refdb-users — List for RefDB users

[Refdb-users] jEdit interface to RefDB

[Damien J. D. <D.J...@cs...>]

Dear all

Resending to RefDB users list.

If anyone has ideas for what they'd like to see in a jEdit interface to 
RefDB please let me know as I am about to start working on one. What I 
will create is a graphical database browsing tool to allow quick entry, 
retrieval and manipulation of references in core formats.

More details below.

Regards
Damien

-------- Original Message --------
Subject: [Refdb-devel] jEdit interface to RefDB
Date: Fri, 23 Jun 2006 12:56:34 +0100
From: Damien Jade Duff <D.J...@cs...>
To: ref...@li...,	Markus Hoenicka 
<mar...@mh...>

Hello all

I am planning to make some improvements to my basic jEdit RefDB
interface and since maybe one day this might be useful to someone else,
I think I'm justified in seeing if anyone wants to comment before I get
up to my armpits in the technical details of java GUI building. If
you're interested in jEdit GUIs for RefDB, read on.

At the moment all I have is a hacked-together jEdit dockable that allows
me to add references and notes in bibtex, ris, risx, update them in ris
or risx, delete them by id, get lists of them via a search field, etc.
as well as dumping an risx template to the editing buffer. It calls
refdbc directly and passes and retrieves info through the command-line,
STDOUT, STDIN, STDERR, etc.

However, I have a sizeable number of references (about 120) in the
system now and my interface is too clunky. It takes a few seconds to
pull back all the references from my local postgresql db, no matter the
format, so I'd like to have a way of browsing the references in an
easier, faster and more intelligent way. Also, linking references and
notes is a bugger because I've got to remember the keys of each one,
etc. Optimally I'd like to be able to jump to a reference and start
entering notes on it, linking it to other references and notes, etc

Essentially, I want to be browsing a visual structure of references and
notes, like a tree (as with the BufferList plugin or something similar).

Incidentally, in order to create links directly between xnotes at
present I would have to create dummy references for these to point to.
Is this sensible, or am I trying to push the system too far?  (i.e. as
well as keeping a bibliography I want to use the system to keep notes
and it seems nearly adapted to this in structure). Whaddya reckon?

Anyway, I think I have two ways forward - a tightly-coupled approach
where I get small chunks of info back from refdbc only when I need it,
and a loosely-coupled approach where I download a whole bunch of barely
pre-filtered info from refdbc into jEdit memory space and make some
effort to keep it synchronised.

The former has the advantage that it doesn't stretch jEdit's memory and
is has a reasonably straightforward partial-synchronisation strategy.
But it means that I need to impose more structure on my reference
database so that I can browse it in a local fashion. refdbc does provide
a facility for extracting the author list, keyword list, journal list,
etc though unfortunately there is no facility for an anadorned list of
citation keys or note keys (I could probably figure how to do this even
though c gives me a headache, but perhaps it could be included in the
next release...? Also, presumably titles are not indexed fields). I
_think_ refdb should be fast enough if I choose my methods of data
extraction right.

The latter has the advantage that I can do quick searches through the
data locally without requiring too much structure in the database (e.g.
title, keyword, author searches). Essentially I can do what I want with
the data. But a lot of the data needs to be kept in jEdit memory space,
and if I want to produce something that is scaleable to industrial
operations it may not be perfect (should I care about this?), and it
somewhat defeats the purpose of keeping them in a database since I
could've just read it all in from a flat file.

Ultimately, the former is an alluring option because it absolutely
forces me to add some more structure to my DB, which I see happening by
exploiting the xnotes facility and exploiting the keyword facility in a
more disciplined way (e.g. rather than adding the keywords "genetic
programming", and "example source", I add the keywords "entered
for/example source", "subject/genetic programming"). But the latter is
going to be faster to use. Any ideas would be welcome.

However I do this part, the visible result will be a jEdit dockable that
contains a tree of references and notes. Filtering is possible, as well
as changing which tree model is displayed (e.g. by author last-name or
title or keyword, or, best, by citation key, if we can change refdbc to
dump an anadorned list of citation keys). Adding of links should be a
case of selecting multiple items and clicking "Link" (probably a
context-sensitive menu). Actual editing of entries is still done using
the jEdit XML tool validating against the risx dtd, or via plaintext RIS
or bibtex mode (though only for new entries). Note, also, I have no
current plans to integrate any of this with docbook or latex because I
don't use docbook and because the command-line latex tools are
sufficient at present (though of course facilities for copying citation
keys to the clipboard are easy enough to do).

Anyway, I've rambled on enough. If you want some input into this
project, or you just have some half-baked ideas, please post back to the
list. If someone has already made a start on something I'd like to hear
more about it. At my expected rate of progress, I don't anticipate
having anything worth sharing for some time (maybe 6 months).

Peace
Damien

Using Tomcat but need to do more? Need to support web services, security?
Get stuff done quickly with pre-integrated technology to make your job 
easier
Download IBM WebSphere Application Server v.1.0.1 based on Apache Geronimo
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Re: [Refdb-users] Numbers only in PY?

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

Daniel O'Donnell <dan...@ul...> was heard to say:

> 1) How would people recommend handling works with a range as a PY?
>

The PY field as mandated by RIS has the following format:

YYYY/MM/DD/<text>

That is, the date proper cannot be a range. However, you can encode the range as
a free-form text in the trailing optional <text>. This is probably less than you
had hoped for, but at least you can preserve the information.


> 2) Am I right that, in mysql at least, searches for non-numerical
> characters in PY don't work? I keep getting errors when I try something
> like getref :PY:~-  or getref :PY:~\- or getref :PY:~[-] getref :PY:=-
>

This is right. :PY: refers only to the publication year. This is treated as a
numerical value internally. I wonder if it should be treated as a date
(including the month and day info, if available) instead.

regards,
Markus

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

[Refdb-users] Numbers only in PY?

[Daniel O'D. <dan...@ul...>]

Hi,

Just checking I've got this right...

My legacy data has a number of entries with ranges in PY (e.g. 1883-1920
or 1933-). When refdb assigns the CK field it treats these as nd.

I have two questions:

1) How would people recommend handling works with a range as a PY?

2) Am I right that, in mysql at least, searches for non-numerical
characters in PY don't work? I keep getting errors when I try something
like getref :PY:~-  or getref :PY:~\- or getref :PY:~[-] getref :PY:=-

I was doing (2) to try an identify the records that have the problematic
- in PY.
-d
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

Re: [Refdb-users] ANN: RefDB 0.9.7 released

[Rich S. <rsh...@ap...>]

On Mon, 26 Jun 2006, Markus Hoenicka wrote:

> No, there is no need to do this.

   Thanks.

> The latter will be available online hopefully tomorrow.

   Are you working over the weekend because your city has been invaded by the
World Cup?

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] ANN: RefDB 0.9.7 released

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

Hi,

Rich Shepard writes:
 > On Sun, 25 Jun 2006, Markus Hoenicka wrote:
 > 
 > > I've uploaded version 0.9.7 of RefDB.
 > 
 > Markus,
 > 
 >    Is this sufficiently different from -pre7 that I should build and install
 > over the existing installation?
 > 

No, there is no need to do this. The binaries are the same except
refdbd which now checks for the main database and database version
only once per parent session (pre7 and earlier check once per child
session). Most of the changes since pre7 are minor changes to the
setup script (which you don't need if pre7 is already running) as well
as an update of the documentation. The latter will be available online
hopefully tomorrow.

regards,
Markus

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

Re: [Refdb-users] ANN: RefDB 0.9.7 released

[Rich S. <rsh...@ap...>]

On Sun, 25 Jun 2006, Markus Hoenicka wrote:

> I've uploaded version 0.9.7 of RefDB.

Markus,

   Is this sufficiently different from -pre7 that I should build and install
over the existing installation?

Thanks,

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] ANN: RefDB 0.9.7 released

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

Hi,

I've uploaded version 0.9.7 of RefDB. Currently only the source
package is available, but I hope that the Cygwin binaries as well as
an updated starter package will follow in due time. Moreover, it is
likely that we will soon see RPM packages.

The new release is available for download here:

http://sourceforge.net/project/showfiles.php?group_id=26091&package_id=19605&release_id=427590

Please report any problems to the list. A list of bugfixes and new
features is appended below. Please note that the ChangeLog included in
the sources covers only the changes that were applied since the
sources were moved from CVS to Subversion. There were more changes
since 0.9.6 while the code was managed with CVS.

regards,
Markus


Bugfixes:

- multiple citation texts are now properly included in the character
  encoding conversion

- periodical titles need to be escaped during import

- a possible segfault during the formatting of journal names in
  bibliographies was fixed

- the formatting (bold, italics, superscript and so on) of intext
  citations was fixed for both the DSSSL and the XSL stylesheets

- fixed missing preceding/following export in journal names during
  style export

- all XML output now correctly exports empty strings as empty elements
  instead of dropping the element

- bibliography titles are now left empty if the style says so, instead
  of inventing a default title

- fixed a crash in the bibliography generation code when an URL was
  missing

- print empty part title instead of none to make the output comply
  with the DTD

- fixed possible segfaults if the automatic keyword scan ran without
  any keywords

- fixed client/server dialog mishap in refdbc:getref, refdbc:getnote
  and getbib

- assorted causes of segfaults during bibliography creation were
  eliminated

- build problems on Debian due to the lack of
  batik-rasterizer. ./configure now checks for this image converter
  and falls back to ImageMagick's convert if the former is not
  available. The latter produces buttugly output from the SVG sources
  but this is better than a build that fails.

- style problems due to bugs in refdb.dump.mysql and
  refdb.dump.mysql41. The *NAMEORDER field sizes were chosen too short
  which caused valid values for these fields to become truncated when
  MySQL was used as the database engine. See the instructions in
  UPGRADING if you're a MySQL user.

- refdbd now uses the path to DB_VERSION from the config file instead
  of a compile-time value

Improvements

- added a refdb-init.sh script that helps setting up RefDB after
  installation

- added a citationlistx backend to support refdb-publist

- some fixes in the bibtex export

- the XML headers now contain a larger selection of predefined
  entities

- FIRSTSPCM (without a dot) was added to the *NAMEORDER values

- support for multi-head tex citations was added

- import and export fixes for CONF, HEAR, and ELEC types

- replaced SGML manual sources by XML sources

- replaced handcrafted man pages by DocBook output

- the logic of the configure switch to build docs was reversed: docs
  are now built by default (this is required to install the prebuilt
  docs), but if you run into problems when building from the CVS
  sources you can disable the docs by means of the --disable-docs
  switch

- alltitles and link0 support was added to the dsssl stylesheets

- the biblioset and bibliomset grouping was improved in the
  bibliography output

- alltitle, which is the only useful title code if you want titles in
  the in-text citations, is now supported

- LINK ROLE="0", MISC, and USERDEF without role attribute are now
  properly imported

- the key/citekey mismatch in the notes import code was fixed

- removed a pair of parens from print/docbook-refdb-dsl which caused a
  warning

- style export now includes the character encoding into the processing
  instruction line

- the Makefile created by refdbnd no longer removes the source file
  using the full citation format when running make clean. If you
  really need to do this, run "make shortclean". This change was done
  to better support refdb-mode which uses the full citation format by
  default.

- fixed a bug in the packaging code which kept refdb-backup and
  refdb-restore out of the tarball

- the main database version check and the update of the database
  version file are now performed only once per refdbd session

- marc2ris now imports the call numbers contained in the MARC fields
  050 (AV) and 082 (U1)


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

Re: [Refdb-users] Field math advice

[Daniel O'D. <dan...@ul...>]

Thanks Damien,

I'm using mysql, but I'll take this as a starting point and see what I
can do.

-d

On Sun, 2006-25-06 at 19:59 +0100, Damien Jade Duff wrote:
> Gidday Daniel
> 
> This may be a bit hacky, it's something I wrote when I first started, 
> working around my own lack of knowledge. It's the script I used once to 
> get arbitrary sql queries out of REFDB using postgresql. I've changed it 
> so that the sql command is close to the one that you'd want. Also you 
> have to enter your database name and you may have to add username and 
> password details if they're not already set up in config files etc. and 
> to use the database client you're using.
> 
> Peace
> Damien
> 
> echo -- start script --
> 
> rm -f out.111
> 
> rm -f out.222
> 
> rm -f out.333
> 
> psql DBNAME -t -c "select refdb_citekey from t_refdb where 
> to_number(refdb_startpage,"9999999999") > 
> to_number(refdb_endpage,"9999999999");">out.111
> 
> cat out.111 | echo :ID:\>9999 `sed -e 's/ / OR :CK:=/g'` > out.222
> 
> refdbc -d djdphd -C getref -t ris `cat out.222` > out.333
> 
> cat out.333
> 
> echo -- end script --
> 
> Daniel O'Donnell wrote:
> > Hi all,
> > 
> > A question:
> > 
> > In adding legacy data to my refdb database, I have inconsistencies in
> > the way end page numbers are represented: they can show up in any of the
> > following formats:
> > 
> > a) 323-324
> > b) 323-24
> > c) 323-4
> > 
> > I think I'd prefer (a), because the others can all be derived from it.
> > What I'd been thinking of doing was trying to extract the records that
> > are in the form (b) or (c) and then manually correct them (if somebody
> > has a better idea, I'd love to hear it).
> > 
> > To find the ones I wanted, I thought I'd use something like this:
> > 
> > refdbc: getref :EP:<:SP:
> > 
> > But this clearly isn't doing what I'm expecting, as here are my first
> > three results (of hundreds); ideally of these three, only the first
> > should show up; the second one in the list actually has an EP that is
> > larger than SP, though it isn't showing up in the output:
> > 
> > ID*:1 (1992)
> > Key: ABRAHAM1992
> > Abraham,Lenore
> > Cædmon's Hymn and the Geþwærnysse (fitness) of things
> > American Benedictine Review 43:331-44
> > 
> > ID*:5 (1998)
> > Key: SZARMACH1998
> > Szarmach,Paul E.
> > Anthem: Auden's Caedmon's Hymn
> > 
> > in: Utz,Richard J., Shippey,T.A., Workman,Leslie J., University of
> > Sydney, Centre for Medieval Studies(ed.), Medievalism in the modern
> > world essays in honour of Leslie J. Workman; part of: Making the Middle
> > Ages
> > Series Volume: v. 1pp. 329-340
> > 
> > 
> > Any suggestions?
> > 
> > -d
> > 
-- 
Daniel Paul O'Donnell
Associate Professor and Chair of English
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
University of Lethbridge
Lethbridge AB T1K 3M4
Canada

Vox +1 403 329-2377
Fax +1 403 382-7191

:@caedmon/ubuntu

Re: [Refdb-users] Field math advice

[Damien J. D. <D.J...@cs...>]

Gidday Daniel

This may be a bit hacky, it's something I wrote when I first started, 
working around my own lack of knowledge. It's the script I used once to 
get arbitrary sql queries out of REFDB using postgresql. I've changed it 
so that the sql command is close to the one that you'd want. Also you 
have to enter your database name and you may have to add username and 
password details if they're not already set up in config files etc. and 
to use the database client you're using.

Peace
Damien

echo -- start script --

rm -f out.111

rm -f out.222

rm -f out.333

psql DBNAME -t -c "select refdb_citekey from t_refdb where 
to_number(refdb_startpage,"9999999999") > 
to_number(refdb_endpage,"9999999999");">out.111

cat out.111 | echo :ID:\>9999 `sed -e 's/ / OR :CK:=/g'` > out.222

refdbc -d djdphd -C getref -t ris `cat out.222` > out.333

cat out.333

echo -- end script --

Daniel O'Donnell wrote:
> Hi all,
> 
> A question:
> 
> In adding legacy data to my refdb database, I have inconsistencies in
> the way end page numbers are represented: they can show up in any of the
> following formats:
> 
> a) 323-324
> b) 323-24
> c) 323-4
> 
> I think I'd prefer (a), because the others can all be derived from it.
> What I'd been thinking of doing was trying to extract the records that
> are in the form (b) or (c) and then manually correct them (if somebody
> has a better idea, I'd love to hear it).
> 
> To find the ones I wanted, I thought I'd use something like this:
> 
> refdbc: getref :EP:<:SP:
> 
> But this clearly isn't doing what I'm expecting, as here are my first
> three results (of hundreds); ideally of these three, only the first
> should show up; the second one in the list actually has an EP that is
> larger than SP, though it isn't showing up in the output:
> 
> ID*:1 (1992)
> Key: ABRAHAM1992
> Abraham,Lenore
> Cædmon's Hymn and the Geþwærnysse (fitness) of things
> American Benedictine Review 43:331-44
> 
> ID*:5 (1998)
> Key: SZARMACH1998
> Szarmach,Paul E.
> Anthem: Auden's Caedmon's Hymn
> 
> in: Utz,Richard J., Shippey,T.A., Workman,Leslie J., University of
> Sydney, Centre for Medieval Studies(ed.), Medievalism in the modern
> world essays in honour of Leslie J. Workman; part of: Making the Middle
> Ages
> Series Volume: v. 1pp. 329-340
> 
> 
> Any suggestions?
> 
> -d
> 

[Refdb-users] Field math advice

[Daniel O'D. <dan...@ul...>]

Hi all,

A question:

In adding legacy data to my refdb database, I have inconsistencies in
the way end page numbers are represented: they can show up in any of the
following formats:

a) 323-324
b) 323-24
c) 323-4

I think I'd prefer (a), because the others can all be derived from it.
What I'd been thinking of doing was trying to extract the records that
are in the form (b) or (c) and then manually correct them (if somebody
has a better idea, I'd love to hear it).

To find the ones I wanted, I thought I'd use something like this:

refdbc: getref :EP:<:SP:

But this clearly isn't doing what I'm expecting, as here are my first
three results (of hundreds); ideally of these three, only the first
should show up; the second one in the list actually has an EP that is
larger than SP, though it isn't showing up in the output:

ID*:1 (1992)
Key: ABRAHAM1992
Abraham,Lenore
Cædmon's Hymn and the Geþwærnysse (fitness) of things
American Benedictine Review 43:331-44

ID*:5 (1998)
Key: SZARMACH1998
Szarmach,Paul E.
Anthem: Auden's Caedmon's Hymn

in: Utz,Richard J., Shippey,T.A., Workman,Leslie J., University of
Sydney, Centre for Medieval Studies(ed.), Medievalism in the modern
world essays in honour of Leslie J. Workman; part of: Making the Middle
Ages
Series Volume: v. 1pp. 329-340


Any suggestions?

-d

-- 
Daniel Paul O'Donnell
Associate Professor and Chair of English
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
University of Lethbridge
Lethbridge AB T1K 3M4
Canada

Vox +1 403 329-2377
Fax +1 403 382-7191

:@caedmon/ubuntu

Re: [Refdb-users] Parsing error ? with addref

[Daniel O'D. <dan...@ul...>]

Thanks Markus and Rich,

The single letter keywords are partially a legacy data issue and
partially disciplinary. In manuscript and textual studies some
manuscripts are known by 1 or 2 letter sigla: Corpus Christi College
Manuscript 41 is known as b1 to most Anglo-Saxonists. Also you could
have an article about the Anglo-Saxon word æ. In previous databases, we
keyworded things like this because searching all fields was more
difficult. My plan in refdb is to rationalise things.

The multiple keywords is also a legacy of some script a student ran
through once.

I'd read the data mangling section but missed the significance of what
refdb was doing. I'll turn it off until the data is in better shape, I
think!

-d

On Sun, 2006-25-06 at 00:02 +0200, Markus Hoenicka wrote:
> Rich Shepard writes:
>  >    As far as the keyword order is concerned, that's a PostgreSQL thing. Rows
>  > (tuples) are returned from a query in no particular order. Unless the query
>  > has an ORDERED BY clause, we'll see this every time. It's not any sort of a
>  > bug or issue of concern.
>  > 
> 
> This is correct. It applies to all database engines as the SQL
> standard does not mandate a particular order of the returned datasets
> unless the ORDERED BY clause is used. RefDB does not use this clause
> here as the order of keywords is not relevant in RIS. It uses the
> clause for author names as their order in the RIS dataset is relevant.
> 
>  > the name. What I don't see in your command line is the option to write the
>  > returned records to a file, e.g., '-o hereiam.ris'. I wonder if you'll see
>  > the same output in a file that you see on screen,
>  > 
> 
> The output is the same except for the summary which is sent to
> stderr. You see it on the screen as it displayes both stuff sent to
> stdout (the data) and to sterr (the summary). If you send the output
> to a file, it will contain the part sent to stout only.
> 
>  > > The problem is the following keyword section
>  > >
>  > > KW  - l
>  > >> KW  - m
>  > >> KW  - o
>  > >> KW  - ld
>  > >> KW  - h
>  > >> KW  - æ
>  > >> KW  - Cædmon
>  > 
>  > > These are all unique keywords drawn from other entries in the original
>  > > RIS file. They show up multiple times in the refdb generated ris files.
>  > 
> 
> This is caused by the automatic keyword scan which is turned on by
> default. RefDB scans the titles and abstracts of new entries for
> keywords already known to the database. This is a very useful feature
> in most cases. However, if you indeed use single-letter keywords, the
> purpose of the automatic keyword scan is pretty much defeated as
> almost all entries will end up containing these keywords. If having
> single-letter keywords is indeed useful and necessary for you, you
> should switch off the automatic keyword scan by setting
> 
> keyword_scan f
> 
> in /usr/local/etc/refdb/refdbrc.
> 
> BTW the RefDB handbook contains a section called "Input data mangling"
> which explains how RefDB may alter your data.
> 
> regards,
> Markus
> 
-- 
Daniel Paul O'Donnell
Associate Professor and Chair of English
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
University of Lethbridge
Lethbridge AB T1K 3M4
Canada

Vox +1 403 329-2377
Fax +1 403 382-7191

:@caedmon/ubuntu

Re: [Refdb-users] Parsing error ? with addref

[Rich S. <rsh...@ap...>]

On Sun, 25 Jun 2006, Markus Hoenicka wrote:

> The output is the same except for the summary which is sent to
> stderr. You see it on the screen as it displayes both stuff sent to
> stdout (the data) and to sterr (the summary). If you send the output
> to a file, it will contain the part sent to stout only.

Markus,

   Good to know.

> This is caused by the automatic keyword scan which is turned on by default.
> RefDB scans the titles and abstracts of new entries for keywords already
> known to the database. This is a very useful feature in most cases.
> However, if you indeed use single-letter keywords, the purpose of the
> automatic keyword scan is pretty much defeated as almost all entries will
> end up containing these keywords. If having single-letter keywords is
> indeed useful and necessary for you, you should switch off the automatic
> keyword scan by setting
>
> keyword_scan f
>
> in /usr/local/etc/refdb/refdbrc.

   Thanks for the lesson.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] Parsing error ? with addref

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

Rich Shepard writes:
 >    As far as the keyword order is concerned, that's a PostgreSQL thi=
ng. Rows
 > (tuples) are returned from a query in no particular order. Unless th=
e query
 > has an ORDERED BY clause, we'll see this every time. It's not any so=
rt of a
 > bug or issue of concern.
 >=20

This is correct. It applies to all database engines as the SQL
standard does not mandate a particular order of the returned datasets
unless the ORDERED BY clause is used. RefDB does not use this clause
here as the order of keywords is not relevant in RIS. It uses the
clause for author names as their order in the RIS dataset is relevant.

 > the name. What I don't see in your command line is the option to wri=
te the
 > returned records to a file, e.g., '-o hereiam.ris'. I wonder if you'=
ll see
 > the same output in a file that you see on screen,
 >=20

The output is the same except for the summary which is sent to
stderr. You see it on the screen as it displayes both stuff sent to
stdout (the data) and to sterr (the summary). If you send the output
to a file, it will contain the part sent to stout only.

 > > The problem is the following keyword section
 > >
 > > KW  - l
 > >> KW  - m
 > >> KW  - o
 > >> KW  - ld
 > >> KW  - h
 > >> KW  - =E6
 > >> KW  - C=E6dmon
 >=20
 > > These are all unique keywords drawn from other entries in the orig=
inal
 > > RIS file. They show up multiple times in the refdb generated ris f=
iles.
 >=20

This is caused by the automatic keyword scan which is turned on by
default. RefDB scans the titles and abstracts of new entries for
keywords already known to the database. This is a very useful feature
in most cases. However, if you indeed use single-letter keywords, the
purpose of the automatic keyword scan is pretty much defeated as
almost all entries will end up containing these keywords. If having
single-letter keywords is indeed useful and necessary for you, you
should switch off the automatic keyword scan by setting

keyword=5Fscan f

in /usr/local/etc/refdb/refdbrc.

BTW the RefDB handbook contains a section called "Input data mangling"
which explains how RefDB may alter your data.

regards,
Markus

--=20
Markus Hoenicka
mar...@ca...
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de

Re: [Refdb-users] Parsing error ? with addref

[Rich S. <rsh...@ap...>]

On Sat, 24 Jun 2006, Daniel O'Donnell wrote:

> I'm importing about 2900 references using addref. If I then output to ris=
,
> I'm finding that keywords seem to be mixed up a little. What seems to be
> happening is that short (one character or word) and unique (one occurrenc=
e
> in the original data) keywords are showing up randomly and repeatedly
> assigned to other entries. These other entries still keep their original
> keywords.

Dan,

   Since I'm another brand-new user, I probably don't know what I'm writing
about, but I'll point out what I don't think is correct, then we can both
learn some more about RefDB.

   As far as the keyword order is concerned, that's a PostgreSQL thing. Row=
s
(tuples) are returned from a query in no particular order. Unless the query
has an ORDERED BY clause, we'll see this every time. It's not any sort of a
bug or issue of concern.

> 1) Original RIS

>> KW  - chapter 6
>> KW  - chapter 1
>> KW  - Dawn
>> KW  - chapter 6
>> KW  - chapter 1
>> KW  - Dawn

   Why the duplicate entries in the original?

> Here's what is coming out the other end:

>> refdbc: getref -d refdbib -t ris :AU:~^Abraham
                   ^^^^^^^^^^
   Unless you have multiple databases with entries, you don't need to speci=
fy
the name. What I don't see in your command line is the option to write the
returned records to a file, e.g., '-o hereiam.ris'. I wonder if you'll see
the same output in a file that you see on screen,

> The problem is the following keyword section
>
> KW  - l
>> KW  - m
>> KW  - o
>> KW  - ld
>> KW  - h
>> KW  - =E6
>> KW  - C=E6dmon

> These are all unique keywords drawn from other entries in the original
> RIS file. They show up multiple times in the refdb generated ris files.

   Are the encodings for all databases the same? Do you really have single
letter keywords on some entries?

   This looks as strange and confusing as my problems with keywords returne=
d
by getref. But, in my case it was caused by asking for an exact match rathe=
r
than a 'like' match.

Rich

--=20
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

[Refdb-users] Parsing error ? with addref

[Daniel O'D. <dan...@ul...>]

I'm getting what looks like an error produced with addref or getref:

I'm importing about 2900 references using addref. If I then output to
ris, I'm finding that keywords seem to be mixed up a little. What seems
to be happening is that short (one character or word) and unique (one
occurrence in the original data) keywords are showing up randomly and
repeatedly assigned to other entries. These other entries still keep
their original keywords.

Here's an example:

1) Original RIS


> TY  - JOUR
> A1  - Abraham, Lenore
> T1  - Cædmon's Hymn and the Geþwærnysse (fitness) of things
> JO  - ABR
> JF  - American Benedictine Review
> Y1  - 1992///
> VL  - 43
> SP  - 331
> EP  - 44
> N2  - folder. 27-ii-01: notes in folder
> N1  - <Fairly long note removed/>
> AV  - Kakelbont Article Abraham1992
> KW  - chapter 6
> KW  - chapter 1
> KW  - Dawn
> KW  - chapter 6
> KW  - chapter 1
> KW  - Dawn
> KW  - caedmon's Hymn
> KW  - structure
> KW  - literary criticism
> KW  - bede
> KW  - Historia ecclesiastia
> KW  - internal criticism
> ER  - 

Here's what is coming out the other end:


> refdbc: getref -d refdbib -t ris :AU:~^Abraham
> 
> TY  - JOUR
> ID  - ABRAHAM1992
> AU  - Abraham,Lenore
> TI  - Cædmon's Hymn and the Geþwærnysse (fitness) of things
> JF  - American Benedictine Review
> JO  - ABR.
> KW  - chapter 6
> KW  - chapter 1
> KW  - Dawn
> KW  - chapter 6
> KW  - chapter 1
> KW  - Dawn
> KW  - caedmon's Hymn
> KW  - structure
> KW  - literary criticism
> KW  - bede
> KW  - Historia ecclesiastia
> KW  - internal criticism
> KW  - Cædmon's Hymn
> KW  - l
> KW  - m
> KW  - o
> KW  - ld
> KW  - h
> KW  - æ
> KW  - Cædmon
> VL  - 43
> SP  - 331
> EP  - 44
> N2  - folder. 27-ii-01: notes in folder
> RP  - NOT IN FILE
> AV  - Kakelbont Article Abraham1992
> N1  - <fairly long note/>
> PY  - 1992///
> ER  -
> 999:1 retrieved:0 failed
> refdbc:
> 

The problem is the following keyword section

KW  - l
> KW  - m
> KW  - o
> KW  - ld
> KW  - h
> KW  - æ
> KW  - Cædmon

These are all unique keywords drawn from other entries in the original
RIS file. They show up multiple times in the refdb generated ris files.

The presence or absence of N2 doesn't affect anything. I don't know if
the long note does, though the same problem occurs with entries that
have no notes. A random selection of these extra keywords seems to be
attached to every entry in the output RIS.

-d


-- 
Daniel Paul O'Donnell
Associate Professor and Chair of English
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
University of Lethbridge
Lethbridge AB T1K 3M4
Canada

Vox +1 403 329-2377
Fax +1 403 382-7191

:@caedmon/ubuntu

Re: [Refdb-users] GOT IT!!! Build to Ubuntu (Debian) system

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

Daniel O'Donnell <dan...@ul...> was heard to say:

> Got it, and in less that 12 hours.
>

Thanks for the comprehensive writeup which other Ubuntu/Debian users certainly
will appreciate. However, I think you stumbled over a few Unix details which
are simpler to resolve than you did.

> * Symlink the libdbi libraries (installed in /usr/local/lib) to /usr/lib
> (where refdb will look for them):
>

This is a fairly rude workaround. The problem here is that ld on Ubuntu (and on
Debian afaik) is set up to look for libraries in /usr/lib. This is set in
ld.so.conf and works fine as long as you use packages. If you build
autotools-based programs from source, they default to /usr/local, that is,
libraries end up in /usr/local/lib. There are two things you can do:

1) you can teach ld to look into /usr/local/lib for libraries as well. Edit
/etc/ld.so.conf and run ldconfig as root

2) you can configure libdbi and libdbi-drivers to install in /usr instead of in
/usr/local. Just pass --prefix=/usr to ./configure to achieve this.

1) is preferable if you tend to build from sources fairly often.

regards,
Markus

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

Re: [Refdb-users] GOT IT!!! Build to Ubuntu (Debian) system

[<J.I...@uv...>]

Hi,

I'm very happy, because I finally could see the output of the "viewstat"
command of refdba. Thank you very much. My refdb installation on ubuntu
seems to work perfectly. I only had to create the symbolic links to
libdbi files.=20

Regards,

Ignasi.

> Got it, and in less that 12 hours.
>=20
> Most of the trouble I've been having comes from not understanding
> details of README files, but since this is probably a common problem, I
> thought I'd write out what worked. Again in  Wiki format.
>=20
> =3D=3DInstalling refdb from a clean install of Ubuntu 6.06 LTS=3D=3D
>=20
> * Ensure that the community and multiverse repositories are enabled.
> ** Open sources.list with your favorite editor
>  sudo nano /etc/apt/sources.list
> ** Remove the comment hashes from the relevant repositories
> ** Reload
>  sudo apt-get update
>=20
> * Load the necessary binaries (place all one one line)
>=20
>  sudo apt-get install make mysql-client mysql-server
libmysqlclient15-dev zlib1g-dev libbtparse0 libbtparse-dev
libreadline5-dev install gcc libexpat1-dev
>=20
> * Add a password to mysql
>=20
>  mysqladmin -u root password '<your favourite password here>'
>=20
> * Get source files for libdbi0 =3D>8.0. In the download directory do the
> following (this assumes you are downloading from the University of
> Minnesota Mirror; you can also choose a different mirror if there is a
> more convenient one):
>=20
>  wget http://umn.dl.sourceforge.net/sourceforge/libdbi/libdbi-0.8.1.tar.g=
z
>  tar zxvf libdbi-0.8.1.tar.gz
>  cd libdbi-0.8.1/
>  ./configure
>  make
>  sudo make install
>  cd ..
>=20
> * Get source files for libdbi drivers and install:
>=20
>  wget
http://umn.dl.sourceforge.net/sourceforge/libdbi-drivers/libdbi-drivers-0.8=
1a.tar.gz
>  tar zxvf libdbi-drivers-0.8.1a.tar.gz
>  cd libdbi-drivers-0.8.1/
>  ./configure --with-mysql
>  make
>  sudo make install
>  cd ..
>=20
> * Symlink the libdbi libraries (installed in /usr/local/lib) to /usr/lib
> (where refdb will look for them):
>=20
>   ln -s /usr/local/lib/libdbi.a /usr/lib/libdbi.a
>   ln -s /usr/local/lib/libdbi.la /usr/lib/libdbi.la
>   ln -s /usr/local/lib/libdbi.so /usr/lib/libdbi.so
>   ln -s /usr/local/lib/libdbi.so.0 /usr/lib/libdbi.so.0
>   ln -s /usr/local/lib/libdbi.so.0.0.5 /usr/lib/libdbi.so.0.0.5
>=20
> * Get install refdb (note: during make you will get a recurring invalid
> pointer error. This is not important):
>=20
>  wget http://refdb.sourceforge.net/pre/refdb-latest.tar.gz
>  tar zxvf refdb-latest.tar.gz
>  cd refdb-0.9.7-pre7/
>  ./configure --sysconfdir=3D/etc --with-refdb-url=3Dhttp://localhost/refd=
b
>  make
>  sudo make install
>  cd ..
>=20
> * Run the installation script (answer all questions)
>  cd /usr/local/bin/
>  sudo refdb-init.sh
>=20
> * test installation (see section 4.9. Testing your installation)
>=20
> --=20
> Daniel Paul O'Donnell, PhD
> Associate Professor and Chair
> Director, Digital Medievalist Project
> <http://www.digitalmedievalist.org/>
> Department of English
> University of Lethbridge
> Lethbridge AB T1K 3M4
>=20
> Tel. +1 (403) 329-2378
> Fax. +1 (403) 382-7191
>=20
> :@wiglaf (dapper ubuntu)
>=20
>=20
> All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> Fully trained technicians. The highest number of Red Hat certifications i=
n
> the hosting industry. Fanatical Support. Click to learn more
> http://sel.as-us.falkag.net/sel?cmd=3Dlnk&kid=3D107521&bid=3D248729&dat=
=3D121642
> _______________________________________________
> Refdb-users mailing list
> Ref...@li...
> https://lists.sourceforge.net/lists/listinfo/refdb-users
>=20
>=20

[Refdb-users] GOT IT!!! Build to Ubuntu (Debian) system

[Daniel O'D. <dan...@ul...>]

Got it, and in less that 12 hours.

Most of the trouble I've been having comes from not understanding
details of README files, but since this is probably a common problem, I
thought I'd write out what worked. Again in  Wiki format.

==Installing refdb from a clean install of Ubuntu 6.06 LTS==

* Ensure that the community and multiverse repositories are enabled.
** Open sources.list with your favorite editor
 sudo nano /etc/apt/sources.list
** Remove the comment hashes from the relevant repositories
** Reload
 sudo apt-get update

* Load the necessary binaries (place all one one line)

 sudo apt-get install make mysql-client mysql-server libmysqlclient15-dev zlib1g-dev libbtparse0 libbtparse-dev libreadline5-dev install gcc libexpat1-dev

* Add a password to mysql

 mysqladmin -u root password '<your favourite password here>'

* Get source files for libdbi0 =>8.0. In the download directory do the
following (this assumes you are downloading from the University of
Minnesota Mirror; you can also choose a different mirror if there is a
more convenient one):

 wget http://umn.dl.sourceforge.net/sourceforge/libdbi/libdbi-0.8.1.tar.gz
 tar zxvf libdbi-0.8.1.tar.gz
 cd libdbi-0.8.1/
 ./configure
 make
 sudo make install
 cd ..

* Get source files for libdbi drivers and install:

 wget http://umn.dl.sourceforge.net/sourceforge/libdbi-drivers/libdbi-drivers-0.8.1a.tar.gz
 tar zxvf libdbi-drivers-0.8.1a.tar.gz
 cd libdbi-drivers-0.8.1/
 ./configure --with-mysql
 make
 sudo make install
 cd ..

* Symlink the libdbi libraries (installed in /usr/local/lib) to /usr/lib
(where refdb will look for them):

  ln -s /usr/local/lib/libdbi.a /usr/lib/libdbi.a
  ln -s /usr/local/lib/libdbi.la /usr/lib/libdbi.la
  ln -s /usr/local/lib/libdbi.so /usr/lib/libdbi.so
  ln -s /usr/local/lib/libdbi.so.0 /usr/lib/libdbi.so.0
  ln -s /usr/local/lib/libdbi.so.0.0.5 /usr/lib/libdbi.so.0.0.5

* Get install refdb (note: during make you will get a recurring invalid
pointer error. This is not important):

 wget http://refdb.sourceforge.net/pre/refdb-latest.tar.gz
 tar zxvf refdb-latest.tar.gz
 cd refdb-0.9.7-pre7/
 ./configure --sysconfdir=/etc --with-refdb-url=http://localhost/refdb
 make
 sudo make install
 cd ..

* Run the installation script (answer all questions)
 cd /usr/local/bin/
 sudo refdb-init.sh

* test installation (see section 4.9. Testing your installation)

-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

[Refdb-users] I give up: perhaps somebody else knows an answer?

[Dan O'D. <dan...@ul...>]

Well having spent all day and done several reinstalls, I can't get it
done. Here's a wikified list of what I did the last time, in case anybody
can figure out how to solve the problem.

The problem seems to lie in a couple of architecture mixups:

1) refdb build from source seems to look in the wrong place for libdbi0
library files, though this should be fixable with an option on
./configure, it doesn't seem to work. You can get around it by symlinking
the libdbi0 librarys from /usr/local/lib/ to /usr/lib

2) libdbi0-drivers is unable to recognise debian installations of mysql.
You should be able to get around this by adding the
--with-mysql-directory, but it is unclear what directory ./configure
wants. I tried every single mysql directory (as far as I can tell) and got
nowhere. I also tried /usr/bin, and similar directories to no avail.

If you follow the instructions here below, you can get refdb up and
running, but will run into the "Initiatialized libdbi, but no drivers were
found!" error. Until point 2) is solved, you won't get past that.

==Installing refdb from a clean install of Ubuntu 6.06 LTS==

* Ensure that the community and multiverse repositories are enabled.

* get the make utility

 sudo apt-get install make

* Install mysql server and client

  sudo apt-get install mysql-client mysql-server

* Get btparse (Universe)

 sudo apt-get install libbtparse0 libbtparse-dev

* Get libreadline5-dev (libreadline5 is already installed)

 sudo apt-get install libreadline5-dev

* Get gcc

 sudo apt-get install gcc

* Get libexpat-dev files (libexpat already installed)

 sudo apt-get install libexpat1-dev

* Get source files for libdbi0 =>8.0. In the download directory do the
following (note: Debian linux stores library files in a different
directory than the source files for libdbi install them in. You need to
symlink the libdbi files to /usr/lib from /usr/local/lib/):

 wget http://umn.dl.sourceforge.net/sourceforge/libdbi/libdbi-0.8.1.tar.gz
 tar zxvf libdbi-0.8.1.tar.gz
 cd libdbi-0.8.1/
 ./configure
 make
 sudo make install
 cd ..

* Get source files for libdbi drivers and install (note this doesn't seem
to work in Debian: the configure file is unable to tell that mysql is
installed, and I for one can't figure out what root directory it is
looking for when I try to specify one with --with-mysql-dir):

 wget
http://umn.dl.sourceforge.net/sourceforge/libdbi-drivers/libdbi-drivers-0.8.1a.tar.gz
 tar zxvf libdbi-drivers-0.8.1a.tar.gz
 cd libdbi-drivers-0.8.1/
 ./configure --with-mysql
 make
 sudo make install
 cd ..

* Get refdb

 wget http://refdb.sourceforge.net/pre/refdb-latest.tar.gz

* install (note: during make you will get a recurring invalid pointer
error. This is not important).

 tar zxvf refdb-latest.tar.gz
 cd refdb-0.9.7-pre7/
 ./configure --sysconfdir=/etc
--with-refdb-url=http://refdb.kakelbont.homelinux.net/refdb
 make
 sudo make install

* Add a password to mysql

 mysqladmin -u root password '<your favourite password here>'

* Run the installation script
 cd /usr/local/bin/
 sudo refdb-init.sh

==Problems==

* Everything works fine except the libdbi0 and libdbi0-drivers.
Unfortunately these are fatal problems. You can get around the build
problems with libdbi0 by symlinking the relevant files as mentioned above,
but nothing I could do could solve the libdbi0-drivers problem.




-- 
Daniel Paul O'Donnell
Director, Digital Medievalist Project (http://www.digitalmedievalist.org/)
Associate Professor of English
University of Lethbridge
Lethbridge AB T1K 3M4
Tel. +1 (403) 329-2377
Fax. +1 (403) 382-7191

(@webmail)

Re: [Refdb-users] make error

[Rich S. <rsh...@ap...>]

On Wed, 21 Jun 2006, Daniel O'Donnell wrote:

> I now am faced with a problem involving libdbi.so.0: the refdb-init.sh
> script reports a refdbd error:
>
> error while loading shared libraries: lbdbi.so.0: cannot open shared
> object file: No such file or directory
>
> The file does seem to be available, though: it is in /usr/local/lib

Dan,

   Make a soft link to /usr/lib and/or /lib. It should then be found by the
startup script.

Rich

-- 
Richard B. Shepard, Ph.D.               |    The Environmental Permitting
Applied Ecosystem Services, Inc.(TM)    |            Accelerator
<http://www.appl-ecosys.com>     Voice: 503-667-4517      Fax: 503-667-8863

Re: [Refdb-users] make error

[Daniel O'D. <dan...@ul...>]

Closing in on it: upon RTFM, I discovered the no drivers were being
installed because you need to configure libdbi-drivers with an explicit
dbase name.Now I'm trying to track down why libdbi-drivers can't find
the mysql root directory.

-d

On Wed, 2006-21-06 at 14:33 -0600, Daniel O'Donnell wrote:
> I reinstalled ubuntu 6.06 and tried again from a fresh install. As far
> as I can tell, there are two problems:
> 
> 1) refdbd is looking in /usr/lib instead of /usr/local/lib for the
> libdbi libraries (if you put a symlink for each libdbi file
> in /usr/local/lib, refdbd loads).
> 
> 2) the libdbi drivers package is creating the
> directory /usr/local/lib/dbd, but not putting any files in it. I've run
> updatedb and searched for the driver files (e.g. libmysql.so) that are
> supposed to be created and was unable to find them anywhere.
> 
> 3) I tried copying some old libdbi drivers I have
> into /usr/local/lib/dbd and then also symlinking them to /usr/lib, but
> they didn't work.
> 
> Any ideas? I swore I was going to get this today!
> 
> -d
> 
> On Wed, 2006-21-06 at 19:52 +0200, J.I...@uv... wrote:
> > Hi,
> > 
> > 
> > > I now am faced with a problem involving libdbi.so.0: the refdb-init.sh
> > > script reports a refdbd error: 
> > > 
> > > error while loading shared libraries: lbdbi.so.0: cannot open shared
> > > object file: No such file or directory
> > 
> > 
> > It is the same problem I have! I am also using ubuntu. I was using old
> > versions of libdbi and libdbi-drivers (those available through the
> > package manager) and I installed the new versions (0.8.1) from sources.
> > And I get the same error when I start refdbd.
> > 
> > Regards,
> > 
> > Ignasi.
> > 
> > 
> > All the advantages of Linux Managed Hosting--Without the Cost and Risk!
> > Fully trained technicians. The highest number of Red Hat certifications in
> > the hosting industry. Fanatical Support. Click to learn more
> > http://sel.as-us.falkag.net/sel?cmd=lnk&kid=107521&bid=248729&dat=121642
> > _______________________________________________
> > Refdb-users mailing list
> > Ref...@li...
> > https://lists.sourceforge.net/lists/listinfo/refdb-users
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

Re: [Refdb-users] make error

[Daniel O'D. <dan...@ul...>]

I reinstalled ubuntu 6.06 and tried again from a fresh install. As far
as I can tell, there are two problems:

1) refdbd is looking in /usr/lib instead of /usr/local/lib for the
libdbi libraries (if you put a symlink for each libdbi file
in /usr/local/lib, refdbd loads).

2) the libdbi drivers package is creating the
directory /usr/local/lib/dbd, but not putting any files in it. I've run
updatedb and searched for the driver files (e.g. libmysql.so) that are
supposed to be created and was unable to find them anywhere.

3) I tried copying some old libdbi drivers I have
into /usr/local/lib/dbd and then also symlinking them to /usr/lib, but
they didn't work.

Any ideas? I swore I was going to get this today!

-d

On Wed, 2006-21-06 at 19:52 +0200, J.I...@uv... wrote:
> Hi,
> 
> 
> > I now am faced with a problem involving libdbi.so.0: the refdb-init.sh
> > script reports a refdbd error: 
> > 
> > error while loading shared libraries: lbdbi.so.0: cannot open shared
> > object file: No such file or directory
> 
> 
> It is the same problem I have! I am also using ubuntu. I was using old
> versions of libdbi and libdbi-drivers (those available through the
> package manager) and I installed the new versions (0.8.1) from sources.
> And I get the same error when I start refdbd.
> 
> Regards,
> 
> Ignasi.
> 
> 
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-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

Re: [Refdb-users] make error

[<J.I...@uv...>]

Hi,


> I now am faced with a problem involving libdbi.so.0: the refdb-init.sh
> script reports a refdbd error:=20
>=20
> error while loading shared libraries: lbdbi.so.0: cannot open shared
> object file: No such file or directory


It is the same problem I have! I am also using ubuntu. I was using old
versions of libdbi and libdbi-drivers (those available through the
package manager) and I installed the new versions (0.8.1) from sources.
And I get the same error when I start refdbd.

Regards,

Ignasi.

Re: [Refdb-users] make error

[Daniel O'D. <dan...@ul...>]

On Wed, 2006-21-06 at 08:30 +0200, Markus Hoenicka wrote:
> Daniel O'Donnell <dan...@ul...> was heard to say:
> 

> Is the error message still the same as in your original post? I don't know how
> to check on the Ubuntu website for the version of a particular package. But if
> you do get the "undefined symbol" error message, you definitely have an
> outdated version of libdbi installed. I'd suggest to remove the packages and to
> build libdbi and libdbi-drivers from the sources instead. You may have to edit
> ld.so.conf and run ldconfig if you install libdbi in its default location.
> /usr/local. If you do get a different error message than the "undefined
> symbol", please post your make output again.

It was the libdbi version, I think. I installed it from source this
time, and made it through make and make install.

BUT...

I now am faced with a problem involving libdbi.so.0: the refdb-init.sh
script reports a refdbd error: 

error while loading shared libraries: lbdbi.so.0: cannot open shared
object file: No such file or directory

The file does seem to be available, though: it is in /usr/local/lib

I config'd refdb with sysconfdir set to /etc

Suggestions? I've just searched the other emails and it doesn't seem to
have come up. I assume refdbd is looking in the wrong directory?


-d

> 
> > I'm wondering if there is not a way of checking that the correct perl
> > and other packages are installed and installing if not? I simply can't
> > get a source install to work.
> >
> 
> The Perl packages are not required for a successful build. Other packages like
> libdbi could be changed to provide the necessary information to check for a
> particular version. However, I'm not familiar with the required libtool tweaks,
> so I'd need external help to get this done.
> 
> > I'd appreciate any experiences in debian: while I have no programming
> > experience, I'm not an inexperienced linux user and it is unusual for me
> > to get as stumped as I currently am.
> >
> 
> I test libdbi and RefDB infrequently on a Debian box (testing). However, as a
> developer I use the source distributions, or sometimes even the CVS/svn
> versions, so I'll never bump into package issues. So far I never had a problem
> building libdbi and RefDB on Debian.
> 
> regards,
> Markus
> 
> 
-- 
Daniel Paul O'Donnell, PhD
Associate Professor and Chair
Director, Digital Medievalist Project
<http://www.digitalmedievalist.org/>
Department of English
University of Lethbridge
Lethbridge AB T1K 3M4

Tel. +1 (403) 329-2378
Fax. +1 (403) 382-7191

:@wiglaf (dapper ubuntu)

Re: [Refdb-users] make error

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

Daniel O'Donnell <dan...@ul...> was heard to say:

> Following up on the libdbi problem:
>
> Has anybody successfully managed the make on a current debian system? I
> did a fresh install of Ubuntu 6.06 to make sure there was no legacy
> data, and have tried loading from the libdbi.sourceforge site as well as
> from the dapper.ubuntu site and simply cannot get through make. I get
> the wrong pointers error even with make dist-clean.
>

Is the error message still the same as in your original post? I don't know how
to check on the Ubuntu website for the version of a particular package. But if
you do get the "undefined symbol" error message, you definitely have an
outdated version of libdbi installed. I'd suggest to remove the packages and to
build libdbi and libdbi-drivers from the sources instead. You may have to edit
ld.so.conf and run ldconfig if you install libdbi in its default location.
/usr/local. If you do get a different error message than the "undefined
symbol", please post your make output again.

> I'm wondering if there is not a way of checking that the correct perl
> and other packages are installed and installing if not? I simply can't
> get a source install to work.
>

The Perl packages are not required for a successful build. Other packages like
libdbi could be changed to provide the necessary information to check for a
particular version. However, I'm not familiar with the required libtool tweaks,
so I'd need external help to get this done.

> I'd appreciate any experiences in debian: while I have no programming
> experience, I'm not an inexperienced linux user and it is unusual for me
> to get as stumped as I currently am.
>

I test libdbi and RefDB infrequently on a Debian box (testing). However, as a
developer I use the source distributions, or sometimes even the CVS/svn
versions, so I'll never bump into package issues. So far I never had a problem
building libdbi and RefDB on Debian.

regards,
Markus


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