refdb-devel — List for RefDB developers

Re: [Refdb-devel] refdbd maintenance mode fails

[David N. <dav...@sw...>]

David Nebauer wrote:
> After upgrading to svn revision 193 I now get an error when running 
> the command
>    refdbd -a -D "sqlite" -i "/var/lib/refdb/db"
> as part of the debian package install.  It announces the error
>    '(null)' cannot be resolved as a hostname
> and exits with a non-zero return value.

This is a quoting problem.  The postinstall script is assembling the 
following command:

    cmd="refdbd -a -D \"sqlite\" -i \"/var/lib/refdb/db\""

and executing it with a simple

    ${cmd}

This reproducibly causes the error message reported earlier.

As a matter of fact, this error is caused by the quoting of the database 
backend:

----------------------------------------------------------------------------------
# cmd="refdbd -a -D \"sqlite\" -i /var/lib/refdb/db"
# ${cmd}
'(null)' cannot be resolved as a hostname
#
----------------------------------------------------------------------------------

Quoting the main database directory causes a different error:

----------------------------------------------------------------------------------
# cmd="refdbd -a -D sqlite -i \"/var/lib/refdb/db\""
# ${cmd}
maintenance of main database failed
#
----------------------------------------------------------------------------------

Use of single quotes for the internal quoting

    cmd="refdbd -a -D 'sqlite' -i '/var/lib/refdb/db'"

produces the same error.

Removing the internal quotes entirely

    cmd="refdbd -a -D sqlite -i /var/lib/refdb/db"

solves the problem and the command executes without a problem.

At a minimum I must be able to quote the main database directory since 
the user may have placed it in a directory path containing spaces.

Regards,
David.

[Refdb-devel] refdbd maintenance mode fails

[David N. <dav...@sw...>]

After upgrading to svn revision 193 I now get an error when running the 
command

    refdbd -a -D "sqlite" -i "/var/lib/refdb/db"

as part of the debian package install.  It announces the error

    '(null)' cannot be resolved as a hostname

and exits with a non-zero return value.

Regards,
David.

[Refdb-devel] [ refdb-Bugs-1562333 ] Trainling backup copies on -pre4

[SourceForge.net <no...@so...>]

Bugs item #1562333, was opened at 2006-09-20 09:41
Message generated for change (Comment added) made by sf-robot
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1562333&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
>Status: Closed
Resolution: Accepted
Priority: 5
Submitted By: steletch (steletch)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Trainling backup copies on -pre4

Initial Comment:
Minor fix, some trailing copies are present in docs:

E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/refnumber.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citestyle.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citekey.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citstyle.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/rangeseparator.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/bibliotitle.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citseparator.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/bibstyle.html~


----------------------------------------------------------------------

>Comment By: SourceForge Robot (sf-robot)
Date: 2006-10-04 19:20

Message:
Logged In: YES 
user_id=1312539

This Tracker item was closed automatically by the system. It was
previously set to a Pending status, and the original submitter
did not respond within 14 days (the time period specified by
the administrator of this Tracker).

----------------------------------------------------------------------

Comment By: Markus Hoenicka (mhoenicka)
Date: 2006-09-20 15:07

Message:
Logged In: YES 
user_id=85809

I've tried to fix this by adding a command to dist-hook
which is supposed to remove the backup files. This doesn't
work, although the same trick does work for the .svn
subdirectories.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1562333&group_id=26091

Re: [Refdb-devel] upgrading the main database

[Markus H. <mar...@mh...>]

David Nebauer writes:
 > You may wish to reverse the recent change to refdbd.
 > 

It doesn't hurt as it will kick in only in very obscure
circumstances, if at all. I'll just leave it as it is.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-devel] Debian packages use debconf for preconfigure and postinstall

[David N. <dav...@sw...>]

The refdb-server package now uses debconf to preconfigure for the 
postinstall script.  It attempts to determine which database backend is 
being used and, if necessary, asks for username and password.

All version testing using DB_VERSION has been stripped as the package 
now relies entirely on refdbd's maintenance mode to upgrade the main 
database when necessary.  It also relies on refdbd to create the main 
database after a fresh install.

Regards,
David.

Re: [Refdb-devel] upgrading the main database

[David N. <dav...@sw...>]

Hi Markus,
> refdbd only requires a username if you use the -a or -c switches. In this case
> no client connection can provide the username and password required to connect
> to the database server. However, you are right that this does not make much
> sense in the case of SQLite. Actually refdbd attempts to guess a username using
> the getlogin() function if none is provided. This is sufficient on all systems
> that I've tested so far. I have no idea why this fails on your system. I've
> changed refdbd to use a dummy username "root" if getlogin() fails. Please check
> whether this fixes the problem.

Mystery solved.  The problem was with my refdbd command.  I was passing 
to the '-i' parameter the full filepath to the database file itself 
</var/lib/refdb/db/refdb> instead of the path to the database 
*directory* </var/lib/refdb/db>.  When I used the latter value the 
command worked fine.

You may wish to reverse the recent change to refdbd.

Regards,
David.

Re: [Refdb-devel] upgrading the main database

[Markus H. <mar...@mh...>]

Hi David,

David Nebauer <dav...@sw...> was heard to say:

> refdbd is now failing unless a username is supplied.  Here is the
> feedback if there is no username:
[...]
> refdbd has not previously required a username when running an sqlite
> backend.
>

refdbd only requires a username if you use the -a or -c switches. In this case
no client connection can provide the username and password required to connect
to the database server. However, you are right that this does not make much
sense in the case of SQLite. Actually refdbd attempts to guess a username using
the getlogin() function if none is provided. This is sufficient on all systems
that I've tested so far. I have no idea why this fails on your system. I've
changed refdbd to use a dummy username "root" if getlogin() fails. Please check
whether this fixes the problem.

