Thread: [Refdb-users] ANN: refdb-0.9.8-pre9 available
Status: Beta
Brought to you by:
mhoenicka
From: Markus H. <mar...@mh...> - 2006-11-30 21:53:05
|
Hi all, we're approaching the next release 0.9.8 which should provide a couple of useful enhancements to the general public. I've uploaded a prerelease which is supposed to be the last one before 0.9.8, unless there are any problems with this prerelease. In order to avoid the (almost customary) build problems on platforms other than FreeBSD, I've set up a SuSE linux test box (SuSE because we already have very active Debian and Mandriva users on board). I didn't run into any problems on that system yet. The prerelease was built from subversion revision 250 and is available right here: http://refdb.sourceforge.net/pre/refdb-latest.tar.gz I've appended the improvements and fixed bugs since 0.9.7 below. Please report any problems to the list to make 0.9.8 a smooth experience. regards, Markus Bugfixes: - queries for UR and L1-L4 fields now work again - en2ris now properly imports the start and end page information from newer EndNote versions - using multiple databases in LaTeX documents now works again properly - bibtex output is now properly escaped - getref now honours backslash-escaped apostrophes in query strings - strings extending the length of limited size fields in t_refdb are now properly truncated during data import - correctly rollback if adding RIS data fails - exclusive queries (e.g. :UR:!~"http") now work as expected for links (UR, L1-L4, authors, and keywords - refdbd now modifies citation keys containing the string "-ID" as this may cause problems when creating bibliographies. "-ID" will be replaced with "_ID" to avoid problems. - if an iconv error occurs during data import, refdbd now returns a meaningful error message. Improvements: - the refdba:listuser command now checks for the required database argument - improved manpage layout by using new DocBook stylesheet capabilities when available, and workarounds for older stylesheet versions - configure now simplifies the task of building modularized RefDB packages. You can now build server, clients, and doc packages separately. Additionally, you can switch off building docs and manpages to build the RefDB binaries from the SVN sourceson systems without an XML/DocBook toolchaiin - the code that generates citation keys from author names was improved by using iconv to transliterate foreign characters. - the default setup now uses UTF-8 as the default input, storage, and output encoding. - the wrapper script bib2ris-utf8 was added to simplify postprocessing of the bib2ris output with the new refdb_latex2uft8txt script. The latter converts foreign characters to their UTF-8 equivalents and strips off other LaTeX commands. - personal reference lists are now implemented on top of extended notes. This means in particular that each user can maintain an unlimited number of reference lists - various fixes to the PHP web interface - use an improved bibtex citation format (\cite{dbname:citekey}) - now supports citation key based citation formats in addition to author/year and numeric - improved citation formats handle more reference types - refdbd can now install and upgrade the main database without external tools. See the file UPGRADING and the refdbd man page for further information. - refdb-init now uses these new refdbd capabilities to simplify the initial setup. - refdbd can also be run to check the database connection and to retrieve the database version. This is mainly useful for package/ports builders. - the help messages of the binaries now show the subversion revision they were built from. This makes it easier to track down bugs to specific builds. - refdbd can now run from a single main+reference database to allow the installation on cheap web space with access to a single MySQL database. - RefDB now provides frequency data for various statistical purposes. The get{au|ed|as|kw|jo|jf|j1|j2} commands allow to display the absolute number of references that use the particular item, or a relative number between 0 and 10 - The xhtml output of getref and checkref now contain frequency data. If you view the output with a new optional stylesheet, the authors, journal names, and keywords will be displayed according to their frequency in terms of font size and colour, similar to the tag clouds in services like del.icio.us. - getref and get{au|ed|as|kw|jo|jf|j1|j2} now support a new option -N limit[:offset] to cut down on the number of returned datasets. This feature can be conveniently used to loop over the result set in e.g. increments of 5 or 10, a feature most useful for graphical frontends. -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: David N. <dav...@sw...> - 2006-11-30 23:39:03
|
Hi Markus, > we're approaching the next release 0.9.8 > In order to avoid the > (almost customary) build problems on platforms other than FreeBSD Build failure on Debian/test: -------------------------------------------------------------------------------- </snip> sed 's%<risxversion>%1.1.0%g' < ../src/refdbd.h.in | \ sed 's%<xnoteversion>%1.2%g' | \ sed 's%<citestylexversion>%1.6%g' | \ sed 's%<citationlistxversion>%1.0%g' | \ sed 's%<db_dir>%/var/lib/refdb/db%' | \ sed 's%<main_db>%refdb%' > refdbd.h ../scripts/statgen.pl c > refstat.h echo -n 'const char* svn_version(void) { const char* SVN_Version = "' > svn_version.c cat svn_dist_version >> svn_version.c cat: svn_dist_version: No such file or directory make[2]: *** [svn_version.c] Error 1 make[2]: Leaving directory `src' make[1]: *** [all-recursive] Error 1 -------------------------------------------------------------------------------- The file 'svn_dist_version' does, indeed, appear to be missing. Proud to be upholding the old customs :-) . Regards, David. |
From: Markus H. <mar...@mh...> - 2006-12-01 08:20:47
|
David Nebauer <dav...@sw...> was heard to say: > > The file 'svn_dist_version' does, indeed, appear to be missing. > $ tar -tzf incoming/refdb-0.9.8-pre9.tar.gz |grep version refdb-0.9.8-pre9/src/svn_version.c refdb-0.9.8-pre9/src/svn_dist_version I reckon there must be a simple way to remove the file after unpacking it. Did you run make clean or make distclean by any chance? If that causes the problem, I'd have to fiddle with the Makefile.am to avoid losing the file. > Proud to be upholding the old customs :-) . > Sigh... Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: David N. <dav...@sw...> - 2006-12-01 08:25:49
|
Hi Markus, >> The file 'svn_dist_version' does, indeed, appear to be missing. > $ tar -tzf incoming/refdb-0.9.8-pre9.tar.gz |grep version > refdb-0.9.8-pre9/src/svn_version.c > refdb-0.9.8-pre9/src/svn_dist_version I haven't tried the pre-release yet. It is svn that fails to build. Regards, David. |
From: Markus H. <mar...@mh...> - 2006-12-01 08:50:39
|
David Nebauer <dav...@sw...>: > Hi Markus, > >> The file 'svn_dist_version' does, indeed, appear to be missing. > > $ tar -tzf incoming/refdb-0.9.8-pre9.tar.gz |grep version > > refdb-0.9.8-pre9/src/svn_version.c > > refdb-0.9.8-pre9/src/svn_dist_version > > > I haven't tried the pre-release yet. It is svn that fails to build. > Could you please send me your config.log and src/Makefile.am? If you build from a svn working copy, svn_dist_version should be created, but not read from. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: David N. <dav...@sw...> - 2006-12-01 09:26:22
|
Hi Markus, >> I haven't tried the pre-release yet. It is svn that fails to build. > > Could you please send me your config.log and src/Makefile.am? Requested files have been sent off-list. Regards, David. |
From: Markus H. <mar...@mh...> - 2006-12-01 10:03:19
|
David Nebauer <dav...@sw...> was heard to say: > Requested files have been sent off-list. > What does the following command return if you run it from the RefDB top-level directory: /usr/bin/svnversion -n '.' The code that seems to work incorrectly on your system is the following chunk in configure.in: if test "X$svnversioncommand" = "X" || test `$svnversioncommand -n '.'` = "exported"; then mysvnversion="cat svn_dist_version" else mysvnversion="svnversion -n '.'" fi As you do have subversion installed *and* work in a svn working copy, $mysvnversion should be set to the svnversion command. In your case it is set to the cat command, for whatever reason. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: David N. <dav...@sw...> - 2006-12-01 09:28:55
Attachments:
config.log
Makefile.am
|
Hi Markus, >> I haven't tried the pre-release yet. It is svn that fails to build. > > Could you please send me your config.log and src/Makefile.am See attached. Regards, David. |
From: Markus H. <mar...@mh...> - 2007-04-16 20:19:50
|
Hi C=E9cile, Cecile Hebert writes: > I am using apache2 and webmin as an administration interface, and I = have=20 > the feeling the example apache configuration example does not look l= ke=20 > the config files I have. I was not able to bring the link from=20 > /usr/local/share/refdb/www/ to /refdb/ to work, neither by using a=20= > symbolic link (even with +FollowSimLinkoption) nor by making the lin= k in=20 > the config file. >=20 > So I tryed to hard copy the www directory to the root directory of= my=20 > web server. This works somehow, I can see the pages, fill the forms,= ask=20 > for references and get no errors messages... but no references at al= l.=20 > And I see nothing happening in the window where refdbd should give l= ogs. >=20 >=20 > Does phpweb needs refdb working as a daemon=3F=3F > Can someone tell me how to set up apache2 properly=3F > Does someone knows where the error can come from=3F >=20 I don't run apache2 over here. I've checked the installation instructions again with my Apache 1.3 installation on FreeBSD. All I needed to do is to follow the instructions in phpweb/INSTALL, using the OS-specific tweaks as usual: - I had to rebuild php5 as it was configured without mod=5Fphp5 support= - then I had to build a matching php5-session package - the changes for httpd.conf were already in place, so everything worked from that point on. I suspect your problems are rooted in some change of the Apache configuration file syntax. Unless someone on this list can provide an apache2 configuration file that works with RefDB, I'd suggest to take this question to an Apache mailing list or forum. As the changes to httpd.conf required by the RefDB PHP interface are very limited, someone might be able to tell you in an instant how to do this with apache2. If you find an answer, please let the list know. I'd like to add this to the documentation. Did you check the Apache log (usually /var/log/httpd-errors.log)=3F You might find additional clues in the error messages. Does php run ok on your box=3F Try "php -v". Finally, refdbd does not have to run as a daemon. The PHP interface calls only the clients, which then access refdbd. The clients don't care whether refdbd runs as a standalone process or as a daemon. If you configure the clients appropriately, you could even run refdbd on a different box without breaking the PHP interface. regards, Markus --=20 Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: David N. <dav...@sw...> - 2006-12-01 11:26:44
|
Hi Markus, > As you do have subversion installed *and* work in a svn working copy, > $mysvnversion should be set to the svnversion command. In your case it is set > to the cat command, for whatever reason. A very simple reason, as it turns out. During the package building process I was copying the build tree using a simple 'cp -r *' command which did not copy hidden directories, including the '.svn/' subdirectory. So, the problem wasn't the svn command but that the svn subdirectory was entirely absent! This only became a problem when you included in the build process an interrogation of the svn revision number. I've modified the copy command to include the '.svn/' subdirectory and all is now well. Regards, David. |
From: Markus H. <mar...@mh...> - 2006-12-01 11:44:15
|
David Nebauer <dav...@sw...> was heard to say: > A very simple reason, as it turns out. During the package building > process I was copying the build tree using a simple 'cp -r *' command > which did not copy hidden directories, including the '.svn/' > subdirectory. So, the problem wasn't the svn command but that the svn > subdirectory was entirely absent! This only became a problem when you > included in the build process an interrogation of the svn revision number. > > I've modified the copy command to include the '.svn/' subdirectory and > all is now well. > You seem to have the obsession to pick the one bordercase that I didn't consider :-) Glad that it works now. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: David N. <dav...@sw...> - 2006-12-01 11:32:49
|
Hi Markus, > I've modified the copy command to include the '.svn/' subdirectory and all is now well. Oh dear, how foolish to tempt the gods with phrasing like that. I have encountered another build failure, this time building documentation: -------------------------------------------------------------------------------- <snip/> dtdformat --html citestylex.xml Formatting HTML. Using plain library. Writing Elements... Writing Entities... Writing Notations... Done. ../scripts/dtdparseweave citestylex line 1 column 1 - Warning: missing <!DOCTYPE> declaration line 6 column 1 - Warning: <table> lacks "summary" attribute line 27 column 1 - Warning: <table> lacks "summary" attribute line 74 column 1 - Warning: trimming empty <p> <snip numerous warnings/> line 1 column 1 - Warning: missing <!DOCTYPE> declaration line 6 column 1 - Warning: <table> lacks "summary" attribute line 62 column 1 - Warning: trimming empty <p> /refdb-0.0-svn-20061201/doc make[2]: *** No rule to make target `chapter-programming.xml', needed by `refdb-manual.pdf'. Stop. make[2]: Leaving directory `/refdb-0.0-svn-20061201/doc' make[1]: *** [all-recursive] Error 1 make[1]: Leaving directory `/refdb-0.0-svn-20061201' make: *** [build-stamp] Error 2 -------------------------------------------------------------------------------- Regards, David. |
From: Markus H. <mar...@mh...> - 2006-12-01 11:51:28
|
David Nebauer <dav...@sw...> was heard to say: > Oh dear, how foolish to tempt the gods with phrasing like that. > > I have encountered another build failure, this time building documentation: > Mea culpa. Looks like I forgot to add the file to the subversion repository. It is included in the pre9 archive though, so this problem does not affect those who want to test the prerelease from the tarball. I'll add this file tonight, as I'm away from my development box right now. Memo to self: thou shalt test a fresh svn checkout as well before releasing code into the wild. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Cecile H. <cec...@tu...> - 2007-04-16 09:23:28
