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From: san <sa...@am...> - 2003-04-12 04:50:17
|
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From: <mar...@mi...> - 2003-04-12 00:29:45
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From: Markus H. <mar...@mh...> - 2003-04-11 16:49:03
|
Hi, first of all, thanks for the complete log information. This helps a lot to see what's going wrong. Fredrik Karlsson writes: > creating database connection structure failed This usually means that you don't have the pgsql driver on your system. If you build libdbi from the sources, you need to add "--with-pgsql" to the configure command line to build the PostgreSQL driver. Otherwise you'll only get the framework. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Fredrik K. <fre...@li...> - 2003-04-11 07:27:33
|
Hi all, I'm new to refdb and trying ot set it up against a PosgreSQL server, but I cannot get it to connect. The error I get when trying to connect using a username and passwd (to refdba) that gives me access to the refdb1 database using the psql client, I get the dump below from the server. The user supplied to the refdba is has full access to the database, but cannot create new databases or users. The refdb-deamon was started by the root user, not the 'postgres' user. Does anyone have an idea as to where the problem may be? /Fredrik ---- refdba output ------ fredrik@theodor:~$ refdba Please enter your password: refdba 0.9.2 ma...@mh... You may redistribute and modify this software under the terms of the GNU General Public License. Type '?' for a command overview refdba: viewstat could not connect to database server refdba: viewstat could not connect to database server refdba: ----- refdbd server output ----- theodor:~# refdbd -s -e 0 -l 7 application server started use /tmp/refdbd_fifo29432 as fifo server waiting n_max_fd=4 adding client on fd 5 server waiting n_max_fd=5 try to read from client serving client on fd 5 with protocol version 1 210-36-09-49 send pseudo-random string to client parent removing client on fd 5 server waiting n_max_fd=4 viewstat -u fredrik -w 118063091064096119117120067 dbi is up (the IP of the server) fredrik (My password) 5432 pgsql /usr/local/share/refdb/db creating database connection structure failed command processing done, finish dialog now child finished client on fd 5 child exited with code 0 server waiting n_max_fd=4 |
From: Markus H. <mar...@mh...> - 2003-04-08 20:34:12
|
Hi, what XSL processor are you trying to use? This is a configurable option in the refdbxml script. Make sure you have all required jars for that processor in your class path or switch to a different processor. You're probably better off asking a list or a newsgroup devoted to Java XSL processors as these are "moving targets" with frequent changes in their class requirements. regards, Markus Daniel Hyduke writes: > I get a java error when creating running "make html" for a document > created using refdbnd (see below). I am using j2re1.4.0_02. Is a > different version of java required? > > refdbxml -d J.Biol.Chem.html.xsl -t html ref_list.xml > java.lang.ClassNotFoundException: > /avalon-framework-4/0/jar:/batik/jar:/fop/jar:/jfor-0/5/1/jar:/jimi-1/0/jar:/logkit-1/0b4/jar:/sax/jar:/saxon/jar:/saxon-fop/jar:/saxon-jdom/jar:/xalan/jar:/xerces/jar:/xp/jar:/xt/jar > at java.lang.Class.forName(Class.java:native) > at java.lang.Class.forName(Class.java:59) > -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Daniel H. <da...@se...> - 2003-04-08 01:42:01
|
I get a java error when creating running "make html" for a document created using refdbnd (see below). I am using j2re1.4.0_02. Is a different version of java required? refdbxml -d J.Biol.Chem.html.xsl -t html ref_list.xml java.lang.ClassNotFoundException: /avalon-framework-4/0/jar:/batik/jar:/fop/jar:/jfor-0/5/1/jar:/jimi-1/0/jar:/logkit-1/0b4/jar:/sax/jar:/saxon/jar:/saxon-fop/jar:/saxon-jdom/jar:/xalan/jar:/xerces/jar:/xp/jar:/xt/jar at java.lang.Class.forName(Class.java:native) at java.lang.Class.forName(Class.java:59) -- Daniel Hyduke <da...@se...> |
From: Marc B. <ba...@sm...> - 2003-04-07 11:45:31
|