> When a spurious username is supplied it attempts to run but still fails:
>
[...]
>
> The database location is correct.
>

Do you have write permissions in the database directory? I see no other reason
why this should fail. I've tested this on FreeBSD and Windows/Cygwin
successfully. I'll give it a try on the weekend on a Debian box to make sure.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-devel] upgrading the main database

[David N. <dav...@sw...>]

Hi Markus,
> refdbd will display some messages and exit. Similarly, to upgrade an
> existing main database, run something like this:
>
> refdbd -a -D sqlite3 -e 0 -l 7 -i /path/to/db

refdbd is now failing unless a username is supplied.  Here is the 
feedback if there is no username:

---------------------------------------------------------------------------------------
# refdbd -a -D sqlite -e 0 -l 7 -i /var/lib/refdb/db/refdb
incorrect username
# refdbctl start
incorrect username
/usr/bin/refdbctl start: bibliography tool application server could not 
be started
/
#
---------------------------------------------------------------------------------------

refdbd has not previously required a username when running an sqlite 
backend.

When a spurious username is supplied it attempts to run but still fails:

---------------------------------------------------------------------------------------
# refdbd -a -D sqlite -u spurious -e 0 -l 7 -i /var/lib/refdb/db/refdb
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
sqlite3
mysql
pgsql
sqlite
Requested libdbi driver found
Database directory:
/var/lib/refdb/db/refdb
check main database version
localhost
david



sqlite
/var/lib/refdb/db/refdb
UTF-8
refdb
failed to connect to database server using database:
refdb
libdbi could not establish a connection
could not open main database
Can't access or create SQLite database
maintenance of main database failed
#
---------------------------------------------------------------------------------------

The database location is correct.

Regards,
David.

Re: [Refdb-devel] upgrading the main database

[Markus H. <mar...@mh...>]

Markus Hoenicka <mar...@mh...> was heard to say:

> > The postinstall script checks for a main refdb database.  If none is
> > found it automatically creates a main sqlite database using the sqlite
> > dump.  Now that you have versioned the dump files it will be difficult
> > for the postinstall script to know which dump file to import.  I could
> > include a loop in which it checks each refdb.[ver].dump.sqlite and
> > determines the largest 'ver'.  It would be easier, however, for me (and,
> > I presume, other packagers) if the newest dump file had a predictable,
> > stable name.  Could you call the newest version 'refdb.dump.sqlite' with
> > only older versions numbered?  When the newest version is replaced it
> > would then be renamed to include the version number and the replacement
> > (now the newest) would receive the unversioned name.  Alternately, and
> > to avoid any possible confusion, the newest dump might be called
> > 'refdb.newest.dump.sqlite' or 'refdb.latest.dump.sqlite'.
> >
>
> I was thinking along these lines too. I think I'll reverse the current
> filenames
> to refdb.dump.sqlite and version only the older ones.
>

Now that I turned my brain on again (it must have been offline yesterday...),
renaming the files is not necessary. Your postinstall script should simply rely
on refdbd -a doing the right thing if it is run unconditionally. As mentioned
before, if the main database is at the current version, this command will do
nothing. If the main database is too old, it will be upgraded. If there is no
main database, it will be created. Therefore you no longer need to know which
dump file to use, and you no longer need a dependency on the sqlite binary
either. refdbd -a will do all this for you.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-devel] upgrading the main database

[Markus H. <mar...@mh...>]

Hi David,

David Nebauer <dav...@sw...> was heard to say:

> The easiest thing to do from a packager's point of view would be to run
> this command unconditionally as part of the postinstall process.  The
> reason is that it is difficult to tell the new db version immediately
> after installation but before the daemon has been started.  Can running
> the upgrade after each server upgrade cause harm?  I hope refdbd is
> smart enough to know when an upgrade is unnecessary and can be skipped.
>

You can do just this. If refdbd -a notices that the installed main database is
already at the latest version, it does nothing.

> The postinstall script checks for a main refdb database.  If none is
> found it automatically creates a main sqlite database using the sqlite
> dump.  Now that you have versioned the dump files it will be difficult
> for the postinstall script to know which dump file to import.  I could
> include a loop in which it checks each refdb.[ver].dump.sqlite and
> determines the largest 'ver'.  It would be easier, however, for me (and,
> I presume, other packagers) if the newest dump file had a predictable,
> stable name.  Could you call the newest version 'refdb.dump.sqlite' with
> only older versions numbered?  When the newest version is replaced it
> would then be renamed to include the version number and the replacement
> (now the newest) would receive the unversioned name.  Alternately, and
> to avoid any possible confusion, the newest dump might be called
> 'refdb.newest.dump.sqlite' or 'refdb.latest.dump.sqlite'.
>

I was thinking along these lines too. I think I'll reverse the current filenames
to refdb.dump.sqlite and version only the older ones.

regards,
Markus


-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-devel] DB_VERSION redux

[Markus H. <mar...@mh...>]

David Nebauer <dav...@sw...> was heard to say:

> I ran the server in standalone mode to capture log output and, lo and
> behold, the version file updated on the first database read.  No idea
> why earlier attempts failed.
>

Come to think of it, the version file will not be updated if you run refdbd -a.
This will update the main database if necessary, but the version file gets
updated only as soon as refdbd forks to handle a client request. I probably ran
refdbd -s after each refdbd -a run to see whether refdbd starts up correctly.
Therefore I always saw the version file being updated.

Would it be hard to change your install scripts and get rid of DB_VERSION in
favour of a refdbd -c call? I'd suggest to drop DB_VERSION then. I could also
make the refdbd -c output easier to parse.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-devel] upgrading the main database

[David N. <dav...@sw...>]

Hi Markus,
> To check the connection to the database engine and to read out the
> version of the main database, run something like this:
>
> refdbd -c -D sqlite3 -e 0 -l 7 -i /path/to/db 2>&1|grep "version:"
>
> refdbd will display some messages and exit. Similarly, to upgrade an
> existing main database, run something like this:
>
> refdbd -a -D sqlite3 -e 0 -l 7 -i /path/to/db

The easiest thing to do from a packager's point of view would be to run 
this command unconditionally as part of the postinstall process.  The 
reason is that it is difficult to tell the new db version immediately 
after installation but before the daemon has been started.  Can running 
the upgrade after each server upgrade cause harm?  I hope refdbd is 
smart enough to know when an upgrade is unnecessary and can be skipped.

> David, if you use the latter in your Debian package postinstall
> script, you may have to explicitly name the database engine and the
> default database location as shown here because the user may have
> changed these settings in refdbdrc after the package was installed. Of
> course you'd run it without dumping the debug log messages to the
> screen.

The postinstall script already checks /etc/refdb/refdbdrc for an 
alternate dbpath.  It is a simple matter to also check the database engine.

> In order to make the upgrades possible in future releases I've
> versioned the refdb dump files. That is, refdb.dump.sqlite(.in) was
> renamed to refdb.2.dump.sqlite(.in) and so on. Future releases will
> probably have to provide several dump files of older database versions
> in order to allow upgrades from these older versions.

The postinstall script checks for a main refdb database.  If none is 
found it automatically creates a main sqlite database using the sqlite 
dump.  Now that you have versioned the dump files it will be difficult 
for the postinstall script to know which dump file to import.  I could 
include a loop in which it checks each refdb.[ver].dump.sqlite and 
determines the largest 'ver'.  It would be easier, however, for me (and, 
I presume, other packagers) if the newest dump file had a predictable, 
stable name.  Could you call the newest version 'refdb.dump.sqlite' with 
only older versions numbered?  When the newest version is replaced it 
would then be renamed to include the version number and the replacement 
(now the newest) would receive the unversioned name.  Alternately, and 
to avoid any possible confusion, the newest dump might be called 
'refdb.newest.dump.sqlite' or 'refdb.latest.dump.sqlite'.

Regards,
David.

Re: [Refdb-devel] DB_VERSION redux

[David N. <dav...@sw...>]

Hi Markus,
>  > The change in database version in svn has exposed some problems.  First, 
>  > use of refdba and refdbc has not caused /var/lib/refdb/db/DB_VERSION to 
>  > increment from 1 to 2.  I've restarted the refdbd daemon and run clients 
>  > as root but it stays at '1'.  I haven't yet investigated log messages.
>  > 
>
> They should be informative. Just grep for "version file". Let me know
> what you find. The upgrade did work on my box. DB_VERSION contains a
> '2' here without any manual intervention.

I ran the server in standalone mode to capture log output and, lo and 
behold, the version file updated on the first database read.  No idea 
why earlier attempts failed.

Regards,
David.

[Refdb-devel] [ refdb-Bugs-1562331 ] some warnings on 0.9.8-pre4

[SourceForge.net <no...@so...>]

Bugs item #1562331, was opened at 2006-09-20 18:39
Message generated for change (Comment added) made by steletch
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1562331&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
>Status: Open
Resolution: Fixed
Priority: 5
Submitted By: steletch (steletch)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: some warnings on 0.9.8-pre4

Initial Comment:
Since some may be harmful, here is the complete list
(unfortunately not providing a patch though, others may):

refdbdref.c:667: warning: passing argument 2 of 'iconv'
from incompatible pointer type
refdbdbib.c:917: warning: passing argument 2 of 'iconv'
from incompatible pointer type
refdbdbib.c:1016: warning: passing argument 2 of
'iconv' from incompatible pointer type
strfncs.c:961:21: warning: unknown escape sequence '\`'
strfncs.c:971:19: warning: unknown escape sequence '\`'
risdb.c:3955: warning: passing argument 2 of 'iconv'
from incompatible pointer type
noteshandler.c:756: warning: passing argument 2 of
'iconv' from incompatible pointer type
risxhandler.c:758: warning: passing argument 2 of
'iconv' from incompatible pointer type
refdbdnote.c:2219: warning: passing argument 2 of
'iconv' from incompatible pointer type
refdbdgetref.c:2680: warning: passing argument 2 of
'iconv' from incompatible pointer type
refdbib.c:777: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
passwd.c:73: warning: incompatible implicit declaration
of built-in function 'strlen'
refdbc.c:3299: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdbc.c:3336: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdbc.c:3978: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdba.c:1989: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdba.c:2048: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result

----------------------------------------------------------------------

>Comment By: steletch (steletch)
Date: 2006-09-21 11:04

Message:
Logged In: YES 
user_id=1129476

Yep, i know for the iconv warning, but having it and
bugzilla may ping someone else ;-)

----------------------------------------------------------------------

Comment By: Markus Hoenicka (mhoenicka)
Date: 2006-09-21 00:02

Message:
Logged In: YES 
user_id=85809

I've fixed all but the "iconv" warnings. I've mentioned in
the refdb-user list before that this problem can be fixed
either for Linux or for *BSD, but not for both. The other
warnings were harmless in their context, but I silenced them
anyway.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1562331&group_id=26091

[Refdb-devel] [ refdb-Bugs-1562333 ] Trainling backup copies on -pre4

[SourceForge.net <no...@so...>]

Bugs item #1562333, was opened at 2006-09-20 18:41
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1562333&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
>Status: Pending
>Resolution: Accepted
Priority: 5
Submitted By: steletch (steletch)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Trainling backup copies on -pre4

Initial Comment:
Minor fix, some trailing copies are present in docs:

E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/refnumber.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citestyle.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citekey.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citstyle.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/rangeseparator.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/bibliotitle.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citseparator.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/bibstyle.html~


----------------------------------------------------------------------

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2006-09-21 00:07

Message:
Logged In: YES 
user_id=85809

I've tried to fix this by adding a command to dist-hook
which is supposed to remove the backup files. This doesn't
work, although the same trick does work for the .svn
subdirectories.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1562333&group_id=26091

[Refdb-devel] [ refdb-Bugs-1562331 ] some warnings on 0.9.8-pre4

[SourceForge.net <no...@so...>]

Bugs item #1562331, was opened at 2006-09-20 18:39
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1562331&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Submitted By: steletch (steletch)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: some warnings on 0.9.8-pre4

