refdb-users — List for RefDB users

[Refdb-users] refdbib segfault

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

Hi,

what version are you working with? I know that the last release 0.9.2a
does have a couple of problems related to citation keys. Most of these
issues have been fixed in CVS and I'd like to know whether this also
holds true for the problem you stumbled in. Could you please provide
everything necessary to reproduce the problem by private mail, i.e. a
zip of the subdirectory containing your Makefile, cepprop.xml, the err
files etc, plus the RIS file containing your references.

BTW why do you assume that refdbib segfaults? Do you get a core file?
I gather from the information that you provided that refdbd bails out
after an error which causes refdbib to call it quits.

regards,
Markus

Dylan Oliver writes:
 > Hi,
 > 
 > I started a document with refdbnd (docbook xml 4.1.2), inserted some
 > references to sources I added to my database (mysql), and have been
 > trying to compile for hours now without any luck. Here's what I'm
 > seeing: 
 > 
 > make html                                 
 > runbib -d rdbib_dao -S J.Biol.Chem. -t db31x cepprop.xml
 > /usr/bin/openjade:cepprop.xml:76:4:E: cannot find "cepprop.bib.xml";
 > tried "cepprop.bib.xml", "/usr/local/share/sgml/cepprop.bib.xml",
 > "/usr/local/lib/sgml/cepprop.bib.xml", "/usr/lib/sgml/cepprop.bib.xml"
 > /usr/bin/openjade:cepprop.xml:78:11:E: end tag for "section" which is
 > not finished
 > /usr/bin/openjade:cepprop.xml:70:129:X: reference to non-existent ID
 > "IDBackstrand2001X"
 > /usr/bin/openjade:cepprop.xml:70:94:X: reference to non-existent ID
 > "IDBackstrand2002X"
 > /usr/bin/openjade:cepprop.xml:70:43:X: reference to non-existent ID
 > "IDBackstrand2002"
 > /usr/bin/openjade:cepprop.xml:70:29:X: reference to non-existent ID
 > "IM0"
 > getbib error: could not create footer:
 > 
 > make: *** [cepprop.bib.xml] Error 1
 > 
 > The base xml file as well as the xsl.err, bib.xml.err and id.xml are all
 > created and look fine. Here's the tail-end of refdbd's debug output:
 > 
 > SELECT DISTINCT dbname, orig_id, author_concat, pubyear, article_title,
 > periodical, volume, issue, startpage, entry_id, citation_pos, xref_pos,
 > multi_id, sorted_pos FROM getbibtemp WHERE citation_pos=0 ORDER BY
 > xref_pos
 > temp table access error
 > could not create footer:
 > command processing done, finish dialog now
 > child finished client on fd 5
 > child exited with code 0
 > 
 > Any help?
 > -- 
 > Dylan Oliver 
 > http://bork.hampshire.edu/~dao
 > AIM: l0sang

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

[Refdb-users] refdbib segfault

[Dylan O. <lo...@st...>]

Hi,

I started a document with refdbnd (docbook xml 4.1.2), inserted some
references to sources I added to my database (mysql), and have been
trying to compile for hours now without any luck. Here's what I'm
seeing:=20

make html                                =20
runbib -d rdbib_dao -S J.Biol.Chem. -t db31x cepprop.xml
/usr/bin/openjade:cepprop.xml:76:4:E: cannot find "cepprop.bib.xml";
tried "cepprop.bib.xml", "/usr/local/share/sgml/cepprop.bib.xml",
"/usr/local/lib/sgml/cepprop.bib.xml", "/usr/lib/sgml/cepprop.bib.xml"
/usr/bin/openjade:cepprop.xml:78:11:E: end tag for "section" which is
not finished
/usr/bin/openjade:cepprop.xml:70:129:X: reference to non-existent ID
"IDBackstrand2001X"
/usr/bin/openjade:cepprop.xml:70:94:X: reference to non-existent ID
"IDBackstrand2002X"
/usr/bin/openjade:cepprop.xml:70:43:X: reference to non-existent ID
"IDBackstrand2002"
/usr/bin/openjade:cepprop.xml:70:29:X: reference to non-existent ID
"IM0"
getbib error: could not create footer:

make: *** [cepprop.bib.xml] Error 1

The base xml file as well as the xsl.err, bib.xml.err and id.xml are all
created and look fine. Here's the tail-end of refdbd's debug output:

SELECT DISTINCT dbname, orig_id, author_concat, pubyear, article_title,
periodical, volume, issue, startpage, entry_id, citation_pos, xref_pos,
multi_id, sorted_pos FROM getbibtemp WHERE citation_pos=3D0 ORDER BY
xref_pos
temp table access error
could not create footer:
command processing done, finish dialog now
child finished client on fd 5
child exited with code 0

Any help?
--=20
Dylan Oliver=20
http://bork.hampshire.edu/~dao
AIM: l0sang

Re: [Refdb-users] ANN: RefDB 0.9.3-pre5 available

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

Hi Jakob,

Jakob Beetz writes:
 > everything runs fine now! Thanks for the great work.
 > BTW when trying to make a fresh checkout from CVS the configure script, 
 > Makefile.*s and other things are missing , but that's maybe just me 
 > missing s.th.
 > 

Yes :-) You need to run ./autogen.sh to build these files. It'll be
mentioned in the next version of the manual.

regards,
Markus

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

Re: [Refdb-users] ANN: RefDB 0.9.3-pre5 available

[Jakob B. <j....@bw...>]

Hi Markus,

Markus Hoenicka wrote:

>I've added a MySQL version check in the CVS version. It does work on
>3.23.x but I'd like to know whether it works on >=4.02 too. Would you
>mind testing the CVS version?
>  
>
everything runs fine now! Thanks for the great work.
BTW when trying to make a fresh checkout from CVS the configure script, 
Makefile.*s and other things are missing , but that's maybe just me 
missing s.th.

best regards
Jakob

Re: [Refdb-users] Links: Open standards and software for bibliographies and cataloging

[John J L. <jj...@po...>]

On Thu, 26 Jun 2003, Bruce D'Arcus wrote:

> On Thu, 26 Jun 2003 21:43:34 +0200, "Markus Hoenicka"
> <mar...@mh...> said:
> > Hi John & Bruce,
> >
> > thanks for the work you put into that list. I believe it is a helpful
> > starting point. Will you attempt to provide more in-depth information,
> > e.g. a comparison of the available tools?
>
> I dunno myself, and am not sure how John feels about the question.  I

I'm happy to let you decide what to do with it, Bruce -- I just tidied it
up and added a couple of descriptions.  I'll add new stuff if people mail
me links, but as you said, my goal was mostly just to get a list of
interesting links out of you.


[...]
> As you can imagine, it becomes a little difficult to weed down even just
> the list.  I'm not sure how I'd propose to do a comprehensive overview of
> it all.  Any ideas?
[...]

Well, of course you're right that surveys of things have to be focused.
And I guess in truth I don't know how comprehensive it is, starting as I
am from a position of ignorance even of the stuff that's already there!

I do have the impression, though, from my limited surfing and mailing-list
lurking, that the list *is* pretty comprehensive within some
hard-to-define-exactly field.  'Bibliographic stuff that interests me',
probably :-)  But quite happy to be proved wrong by the contents of my
INBOX, of course!


John

Re: [Refdb-users] Links: Open standards and software for bibliographies and cataloging

[John J L. <jj...@po...>]

On Thu, 26 Jun 2003, Markus Hoenicka wrote:
> thanks for the work you put into that list. I believe it is a helpful
> starting point. Will you attempt to provide more in-depth information,
> e.g. a comparison of the available tools?

Nope.  :-)

Well, not unless Bruce wants to do it, but I think he's busy with other
things (at least he should be ;-)...

OTOH, I'd certainly like to hear of interesting projects we haven't listed
(as I said, please send all comments to me, not Bruce).


John

Re: [Refdb-users] ANN: RefDB 0.9.3-pre5 available

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

Hi Jakob,

Markus Hoenicka writes:
 > I'm glad the Perl issues are sorted out. I've checked the MySQL docs
 > today. Turns out that the LOCK TABLES privilege was indeed introduced
 > in MySQL 4.02, so it is a simple version issue that I have to work
 > around somehow.
 > 

I've added a MySQL version check in the CVS version. It does work on
3.23.x but I'd like to know whether it works on >=4.02 too. Would you
mind testing the CVS version?

regards,
Markus

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

Re: [Refdb-users] Links: Open standards and software for bibliographies and cataloging

[Bruce D'A. <bd...@fa...>]

On Thu, 26 Jun 2003 21:43:34 +0200, "Markus Hoenicka"
<mar...@mh...> said:
> Hi John & Bruce,
> 
> thanks for the work you put into that list. I believe it is a helpful
> starting point. Will you attempt to provide more in-depth information,
> e.g. a comparison of the available tools?

I dunno myself, and am not sure how John feels about the question.  I
suppose I'd like to sit on it awhile and see what people have to say. 
The list started out because John wanted a comprehensive overview of
*links* to the open bib universe.  I opted to add short descriptions, and
to focus on the interesting, more forward-looking, stuff.  As I put it to
John, it ought to be a list with a purpose; namely to promote the more
interesting open projects.

As you can imagine, it becomes a little difficult to weed down even just
the list.  I'm not sure how I'd propose to do a comprehensive overview of
it all.  Any ideas?

To my mind, the most interesting stuff relevant to bibliographic software
of the sort we're all interested in is refdb and pybliographer (not the
current version, but the planned v2) in the applications space, and mods
and bibx (along with citestylex) in the data standards space. I'm most
interested in the data models/standards that various projects can then
put to use.

Bruce

-- 
http://www.fastmail.fm - One of many happy users:
  http://www.fastmail.fm/docs/quotes.html

[Refdb-users] Links: Open standards and software for bibliographies and cataloging

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

Hi John & Bruce,

thanks for the work you put into that list. I believe it is a helpful
starting point. Will you attempt to provide more in-depth information,
e.g. a comparison of the available tools?

regards,
Markus

John J Lee writes:
 > http://wwwsearch.sourceforge.net/bib/openbib.html
 > 
 > Bruce D'Arcus and I (mostly Bruce, actually) have put up a relatively
 > comprehensive list of interesting open standards and open-source software
 > related to bibliographies and cataloging.
 > 
 > Currently, the emphasis is on the needs of individuals and small groups
 > rather than libraries, but given the growing overlap in the interests of
 > these groups, the list is likely to expand to some extent to cover more
 > library software.
 > 
 > Apologies for sp*mming everybody, this is a one-off message.  Please edit
 > the list down if you reply, or reply in a separate thread.  I don't read
 > all these lists, so please reply to me directly if you want to get through
 > to me.  Also, note that though Bruce compiled most of the list and wrote
 > much of the text, I'm doing the drudge work, so please reply to me, not
 > Bruce.  Thanks
 > 
 > 
 > John
 > 
 > 
 > 
 > -------------------------------------------------------
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 > 
 > 

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

Re: [Refdb-users] ANN: RefDB 0.9.3-pre5 available

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

Hi Jakob,

Jakob Beetz writes:
 > Hi Markus, all,
 > 
 > great work! runs very smooth, all tests ok (that is: with the 0.9.3-pre6 
 > with additional GRANT LOCK TABLES in dbfncs.c and  refdbda.c for 
 > mySQL-nt. Without these additional grants I still got "cannot lock 
 > tables" with make test)

I'm glad the Perl issues are sorted out. I've checked the MySQL docs
today. Turns out that the LOCK TABLES privilege was indeed introduced
in MySQL 4.02, so it is a simple version issue that I have to work
around somehow.

 > Im going to start a CGI module on that basis now.
 > 

I'm looking forward to seeing your work. I'd greatly appreciate if
you decide to share the results.

regards,
Markus

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

[Refdb-users] Links: Open standards and software for bibliographies and cataloging

[John J L. <jj...@po...>]

http://wwwsearch.sourceforge.net/bib/openbib.html

Bruce D'Arcus and I (mostly Bruce, actually) have put up a relatively
comprehensive list of interesting open standards and open-source software
related to bibliographies and cataloging.

Currently, the emphasis is on the needs of individuals and small groups
rather than libraries, but given the growing overlap in the interests of
these groups, the list is likely to expand to some extent to cover more
library software.

Apologies for sp*mming everybody, this is a one-off message.  Please edit
the list down if you reply, or reply in a separate thread.  I don't read
all these lists, so please reply to me directly if you want to get through
to me.  Also, note that though Bruce compiled most of the list and wrote
much of the text, I'm doing the drudge work, so please reply to me, not
Bruce.  Thanks


John

Re: [Refdb-users] ANN: RefDB 0.9.3-pre5 available

[Jakob B. <J....@bw...>]

Hi Markus, all,

great work! runs very smooth, all tests ok (that is: with the 0.9.3-pre6 
with additional GRANT LOCK TABLES in dbfncs.c and  refdbda.c for 
mySQL-nt. Without these additional grants I still got "cannot lock 
tables" with make test)
Im going to start a CGI module on that basis now.

Thanks again.
Cheers
Jakob

Markus Hoenicka wrote:

>Hi,
>
>Markus Hoenicka writes:
> > I've had problems with this encryption stuff before on some particular
> > platforms (PPC, but that's been fixed), but never on Windows, the
> > BSDs, Linux, or OSX. Did you run a reasonable number of tests using
> > the C clients directly? I'd like to know whether Perl has something to
> > do with it, because this part has been tested much less than the C
> > clients. Could be some weird quoting issue or something like that. If
> > I knew Perl better I'd go ahead and write a native implementation of
> > the encryption in Perl but I'm afraid this would take too much time
> > off my efforts to get 0.9.3 out the door. Any Perl gurus out there
> > with some spare time?
> > 
>
>Ok, forget about all this. The Perl module was utterly broke. I've
>uploaded a fixed version to:
>
>http://refdb.sourceforge.net/pre/RefDBClient-Client-1.7.tar.gz
>
>Please try again.
>
>Thanks
>Markus
>
>  
>

Re: [Refdb-users] ANN: RefDB 0.9.3-pre5 available

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

Hi,

Markus Hoenicka writes:
 > I've had problems with this encryption stuff before on some particular
 > platforms (PPC, but that's been fixed), but never on Windows, the
 > BSDs, Linux, or OSX. Did you run a reasonable number of tests using
 > the C clients directly? I'd like to know whether Perl has something to
 > do with it, because this part has been tested much less than the C
 > clients. Could be some weird quoting issue or something like that. If
 > I knew Perl better I'd go ahead and write a native implementation of
 > the encryption in Perl but I'm afraid this would take too much time
 > off my efforts to get 0.9.3 out the door. Any Perl gurus out there
 > with some spare time?
 > 

Ok, forget about all this. The Perl module was utterly broke. I've
uploaded a fixed version to:

http://refdb.sourceforge.net/pre/RefDBClient-Client-1.7.tar.gz

Please try again.

Thanks
Markus

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

Re: [Refdb-users] ANN: RefDB 0.9.3-pre5 available

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

Jakob Beetz writes:
 > Hi Markus, all,
 > 
 > thanks for the quick fix!
 > I testested it this morning, the numberized_passwd issues went like a 
 > charm out-of-the-box.
 > However, the "cannot lock tables" issue remains the same for my setup (I 
 > suppose this is a mySQL w32 issue, so maybe it is not worth investigating).

I'll browse the MySQL docs and see whether anything has changed
between 3.23 and 4.x that would cause this problem. I wouldn't bet
this is a platform issue, and even if it was I'd have to work around
it.

 > And now to the weird part ;-)
 > There seems to be a bug within enigma_encrypt: On _random_ occasions 
 > (though at least once a test.pl run) the denumberized password is 
 > incorectly decrypted. Here is from my refdbd log (I uncommented the 
 > printf in refdbd.c line 1031, hence the additional "encrypted:"... line)
 > 

I've had problems with this encryption stuff before on some particular
platforms (PPC, but that's been fixed), but never on Windows, the
BSDs, Linux, or OSX. Did you run a reasonable number of tests using
the C clients directly? I'd like to know whether Perl has something to
do with it, because this part has been tested much less than the C
clients. Could be some weird quoting issue or something like that. If
I knew Perl better I'd go ahead and write a native implementation of
the encryption in Perl but I'm afraid this would take too much time
off my efforts to get 0.9.3 out the door. Any Perl gurus out there
with some spare time?

regards,
Markus

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

Re: [Refdb-users] ANN: RefDB 0.9.3-pre5 available

[Jakob B. <J....@bw...>]

Hi Markus, all,

thanks for the quick fix!
I testested it this morning, the numberized_passwd issues went like a 
charm out-of-the-box.
However, the "cannot lock tables" issue remains the same for my setup (I 
suppose this is a mySQL w32 issue, so maybe it is not worth investigating).
And now to the weird part ;-)
There seems to be a bug within enigma_encrypt: On _random_ occasions 
(though at least once a test.pl run) the denumberized password is 
incorectly decrypted. Here is from my refdbd log (I uncommented the 
printf in refdbd.c line 1031, hence the additional "encrypted:"... line)

/usr/src/RefDBClient-Client-1.6$> make test
logfile output:

healty - looking output here

---------------------------snip 8< --------------------

connected to database server using database:
perltest
command processing done, finish dialog now
child finished client on fd 4
adding client on fd 4
server waiting n_max_fd=4
parent removing client on fd 4
server waiting n_max_fd=3
try to read from client
serving client on fd 4 with protocol version 1
201-04-63-23
send pseudo-random string to client
listdb  -u testuser -w 121092107075
wheelpos:121092107075
encrypted:y\kK<< plain:pass<<
dbi_driver_dir went to:

dbi is up using default driver dir
131.155.xxx.xx
testuser
pass

3306
mysql

connected to database server using database:
refdb1
command processing done, finish dialog now
child finished client on fd 4
adding client on fd 4
server waiting n_max_fd=4
parent removing client on fd 4
server waiting n_max_fd=3
try to read from client
serving client on fd 4 with protocol version 1
120-80-71-20
send pseudo-random string to client
gettexbib -d perltest -s refdbteststyle -u testuser -w 121092107075  1
wheelpos:121092107075
encrypted:y\kK<< plain:Al6`<<
dbi_driver_dir went to:

dbi is up using default driver dir
131.155.xxx.xxx
testuser
Al6`
perltest
3306
mysql

failed to connect to database server
could not connect to database server
command processing done, finish dialog now
child finished client on fd 4

---------------------------snip 8< --------------------


(x-ed out my IP)

now the strange lines are
encrypted:y\kK<< plain:pass<<

and

encrypted:y\kK<< plain:Al6`<<

As I mentioned I could not find special conditions to reproduce this, it 
seems to happen at random with 'testuser:pass' . I tried with diffent 
"user:pass", same thing.
The enigma - stuff is a little bit over my head ;-), maybe you can make 
s.th. from this.

Do you have any idea?

Keep up the good work,

Cheers
Jakob


Markus Hoenicka wrote:

>Hi Jakob,
>
>(moving back to the list where you apparently meant to send your mail)
>
>Jakob Beetz writes:
> > 1. I was not able to get make test through, none of the subtests in 
> > test.pl was able to connect to the database when sending plain passwords 
> > in the coresponding subs in  Client.pm ( $cmd .= "-w $self->{passwd} "; 
> > ).  I could partly "solve" this by replacing the above lines with $cmd 
> > .= "-w $self->{numberized_passwd} "; which resolved the issue for most 
> > tests (however  10..21 still fails with "failed to connect to database 
> > server", strange enough the second call to $clientc->refdb_addref passes 
> > a different -w $self->{numberized_passwd} to refdbd after 9..10 
> > succeeded...)
> > 
>
>Your fix was absolutely correct. I never came across these typos as I
>run tests mostly on a SQLite database which doesn't care about
>username and password.
>
>$self->{numberized_passwd} will be different for each test as each
>connection to refdbd will result in a fresh scramble string which is
>used to encode the password.
>



>
> > 
> > 2. after "solving" this issue, refdb_addref could not be executed, 
> > stating "cannot lock tables" for  "testuser" created during the 
> > execution of test.pl. What I did was adding LOCK TABLES to the GRANT 
> > statements in refdba.c line 1176 ff. (However, as I did not want to 
> > touch the default rights to refdb1 I manually added LOCK TABLES for 
> > "testuser" (for the call  "LOCK TABLES [...] refdb1.t_journal_words 
> > WRITE" in 9..21))
> > 
>
>This fix should not be required unless there is a MySQL version issue
>at work (I still use a 3.23 release). The real problem was an
>uninitialized pointer that happened to be NULL in all my previous
>tests. Besides, the reference data used in make test did not match the
>latest risx.dtd and thus would have given strange results anyway.
>
>I've fixed all these issues. Please test the new prereleases as
>announced in a separate mail and see whether your table locking issue
>still persists.
>
>thanks for your testing
>Markus
>
>

[Refdb-users] ANN: RefDB-0.9.3-pre6 available

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

Hi all,

this new prerelease fixes a segfault in the import of risx
data. There's a couple of other minor changes, among them a relaxation
of the risx.dtd (contents is now optional). The RefDBClient module
required an update too, so please use these files for testing:

http://refdb.sourceforge.net/pre/refdb-0.9.3-pre6.tar.gz
http://refdb.sourceforge.net/pre/RefDB-perlmod-0.3_pre1.tar.gz
http://refdb.sourceforge.net/pre/RefDBClient-Client-1.6.tar.gz

regards
Markus

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

Re: [Refdb-users] ANN: RefDB 0.9.3-pre5 available

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

Hi Jakob,

(moving back to the list where you apparently meant to send your mail)

Jakob Beetz writes:
 > 1. I was not able to get make test through, none of the subtests in 
 > test.pl was able to connect to the database when sending plain passwords 
 > in the coresponding subs in  Client.pm ( $cmd .= "-w $self->{passwd} "; 
 > ).  I could partly "solve" this by replacing the above lines with $cmd 
 > .= "-w $self->{numberized_passwd} "; which resolved the issue for most 
 > tests (however  10..21 still fails with "failed to connect to database 
 > server", strange enough the second call to $clientc->refdb_addref passes 
 > a different -w $self->{numberized_passwd} to refdbd after 9..10 
 > succeeded...)
 > 

Your fix was absolutely correct. I never came across these typos as I
run tests mostly on a SQLite database which doesn't care about
username and password.

$self->{numberized_passwd} will be different for each test as each
connection to refdbd will result in a fresh scramble string which is
used to encode the password.

 > 
 > 2. after "solving" this issue, refdb_addref could not be executed, 
 > stating "cannot lock tables" for  "testuser" created during the 
 > execution of test.pl. What I did was adding LOCK TABLES to the GRANT 
 > statements in refdba.c line 1176 ff. (However, as I did not want to 
 > touch the default rights to refdb1 I manually added LOCK TABLES for 
 > "testuser" (for the call  "LOCK TABLES [...] refdb1.t_journal_words 
 > WRITE" in 9..21))
 > 

This fix should not be required unless there is a MySQL version issue
at work (I still use a 3.23 release). The real problem was an
uninitialized pointer that happened to be NULL in all my previous
tests. Besides, the reference data used in make test did not match the
latest risx.dtd and thus would have given strange results anyway.

I've fixed all these issues. Please test the new prereleases as
announced in a separate mail and see whether your table locking issue
still persists.

thanks for your testing
Markus

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

[Refdb-users] Re: Hello Hello Hello???

[<mar...@gm...>]

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        TRY IF I AM ON LINE<br>
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Re: [Refdb-users] RefMan/RIS questions

[Bruce D'A. <bd...@fa...>]

On Tue, 24 Jun 2003 07:28:38 -0800, "Bruce D'Arcus" <bd...@fa...>
said:
> I'm not sure if RefMan has something like Endnote's label field and the
> ability to use it in the temporary citation.  From what I can tell, it
> does not, so maybe that complicates my suggestion.  Still worth
> considering though...

Followup number 2: I didn't realize RefMan allows you to specify a
citation key in the ID field, but it does indeed.  Good!

Bruce

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                          wherever you are

Re: [Refdb-users] RefMan/RIS questions

[Bruce D'A. <bd...@fa...>]

On Tue, 24 Jun 2003 06:56:04 -0800, "Bruce D'Arcus" <bd...@fa...>
said:

> So, does RefMan have something equivalent, and if so, what is the
> temporary record syntax?

Ah, I found an answer at (especially starting on p253):

http://www.refman.com/support/docs/User%20Manual%20RM10.pdf

RefMan does indeed have something analogous to Endnote's sytem, but it is
also a little different. My reason for asking is some ideas I
communicated to Markus previously that relate to the next release (0.9.4)
and planned support for extended citations.  What I am proposing for
consideration is this:

Allowing for a "citation-compatability mode" feature, in which RefDB
could use the temporary citation forms of Endnote or RefMan as variant
short citation styles.  

In Endnote, I can specify that the "label" field -- which is where I
manually enter the citation key that gets exported to the RIS "ID" tag --
be used in place of the record ID.  This means I have citations like
{Jones, 1987, Jones1987a}, which would be the same as what I'd have in
RefDB, plus the additional comma-delimited author and year info.  If I
want to omit the author from the formatted citation, then I'd have {,
1987, Jones1987a}. 

I'd like to be able to use this form if possible, so that I don't have to
hassle with going through every single citation in my existing documents,
and so that I can also allow for collaboration with non-refdb users in
the future.

I'm not sure if RefMan has something like Endnote's label field and the
ability to use it in the temporary citation.  From what I can tell, it
does not, so maybe that complicates my suggestion.  Still worth
considering though...

Note: this document is also VERY useful for the RIS information, and the
field name mapping.  Download it Markus; it'll be useful if you get
around to your input DTD.  I'll also take a look to make sure my Endnote
export filter is right.  To answer my question about type, though, it
appears there is no such field, but RefMan uses the "misc 1" field to map
that info for various reference types.  Perhaps we ought to consider
something like this for RefDB, at least as suggested practice?

Bruce


-- 
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[Refdb-users] RefMan/RIS questions

[Bruce D'A. <bd...@fa...>]

For anyone with access to a copy of Reference Manager, I've got two
questions:

1) I've seen conflicting information on whether there is an RIS tag for
"type."  This is not reference type, but rather lower-level.  Example:
you might have an "email" type in a PCOMM record.  So, does RefMan in
fact have a field for this kind of thing, and what does it do with these
data when exported?

2) How does RefMan actually format citations?  In Endnote, for example,
one inserts a temporary citation with syntax like: [see also \Jones, 1998
#52@23]. (Note: the default citation delimters are actually
curly-brackets, but I don't know how to access them on this keyboard). In
this example, the backslash delimits where the actual citation begins,
the temporary citation itself is author, year, and record number,
followed by the @ symbol which indicates the following is the page
number(s) that ought to be added to the citation.

There is then a formatting stage in which Endnote scans for these
temporary citations, and replaces them with their formatted counterparts.
 This is thus analogous (sort of) to what refdb does.

So, does RefMan have something equivalent, and if so, what is the
temporary record syntax?

Bruce


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Re: [Refdb-users] can't create database conn struct

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

Hi,

Antti Vanne writes:
 > I tried the 0.9.3-pre5, and got a notch further:
 > 
 > connected to database server using database:
 > refdb1
 > SELECT VERSION()
 > 

Is that really the end of refdbd's log output? This would mean it
crashes right away. The whole log output of a viewstat command looks
like this on my box:

server waiting n_max_fd=4
try to read from client
serving client on fd 5 with protocol version 1
102-86-47-14
send pseudo-random string to client
viewstat  -u root -w 102073083099101051051
dbi_driver_dir went to:

dbi is up using default driver dir
localhost
root
xxx

5432
mysql

connected to database server using database:
refdb1
SELECT VERSION()
command processing done, finish dialog now
child finished client on fd 5
child exited with code 0
server waiting n_max_fd=4


 > this is refdbd's output when viewstat is run and this is from the rfdba 
 > screen:
 > 
 > refdba: viewstat
 > 
 > Connected via mysql driver (dbd_mysql v0.6.7)
 > to: ERROR
 > serverip: localhost
 > timeout: 60
 > dbs_port: 3306
 > logfile: /var/log/refdbd.log
 > logdest: 0
 > loglevel: 7
 > remoteadmin: off
 > pidfile: /var/run/refdbd.pid
 > 
 > So I guess it almost works now :)  However, trying for example 
 > "listword" gives me:
 > 

I beg to differ. The "ERROR" thing above means that libdbi cannot
execute the simple query "SELECT VERSION()" properly. If your make
check results in libdbi wouldn't tell me otherwise, I'd say libdbi is
broke on your box.

 > connected to database server using database:
 > refdb1
 > SELECT DISTINCT name FROM t_journal_words WHERE name RLIKE '.*'
 > 
 > and
 > 
 > refdba: listword
 > ERROR
 > 
 > aborting...
 > could not read from refdbd. Stop
 > 
 > This in the refdba prompt.
 > 

This again would point to a refdbd crash. I've never seen this on any
of my platforms.

 > > As for the failed connection, the most likely reason is that you run
 > > your mysqld with the --skip-networking option (or the corresponding entry
 > > in my.cnf). refdbd always uses TCP/IP even when it talks to a database
 > > server on the local machine.
 > 
 > I start the mysqld from the standard mdk /etc/init.d/mysql, and nmapping 
 > localhost shows that 3306 is open and I can also telnet localhost 3306 
 > just fine. So this is like it should be right?
 > 

Yeah, this looks ok to me.

I'm at a loss how to debug this problem. It just looks weird to
me. Did you build your libdbi from the sources or did you use some
RPM's? Did you try building and installing again from scratch?

regards,
Markus

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

Re: [Refdb-users] can't create database conn struct

[Antti V. <Ant...@uk...>]

Markus Hoenicka wrote:
> added some debug information to track this down. Could you please try
> the prerelease that I've just announced in a separate mail?

I tried the 0.9.3-pre5, and got a notch further:

connected to database server using database:
refdb1
SELECT VERSION()

this is refdbd's output when viewstat is run and this is from the rfdba 
screen:

refdba: viewstat

Connected via mysql driver (dbd_mysql v0.6.7)
to: ERROR
serverip: localhost
timeout: 60
dbs_port: 3306
logfile: /var/log/refdbd.log
logdest: 0
loglevel: 7
remoteadmin: off
pidfile: /var/run/refdbd.pid

So I guess it almost works now :)  However, trying for example 
"listword" gives me:

connected to database server using database:
refdb1
SELECT DISTINCT name FROM t_journal_words WHERE name RLIKE '.*'

and

refdba: listword
ERROR

aborting...
could not read from refdbd. Stop

This in the refdba prompt.

> As for the failed connection, the most likely reason is that you run
> your mysqld with the --skip-networking option (or the corresponding entry
> in my.cnf). refdbd always uses TCP/IP even when it talks to a database
> server on the local machine.

I start the mysqld from the standard mdk /etc/init.d/mysql, and nmapping 
localhost shows that 3306 is open and I can also telnet localhost 3306 
just fine. So this is like it should be right?

Thanks a lot for you time, really appreciate it.

-- 
Ant...@uk...   | Department of Applied Physics
tel. +358 17 162 279 | University of Kuopio

Re: [Refdb-users] can't create database conn struct

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

Hi,

Antti Vanne writes:
 > After starting the refdbd with options -s -e0 -l7 -Y /usr/local/lib/dbd/ 
 > I get a different error:
 > 
 > 3306
 > mysql
 > /usr/local/share/refdb/db
 > failed to connect to database server
 > 
 > but I don't get anything related to mysql to logfiles in /var/log or 
 > /var/lib/mysql. I'm still running refdbd & refdba as root, and root is 
 > able to use the refdb1 database using the mysql client.
 > 

This at least gives me a clue. Some sort of memory corruption
apparently overwrites the dbi_driver_dir string (or is it never
initialized to an empty string due to some weird compiler
"optimization"?). I've fixed a couple of minor issues in refdbd.c and
added some debug information to track this down. Could you please try
the prerelease that I've just announced in a separate mail?

As for the failed connection, the most likely reason is that you run
your mysqld with the --skip-networking option (or the corresponding entry
in my.cnf). refdbd always uses TCP/IP even when it talks to a database
server on the local machine.

 > My box is behind a firewall, and I'd get cold feet giving access to 
 > people outside my organization. But yes I could try out modified 
 > versions, if this new info doesn't help any further.
 > 

That's fine with me. Having control over other people's machines makes
me nervous anyway. If the prerelease doesn't fix the problem for you,
I'll send you patches for testing.

regards,
Markus

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

Re: [Refdb-users] CGI query interface docs?

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

Jakob Beetz writes:
 > The installation went really smooth on cygwin, (nearly) no complains 
 > here. The only thing that could maybe be mentioned in the documentation 
 > is that for cygwin users who work with the binary distro of mySQL  (and 
 > evt. compiled an additional mysql --without-server it  within cygwin, as 
 > I did) it is very important to start the server with  -i 
 > my.real.ip.address because the binary has no socket-support. and thus 
 > calls to localhost will fail.

Ah, I remember this from an earlier post. I'll add this to the docs.

thanks,
Markus

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