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Dr. Martin Goik | 3 Apr 2009 20:02
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Error creating docbook bibliography

I've tried to follow the instructions given in 
http://refdb.sourceforge.net/tutorial/x1442.html to generate a docbook 
bibliograpy for the following docbook5 document test instance mydoc.xml:

<?xml version="1.0" encoding="UTF-8"?>
<book version="5.0" xmlns="http://docbook.org/ns/docbook"
       xmlns:xlink="http://www.w3.org/1999/xlink"
       xmlns:xi="http://www.w3.org/2001/XInclude"
       xmlns:svg="http://www.w3.org/2000/svg"
       xmlns:m="http://www.w3.org/1998/Math/MathML"
       xmlns:html="http://www.w3.org/1999/xhtml"
       xmlns:db="http://docbook.org/ns/docbook">
   <chapter>
     <title>Test</title>

     <section>
       <title>A citation</title>
       <para>We only need <citation role="REFDB">date83</citation>.</para>
     </section>
   </chapter>
        <xi:include href="mydoc.bib.xml">
   <xi:fallback>mydoc.bib.xml appears to be missing</xi:fallback>
   </xi:include>
</book>

Now the runbib execution on behalf of the generated Makefile fails. The 
command actually reads:

 >runbib -u goik -w XXX -d mi -G raw.css -r -t db50x -E utf-8 mydoc.xml
 >select failed
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Markus Hoenicka | 3 Apr 2009 22:11
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Error creating docbook bibliography

Hi,

 > <citationlist>
 > 	<citation>date83</citation>
 > 	</citationlist>

The problem here is that the tutorial apparently did not tell you
explicitly that you need to edit mydoc.short.xml if you intend to use
the short notation of references. If you edit mydoc.xml, you need to
use the full notation. In any case, the id file should look like this:

<citationlist>
   <citation>
      <xref>IDOkuda1993</xref>
   </citation>
</citationlist>

 > 
 > The only problem here is the inexistence of 
 > http://refdb.sourceforge.net/dtd/citationlistx.dtd.
 > 

The DTDs were reorganized on the web page quite a while
ago. Unfortunately the tutorial is even older, so the links are dead
indeed. The correct URL is:

http://refdb.sourceforge.net/dtd/citationlistx/citationlistx.dtd

 > t_refdb.refdb_citekey IN () ORDER BY t_refdb.refdb_id
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Torsten Bronger | 4 Apr 2009 11:53
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About IDs and citation keys

Hallöchen!

I need something that *never* changes for a reference entry, so I
plan to use the ID.  My problem is that I don't easily get it after
addition of the reference.  I only get the generated citation key.
But the citation key can change.

So after having added the references, I must search for them with
the citation keys in order to get the IDs.

Is all this correct?

Tschö,
Torsten.

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Markus Hoenicka | 5 Apr 2009 23:04
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Re: About IDs and citation keys

Quoting Torsten Bronger <bronger <at> physik.rwth-aachen.de>:

> Hallöchen!
>
> I need something that *never* changes for a reference entry, so I
> plan to use the ID.  My problem is that I don't easily get it after
> addition of the reference.  I only get the generated citation key.
> But the citation key can change.
>

The citation key is not supposed to change. In fact, it takes quite  
some effort to change the citation key. I'm not aware of a simple way  
using RIS, and risx prefers the citation key over the ID if both are  
specified. Also, if you have to re-create a database from a RIS or  
risx dump, the ID is more likely to change than the citation key.

Do you have some scenario in mind which is likely to alter the citation key?

regards,
Markus

--

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

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Torsten Bronger | 5 Apr 2009 23:27
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Re: About IDs and citation keys

Hallöchen!

Markus Hoenicka writes:

> Quoting Torsten Bronger <bronger <at> physik.rwth-aachen.de>:
>
>> I need something that *never* changes for a reference entry, so I
>> plan to use the ID.  My problem is that I don't easily get it
>> after addition of the reference.  I only get the generated
>> citation key.  But the citation key can change.
>
> The citation key is not supposed to change. In fact, it takes
> quite some effort to change the citation key. I'm not aware of a
> simple way using RIS, and risx prefers the citation key over the
> ID if both are specified. Also, if you have to re-create a
> database from a RIS or risx dump, the ID is more likely to change
> than the citation key.

This all sounds like the CK in RefDB is what the ID is in general
database applications: A primary key that doesn't change.

My scenario is this: In my RefDB web frontend, the user can upload
PDF files which are stored in the file system.  Every reference gets
a sub-directory with its PDF file.  The question is, which name
should the sub-directory have?  In order to avoid re-naming it, it
should never change.  At the moment, I use the ID but probably the
CK is better?

> Do you have some scenario in mind which is likely to alter the
> citation key?
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Markus Hoenicka | 6 Apr 2009 00:06
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Re: About IDs and citation keys

Quoting Torsten Bronger <bronger <at> physik.rwth-aachen.de>:

> This all sounds like the CK in RefDB is what the ID is in general
> database applications: A primary key that doesn't change.
>

Basically yes. Providing both a unique ID and a unique citation key  
combines the best of both worlds: You can file paper copies by ID, and  
electronic offprints by citation key. Without legacy support for paper  
copies, CK would be sufficient.

> My scenario is this: In my RefDB web frontend, the user can upload
> PDF files which are stored in the file system.  Every reference gets
> a sub-directory with its PDF file.  The question is, which name
> should the sub-directory have?  In order to avoid re-naming it, it
> should never change.  At the moment, I use the ID but probably the
> CK is better?
>

I suggest to use CK instead.

regards,
Markus

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markus.hoenicka <at> cats.de
(Spam-protected email: replace the quadrupeds with "mhoenicka")
http://www.mhoenicka.de
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Torsten Bronger | 10 Apr 2009 21:50
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Re: About the AV and L1 fields

Hallöchen!

Markus Hoenicka writes:

> Torsten Bronger writes:
>
>> But is L2 a personal or a global field?  According to the manual,
>> they "hold information which is stored for each user separately".
>> 
>> The RISX DTD has <link> tags in both the pubinfo (global) and the
>> libinfo (personal) elements.
>
> The sources say that L1 through L4 elements from risx pubinfo elements
> are imported without being attached to a particular user. In contrast,
> L1 through L4 elements from libinfo elements are owned by the
> corresponding user. When you retrieve risx data, you'll get back both
> types, i.e. the "global" pubinfo links and the personal libinfo
> links.

Are pubinfo and libinfo inextricably intertwined or perfectly
separated?

An example which confuses me: I send the following to RefDB with the
updateref command:

    <entry citekey="Bld2006" id="1" type="JOUR">
      <part>
        <title>Electron Spin Resonance in thin film silicon after low
temperature electron irradiation</title>
        <author>
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Markus Hoenicka | 17 Apr 2009 21:27
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Re: About the AV and L1 fields

Torsten Bronger writes:
 > Are pubinfo and libinfo inextricably intertwined or perfectly
 > separated?
 > 

They are supposed to be treated separately. Your example helped to fix
two unrelated bugs which caused the behaviour you saw.

First, a bug prevented public links to be added to the returned string
if pubinfo does not contain anything else but link elements. That is,
the data were correctly added to the database and correctly retrieved,
but they were simply not added to the result string.

Second, a SQL query bug requested both public and private links when
retrieving the libinfo link elements.

This is now fixed in svn. However, there is one thing to keep in
mind. The current implementation uses a simple check for "file://" at
the start of each link to make sure a libinfo link is an URL pointing
to a file resource owned by the user, and not a public URL accessible
via http or ftp. That is, libinfo links using any protocol other than
"file://" or none at all end up being added as public links. This code
has been added too long ago to exactly remember why it was added. It
now looks a little strange to me, and I'm open to suggestions whether
or not to remove this restriction.

regards,
Markus

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Torsten Bronger | 18 Apr 2009 12:51
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How to mark institute's publication

Hallöchen!

For a change, I have a question which may also be answered by
readers other than Markus.  ;-)

I need to mark publications which were made by our scientific
institute, in order to be able to automate the generation of the
publication report which needs to be submitted annually in our
research centre.

I try to avoid the U1-U5 fields of RIS because I don't like their
arbitrary semantics, and I run out of them quickly.

Okay, I see four possibilities:

* Use a U1..U5 field anyway

* Add a bogus series (aka set) with the title "IEF-5 publications"

* Use RISX' <address> tag with a special micro syntax,
  e.g. "[institution: IEF-5]"

* Store it in the Web client instead of in RefDB

What do you think?

Tschö,
Torsten.

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Bruce D'Arcus | 19 Apr 2009 15:21
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Re: How to mark institute's publication

On Sat, Apr 18, 2009 at 6:51 AM, Torsten Bronger
<bronger <at> physik.rwth-aachen.de> wrote:

> Okay, I see four possibilities:
>
> * Use a U1..U5 field anyway
>
> * Add a bogus series (aka set) with the title "IEF-5 publications"
>
> * Use RISX' <address> tag with a special micro syntax,
>  e.g. "[institution: IEF-5]"
>
> * Store it in the Web client instead of in RefDB

Aren't they all hacks of sort that abuse the (limited) RIS semantics?
What you're really wanting to model is that a contributor is
affiliated with a particular institution (your's), and then to grab
items based on that affiliation.

In the Drupal-based biblio module, one can associate a a contributor
with a Drupal user, and then use that to generate reports and such. So
I guess his approach was your option #4.

There's a fifth possibility, BTW: use a keyword/tag.

Bruce

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