Initial Comment:
Since some may be harmful, here is the complete list
(unfortunately not providing a patch though, others may):

refdbdref.c:667: warning: passing argument 2 of 'iconv'
from incompatible pointer type
refdbdbib.c:917: warning: passing argument 2 of 'iconv'
from incompatible pointer type
refdbdbib.c:1016: warning: passing argument 2 of
'iconv' from incompatible pointer type
strfncs.c:961:21: warning: unknown escape sequence '\`'
strfncs.c:971:19: warning: unknown escape sequence '\`'
risdb.c:3955: warning: passing argument 2 of 'iconv'
from incompatible pointer type
noteshandler.c:756: warning: passing argument 2 of
'iconv' from incompatible pointer type
risxhandler.c:758: warning: passing argument 2 of
'iconv' from incompatible pointer type
refdbdnote.c:2219: warning: passing argument 2 of
'iconv' from incompatible pointer type
refdbdgetref.c:2680: warning: passing argument 2 of
'iconv' from incompatible pointer type
refdbib.c:777: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
passwd.c:73: warning: incompatible implicit declaration
of built-in function 'strlen'
refdbc.c:3299: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdbc.c:3336: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdbc.c:3978: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdba.c:1989: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdba.c:2048: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result

----------------------------------------------------------------------

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2006-09-21 00:02

Message:
Logged In: YES 
user_id=85809

I've fixed all but the "iconv" warnings. I've mentioned in
the refdb-user list before that this problem can be fixed
either for Linux or for *BSD, but not for both. The other
warnings were harmless in their context, but I silenced them
anyway.

----------------------------------------------------------------------

You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1562331&group_id=26091

[Refdb-devel] [ refdb-Bugs-1562333 ] Trainling backup copies on -pre4

[SourceForge.net <no...@so...>]

Bugs item #1562333, was opened at 2006-09-20 18:41
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1562333&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: steletch (steletch)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Trainling backup copies on -pre4

Initial Comment:
Minor fix, some trailing copies are present in docs:

E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/refnumber.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citestyle.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citekey.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citstyle.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/rangeseparator.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/bibliotitle.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/citseparator.html~
E: refdb backup-file-in-package
/usr/share/doc/refdb-0.9.8/citestylex/ele-desc/bibstyle.html~


----------------------------------------------------------------------

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[Refdb-devel] [ refdb-Bugs-1562331 ] some warnings on 0.9.8-pre4

[SourceForge.net <no...@so...>]

Bugs item #1562331, was opened at 2006-09-20 18:39
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1562331&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: steletch (steletch)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: some warnings on 0.9.8-pre4

Initial Comment:
Since some may be harmful, here is the complete list
(unfortunately not providing a patch though, others may):

refdbdref.c:667: warning: passing argument 2 of 'iconv'
from incompatible pointer type
refdbdbib.c:917: warning: passing argument 2 of 'iconv'
from incompatible pointer type
refdbdbib.c:1016: warning: passing argument 2 of
'iconv' from incompatible pointer type
strfncs.c:961:21: warning: unknown escape sequence '\`'
strfncs.c:971:19: warning: unknown escape sequence '\`'
risdb.c:3955: warning: passing argument 2 of 'iconv'
from incompatible pointer type
noteshandler.c:756: warning: passing argument 2 of
'iconv' from incompatible pointer type
risxhandler.c:758: warning: passing argument 2 of
'iconv' from incompatible pointer type
refdbdnote.c:2219: warning: passing argument 2 of
'iconv' from incompatible pointer type
refdbdgetref.c:2680: warning: passing argument 2 of
'iconv' from incompatible pointer type
refdbib.c:777: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
passwd.c:73: warning: incompatible implicit declaration
of built-in function 'strlen'
refdbc.c:3299: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdbc.c:3336: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdbc.c:3978: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdba.c:1989: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result
refdba.c:2048: warning: ignoring return value of
'fwrite', declared with attribute warn_unused_result

----------------------------------------------------------------------

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[Refdb-devel] [ refdb-Bugs-1559912 ] Prevent use of -ID in citation keys

[SourceForge.net <no...@so...>]

Bugs item #1559912, was opened at 2006-09-16 23:40
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1559912&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
>Status: Closed
>Resolution: Fixed
Priority: 5
Submitted By: Markus Hoenicka (mhoenicka)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Prevent use of -ID in citation keys

Initial Comment:
The character sequence "-ID" is used to separate the
(optional) database name from the citation key or ID
proper in citations. If a citation key contains the
sequence "-ID" somewhere, as in
"Johnson2001The-Idea-of-ICA", creating bibliographies
will fail. refdbd must not accept or create such
citation keys.

----------------------------------------------------------------------

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2006-09-19 10:33

Message:
Logged In: YES 
user_id=85809

fixed in svn. refdbd now replaces "-ID" with "_ID" to avoid
this problem.

----------------------------------------------------------------------

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[Refdb-devel] [ refdb-Bugs-1559912 ] Prevent use of -ID in citation keys

[SourceForge.net <no...@so...>]

Bugs item #1559912, was opened at 2006-09-16 23:40
Message generated for change (Tracker Item Submitted) made by Item Submitter
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1559912&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: None
Group: None
Status: Open
Resolution: None
Priority: 5
Submitted By: Markus Hoenicka (mhoenicka)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Prevent use of -ID in citation keys

Initial Comment:
The character sequence "-ID" is used to separate the
(optional) database name from the citation key or ID
proper in citations. If a citation key contains the
sequence "-ID" somewhere, as in
"Johnson2001The-Idea-of-ICA", creating bibliographies
will fail. refdbd must not accept or create such
citation keys.

----------------------------------------------------------------------

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Re: [Refdb-devel] upgrading the main database

[David N. <dav...@sw...>]

Hi Markus,
> Similarly, to upgrade an
> existing main database, run something like this:
>
> refdbd -a -D sqlite3 -e 0 -l 7 -i /path/to/db
>
> David, if you use the latter in your Debian package postinstall
> script, you may have to explicitly name the database engine and the
> default database location as shown here because the user may have
> changed these settings in refdbdrc after the package was installed. Of
> course you'd run it without dumping the debug log messages to the
> screen.

Thanks for adding this feature with your customary speed.  I'm afraid I 
won't get around to building the new debs till later this week as I have 
a few other things on my plate.

Regards,
David.

[Refdb-devel] upgrading the main database

[Markus H. <mar...@mh...>]

Hi,

the current SVN version (revision 167) implements a first stab at the
main database upgrading mechanism required for smooth upgrades of
packages and ports. It is currently only implemented for
SQLite/SQLite3, but the implementation for MySQL and PostgreSQL is
mainly monkey business. I'll try to add that code during the next
week.

In addition to the standalone and daemonized ways of running refdbd
there is an additional mode now. You can use it to either check the
database connection or to upgrade an existing main database. In both
cases refdbd will evaluate <prefix>/etc/refdb/refdbdrc as usual, so
you may get away using the existing connection parameters.

To check the connection to the database engine and to read out the
version of the main database, run something like this:

refdbd -c -D sqlite3 -e 0 -l 7 -i /path/to/db 2>&1|grep "version:"

refdbd will display some messages and exit. Similarly, to upgrade an
existing main database, run something like this:

refdbd -a -D sqlite3 -e 0 -l 7 -i /path/to/db

David, if you use the latter in your Debian package postinstall
script, you may have to explicitly name the database engine and the
default database location as shown here because the user may have
changed these settings in refdbdrc after the package was installed. Of
course you'd run it without dumping the debug log messages to the
screen.

In order to make the upgrades possible in future releases I've
versioned the refdb dump files. That is, refdb.dump.sqlite(.in) was
renamed to refdb.2.dump.sqlite(.in) and so on. Future releases will
probably have to provide several dump files of older database versions
in order to allow upgrades from these older versions.

Please give the upgrade code a try. I use a 0.9.7 version to create
the database and to add a few styles. Then I try to upgrade it with
the current SVN version. Finally I read out the styles with
the SVN version. So far the tests looked ok.

regards,
Markus

-- 
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

[Refdb-devel] [ refdb-Bugs-1550514 ] Trouble while importing chapters

[SourceForge.net <no...@so...>]

Bugs item #1550514, was opened at 2006-09-01 15:15
Message generated for change (Comment added) made by dreusser
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1550514&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
>Status: Closed
Resolution: Works For Me
Priority: 5
Submitted By: Dominik (dreusser)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Trouble while importing chapters

Initial Comment:
Queries are not assembled correctly (cutting of either
the refdb_title or redb_booktitile) while importing
chapters from a file with multiple records. For some
reason, writing the records to a seprate file and
importing from there works for some records. I attached
a file with example records that failed.


Example 1
----------
UPDATE t_refdb SET refdb_pubyear=2003, refdb_secyear=0,
refdb_pyother_info='///', refdb_secother_info=NULL,
refdb_citekey='Bardsley2003a', refdb_user1=NULL,
refdb_user2='schaeffli', refdb_user3=NULL,
refdb_user4=NULL, refdb_user5=NULL, refdb_misc1=NULL,
refdb_misc2=NULL, refdb_misc3=NULL, refdb_issn=NULL,
refdb_issue=NULL, refdb_publisher='IAHS Publication no.
281', refdb_city='Wallingford, Oxfordshire UK',
refdb_volume=NULL, refdb_endpage='74',
refdb_startpage='67', refdb_type='CHAP',
refdb_booktitle='Water resources systems - hydrological
risk, management and development  (Proceedings of an
international symposium the XXIII General Assembly of
the International Union of Geodesy and Geophysics, at
Sapporo, Japan, from 30 June to 11 July 2003)',
refdb_title='An approach to creating lumped-parameter
rainfall-runoff models for drainage basins experiencing
envrionemental WHERE refdb_id=2393
1064: You have an error in your SQL syntax; check the
manual that corresponds to your MySQL server version
for the right syntax to use near ''An approach to
creating lumped-parameter rainfall-runoff models
inserting reference data failed

Example 2
---------
UPDATE t_refdb SET refdb_pubyear=1998, refdb_secyear=0,
refdb_pyother_info='///', refdb_secother_info=NULL,
refdb_citekey='Aizen1998', refdb_user1=NULL,
refdb_user2='schaeffli', refdb_user3=NULL,
refdb_user4=NULL, refdb_user5=NULL, refdb_misc1=NULL,
refdb_misc2=NULL, refdb_misc3=NULL, refdb_issn=NULL,
refdb_issue=NULL, refdb_publisher='IAHS Publication No.
248', refdb_city='Wallingford, Oxfordshire UK',
refdb_volume=NULL, refdb_endpage='198',
refdb_startpage='191', refdb_type='CHAP',
refdb_booktitle='Hydrology, Water Resources and Ecology
in Headwaters (P, refdb_title='Estimation of glacial
runoff to the Tarim River, central Tien Shan' WHERE
refdb_id=2352
1064: You have an error in your SQL syntax; check the
manual that corresponds to your MySQL server version
for the right syntax to use near 'Estimation of glacial
runoff to the Tarim River, central Tien Sh
inserting reference data failed

refdb-bug:
Linux aare 2.6.17-1-686 #1 SMP Sat Jul 29 15:32:47 UTC
2006 i686 GNU/Linux
RefDB binaries and scripts in the path:
/usr/bin/refdbd
/usr/bin/refdba
/usr/bin/refdbc
/usr/bin/refdbib
/usr/bin/bib2ris
and their version numbers:
refdbd 0.9.8-pre2
refdba 0.9.8-pre2
refdbc 0.9.8-pre2
refdbib 0.9.8-pre2
/usr/bin/refdb-bug: line 41: nmed2ris: command not found
bib2ris 0.9.8-pre2
DSSSL engines in the path:
and their version numbers:

$REFDBLIB is /usr/share/refdb
global refdbd config file:
refdblib /usr/share/refdb
serverip        localhost
dbsport 3306
dbserver        mysql
dbpath          /var/lib/refdb/db
port    9734
logfile /var/log/refdbd.log
logdest file
loglevel info
pidfile         /var/run/refdbd.pid
remoteadmin f
remoteconnect f
keep_pnames t
keyword_scan t
db_encoding
in_encoding     UTF-8

global refdba config file:
serverip        127.0.0.1
port    9734
pager   less
username        joeuser
passwd  <protected>
logdest file
loglevel info
logfile /var/log/refdba.log

global refdbc config file:
serverip        127.0.0.1
port    9734
pager   less
username        joeuser
passwd  <protected>
logdest file
loglevel info
logfile /var/log/refdbc.log
cssurl /usr/share/refdb/css/refdb.css
fromencoding UTF-8
toencoding UTF-8

global refdbc config file (cgi):

global refdbib config file:

global nmed2ris config file:

global bib2ris config file:

