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From: <inf...@af...> - 2002-05-28 06:45:15
|
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From: Markus H. <hoe...@co...> - 2002-05-27 21:29:24
|
Janusz S. Bie=F1 writes: > I hope so. On the other hand, the problem of different endianness > occurs only if you use UTF-16, while in practice more popular seems > UTF-8 form, already supported `out of the box' by GNU Emacs. >=20 You're right, I had multibyte character sets in mind, not Unicode per se. > Are you aware that the most official (ISO 2709) and popular MARC > format for bibliographic records has also an SGML/XML form? It's > somewhere on Library of Congress pages. When EndNote downloads a > record from a real library catalog, it probably get its in MARC form= at > and only later converts it and stores in the RIS file. I had no time= My background is Biochemistry, and the bibliographic data I use mostly come from Pubmed. There are only three formats available: XML, ASN.1, and Medline, the latter being almost identical to RIS. This is the official download format for importing Pubmed data into reference manager programs. The XML DTD is pretty specific to the Pubmed database, so I currently do not plan to support it as an input format. MARC is not supported at all, so apparently it depends on your field of expertise what you consider as "most popular". > yet to check what is the output of free Z39.50 clients such as YAZ > (which hopefully will be some time in future integrated with refdb > :-)), but I suspect it must be quite close to MARC. Well, at least I did the first steps towards this goal a while ago, but I didn't start to code yet. I just browsed the YAZ documentation again but couldn't find any mentioning of MARC. My understanding of both YAZ and MARC is quite poor, so I can't tell whether this is a problem. >=20 > Now the question is: do you have an idea how difficult it would be t= o > provide support for MARC format either as an advanced option or as t= he > primary format? Perhaps it is just switching to a different DTD in t= he > right place? >=20 www.loc.gov was down when I tried, so I don't have all the information I'd like to have about MARC yet. Without a documentation the MARC XML DTD looks like complete nonsense (I'm sure this impression will change as soon as I have access to the docs). In general, XML would be the best way to feed MARC datasets to RefDB. There are two different issues when adding new input formats to RefDB: - teaching refdbd to digest a new reference format is fairly easy. The current implementation simply sends the incoming chunk of data to a RIS parser. Adding a switch to send it to an XML parser would be trivial. The hard thing would then be to add the handlers for a specific XML DTD. - teaching RefDB databases to hold full MARC datasets could turn out to be a complex task, depending on the complexity of the MARC DTD. I'd prefer a way to use a common database format for both RIS and MARC stuff. Another issue is which MARC standard should be supported. USMARC sounds fairly straightforward as it uses ASCII, but this wouldn't solve your problem. UNIMARC allows to specify the ISO character set in each dataset, though. > I had a very, very quick look at EndNote demo and I am intrigued by > the lack of any mention of character code issue. This is strange, > because bibliographic references are inherently multilingual (the > libraries, before switching to UNICODE, seemed to use internally som= e > other multibyte encodings). Looks like there is a need for some > experiments consisting in downloading bibliographic references in > different languages and checking the character code in the resulting= > RIS file. >=20 I'd be thrilled to read the results of your experiments. I don't have access to a Windows box currently so I can't run these tests myself. regards, Markus --=20 Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
|
From: <js...@mi...> - 2002-05-27 04:22:40
|
On Sat, 25 May 2002 "Markus Hoenicka" <hoe...@co...> wro= te: > Janusz S. Bie=F1 writes: > > I hope MySQL supports UNICODE in some form, which would be the optimal > > solution. >=20 > Apparently it does, but in the case of multibyte character sets RefDB > might actually be limiting. There are no provisions whatsoever to deal > with multibyte characters. I'm not sure whether this really matters, > but at least the transfer between computers with different endianness > would fail. This could be fixed, however, with only little overhead. I hope so. On the other hand, the problem of different endianness occurs only if you use UTF-16, while in practice more popular seems UTF-8 form, already supported `out of the box' by GNU Emacs. >=20 > >=20 > > Another limiting factor may be the RIS format. Do I understand > > correctly that it is an informal standard introduced by commercial > > software? >=20 > It is a de-facto standard used by the top 3 commercial reference > management and bibliography tools. Meanwhile all 3 are sold by the > same company (www.risinc.com), so the free transfer between these > tools might be of some interest to the company. Unfortunately it is no > "real" standard: no RFCs, no publicly available description etc. All I > know about RIS is from the Reference Manager help file. >=20 > > BTW, I think it would be good to include the explicit > > answer to this question in the documentation. >=20 > Sure, as soon as I know the answer... This is already a (kind of) answer. Are you aware that the most official (ISO 2709) and popular MARC format for bibliographic records has also an SGML/XML form? It's somewhere on Library of Congress pages. When EndNote downloads a record from a real library catalog, it probably get its in MARC format and only later converts it and stores in the RIS file. I had no time yet to check what is the output of free Z39.50 clients such as YAZ (which hopefully will be some time in future integrated with refdb :-)), but I suspect it must be quite close to MARC. Now the question is: do you have an idea how difficult it would be to provide support for MARC format either as an advanced option or as the primary format? Perhaps it is just switching to a different DTD in the right place? >=20 > > Anyway, what character > > codes are used in practice in existing RIS files? Is UNICODE > > explicitly allowed? > >=20 >=20 > There is no mentioning of character sets in the last Reference Manager > version that I had access to (8.5, today they sell version 10). ISI > Research Soft (their current name) are a US company, and the products > seemed to be geared towards life sciences. The largest public database > is Pubmed which uses latin-1 afaik. So you can imagine that they might > not feel the urge to support lots of different character sets. But > then, only the company knows for sure. >=20 > >From a practical point of view, as long as the tags are ok, you should > be able to use any character set in your RIS files. They might no > longer be compatible to commercial software, though. I had a very, very quick look at EndNote demo and I am intrigued by the lack of any mention of character code issue. This is strange, because bibliographic references are inherently multilingual (the libraries, before switching to UNICODE, seemed to use internally some other multibyte encodings). Looks like there is a need for some experiments consisting in downloading bibliographic references in different languages and checking the character code in the resulting RIS file. >=20 > > Yesterday I made a quick try to install refdb in my office on Debian > > Woody. I don't remember exactly the messages (I write now from home), > > but the configure failed because libreadline is not present in Woody - > > it has been replaced by something else, which in turn is not > > recognized by refdb's configure. >=20 > I just checked the Debian package list, and libreadline4 is available > in unstable, testing, and stable. I'd be surprised if this lib would > actually be dropped. You just need to make sure that you have the > development libraries too, i.e. you need libreadline4 *and* > libreadline4-dev. Probably I was missing libreadline4-dev. On the other hand, I really got some message about a missing library and I will try to reproduce it. Best regards Janusz --=20 ,=20=20=20 dr hab. Janusz S. Bien, prof. UW Prof. Janusz S. Bien, Warsaw Uniwersity http://www.orient.uw.edu.pl/~jsbien/ --------------------------------------------------------------------- Na tym koncie czytam i wysylam poczte i wiadomosci offline. On this account I read/post mail/news offline. |
|
From: Markus H. <hoe...@co...> - 2002-05-26 21:48:58
|
Bugfixes: - Password encryption bug on PPC Linux (and other PPC OSes?) was fixed - It is now possible to specify empty variable values with the set command in refdba and refdbc - The RIS backend accidentally returned the value of USER1 for all USERX fields and MISC1 for all MISCX fields. This is corrected now. - The application server now handles SIGCHLD correctly to avoid zombies on BSD-style systems. - refdba and refdbc now correctly pass non-option arguments to the command if run in batch mode - the "'' could not be resolved as hostname" bug in refdbc and refdbib was fixed - a bug in the detection of unabbreviated words in journal names was fixed - a bug in the post-processing of the default_ris variable was fixed - the address, ISSN, URL, publisher, and city fields are now available for display in the screen and HTML backends as well as in the web interface Improvements: - New refdba functions addword and listword to manage reserved journal words - The getref HTML output now generates output suitable for CSS stylesheets. A new command-line option/configuration file variable allows to specify the URL of the CSS file to use. - All RefDB applications now look into /usr/local/etc (or whatever you choose as "sysconfdir" during configuration) to find their global configuration files. Only if they're not found there, the apps will consult $REFDBLIB. The latter is done in order not to break existing installations, but you should move your config files to the proper location now (unless you really share them between machines). This change was made to separate the shareable data in $REFDBLIB from machine-specific configuration data. - Building and installing is now possible from a separate build directory - The script refdb is now suitable for use on both SysV-style and BSD-style systems to start and stop the refdbd daemon Other changes: - ris.el is now no longer byte-compiled. This simplifies building Debian packages and does not really hurt speed-wise. You can still byte-compile this file manually if you believe it helps. Unfortunately I can't provide a Cygwin package at this time as I don't have access to a Windoze box currently. If someone wants to jump in, please let me know. Comments, bug reports, and praise \\;^) are appreciated as usual. regards, Markus -- Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
|
From: Markus H. <hoe...@co...> - 2002-05-25 20:36:38
|
Janusz S. Bie=F1 writes: > I hope MySQL supports UNICODE in some form, which would be the optim= al > solution. Apparently it does, but in the case of multibyte character sets RefDB might actually be limiting. There are no provisions whatsoever to deal with multibyte characters. I'm not sure whether this really matters, but at least the transfer between computers with different endianness would fail. This could be fixed, however, with only little overhead. >=20 > Another limiting factor may be the RIS format. Do I understand > correctly that it is an informal standard introduced by commercial > software? It is a de-facto standard used by the top 3 commercial reference management and bibliography tools. Meanwhile all 3 are sold by the same company (www.risinc.com), so the free transfer between these tools might be of some interest to the company. Unfortunately it is no "real" standard: no RFCs, no publicly available description etc. All I know about RIS is from the Reference Manager help file. > BTW, I think it would be good to include the explicit > answer to this question in the documentation. Sure, as soon as I know the answer... > Anyway, what character > codes are used in practice in existing RIS files? Is UNICODE > explicitly allowed? >=20 There is no mentioning of character sets in the last Reference Manager version that I had access to (8.5, today they sell version 10). ISI Research Soft (their current name) are a US company, and the products seemed to be geared towards life sciences. The largest public database is Pubmed which uses latin-1 afaik. So you can imagine that they might not feel the urge to support lots of different character sets. But then, only the company knows for sure. From a practical point of view, as long as the tags are ok, you should be able to use any character set in your RIS files. They might no longer be compatible to commercial software, though. > Yesterday I made a quick try to install refdb in my office on Debian= > Woody. I don't remember exactly the messages (I write now from home)= , > but the configure failed because libreadline is not present in Woody= - > it has been replaced by something else, which in turn is not > recognized by refdb's configure. I just checked the Debian package list, and libreadline4 is available in unstable, testing, and stable. I'd be surprised if this lib would actually be dropped. You just need to make sure that you have the development libraries too, i.e. you need libreadline4 *and* libreadline4-dev. regards, Markus --=20 Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
|
From: <js...@mi...> - 2002-05-25 05:34:42
|
On Fri, 24 May 2002 "Markus Hoenicka" <hoe...@co...> wrote: > This is a good question. I personally do not have any experience with > non-standard character sets, but the limiting step is basically the > storage in the SQL database. Recent versions of MySQL allow to select > the character set (per server, afaik). Information about supported > character sets is available in the MySQL handbook at www.mysql.com. I hope MySQL supports UNICODE in some form, which would be the optimal solution. Another limiting factor may be the RIS format. Do I understand correctly that it is an informal standard introduced by commercial software? BTW, I think it would be good to include the explicit answer to this question in the documentation. Anyway, what character codes are used in practice in existing RIS files? Is UNICODE explicitly allowed? > > It would be great if you could test the setup with your specific > language needs and see whether refdb adds any unnecessary > constraints. I'll be happy to work out these problems. I definitely intend to make some experiments, as I am quite impressed by the system. Yesterday I made a quick try to install refdb in my office on Debian Woody. I don't remember exactly the messages (I write now from home), but the configure failed because libreadline is not present in Woody - it has been replaced by something else, which in turn is not recognized by refdb's configure. Best regards Janusz -- , dr hab. Janusz S. Bien, prof. UW Prof. Janusz S. Bien, Warsaw Uniwersity http://www.orient.uw.edu.pl/~jsbien/ --------------------------------------------------------------------- Na tym koncie czytam i wysylam poczte i wiadomosci offline. On this account I read/post mail/news offline. |
|
From: Markus H. <hoe...@co...> - 2002-05-25 02:33:47
|
This is a good question. I personally do not have any experience with non-standard character sets, but the limiting step is basically the storage in the SQL database. Recent versions of MySQL allow to select the character set (per server, afaik). Information about supported character sets is available in the MySQL handbook at www.mysql.com. It would be great if you could test the setup with your specific language needs and see whether refdb adds any unnecessary constraints. I'll be happy to work out these problems. regards, Markus Janusz S. Bie=F1 writes: > I have just learned (from TEI-L) about refdb. It looks like an > exciting piece of software, but I was unable to find in the > documentation an answer to a simple question: which character sets a= re > supported? --=20 Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
|
From: <js...@mi...> - 2002-05-24 12:49:16
|
Hi!
I have just learned (from TEI-L) about refdb. It looks like an
exciting piece of software, but I was unable to find in the
documentation an answer to a simple question: which character sets are
supported?
Best regards
Janusz
--
,
dr hab. Janusz S. Bien, prof. UW
Prof. Janusz S. Bien, Warsaw Uniwersity
http://www.orient.uw.edu.pl/~jsbien/
---------------------------------------------------------------------
Na tym koncie czytam i wysylam poczte i wiadomosci offline.
On this account I read/post mail/news offline.
|
|
From: Markus H. <hoe...@co...> - 2002-05-10 21:51:56
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Where does the part "pp. 2-5" stem from? Is this a particular section of the whole reference which is addressed only in this citation? As an example, the reference would be: Someone: An investigation of foo with a special focus on bar. University Press, Princeton 2007. but in your citation you point out only the pages 2-5 while in another citation you might talk about other pages? I'm afraid this is currently beyond the capabilities of RefDB. The available tricks (X, S and so on) deal only with information that is already in the database, so merely extending this feature wouldn't help much. What we would need is a method to specify a page, a list of pages, or a page range as an attribute of the xref and ptr elements. The question is whether there are unused attributes available in all supported DTDs that would allow to implement this feature without extending the DTDs. If nothing else helps, the linkend (DocBook) and target (TEI) attributes could be overloaded by adding a page string, but these attributes will get increasingly difficult to parse with DSSSL or XSL. I'll have to think about this. One ugly way to achieve this with the current capabilities could be to assemble the citation from two in-text citations (authoronly, yearonly) and manually add parens and the page range. But again, this is kludgy. regards, Markus Denis Crowdy writes: > > Hi, > > In the referencing style for my thesis I need to create entries of the > kind: > > Text blah blah blah (Someone, 2007, pp. 2-5). > > Using the current reference types in refdb (X, S and so on) appended to > the ID part of the tag I haven't managed to cover this yet. > > Any ideas? Even a pointer to which part of the source I might > investigate would help. -- Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Denis C. <dc...@pi...> - 2002-05-10 09:49:48
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Hi, In the referencing style for my thesis I need to create entries of the kind: Text blah blah blah (Someone, 2007, pp. 2-5). Using the current reference types in refdb (X, S and so on) appended to the ID part of the tag I haven't managed to cover this yet. Any ideas? Even a pointer to which part of the source I might investigate would help. Thanks in advance, Denis Crowdy -- Department for Contemporary Music Studies Macquarie University NSW 2109 Australia, ph: +61 (0)2 9850 6787, fax: 9850 6593 |
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From: Markus H. <hoe...@co...> - 2002-05-06 20:13:26
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Dylan Oliver writes: > Almost, because of a minor but annoying mishandling of the ampersand (\&) > character. While getref shows that it was preserved through the conversion of > my original .bib to .ris (with bib2ris) and importation with refdbc's addref, > refdbib outputs it as \& , which bibtex doesn't like. > > Now that I think of it, the \& really shouldn't be preserved by bib2ris, as it > wouldn't make sense to any of the other formats. Shouldn't it be translated > by bib2ris into something (what?) the rest of the bibliography formats can > deal with, and then translated back to \& by refdbib when using the bibtex > output type? Would this be a difficult fix? I've got a wee bit of experience > with C, and would be willing to look at it after I'm done with all of my work > for the semester.. Did you run the bib2ris output through the supplied perl script tex2mail? I'm not sure about \& but in general this script should take care of these TeX constructs (in terms of removing them without a trace). If you plan to use your references for other purposes than LaTeX, then indeed the references should not contain any LaTeX-specific commands. Unfortunately RefDB is not yet capable to export LaTeX/BibTeX correctly, so only simple cases will work. I'm afraid it shows here that the BibTeX support was added "real quick" and that many issues have simply not been addressed yet. I'm still pondering the proper way of handling LaTeX formatting commands in the database. As it is next to impossible to re-create the original markup after stripping it, I favour the possibility to keep the markup in the database, but strip it for any output other than BibTeX. This might have funny results on queries though, so it would be a less than perfect solution. Your input, be it in form of code or of mere suggestions, is always welcome. regards, Markus -- Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Dylan O. <lo...@st...> - 2002-05-06 00:34:13
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Sunday 05 May 2002 18:18, Markus Hoenicka wrote: > Ok, this is bad. Even if it was no RefDB bug, there should be more > debug output to locate the bug. I'll put this on my todo-list. > - did you add the styles to the style database? Ah, no! I really wasn't clear on this. I added the styles to the database= , and=20 then it worked almost perfectly.=20 Almost, because of a minor but annoying mishandling of the ampersand (\&)= =20 character. While getref shows that it was preserved through the conversio= n of=20 my original .bib to .ris (with bib2ris) and importation with refdbc's add= ref,=20 refdbib outputs it as \& , which bibtex doesn't like.=20 Now that I think of it, the \& really shouldn't be preserved by bib2ris, = as it=20 wouldn't make sense to any of the other formats. Shouldn't it be translat= ed=20 by bib2ris into something (what?) the rest of the bibliography formats ca= n=20 deal with, and then translated back to \& by refdbib when using the bibte= x=20 output type? Would this be a difficult fix? I've got a wee bit of experie= nce=20 with C, and would be willing to look at it after I'm done with all of my = work=20 for the semester.. - --=20 Dylan Oliver=20 http://www.steelbend.org/~losang=20 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQE81dBFwDB3hYDfCecRAkHSAJ9Fuxib9DyGJOAiEGTKqFos3/+8VACcD9hN bXj5ZYeDwsNnLdKpYHCwoko=3D =3DDpIb -----END PGP SIGNATURE----- |
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From: Markus H. <hoe...@co...> - 2002-05-05 22:44:13
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Ok, this is bad. Even if it was no RefDB bug, there should be more debug output to locate the bug. I'll put this on my todo-list. The next step would be that you send me your references and your document to reproduce the problem. Before doing that, just a few more questions: - does the error occur with any references or just with some particular ones? Try test documents with just one reference, and change the ID to see what happens. - did you add the styles to the style database? regards, Markus Dylan Oliver writes: > I did try that, and don't see any interesting output - I abort, and refdbib > only reports that it started, ran gettexbib, and finished. refdbd just says > "added client". Both were run -l 7. -- Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Dylan O. <lo...@st...> - 2002-05-03 05:14:51
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 On Thursday 02 May 2002 23:37, Markus Hoenicka wrote: > Hi, > > did you try to switch the log level to 7 for refdbib *and* for refdbd > and see whether this tells you something? If not, please do so and > send the log output to the list. I did try that, and don't see any interesting output - I abort, and refdb= ib=20 only reports that it started, ran gettexbib, and finished. refdbd just sa= ys=20 "added client". Both were run -l 7. - --=20 Dylan Oliver - ------------ Hampshire College=09web:http://www.steelbend.org Box 927=09=09=09AIM:l0sang Amherst, MA 01002=09phone:413-559-5193 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQE80h1uwDB3hYDfCecRAox5AJ0Ssb9+BWEvShAekpHqkeZW31Bj+QCfR+So SP7SZ+yiDMNTy5Bk3kBwRE4=3D =3DCe90 -----END PGP SIGNATURE----- |
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From: Markus H. <hoe...@co...> - 2002-05-03 03:36:05
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Hi, did you try to switch the log level to 7 for refdbib *and* for refdbd and see whether this tells you something? If not, please do so and send the log output to the list. Thanks Markus Dylan Oliver writes: > aborting... > could not read from refdbd. Stop > > <document>.bib is not created. What's going on? Am I using the style > correctly? -- Markus Hoenicka <hoe...@co...> http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Dylan O. <lo...@st...> - 2002-05-03 00:21:57
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-----BEGIN PGP SIGNED MESSAGE----- Hash: SHA1 Hi, I'm trying to generate a bibtex bibliography with refdb. I've added m= y=20 references to the rdbib database, and have cited them in my LaTeX documen= t.=20 I've run latex to generate the .aux file. When I run `runbib -S=20 bibtex-full.xml -t bibtex <document>`, the refdbib process starts sucking= 99%=20 of my CPU and doesn't appear to do anything. I abort the process, and it=20 says:=20 aborting... could not read from refdbd. Stop <document>.bib is not created. What's going on? Am I using the style=20 correctly?=20 - --=20 Dylan Oliver - ------------ Hampshire College=09web:http://www.steelbend.org Box 927=09=09=09=09AIM:l0sang Amherst, MA 01002=09phone:413-559-5193 -----BEGIN PGP SIGNATURE----- Version: GnuPG v1.0.6 (GNU/Linux) Comment: For info see http://www.gnupg.org iD8DBQE80di2wDB3hYDfCecRAkFUAJ9jQbsqaetvnovug/NAQOfVfkWBHQCfcfFM RYTudqG/rAMo+xZAxFXmeAc=3D =3D7h2m -----END PGP SIGNATURE----- |
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From: Markus H. <hoe...@co...> - 2002-04-04 07:57:40
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Hi Denis, your statement is in no way ignorant! The endianness issue was indeed what I was heading towards. Unfortunately I don't have a ppc box or similar available, so I'll have to think. I'll try to fiddle with this tomorrow (2am - bed is calling) and let you know when it is worth to try a CVS version (the current version certainly has the same issue). thanks for your help to track this down Markus Denis Crowdy writes: > <ignorant statement role="musician" codingability="verypoor"> > Could the endian status of this ppc box be a potential source of such a > problem? I just know from playing around with some open source music > software (the MusicKit - runs using GNUstep) that audio data had to be > adjusted appropriately. > </ignorant statement> -- Markus Hoenicka hoe...@co... http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Markus H. <hoe...@co...> - 2002-04-04 04:45:46
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Hi Denis,
this does not sound too promising. I'm afraid you'll have to lend me a
hand to debug this. I have not seen this kind of error since about two
versions back, so I just can't debug it here.
I've got a few questions, and a suggestion. First you might try
the following:
Please edit the file src/refdbd.c. Look for an outcommented line saying:
printf("encrypted:%s<< plain:%s<<\n", passwd, descrambled_passwd);
This is line 942 in my sources, but it might be shifted a little
compared to your version.
Please uncomment this line and rebuild refdbd.
Now run this new server in the foreground again, like refdbd -s, and
run a command with refdba. This should tell you whether your password
is indeed correctly encrypted and decrypted (the string after plain:
should be exactly what you entered in refdba). If this test is ok,
we'd have to look at MySQL for the problem. If this test fails, I'll
stand caught with my pants down and I'll have to fix the code.
Some other questions:
- Is there any difference in your MySQL setup between your home and
office box? Are the versions the same? Do you use password-protected
access at home as well?
- Do you have any problems connecting with mysql (the MySQL
command-line client) on your office box?
regards,
Markus
Denis Crowdy writes:
>
> Now a bizarre thing happened prior to this - I did manage to
> successfully carry out a listdb, but subsequent attempts (while still
> logged in), failed. I haven't been able to repeat this so far. It's
> late and upside down on this side of the planet - I'll try again in the
> morning...
--
Markus Hoenicka
hoe...@co...
http://ourworld.compuserve.com/homepages/hoenicka_markus/
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From: Markus H. <hoe...@co...> - 2002-04-03 05:41:35
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Hi Denis, do you try to access your database "test" on the local machine? In this case your mysql.db lacks an entry for "test" and localhost. If this should not solve the problem, I would greatly appreciate if you could send the relevant piece of the refdbd log output with log_level set to 7. A simple way to do this is to start refdbd manually like this (make sure no daemon is running in the background): refdbd -s -e 0 -l 7 This would print the log output to stderr, so you could either redirect this to a file or cut+paste this into your mail. regards, Markus Denis Crowdy writes: > > Hi All, > > I have successfully set up refdb on a box at home, but am having great > trouble getting it set up on my office box (Debian ppc - woody). I keep > getting "could not connect to database server" messages. I've tried > commenting out "skip networking" in the mysql config file, have allowed > remote admin in the refdb config file. I've tried a variety of access > permissions in mysql. My current mysql.db table is listed below. > -- Markus Hoenicka hoe...@co... http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Denis C. <dc...@pi...> - 2002-04-03 00:16:03
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Hi All, I have successfully set up refdb on a box at home, but am having great trouble getting it set up on my office box (Debian ppc - woody). I keep getting "could not connect to database server" messages. I've tried commenting out "skip networking" in the mysql config file, have allowed remote admin in the refdb config file. I've tried a variety of access permissions in mysql. My current mysql.db table is listed below. I feel like I'm missing something very simple! Love the program though and am looking forward to getting it going. Thanks, Denis Crowdy | Host | Db | User | Select_priv | Insert_priv | Update_priv | Delete_priv | Create_priv | Drop_priv | Grant_priv | References_priv | Index_priv | Alter_priv | +-----------+----------+---------+-------------+-------------+-------------+-------------+-------------+-----------+------------+-----------------+------------+------------+ | % | test | | Y | Y | Y | Y | Y | Y | N | Y | Y | Y | | % | test\_% | | Y | Y | Y | Y | Y | Y | N | Y | Y | Y | | % | refdb | dcrowdy | Y | Y | Y | Y | Y | Y | Y | Y | Y | Y | | localhost | refdb | dcrowdy | Y | Y | Y | Y | Y | Y | Y | Y | Y | Y | | localhost | refdbvar | dcrowdy | Y | Y | Y | Y | Y | Y | Y | Y | Y | Y | | % | refdbvar | dcrowdy | Y | Y | Y | Y | Y | Y | Y | Y | Y | Y | | localhost | refdbvar | root | Y | Y | Y | Y | Y | Y | Y | Y | Y | Y | | localhost | refdb | root | Y | Y | Y | Y | Y | Y | Y | Y | Y | Y | +-----------+----------+---------+-------------+-------------+-------------+-------------+-------------+-----------+------------+-----------------+------------+------------+ -- Department for Contemporary Music Studies Macquarie University NSW 2109 Australia, ph: +61 (0)2 9850 6787, fax: 9850 6593 |
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From: Markus H. <hoe...@co...> - 2002-03-22 05:04:32
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David Kilgour writes: > on this, but Markus is convinced refdb should function regardless of the > operator's mental health :>) This sure was one of the major design goals, more important than all this SGML stuff! regards, Markus -- Markus Hoenicka hoe...@co... http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Markus H. <hoe...@co...> - 2002-03-22 05:03:29
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Hi Juan, Juan de la Figuera writes: > I can connect through either refdba or refdbc as root to the mysql > server (say doing a "listdb"). No problem there. But when I try as my > username, I get the "cannot connect to database server". The strange > thing is that using the same user name and password, I can use the > mysql client and list the databases (show databases), or look inside > them (the permissions look ok). For example, the output from status > is: In which databases precisely can you look inside? It might actually be a problem with your MySQL access rights for the database "refdb" (not the database with your references). When RefDB tries to connect to MySQL, it uses the database "refdb" as a dummy. This should no longer be necessary in MySQL 3.23 and later, but I have to keep it this way for compatibility with MySQL 3.22. If you do not have sufficient access rights to refdb (and refdbvar, but this is only used for bibliographies), you'd get this error. Could you check your access rights again? Send the contents of your mysql.db and mysql.user tables if you're not sure. FWIW I use the following access rights for a test database "lall" and entries to allow local and remote access: | Host | Db | User | Select_priv | Insert_priv | Update_priv | Delete_priv | Create_priv | Drop_priv | Grant_priv | References_priv | Index_priv | Alter_priv | +-----------+----------+--------+-------------+-------------+-------------+-------------+-------------+-----------+------------+-----------------+------------+------------+ | % | refdb | markus | Y | Y | Y | Y | N | N | N | N | N | N | | localhost | refdb | markus | Y | Y | Y | Y | N | N | N | N | N | N | | % | lall | markus | Y | Y | Y | Y | N | N | N | N | N | N | | % | refdbvar | markus | Y | Y | Y | Y | Y | Y | N | Y | Y | Y | | localhost | refdbvar | markus | Y | Y | Y | Y | Y | Y | N | Y | Y | Y | | localhost | lall | markus | Y | Y | Y | Y | N | N | N | N | N | N | NB If you add users with the refdba adduser command, the access rights should automatically be set correctly for the reference database as well as for refdb and refdbvar. If this does not work in your case, then it is a bug. > (BTW, the mysql client changes the password to "xxx" when doing the ps ax, but not refdbc. Not a big worry though) > This is very neat, and I believe it is very simple to implement. This would make things a bit more secure. regards, Markus -- Markus Hoenicka hoe...@co... http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: Markus H. <hoe...@co...> - 2002-03-22 05:03:14
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Hi, Octavio Martinez de la Vega writes: > - libreadline* in: > ./lib/libreadline.so.4 > ./lib/libreadline.so.4.1 [...] > > Do I have the wrong version of "libreadline" or why the configure script > cannot find it? I try to analyse it a bit, but I am lost... Thanks again. This is the case that I was talking about in my previous reply. You have the shared libraries (.so), but not the development libraries (.a or .la or whatever). You possibly have to install a separate package libreadline-dev. regards, Markus -- Markus Hoenicka hoe...@co... http://ourworld.compuserve.com/homepages/hoenicka_markus/ |
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From: David K. <to...@xt...> - 2002-03-21 21:31:51
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Juan did you see a change in a recent Debian\unstable where /etc/mysql/my.cnf has an entry "skip networking"? I commented this entry out and was able to connect to server with refdb 0.8.3 through refdba and refdbc as various users. I am having other "cannot connect to server" problems when running refdbib and runbib which I have mentioned here recently, and Markus has asked for specific details which I will send send shortly. There has been a delay bacause I also find "it is somewhat late" when I am working on this, but Markus is convinced refdb should function regardless of the operator's mental health :>) David |
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From: Juan de la F. <ju...@ca...> - 2002-03-21 09:59:23
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Hello, I am having some funny behavior. Ok, it is somewhat late. It is a refdb 0.8.3 installed on Debian 3.0 unstable/ppc. I can connect through either refdba or refdbc as root to the mysql server (say doing a "listdb"). No problem there. But when I try as my username, I get the "cannot connect to database server". The strange thing is that using the same user name and password, I can use the mysql client and list the databases (show databases), or look inside them (the permissions look ok). For example, the output from status is: -------------- mysql Ver 11.15 Distrib 3.23.47, for unknown-linux-gnu (powerpc) Connection id: 44 Current database: Current user: juan@localhost Current pager: stdout Using outfile: '' Server version: 3.23.47-log Protocol version: 10 Connection: Localhost via UNIX socket Client characterset: latin1 Server characterset: latin1 UNIX socket: /var/run/mysqld/mysqld.sock Uptime: 1 hour 14 sec Threads: 1 Questions: 45 Slow queries: 0 Opens: 7 Flush tables: 1 Open tables: 1 Queries per second avg: 0.012 -------------- The output of ps ax | grep ref is: 1432 ? S 0:00 /usr/local/bin/refdbd 1563 pts/4 S 0:00 refdbc -u juan -w myspasswd 1568 pts/2 S 0:00 grep ref and the one from ps ax | grep "mysql -u" is: 1599 pts/3 S 0:00 mysql -u juan --password=x xxxxx 1606 pts/2 S 0:00 grep mysql -u (BTW, the mysql client changes the password to "xxx" when doing the ps ax, but not refdbc. Not a big worry though) The variable in the refdbc are: serverip 127.0.0.1 port 9734 verbose f pager less username juan defaultdb papers pdfroot /home/juan/papers_bib/PDF/ timeout 60 logfile /var/log/refdbc.log logdest FILE loglevel DEBUG autokill 1800 fields RPAB Ok, on this computer I can run it as root. But I am curious... I am also including the "refdb-bug" output as an attachment... Regards, Juan -- ---------------------------------------- Juan de La Figuera Sandia National Laboratories Mail Stop 9161 Livermore, CA 94550 Fax: 925-294-3231 Phone: 925-294-1201 e-mail: gap...@at... ju...@ca... jd...@sa... Web: http://www.ca.sandia.gov/materials_science http://castelar.dhs.org ---------------------------------------- |
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