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From: Markus H. <mar...@mh...> - 2007-01-23 22:04:16
|
Martin Hicks writes: > All of the manpages talk about regexps, as does the manual. Which > backends support this? Both MySQL and pgsql? > Yes, both MySQL and PostgreSQL support full-fledged Unix regexps. SQLite is the only supported database engine that doesn't. However, as Josef pointed out already, you may get by with SQL regular expressions. > Ditto...If I do "getref" with no arguments no further valid getref > queries work. > RefDB is a unixish app, therefore many commands can read from stdin. In fact, they automatically attempt to read from stdin if there is no argument providing or pointing to the data. E.g. if you don't specify a file with addref, refdbc will try to read the data from stdin. Same with getref. If there is no query string, refdbc waits for one on stdin. While refdbc appears to hang here, you can type in a query string and terminate it with Ctrl-d Ctrl-d (there is still a bug in the implementation as this appears to work only once per session). This is in fact a feature, as you can store live queries in text files and pipe them into refdbc to your heart's content. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Josef K. <jo...@ta...> - 2007-01-23 20:48:17
|
On Tue, Jan 23, 2007 at 02:34:35PM -0500, Martin Hicks wrote: >=20 > > return anything? I'm not sure about the hang, but certainly SQLite > > doesn't support regular expression in query strings, and so you need to > > use SQL LIKE syntax, which is basically using '%' instead of '.*' > > and '_' instead of '.'. >=20 > Hmm...No regular expressions, eh? Well this really isn't sister > friendly (the person who is actually going to be using this). I could > probably teach her regexps but I don't know enough SQL foo to get by. >=20 Actually there is not SQL foo to know. Everything there is I've described above. Basically use an underscore (_) like a single character wild card, and a percent (%) like a multicharacter wild card, and that's your lot. Regular expressions give you more flexibility, but in my opinion are far less "sister friendly" than using a '%'. So you're probably good as you are. > All of the manpages talk about regexps, as does the manual. Which > backends support this? Both MySQL and pgsql? I'm not sure of pgsql, but mysql does. However it only does when the client code uses the right query operator. The SQL standard only supports a pattern matching query (LIKE) with % and _ as special characters, which is why SQLite does that. To be honest use of regular expressions in refdbc is a bit overkill for most queries. > > I'm not sure about the hanging. I had the same problem myself, until I > > started using strings that worked. For instance 'getref' on its own > > hung, and I needed to press 'control C' to return control, but then the > > database connection appeared to have broken, and I needed to close > > refdbc and reload it again. >=20 > Ditto...If I do "getref" with no arguments no further valid getref > queries work. Yes. I'm sure that's a bug (or feature)! Joe --=20 =3D=3D=3D Josef Karthauser (jo...@ta...) =3D=3D=3D http://x2obuilder.com= /tao =3D=3D=3D |
From: Martin H. <mo...@bo...> - 2007-01-23 19:34:52
|
On Tue, Jan 23, 2007 at 06:16:47PM +0000, Josef Karthauser wrote: > On Tue, Jan 23, 2007 at 12:39:40PM -0500, Martin Hicks wrote: > >=20 > > Should actually return something. And I can't get getref to work > > either. Using an example similar to that found in the Query Lanuage > > section of the manual: > >=20 > > refdbc: getref :AU:~^Tyson > >=20 >=20 > Does=20 > refdbc: getref :AU:~'tyson%' Yes, this does work... >=20 > return anything? I'm not sure about the hang, but certainly SQLite > doesn't support regular expression in query strings, and so you need to > use SQL LIKE syntax, which is basically using '%' instead of '.*' > and '_' instead of '.'. Hmm...No regular expressions, eh? Well this really isn't sister friendly (the person who is actually going to be using this). I could probably teach her regexps but I don't know enough SQL foo to get by. All of the manpages talk about regexps, as does the manual. Which backends support this? Both MySQL and pgsql? > I'm not sure about the hanging. I had the same problem myself, until I > started using strings that worked. For instance 'getref' on its own > hung, and I needed to press 'control C' to return control, but then the > database connection appeared to have broken, and I needed to close > refdbc and reload it again. Ditto...If I do "getref" with no arguments no further valid getref queries work. mh --=20 Martin Hicks || mo...@bo... || PGP/GnuPG: 0x4C7F2BEE |
From: Josef K. <jo...@ta...> - 2007-01-23 18:17:07
|
On Tue, Jan 23, 2007 at 12:39:40PM -0500, Martin Hicks wrote: >=20 > Should actually return something. And I can't get getref to work > either. Using an example similar to that found in the Query Lanuage > section of the manual: >=20 > refdbc: getref :AU:~^Tyson >=20 Does=20 refdbc: getref :AU:~'tyson%' return anything? I'm not sure about the hang, but certainly SQLite doesn't support regular expression in query strings, and so you need to use SQL LIKE syntax, which is basically using '%' instead of '.*' and '_' instead of '.'. I'm not sure about the hanging. I had the same problem myself, until I started using strings that worked. For instance 'getref' on its own hung, and I needed to press 'control C' to return control, but then the database connection appeared to have broken, and I needed to close refdbc and reload it again. Joe --=20 =3D=3D=3D Josef Karthauser (jo...@ta...) =3D=3D=3D http://x2obuilder.com= /tao =3D=3D=3D |
From: Martin H. <mo...@bo...> - 2007-01-23 18:01:12
|
Hi, My first attempt at installing refdb. On Linux, using sqlite. I've managed to stick in two rif entries, and I can see that they were entered because 'getau' with no arguments produces: refdbc: getau Cinnamon,Jerry Tyson,Andy 999:2 refdbc: However, I don't seem to be able to figure out how to formulate a query that will pull out all the information. It would seem that refdbc: getau '^Tyson' 999:0 refdbc: Should actually return something. And I can't get getref to work either. Using an example similar to that found in the Query Lanuage section of the manual: refdbc: getref :AU:~^Tyson Just hangs and I see the following in the logs: adding client 127.0.0.1 on fd 5 server waiting n_max_fd=5 try to read from client serving client on fd 5 with protocol version 5 210-40-54-21 send pseudo-random string to client parent removing client on fd 5 server waiting n_max_fd=4 Any ideas? thanks mh -- Martin Hicks || mo...@bo... || PGP/GnuPG: 0x4C7F2BEE |
From: Josef K. <jo...@ta...> - 2007-01-21 11:06:15
|
On Sat, Jan 20, 2007 at 11:28:30PM +0100, Markus Hoenicka wrote: > Josef Karthauser writes: > > On another note, the version of refdbib I'm running appears to write > > duplicate entries to the bib file for things that are cited more than > > once. Can this be prevented? > >=20 >=20 > The simplest way to avoid this is to run runbib instead of > refdbib. runbib preprocesses the aux file to avoid duplicates. If you > need to do this manually, use something like: >=20 > sort file.aux | uniq | refdbib [options] > bib.bib >=20 Yay. Thanks for that. Joe --=20 =3D=3D=3D Josef Karthauser (jo...@ta...) =3D=3D=3D http://x2obuilder.com= /tao =3D=3D=3D |
From: Markus H. <mar...@mh...> - 2007-01-20 22:29:11
|
Josef Karthauser writes: > On another note, the version of refdbib I'm running appears to write > duplicate entries to the bib file for things that are cited more than > once. Can this be prevented? > The simplest way to avoid this is to run runbib instead of refdbib. runbib preprocesses the aux file to avoid duplicates. If you need to do this manually, use something like: sort file.aux | uniq | refdbib [options] > bib.bib regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Josef K. <jo...@ta...> - 2007-01-20 21:46:47
|
On Sat, Jan 20, 2007 at 10:40:38PM +0100, Markus Hoenicka wrote: > Josef Karthauser writes: > > Sure. See the attached. It looks like it might be complaining about a > > missing style, however I couldn't find anything in the documentation > > which talked about setting up styles for bibtex output; it would also = be > > useful for revdbib to report the reason for the error if this is the > > case. > >=20 >=20 > The current svn version now reports correctly if it can't find a style > or if it can't load the selected style. >=20 Brilliant. On another note, the version of refdbib I'm running appears to write duplicate entries to the bib file for things that are cited more than once. Can this be prevented? Joe --=20 =3D=3D=3D Josef Karthauser (jo...@ta...) =3D=3D=3D http://x2obuilder.com= /tao =3D=3D=3D |
From: Markus H. <mar...@mh...> - 2007-01-20 21:41:24
|
Josef Karthauser writes: > Sure. See the attached. It looks like it might be complaining about a > missing style, however I couldn't find anything in the documentation > which talked about setting up styles for bibtex output; it would also be > useful for revdbib to report the reason for the error if this is the > case. > The current svn version now reports correctly if it can't find a style or if it can't load the selected style. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2007-01-19 15:59:15
|