|
Dear all, I am trying to set up pwpweb under suse linux 10.1, without much success :-( refdfworks fine, still in the "debug" mode (refdbd -s -e 0 -l 7), I can connect thru refdba and refdbc, manage users and references... I am using apache2 and webmin as an administration interface, and I have the feeling the example apache configuration example does not look lke the config files I have. I was not able to bring the link from /usr/local/share/refdb/www/ to /refdb/ to work, neither by using a symbolic link (even with +FollowSimLinkoption) nor by making the link in the config file. So I tryed to hard copy the www directory to the root directory of my web server. This works somehow, I can see the pages, fill the forms, ask for references and get no errors messages... but no references at all. And I see nothing happening in the window where refdbd should give logs. Does phpweb needs refdb working as a daemon?? Can someone tell me how to set up apache2 properly? Does someone knows where the error can come from? Thank you for any help! Cécile -- Dr. Cécile Hébert, Inst. f. Festkörperphysik TU Wien, Wiedner Hauptstrasse 8-10 A-1040 WIEN cec...@tu... tel +43 1 58 801 138 15 fax - 138 99 http://tem.atp.tuwien.ac.at/leute/cecile.html http://www.ncc.at/cecile/photos/index.html |
From: Cecile H. <cec...@tu...> - 2007-04-16 21:24:54
|
Markus Hoenicka wrote: > I suspect your problems are rooted in some change of the Apache > configuration file syntax. Unless someone on this list can provide an > apache2 configuration file that works with RefDB, I'd suggest to take > this question to an Apache mailing list or forum. As the changes to > httpd.conf required by the RefDB PHP interface are very limited, > someone might be able to tell you in an instant how to do this with > apache2. If you find an answer, please let the list know. I'd like to > add this to the documentation. What I did is - make a symbolik link: ln -s /usr/local/share/refdb/web /my_server_root/refdb Add the following to the config file: <VirtualHost XX.XX.XX.XX:80> DocumentRoot /my_server_root ServerName tem.atp.tuwien.ac.at ScriptAlias /cgi-bin/ "/XXX/cgi-bin" Alias /refdb/ "/usr/local/share/refdb/www/" <Directory "/usr/local/share/refdb/www"> Options FollowSymLinks +ExecCGI AllowOverride None Order allow,deny Allow from all AddType application/x-httpd-php .php .phtml </Directory> It works, I just have to call http://tem.atp.tuwien.ac.at/refdb/ *WITH* the trailing slash. Does not work without. I am not sure this is the most "academic" way, but at least I get the pages... (somehow I feel the symbolic linkt should not be necessary...) > Did you check the Apache log (usually /var/log/httpd-errors.log)? > You might find additional clues in the error messages. Mh, seems to be a php problem: [Mon Apr 16 23:06:32 2007] [error] [client 195.230.58.82] PHP Notice: Undefined variable: passwd in /usr/local/share/refdb/www/login.php on line 6, referer: http://tem.atp.tuwien.ac.at/refdb/index.html But : miraculix 114> httpd2 -M Loaded Modules: . . . php5_module (shared) Syntax OK > Does php run ok on your box? Try "php -v". miraculix 102> php5 -v PHP 5.1.2 (cli) (built: May 2 2006 10:19:57) Copyright (c) 1997-2006 The PHP Group Zend Engine v2.1.0, Copyright (c) 1998-2006 Zend Technologies So I would say php seems to run ? Cécile -- Dr. Cécile Hébert, Inst. f. Festkörperphysik TU Wien, Wiedner Hauptstrasse 8-10 A-1040 WIEN cec...@tu... tel +43 1 58 801 138 15 fax - 138 99 http://tem.atp.tuwien.ac.at/leute/cecile.html http://www.ncc.at/cecile/photos/index.html |
From: Markus H. <mar...@mh...> - 2007-04-17 07:38:50
|
Quoting Cecile Hebert <cec...@tu...>: > > It works, I just have to call > http://tem.atp.tuwien.ac.at/refdb/ > *WITH* the trailing slash. Does not work without. > This is correct, but the phpweb/INSTALL file already mentions this. > I am not sure this is the most "academic" way, but at least I get the > pages... (somehow I feel the symbolic linkt should not be necessary...) > It certainly isn't necessary in my case. I wonder if this is an Apache =20 1.3 vs. 2.0 issue. > [Mon Apr 16 23:06:32 2007] [error] [client 195.230.58.82] PHP Notice: > Undefined variable: passwd in /usr/local/share/refdb/www/login.php on > line 6, referer: http://tem.atp.tuwien.ac.at/refdb/index.html > PHP calls this a "Notice". I'm not sure whether it really hurts. > So I would say php seems to run ? > Yes it does. I was just asking because I had accidentally upgraded =20 php5 without upgrading php-session. In my case php5 refused to run =20 because it couldn't load php-session. regards, Markus --=20 Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |