these references to a RefDB
database. Try that with a commercial product.
Taken together, RefDB does not try to simulate the usability features
of commercial Windows products. It uses a different approach to arrive
at the same final result, a formatted bibliography.
Z39.50 support will eventually be implemented, but strictly according
to this philosophy: as an external application.
> o Comments and questions on the installation documentation
>
> - Why during the make install, the style files (bibtex-full.xml etc.) are
> copied to /usr/local/share/refdb/styles ? It seems that during a:
> refdbib -u username -d foo -S bibtex-full -t bibtex foo.aux
> command, refdbib does not look at that style file directory. Ok, I
> understand that the styles have to be loaded into the refdb mysql database
> but why, again, the refdba command:
> addstyle bibtex-full.xml
> does not look at that special directory? The only way I found to add styles
> was to enter the complete path
> addstyle /usr/local/share/refdb/styles/bibtex-full.xml
> Is there another way? (I spent hours on this!)
No. It is a basic feature of the Unix command line that if you want to
work with a particular file you use its path to specify this
file. RefDB installs the example styles in a useful place, but it does
not force you to add your own styles to this particular directory.
> What means the line
> stylespecdir $REFDBLIB/stylespec
> in refdbibrc?
Sorry about that. This is leftover junk that needs to be cleaned up.
>
> It is not clear in your README or INSTALL file that after "make install" you
> should have a refdbd running...
> ...and refdba works without a refdbd running...
> I mean that there is no error message if you create a database with refdba
> without a refdbd running!
I can't reproduce this. If I run any command from refdba or refdbc
without a refdbd instance running I get:
could not establish server connection
which should be pretty descriptive. Please verify that you don't have
a refdbd process running in the background.
> Many of the refdb client don't have error messages (like refdbib if the
> foo.aux does not exist).
>
> What is the default style of refdbib?
There is no default style. If you don't specify a particular style,
you'll get an error message.
> Why isn't the default style not included into the mysql database during the
> make install, or during the input of a mysql install dump.
>
> In fact you could add also the inclusion of a sample database (foo) whith a
> dump.
>
Yep. Dumps would be good.
> Instead of long documentation sections on how to implement refdbd daemon
> which every one knows (/etc/rc.d/init.d/refdbd start) you could simply tell
*You* happen to know that. But you are not everyone. And what you
suggest happens to work on your favourite Linux distro, but not on
FreeBSD or Cygwin or a dozen other systems. This is why this stuff is
an integral part of any comprehensive documentation.
> people to launch refdbd as:
> refdbd -s -V -e 0 -l 7
> in order to test the connection.
>
> For example the creation of 'root' and other user is not clear. Even if I
> use mysql for other product like the 'sympa' mailing list server,
> phpmyAdmin, and other private services I spent a lot of time until it works.
>
> For example, refdb seems to need "localhost.localdomain" as the local host.
> It is not true with other standard mysql services where simply "localhost"
> is the host. I have had to create a root user for localhost.localdomain,
> because the standard one did not work: only an interactive (-e 0) refdbd
> launch can help you to see the:
> Access denied root@localhost.localdomain
> messages.
>
It is frankly stated in the manual that you still need some MySQL
administration skills to set up RefDB (and it is a stated goal for
the first stable release 1.0 to change that...). This includes reading
the excellent MySQL manual. I don't know why you had to create 'root'
as it is the default administrator on fresh MySQL installations. If
you removed this user for security reasons, I can assume you know what
you were doing.
I've never seen the "localhost.localdomain" issue on any of my
installations. It would be great if you could supply more information
about your setup in order to find out what happens. I can use
"localhost" or "127.0.0.1" (if I allow TCP/IP connections) without any
problems on several platforms (FreeBSD, Debian, WinNT).
> Also, there is no documentation on the port that you use and, if you are
> protected by a firewall, which one you can use. Is port 9734 planned to be
> included in /etc/services like 3306 is for mysql?
>
This depends on how you set up RefDB. If you run clients outside the
firewall, then you have to allow access to port 9734. If refdbd and
mysqld run on the same box, port 3306 does not have to be accessible
from outside.
> It seems to me that if you use a WebInterface of refdb the access are done
> from localhost so you don't need to open the 9734 port for input with your
> firewall.
If you use the web interface, Apache locally runs refdbc which in turn
connects to refdbd which in turn connects to mysqld. If all of this
happens on the same box, you don't need any publicly accessible port
except 80 for Apache.
>
> Your documentation is mainly written as if clients were all on Unix boxes in
> a World without firewalls. I think that reality changed. It is not necessary
> to create users with -H % privileges if your mysql databases are used for
> other purposes like confidential mailing lists with protected passwords.
>
Again, the RefDB manual can't repeat the MySQL manual and your
favourite Firewall's manual. If you use these tools, you should use
the appropriate documentation. The -H % examples are nothing but
examples with the hints that you should use restrictions appropriate
to your local installation.
> There is no section on "Common Errors" like "What to do if
> you get Access denied" or other things like that. The use of phpMyAdmin
> could be mentioned and emphasized as it really simplifies the management of
> databases.
Granted. The common errors section is badly missing.
>
> Also I don't understand the personal reference list. What is the hierarchy
> between users? What are the privileges to setup? If someone uploads a
> bibliography from the Web interface, would it be a common database or a
> personal database? Also a guided tour could be nice.
There is no such thing as a hierarchy. Personal reference lists are a
tool to *avoid* personal databases. The idea is to pool all references
that a workgroup or a department collects in one database and still allow
each user to have a view of those references that he personally added
(or picked from those that others added), just as if he had used a
private database. This is independent of whether you use the web
interface or the CLI.
>
> Your documentation is not numbered and its structure is not clear.
> For example in your Table of Contents you have Parts and Chapters but
> chapters are not renumbered from one after each part. Under each chapter,
> sections are not numbered at all. It is very confusing with subsections. For
> example why "Finishing the refdb installation" which is a major section is
> before the "Seting up the refdb web services". Again "Add or delete
> bibliography styles" should be partly dupplicated in a sub-section of
> Finishing the refdb installation if not setup through a mysql command file
> or dump.
The manual was transformed with the default DocBook DSSSL
stylesheets. The numbering stuff could be altered by a driver file if
you feel this improves readability.
As for the other issues, the manual is certainly far from perfect.
>
> There is actually no documentation on the Web interface which is what I am
> interested mostly in. The "login" button is confusing: whatever username and
> password you enter, the message is that "Your are logged in". What is this
> button doing? The java script could be included in the HTML to be more
> clear. I understand that you need a username, a password and a database to
> submit a query. So the Login button is not mandatory. In your simple query a
> book title is not searched, only a title of an article is searched.
>
Including the Javascript code in the HTML would duplicate the code in
a dozen files. This is why it is in an easily maintainable external
file that you can view with your browser as easily as a HTML page.
The purpose of the login button is to set the cookies for the
authentication stuff. This is necessary if you immediately switch to a
different page without running a query (the latter creates the cookies
on the fly), because all other pages assume that the cookies already
exist.
> I know that criticism is easy but when I see that the todo list is mostly
> concerned by new facilities I am afraid that many potential users,
> sourceforge downloaders, did not try the product only because the
> documentation is not clear and not because of the limitations of refdb.
>
> Also it is not difficult to describe briefly in the introduction what are
> the other softwares or concepts that you use (BibTeX, SGML, XML, TEI,
> DocBook etc.). Even LaTeX is not described at all.
RefDB is a tool for people that have specific requirements to get
something done. If a XML author needs bibliographies, I don't have to
explain XML to him. If a LaTeX author needs bibliographies, I don't
have to explain LaTeX to him. If you don't know it, you most likely
don't use it. I believe what you ask for is beyond the scope of a user
manual. It would be a nice introductory chapter of an O'Reilly book on
RefDB (just kidding).
[...]
> I hope that my remarks and comments were helpful and not offensive because
> refdb is probably one of the most "opensource" innovative product for
> scientists I have found.
Again, I appreciate your comprehensive comments. Still you should keep
one thing in mind: RefDB is essentially a one-man show (but thanks to
all who sent in bug reports, did testing on arcane platforms, and sent
in Makefile patches etc). I'm hacking RefDB in my spare time according
to my personal needs, but I always try to listen what others would
like to see implemented. But you simply can't expect a free Reference
Manager clone from me for all platforms that Reference Manager ignores
and for all document types that Reference Manager ignores with all the
nifty usability features of a $500 package. (And now the free software
mantra:) RefDB is free software. If you want to improve RefDB, take
the source, implement missing features, and send in the patches. If
you want a better documentation, take the DocBook sources, improve the
document, and send in the patches. I hope this doesn't sound rude but
this is how most non-commercial software packages are developed these
days.
best regards,
Markus
--
Markus Hoenicka <hoe...@co...>
http://ourworld.compuserve.com/homepages/hoenicka_markus/
|
|
From: Vanessa L. <re...@se...> - 2002-09-12 19:54:40
|
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|
|
From: Nicolas B. <br...@in...> - 2002-09-12 16:27:59
|
Hi, I got again a segmentation fault in refdbib on a Linux box (Mandrake 8.2) just at starting when it tries to read the 'rc' files. I changed, in line 213, of refdbib.c a 0 with a 1 (as it is on some other clients): read_prefs (prefs, "refdbibrc",1); I already did it in version 0.8.5 and thought that it was solved in the new version. I don't know exactly the meaning of this 0 or 1 option, I aggree. Nicolas Brouard INED, Paris |
|
From: Nicolas B. <br...@in...> - 2002-09-12 10:46:12
|
Hi all,
I am new on RefDB.
I downloaded version 0.8.5, found the refdbib segmentation fault bug and
downloaded latest version 0.8.6 which suppresses the bug. RefDb is now
working on my linux box and I want to make some comments on the
documentation and on the product itself which could be easily improved by a
better documentation (the implementation of Postgresql is a secondary
priority).
- At first, there is no sample files in order to test the local
installation. This is a pity.
For example, my BibTeX file could not be input from the refdb WEB interface
for an unknown reason (with a javascript warning saying that it was not a
BibTeX file!); and I had liked to see how is a standard BibTeX/refdb input
(is it with { or ( etc.?). Also there is no documentation on what refdb does
with the "\citekey" field.
I name citekey the text as in: @article(citekey,
The citekey appears as the ID field of the RIS file after a bib2ris
conversion but it disappears in the database and is replaced by a numbered
ID
@article(db-1,
It is a severe limitation and truncation of your bibtex file which has to be
documented.
- The first description and advertisement of RefDB on sourceforge.net
compares RefDB with Reference Manager and EndNote; it is far from real. The
main two advantages of these commercial products (and Procite too) consist
in my view in: (1-import) on the "rapid" selection and "automatic" inclusion
in an temporary database of references obtained from a search on Medline (or
whatever bibliographic server), (2-export) on the "cite while you type"
facility which you can use from Word or Word perfect by querying your
reference manager.
As far as I understand refdb today in order to simulate the first feature
(1-import) you have to search your Medline with your own browser, copy and
paste the different parts of the text of interest into your refdb browser
(same browser but another and appropriate window). You can do it also from
the command line but it doesn't seem to be more simple.
Feature (2-export) can only be done with LaTeX/BibTeX (I am happy because
LaTeX was what I wanted but most of the people here would like to use the
refdb database with Word!). In most of these commercial products you can
enter some "citekeys" into your text and if you don't remember the exact ID
of your reference you can enter an author and/or a keyword and/or a date
(which have to be enclosed by braces or something like that) and then by
clicking from Word on the "Scan document" button you can select from your
reference database one or more exact references to be inserted. Also refdb
is not a Z39.50 server and can't be used with such, commercial or not,
reference seekers. It has to be documented.
o Comments and questions on the installation documentation
- Why during the make install, the style files (bibtex-full.xml etc.) are
copied to /usr/local/share/refdb/styles ? It seems that during a:
refdbib -u username -d foo -S bibtex-full -t bibtex foo.aux
command, refdbib does not look at that style file directory. Ok, I
understand that the styles have to be loaded into the refdb mysql database
but why, again, the refdba command:
addstyle bibtex-full.xml
does not look at that special directory? The only way I found to add styles
was to enter the complete path
addstyle /usr/local/share/refdb/styles/bibtex-full.xml
Is there another way? (I spent hours on this!)
What means the line
stylespecdir $REFDBLIB/stylespec
in refdbibrc?
It is not clear in your README or INSTALL file that after "make install" you
should have a refdbd running...
...and refdba works without a refdbd running...
I mean that there is no error message if you create a database with refdba
without a refdbd running!
Many of the refdb client don't have error messages (like refdbib if the
foo.aux does not exist).
What is the default style of refdbib?
Why isn't the default style not included into the mysql database during the
make install, or during the input of a mysql install dump.
In fact you could add also the inclusion of a sample database (foo) whith a
dump.
Instead of long documentation sections on how to implement refdbd daemon
which every one knows (/etc/rc.d/init.d/refdbd start) you could simply tell
people to launch refdbd as:
refdbd -s -V -e 0 -l 7
in order to test the connection.
For example the creation of 'root' and other user is not clear. Even if I
use mysql for other product like the 'sympa' mailing list server,
phpmyAdmin, and other private services I spent a lot of time until it works.
For example, refdb seems to need "localhost.localdomain" as the local host.
It is not true with other standard mysql services where simply "localhost"
is the host. I have had to create a root user for localhost.localdomain,
because the standard one did not work: only an interactive (-e 0) refdbd
launch can help you to see the:
Access denied root@localhost.localdomain
messages.
Also, there is no documentation on the port that you use and, if you are
protected by a firewall, which one you can use. Is port 9734 planned to be
included in /etc/services like 3306 is for mysql?
It seems to me that if you use a WebInterface of refdb the access are done
from localhost so you don't need to open the 9734 port for input with your
firewall.
Your documentation is mainly written as if clients were all on Unix boxes in
a World without firewalls. I think that reality changed. It is not necessary
to create users with -H % privileges if your mysql databases are used for
other purposes like confidential mailing lists with protected passwords.
There is no section on "Common Errors" like "What to do if
you get Access denied" or other things like that. The use of phpMyAdmin
could be mentioned and emphasized as it really simplifies the management of
databases.
Also I don't understand the personal reference list. What is the hierarchy
between users? What are the privileges to setup? If someone uploads a
bibliography from the Web interface, would it be a common database or a
personal database? Also a guided tour could be nice.
Your documentation is not numbered and its structure is not clear.
For example in your Table of Contents you have Parts and Chapters but
chapters are not renumbered from one after each part. Under each chapter,
sections are not numbered at all. It is very confusing with subsections. For
example why "Finishing the refdb installation" which is a major section is
before the "Seting up the refdb web services". Again "Add or delete
bibliography styles" should be partly dupplicated in a sub-section of
Finishing the refdb installation if not setup through a mysql command file
or dump.
There is actually no documentation on the Web interface which is what I am
interested mostly in. The "login" button is confusing: whatever username and
password you enter, the message is that "Your are logged in". What is this
button doing? The java script could be included in the HTML to be more
clear. I understand that you need a username, a password and a database to
submit a query. So the Login button is not mandatory. In your simple query a
book title is not searched, only a title of an article is searched.
I know that criticism is easy but when I see that the todo list is mostly
concerned by new facilities I am afraid that many potential users,
sourceforge downloaders, did not try the product only because the
documentation is not clear and not because of the limitations of refdb.
Also it is not difficult to describe briefly in the introduction what are
the other softwares or concepts that you use (BibTeX, SGML, XML, TEI,
DocBook etc.). Even LaTeX is not described at all.
"TeX and LaTeX (one of the first markup language) are mostly but heavily
used by people who needs to type mathematics. BiBTeX was included in the
LaTeX package to manage scientific bibliography databases. Since libraries
have been computerized, the BibTeX format was too simple to locate physical
books in a real library and many formats have been used in the world, like
the RIS format used in RefDB. Also Internet offered the possibility to
exchange documents and bibliographies, markup languages like SGML HTML and
now XML are more and more used and sometimes output by bibliographic web
servers like Medline but also RefDB.
The Z39.50 protocol is actually the most important protocol used to query a
bibliographic server even if its possibilities of searching documents are
poor (ISI said that recently). RefDB is actually not a Z39.50 server like
Zebra/Zap (opensource) is but it can output XML as well as formatted
bibliographies. Unlike Reference Manager, Endnote, Procite and other
commercial products it has no automatic procedure to query the Medline
server and to select and store results in a refdb database but it can import
results of internet queries through a Web Interface as well as through
unix-like typed commands. For example you can export from Reference Manager
or Endnote, your databases as Ris-Export-Text files and then import them
into a refdb database with a simple refdbc client. But the main adavantage
of RefDB is probably for LaTeX users who want to share a local bibliographic
database. In fact a LaTeX user, who can use LaTeX on an Unix box as on a PC
or Mac, can search the refdb database (named "db" for example) with a
browser (http://foo.net/refdbquery.html) , locate the appropriate reference
ID ("243" for example), insert the \cite{db-243} command in her LaTeX text
to get a correct bibliography with the \bibliography{db} command. The
"refdbib" client is only the additional step (before bibtex) to extract the
references cited in the ".aux" file from the "db" refdb database, create a
local db.bib bibtex file which can be used by BibTeX to create a db.bbl
which, finally, is used by latex.
Refdbib clients (on Pc or whatever box) should be able to query a refdb
server through the 9734 tcp port. As far as I understand refdb, the refdb
server (not refdbib itself) calls the mysql server on port 3306 (it is not
necessary to open 3306 outside a firewall). RefDB is only at a very early
stage of functionning. We are waiting for the implementation of a Z39.50
protocol in order to allow easy search/download from commercial products
like Reference Manager, EndNote, ProCite and others."
I know that English is not my native language but I had like to find some
explanations like the above to know more precisely some of the features of
refdb.
I hope that my remarks and comments were helpful and not offensive because
refdb is probably one of the most "opensource" innovative product for
scientists I have found.
Nicolas Brouard
Institut national d'études démographiques
Mortality, Health and Epidemiology Research Unit
Paris
br...@in...
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From: Markus H. <hoe...@co...> - 2002-09-11 20:48:10
|
The file xmlhandler.c contains a few bugs that affect only the PowerPC platform. Anyone using RefDB on PowerPC need to upgrade this file. Until a new maintenance release is finished, please contact me off list. NB The libdbi-pre1 branch in CVS, which eventually will be released as RefDB 0.9 is not affected by this bug. regards, Markus Juan de la Figuera writes: > > Hi, > > I still have the DUMMY problem under ref 0.8.6 (which I guess is to be > expected as xmlhandler.c didn't change). If there is anything I can test from > this side on the powerpc platform, I would be happy to help (time > permitting). -- Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Juan de la F. <jua...@ua...> - 2002-09-09 10:03:48
|
Hi, I still have the DUMMY problem under ref 0.8.6 (which I guess is to be=20 expected as xmlhandler.c didn't change). If there is anything I can test = from=20 this side on the powerpc platform, I would be happy to help (time=20 permitting). Regards, Juan --=20 -------------------------------------------------------------------------= ----------------- Juan de la Figuera Profesor contratado Ram=F3n y Cajal/ Assistant Professor Dpto. de F=EFsica de la Materia Condensada C-III Universidad Aut=F3noma de Madrid Madrid 28049 Spain Phone: 913974758 Fax: 913973961 -------------------------------------------------------------------------= ------------------ |
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From: Markus H. <hoe...@co...> - 2002-08-28 20:24:13
|
Hi, just to let you know that the latest and greatest RefDB is available at http://sourceforge.net/projects/refdb The noteworthy changes are: Bugfixes: - fixed a segfault in refdbib - the adduser command was fixed for host names containing wildcards - retrieving journal abbreviations through the web interface now works as expected - etc/Makefile now correctly creates the sysconfdir directory if it doesn't exist yet - fixed a protocol error in the bibliography code - fixed handling of visible and hidden user config files - the additional information in PY fields is now correctly added to the appropriate row Improvements: - a new command line option (-y) allows to specify the directory containing the configuration files. This is important only if you move around precompiled binaries, e.g. when relocating a rpm package. In addition to this release I'd like to point out the existence of a libdbi-pre1 branch in CVS. This branch uses libdbi as a database abstraction layer and works with both MySQL and PostgreSQL. Unfortunately the current libdbi release needs a few patches to work properly, so I'll wait with an official release of this new branch until libdbi is updated. If anyone is interested in test-driving this branch, I'd be happy to write up the necessary libdbi fixes (they're all submitted to the libdbi list BTW) and to provide installation and setup instructions. regards, Markus -- Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Markus H. <hoe...@co...> - 2002-08-13 18:24:53
|
Hi Juan,
jua...@ua... writes:
> behavior: I cannot add styles (even using the original ones from the refdb
> tar.gz)
>
> This is the syslog output of refdba "addstyle bibtex-full.xml". I end up
> with
> an entry called "DUMMY". The mysql version is 3.23.51, refdb is 0.8.5a.
> Everything running under Debian/sid for powerpc. I have to say I didn't clean
> everything from 0.8.4, I just compiled and installed 0.8.5a and used the same
> configuration files... and the same databases...but if I recall correctly I
> also had the same problem. I also attach the dump of the CITSTYLE part of
> refdb. As far as I understand, it is getting confused getting a new ID
> (something related to endiannes?)
>
This is correct. I believe it is some weird problem with the size of
integers on your platform. Interestingly the new ID is retrieved
correctly into an int when adding references (this is a size
limitation to be removed in future refdb releases), but it fails if
you assign it to a my_ulonglong (which translates to unsigned long
long on most platforms). This unfortunately means that fixing RefDB to
use my_ulonglong in all cases would break it completely on your
platform.
Please give me another day or two to investigate the peculiarities of
the powerpc platform. Unfortunately I don't have such a beast around,
so I'll probably have to ask you to run a few tests for me.
regards,
Markus
> Aug 2 16:08:15 ibuk refdbd[3588]: serving client on fd 6 with protocol
> version 0
> Aug 2 16:08:15 ibuk refdbd[3588]: 210-27-79-57
> Aug 2 16:08:16 ibuk refdbd[3588]: INSERT INTO CITSTYLE (JOURNAL) VALUES
> ('DUMMY')
> Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE CITSTYLE SET JOURNAL='bibtex-full'
> WHERE ID=0
--
Markus Hoenicka <hoe...@co...>
http://ourworld.compuserve.com/homepages/hoenicka_markus/
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|
From: <jua...@ua...> - 2002-08-10 22:58:01
|
Hello,
After moving to Spain I am back (sort of). I still have to unpack=
all the
books, but they are in a nice refdb database :-)
What is the status of the so-called DUMMY style problem? I am hav=
ing the
same
behavior: I cannot add styles (even using the original ones from the refd=
b
tar.gz)
This is the syslog output of refdba "addstyle bibtex-full.xml". I=
end up
with
an entry called "DUMMY". The mysql version is 3.23.51, refdb is 0.8.5a.
Everything running under Debian/sid for powerpc. I have to say I didn't c=
lean
everything from 0.8.4, I just compiled and installed 0.8.5a and used the =
same
configuration files... and the same databases...but if I recall correctly=
I
also had the same problem. I also attach the dump of the CITSTYLE part of
refdb. As far as I understand, it is getting confused getting a new ID
(something related to endiannes?)
Aug 2 16:08:15 ibuk refdbd[3588]: serving client on fd 6 with protocol
version 0
Aug 2 16:08:15 ibuk refdbd[3588]: 210-27-79-57
Aug 2 16:08:16 ibuk refdbd[3588]: INSERT INTO CITSTYLE (JOURNAL) VALUES
('DUMMY')
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE CITSTYLE SET JOURNAL=3D'bibtex-=
full'
WHERE ID=3D0
Aug 2 16:08:16 ibuk refdbd[3588]: INSERT INTO REFSTYLE (CITSTYLEID, PUBT=
YPE)
VALUES (0, 'GEN')
Aug 2 16:08:16 ibuk refdbd[3588]: INSERT INTO POSITIONS
(POS,TYPE,SEPARATORID,REFSTYLEID) VALUES (0, 'JOURNALNAME', 0, 0)
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE REFSTYLE SET
JOURNALNAMEPUNCTUATION=3D'SPACE' WHERE CITSTYLEID=3D0 AND PUBTYPE=3D'GEN'
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE REFSTYLE SET
JOURNALNAMEALTERNATETEXT=3D'AABBREV' WHERE CITSTYLEID=3D0 AND PUBTYPE=3D'=
GEN'
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE REFSTYLE SET
JOURNALNAMEDEFAULTTEXT=3D'FULL' WHERE CITSTYLEID=3D0 AND PUBTYPE=3D'GEN'
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE REFSTYLE SET JOURNALNAMECASE=3D=
'ASIS'
WHERE CITSTYLEID=3D0 AND PUBTYPE=3D'GEN'
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE CITSTYLE SET PRECEEDING=3D'(' W=
HERE
ID=3D2139062143
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE CITSTYLE SET FOLLOWING=3D')' WH=
ERE
ID=3D2139062143
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE CITSTYLE SET CITSEPARATOR=3D'; =
' WHERE
ID=3D2139062143
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE CITSTYLE SET RANGESEPARATOR=3D'=
-'
WHERE ID=3D2139062143
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE CITSTYLE SET BIBLIOTITLE=3D'Ref=
erence
List' WHERE ID=3D2139062143
Aug 2 16:08:16 ibuk refdbd[3588]: INSERT INTO REFSTYLE (CITSTYLEID, PUBT=
YPE)
VALUES (0, 'INTEXT')
Aug 2 16:08:16 ibuk refdbd[3588]: INSERT INTO POSITIONS
(POS,TYPE,SEPARATORID,REFSTYLEID) VALUES (0, 'REFNUMBER', 0, 0)
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE CITSTYLE SET BIBLIOSEQUENCE=3D'=
BASIS'
WHERE ID=3D2139062143
Aug 2 16:08:16 ibuk refdbd[3588]: UPDATE CITSTYLE SET INTEXTSEQUENCE=3D'=
ASIS'
WHERE ID=3D2139062143
Aug 2 16:08:16 ibuk refdbd[3588]: SELECT ID FROM CITSTYLE WHERE
JOURNAL=3D'bibtex-full' ORDER BY ID ASC
Aug 2 16:08:16 ibuk refdbd[3588]: chunk added successfully
Aug 2 16:08:16 ibuk refdbd[3588]: command processing done, finish dialog=
now
Aug 2 16:08:16 ibuk refdbd[3588]: child finished client on fd 6
Aug 2 16:08:16 ibuk refdbd[2078]: child exited with code 0
Aug 2 16:08:16 ibuk refdbd[2078]: server waiting n_max_fd=3D5
And the refdb dump looks like:
-- MySQL dump 8.22
--
-- Host: localhost Database: refdb
---------------------------------------------------------
-- Server version 3.23.51-log
--
-- Current Database: refdb
--
CREATE DATABASE /*!32312 IF NOT EXISTS*/ refdb;
USE refdb;
--
-- Table structure for table 'CITSTYLE'
--
CREATE TABLE CITSTYLE (
ID int(11) NOT NULL auto_increment,
JOURNAL tinytext,
CITSEPARATOR tinytext,
FOLLOWING tinytext,
PRECEEDING tinytext,
RANGESEPARATOR tinytext,
BIBLIOTITLE tinytext,
INTEXTSEQUENCE varchar(10) default NULL,
BIBLIOSEQUENCE varchar(11) default NULL,
STYLE varchar(12) default NULL,
JANABBREV varchar(16) default NULL,
FEBABBREV varchar(16) default NULL,
MARABBREV varchar(16) default NULL,
APRABBREV varchar(16) default NULL,
MAYABBREV varchar(16) default NULL,
JUNABBREV varchar(16) default NULL,
JULABBREV varchar(16) default NULL,
AUGABBREV varchar(16) default NULL,
SEPABBREV varchar(16) default NULL,
OCTABBREV varchar(16) default NULL,
NOVABBREV varchar(16) default NULL,
DECABBREV varchar(16) default NULL,
JANFULL varchar(255) default NULL,
FEBFULL varchar(255) default NULL,
MARFULL varchar(255) default NULL,
APRFULL varchar(255) default NULL,
MAYFULL varchar(255) default NULL,
JUNFULL varchar(255) default NULL,
JULFULL varchar(255) default NULL,
AUGFULL varchar(255) default NULL,
SEPFULL varchar(255) default NULL,
OCTFULL varchar(255) default NULL,
NOVFULL varchar(255) default NULL,
DECFULL varchar(255) default NULL,
JANTHREELET varchar(16) default NULL,
FEBTHREELET varchar(16) default NULL,
MARTHREELET varchar(16) default NULL,
APRTHREELET varchar(16) default NULL,
MAYTHREELET varchar(16) default NULL,
JUNTHREELET varchar(16) default NULL,
JULTHREELET varchar(16) default NULL,
AUGTHREELET varchar(16) default NULL,
SEPTHREELET varchar(16) default NULL,
OCTTHREELET varchar(16) default NULL,
NOVTHREELET varchar(16) default NULL,
DECTHREELET varchar(16) default NULL,
PRIMARY KEY (ID)
) TYPE=3DMyISAM;
--
-- Dumping data for table 'CITSTYLE'
--
INSERT INTO CITSTYLE VALUES
(20,'DUMMY',NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,N=
ULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL=
,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NULL,NU=
LL,NULL,NULL);
Ciao
Juan
--
-------------------------------------------------------------------------=
-----------------
Juan de la Figuera
Profesor contratado Ram=F3n y Cajal/ Assistant Professor
Dpto. de F=EFsica de la Materia Condensada C-III
Universidad Aut=F3noma de Madrid
Madrid 28049 Spain
Phone: 913974758 Fax: 913973961
-------------------------------------------------------------------------=
------------------
-------------------------------------------------------------------------=
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