Hi, I mentioned a little while ago that there was a problem with catalog files on Debian. In fact the problem appeared because I defined the catalog environment variable in ~/.bashrc as export SGML_CATALOG_FILES=/usr/local/share/refdb/refdb.cat which is *not* the preferred way in Debian (as it overrides the default search in the system-wide catalog). So for all people using Debian and who did not yet know, the prefered way to add the refdb stylesheets is update-catalog --add /etc/sgml/catalog /usr/local/share/refdb/refdb.cat works like a charm now .. Cheers, Marc -- Dr. Marc Baaden - Institut de Biologie Physico-Chimique, Paris mailto:ba...@sm... - http://www.marc-baaden.de FAX: +49 697912 39550 - Tel: +33 15841 5176 ou +33 609 843217 |
From: Thomas B. <tkb...@fs...> - 2003-04-07 09:17:41
|
>Hi, >the easiest way to analyze the problem is to run both refdbd and >refdbc (in CGI mode) with a log level of 7. This will give a very >detailed record of what RefDB attempts to do based on the data that >you send via CGI. Please post a reference that reproduces the problem >along with the two logs created by your attempt to add it to the >database. >I'll be happy to provide further assistance if you don't know how to >do this. >regards, >Markus >TKB 5. Prak. writes: >> Hi >> Got another little Problem with the Web Interface of RefDB. Most of the >> functionalities make no problems but if I want to add a new Reference or >> update a Reference I get almost every time an Internal Server Error and >> I really don't know why. In the error_log of the Apache ist the >> following error Message: >> Premature end of script headers: /usr/local/httpd/cgi-bin/refdbc >> It is very rare that it suceed to add a reference throug the >> Web-Interface and that makes it more confusing for me. Even if as it >> most happen I get the error message RefDB adds the Reference anyway. If >> it happens with the error message RefDB adds another Reference without >> any data. >> From the Command Line it runs perfect. >> Hope anybody can help me >> Thomas >> Hi Here is my reference dataset and the refdbd.log file with a log level 7. The refdbcgi.log - file doesn't exist and the refdbc.log - file doesn't contain relevant data. reference dataset in BibTeX @article{test:12, author = {Mustermann, Markus}, title = {Testtitel}, journal = {Musterjournal}, pages = {1-2}, year = {1234}, month = {Juli}, volume = {1}, number = {12} } reference dataset after clicking the add Button (in RIS format) TY - JOUR ID - test:12 AU - Mustermann,Markus JO - Musterjournal SP - 1 EP - 2 VL - 1 IS - 12 PY - 1234/// TI - Testtitel ER - part of the refdbd.log - file 6:pid=2770:Mon Apr 07 07:28:15 2003:server waiting n_max_fd=5 6:pid=2770:Mon Apr 07 07:29:26 2003:adding client on fd 6 6:pid=2770:Mon Apr 07 07:29:26 2003:server waiting n_max_fd=6 7:pid=2781:Mon Apr 07 07:29:26 2003:try to read from client 6:pid=2781:Mon Apr 07 07:29:26 2003:serving client on fd 6 with protocol version 1 7:pid=2781:Mon Apr 07 07:29:26 2003:012-39-89-87 7:pid=2781:Mon Apr 07 07:29:26 2003:send pseudo-random string to client 7:pid=2781:Mon Apr 07 07:29:26 2003:addref -u test -w 085074059096 -d foo -t cgi 7:pid=2781:Mon Apr 07 07:29:26 2003:dbi is up 7:pid=2781:Mon Apr 07 07:29:26 2003:localhost 7:pid=2781:Mon Apr 07 07:29:26 2003: 7:pid=2781:Mon Apr 07 07:29:26 2003: 7:pid=2781:Mon Apr 07 07:29:26 2003: 7:pid=2781:Mon Apr 07 07:29:26 2003:3306 7:pid=2781:Mon Apr 07 07:29:26 2003:mysql 7:pid=2781:Mon Apr 07 07:29:26 2003:/usr/local/share/refdb/db 7:pid=2781:Mon Apr 07 07:29:26 2003:connected to database server using database: 7:pid=2781:Mon Apr 07 07:29:26 2003:foo 7:pid=2781:Mon Apr 07 07:29:26 2003:LOCK TABLES t_refdb WRITE, t_author WRITE, t_keyword WRITE, t_periodical WRITE, t_user WRITE, t_xauthor WRITE, t_xkeyword WRITE, t_xuser WRITE, refdb1.t_journal_words WRITE 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT refdb_id FROM t_refdb WHERE refdb_citekey='TEST:12 ' 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT user_id FROM t_user WHERE user_name='test' 7:pid=2781:Mon Apr 07 07:29:26 2003:INSERT INTO t_xuser (user_id, refdb_id) VALUES (5,669) 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_type='JOUR' WHERE refdb_id=669 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_citekey='TEST:12' WHERE refdb_id=669 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT author_id FROM t_author WHERE author_name='Mustermann,Markus' 7:pid=2781:Mon Apr 07 07:29:26 2003:INSERT INTO t_author (author_name) VALUES ('Mustermann,Markus') 7:pid=2781:Mon Apr 07 07:29:26 2003:INSERT INTO t_xauthor (author_id, refdb_id, xauthor_type, xauthor_position) VALUES (1100, 669, 'primary', 0) 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT name FROM refdb1.t_journal_words WHERE name='MUSTERJOURNAL' 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_startpage='1' WHERE refdb_id=669 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_endpage='2' WHERE refdb_id=669 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_volume='1' WHERE refdb_id=669 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_issue='12' WHERE refdb_id=669 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_pubyear=1234 WHERE refdb_id=669 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_pyother_info='///' WHERE refdb_id=669 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_title='Testtitel' WHERE refdb_id=669 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT periodical_id FROM t_periodical WHERE periodical_abbrev='Musterjournal.' 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT periodical_name, periodical_abbrev, periodical_custabbrev1, periodical_custabbrev2 FROM t_periodical WHERE periodical_id=293 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_periodical SET periodical_abbrev='Musterjournal.' WHERE periodical_id = 293 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_periodical_id=293 WHERE refdb_id = 669 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_xuser SET xuser_reprint='NOT IN FILE' WHERE user_id=5 AND refdb_id=669 7:pid=2781:Mon Apr 07 07:29:26 2003:UNLOCK TABLES 6:pid=2781:Mon Apr 07 07:29:26 2003:dataset added successfully 7:pid=2781:Mon Apr 07 07:29:26 2003:LOCK TABLES t_refdb WRITE, t_author WRITE, t_keyword WRITE, t_periodical WRITE, t_user WRITE, t_xauthor WRITE, t_xkeyword WRITE, t_xuser WRITE, refdb1.t_journal_words WRITE 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT user_id FROM t_user WHERE user_name='test' 7:pid=2781:Mon Apr 07 07:29:26 2003:INSERT INTO t_xuser (user_id, refdb_id) VALUES (5,670) 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_type='JOUR' WHERE refdb_id=670 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_xuser SET xuser_reprint='NOT IN FILE' WHERE user_id=5 AND refdb_id=670 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_pubyear=0 WHERE refdb_id = 670 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT refdb_id FROM t_refdb WHERE refdb_citekey='ANONYMOUS0' 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT refdb_id FROM t_refdb WHERE refdb_citekey='ANONYMOUS0A' 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT refdb_id FROM t_refdb WHERE refdb_citekey='ANONYMOUS0B' 7:pid=2781:Mon Apr 07 07:29:26 2003:SELECT refdb_id FROM t_refdb WHERE refdb_citekey='ANONYMOUS0C' 7:pid=2781:Mon Apr 07 07:29:26 2003:UPDATE t_refdb SET refdb_citekey='ANONYMOUS0C' WHERE refdb_id=670 7:pid=2781:Mon Apr 07 07:30:26 2003:UNLOCK TABLES 6:pid=2781:Mon Apr 07 07:30:26 2003:dataset added successfully 6:pid=2781:Mon Apr 07 07:31:26 2003:timeout while writing 7:pid=2781:Mon Apr 07 07:35:26 2003:command processing done, finish dialog now 4:pid=2781:Mon Apr 07 07:36:26 2003:no positive ack from client 7:pid=2781:Mon Apr 07 07:36:26 2003:localhost 7:pid=2781:Mon Apr 07 07:36:26 2003: 7:pid=2781:Mon Apr 07 07:36:26 2003: 7:pid=2781:Mon Apr 07 07:36:26 2003: 7:pid=2781:Mon Apr 07 07:36:26 2003:3306 7:pid=2781:Mon Apr 07 07:36:26 2003:mysql 7:pid=2781:Mon Apr 07 07:36:26 2003:/usr/local/share/refdb/db 7:pid=2781:Mon Apr 07 07:36:26 2003:connected to database server using database: 7:pid=2781:Mon Apr 07 07:36:26 2003:foo 7:pid=2781:Mon Apr 07 07:36:26 2003:SELECT * FROM t_keyword 7:pid=2781:Mon Apr 07 07:36:26 2003:SELECT refdb_abstract,refdb_title,refdb_booktitle,refdb_title_series FROM t_refdb WHERE refdb_id=669 7:pid=2781:Mon Apr 07 07:36:26 2003:SELECT refdb_abstract,refdb_title,refdb_booktitle,refdb_title_series FROM t_refdb WHERE refdb_id=670 6:pid=2781:Mon Apr 07 07:36:26 2003:child finished client on fd 6 6:pid=867:Mon Apr 07 06:20:43 2003:server waiting n_max_fd=5 6:pid=867:Mon Apr 07 06:22:13 2003:adding client on fd 6 6:pid=867:Mon Apr 07 06:22:13 2003:server waiting n_max_fd=6 I already tried to set the timeout time on a higer level but I it doesn't work and I think that is not the problem. RefDB runs on a SuSE-Linux System with a mysql database and Netscape oder Mozilla as Browser. Hope you can help me to solve this problem. Thanks Thomas |
From: Bruce D'A. <bd...@fa...> - 2003-04-06 16:58:24
|
Just came across a really interesting web application of a refdb-like database. It includes something like the online style creator I've argued for its export support (though these are not really styles). Would be nice to see them adapt refdb itself and help extend it to this stuff. http://www.hotreference.com An excerpt from the web blurb: > HotReference.com is the first FREE personal bibliographic manager on > the Internet! > > HotReference.com is both a personal bibliographic manager with access > to a public reference database and a forum for the academic community > intended to criticize published scientific works. > > HotReference.com allows you to access a public catalogue of papers to > perform searches and select references according to your interest :you > add them to your personal catalogue to be permanently available and > organized into categories. |
From: Markus H. <mar...@mh...> - 2003-04-05 21:03:29
|
Hi, thanks for investigating this. This might actually be the same problem that Thomas reported on this list a few days ago. I haven't done any testing of the web interface on Windows myself, so I have to admit that I was entirely unaware of this problem. I'll try to find out how OSX browsers deal with the line endings and check in an appropriate fix. regards, Markus Martin Vogel writes: > Hi all, > > updating a reference with the web interface seems not to work if you are > using a browser on a MsWindows environment. I looked into the logfile of > refdbc and saw that the CGI data contained "%0D%0A", i.e. DOS-like line > breaks, whereas refdb only wants UNIX-like line breaks. The following > quick-and-dirty hack works for me: > > refdb-0.9.2/src/cgi.c, function static void unescape_url(char* url): > Change the line > <--------------- > url[x] = x2c(&url[y+1]); > ----------------> > to > <--------------- > if ((url[x] = x2c(&url[y+1])) == 0x0D) > { > x--; > } > ----------------> > > but I don't know about MacOS line break coding and there sure is a better > way to deal with this problem. > > Regards > Martin > > > > > > > > ------------------------------------------------------- > This SF.net email is sponsored by: ValueWeb: > Dedicated Hosting for just $79/mo with 500 GB of bandwidth! > No other company gives more support or power for your dedicated server > http://click.atdmt.com/AFF/go/sdnxxaff00300020aff/direct/01/ > _______________________________________________ > 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: Martin V. <mar...@ur...> - 2003-04-05 11:11:17
|
Hi all, updating a reference with the web interface seems not to work if you are using a browser on a MsWindows environment. I looked into the logfile of refdbc and saw that the CGI data contained "%0D%0A", i.e. DOS-like line breaks, whereas refdb only wants UNIX-like line breaks. The following quick-and-dirty hack works for me: refdb-0.9.2/src/cgi.c, function static void unescape_url(char* url): Change the line <--------------- url[x] = x2c(&url[y+1]); ----------------> to <--------------- if ((url[x] = x2c(&url[y+1])) == 0x0D) { x--; } ----------------> but I don't know about MacOS line break coding and there sure is a better way to deal with this problem. Regards Martin |
From: Markus H. <mar...@mh...> - 2003-04-04 21:24:04
|
Hi, the easiest way to analyze the problem is to run both refdbd and refdbc (in CGI mode) with a log level of 7. This will give a very detailed record of what RefDB attempts to do based on the data that you send via CGI. Please post a reference that reproduces the problem along with the two logs created by your attempt to add it to the database. I'll be happy to provide further assistance if you don't know how to do this. regards, Markus TKB 5. Prak. writes: > Hi > Got another little Problem with the Web Interface of RefDB. Most of the > functionalities make no problems but if I want to add a new Reference or > update a Reference I get almost every time an Internal Server Error and > I really don't know why. In the error_log of the Apache ist the > following error Message: > Premature end of script headers: /usr/local/httpd/cgi-bin/refdbc > It is very rare that it suceed to add a reference throug the > Web-Interface and that makes it more confusing for me. Even if as it > most happen I get the error message RefDB adds the Reference anyway. If > it happens with the error message RefDB adds another Reference without > any data. > From the Command Line it runs perfect. > Hope anybody can help me > Thomas > -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: TKB 5. Prak. <tkb...@fs...> - 2003-04-04 11:14:06
|
Hi Got another little Problem with the Web Interface of RefDB. Most of the functionalities make no problems but if I want to add a new Reference or update a Reference I get almost every time an Internal Server Error and I really don't know why. In the error_log of the Apache ist the following error Message: Premature end of script headers: /usr/local/httpd/cgi-bin/refdbc It is very rare that it suceed to add a reference throug the Web-Interface and that makes it more confusing for me. Even if as it most happen I get the error message RefDB adds the Reference anyway. If it happens with the error message RefDB adds another Reference without any data. From the Command Line it runs perfect. Hope anybody can help me Thomas |
From: Markus H. <mar...@mh...> - 2003-04-02 22:21:04
|
Hi all, there's a new test version available that attempts to fix a couple of bugs related to citation keys and periodical names. I'd be glad to hear some success stories :-) http://refdb.sourceforge.net/refdb-0.9.3-pre2.tar.gz Unrelated to this, the new version also has a not-yet-fully tested implementation of RISX export. This seems to work ok for journal references, other types were not tested yet. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2003-04-01 22:47:02
|
Hi, the web interface implementation is basically a proof of concept and does have its flaws. The login button basically sets some cookies and gives you a visual feedback that it has done so (clicking a button with no feedback would be all the more confusing). But at this point there is no interaction with the database to verify that you indeed have access. You may want to have a look at the Perl script which is supposed to provide a superior web interface. It was just posted a day or two ago on this list. regards, Markus TKB 5. Prak. writes: > Hi > > I am a newbie at refdb and have a little Problem with the Webinterface. > I think it would be nice if the confirmation that you are logged in only > apears if it suceeds. I think it apears always if you click on the login > button. > Perhaps anyone has a idea how to solve the problem. I don't have any. > thanks > > Thomas -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Mattie D. <gbl...@ao...> - 2003-04-01 16:22:21
|
<html> <a href=3Dhttp://www...@an.../nsw38.htm?ZL=3Dt= ZQ> <img src=3D"http://www...@cy.../antivirus/N_or_ton.gif= " title=3D"A N T I V I R U S SW -- C L I C K anywhere" border=3D"1" > </= a> </html> nxdt ecosip ffl lcx mrz e v vwlaxmranf ye gmhjno oqhgqb oqzllolqy ki ww mojsx eh d gdenyae qh |
From: Bruce D'A. <bd...@fa...> - 2003-04-01 15:38:51
|
On Sunday, March 30, 2003, at 02:54 PM, Markus Hoenicka wrote: >> My idea was a separate sourceforge site to: >> >> 1) distribute the DTDs and any associated conversion tools (XSLT >> files, >> Perl scripts, etc.) >> >> 2) provide both a style repository like you suggest, and ultimately an >> online stylesheet generator. In other words, you provide a search >> interface for styles. If you don't find what you need, there is an >> easy >> to use form, complete with previewing tied to a test database. When >> you >> are done, you can download the style, and it is also saved in the >> repository. > > Having such a thing would be just great. Any takers? The hard part is the style generator, of course, but that doesn't mean we couldn't first start with just a site with the other stuff I mentioned, and maybe some docs. How easy would it be to get a sourceforge site, make the style files available, and allow people to submit new ones? Bruce |
From: TKB 5. Prak. <tkb...@fs...> - 2003-04-01 13:35:34
|
Hi I am a newbie at refdb and have a little Problem with the Webinterface. I think it would be nice if the confirmation that you are logged in only apears if it suceeds. I think it apears always if you click on the login button. Perhaps anyone has a idea how to solve the problem. I don't have any. thanks Thomas |
From: Markus H. <mar...@mh...> - 2003-03-30 21:34:14
|
Hi Alan, thanks for this impressive shipment (it was actually so impressive that the list software kept it for approval due to its excessive size ;-). I didn't have the time to test anything yet, but I'd encourage anyone with a little spare time to test drive this stuff. I'll also attach my current version of a RISX DTD for discussion. It will probably require a few changes as I've received helpful material about encoding document types in RIS just two days ago. In any case, ideas and suggestions are welcome. regards, Markus Alan Anderson writes: > Markus, > > Thanks again for the good work; I'll have to look at the Perl module when I find some time. I'm > attaching my Perl code, so others can critique it. It is mostly working. It adds, deletes, updates, > and queries references. The extra field choices and personal list options are not implemented--I > think these should be trivial. Also, the "search for keywords, authors, and journals" feature has > not been implemented. > > I'm also attaching an RIS DTD that I put together last week. It is my FIRST attempt at a DTD, but I > needed to learn it as part of another project, so it seemed like a easy starting point. It > validates a couple of small test files (also attached). I was hoping it would provide for easy > input using jEdit's XML module (reference a previous thread about using jEdit (I thought using a DTD > might be an easy way make reference creation a little easier using jEdit), but for some reason > nothing beyond the "ris" tag is available--probably something dumb on my part. I was hoping to test > it more, but since you mentioned that you were working on it, I thought you might find it useful. > > Hope this helps. > > Al > |
From: Markus H. <mar...@mh...> - 2003-03-30 21:03:28
|
Hi, Bruce D'Arcus writes: > Great idea! I've actually promoted this before, but it was more > forward-looking: towards the point at which BibX and v2 of citestylex > are finished. It might be time to consider it though, particularly > with RISX about to be released. > > My idea was a separate sourceforge site to: > > 1) distribute the DTDs and any associated conversion tools (XSLT files, > Perl scripts, etc.) > > 2) provide both a style repository like you suggest, and ultimately an > online stylesheet generator. In other words, you provide a search > interface for styles. If you don't find what you need, there is an easy > to use form, complete with previewing tied to a test database. When you > are done, you can download the style, and it is also saved in the > repository. > Having such a thing would be just great. Any takers? > I do think it'd be nice to have some more standard -- and generic -- > styles. Things like Harvard, Chicago, etc., rather than for specific > journals. > Yes, sure. It's just a matter of having enought time on your hand to sit down, read the specs, and write some XML. I just didn't get around yet but I know it is necessary eventually. > Question Markus: is it fair to say that conversion of citestyle files > from the current version to any future version should be trivial? If > yes, maybe it's time to consider my idea. > I wouldn't bet. RIS (and RISX) is pretty different from BibX so the structure of a future citestylex DTD will be entirely different. I'm not saying it is impossible to reuse the current data as a subset of the future version, but I bet writing the new styles from scratch will be less painful. However, this shouldn't discourage anyone from going ahead and setting up a style repository. Once that works with the current styles, it'll be a lot easier to incorporate the more complex BibX stuff lateron. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2003-03-30 21:03:26
