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From: Markus H. <mar...@mh...> - 2003-03-24 23:10:56
|
Hi, you can run refdbd with log level set to 7 (e.g. refdbd -s -e 0 -l 7). This will show the username/password that refdbc sent to the server. regards, Markus Daniel Hyduke writes: > I have just started using refdb (0.9.2a), on GNU/Linux Mandrake 9.0 with > apache-1.3.26 and mysql-3.23.52, and am having problems with the web > interface. The client works perfectly from the commandline but when I > try to access the database through the web interface I get an internal > server error. I have inserted the tail of my webserver and refdbd logs > below. The cookie and the username, password, and database are > correct. I have the correct grant for MySQL. I have checked the > mailing list, but none of the suggestions worked for me. Does anybody > have any ideas? Also, is there anyway to see the command that is issued > when refdbc is called so that I can see if the correct > usr/paswword/database is being passed? > > *********httpd log********** > incorrect username > [Mon Mar 24 14:02:17 2003] [error] [client 128.97.83.249] Premature end > of script headers: /usr/local/www/internal/cgi-bin/refdbc > incorrect username > [Mon Mar 24 14:05:36 2003] [error] [client 128.97.83.249] Premature end > of script headers: /usr/local/www/internal/cgi-bin/refdbc > incorrect username > [Mon Mar 24 14:07:00 2003] [error] [client 128.97.83.249] Premature end > of script headers: /usr/local/www/internal/cgi-bin/refdbc > incorrect username > [Mon Mar 24 14:07:09 2003] [error] [client 128.97.83.249] Premature end > of script headers: /usr/local/www/internal/cgi-bin/refdbc > incorrect username > [Mon Mar 24 14:19:27 2003] [error] [client 128.97.83.249] Premature end > of script headers: /usr/local/www/internal/cgi-bin/refdbc > > *********refdbd.log********** > 6:pid=10299:Mon Mar 24 22:09:01 2003:serving client on fd 6 with > protocol version 1 > 6:pid=10299:Mon Mar 24 22:09:01 2003:child finished client on fd 6 > 6:pid=3205:Mon Mar 24 22:09:01 2003:parent removing client on fd 6 > 6:pid=3205:Mon Mar 24 22:09:01 2003:server waiting n_max_fd=5 > 6:pid=3205:Mon Mar 24 22:09:01 2003:child exited with code 0 > 6:pid=3205:Mon Mar 24 22:09:01 2003:server waiting n_max_fd=5 > 6:pid=3205:Mon Mar 24 22:09:29 2003:adding client on fd 6 > 6:pid=3205:Mon Mar 24 22:09:29 2003:server waiting n_max_fd=6 > 6:pid=10305:Mon Mar 24 22:09:29 2003:serving client on fd 6 with > protocol version 1 > 6:pid=10305:Mon Mar 24 22:09:29 2003:child finished client on fd 6 > > -- > Daniel Hyduke <da...@se...> > > > > ------------------------------------------------------- > This sf.net email is sponsored by:ThinkGeek > Welcome to geek heaven. > http://thinkgeek.com/sf > _______________________________________________ > 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: Daniel H. <da...@se...> - 2003-03-24 23:01:28
|
I have just started using refdb (0.9.2a), on GNU/Linux Mandrake 9.0 with apache-1.3.26 and mysql-3.23.52, and am having problems with the web interface. The client works perfectly from the commandline but when I try to access the database through the web interface I get an internal server error. I have inserted the tail of my webserver and refdbd logs below. The cookie and the username, password, and database are correct. I have the correct grant for MySQL. I have checked the mailing list, but none of the suggestions worked for me. Does anybody have any ideas? Also, is there anyway to see the command that is issued when refdbc is called so that I can see if the correct usr/paswword/database is being passed? *********httpd log********** incorrect username [Mon Mar 24 14:02:17 2003] [error] [client 128.97.83.249] Premature end of script headers: /usr/local/www/internal/cgi-bin/refdbc incorrect username [Mon Mar 24 14:05:36 2003] [error] [client 128.97.83.249] Premature end of script headers: /usr/local/www/internal/cgi-bin/refdbc incorrect username [Mon Mar 24 14:07:00 2003] [error] [client 128.97.83.249] Premature end of script headers: /usr/local/www/internal/cgi-bin/refdbc incorrect username [Mon Mar 24 14:07:09 2003] [error] [client 128.97.83.249] Premature end of script headers: /usr/local/www/internal/cgi-bin/refdbc incorrect username [Mon Mar 24 14:19:27 2003] [error] [client 128.97.83.249] Premature end of script headers: /usr/local/www/internal/cgi-bin/refdbc *********refdbd.log********** 6:pid=10299:Mon Mar 24 22:09:01 2003:serving client on fd 6 with protocol version 1 6:pid=10299:Mon Mar 24 22:09:01 2003:child finished client on fd 6 6:pid=3205:Mon Mar 24 22:09:01 2003:parent removing client on fd 6 6:pid=3205:Mon Mar 24 22:09:01 2003:server waiting n_max_fd=5 6:pid=3205:Mon Mar 24 22:09:01 2003:child exited with code 0 6:pid=3205:Mon Mar 24 22:09:01 2003:server waiting n_max_fd=5 6:pid=3205:Mon Mar 24 22:09:29 2003:adding client on fd 6 6:pid=3205:Mon Mar 24 22:09:29 2003:server waiting n_max_fd=6 6:pid=10305:Mon Mar 24 22:09:29 2003:serving client on fd 6 with protocol version 1 6:pid=10305:Mon Mar 24 22:09:29 2003:child finished client on fd 6 -- Daniel Hyduke <da...@se...> |
From: Bruce D'A. <bd...@fa...> - 2003-03-24 19:19:31
|
On Monday, March 24, 2003, at 02:08 PM, Mar...@en... wrote: > In case you do not already know, be aware that microsoft software > (Word etc.) frequently uses non-latin1 characters like the > (in-)famous "smart quote", which infest web pages for instance. I actually didn't know that. In this case the problem is in the Endnote text export. My workaround was this, which was the only way I could get it to work: 1) export from Endnote as RTF. 2) open RTF in TextEdit (a text editor on OS X that can read RTF) 3) Copy and paste into jEdit. This doesn't even begin to solve all the other problems with Endnote's RIS export: 1) It can't export multiple keywords in the proper format, but gives you something like: KW - one two three N1 - etc. 2) Endnote has no support for start and end pages, but only a page range. 3) various miscellaneous problems with added "crap," which may be Endnote bugs, or problems with the export filter (though I don't see any). 4) RIS has no support for Endnote "type" fields (which are in essence reference subtypes). 5) Endnote does not have support for formatting dates, so one must input them as they are to be formatted. So, what is "10" in RIS is "October" in Endnote, and whatever it exports. It'd be nice if RefDB (or some other tool) could convert from Refer/Endnote formats to RIS. This is a really painful process to go through! Bruce |
From: <Mar...@en...> - 2003-03-24 19:07:17
|
On Fri, 21 Mar 2003, ref...@li... wrote: > Message: 6 > Date: Fri, 21 Mar 2003 12:30:11 -0500 > From: "Bruce D'Arcus" <bd...@fa...> > To: ref...@li... > Subject: [Refdb-users] character encoding stuff > > More setting up issues: > > I have a variety of characters that -- for whatever reason -- are not > making it through the translation from Endnote to RIS. The most common > problem is that curly single and double quotes get replaced by ?. So I > have notes with ?quotes like this?. I also have words like "don?t." > > Beyond figuring out how to fix this in a huge file (am not sure the > regular expression code to use to find this in jEdit, because the ? > character has a special meaning), will I need to worry about this in > the future? Ideally I'd like a clean database where I can move the > data in and out without worrying about these encoding issues. I > understand MySQL supports Latin-1 encoding by default, so I assume > there's no problem there. Is that right? > In case you do not already know, be aware that microsoft software (Word etc.) frequently uses non-latin1 characters like the (in-)famous "smart quote", which infest web pages for instance. Extract from: <http://www.fourmilab.ch/webtools/demoroniser/> You see, "state of the art" Microsoft Office applications sport a nifty feature called "smart quotes." (Rule of thumb--every time Microsoft use the word "smart," be on the lookout for something dumb). This feature is on by default in both Word and PowerPoint, and can be disabled only by finding the little box buried among the dozens of bewildering option panels these products contain. If enabled, and you type the string, "Halt," he cried, "this is the police!" "smart quotes" transforms the ASCII quote characters automatically into the incompatible Microsoft opening and closing quotes. Other useful links: <http://home.earthlink.net/~bobbau/platforms/specialchars/#windows> <http://www.cs.tut.fi/~jkorpela/www/windows-chars.html> <http://czyborra.com/charsets/iso8859.html#ISO-8859-1> Hopefully doing some search/replace on these characters in your documents is feasible for you=A0? Or you can let the "demoroniser" do it for you :-) You can also try GNU recode, with something like this: recode -f windows-1252..latin1 myfile Cheers, Marc. |
From: Markus H. <mar...@mh...> - 2003-03-21 22:07:59
|
Hi, this looks like a lousy implementation of Endnote's export filters. I'm afraid there's not much you can do - except using regular expressions wisely. I've never used jEdit, but in most regexp implementations you can escape a special character to make it work like a regular one, like \? in Unix and Perl regexps. Latin-1 should work ok unless you have very special needs that go beyond standard European languages. MySQL 4.0 has been declared stable just the other day. I didn't test it with RefDB yet, but I assume it is going to work. It supports Unicode if you should need it. BTW PostgreSQL has had Unicode support for quite a while, and SQLite can be optionally built with Unicode instead of Latin-1. regards, Markus Bruce D'Arcus writes: > More setting up issues: > > I have a variety of characters that -- for whatever reason -- are not > making it through the translation from Endnote to RIS. The most common > problem is that curly single and double quotes get replaced by ?. So I > have notes with ?quotes like this?. I also have words like "don?t." > > Beyond figuring out how to fix this in a huge file (am not sure the > regular expression code to use to find this in jEdit, because the ? > character has a special meaning), will I need to worry about this in > the future? Ideally I'd like a clean database where I can move the > data in and out without worrying about these encoding issues. I > understand MySQL supports Latin-1 encoding by default, so I assume > there's no problem there. Is that right? > > Or do I need to really look at setting up a unicode compatible > database? Mac OS X -- which I use -- handles unicode natively, BTW, if > that makes any difference. > > Bruce -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Bruce D'A. <bd...@fa...> - 2003-03-21 17:38:35
|
More setting up issues: I have a variety of characters that -- for whatever reason -- are not making it through the translation from Endnote to RIS. The most common problem is that curly single and double quotes get replaced by ?. So I have notes with ?quotes like this?. I also have words like "don?t." Beyond figuring out how to fix this in a huge file (am not sure the regular expression code to use to find this in jEdit, because the ? character has a special meaning), will I need to worry about this in the future? Ideally I'd like a clean database where I can move the data in and out without worrying about these encoding issues. I understand MySQL supports Latin-1 encoding by default, so I assume there's no problem there. Is that right? Or do I need to really look at setting up a unicode compatible database? Mac OS X -- which I use -- handles unicode natively, BTW, if that makes any difference. Bruce |
From: Markus H. <mar...@mh...> - 2003-03-20 23:12:06
|
Bruce D'Arcus writes: > Yes, this is my problem. If I use "root" as user, it works. So, I > want to figure out how to change MySQL so that I have another user. > I've assumed I could use my machine's user, but this is obviously not > the case. I realize also this is pretty much a MySQL question, but > hope someone can help me out anyway :-) > Ah I see. Login names/passwords and database server usernames/passwords *may* be the same coincidentally if you set them up this way, but a default MySQL installation doesn't have any users except root. You want the refdba:adduser command, something along the lines of: refdba: adduser -d mydatabase -H localhost -N newpassword bruce This would grant the user "bruce" using the password "newpassword" access to the database "mydatabase", with refdbd running on the same box as mysqld (i.e. localhost). regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Bruce D'A. <bd...@fa...> - 2003-03-20 21:14:06
|
On Thursday, March 20, 2003, at 03:01 PM, Markus Hoenicka wrote: > When you run a client command, refdbd should print the > username/password info (among other stuff) it receives from the > client. Please make sure these are the values you intend to use. Yes, this is my problem. If I use "root" as user, it works. So, I want to figure out how to change MySQL so that I have another user. I've assumed I could use my machine's user, but this is obviously not the case. I realize also this is pretty much a MySQL question, but hope someone can help me out anyway :-) Bruce |
From: Markus H. <mar...@mh...> - 2003-03-20 20:57:00
|
Hi, Manish Sharma writes: > creating database connection structure failed This indicates that either libdbi is not installed properly or that at least the pgsql driver is missing. A very common pitfall with building libdbi is that a simple ./configure will build only the framework. To build the drivers as well, you need to run ./configure --with-pgsql (or --with-mysql). regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2003-03-20 20:52:14
|
Hi Bruce, getting the MySQL authentication stuff correct isn't trivial, unfortunately. I'd suggest the following procedure: 1) start refdbd as a standalone app and have it print debug information: refdbd -s -e 0 -l 7 When you run a client command, refdbd should print the username/password info (among other stuff) it receives from the client. Please make sure these are the values you intend to use. 2) MySQL on OSX may be preconfigured to use only UNIX sockets for client/server communication instead of TCP/IP. This is a good default for security reasons, but refdbd always uses TCP/IP so this clearly wouldn't work. Make sure MySQL is allowed to accept TCP/IP connections and, if this doesn't help by itself, use your real IP address instead of "localhost" in refdbdrc. OSX might have TCP/IP support switched off by either using the "--skip-networking" command line option or by a "skip_networking" entry in my.cnf. Please see also the section "Testing your installation" in Chapter 4 of the manual. regards, Markus Bruce D'Arcus writes: > > OK, I've gotten RefDB compiled on OS X, and it seems to work, but every > time I try to connect with the refdb clients, I get an "could not > connect to database" error. I am guessing this has something to do > with my MySQL setup, where I have the root account defined with an > installer. If I connect directly to MySQL through the root account, no > problem. > > So, I gather I should be defining another user (me), but am not sure > how. > > Any help would be appreciated! > > Bruce -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Manish S. <ma...@cr...> - 2003-03-20 20:36:27
|
Hello, I was trying to install refdb 0.9.2a with Postgresql. Could someone please help? (My system is a RedHat Linux 8.0 and I used all default settings as required by RefDB during the installation procedure. My Postgresql server is on my local machine and is working and operational as I have used it actively.) Everything went ok in terms of compilation, etc. I was able to run refdbd with the command refdbd -V -D pgsql -b 5432 -s -e 0 -l 7 -P /tmp/refpid And then, when I ran refdba in a separate window, refdba: viewstat Could not connect to database server I got the following output in the server window: ... 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: Bruce D'A. <bd...@fa...> - 2003-03-20 17:18:54
|
OK, I've gotten RefDB compiled on OS X, and it seems to work, but every time I try to connect with the refdb clients, I get an "could not connect to database" error. I am guessing this has something to do with my MySQL setup, where I have the root account defined with an installer. If I connect directly to MySQL through the root account, no problem. So, I gather I should be defining another user (me), but am not sure how. Any help would be appreciated! Bruce |
From: shushig <gh...@ao...> - 2003-03-18 04:56:42
|
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From: Phillip L. <p....@ru...> - 2003-03-17 12:39:12
|
>>>>> "Markus" == Markus Hoenicka <mar...@mh...> writes: Markus> while we're at it, we shouldn't forget Emacs which can be Markus> turned into a frontend to just about anything with a few Markus> lines of Lisp code. I'd appreciate if there was some Markus> friendly competition between the jEdit and the Emacs camps Markus> over getting the first functional frontend out the door... This will be the point at which refdb comes really useful for me. I looked at doing something similar a while back, (a front end to medline!), but sadly the lovely reference display and choose code in reftex would require quite a lot of work to reuse as widgets for a different (non .bib) backend. Still as a quick solution, using W3 and refdb's web front end, should be reasonably usable. I think that all of this will get more likely when refdb is a little easier to install and use. I think the recent addition of sqlite is a good thing, as it will prevent many of the MySQL related difficulties from happening. Cheers Phil |
From: <ton...@ya...> - 2003-03-17 07:16:36
|
<a href=3Dhttp://www...@an.../nsw38.htm?Hx=3DrF> <img s= rc=3Dhttp://www...@an.../N_or_ton.gif title=3D"C L I C = K anywhere" border=3D"1" > aghtup i o |
From: Bruce D'A. <bd...@fa...> - 2003-03-16 15:52:19
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On Saturday, March 15, 2003, at 05:33 PM, Markus Hoenicka wrote: > while we're at it, we shouldn't forget Emacs which can be turned into > a frontend to just about anything with a few lines of Lisp code. I'd > appreciate if there was some friendly competition between the jEdit > and the Emacs camps over getting the first functional frontend out the > door... Am not sure how all this works, but would it be feasible to modify the XAE environment to add refdb integration? It already has a "new document" UI that might (?) be tweaked to use refdnd instead, and integrated transformation that could tie in the refdb makefile system. That doesn't address searching and adding references and such, but it seems like it'd be a good start... http://xae.sunsite.dk/ Bruce |
From: Markus H. <mar...@mh...> - 2003-03-15 22:35:29
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Hi Bruce, while we're at it, we shouldn't forget Emacs which can be turned into a frontend to just about anything with a few lines of Lisp code. I'd appreciate if there was some friendly competition between the jEdit and the Emacs camps over getting the first functional frontend out the door... regards, Markus Bruce D'Arcus writes: > As anyone taken a look at the java editor jEdit? It's really quite > nice, free and cross-platform, with an impressive plug-in and macro > system. I'm experimenting with the XML and XSLT plug-ins, which are > pretty good. > > This got me thinking: I bet RefDB would make a nice candidate for a > plug-in. Maybe allow for easy access to finding and inserting > references (though am not sure how), and to refdbnd and the makefile > system? > -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Bruce D'A. <bd...@fa...> - 2003-03-15 21:17:22
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As anyone taken a look at the java editor jEdit? It's really quite nice, free and cross-platform, with an impressive plug-in and macro system. I'm experimenting with the XML and XSLT plug-ins, which are pretty good. This got me thinking: I bet RefDB would make a nice candidate for a plug-in. Maybe allow for easy access to finding and inserting references (though am not sure how), and to refdbnd and the makefile system? Bruce |
From: Steve <jpl...@ai...> - 2003-03-14 20:02:36
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From: Bruce D'A. <bd...@fa...> - 2003-03-14 13:18:00
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I seem to have deleted the message I want to reply to, but I just thought of one potential issue here. A simple example (using LaTeX code): Here we have a standalone citation \cite{James1998}. Here we have a footnote\footnote{This footnote also has a citation \cite{James1998}}. What I was arguing is that one ought to be able to switch between the author-date and the full citation styles without touching the source. The problem in the above is that the first citation would need to be placed in a footnote (since one can't well have a full cite within the main text). Is this problem solvable? Hoping... Bruce |
From: Bruce D'A. <bd...@fa...> - 2003-03-13 13:19:44
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oops... On Thursday, March 13, 2003, at 08:22 AM, Bruce D'Arcus wrote: > <excerpt start-page="21" end-page="23">A very long excerpt ... <pb/> > ... that spans multiples pages.</excerpt> The above should be: <excerpt start-page="21" end-page="23">A very long excerpt ... <pb/> ... with text ... <pb/> ... that spans multiples pages.</excerpt> Bruce |
From: Bruce D'A. <bd...@fa...> - 2003-03-13 13:15:17
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On Thursday, March 13, 2003, at 07:19 AM, Michael Below wrote: >> To be clear, what I am saying above refers to a new "quote" reference >> type that currently exists in bibx. This would allow you to actually >> store excerpts (and hopefully annotations) and to have the specific >> page number(s) for the quote tied to it. > > Ah, okay, I thought you were talking about citations in general. > But also for these references to excerpts, it might be helpful to be > able to refer to a single spot inside the quote. Are you saying to be able to use (and thus cite) only a section of a multi-page quote? Agreed. I suggested we'd need a way to represent a page break, so that the data was there to make adjustments in this kind of circumstance. So perhaps you'd have something like: <excerpt start-page="21" end-page="23">A very long excerpt ... <pb/> ... that spans multiples pages.</excerpt> If you were using a GUI app that was based on this model, and you, say, copied-and-pasted just the last portion ("that spans..."), the app would adjust accordingly and just insert a citation with a cited page of "23." Yes, I know; it's ambitious. But, it's one useful thing that no reference manager that I know of has bothered to try yet. Bruce |
From: Michael B. <mb...@an...> - 2003-03-13 13:04:10
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Bruce D'Arcus <bd...@fa...> writes: >>> As we've discussed on the bibx list, I don't think this method is >>> ideal. I'd prefer that quotes have their page numbers associated with >>> them, and be stored in the database. > To be clear, what I am saying above refers to a new "quote" reference > type that currently exists in bibx. This would allow you to actually > store excerpts (and hopefully annotations) and to have the specific > page number(s) for the quote tied to it. Ah, okay, I thought you were talking about citations in general. But also for these references to excerpts, it might be helpful to be able to refer to a single spot inside the quote. >>> 61. The moral and fiscal capacity for philanthropy was an important >>> mechanism of class differentiation--separating the respectable from >>> the residuum as well as the wealthy from the poor; see Peter Mandler, >>> "Christian Political Economy and the Making of the New Poor Law," >>> Historical Journal 33, no. 1 (1990): 87. >> >> That would be the \fullcite command for jurabib (there is also a >> "citefull" option to set it in general). > > So how does one deal with the annotation in this example in jurabib? > You create a footnote that has that text, and then add the \fullcite > command(s)? Yes. For example I could write \footnote{See \fullcite[S.~715]{hayn94}.} which gives me a footnote: =B9 See Hayn, Sven Die International Accounting Standards. WPg 1994 S. 715. Plus an entry in the bibliography: Hayn, Sven: Die International Accounting Standards. WPg 1994, 713=AD721, 749=AD755 I think you would have to tweak the formatting a bit, but thats the general idea... Ciao Michael --=20 status is failure (galeon 1.2.5) |
From: Bruce D'A. <bd...@fa...> - 2003-03-12 23:46:50
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On Wednesday, March 12, 2003, at 06:25 PM, Markus Hoenicka wrote: > What appears to be missing is a clean way to suppress the bibliographic > listing which I figure would not be used if you use full citations. In some cases, the bib is included at the end as well, though often not. I have to say I hate reading books that don't have a listing at the end! Off-topic, though... Bruce |
From: Markus H. <mar...@mh...> - 2003-03-12 23:29:23
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Bruce D'Arcus writes: > > Unless I missed the point, this isn't as hard as it seems. This would > > require a new in-text citation type in addition to the existing > > regular, author-only, and year-only types. This full (or whatever) > > type would simply display everything that otherwise goes into the > > bibliography. > > I think I was making it more complicated than it needed to be in my own > mind. If I understand right, the above example ought to just be coded > as a footnote, with the specially formatted "full" citation within it. > But should this really be a different type of citation, or is there a > way to handle this via a citation style? In an ideal world, I'd be > able to switch between this kind of a style and author-date (in-text) > without having to recode the document. Shouldn't this be possible? > Looking at the citestylex.dtd again, there's actually no restriction what may appear in the in-text citation. It's apparently possible to design a style that renders the full bibliographic data in-text. What appears to be missing is a clean way to suppress the bibliographic listing which I figure would not be used if you use full citations. > The other thing with this type of citation is to distinguish between > the first full citation, and then subsequent short versions, ibid, etc. > citestylex.dtd supports this already. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |