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From: Markus H. <mar...@mh...> - 2007-03-21 16:40:44
|
Hi Bruce, are you sure you have to? I've just checked the UPGRADING file, and it =20 reports no changes in the reference database schema since 0.9.6. I'd =20 expect that you can continue to access your databases. Are there =20 specific error messages that make you think so? Or did you =20 accidentally hose the databases? Adding more than one file at a time is supposed to work. However, the =20 "*.ris" notation depends on shell expansion. I do not think that this =20 works in interactive use. OTOH, refdbc -C addref *.ris should work ok. If it doesn't, it is a bug which I'll be happy to fix. regards, Markus Quoting Bruce Hayward <b.h...@le...>: > Markus, > Looks like I need to recreate my database. Is there a way of doing > "addref *.ris"? I just tried it and got a 51K file instead of a 3.6M > file and a refdbc program occupying most of the CPU! > Bruce > --=20 Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Bruce H. <b.h...@le...> - 2007-03-21 15:45:49
|
Markus, Looks like I need to recreate my database. Is there a way of doing "addref *.ris"? I just tried it and got a 51K file instead of a 3.6M file and a refdbc program occupying most of the CPU! Bruce > > - run refdbd -a -u <username> -w <password>. You have to provide the > username and password of the database admin, the ones you'd use for > refdba. > > - if this results in an error message or does not have the desired > effect, delete your existing main database (delete the file if you use > SQLite, run "DROP DATABASE refdb" in the appropriate command-line > client when using MySQL or PostgreSQL) and go back to the manual to > re-create the main database. You'll have to add your citation styles > again after this procedure. |
From: Markus H. <mar...@mh...> - 2007-03-21 14:18:44
|
Hi Bruce, there were a few changes in the main database schema between 0.9.6 and =20 0.9.8. I'm pretty sure that the FreeBSD port does not automatically =20 attempt to upgrade the main database (and fails to tell you so). I'm =20 not perfectly sure whether auto-updating the main database will work =20 from 0.9.6, but it is worth a try. - depending on your database engine (you have installed all of them, =20 so I don't know which one you're going to use) make a backup copy =20 (sqlite) or a SQL dump (MySQL, PostgreSQL) of your current main =20 database (refdb), just in case. - run refdbd -a -u <username> -w <password>. You have to provide the =20 username and password of the database admin, the ones you'd use for =20 refdba. - if this results in an error message or does not have the desired =20 effect, delete your existing main database (delete the file if you use =20 SQLite, run "DROP DATABASE refdb" in the appropriate command-line =20 client when using MySQL or PostgreSQL) and go back to the manual to =20 re-create the main database. You'll have to add your citation styles =20 again after this procedure. hope this helps Markus Quoting Bruce Hayward <b.h...@le...>: > I've just upgraded most of the software on my FreeBSD 5.5 computer. > Refdb is now complaining about the main database: > --=20 Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Bruce H. <b.h...@le...> - 2007-03-21 13:29:18
|
I've just upgraded most of the software on my FreeBSD 5.5 computer. Refdb is now complaining about the main database: 404 >refdbc Please enter your password: refdbc: selectdb refs main database version is not supported refdbc: quit Upgrades included: mysql-client-5.0.24a_1 < needs updating (port has 5.0.33) postgresql-client-7.4.13 < needs updating (port has 7.4.16) refdb-0.9.6_2 < needs updating (port has 0.9.8) sqlite-3.3.7 < needs updating (port has 3.3.12) Libdbi is currently: libdbi-0.8.1_1 Database Independent Abstraction Layer for C libdbi-drivers-0.8.1_1 Drivers for libdbi Haven't done any upgrades outside the FreeBSD ports. Suggestions? |
From: <do...@gm...> - 2007-03-21 13:13:28
|
Hi Markus, explanation is simple. The script is lookign for the file in /etc/refdb/ directory, but file itself is located in /usr/share/refdb/etc/. The same problem is with refdbarc.example and very likely with some more files. So script does not match the data structure. But at the end it does not succeed anyway ... I've finished collecting all required information, and the checks look ok. If you don't want to touch your existing installation, answer with 'n'. Shall I proceed and set up RefDB [y/n]? y Saved existing refdbd configuration file as /etc/refdb/refdbdrc.200703211409.57 Failed to install or upgrade main database refdbd-init.sh failed. refdb-init is finished. mvolav:/etc/refdb# In the attachment is my refdb-init file. BTW, fresh instalation from: deb http://refdb.sourceforge.net/debian/release testing main Is there some updated deb package or should I fight with current one? thanks Jozef > I'm not sure whether this