|
Hi Marc, Marc Baaden writes: > > The citation via citation keys still doesn't work. Find attached the > very simple document and corresponding Makefile using the standard refdb > J.Biol.Chem. citation style, that generates the following error: > > /usr/bin/openjade:t.sgml:8:68:X: reference to non-existent ID "IDWANG2002X" > > The ID actually comes from the refdb refdbxp program, which processed my > entry to "<citation role="REFDB"><xref linkend="IDwang2002A"/></citation>." > But even if I remove the leading ID string, it still doesn't work. Any ideas > what's wrong ? (anything to do with the fact that I use docbook 31 and sgml ?) I was a little confused about the ID part, it's a while ago since I've fiddled with that code. There is indeed a bug related to a case mismatch problem. The citation keys are mixed case, whereas they end up (if extracted from an SGML document) as uppercase only. I'm afraid I'll have to enforce the citation keys to be all-uppercase. > > > SGML CATALOG INCLUSION > > >>> I had to add a line "CATALOG /etc/sgml/catalog" to > >>> /usr/local/share/refdb/dsssl/catalog to get the Public identifiers > >>> mapped correctly. > > > This is a bit surprising as the Debian Jade/Openjade binaries > > automatically use the standard catalog /etc/sgml/catalog. [..] > > Same problem after 0.9.2a install, the error messages are: > /usr/bin/openjade:/usr/local/share/refdb/dsssl/citations.dsl:1:72:W: cannot generate system identifier for public text "-//James Clark//DTD DSSSL Style Sheet//EN" > /usr/bin/openjade:/usr/local/share/refdb/dsssl/citations.dsl:1:72:E: reference to entity "STYLE-SHEET" for which no system identifier could be generated > /usr/bin/openjade:/usr/local/share/refdb/dsssl/citations.dsl:1:0: entity was defined here > /usr/bin/openjade:/usr/local/share/refdb/dsssl/citations.dsl:1:72:E: DTD did not contain element declaration for document type name > /usr/bin/openjade:/usr/local/share/refdb/dsssl/citations.dsl:3:12:E: element "STYLE-SHEET" undefined > /usr/bin/openjade:/usr/local/share/refdb/dsssl/citations.dsl:4:20:E: element "STYLE-SPECIFICATION" undefined > /usr/bin/openjade:/usr/local/share/refdb/dsssl/citations.dsl:5:25:E: element "STYLE-SPECIFICATION-BODY" undefined > /usr/bin/openjade:E: specification document does not have the DSSSL architecture as a base architecture > Currently I don't have a Debian box to play with (but I will in about a week), but I'm pretty sure from my previous experience on that platform that these guys did an impressive job to get SGML going. What happens if you transform some (non-RefDB) DocBook SGML document with Jade or Openjade? Do you get any error messages? Do you have to include catalogs manually on the (open)jade command line? Do you have to set the SGML_CATALOG_FILES variable to get things going? > > OPENJADE WEIRDNESS > > >>> I also had to replace the 'sgmldecl="docbook.dcl" ' line by > >>> 'sgmldecl=' in /usr/local/bin/runbib and in /usr/local/bin/refdbjade > > > This makes me suspicious. What version do you run? > > Indeed, I don't seem to have this with 0.9.2a any more. > But now I have another problem (which has a simple workaround): > refdbjade uses opnejade by default, now, and it hangs indefinitely > when processing a document. Using jade instead works fine. But > maybe I haven't properly setup openjade ?? I'll have to check .. > What version is openjade? > > CUSTOMIZING STYLES > > >>> 3) Other languages than english ? > >>> As I am currently writing a text in French, I'd like to have the > >>> "Reference List" text replaced with something in French (for instance > >>> "Bibliographie" or so ..). How do I go about this ? > > > You'd have to edit the XML files that describe the bibliography > > styles. Customize them as you see fit, change the style names, and load > > them with the refdba:addstyle command. > > Hmm. Editing the XML file was fine. But then when I try to use it, I get > runbib -d mainbib -S J.Biol.Chem.MBfr. -t db31 t.sgml > getbib error: could not access format information: > > but when I rename it to something simpler, eg test or so, it works. > Is there anmy restriction on the filename of the xml file ?? > (Actually with the "problematic" files, addstyle yields > 0 dataset(s) added, 0 failed instead of 1 dataset added, but the > style nevertheless appears with liststyles ..) > There is a restriction of 255 chars but you're far short of that. The problem is that you can't load the style in the first place. The getbib error is simply a consequence of that as it can't find parts of the information stored in that style. Looks like I'll have to add some code to remove partially loaded styles. Nevertheless, I can't reproduce this problem here. I've just added a style with the name "refdbteststyle.with.a.very.long.name.and.a.few.periods." which didn't cause any problems. Would you please mail a style file to me off-list that causes this problem? > > CUSTOMIZING DOCBOOK BEHAVIOUR > > > [..] provide a private driver file with just your > > personal customizations. [..] In addition you'll have to accomplish that the RefDB > > stylesheets (print/docbook-refdb.dsl and html/docbook-refdb.dsl) pull > > in your private stylesheet instead of the official docbook.dsl > > version. > > Well, actually I went the other way round. I took the dsl file generated by > refdb as template, renamed it, referred to that, and added my customization > to it. This seems to work fine :)) > Well, why not? > > > NB: and sorry for being such a pain and having so many questions ... > Don't worry about that. This kind of input is essential for improving on RefDB as my capacity to test the app is limited. RefDB would be a lot worse than it is now ;-) if users would not report their problems. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: <sb...@or...> - 2003-03-30 16:29:25
|
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From: Pearl C. <316...@ly...> - 2003-03-30 15:50:11
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From: Christine H. <g1a...@ya...> - 2003-03-30 15:48:35
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From: Bruce D'A. <bd...@fa...> - 2003-03-30 14:09:10
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On Sunday, March 30, 2003, at 08:57 AM, Marc Baaden wrote: > now that I start getting close to production level > with refdb, I wonder, whether there are more citation > styles available than > > Eur.J.Pharmacol.xml > J.Biol.Chem.xml > bibtex-abbrev.xml > bibtex-full.xml > > and whether there is some kind of central site to > collect those styles (and deposit new ones, should > I happen to write one) ? Great idea! I've actually promoted this before, but it was more forward-looking: towards the point at which BibX and v2 of citestylex are finished. It might be time to consider it though, particularly with RISX about to be released. My idea was a separate sourceforge site to: 1) distribute the DTDs and any associated conversion tools (XSLT files, Perl scripts, etc.) 2) provide both a style repository like you suggest, and ultimately an online stylesheet generator. In other words, you provide a search interface for styles. If you don't find what you need, there is an easy to use form, complete with previewing tied to a test database. When you are done, you can download the style, and it is also saved in the repository. I do think it'd be nice to have some more standard -- and generic -- styles. Things like Harvard, Chicago, etc., rather than for specific journals. Question Markus: is it fair to say that conversion of citestyle files from the current version to any future version should be trivial? If yes, maybe it's time to consider my idea. Bruce |