refdb-users — List for RefDB users

[Refdb-users] new (potental) user with problems (debian/sid)

[Dot D. <do...@gm...>]

        Hi everybody,

        I'm new to this list and I start with an installation problem.

        I wanted to install refdb on a debian/sid but I came across a
        problem since the beginning. Here is briefly what I did:

        1. put refdb repositories in /etc/apt/sources.list
deb http://refdb.sourceforge.net/debian/release unstable main
deb http://refdb.sourceforge.net/debian/addons unstable main

        2. apt-get update + apt-get install refdb
[...]
The following packages have unmet dependencies:
  refdb: Depends: libreadline4 (>=3D 4.3-1) but it is not installable
E: Broken packages

        I know that in debian/sid libreadline4 is replaced by
        readline-common: apt-get install libreadline4, says:
[...]
However the following packages replace it:
  readline-common

        Is it possible for the debian package maintainer to update this
        information?

        Thank you,
        augh

Re: [Refdb-users] The return of "An invalid or out-of-range index was passed to libdbi"

[Jeremy M. <Je...@Ma...>]

Markus Hoenicka wrote:
> 
> Is this error associated with particular datasets or does it occur randomly?
> Does the error occur only if you have more than a fixed number of entries in
> your bibliography?

Good point - it seems to fail as soon as you have 128 entries or more. 
That's why I didn't get the error until I had completed another chapter 
with more references in it!  I'm using MySQL and so this sounds very 
much like a TINYINT problem to me, however there are no TINYINTs in my 
databases...

-- 
JEREMY MALCOLM <Je...@Ma...> - lawyer, IT consultant and actor.
Internet and Open Source specialist. Web site: http://www.malcolm.id.au.
Disclaimer: http://www.terminus.net.au/disclaimer.html. GPG key: finger.

Re: [Refdb-users] The return of "An invalid or out-of-range index was passed to libdbi"

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

Hi,

Jeremy Malcolm <Je...@Ma...> was heard to say:


> An invalid or out-of-range index was passed to libdbi
>
> I'm using refdb 0.9.7-pre1 and libdbi 0.8.1-1 on Mac OS X 10.3.9.  Is
> there anything I can do to narrow down the reason for this error?
>

Is this error associated with particular datasets or does it occur randomly?
Does the error occur only if you have more than a fixed number of entries in
your bibliography?

In any case it would be helpful to try and reproduce this problem on a different
box. Maybe we still have some big vs. low-endianness problems that are triggered
only by particular datasets. Could you please send me your complete reference
database as a RIS or risx file and the basename.id.xml file that is generated
when running runbib (this way I don't need to peek at your thesis)?

regards,
Markus

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

Re: [Refdb-users] Adduser problem

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

Hi,

Z F <mai...@ya...> was heard to say:

> Using mysql --protocol=tcp -h hostname -u username -p password
> works no problems. I connect and can browse the databases. Since I have
> provided serverip in refdbarc file, refdba should be able to connect to
> mysql server. And it does, but can not seem to perfrom all the tasks it
> needs.
>
>

This is a good sign indeed. refdbd should be able to connect all the same if the
username/password authentication is set up properly. To find out why mysqld
won't let you in as a regular RefDB user, please try and find the mysql error
log. By default it is in MySQL's data directory, but an entry in my.ini may put
it somewhere else. The default name of the query log file is servername.log.
servername.err which I mentioned previously logs only the mysqld startup and
stop messages but no query errors.

If you can connect through mysql --protocol=tcp but not with refdbc, you should
see one of these error messages:

Access denied for user '%s'@'%s' to database '%s'
Access denied for user '%s'@'%s' (using password: %s)

The latter message indicates whether or not a password was sent to mysqld. To
the best of my knowledge MySQL also issues an error if you have a user account
w/o password but try to connect with a password.

If nothing else helps, could you please send me the results of

select * from db
select * from host
select * from user

after opening the database mysql as root?

regards,
Markus


-- 
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[Refdb-users] The return of "An invalid or out-of-range index was passed to libdbi"

[Jeremy M. <Je...@Ma...>]

I have written another chapter of my thesis and now errors that were 
gone before have come back.  Last time that I got "An invalid or 
out-of-range index was passed to libdbi", there were obvious signs of 
software bugs in the log, but now there is nothing obvious:

SELECT refdb_id, refdb_type FROM thesis.t_refdb WHERE 
refdb_citekey='NTIA2005US-PRINCIPLES-O' AND refdb_type!='DUMMY'
SELECT QAEMPTY,XAEMPTY FROM refdb.REFSTYLE, refdb.CITSTYLE WHERE 
REFSTYLE.CITSTYLEID=CITSTYLE.ID AND REFSTYLE.PUBTYPE='ELEC' AND 
JOURNAL='Murdoch.Law.'
INSERT INTO getbibtemp (article_title,volume,issue,startpage,pubyear) 
SELECT 
refdb_title,refdb_volume,refdb_issue,refdb_startpage,refdb_pubyear FROM 
thesis.t_refdb WHERE refdb_id=48
SELECT 
refdb_title,refdb_volume,refdb_issue,refdb_startpage,refdb_pubyear FROM 
t_refdb WHERE refdb_id=48
UPDATE getbibtemp SET 
dbname='thesis',citation_pos=72,xref_pos=0,orig_id=48,entry_id='IDNTIA2005US-PRINCIPLES-O', 
multi_id='' WHERE id=73
SELECT 
thesis.t_author.author_name,thesis.t_author.author_lastname,thesis.t_author.author_firstname,thesis.t_author.author_middlename,thesis.t_author.author_suffix,thesis.t_xauthor.xauthor_role 
FROM thesis.t_author, thesis.t_xauthor WHERE 
thesis.t_author.author_id=thesis.t_xauthor.author_id AND 
thesis.t_xauthor.xauthor_type='primary' AND thesis.t_xauthor.refdb_id=48 
ORDER BY t_xauthor.xauthor_position
UPDATE getbibtemp SET author_concat='NTIA' WHERE id=73
SELECT thesis.t_periodical.periodical_abbrev FROM thesis.t_periodical, 
thesis.t_refdb WHERE 
thesis.t_refdb.refdb_periodical_id=thesis.t_periodical.periodical_id AND 
thesis.t_refdb.refdb_id=48
chunk added successfully
chunk added successfully
error
An invalid or out-of-range index was passed to libdbi

I'm using refdb 0.9.7-pre1 and libdbi 0.8.1-1 on Mac OS X 10.3.9.  Is 
there anything I can do to narrow down the reason for this error?

TIA

-- 
JEREMY MALCOLM <Je...@Ma...> - lawyer, IT consultant and actor.
Internet and Open Source specialist. Web site: http://www.malcolm.id.au.
Disclaimer: http://www.terminus.net.au/disclaimer.html. GPG key: finger.

Re: [Refdb-users] Adduser problem

[Z F <mai...@ya...>]

Dear Markus,

>  > Hm, this is interesting. The thing is that a mysql user is added
> by
>  > refdba. That is, after adding the user to refdb database, 
>  > I can use mysql with that username and password. So, it seems that
> 
>  > mysql part worked.
> 
> The situation is a bit confusing because the mysql client uses a
> socket or a named pipe to connect to the daemon if it runs on the
> same
> box. refdbd always uses TCP/IP connections. This makes a difference
> for the user authentication.

Confusing, indeed! Apparently mysql client uses unix socket by default.
(I do not see where it is configured in mysql my.cnf file). So I was
using
the socket to connect to the mysql database all the time.


> Alternatively, try to connect with the mysql client by using:
> 
> mysql --protocol=tcp -u username -p password
> 
> This makes mysql behave like refdbc w/regard to user
> authentication. mysql will send the error messages to stderr.
> 

Using mysql --protocol=tcp -h hostname -u username -p password
works no problems. I connect and can browse the databases. Since I have
provided serverip in refdbarc file, refdba should be able to connect to
mysql server. And it does, but can not seem to perfrom all the tasks it
needs.


> Actually things work a bit different. refdbd adds an entry to the
> t_user database only if you add references or notes. If your
> reference
> database contains "root" in t_user, you must have added a reference
> when using "root" as your username in refdbc. Just adding a user with
> refdba:adduser does not modify t_user.

Ok, understood.

> This is my practical experience. The MySQL manual says "%" means any
> host but I can't quite agree with this. This does not exclude the
> possibility that I'm doing something very dumb.

I found the same thing here :-)

Lazar

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Re: [Refdb-users] Adduser problem

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

Hi,

Z F writes:
 > Dear Markus,
 > 
 > Hm, this is interesting. The thing is that a mysql user is added by
 > refdba. That is, after adding the user to refdb database, 
 > I can use mysql with that username and password. So, it seems that 
 > mysql part worked.

The situation is a bit confusing because the mysql client uses a
socket or a named pipe to connect to the daemon if it runs on the same
box. refdbd always uses TCP/IP connections. This makes a difference
for the user authentication.

 > In addition, refdba should have added the same user
 > to its internal user table t_user which is stored inside the  citation 
 > database (refdb_csi in my case) not in the helper database(refdb).
 > This is not happening. As a result, the user can login using mysql,
 > but refdbc does not work. I think I misconfigured refdb, but I can not
 > find 
 > where... I look at t_user table of refdb_csi and see only "root"
 > there...

Actually things work a bit different. refdbd adds an entry to the
t_user database only if you add references or notes. If your reference
database contains "root" in t_user, you must have added a reference
when using "root" as your username in refdbc. Just adding a user with
refdba:adduser does not modify t_user.

 > 
 > I have tried your suggestion of putting "localhost", ip address
 > with the same result.
 > 

Could you please send me the mysql error log? I'd like to see the
error message mysql generates when you try to use refdbc with your
user account instead of "root". The error log can be just about
anywhere on your system and have just about any name, please read the
documentation on your system. On my box it is
/var/db/mysql/yeti.mininet.err

Alternatively, try to connect with the mysql client by using:

mysql --protocol=tcp -u username -p password

This makes mysql behave like refdbc w/regard to user
authentication. mysql will send the error messages to stderr.

 > i would use sqlite as the database as it is much easier. The question
 > is:
 > Is it possible to configure refdb/mysql so a user can have read only
 > access? I think that the answer to this question is "yes". It can be
 > done using mysql administration after the user is added to the refdb 
 > database.
 > 

refdba does not yet have an option to add users read-only, but as you
correctly state you can achieve this by setting the permissions
manually with the mysql client.

 > The problem is that, I am afraid, some users will mess-up the database
 > if they are allowed to write to it (add references). I would want to 
 > set up certain users so they can only get citation references without
 > any ability to add/edit references. If this is not possible due to 
 > the design of refdb, I will simply switch to sqlite :-)
 > 
 > Regardless, the situation with mysql is strange. Your remark that
 > % means any other than localhost is very interesting.
 > 

This is my practical experience. The MySQL manual says "%" means any
host but I can't quite agree with this. This does not exclude the
possibility that I'm doing something very dumb.

regards,
Markus

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

Re: [Refdb-users] 0.9.6 Compile problem

[Doug du B. <dou...@gm...>]

On Sunday 29 January 2006 16:40, Doug du Boulay wrote:
> On Thursday 26 January 2006 01:34, Markus Hoenicka wrote:
> > Thomas Bartolucci <tba...@nn...> was heard to say:
> > > refdbdref.c:2363: error: `DBI_ROW_ERROR' undeclared (first use in this
> > > function)
> >
> > This is due to an outdated version of libdbi. Please install libdbi-0.8.1
> > and libdbi-drivers-0.8.1.
>
> I'm guessing the sourceforge libdbi CVS repository is missing a ./configure
> script to build it, according to the README in any case.
>
> Any ideas where I could get a copy?

Oops. I see now that its created by autogen.sh
Sorry.
Doug

Re: [Refdb-users] 0.9.6 Compile problem

[Doug du B. <dou...@gm...>]

On Thursday 26 January 2006 01:34, Markus Hoenicka wrote:
> Thomas Bartolucci <tba...@nn...> was heard to say:
> > refdbdref.c:2363: error: `DBI_ROW_ERROR' undeclared (first use in this
> > function)
>
> This is due to an outdated version of libdbi. Please install libdbi-0.8.1
> and libdbi-drivers-0.8.1.

I'm guessing the sourceforge libdbi CVS repository is missing a ./configure 
script to build it, according to the README in any case.

Any ideas where I could get a copy?

Thanks
Doug

Re: [Refdb-users] Adduser problem

[Z F <mai...@ya...>]

Dear Markus,

Hm, this is interesting. The thing is that a mysql user is added by
refdba. That is, after adding the user to refdb database, 
I can use mysql with that username and password. So, it seems that 
mysql part worked. In addition, refdba should have added the same user
to its internal user table t_user which is stored inside the  citation 
database (refdb_csi in my case) not in the helper database(refdb).
This is not happening. As a result, the user can login using mysql,
but refdbc does not work. I think I misconfigured refdb, but I can not
find 
where... I look at t_user table of refdb_csi and see only "root"
there...

I have tried your suggestion of putting "localhost", ip address
with the same result.

i would use sqlite as the database as it is much easier. The question
is:
Is it possible to configure refdb/mysql so a user can have read only
access? I think that the answer to this question is "yes". It can be
done using mysql administration after the user is added to the refdb 
database.

The problem is that, I am afraid, some users will mess-up the database
if they are allowed to write to it (add references). I would want to 
set up certain users so they can only get citation references without
any ability to add/edit references. If this is not possible due to 
the design of refdb, I will simply switch to sqlite :-)

Regardless, the situation with mysql is strange. Your remark that
% means any other than localhost is very interesting.

Thank you very much for your kind help

Lazar

--- Markus Hoenicka <mar...@mh...> wrote:

> Hi,
> 
> Z F writes:
>  > Anyway, if I add a user
>  > refdba: adduser -d refdb_csi -H % lazarf
>  > 999:1 added:0 failed
>  > 
>  > and then do:
>  > 
>  > refdba: listuser -d refdb_csi
>  > root
>  > 999:1
>  > 
> 
> This is one of the few things that I couldn't figure out completely
> yet. MySQL distinguishes strictly between local and remote
> connections. "%" means all connections except localhost. On most
> installations you have to use the following command to add a user if
> refdbd and mysqld run on the same box:
> 
> adduser -d refdb_csi -H localhost lazarf
> 
> However, this does not work on other systems. E.g. on Windows I have
> to use:
> 
> adduser -d refdb_csi -H 123.4.5.6 lazarf
> 
> i.e. by using the real IP of the box instead of "localhost".
> 
> Please try one of these options and let me know if you get further.
> 
> regards,
> Markus
> 
> -- 
> Markus Hoenicka
> mar...@ca...
> (Spam-protected email: replace the quadrupeds with "mhoenicka")
> http://www.mhoenicka.de
> 
> 


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Re: [Refdb-users] Adduser problem

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

Hi,

Z F writes:
 > Anyway, if I add a user
 > refdba: adduser -d refdb_csi -H % lazarf
 > 999:1 added:0 failed
 > 
 > and then do:
 > 
 > refdba: listuser -d refdb_csi
 > root
 > 999:1
 > 

This is one of the few things that I couldn't figure out completely
yet. MySQL distinguishes strictly between local and remote
connections. "%" means all connections except localhost. On most
installations you have to use the following command to add a user if
refdbd and mysqld run on the same box:

adduser -d refdb_csi -H localhost lazarf

However, this does not work on other systems. E.g. on Windows I have
to use:

adduser -d refdb_csi -H 123.4.5.6 lazarf

i.e. by using the real IP of the box instead of "localhost".

Please try one of these options and let me know if you get further.

regards,
Markus

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

Re: [Refdb-users] Adduser problem

[Z F <mai...@ya...>]

Hello Markus

--- Markus Hoenicka <mar...@mh...> wrote:

> Hi,
> 
> Z F writes:
>  > refdba: listuser
>  > select failed
>  > 
> 
> This is a misunderstanding of the command syntax. The refdba:listuser
> command takes one mandatory argument, the name of the reference
> database you're interested in. If you want to see whether you added
> yourself properly to the refdb_csi database, you should run
> 
> listuser refdb_csi

Yes, I thought that if no database is supplied, the default one
is used from configuration files. But you are right, again, only
refdbc has a default database. I got confused. There should not be any
default database for administration client.

Anyway, if I add a user
refdba: adduser -d refdb_csi -H % lazarf
999:1 added:0 failed

and then do:

refdba: listuser -d refdb_csi
root
999:1

So only root is the user. This is confirmed with mysql:

Welcome to the MySQL monitor.  Commands end with ; or \g.
Your MySQL connection id is 32 to server version: 5.0.18-Debian_7-log

mysql> use refdb_csi;
mysql> select * from t_user;

+---------+-----------+
| user_id | user_name |
+---------+-----------+
|       1 | root      |
+---------+-----------+

So no user is added to the database.
I must have done something wrong, once again, but I do not see what.
Could you suggest where I should look next?

As root, I was able to add some references to the citation database, so
I know that works -)

Thank you very much for your help

Lazar

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[Refdb-users] Adduser problem

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

Hi,

Z F writes:
 > refdba: listuser
 > select failed
 > 

This is a misunderstanding of the command syntax. The refdba:listuser
command takes one mandatory argument, the name of the reference
database you're interested in. If you want to see whether you added
yourself properly to the refdb_csi database, you should run

listuser refdb_csi

regards,
Markus

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

[Refdb-users] Adduser problem

[Z F <mai...@ya...>]

Hello everybody,

Thank you Markus for helping me setup the system. Now all initial tests
work. The next step is to add a user. Here is a problem.

refdba: adduser -d refdb_csi -H 10.135.148.96 -N refdb lazarf
999:1 added:0 failed
refdba: listuser
select failed

If I look at the database from mysql than I see that the user is
created with the right password and host. As to the access rights for
refdb database and for the citation database (refdb_csi, which I
created),they
are also reasonable (to me).


refdb producess this error:

refdb
connected to database server using database:
refdb
SELECT VERSION()
1146: Table 'refdb.t_user' doesn't exist
SELECT DISTINCT user_name FROM t_user WHERE user_name RLIKE '.*'
select failed
child finished client on fd 5
child exited with code 1
server waiting n_max_fd=4


Indeed, refdb.t_user is not there. As far as I understand,
t_user should be in the citation database (refdb_csi) not in the
refdb (refbd) dababase.

I think I lost something while reading the manuals again. Could someone
point out how I could debug this problem?

Thank you very much for your kind help

Lazar

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Re: [Refdb-users] forced to use sqlite

[Z F <mai...@ya...>]

Dear Markus,

I think I found what the problem is. Maybe I did not read the
manual correctly, but it appears that refdb database is a reserved
name. That is, I should have created the refdb database from refdb.dump
and namded it refdb. I, instead, named it refdb_csi as I thought that
this is the reference database. But in reality, refdb contains 
information needed for refdb and is NOT a reference database. 
reference database is created separately by refdba create. This was 
not clear to me :-)

So, this solved this problem. The test works and I can connect to
the database and viewstat works.

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Re: [Refdb-users] forced to use sqlite

[Z F <mai...@ya...>]

Dear Markus,

Sorry, you are right, there was another server running. Apparently
I started it by eccident, but refdbctl stop did not kill it.
Anyway, I killed it manually. and repeated the test. Now, the error
message is different. It appears refdba is trying to connect to wrong
database. I have created database named refdb_csi, but it searches for
refdb.

Attached are script files from refdbd terminal and from refdba terminal

I ran ps aux before the test and during the test. (the output of
ps aux during the test is in a separate file). Could you suggest where
I made a mistke in the configuration after reviewing this?

Thank you for pointing me to web interface. I will look at it.
It is needed so that people who do not like command line interface
can use the database. I am fine with learning the comman line version
:-)

Thank you for your help

Lazar

> Now if you repeat your test as per the manual, with refdba running in
> xterm 1 and refdbd -s -e 0 -l 7 -D mysql running in xterm 2. If you
> issue the viewstat command in xterm 1, what happens in xterm 2? Does
> refdbd produce output that indicates a client connection? Can you
> send
> a copy of that output? And please make sure to add the output of "ps
> ax" in the very moment you run this test.
> The old web interface was dropped, and the instructions were removed
> from the manual. Just before 0.9.6 was released, a new PHP-based
> version of the web interface was kindly contributed by Tom
> Bartolucci. I simply didn't get round to update the manual. There are
> some setup instructions in the refdb/phpweb/INSTALL file in the
> sources. If you are an Emacs user, please also give refdb-mode a try
> which is currently a superior alternative to the web interface.
> 


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Re: [Refdb-users] forced to use sqlite

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

Hi,

Z F writes:
 > Thank you very much for your help. The output of
 > the refdb-debug script is attached. I do not have any configuration
 > files in my home directory. The rest, you can see.
 > 

There is nothing strange in your setup, which makes the result all the
more mysterious. According to the sources there is not the slightest
chance that you accidentally use the sqlite driver. The priorities are
as follows:

1) the hardcoded default is mysql. This driver is used if neither the
config files nor the command line sets a db engine explicitly.

2) the config file in your case sets mysql too. This is used unless
you use the -D command line option to override this.

3) the command line switch -D overrides everything else.

Now if you repeat your test as per the manual, with refdba running in
xterm 1 and refdbd -s -e 0 -l 7 -D mysql running in xterm 2. If you
issue the viewstat command in xterm 1, what happens in xterm 2? Does
refdbd produce output that indicates a client connection? Can you send
a copy of that output? And please make sure to add the output of "ps
ax" in the very moment you run this test.

 > And, no user can run refdb since I am the only one who knows about it
 > and I do not know how to use it yet :-) I just started ....
 > By the way, the webpage says that there is web interface to the
 > database, but I did not find any instructions in the manual on how
 > to set it up. But that is the next step.
 > 

The old web interface was dropped, and the instructions were removed
from the manual. Just before 0.9.6 was released, a new PHP-based
version of the web interface was kindly contributed by Tom
Bartolucci. I simply didn't get round to update the manual. There are
some setup instructions in the refdb/phpweb/INSTALL file in the
sources. If you are an Emacs user, please also give refdb-mode a try
which is currently a superior alternative to the web interface.

regards,
Markus

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

[Refdb-users] incomplete client command

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

Thomas Bartolucci writes:
 > I got refdb0.9.6 to compile, and I run the server. In refdba I try the 
 > viewstat command and I get the error:
 > 
 > "password transfer failed"
 > 
 > the corresponding line in the logs show:
 > 
 > "incomplete client command"
 > 
 > Any ideas on why this is happening?

One way to cause this error is to use a 0.9.5 client to connect to a
0.9.6 server. Do you have both versions of RefDB installed, maybe in
/usr/bin and /usr/local/bin? If you test a freshly compiled version,
make sure to run the new executables explicitly, e.g. by cd'ing to
refdb/src and starting them as ./refdbd, ./refdba and so on.

BTW 0.9.6 introduced a versioned client/server protocol that is
supposed to allow an easier analysis of this kind of problem in the future.

regards,
Markus

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

[Refdb-users] incomplete client command

[Thomas B. <tba...@nn...>]

I got refdb0.9.6 to compile, and I run the server. In refdba I try the 
viewstat command and I get the error:

"password transfer failed"

the corresponding line in the logs show:

"incomplete client command"

Any ideas on why this is happening?
-- 
Thomas Bartolucci
National Nanotechnology Coordination Office
Systems Administrator
4201 Wilson Blvd
Stafford II Room 405
Arlington, VA 22230
703-292-4533
tba...@nn...

Re: [Refdb-users] 0.9.6 Compile problem

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

Thomas Bartolucci <tba...@nn...> was heard to say:

> refdbdref.c:2363: error: `DBI_ROW_ERROR' undeclared (first use in this
> function)

This is due to an outdated version of libdbi. Please install libdbi-0.8.1 and
libdbi-drivers-0.8.1.

regards,
Markus

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

[Refdb-users] 0.9.6 Compile problem

[Thomas B. <tba...@nn...>]

On a debian system I use this config line:
./configure --sysconfdir=/etc 
--with-docbook-xsl=/usr/share/sgml/docbook/stylesheet/xsl/nwalsh 
--with-tei-xsl=/usr/local/lib/sgml/stylesheet/xsl 
--with-refdb-url=https://nnco2.nano.gov/refdb --with-db-server=mysql

make && make install

I get the following error:

refdbdref.c: In function `read_ris_data':
refdbdref.c:667: warning: passing arg 2 of `libiconv' from incompatible 
pointer type
refdbdref.c: In function `is_journal':
refdbdref.c:2363: error: `DBI_ROW_ERROR' undeclared (first use in this 
function)
refdbdref.c:2363: error: (Each undeclared identifier is reported only once
refdbdref.c:2363: error: for each function it appears in.)
refdbdref.c: In function `getref':
refdbdref.c:4585: warning: passing arg 2 of `libiconv' from incompatible 
pointer type
make[2]: *** [refdbdref.o] Error 1
make[2]: Leaving directory `/usr/local/refdb-0.9.6/src'
make[1]: *** [all] Error 2
make[1]: Leaving directory `/usr/local/refdb-0.9.6/src'
make: *** [all-recursive] Error 1

-- 
Thomas Bartolucci
National Nanotechnology Coordination Office
Systems Administrator
4201 Wilson Blvd
Stafford II Room 405
Arlington, VA 22230
703-292-4533
tba...@nn...

Re: [Refdb-users] forced to use sqlite

[Z F <mai...@ya...>]

--- Markus Hoenicka <mar...@mh...> wrote:

> Z F <mai...@ya...> was heard to say:
> 
> > This is exactly what I did. I followed the manual :-)
> > killed the daemon and used refdbd -s -e 0 -l 7 -D mysql
> > in one window and refdba in another.
> >
> > when I execute viewstat, it sais that I am connected to sqlite
> > database...
> >
> 
> This is really mysterious. If you use the -D command line option,
> refdbd will
> try to connect through the mysql driver no matter what the config
> files say.
> There is no fallback mechanism that would use a different driver if
> the one
> asked for does not work. If refdbd can't connect to mysql, it will
> report an
> error.
> 
> I'd like to have a look at the following information:
> 
> 1) Please run refdb-bug. This is a little script which collects a lot
> of
> information about your RefDB setup, including all config files.
> Please send me
> the file refdb-bug.txt which the script creates in your current
> working
> directory.
> 
> 2) Please send me the output of "ps ax". Is it possible that another
> user runs
> refdbd on your box?

Dear Markus,

Thank you very much for your help. The output of
the refdb-debug script is attached. I do not have any configuration
files in my home directory. The rest, you can see.

And, no user can run refdb since I am the only one who knows about it
and I do not know how to use it yet :-) I just started ....
By the way, the webpage says that there is web interface to the
database, but I did not find any instructions in the manual on how
to set it up. But that is the next step.

Thanks again for your help

Lazar

__________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

Re: [Refdb-users] Problem after updating to 0.9.6 on FreeBSD

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

Bruce Hayward <b.h...@le...> was heard to say:

> Hi,
> I get this error message "main database is too old or corrupt" after
> updating from 0.9.5.
>

>  111 >ll /usr/local/share/refdb/db/
> total 2516
> -rw-r--r--  1 root  wheel    40K Aug 10 16:22 refdb

First of all, thanks for the wealth of debug information. This makes it so much
easier to find out what's going wrong.

I believe the error message indeed catches the underlying problem very well
[something that does not always hold true with RefDB :-( ] . Your system
database has a timestamp as of Aug 10, so it seems to be the version you
installed with 0.9.5. The database schemas of 0.9.6 were changed a bit (both
the system database and the reference databases), so you'd just have to create
the databases again, using the tools shipped with 0.9.6. There is a file called
UPGRADING and an appropriately named section in the manual which describe how to
upgrade without losing data. Please let me know if that does not fix your
problem.

regards,
Markus

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

[Refdb-users] Problem after updating to 0.9.6 on FreeBSD

[Bruce H. <b.h...@le...>]

Hi,
I get this error message "main database is too old or corrupt" after
updating from 0.9.5.

My original build didn't quite follow the approved pattern but worked:
 113 >more RefDB/My_Notes.txt 
"I built RefDB using the FreeBSD port of RefDB then added, from
sourceforge, the RefDB-Client module (by mistake) and then the
RefDB-perlmod module to translate PubMed references into RefDB style.
None of these contained the Text-Iconv-1.4 module which is necessary for
perlmod to function so I added that last from the meta-starter kit which
wasn't the order suggested in the meta-starter kit but it seems to work
anyway."

RefDB is installed on my machine and I'm the sole user.

Having read some previous posts I collected the following info- 
refdbd -s -e 0 -l 7
pkg_info | grep sql
ll /usr/local/share/refdb/db/
refdb-bug

Any suggestions?
Bruce Hayward


mme-pc2132# refdbd -s -e 0 -l 7
dbi_driver_dir went to:

dbi is up using default driver dir
Available libdbi database drivers:
mysql
pgsql
sqlite
sqlite3
Requested libdbi driver found
Database directory:
/usr/local/share/refdb/db
application server started
share extended notes by default
use /tmp/refdbd_fifo9639 as fifo
server waiting n_max_fd=4
adding client 127.0.0.1 on fd 5
server waiting n_max_fd=5
parent removing client on fd 5
server waiting n_max_fd=4
try to read from client
serving client on fd 5 with protocol version 4
210-02-30-68
send pseudo-random string to client
viewstat  -u medbha
dbi is up
localhost
medbha



sqlite
/usr/local/share/refdb/db

refdb
connected to database server using database:
refdb


main database is too old or corrupt
child finished client on fd 5
child exited with code 1
server waiting n_max_fd=4


 109 >pkg_info | grep sql
mysql-client-4.1.15 Multithreaded SQL database (client)
postgresql-client-7.4.9 PostgreSQL database (client)
sqlite-2.8.17       An SQL database engine in a C library w/ Tcl wrapper
sqlite-3.2.8        An SQL database engine in a C library w/ Tcl wrapper


 111 >ll /usr/local/share/refdb/db/
total 2516
-rw-r--r--  1 root  wheel    40K Aug 10 16:22 refdb
-rw-r--r--  1 root  wheel   2.2M Jan 24 09:44 refs
-rw-r--r--  1 root  wheel   171K Aug 23 15:02 test

And the refdb-bug output is:
FreeBSD mme-pc2132.leeds.ac.uk 5.4-STABLE FreeBSD 5.4-STABLE #1: Tue Aug
23 09:34:
31 BST 2005     me...@mm...:/usr/obj/usr/src/sys/BRUCE
i386
RefDB binaries and scripts in the path:
/usr/local/bin/refdbd
/usr/local/bin/refdba
/usr/local/bin/refdbc
/usr/local/bin/refdbib
/usr/local/bin/nmed2ris
/usr/local/bin/bib2ris
and their version numbers:
refdbd 0.9.6
refdba 0.9.6
refdbc 0.9.6
refdbib 0.9.6
nmed2ris 0.9.6
nmed2ris is
bib2ris 0.9.6
DSSSL engines in the path:
and their version numbers:

$REFDBLIB is /usr/local/share/refdb
global refdbd config file:
refdblib /usr/local/share/refdb
serverip        localhost
dbsport         
dbserver        sqlite
dbpath          /usr/local/share/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     UNICODE
in_encoding     ISO-8859-1

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

global refdbc config file:
serverip        127.0.0.1
port    9734
pager   less
passwd  <protected>
logdest file
loglevel info
logfile /var/log/refdbc.log
cssurl /usr/local/share/refdb/css/refdb.css
fromencoding ISO-8859-1

global refdbc config file (cgi):
refdblib /usr/local/share/refdb
serverip        127.0.0.1
port    9734
logfile /var/log/refdbcgi.log
logdest file
loglevel info
autokill 1800

global refdbib config file:
refdblib /usr/local/share/refdb
serverip        127.0.0.1
port    9734
pager   less
passwd  <protected>
outtype db31
logfile /var/log/refdbib.log
logdest file
loglevel info
stylespecdir    .
ignore_missing  f

global nmed2ris config file:
medsource       PUBMED
outappend       t
ignoretag       t
logfile /var/log/nmed2ris.log
logdest file
loglevel info

global bib2ris config file:
refdblib /usr/local/share/refdb
logfile /var/log/bib2ris.log
logdest file
loglevel info
abbrevfirst     t
forcejabbrev    t
listsep ;

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

user refdba config file (hidden):

user refdbc config file:

user refdbc config file (hidden):

user refdbib config file:

user refdbib config file (hidden):

user nmed2ris config file:

user nmed2ris config file (hidden):

user bib2ris config file:

user bib2ris config file (hidden):

Re: [Refdb-users] forced to use sqlite

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

Z F <mai...@ya...> was heard to say:

> This is exactly what I did. I followed the manual :-)
> killed the daemon and used refdbd -s -e 0 -l 7 -D mysql
> in one window and refdba in another.
>
> when I execute viewstat, it sais that I am connected to sqlite
> database...
>

This is really mysterious. If you use the -D command line option, refdbd will
try to connect through the mysql driver no matter what the config files say.
There is no fallback mechanism that would use a different driver if the one
asked for does not work. If refdbd can't connect to mysql, it will report an
error.

I'd like to have a look at the following information:

1) Please run refdb-bug. This is a little script which collects a lot of
information about your RefDB setup, including all config files. Please send me
the file refdb-bug.txt which the script creates in your current working
directory.

2) Please send me the output of "ps ax". Is it possible that another user runs
refdbd on your box?

regards,
Markus


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