$HOME is /home/dreusser
user refdba config file:

user refdba config file (hidden):
serverip        127.0.0.1
username        root
passwd          <protected>
pager           less
toencoding      ISO-8859-1
fromencoding    ISO-8859-1

user refdbc config file:

user refdbc config file (hidden):
serverip        127.0.0.1
username        dominik
passwd          <protected>
defaultdb       hykli
pager           less
toencoding      ISO-8859-1
fromencoding    ISO-8859-1

user refdbib config file:

user refdbib config file (hidden):
serverip        127.0.0.1
username        dominik
passwd          <protected>
defaultdb       refdb_test
pager           less
toencoding      ISO-8859-1

user nmed2ris config file:

user nmed2ris config file (hidden):

user bib2ris config file:

user bib2ris config file (hidden):
logfile bib2ris.log
logdest 2
loglevel 7
nsf_abstract N2
nsf_url UR
nsf_url2 UR
nsf_pdf UR
nsf_keywords KW
nsf_owner U2
nsf_comment U3
nsf_issn SN


----------------------------------------------------------------------

>Comment By: Dominik (dreusser)
Date: 2006-09-08 16:06

Message:
Logged In: YES 
user_id=1572139

I agree that the problem probably is related to my box.
Sorry for taking up your time... 

----------------------------------------------------------------------

Comment By: Markus Hoenicka (mhoenicka)
Date: 2006-09-07 20:57

Message:
Logged In: YES 
user_id=85809

I've sent this problem to the user list without any
response. I reckon that this is not a general problem, but a
problem on a particular (probably screwed-up) box. I'm
afraid that trying to debug this on the affected box is
above my head, as the code that assembles the query strings
is fairly straightforward and not likely to fail just so. We
might end up debugging your system instead of debugging
RefDB. Therefore I suggest to close this bug for the time
being. Whenever you can reproduce this behaviour on a
different system, feel free to open the bug report again.

BTW I assume you have tried the obvious, like rebuilding
/reinstalling RefDB and all libraries it depends on.

----------------------------------------------------------------------

Comment By: Dominik (dreusser)
Date: 2006-09-07 14:19

Message:
Logged In: YES 
user_id=1572139

I still get similar errors with the 0.9.8-pre3 version on
the same system. Importing works on a different system which
I just set up. Either we'll drop the issue or I can provide
you an account on my "broken" system. 

----------------------------------------------------------------------

Comment By: Markus Hoenicka (mhoenicka)
Date: 2006-09-02 01:36

Message:
Logged In: YES 
user_id=85809

I've never encountered problems like this one on any of my
installations. To make sure I've installed 0.9.8-pre3 (the
only difference to pre2 is the inclusion of two headers in
refdbdgetref.c to avoid compiler errors) on a pristine
Debian 3.1 box. I can import your test data without any
problems.

I'll post a message to the refdb-users list to see whether
anyone else has seen this. Unless we can pin down the
environment or the circumstances that lead to this problem,
I'll not be able to fix it.


----------------------------------------------------------------------

Comment By: Dominik (dreusser)
Date: 2006-09-01 15:33

Message:
Logged In: YES 
user_id=1572139

It is not just while adding chapters. But I haven't found
out when addref fails exactly..

----------------------------------------------------------------------

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[Refdb-devel] [ refdb-Bugs-1550514 ] Trouble while importing chapters

[SourceForge.net <no...@so...>]

Bugs item #1550514, was opened at 2006-09-01 15:15
Message generated for change (Comment added) made by mhoenicka
You can respond by visiting: 
https://sourceforge.net/tracker/?func=detail&atid=385991&aid=1550514&group_id=26091

Please note that this message will contain a full copy of the comment thread,
including the initial issue submission, for this request,
not just the latest update.
Category: refdbd
Group: None
Status: Open
Resolution: Works For Me
Priority: 5
Submitted By: Dominik (dreusser)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Trouble while importing chapters

Initial Comment:
Queries are not assembled correctly (cutting of either
the refdb_title or redb_booktitile) while importing
chapters from a file with multiple records. For some
reason, writing the records to a seprate file and
importing from there works for some records. I attached
a file with example records that failed.


Example 1
----------
UPDATE t_refdb SET refdb_pubyear=2003, refdb_secyear=0,
refdb_pyother_info='///', refdb_secother_info=NULL,
refdb_citekey='Bardsley2003a', refdb_user1=NULL,
refdb_user2='schaeffli', refdb_user3=NULL,
refdb_user4=NULL, refdb_user5=NULL, refdb_misc1=NULL,
refdb_misc2=NULL, refdb_misc3=NULL, refdb_issn=NULL,
refdb_issue=NULL, refdb_publisher='IAHS Publication no.
281', refdb_city='Wallingford, Oxfordshire UK',
refdb_volume=NULL, refdb_endpage='74',
refdb_startpage='67', refdb_type='CHAP',
refdb_booktitle='Water resources systems - hydrological
risk, management and development  (Proceedings of an
international symposium the XXIII General Assembly of
the International Union of Geodesy and Geophysics, at
Sapporo, Japan, from 30 June to 11 July 2003)',
refdb_title='An approach to creating lumped-parameter
rainfall-runoff models for drainage basins experiencing
envrionemental WHERE refdb_id=2393
1064: You have an error in your SQL syntax; check the
manual that corresponds to your MySQL server version
for the right syntax to use near ''An approach to
creating lumped-parameter rainfall-runoff models
inserting reference data failed

Example 2
---------
UPDATE t_refdb SET refdb_pubyear=1998, refdb_secyear=0,
refdb_pyother_info='///', refdb_secother_info=NULL,
refdb_citekey='Aizen1998', refdb_user1=NULL,
refdb_user2='schaeffli', refdb_user3=NULL,
refdb_user4=NULL, refdb_user5=NULL, refdb_misc1=NULL,
refdb_misc2=NULL, refdb_misc3=NULL, refdb_issn=NULL,
refdb_issue=NULL, refdb_publisher='IAHS Publication No.
248', refdb_city='Wallingford, Oxfordshire UK',
refdb_volume=NULL, refdb_endpage='198',
refdb_startpage='191', refdb_type='CHAP',
refdb_booktitle='Hydrology, Water Resources and Ecology
in Headwaters (P, refdb_title='Estimation of glacial
runoff to the Tarim River, central Tien Shan' WHERE
refdb_id=2352
1064: You have an error in your SQL syntax; check the
manual that corresponds to your MySQL server version
for the right syntax to use near 'Estimation of glacial
runoff to the Tarim River, central Tien Sh
inserting reference data failed

refdb-bug:
Linux aare 2.6.17-1-686 #1 SMP Sat Jul 29 15:32:47 UTC
2006 i686 GNU/Linux
RefDB binaries and scripts in the path:
/usr/bin/refdbd
/usr/bin/refdba
/usr/bin/refdbc
/usr/bin/refdbib
/usr/bin/bib2ris
and their version numbers:
refdbd 0.9.8-pre2
refdba 0.9.8-pre2
refdbc 0.9.8-pre2
refdbib 0.9.8-pre2
/usr/bin/refdb-bug: line 41: nmed2ris: command not found
bib2ris 0.9.8-pre2
DSSSL engines in the path:
and their version numbers:

$REFDBLIB is /usr/share/refdb
global refdbd config file:
refdblib /usr/share/refdb
serverip        localhost
dbsport 3306
dbserver        mysql
dbpath          /var/lib/refdb/db
port    9734
logfile /var/log/refdbd.log
logdest file
loglevel info
pidfile         /var/run/refdbd.pid
remoteadmin f
remoteconnect f
keep_pnames t
keyword_scan t
db_encoding
in_encoding     UTF-8

global refdba config file:
serverip        127.0.0.1
port    9734
pager   less
username        joeuser
passwd  <protected>
logdest file
loglevel info
logfile /var/log/refdba.log

global refdbc config file:
serverip        127.0.0.1
port    9734
pager   less
username        joeuser
passwd  <protected>
logdest file
loglevel info
logfile /var/log/refdbc.log
cssurl /usr/share/refdb/css/refdb.css
fromencoding UTF-8
toencoding UTF-8

global refdbc config file (cgi):

global refdbib config file:

global nmed2ris config file:

global bib2ris config file:

$HOME is /home/dreusser
user refdba config file:

user refdba config file (hidden):
serverip        127.0.0.1
username        root
passwd          <protected>
pager           less
toencoding      ISO-8859-1
fromencoding    ISO-8859-1

user refdbc config file:

user refdbc config file (hidden):
serverip        127.0.0.1
username        dominik
passwd          <protected>
defaultdb       hykli
pager           less
toencoding      ISO-8859-1
fromencoding    ISO-8859-1

user refdbib config file:

user refdbib config file (hidden):
serverip        127.0.0.1
username        dominik
passwd          <protected>
defaultdb       refdb_test
pager           less
toencoding      ISO-8859-1

user nmed2ris config file:

user nmed2ris config file (hidden):

user bib2ris config file:

user bib2ris config file (hidden):
logfile bib2ris.log
logdest 2
loglevel 7
nsf_abstract N2
nsf_url UR
nsf_url2 UR
nsf_pdf UR
nsf_keywords KW
nsf_owner U2
nsf_comment U3
nsf_issn SN


----------------------------------------------------------------------

>Comment By: Markus Hoenicka (mhoenicka)
Date: 2006-09-07 20:57

Message:
Logged In: YES 
user_id=85809

I've sent this problem to the user list without any
response. I reckon that this is not a general problem, but a
problem on a particular (probably screwed-up) box. I'm
afraid that trying to debug this on the affected box is
above my head, as the code that assembles the query strings
is fairly straightforward and not likely to fail just so. We
might end up debugging your system instead of debugging
RefDB. Therefore I suggest to close this bug for the time
being. Whenever you can reproduce this behaviour on a
different system, feel free to open the bug report again.

BTW I assume you have tried the obvious, like rebuilding
/reinstalling RefDB and all libraries it depends on.

----------------------------------------------------------------------

Comment By: Dominik (dreusser)
Date: 2006-09-07 14:19

Message:
Logged In: YES 
user_id=1572139

I still get similar errors with the 0.9.8-pre3 version on
the same system. Importing works on a different system which
I just set up. Either we'll drop the issue or I can provide
you an account on my "broken" system. 

----------------------------------------------------------------------

Comment By: Markus Hoenicka (mhoenicka)
Date: 2006-09-02 01:36

Message:
Logged In: YES 
user_id=85809

I've never encountered problems like this one on any of my
installations. To make sure I've installed 0.9.8-pre3 (the
only difference to pre2 is the inclusion of two headers in
refdbdgetref.c to avoid compiler errors) on a pristine
Debian 3.1 box. I can import your test data without any
problems.

I'll post a message to the refdb-users list to see whether
anyone else has seen this. Unless we can pin down the
environment or the circumstances that lead to this problem,
I'll not be able to fix it.


----------------------------------------------------------------------

Comment By: Dominik (dreusser)
Date: 2006-09-01 15:33

Message:
Logged In: YES 
user_id=1572139

It is not just while adding chapters. But I haven't found
out when addref fails exactly..

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[Refdb-devel] [ refdb-Bugs-1550514 ] Trouble while importing chapters

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Bugs item #1550514, was opened at 2006-09-01 15:15
Message generated for change (Comment added) made by dreusser
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Category: refdbd
Group: None
Status: Open
Resolution: Works For Me
Priority: 5
Submitted By: Dominik (dreusser)
Assigned to: Markus Hoenicka (mhoenicka)
Summary: Trouble while importing chapters

Initial Comment:
Queries are not assembled correctly (cutting of either
the refdb_title or redb_booktitile) while importing
chapters from a file with multiple records. For some
reason, writing the records to a seprate file and
importing from there works for some records. I attached
a file with example records that failed.


Example 1
----------
UPDATE t_refdb SET refdb_pubyear=2003, refdb_secyear=0,
refdb_pyother_info='///', refdb_secother_info=NULL,
refdb_citekey='Bardsley2003a', refdb_user1=NULL,
refdb_user2='schaeffli', refdb_user3=NULL,
refdb_user4=NULL, refdb_user5=NULL, refdb_misc1=NULL,
refdb_misc2=NULL, refdb_misc3=NULL, refdb_issn=NULL,
refdb_issue=NULL, refdb_publisher='IAHS Publication no.
281', refdb_city='Wallingford, Oxfordshire UK',
refdb_volume=NULL, refdb_endpage='74',
refdb_startpage='67', refdb_type='CHAP',
refdb_booktitle='Water resources systems - hydrological
risk, management and development  (Proceedings of an
international symposium the XXIII General Assembly of
the International Union of Geodesy and Geophysics, at
Sapporo, Japan, from 30 June to 11 July 2003)',
refdb_title='An approach to creating lumped-parameter
rainfall-runoff models for drainage basins experiencing
envrionemental WHERE refdb_id=2393
1064: You have an error in your SQL syntax; check the
manual that corresponds to your MySQL server version
for the right syntax to use near ''An approach to
creating lumped-parameter rainfall-runoff models
inserting reference data failed

Example 2
---------
UPDATE t_refdb SET refdb_pubyear=1998, refdb_secyear=0,
refdb_pyother_info='///', refdb_secother_info=NULL,
refdb_citekey='Aizen1998', refdb_user1=NULL,
refdb_user2='schaeffli', refdb_user3=NULL,
refdb_user4=NULL, refdb_user5=NULL, refdb_misc1=NULL,
refdb_misc2=NULL, refdb_misc3=NULL, refdb_issn=NULL,
refdb_issue=NULL, refdb_publisher='IAHS Publication No.
248', refdb_city='Wallingford, Oxfordshire UK',
refdb_volume=NULL, refdb_endpage='198',
refdb_startpage='191', refdb_type='CHAP',
refdb_booktitle='Hydrology, Water Resources and Ecology
in Headwaters (P, refdb_title='Estimation of glacial
runoff to the Tarim River, central Tien Shan' WHERE
refdb_id=2352
1064: You have an error in your SQL syntax; check the
manual that corresponds to your MySQL server version
for the right syntax to use near 'Estimation of glacial
runoff to the Tarim River, central Tien Sh
inserting reference data failed

refdb-bug:
Linux aare 2.6.17-1-686 #1 SMP Sat Jul 29 15:32:47 UTC
2006 i686 GNU/Linux
RefDB binaries and scripts in the path:
/usr/bin/refdbd
/usr/bin/refdba
/usr/bin/refdbc
/usr/bin/refdbib
/usr/bin/bib2ris
and their version numbers:
refdbd 0.9.8-pre2
refdba 0.9.8-pre2
refdbc 0.9.8-pre2
refdbib 0.9.8-pre2
/usr/bin/refdb-bug: line 41: nmed2ris: command not found
bib2ris 0.9.8-pre2
DSSSL engines in the path:
and their version numbers:

$REFDBLIB is /usr/share/refdb
global refdbd config file:
refdblib /usr/share/refdb
serverip        localhost
dbsport 3306
dbserver        mysql
dbpath          /var/lib/refdb/db
port    9734
logfile /var/log/refdbd.log
logdest file
loglevel info
pidfile         /var/run/refdbd.pid
remoteadmin f
remoteconnect f
keep_pnames t
keyword_scan t
db_encoding
in_encoding     UTF-8

global refdba config file:
serverip        127.0.0.1
port    9734
pager   less
username        joeuser
passwd  <protected>
logdest file
loglevel info
logfile /var/log/refdba.log

global refdbc config file:
serverip        127.0.0.1
port    9734
pager   less
username        joeuser
passwd  <protected>
logdest file
loglevel info
logfile /var/log/refdbc.log
cssurl /usr/share/refdb/css/refdb.css
fromencoding UTF-8
toencoding UTF-8

global refdbc config file (cgi):

global refdbib config file:

global nmed2ris config file:

global bib2ris config file:

$HOME is /home/dreusser
user refdba config file:

user refdba config file (hidden):
serverip        127.0.0.1
username        root
passwd          <protected>
pager           less
toencoding      ISO-8859-1
fromencoding    ISO-8859-1

user refdbc config file:

user refdbc config file (hidden):
serverip        127.0.0.1
username        dominik
passwd          <protected>
defaultdb       hykli
pager           less
toencoding      ISO-8859-1
fromencoding    ISO-8859-1

user refdbib config file:

user refdbib config file (hidden):
serverip        127.0.0.1
username        dominik
passwd          <protected>
defaultdb       refdb_test
pager           less
toencoding      ISO-8859-1

user nmed2ris config file:

user nmed2ris config file (hidden):

user bib2ris config file:

user bib2ris config file (hidden):
logfile bib2ris.log
logdest 2
loglevel 7
nsf_abstract N2
nsf_url UR
nsf_url2 UR
nsf_pdf UR
nsf_keywords KW
nsf_owner U2
nsf_comment U3
nsf_issn SN


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>Comment By: Dominik (dreusser)
Date: 2006-09-07 14:19

Message:
Logged In: YES 
user_id=1572139

I still get similar errors with the 0.9.8-pre3 version on
the same system. Importing works on a different system which
I just set up. Either we'll drop the issue or I can provide
you an account on my "broken" system. 

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Comment By: Markus Hoenicka (mhoenicka)
Date: 2006-09-02 01:36

Message:
Logged In: YES 
user_id=85809

I've never encountered problems like this one on any of my
installations. To make sure I've installed 0.9.8-pre3 (the
only difference to pre2 is the inclusion of two headers in
refdbdgetref.c to avoid compiler errors) on a pristine
Debian 3.1 box. I can import your test data without any
problems.

I'll post a message to the refdb-users list to see whether
anyone else has seen this. Unless we can pin down the
environment or the circumstances that lead to this problem,
I'll not be able to fix it.


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Comment By: Dominik (dreusser)
Date: 2006-09-01 15:33

Message:
Logged In: YES 
user_id=1572139

It is not just while adding chapters. But I haven't found
out when addref fails exactly..

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