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From: Markus H. <mar...@mh...> - 2009-06-15 18:19:25
|
-- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2009-06-04 14:53:33
|
Hi, Quoting "O. Hartmann" <oha...@ze...>: > The server (refdbd) is running on a FreeBSD 8.0-CURRENT/AMD64 SMP box, > another test facility is located on an older FreeBSD 7.2-STABLE/i386 box. My laptop runs 7.2-STABLE as well. This should make it fairly easy to compare setups. > I can add references from a file very easily as far as no UTF-8 or ISO > specific encodings (Umlaute) are used. This is unusual and probably a configuration problem. Before going into the details, I'd ask you to provide the following information: - the versions of RefDB, libdbi, libdbi-drivers, and of your database engine - the contents of your configuration files. Running "refdb-bug" retrieves your config files and a few other things. Please post the file created by this tool. - what kind of reference data are you using? The /examples subdirectory of the source distribution contains some test data that should just work. If you're experiencing the problems with some kind of non-standard data (e.g. exported from other software), feel free to zip or tar.gz some examples and send them to me off-list. > When using then a client, refdbc, I'm able to retrieve via 'getau' all > auhors, but trying 'getref' results in a got-stuck process which I can > only leave by hitting Ctrl-C. That is, the client gets stuck? Or the server child process? If the client appears to be stuck, most likely the server child process has run into trouble. In that case, please set the debug level of refdbd to "7", truncate the server log (usually /var/log/refdbd.log), and restart the server. Repeat the queries which fail and post the log. > > I also installed the web based contributed interface, but with this, on > no server I'm able to insert references or retrieve references. The only > way to retrieve anything is searching by 'Search indices', 'authors'. > There I can retrieve author names. > I don't recommend to fiddle with the web interface at this moment. The web interface calls the C clients, so if these don't work ok in the first place, the web interface won't either. > I digged the database server and there the tables (most recent > PostgreSQL), the references are accurate stored. > > Even with the supervisor/administration account for PostgreSQL I'm > incapable of retrieving references. Did you check the PostgreSQL error logs for anything unusual? I don't expect any permission problems though, as you seem to be able to create and fill the tables. > Another problem concerns trouble when inserting references taken from > our 'JabRef' output or BibTeX in gemeral. I use bib2ris-utf creating RIS > files for insertion into RefDB, but something gets confused. In most > cases, the end tag 'ER - ' is corrupted that way that the trailing > space gets lost. > Another issue targets LaTeX/TeX tags, like {\'C}uk. As often special > tags occur at the beginning of a line, say the first author's name, the > whole entry gets corrupted, the end of line gets lost and the next line > seems to merge with the first, faulty one. > This is probably due to limitations of the RefDB tools in question. It would be helpful if you could send me a couple of JabRef/BibTeX datasets, along with the datasets after running them through bib2ris-utf8, and with some comments on how the converted datasets should look like (I'm no BibTeX expert, so some conversion problems might not be obvious to me). regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: O. H. <oha...@ze...> - 2009-06-04 14:00:08
|
Hello. Since a while we check out RefDB as a poential backbone for our institute's literature and reference system. The server (refdbd) is running on a FreeBSD 8.0-CURRENT/AMD64 SMP box, another test facility is located on an older FreeBSD 7.2-STABLE/i386 box. Well, I ran into several severe problems, but I will target the first and possibly simple-to-fix one first. I can add references from a file very easily as far as no UTF-8 or ISO specific encodings (Umlaute) are used. When using then a client, refdbc, I'm able to retrieve via 'getau' all auhors, but trying 'getref' results in a got-stuck process which I can only leave by hitting Ctrl-C. I also installed the web based contributed interface, but with this, on no server I'm able to insert references or retrieve references. The only way to retrieve anything is searching by 'Search indices', 'authors'. There I can retrieve author names. I digged the database server and there the tables (most recent PostgreSQL), the references are accurate stored. Even with the supervisor/administration account for PostgreSQL I'm incapable of retrieving references. At this very moment I'm floating like a dead man in the water. Another problem concerns trouble when inserting references taken from our 'JabRef' output or BibTeX in gemeral. I use bib2ris-utf creating RIS files for insertion into RefDB, but something gets confused. In most cases, the end tag 'ER - ' is corrupted that way that the trailing space gets lost. Another issue targets LaTeX/TeX tags, like {\'C}uk. As often special tags occur at the beginning of a line, say the first author's name, the whole entry gets corrupted, the end of line gets lost and the next line seems to merge with the first, faulty one. It would be kind if someone could give me advice. Thanks in advance, Oliver |
From: Markus H. <mar...@mh...> - 2009-05-22 20:51:33
|
Torsten Bronger writes: > Hallöchen! > > If I connect to refdbd using sockets, why does the command > > addlink -u user -w password :NCK:=django-refdb-offprints-1 :CK:=Bld2006 > > not work, however, > > addlink -u user -w password ":NCK:=django-refdb-offprints-1 :CK:=Bld2006" > > does work? > I haven't analyzed this situation in detail, but I suspect it is caused by the use of getopt() to parse the command. Looks like getopt attempts to interpret the characters of the query string preceded by a dash as option characters unless they are enclosed in quotes. Let me know if this does not explain your experiences in full, I'd then have to have a second look. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Torsten B. <br...@ph...> - 2009-05-22 11:16:22
|
Hallöchen! If I connect to refdbd using sockets, why does the command addlink -u user -w password :NCK:=django-refdb-offprints-1 :CK:=Bld2006 not work, however, addlink -u user -w password ":NCK:=django-refdb-offprints-1 :CK:=Bld2006" does work? Tschö, Torsten. -- Torsten Bronger, aquisgrana, europa vetus Jabber ID: tor...@ja... |
From: Wei-Wei G. <ww...@gm...> - 2009-05-14 02:03:10
|
Markus Hoenicka 写道: > > I've checked in a patch which fixes this problem, see revision 675. > Thanks a lot! Best wishes, Wei-Wei |
From: Markus H. <mar...@mh...> - 2009-05-13 20:07:07
|
Markus Hoenicka writes: > Quoting Wei-Wei Guo <ww...@gm...>: > > > After changing the variable, the refdbd can be stopped correctly. It seems > > refdbctl doesn't use the variable set in refdbdrc. > > > > Ah, I see. I'll try to fix this asap. > I've checked in a patch which fixes this problem, see revision 675. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2009-05-11 09:50:15
|
Quoting Wei-Wei Guo <ww...@gm...>: > After changing the variable, the refdbd can be stopped correctly. It seems > refdbctl doesn't use the variable set in refdbdrc. > Ah, I see. I'll try to fix this asap. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Wei-Wei G. <ww...@gm...> - 2009-05-11 09:44:30
|
Markus Hoenicka 写道: > Thanks again. Both commands work as expected. Therefore the script > should work as well. Can you still reproduce the script failure? Also, > which shell did you use for these tests, i.e. what is your login shell? > If it is not bash, you may try repeating the above tests using bash: > type "bash" at your prompt, repeat the above tests, and type exit again > to return to your login shell. If that should give different results, > try editing the first line of refdbctl (something like > "#!/usr/bin/bash") and make it point to your login shell. > I opened /usr/bin/refdbctl and happened to find the problem. the script refdbctl set PIDFILE to: PIDFILE='/var/lib/run/refdbd.pid' instead of PIDFILE='/var/run/refdbd.pid' After changing the variable, the refdbd can be stopped correctly. It seems refdbctl doesn't use the variable set in refdbdrc. Thanks for help! Best wishes, Wei-Wei |
From: Markus H. <mar...@mh...> - 2009-05-11 09:13:43
|
Quoting Wei-Wei Guo <ww...@gm...>: > Is this what you mean? > > $ ls /var/run/refdb* > /var/run/refdbd.pid > > $ ps -C refdbd > PID TTY TIME CMD > 2904 ? 00:00:00 refdbd > > $ cat /var/run/refdbd.pid|sed 's/^ *\([0-9]*\).*/\1/' > 2904 > > $ ps ax | grep -i "^ *2904.*[r]efdbd" | sed 's/^ *\([0-9]*\).*/ 1/' > 2904 > Thanks again. Both commands work as expected. Therefore the script should work as well. Can you still reproduce the script failure? Also, which shell did you use for these tests, i.e. what is your login shell? If it is not bash, you may try repeating the above tests using bash: type "bash" at your prompt, repeat the above tests, and type exit again to return to your login shell. If that should give different results, try editing the first line of refdbctl (something like "#!/usr/bin/bash") and make it point to your login shell. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Wei-Wei G. <ww...@gm...> - 2009-05-11 08:42:37
|
Markus Hoenicka 写道: > Thanks for running these tests. Both look ok, so I'm entirely clueless > why the script fails on your box. refdbctl uses two shell commands to > isolate the process ID from the ps output and from the PID file. Maybe > one of these commands fails on your box. Could you please test those > shell commands manually? You'll have to replace two variables with their > real values, like this (using the values "2908" as the PID and > "/var/run/refdbd.pid" as the full path of the PID file in this example): > > cat /var/run/refdbd.pid|sed 's/^ *\([0-9]*\).*/\1/' > > and > > ps ax | grep -i "^ *2908.*[r]efdbd" | sed 's/^ *\([0-9]*\).*/\1/' > > Both commands should return the process ID, i.e. "2908" in this example. > Is this what you mean? $ ls /var/run/refdb* /var/run/refdbd.pid $ ps -C refdbd PID TTY TIME CMD 2904 ? 00:00:00 refdbd $ cat /var/run/refdbd.pid|sed 's/^ *\([0-9]*\).*/\1/' 2904 $ ps ax | grep -i "^ *2904.*[r]efdbd" | sed 's/^ *\([0-9]*\).*/ 1/' 2904 Best wishes, Wei-Wei |
From: Markus H. <mar...@mh...> - 2009-05-11 08:18:30
|
Quoting Wei-Wei Guo <ww...@gm...>: > There is only one line in /var/run/refdbd.pid: > > 2908 > > It is the PID of refdbd. > > $ ps -C refdbd > PID TTY TIME CMD > 2908 ? 00:00:00 refdbd > > >> Please also check the setting of the "pidfile" variable in your >> refdbdrc. It should have the value "/var/run/refdbd.pid" as well. >> > > Here is the 'pidfile' line in refdbdrc: > > pidfile /var/run/refdbd.pid > > Thanks for running these tests. Both look ok, so I'm entirely clueless why the script fails on your box. refdbctl uses two shell commands to isolate the process ID from the ps output and from the PID file. Maybe one of these commands fails on your box. Could you please test those shell commands manually? You'll have to replace two variables with their real values, like this (using the values "2908" as the PID and "/var/run/refdbd.pid" as the full path of the PID file in this example): cat /var/run/refdbd.pid|sed 's/^ *\([0-9]*\).*/\1/' and ps ax | grep -i "^ *2908.*[r]efdbd" | sed 's/^ *\([0-9]*\).*/\1/' Both commands should return the process ID, i.e. "2908" in this example. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Wei-Wei G. <ww...@gm...> - 2009-05-11 07:40:19
|
Markus Hoenicka 写道: >> # refdbctl stop >> /usr/bin/refdbctl stop: /usr/bin/refdbd is not running >> >> Am I do anything wrong? >> > > Not necessarily. It might be a permission problem or a parsing problem > of the grep output as well. After starting refdbd using refdbctl, do you > see a file called "refdbd.pid" in /var/run/? If yes, could you please > post the contents? There is only one line in /var/run/refdbd.pid: 2908 It is the PID of refdbd. $ ps -C refdbd PID TTY TIME CMD 2908 ? 00:00:00 refdbd > Please also check the setting of the "pidfile" > variable in your refdbdrc. It should have the value > "/var/run/refdbd.pid" as well. > Here is the 'pidfile' line in refdbdrc: pidfile /var/run/refdbd.pid Best wishes, Wei-Wei |
From: Markus H. <mar...@mh...> - 2009-05-11 06:49:38
|
Quoting Wei-Wei Guo <ww...@gm...>: > # refdbctl stop > /usr/bin/refdbctl stop: /usr/bin/refdbd is not running > > Am I do anything wrong? > Not necessarily. It might be a permission problem or a parsing problem of the grep output as well. After starting refdbd using refdbctl, do you see a file called "refdbd.pid" in /var/run/? If yes, could you please post the contents? Please also check the setting of the "pidfile" variable in your refdbdrc. It should have the value "/var/run/refdbd.pid" as well. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Wei-Wei G. <ww...@gm...> - 2009-05-09 03:34:52
|
Hi Markus, I got a new problem. refdbctl can start daemon, but cannot stop it. # ps -C refdbd PID TTY TIME CMD 2860 ? 00:00:00 refdbd 3255 ? 00:00:00 refdbd # refdbctl stop /usr/bin/refdbctl stop: /usr/bin/refdbd is not running Am I do anything wrong? Best wishes, Wei-Wei |
From: Wei-Wei G. <ww...@gm...> - 2009-05-09 03:32:22
|
Markus Hoenicka 写道: > It turned out that this was not a driver problem, but a bug in the > libdbi library itself. I've checked in a fix today. I assume you won't > be able to wait until the next libdbi release, which may take some > time to be picked up by package maintainers. If you feel comfortable > with installing libdbi from the sources, please use the appended patch > for src/dbi_main.c. > Thanks, it solves the problem. Best wishes, Wei-Wei |
From: Markus H. <mar...@mh...> - 2009-05-08 23:41:25
|
Wei-Wei Guo writes: > Thanks. I'd better wait since PG or MySql is kind of heavy for me. Hope the > driver problem could be solved soon :> > It turned out that this was not a driver problem, but a bug in the libdbi library itself. I've checked in a fix today. I assume you won't be able to wait until the next libdbi release, which may take some time to be picked up by package maintainers. If you feel comfortable with installing libdbi from the sources, please use the appended patch for src/dbi_main.c. regards, Markus --- dbi_main.c 2008/11/28 22:28:51 1.95 +++ dbi_main.c 2009/05/08 23:22:33 1.96 @@ -1570,8 +1574,19 @@ /* hahaha! who woulda ever thunk strawberry's code would come in handy? */ // find first (highest) bit set; methods not using FP can be found at // http://graphics.stanford.edu/~seander/bithacks.html#IntegerLogObvious - unsigned startbit = log(rangemin)/log(2); - unsigned endbit = log(rangemax)/log(2); +/* unsigned startbit = log(rangemin)/log(2); */ +/* unsigned endbit = log(rangemax)/log(2); */ + unsigned int startbit = 0; + unsigned int endbit = 0; + + while (rangemin >>= 1) { + startbit++; + } + + while (rangemax >>= 1) { + endbit++; + } + // construct mask from startbit to endbit inclusive unsigned attrib_mask = ((1<<(endbit+1))-1) ^ ((1<<startbit)-1); return attribs & attrib_mask; -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Wei-Wei G. <ww...@gm...> - 2009-05-08 15:53:14
|
Markus Hoenicka 写道: Hi Markus, Sorry for late rely. I just settled down. > I'll investigate this driver problem in the next days. I'll let you > know as soon as there are good news. Also, feel free to watch the > libdbi-drivers-devel list for further news > (http://sourceforge.net/mailarchive/forum.php?forum_name=libdbi-drivers-devel). > > Unfortunately, at this time there are only two options to get RefDB up > and running: use FreeBSD (or any other OS not affected by this bug), > or use a different database engine. > Thanks. I'd better wait since PG or MySql is kind of heavy for me. Hope the driver problem could be solved soon :> Best wishes, Wei-Wei |
From: Markus H. <mar...@mh...> - 2009-05-06 20:27:18
|
Wei-Wei Guo writes: > The new refdbd.log has 'ulonglong' now. I should restart refdbd before run > the test procedure. Yes, it is all too easy to forget this. Maybe I should have mentioned it. Your log indicates that this is apparently not a RefDB problem, but a problem of the libdbi driver which you use to access the SQLite database. We (that is, a few libdbi developers and myself) came across a platform-dependent problem with the sqlite and sqlite3 drivers just the other day. In a nutshell, these drivers do not handle 8 byte integers correctly on Linux, returning 0 instead of the real value. This is what your logs indicate as well. The id value returned by this query: 7:pid=3251:Wed May 06 10:55:45 2009:SELECT note_id, note_user_id FROM t_note WHERE note_key='wwguo-wwguo' 7:pid=3251:Wed May 06 10:55:45 2009:ulonglong: u 0<< lu 0<< llu 0 ought to be 1, which you already confirmed by running this query in the sqlite command line app. However, the driver returns 0 as indicated by the debug log output. I'll investigate this driver problem in the next days. I'll let you know as soon as there are good news. Also, feel free to watch the libdbi-drivers-devel list for further news (http://sourceforge.net/mailarchive/forum.php?forum_name=libdbi-drivers-devel). Unfortunately, at this time there are only two options to get RefDB up and running: use FreeBSD (or any other OS not affected by this bug), or use a different database engine. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Wei-Wei G. <ww...@gm...> - 2009-05-06 10:48:59
|
Markus Hoenicka 写道: > > Thanks for repeating the test. Unfortunately I can't find the additional > log output from the latest patch. There should be couple of lines > starting with either "uint:" or "ulonglong:" providing additional clues. > Could you please retry patching the sources with dbfncs.c.patch? > The new refdbd.log has 'ulonglong' now. I should restart refdbd before run the test procedure. Best wishes, Wei-Wei |
From: Markus H. <mar...@mh...> - 2009-05-06 07:49:54
|
Quoting Wei-Wei Guo <ww...@gm...>: > Markus Hoenicka 写道: >> I've checked your log output. I've designed another small patch to >> drill a bit deeper. Please apply it in addition to the previous patch >> and rebuild RefDB again. The procedure you used last time was >> apparently successful. >> > > I attached the newly produced refdbd.log with the same procedure. Thanks for repeating the test. Unfortunately I can't find the additional log output from the latest patch. There should be couple of lines starting with either "uint:" or "ulonglong:" providing additional clues. Could you please retry patching the sources with dbfncs.c.patch? thanks Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Wei-Wei G. <ww...@gm...> - 2009-05-05 23:39:31