Josef Karthauser <jo...@ta...> was heard to say: > Ahha. I didn't find the refdb-init script, but I found the style files > in the distribution and used 'refdba' to load them manually. > > It now works using > > % refdbib -d joe -S bibtex-abbrev -t bibtex tc.aux > tc.bib > > The installation I got was from the FreeBSD ports system. > There was no refdb-init script in 0.9.6. The FreeBSD port is a bit outdated, unfortunately. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Josef K. <jo...@ta...> - 2007-01-19 15:33:01
|
On Fri, Jan 19, 2007 at 04:06:04PM +0100, Markus Hoenicka wrote: > Josef Karthauser <jo...@ta...> was heard to say: >=20 > > Sure. See the attached. It looks like it might be complaining about a > > missing style, however I couldn't find anything in the documentation > > which talked about setting up styles for bibtex output; >=20 > Looks like an omission from the docs. Even bibtex output requires one of = two > very simple styles: bibtex-full and bibtex-abbrev. You can use these to c= ontrol > whether the journal names are printed in full or if you prefer the abbrev= iated > names - something that is hard to achieve in bibtex alone. Add these styl= es to > your refdb database, and the error should go away. >=20 > BTW did you set up RefDB manually? The refdb-init script should load all > available styles to avoid this problem. Ahha. I didn't find the refdb-init script, but I found the style files in the distribution and used 'refdba' to load them manually. It now works using % refdbib -d joe -S bibtex-abbrev -t bibtex tc.aux > tc.bib The installation I got was from the FreeBSD ports system. > > it would also be > > useful for revdbib to report the reason for the error if this is the > > case. > > >=20 > There is certainly some wiggle room for improvements! I'll try to figure = out > something appropriate. Would you mind posting a feature request on the > SourceForge RefDB site to remind me? >=20 I'll do that in due course. Thanks, Joe --=20 =3D=3D=3D Josef Karthauser (jo...@ta...) =3D=3D=3D http://x2obuilder.com= /tao =3D=3D=3D |
From: Markus H. <mar...@mh...> - 2007-01-19 15:06:09
|
Josef Karthauser <jo...@ta...> was heard to say: > Sure. See the attached. It looks like it might be complaining about a > missing style, however I couldn't find anything in the documentation > which talked about setting up styles for bibtex output; Looks like an omission from the docs. Even bibtex output requires one of two very simple styles: bibtex-full and bibtex-abbrev. You can use these to control whether the journal names are printed in full or if you prefer the abbreviated names - something that is hard to achieve in bibtex alone. Add these styles to your refdb database, and the error should go away. BTW did you set up RefDB manually? The refdb-init script should load all available styles to avoid this problem. > it would also be > useful for revdbib to report the reason for the error if this is the > case. > There is certainly some wiggle room for improvements! I'll try to figure out something appropriate. Would you mind posting a feature request on the SourceForge RefDB site to remind me? regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Josef K. <jo...@ta...> - 2007-01-19 12:30:34
|
On Fri, Jan 19, 2007 at 10:10:34AM +0100, Markus Hoenicka wrote: > Josef Karthauser <jo...@ta...> was heard to say: > > > As you can see, the .aux file contains a single citation > > 'Overduin1998pn', which it appears to retrieve ok '1 retrieved', but > > then it also says '1 failed' and no output is produced. > > Could you please run the application server refdbd with a log level of 7 and > send me the log output of the getbib command? E.g. stop the server using > "refdbctl stop", then run refdbd -s -e 2 -l 7 -L /home/joe/getbib.log, run > refdbib in a separate terminal, and kill refdbd with Ctrl-C when done. > Sure. See the attached. It looks like it might be complaining about a missing style, however I couldn't find anything in the documentation which talked about setting up styles for bibtex output; it would also be useful for revdbib to report the reason for the error if this is the case. > > BTW, how do I do a query in refdbc on the citation key? I don't appear > > to be able to do: > > > > refdbc: getref :ID:~'Overduin1998pn' > > RefDB treats numerical ID values and citation keys separately, although they > have to share the same field (ID - ) in RIS datasets. :ID: looks for a > numerical ID, whereas :CK: looks for a citation key. The following command > should work: > > refdbc: getref :CK:=Overduin1998pn > Brilliant, I was wondering - I didn't find this in the documentation anywhere. Joe -- === Josef Karthauser (jo...@ta...) === http://x2obuilder.com/tao === |
From: Markus H. <mar...@mh...> - 2007-01-19 09:10:42
|
Josef Karthauser <jo...@ta...> was heard to say: > As you can see, the .aux file contains a single citation > 'Overduin1998pn', which it appears to retrieve ok '1 retrieved', but > then it also says '1 failed' and no output is produced. Could you please run the application server refdbd with a log level of 7 and send me the log output of the getbib command? E.g. stop the server using "refdbctl stop", then run refdbd -s -e 2 -l 7 -L /home/joe/getbib.log, run refdbib in a separate terminal, and kill refdbd with Ctrl-C when done. > BTW, how do I do a query in refdbc on the citation key? I don't appear > to be able to do: > > refdbc: getref :ID:~'Overduin1998pn' > RefDB treats numerical ID values and citation keys separately, although they have to share the same field (ID - ) in RIS datasets. :ID: looks for a numerical ID, whereas :CK: looks for a citation key. The following command should work: refdbc: getref :CK:=Overduin1998pn regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Josef K. <jo...@ta...> - 2007-01-18 22:18:35
|
Hi, I wonder. Can someone help me? I can't get refdbib to function properly. I'm trying to get it to export a bibtex file for a latex document, but it returns an error and no output. Here's the command I'm running: % refdbib -d joe -S name -m -l 7 -t bibtex -e 0 tc.aux > foo=20 Please enter your password:=20 refdbib started gettexbib -u joe -d joe -s name 18 Overduin1998pn 999:1 retrieved:1 failed refdbib finished % cat foo %=20 As you can see, the .aux file contains a single citation 'Overduin1998pn', which it appears to retrieve ok '1 retrieved', but then it also says '1 failed' and no output is produced. As you can see, this entry is in the database: TY - JOUR ID - Overduin1998pn AU - Overduin,J.M. AU - Wesson,P.S. TI - Kaluza-Klein Gravity JF - Physics Reports JO - Phys.Rept. KW - Cosmology KW - KaluzaKlein KW - ReviewPaper VL - 283 SP - 303 EP - 378 N2 - Read the cosmology section especially, for the thesis. RP - NOT IN FILE IS - 5-6 UR - http://lanl.arxiv.org/abs/gr-qc/9805018 N1 - We review higher-dimensional unified theories from the general re= lativity, rather than the particle physics side. Three distinct approaches = to the subject are identified and contrasted: compactified, projective and = noncompactified. We discuss the cosmological and astrophysical implications= of extra dimensions, and conclude that none of the three approaches can be= ruled out on observational grounds at the present time. PY - 1997/April// ER -=20 999:1 retrieved:0 failed refdbc:=20 What's going wrong? BTW, how do I do a query in refdbc on the citation key? I don't appear to be able to do: refdbc: getref :ID:~'Overduin1998pn' Joe --=20 =3D=3D=3D Josef Karthauser (jo...@ta...) =3D=3D=3D http://x2obuilder.com= /tao =3D=3D=3D |
From: <ste...@jo...> - 2007-01-18 16:37:33
|
Markus Hoenicka a =E9crit : > Hi all, >=20 > 0.9.8 unfortunately contained a few bugs which require a bugfix > release. 0.9.8-1 does not contain any new features. See below for a > description of the fixed bugs. The new release was built from the > subversion revision 273. The bugfixes also required a new release of > the perlclient module, now at version 1.16. Updated Cygwin binaries > will be released shortly. >=20 > The new releases can be grabbed here: >=20 > http://sourceforge.net/project/showfiles.php?group_id=3D26091 >=20 RPMs available for Mandriva 2007.0 at: http://distrib-coffee.ipsl.jussieu.fr/pub/linux/MandrivaLinux/official/20= 07.0/i586/media/contrib/testing/ Cheers, St=E9phane --=20 St=E9phane T=E9letch=E9a, PhD. http://www.steletch.org Unit=E9 Math=E9matique Informatique et G=E9nome http://migale.jouy.inra.f= r/mig INRA, Domaine de Vilvert T=E9l : (33) 134 652 891 78352 Jouy-en-Josas cedex, France Fax : (33) 134 652 901 |
From: Markus H. <mar...@mh...> - 2007-01-16 08:27:38
|
Hi all, I've uploaded updated Cygwin binaries which were built from the recently announced 0.9.8-1 bugfix release. The package is available here: http://sourceforge.net/project/showfiles.php?group_id=26091 Please remember that this is not a real Cygwin package. It is a simple archive that you should extract in / (the root directory of your Cygwin installation). All files will then drop into the /usr/local hierarchy. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2007-01-14 13:12:42
|
Hi all, 0.9.8 unfortunately contained a few bugs which require a bugfix release. 0.9.8-1 does not contain any new features. See below for a description of the fixed bugs. The new release was built from the subversion revision 273. The bugfixes also required a new release of the perlclient module, now at version 1.16. Updated Cygwin binaries will be released shortly. The new releases can be grabbed here: http://sourceforge.net/projects/showfiles.php?group_id=26091 regards, Markus Bugfixes: - the implementation of the addref/updateref/checkref client/server dialog was incorrect. The bug did not cause a loss of data under any circumstances. In fact, the bug was silent on most systems. However, the bug showed up randomly on Cygwin. The bug in the client/server dialog was *after* all data were added to the database, but *before* the result summary was transmitted to the client. Due to the bug refdbc would in some cases indicate an error when in fact the command had been processed successfully. - the checkref command suffered from a possible segfault which was fixed - getbib returned an error if one of the references did not contain any titles. This is now handled more gracefully. - while at it, several memory leaks were plugged. -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2006-12-15 08:38:34
|
Hi, I've uploaded a binary package of RefDB-0.9.8 for Windows/Cygwin: http://sourceforge.net/project/showfiles.php?group_id=26091&package_id=17592 As with all binary Cygwin releases before, this is not a real Cygwin package. It is a simple tar.gz archive which you should extract in /. The binaries, documentation, man pages, and shared files will then end up in /usr/local. Inquiries to become a Cygwin package maintainer to do a real Cygwin package will be generously considered :-) Let me know if you encounter any problems. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2006-12-14 12:39:34
|
Hi, refdb-elisp is a minor mode for Emacs which implements a graphical interface and an integrated editing environment for RefDB. I've uploaded refdb-elisp 1.3 last night. There are no new features in the tool itself, but it provides support for the new checkref command and it also supports the changed command-line options in some of the RefDB clients. If you upgraded RefDB to 0.9.8 or plan to do so, please grab the new version of refdb-elisp here: http://sourceforge.net/project/showfiles.php?group_id=26091&package_id=169552 regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: David N. <dav...@sw...> - 2006-12-12 15:10:47
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The Debian svn repository has been updated so that all packages now are at revision 261. Regards, David. |
From: David N. <dav...@sw...> - 2006-12-12 15:10:41
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The Debian (pre-)release repository has been updated so that all packages now are version 0.9.8. Regards, David. |
From: Markus H. <mar...@mh...> - 2006-12-12 10:17:38
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:-( I should know by now! thanks for the correction Markus David Nebauer <dav...@sw...> was heard to say: > Hi Markus, > > > after another 6 months of work, RefDB 0.9.8 has been released into the > > wild today. Please grab your copy right here: > > > > http://sourceforge.net/projects/showfiles.php?group_id=26091 > > That link should use 'project' instead of 'projects': > > http://sourceforge.net/project/showfiles.php?group_id=26091 > > Regards, > David. > > -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: David N. <dav...@sw...> - 2006-12-12 09:01:32
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Hi Markus, > after another 6 months of work, RefDB 0.9.8 has been released into the > wild today. Please grab your copy right here: > > http://sourceforge.net/projects/showfiles.php?group_id=26091 That link should use 'project' instead of 'projects': http://sourceforge.net/project/showfiles.php?group_id=26091 Regards, David. |
From: Markus H. <mar...@mh...> - 2006-12-07 22:38:21
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Hi, I've just noticed that yesterday's announcement mentioned the checkref command twice, but it did not explain it anywhere. This is quite funny as probably the largest part of my coding time since 0.9.7 went into this feature. So for all who missed earlier prerelease announcement, this is what the checkref command is all about: The checkref command adds your RIS or risx data to your database much like addref does. However, the data end up in temporary tables and are not added permanently. Instead, refdbd uses the temporary data to compare the new references against the ones in the database. This will help you identify duplicate entries as well as synonyms or spelling variants of keywords, author names, and periodicals. If you use the xhtml output of the checkref command, you'll even be able to see what the imported data is going to look like. I'm sorry for that omission. regards, Markus Markus Hoenicka writes: > Hi all, > > after another 6 months of work, RefDB 0.9.8 has been released into the > wild today. Please grab your copy right here: > -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |