MK | 31 Aug 03:33 2015

Deprecated function PHP 5.4+: session_register

I'm using PHP 5.6 and received some errors regarding a deprecated
function (session_register). I was able to fix these by adding some
code to index.php. (Code from


// Fix for removed Session functions
function fix_session_register(){
    function session_register(){
        $args = func_get_args();
        foreach ($args as $key){
    function session_is_registered($key){
        return isset($_SESSION[$key]);
    function session_unregister($key){
if (!function_exists('session_register')) fix_session_register();
(Continue reading)

MK | 31 Aug 03:13 2015

Fatal error: Call-time pass-by-reference

when trying out PHP-interface i received a fatal error. I could fix it
by using the instructions listed here:

+- if (!yaz_ccl_parse($id[$i], $term, &$cclresult)) {
++ if (!yaz_ccl_parse($id[$i], $term, $cclresult)) {


MK | 31 Aug 03:08 2015

Results found (counted), but not displayed, in PHP-interface with sqlite3

I'm trying out the PHP interface for refdb, using sqlite3 as my
database. I am able to add new references to the database by uploading
.ris files. The searching of references, however, is only partially
working. If I do a "simple field-based search" I am greeted with
results of the following kind:

Your search for :AX:~Marder% generated 1 result.

But no actual result is displayed on the page. (There is nothing in
the HTML code.)

If I search for indices, I am greeted with the following:
Your index search for retina in keyword generated 1 entries.

Sorry, there were no results.

It seems like the "first part" of the search works -- as something is
found, and counted but that something breaks in section that follows.

Any clues on what's going on?


(Continue reading)

Markus Hoenicka | 12 Sep 16:15 2012

Re: docbook5, getting started

Tim Arnold <jtim.arnold <at>> was heard to say:

> As for the problem with the chapter vs book root element:
> When I have a source xml file (test1_full.xml) with chapter as the
> root and citations like this:
> <citation role="REFDB"><xref linkend="IDbart_m66-X"/></citation>.
> runbib gives me an error:
> -----------------------------------
> runbib -d saslatexbib -S Chicago -t db50x test1_full.xml
> Variable $SGML_CATALOG_FILES not set
> Please enter your password:
> Parse error at line 1:
> no element found
> error
> -----------------------------------

I see. This is caused by a limitation of  
/usr/local/share/refdb/xsl/citations.xsl. This stylesheet is used to  
extract the citations from the source document and write them into the file. For reasons that I don't quite understand right now,  
the script limits itself to processing book and article elements. As a  
short term fix you could simply extend the regexp in line 39 like this  

         <xsl:template match="article|d:article|chapter|d:chapter">

I'll try to figure out if there was some obscure reason for this  
(Continue reading)

markus.hoenicka | 11 Sep 23:07 2012

Re: docbook5, getting started

Tim Arnold writes:
 > Hi Markus,
 > Here are some notes:
 > Using refdbxp 0.9.9-1 built from svn revision 531 markus <at>
 > (1) invalid xml generated
 > This citation:
 >     <citation role="REFDB">bart_m66</citation>
 > After the command
 > refdbxp -t db50x < test1.xml > test1_full.xml
 > becomes (note the non-terminated xref)
 >     <citation role="REFDB"><xref linkend="IDbart_m66-X"></citation>

This is an odd inconsistency. As refdbxp need not be aware of the
DocBook or TEI version you're using, you can only choose between
DocBook SGML, DocBook XML, and TEI XML. The first one is the default
if no type or an incorrect type is specified. Try "-t db31x" instead
and you should get valid XML. See the man page for further
details. The default stems from the days of yore when XML was all
fresh and new and no one used it because the tools weren't as good as
they are now. XML should probably be the default these days, but I'm
always careful not to break old behaviour.

 > (2) documentation typo
 > Page 102 (section, step 1) the xinclude path is incorrect:
 > /usr/local/share/xsl should be
 > /usr/local/share/refdb/xsl
(Continue reading)

markus.hoenicka | 10 Sep 21:12 2012

Re: docbook5, getting started

Tim Arnold writes:
 > failed to access style data

Hi Tim,

this usually means that you did not add that particular style to the
database. The style data have to be available to the application
server refdbd rather than to any of the clients. You'll have to run a
command along the lines of:

refdba -C addstyle APA.xml

although this should have been taken care of during the initial setup
of RefDB with refdb-init. You can list the available styles with the

refdbc -C liststyle



Markus Hoenicka
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Tim Arnold | 7 Sep 16:54 2012

docbook5, getting started

hi, I must be doing something wrong since I can't get to the first
step of creating a DocBook5.0 raw bibliography.
I converted my bibtex database to ris format and I can use refdba, so
my installation is okay I think.

In my docbook test.xml file I have a couple of citations like this:
<citation role="REFDB">kuma_v92</citation>.

runbib -d mybib -r -t db50x test.xml
I get
Variable $SGML_CATALOG_FILES not set
Parse error at line 4 column 2:
syntax error

The terminal where the refdbd instance is running (refdbd -s -e 0 -l
7) says this when I exec the runbib in another terminal:

SELECT meta_app,meta_type,meta_dbversion FROM t_meta WHERE meta_type='risx'
connected to database server using database:
no character encoding conversion required
output encoding is:
XML parse error

child exited with code 1
(Continue reading)

Stephan Gatzka | 23 Jan 22:28 2012

DOI and edition


I'm a somehow newbie to refdb, but I got it running and I'm impressed by 
the capabilities. I'm using the latest official version 0.9.9-1

Currently I've two questions I didn't found answers yet.

Is it possible or planned to include a
<biblioid class="doi">xxxx</biblioid>
when exporting to docbook5? I've imported RIS data sets including DO tags.

The second question is which RIS tag is the correct one for the 
"edition" of a book and is this tag already exported to an <edition> tag 
in docbook?

Kind regards,


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markus.hoenicka | 15 Jul 23:15 2011

Re: RefDB chooses NOT to communicate with latest version of PostgreSQL

Hi Frank,

Frank M Salter writes:
 > main database version is not supported

this in fact indicates that the libdbi driver somehow doesn't manage
to talk to the PostgreSQL engine properly.

 > At some point: I was using a number of terminal screens and did not
 > see the exact moment
 > when the following (transcribed by me) appeared:
 > =======================================================
 > *** glibc detected  *** refdb *** munmap_chunk(): invalid pointer
 > 0xb75f48e0  ***
 > =======  Backtrace:  =======
 > /lib/[0xb76f068a]
 > /usr/local/lib/ + 0x14c)[0xb782827c]
 > refdbd[0x804d9a5]
 > /lib/[0xb7697db6]
 > refdbd[0x804aa21]

This looks like a crash in libdbi. This may be caused by some
incompatibility between the driver and the engine, or it's just a
plain libdbi bug. However, I've never had any such crashes with any of
the drivers that I've used, so I still suspect the pgsql driver does
not work well with the latest PostgreSQL releases.

 > Thank you for your prompt reply. If you need any more information,
 > please let me know.

(Continue reading)

Frank M Salter | 12 Jul 15:57 2011

RefDB chooses NOT to communicate with latest version of PostgreSQL

Refdb complains about the version number of the latest version of
PostgreSQL 9.0.4 and does not continue.

Is there real incompatibility?

Is there a workaround to allow access?

If not, what is the latest version of PostgreSQL with which RefDB will
work successfully?


Frank Salter

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Torsten Bronger | 18 Jun 21:07 2011

Problems with adduser


I use RefDB SVN-747 with PostgreSQL.  With refdba, I experience the

bronger <at> wilson:~$ refdba -u chantal
Please enter your password:
refdba: listuser -d biblio
main database version is not supported
refdba: listuser -d biblio
refdba: adduser -d biblio toll
999:1 added:0 failed
refdba: listuser -d biblio

(The first "main database version is not supported" is stange
because a second try works.  But this is not the main reason for my

My problem is that I cannot see the user "toll" after having added
him.  The user "chantal" is allowed to add new users.  And what does
"238 - revoke user permissions successful" mean in this context?
(Continue reading)