is a packaging error or a problem with an > older RefDB version which has been fixed since. There's two > explanations: > > 1) Your installation indeed may lack the requested file. Please check > whether /usr[/local]/etc/refdb/refdbdrc.mysql.example exists > > 2) The script may be broken and look for the incorrect file. There is > still a typo in the current version of the script (it looks for > refdbdrc.mysql.example, but complains about refdb.mysql.example if the > former is missing), but that should not affect the proper operation. > Could you please send me your version of the refdb-init script? > > If nothing else helps, please try a manual configuration as described > in the handbook. I'll be happy to provide further guidance if you need > help. > > regards, > Markus > > > > Quoting ?o?o <do...@gm...>: > > > Hi guys, > > > > I have again a bit time to fight with refdb instalation under debian. > > Shell I report debian problems somewhere, or just use brute force to > > get it running? > > Current status is: > > Please select the database engine you want to use. > > Available are: mysql pgsql sqlite sqlite3 > > > > mysql > > > > === > > What is the version of the MySQL database engine that you want > > to connect to? > > If the version is 4.0 or earlier, type 'pre' > > If the version is 4.1 or later, type 'post' > > post > > > > refdb.mysql.example is not readable or missing > > > > refdbd-init.sh failed. > > refdb-init is finished. > > > > > > So I run refdb-init, but looks like example are either missing or renamed. > > > > best regards > > > > Jozef > > > > ------------------------------------------------------------------------- > > Take Surveys. Earn Cash. Influence the Future of IT > > Join SourceForge.net's Techsay panel and you'll get the chance to share your > > opinions on IT & business topics through brief surveys-and earn cash > > http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV > > _______________________________________________ > > Refdb-users mailing list > > Ref...@li... > > https://lists.sourceforge.net/lists/listinfo/refdb-users > > > > > > -- > Markus Hoenicka > mar...@ca... > (Spam-protected email: replace the quadrupeds with "mhoenicka") > http://www.mhoenicka.de > > |
From: Markus H. <mar...@mh...> - 2007-03-21 12:48:11
|
Quoting Dominik Reusser <dre...@un...>: > Is this a problem specific to my set-up or does refdbd fail to check what > authentication protocol should be used? > refdbd does not perform any specific checks. It simply passes the authentication information to libdbi, which in turn passes them to the requested driver. The driver uses (in your case) the libmysqlclient library provided by the MySQL database engine. I can only imagine that your libdbi driver is linked against an older version of the libmysqlclient library than what the database server expects. Rebuilding libdbi-drivers with the latest libmysqlclient library should fix this. I'm a bit puzzled that only one user runs into this problem. Do the other users have OLD_PASSWORDs by default, e.g. because their accounts are older? regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Dominik R. <dre...@un...> - 2007-03-21 12:21:50
|
Today I encountered the following problem: For one user, I always got the error: > could not open main database even though rights were appropriate. And login worked for other users. In the log-file, I found: > 1251: Client does not support authentication protocol requested by server; consider upgrading MySQL client I was able to fix the problem by reseting the password in mysql to an older password-version: SET PASSWORD FOR 'someuser'@'localhost' = OLD_PASSWORD('*******') Is this a problem specific to my set-up or does refdbd fail to check what authentication protocol should be used? Regards -- Dominik Reusser |
From: Markus H. <mar...@mh...> - 2007-03-21 08:45:50
|
Hi, I'm not sure whether this is a packaging error or a problem with an =20 older RefDB version which has been fixed since. There's two =20 explanations: 1) Your installation indeed may lack the requested file. Please check =20 whether /usr[/local]/etc/refdb/refdbdrc.mysql.example exists 2) The script may be broken and look for the incorrect file. There is =20 still a typo in the current version of the script (it looks for =20 refdbdrc.mysql.example, but complains about refdb.mysql.example if the =20 former is missing), but that should not affect the proper operation. =20 Could you please send me your version of the refdb-init script? If nothing else helps, please try a manual configuration as described =20 in the handbook. I'll be happy to provide further guidance if you need =20 help. regards, Markus Quoting ?o?o <do...@gm...>: > Hi guys, > > I have again a bit time to fight with refdb instalation under debian. > Shell I report debian problems somewhere, or just use brute force to > get it running? > Current status is: > Please select the database engine you want to use. > Available are: mysql pgsql sqlite sqlite3 > > mysql > > =3D=3D=3D > What is the version of the MySQL database engine that you want > to connect to? > If the version is 4.0 or earlier, type 'pre' > If the version is 4.1 or later, type 'post' > post > > refdb.mysql.example is not readable or missing > > refdbd-init.sh failed. > refdb-init is finished. > > > So I run refdb-init, but looks like example are either missing or renamed. > > best regards > > Jozef > > ------------------------------------------------------------------------- > Take Surveys. Earn Cash. Influence the Future of IT > Join SourceForge.net's Techsay panel and you'll get the chance to share yo= ur > opinions on IT & business topics through brief surveys-and earn cash > http://www.techsay.com/default.php?page=3Djoin.php&p=3Dsourceforge&CID=3DD= EVDEV > _______________________________________________ > Refdb-users mailing list > Ref...@li... > https://lists.sourceforge.net/lists/listinfo/refdb-users > --=20 Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: <do...@gm...> - 2007-03-20 15:54:15
|
Hi guys, I have again a bit time to fight with refdb instalation under debian. Shell I report debian problems somewhere, or just use brute force to get it running? Current status is: Please select the database engine you want to use. Available are: mysql pgsql sqlite sqlite3 mysql === What is the version of the MySQL database engine that you want to connect to? If the version is 4.0 or earlier, type 'pre' If the version is 4.1 or later, type 'post' post refdb.mysql.example is not readable or missing refdbd-init.sh failed. refdb-init is finished. So I run refdb-init, but looks like example are either missing or renamed. best regards Jozef |
From: Markus H. <mar...@mh...> - 2007-03-15 23:51:25
|
Mathias Krueger writes: > 7:pid=29339:Thu Mar 15 16:43:53 2007:ERROR: failed to re-find parent key in > "pg_attribute > _relid_attnam_index" > > 3:pid=29339:Thu Mar 15 16:43:53 2007:create t_refdb failed > 2:pid=29339:Thu Mar 15 16:43:53 2007:create temporary table failed > 6:pid=29339:Thu Mar 15 16:43:53 2007:child finished client on fd 6 > > i use postgres as the database-server, any ideas? > other command like getref work. > This seems to be a bug in some versions of PostgreSQL. I don't see this problem with 8.08 on FreeBSD, but Google mentions it a couple of times for 7.4.x and 8.1.x versions. Do you have a chance to up- or downgrade to a different version? regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Mathias K. <m.k...@di...> - 2007-03-15 16:54:12
|
After execute the checkref command I got the following error n the refdbd.log: 7:pid=29339:Thu Mar 15 16:43:49 2007:CREATE TEMPORARY TABLE t_temp_meta (meta_app VARCHAR( 20),meta_type VARCHAR(20),meta_version VARCHAR(20),meta_dbversion SMALLINT,meta_create_dat e TIMESTAMP,meta_modify_date TIMESTAMP) 7:pid=29339:Thu Mar 15 16:43:51 2007:CREATE TEMPORARY TABLE t_temp_refdb (refdb_id BIGSERI AL,refdb_citekey VARCHAR(255) UNIQUE,refdb_type VARCHAR(6),refdb_pubyear SMALLINT,refdb_se cyear SMALLINT,refdb_startpage VARCHAR(255),refdb_endpage VARCHAR(255),refdb_abstract TEXT ,refdb_title TEXT,refdb_volume VARCHAR(255),refdb_issue VARCHAR(255),refdb_booktitle TEXT, refdb_city VARCHAR(255),refdb_publisher VARCHAR(255),refdb_title_series TEXT,refdb_address TEXT,refdb_issn VARCHAR(255),refdb_pyother_info VARCHAR(255),refdb_secother_info VARCHAR( 255),refdb_periodical_id BIGINT,refdb_user1 VARCHAR(255),refdb_user2 VARCHAR(255),refdb_us er3 VARCHAR(255),refdb_user4 VARCHAR(255),refdb_user5 VARCHAR(255),refdb_misc1 VARCHAR(255 ),refdb_misc2 VARCHAR(255),refdb_misc3 VARCHAR(255),PRIMARY KEY (refdb_id)) 7:pid=29339:Thu Mar 15 16:43:53 2007:ERROR: failed to re-find parent key in "pg_attribute _relid_attnam_index" 3:pid=29339:Thu Mar 15 16:43:53 2007:create t_refdb failed 2:pid=29339:Thu Mar 15 16:43:53 2007:create temporary table failed 6:pid=29339:Thu Mar 15 16:43:53 2007:child finished client on fd 6 i use postgres as the database-server, any ideas? other command like getref work. |
From: <do...@gm...> - 2007-03-14 11:48:15
|
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From: Markus H. <mar...@mh...> - 2007-03-14 10:56:25
|
Hi Jozef, did you try to use the .debs provided by libdbi (see =20 http://libdbi.sourceforge.net/download.html)? They should be fresher =20 than those in the Debian repositories. In any case, both the RefDB and the libdbi/libdbi-drivers Debian =20 packages are outdated compared to the source releases. David, are you =20 listening? Will you be able to update the packages anytime soon? regards, Markus Quoting =C4=8Eo=C4=8Fo <do...@gm...>: > Markus, > > I tried year ago with SQLite and I was not able to get it running. May > be you recall. Problem with database version with RefDb. > Now I gave a second try but with the mySql. On the standard debian > system.(Sarge). > I have nothing against installing one more library - I fully agree > with your args - but the version of libdb-sqlite required by > refdb-server in testing version is not available in any of Debian > distributio. There such package only in stable and unstable version > and just 0.7.1. But version required by refdb server is >=3D 0.8.1-2. > So if the plan was to have simple instalation, then it failed ;) > --=20 Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: <do...@gm...> - 2007-03-14 10:43:58
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From: Markus H. <mar...@mh...> - 2007-03-14 10:27:54
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Hi, it would be helpful to know what platform you are using. Are you using =20 the Debian packages? In that case, David should have the authoritative =20 answer. But I recall that the packages depend on libdbd-sqlite and =20 thus indirectly on sqlite in order to provide a working setup with the =20 smallest possible download. Having sqlite installed even if you're not =20 going to use it adds just a few kb to your box (sqlite is tiny =20 compared to MySQL or PostgreSQL). If you change the database =20 dependency from required to suggested, lots of users may end up with a =20 RefDB installation that simply does not work due to a lack of a =20 database engine. regards, Markus Quoting =C4=8Eo=C4=8Fo <do...@gm...>: > Hi Markus, > > I have one more issue. Why: > > The following packages have unmet dependencies: > refdb-server: Depends: libdbd-sqlite (>=3D 0.8.1-2) but it is not > going to be installed > E: Broken packages > > if I do not want to use sqlite at all and I plan to use mysql? I > understand that during the instalation process it is difficul to know > what user will use, but to have the package in suggested package would > may be O.K. > --=20 Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2007-03-14 09:40:53
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Hi Jozef, thanks for catching this. Boon and bane of copy and paste... regards, Markus Quoting ?o?o <do...@gm...>: > Hi guys, > > I have a feeling that on RefDB web pages, in the news, is incorrect > year. First I thought that web page was not modified for more then one > year, but now I am sure it is a typo. > > Jozef > -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: <do...@gm...> - 2007-03-14 09:26:25
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Hi guys, I have a feeling that on RefDB web pages, in the news, is incorrect year. First I thought that web page was not modified for more then one year, but now I am sure it is a typo. Jozef |
From: Markus H. <mar...@mh...> - 2007-03-06 23:29:28
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Dominik Reusser writes: > Hi there, > I have refdbd running on a rather old debian box with quite a large database > (~2400 records). If I try to run checkref with this setup, I end up with > timeouts and no results. So I am still required to check references manually. This is just a matter of increasing your timeout settings both on the server and client side. The default timeouts turned out to be too short for the kind of database processing required for checkref. If you're running refdbc and refdbd on the same computer, you can set both timeouts to zero to avoid this problem altogether (there should be no networking problems on the loopback device, after all). > > Would it be possible to turn off certain checks (such as keywords, user > notes,..) and just compare for example author, year, journal, issue, pages > and title? > I've been pondering this too. I get a serious number of possible keyword duplicates when using Pubmed data, which is well endowed with keywords of all sorts. Maybe we should use the -S switch to select the fields to check, instead of to select the additional fields for the xhtml output. > Also, I do have some duplicates in my database. Is there an efficient way to > get a list of possible duplicates through refdbc/refdba? Of course I could > run SQL-queries to get this information. But maybe there is a more efficient > way? > Currently not. You might of course checkref a ris(x) dump of your entire database and filter the (humongous) report e.g. for exact title matches. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Dominik R. <dre...@un...> - 2007-03-06 17:29:32
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Hi there, I have refdbd running on a rather old debian box with quite a large database (~2400 records). If I try to run checkref with this setup, I end up with timeouts and no results. So I am still required to check references manually. Would it be possible to turn off certain checks (such as keywords, user notes,..) and just compare for example author, year, journal, issue, pages and title? Also, I do have some duplicates in my database. Is there an efficient way to get a list of possible duplicates through refdbc/refdba? Of course I could run SQL-queries to get this information. But maybe there is a more efficient way? Thanks Dominik |
From: Markus H. <mar...@mh...> - 2007-02-28 12:21:32
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Hi Mathias, Quoting Mathias Kr=FCger <m.k...@di...>: > So I really don't unterstand, how to use the checkref-function in the > Perl-Module, in last parameter I am able to submit $output-parameter, > but how I get the output? the only out I get is: > > 999:1 checked:0 skipped:0 failed > [...] > > print $client->refdb_checkref($data, "ris", "utf-8", "scrn"); > > After that, just run: print $client->get_data(); The Perl Client module functions always return the command summary =20 (i.e. the brief message which the C clients send to stderr, which is =20 the one you saw in your tests). The most recently returned data, if =20 any, are always accessible via the get_data() member function. The =20 reason for this somewhat obscure design is that some commands do not =20 return data, but only a summary. For the sake of consistency, these =20 functions would have to return undef if we'd use the data proper as a =20 return value throughout. BTW the test script test.pl runs each function at least once. It is a =20 good resource for finding out how these functions work. regards, Markus --=20 Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Mathias <m.k...@di...> - 2007-02-28 10:50:51
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Hello List, So I really don't unterstand, how to use the checkref-function in the Perl-Module, in last parameter I am able to submit $output-parameter, but how I get the output? the only out I get is: 999:1 checked:0 skipped:0 failed For this, I used the following test-script: use strict; use warnings; use RefDBClient::Client; my $client= new RefDBClient::Client(); my $data = new RefDBClient::Risdata(); $client->set_conninfo("127.0.0.1","9734","xxxxxxxx", "xxxxxx","xxxxxx","",""); $data->read_ris("./test"); print $client->refdb_checkref($data, "ris", "utf-8", "scrn"); while the dataset in test is in database. Thanx for support, m. |
From: Markus H. <mar...@mh...> - 2007-01-31 16:28:52
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Josef Karthauser <jo...@ta...> was heard to say: > Cool. Tell you what, I'll get someone to update the FreeBSD port so > that you don't keep getting error reports on old versions! :) Much appreciated. Paul, who managed to get RefDB into the ports system, unfortunately is no longer able to take care of the port. I'd love to see someone else looking after the port. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Josef K. <jo...@ta...> - 2007-01-31 16:18:32
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On Wed, Jan 31, 2007 at 04:55:04PM +0100, Markus Hoenicka wrote: >=20 > If you still run the version you installed from the FreeBSD ports system,= then > it is indeed easy to fix: just upgrade to the current version (the port h= as not > been updated unfortunately, but RefDB builds straight out of the tarball = on > FreeBSD). RefDB is supposed to handle multi-head bibtex citations correct= ly > since 0.9.7. If you run a version later than 0.9.6 which can't handle the= se > citations, then this will qualify as a bug. >=20 Cool. Tell you what, I'll get someone to update the FreeBSD port so that you don't keep getting error reports on old versions! :) Joe --=20 =3D=3D=3D Josef Karthauser (jo...@ta...) =3D=3D=3D http://x2obuilder.com= /tao =3D=3D=3D |
From: Markus H. <mar...@mh...> - 2007-01-31 15:55:25
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Josef Karthauser <jo...@ta...> was heard to say: > Hi there, > > I think I've found another bug in refdbib. It doesn't know how to parse > aux file lines like this: > > \citation{Karthauser2006,Karthauser2006b} > > which are perfectly valid latex. I assume it doesn't know that more > than reference can appear separated by a comma. > > Is this something that's easy to fix? If you still run the version you installed from the FreeBSD ports system, then it is indeed easy to fix: just upgrade to the current version (the port has not been updated unfortunately, but RefDB builds straight out of the tarball on FreeBSD). RefDB is supposed to handle multi-head bibtex citations correctly since 0.9.7. If you run a version later than 0.9.6 which can't handle these citations, then this will qualify as a bug. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Josef K. <jo...@ta...> - 2007-01-31 15:28:32
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Hi there, I think I've found another bug in refdbib. It doesn't know how to parse aux file lines like this: \citation{Karthauser2006,Karthauser2006b} which are perfectly valid latex. I assume it doesn't know that more than reference can appear separated by a comma. Is this something that's easy to fix? Joe --=20 =3D=3D=3D Josef Karthauser (jo...@ta...) =3D=3D=3D http://x2obuilder.com= /tao =3D=3D=3D |