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Dominik Reusser | 6 Mar 2007 18:28
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reduced version of checkref

Hi there,
I have refdbd running on a rather old debian box with quite a large database 
(~2400 records). If I try to run checkref with this setup, I end up with 
timeouts and no results. So I am still required to check references manually.

Would it be possible to turn off certain checks (such as keywords, user 
notes,..) and just compare for example author, year, journal, issue, pages 
and title?

Also, I do have some duplicates in my database. Is there an efficient way to 
get a list of possible duplicates through refdbc/refdba? Of course I could 
run SQL-queries to get this information. But maybe there is a more efficient 
way?

Thanks
Dominik

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Markus Hoenicka | 7 Mar 2007 00:01
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reduced version of checkref

Dominik Reusser writes:
 > Hi there,
 > I have refdbd running on a rather old debian box with quite a large database 
 > (~2400 records). If I try to run checkref with this setup, I end up with 
 > timeouts and no results. So I am still required to check references manually.

This is just a matter of increasing your timeout settings both on the
server and client side. The default timeouts turned out to be too
short for the kind of database processing required for checkref. If
you're running refdbc and refdbd on the same computer, you can set
both timeouts to zero to avoid this problem altogether (there should
be no networking problems on the loopback device, after all).

 > 
 > Would it be possible to turn off certain checks (such as keywords, user 
 > notes,..) and just compare for example author, year, journal, issue, pages 
 > and title?
 > 

I've been pondering this too. I get a serious number of possible
keyword duplicates when using Pubmed data, which is well endowed with
keywords of all sorts. Maybe we should use the -S switch to select the
fields to check, instead of to select the additional fields for the
xhtml output.

 > Also, I do have some duplicates in my database. Is there an efficient way to 
 > get a list of possible duplicates through refdbc/refdba? Of course I could 
 > run SQL-queries to get this information. But maybe there is a more efficient 
 > way?
 >
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Ďoďo | 14 Mar 2007 10:26
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RefDB web page..

Hi guys,

I have a feeling that on RefDB web pages, in the news, is incorrect
year. First I thought that web page was not modified for more then one
year, but now I am sure it is a typo.

Jozef

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Markus Hoenicka | 14 Mar 2007 10:40
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Re: RefDB web page..

Hi Jozef,

thanks for catching this. Boon and bane of copy and paste...

regards,
Markus

Quoting ?o?o <dodo.sk <at> gmail.com>:

> Hi guys,
>
> I have a feeling that on RefDB web pages, in the news, is incorrect
> year. First I thought that web page was not modified for more then one
> year, but now I am sure it is a typo.
>
> Jozef
>

--

-- 
Markus Hoenicka
markus.hoenicka <at> cats.de
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

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Markus Hoenicka | 14 Mar 2007 11:27
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Re: RefDB web page..

Hi,

it would be helpful to know what platform you are using. Are you using  
the Debian packages? In that case, David should have the authoritative  
answer. But I recall that the packages depend on libdbd-sqlite and  
thus indirectly on sqlite in order to provide a working setup with the  
smallest possible download. Having sqlite installed even if you're not  
going to use it adds just a few kb to your box (sqlite is tiny  
compared to MySQL or PostgreSQL). If you change the database  
dependency from required to suggested, lots of users may end up with a  
RefDB installation that simply does not work due to a lack of a  
database engine.

regards,
Markus

Quoting Ďoďo <dodo.sk <at> gmail.com>:

> Hi Markus,
>
> I have one more issue. Why:
>
> The following packages have unmet dependencies:
>  refdb-server: Depends: libdbd-sqlite (>= 0.8.1-2) but it is not
> going to be installed
> E: Broken packages
>
> if I do not want to use sqlite at all and I plan to use mysql? I
> understand that during the instalation process it is difficul to know
> what user will use, but to have the package in suggested package would
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Ďoďo | 14 Mar 2007 11:43
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Re: RefDB web page..

Markus,

I tried year ago with SQLite and I was not able to get it running. May
be you recall. Problem with database version with RefDb.
Now I gave a second try but with the mySql.  On the standard debian
system.(Sarge).
I have nothing against installing one more library - I fully agree
with your args - but  the version of libdb-sqlite required by
refdb-server in testing version is not available in any of Debian
distributio. There such package only in stable and unstable version
and just  0.7.1. But version required by refdb server is >= 0.8.1-2.
So if the plan was to have simple instalation, then it failed ;)

Jozef

On 3/14/07, Markus Hoenicka <markus.hoenicka <at> mhoenicka.de> wrote:
> Hi,
>
> it would be helpful to know what platform you are using. Are you using
> the Debian packages? In that case, David should have the authoritative
> answer. But I recall that the packages depend on libdbd-sqlite and
> thus indirectly on sqlite in order to provide a working setup with the
> smallest possible download. Having sqlite installed even if you're not
> going to use it adds just a few kb to your box (sqlite is tiny
> compared to MySQL or PostgreSQL). If you change the database
> dependency from required to suggested, lots of users may end up with a
> RefDB installation that simply does not work due to a lack of a
> database engine.
>
> regards,
(Continue reading)

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Markus Hoenicka | 14 Mar 2007 11:56
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Re: RefDB web page..

Hi Jozef,

did you try to use the .debs provided by libdbi (see  
http://libdbi.sourceforge.net/download.html)? They should be fresher  
than those in the Debian repositories.

In any case, both the RefDB and the libdbi/libdbi-drivers Debian  
packages are outdated compared to the source releases. David, are you  
listening? Will you be able to update the packages anytime soon?

regards,
Markus

Quoting Ďoďo <dodo.sk <at> gmail.com>:

> Markus,
>
> I tried year ago with SQLite and I was not able to get it running. May
> be you recall. Problem with database version with RefDb.
> Now I gave a second try but with the mySql.  On the standard debian
> system.(Sarge).
> I have nothing against installing one more library - I fully agree
> with your args - but  the version of libdb-sqlite required by
> refdb-server in testing version is not available in any of Debian
> distributio. There such package only in stable and unstable version
> and just  0.7.1. But version required by refdb server is >= 0.8.1-2.
> So if the plan was to have simple instalation, then it failed ;)
>

--

--
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Ďoďo | 14 Mar 2007 12:48
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Re: RefDB web page..

Thanks Markus,

by adding also second deb pkg source from SF the isntalation run
without any problem. Let's see what will happend during the
configuration ;)

Jozef

On 3/14/07, Markus Hoenicka <markus.hoenicka <at> mhoenicka.de> wrote:
> Hi Jozef,
>
> did you try to use the .debs provided by libdbi (see
> http://libdbi.sourceforge.net/download.html)? They should be fresher
> than those in the Debian repositories.
>
> In any case, both the RefDB and the libdbi/libdbi-drivers Debian
> packages are outdated compared to the source releases. David, are you
> listening? Will you be able to update the packages anytime soon?
>
> regards,
> Markus
>
> Quoting Ďoďo <dodo.sk <at> gmail.com>:
>
> > Markus,
> >
> > I tried year ago with SQLite and I was not able to get it running. May
> > be you recall. Problem with database version with RefDb.
> > Now I gave a second try but with the mySql.  On the standard debian
> > system.(Sarge).
(Continue reading)

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Mathias Krueger | 15 Mar 2007 17:55
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error after checkref

After execute the checkref command I got the following error n the 
refdbd.log: 

7:pid=29339:Thu Mar 15 16:43:49 2007:CREATE TEMPORARY TABLE t_temp_meta 
(meta_app VARCHAR(
20),meta_type VARCHAR(20),meta_version VARCHAR(20),meta_dbversion 
SMALLINT,meta_create_dat
e TIMESTAMP,meta_modify_date TIMESTAMP)
7:pid=29339:Thu Mar 15 16:43:51 2007:CREATE TEMPORARY TABLE t_temp_refdb 
(refdb_id BIGSERI
AL,refdb_citekey VARCHAR(255) UNIQUE,refdb_type VARCHAR(6),refdb_pubyear 
SMALLINT,refdb_se
cyear SMALLINT,refdb_startpage VARCHAR(255),refdb_endpage 
VARCHAR(255),refdb_abstract TEXT
,refdb_title TEXT,refdb_volume VARCHAR(255),refdb_issue 
VARCHAR(255),refdb_booktitle TEXT,
refdb_city VARCHAR(255),refdb_publisher VARCHAR(255),refdb_title_series 
TEXT,refdb_address
TEXT,refdb_issn VARCHAR(255),refdb_pyother_info 
VARCHAR(255),refdb_secother_info VARCHAR(
255),refdb_periodical_id BIGINT,refdb_user1 VARCHAR(255),refdb_user2 
VARCHAR(255),refdb_us
er3 VARCHAR(255),refdb_user4 VARCHAR(255),refdb_user5 
VARCHAR(255),refdb_misc1 VARCHAR(255
),refdb_misc2 VARCHAR(255),refdb_misc3 VARCHAR(255),PRIMARY KEY (refdb_id))
7:pid=29339:Thu Mar 15 16:43:53 2007:ERROR:  failed to re-find parent key in 
"pg_attribute
_relid_attnam_index" 

3:pid=29339:Thu Mar 15 16:43:53 2007:create t_refdb failed
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Markus Hoenicka | 16 Mar 2007 00:50
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error after checkref

Mathias Krueger writes:
 > 7:pid=29339:Thu Mar 15 16:43:53 2007:ERROR:  failed to re-find parent key in 
 > "pg_attribute
 > _relid_attnam_index" 
 > 
 > 3:pid=29339:Thu Mar 15 16:43:53 2007:create t_refdb failed
 > 2:pid=29339:Thu Mar 15 16:43:53 2007:create temporary table failed
 > 6:pid=29339:Thu Mar 15 16:43:53 2007:child finished client on fd 6 
 > 
 > i use postgres as the database-server, any ideas?
 > other command like getref work. 
 > 

This seems to be a bug in some versions of PostgreSQL. I don't see
this problem with 8.08 on FreeBSD, but Google mentions it a couple of
times for 7.4.x and 8.1.x versions. Do you have a chance to up- or
downgrade to a different version?

regards,
Markus

--

-- 
Markus Hoenicka
markus.hoenicka <at> cats.de
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

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