|
Markus Hoenicka 写道: > I've checked your log output. I've designed another small patch to > drill a bit deeper. Please apply it in addition to the previous patch > and rebuild RefDB again. The procedure you used last time was > apparently successful. > I attached the newly produced refdbd.log with the same procedure. > BTW which type of processor do you use? Is it a non-x86, by any > chance? > My processor is Intel Pentium 4. Best wishes, Wei-Wei |
From: Torsten B. <br...@ph...> - 2009-05-05 23:31:24
|
Hallöchen! Markus Hoenicka writes: > [...] > > The mapping is not documented at this time except in the source > code. The tricky thing to understand is that RIS uses weird rules > to assign authors and titles to the A1-A3 and T1-T3 fields, > whereas risx attempts to use a much saner analytical=1, > monographic=2, series=3 approach. The other risx elements map to > RIS fields according to the RefMan table in a fairly > straightforward fashion. I think I can cope with RISX' semantics quite well now. I just want to grey out some fields sometimes and rename them (e.g. "article title" -- "journal title" for journal articles). I think this helps my collegues a lot because analytical vs. monographic must be learnt by them first. For this renaming, the tables in the RIS specification were helpful. What's missing is "edition" in RISX. One can use the "otherinfo" for the publishing date but this doesn't survive in BibTeX output. If you use "edition" with RIS however, RefDB creates an "edition" field for BibTeX. Additionally, the explanation of "city" should be expanded to "publication place" and not just the name of a town. In case of patents, for example, it's the name of a country. (The tag name may stay, however.) Tschö, Torsten. -- Torsten Bronger, aquisgrana, europa vetus Jabber ID: tor...@ja... |
From: Markus H. <mar...@mh...> - 2009-05-05 20:46:51
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Torsten Bronger writes: > I investigated further and now I'm slightly confused. The RefDB > manual says that RISX should be prefered for communicating with the > database, and even that it should be used for backup dumps. > However, it can't hold all the data in the database. For example, > if I store a book reference, there is a "volume" and an "edition" > field, however in RISX, only "volume" survives. In other words, the > RISX dump is not lossless. An RIS dump contains all fields, though. > If a risx dump does not contain all data, the risx backend must be considered broken. Could you please send some test data which help me reproduce the problem? thanks Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |
From: Markus H. <mar...@mh...> - 2009-05-05 20:45:13
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Torsten Bronger writes: > The data model of my front-end is RISX. Where can I get information > about how to interpret the RISX fields for the different types? > http://refdb.sourceforge.net/risx/index.html is of some help but it > is rather limited. The most comprehensive tables can be found in > <http://www.referencemanager.com/support/docs/ReferenceManager11.pdf>, > pp 525 ff. But this makes is necessary to map RISX to RIS. Is > there information about this? > The mapping is not documented at this time except in the source code. The tricky thing to understand is that RIS uses weird rules to assign authors and titles to the A1-A3 and T1-T3 fields, whereas risx attempts to use a much saner analytical=1, monographic=2, series=3 approach. The other risx elements map to RIS fields according to the RefMan table in a fairly straightforward fashion. I guess you're asking for an even larger table which shows the mapping between real world items, RIS fields, and risx elements. I realize that this information is helpful, but I won't be able to cough it up in a matter of days. > By the way, RIS seems to have four titles (primary, secondary, > series, periodical), whereas RISX has only three of them. In case > of conferences, RIS uses all four (see page 527). How is this > mapped to RISX? > risx currently does not handle four titles, as I was not able to figure out the difference between "series title" and "proceedings title". With my limited knowledge about conference proceedings I concluded these are the same, but I'm willing to learn. regards, Markus -- Markus Hoenicka mar...@ca... (Spam-protected email: replace the quadrupeds with "mhoenicka") http://www.mhoenicka.de |