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Torsten Bronger | 12 Aug 2009 23:37
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RefDB's source code organisation

Hallöchen!

I package RefDB for Ubuntu in order to make the server insallation
easier.  (Maybe eventually I'll upload it to the official Ubuntu
archives if nobody objects.)

Apparatently, there used to be a Debianisation but I cannot find it.
Where is the old material for Debian/Ubuntu packaging (i.e. the
debian/ directory)?

I'd like to have preferably only one package containing everything.
Unfortunately, RefDB is split into a couple of tarballs
(refdb-0.9.9.tar.gz, RefDB-perlmod-1.2.tar.gz,
RefDB-Client-1.18.tar.gz, RefDB-SRU-0.7.tar.gz, and
refdb-publist-1.1.tar.gz).  What should be packaged?  Since all
except the first package are tiny, what was the rationale to have
them separately?

Tschö,
Torsten.

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Markus Hoenicka | 19 Aug 2009 22:28
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RefDB's source code organisation

Torsten Bronger writes:
 > Hallöchen!
 > 
 > I package RefDB for Ubuntu in order to make the server insallation
 > easier.  (Maybe eventually I'll upload it to the official Ubuntu
 > archives if nobody objects.)
 > 

This would be greatly appreciated by many users. I keep getting
requests about the outdated Debian repository that we used to have.

 > Apparatently, there used to be a Debianisation but I cannot find it.
 > Where is the old material for Debian/Ubuntu packaging (i.e. the
 > debian/ directory)?
 > 

I've checked the (usually disabled) CVS repository, but I couldn't
find a debian subdirectory. I faintly recall that the developer who
built the Debian packages did so in a local copy. Unfortunately the
debianization appears to be lost.

 > I'd like to have preferably only one package containing everything.
 > Unfortunately, RefDB is split into a couple of tarballs
 > (refdb-0.9.9.tar.gz, RefDB-perlmod-1.2.tar.gz,
 > RefDB-Client-1.18.tar.gz, RefDB-SRU-0.7.tar.gz, and
 > refdb-publist-1.1.tar.gz).  What should be packaged?  Since all
 > except the first package are tiny, what was the rationale to have
 > them separately?
 >
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Torsten Bronger | 21 Aug 2009 09:24
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Re: RefDB's source code organisation

Hallöchen!

Markus Hoenicka writes:

> Torsten Bronger writes:
>
> [...]
>
>> I'd like to have preferably only one package containing
>> everything.  Unfortunately, RefDB is split into a couple of
>> tarballs (refdb-0.9.9.tar.gz, RefDB-perlmod-1.2.tar.gz,
>> RefDB-Client-1.18.tar.gz, RefDB-SRU-0.7.tar.gz, and
>> refdb-publist-1.1.tar.gz).  What should be packaged?  Since all
>> except the first package are tiny, what was the rationale to have
>> them separately?
>
> The reason to keep them separately was to avoid unnecessary
> dependencies for packaging efforts. [...] Therefore the most
> "Debianish" way might be to provide separate packages for each
> tarball.

Good.  What are the dependencies *within* the above tarballs?  First
I though that all tarballs simply depend on refdb, so I packaged it
first.  Then, I found an SRU server in refdb-0.9.9.tar.gz, but the
Perl code for this is (probably) in RefDB-SRU-0.7.tar.gz.  So what
depends on what?

Tschö,
Torsten.
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Markus Hoenicka | 22 Aug 2009 00:09
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Re: RefDB's source code organisation

Torsten Bronger writes:
 > Good.  What are the dependencies *within* the above tarballs?  First
 > I though that all tarballs simply depend on refdb, so I packaged it
 > first.  Then, I found an SRU server in refdb-0.9.9.tar.gz, but the
 > Perl code for this is (probably) in RefDB-SRU-0.7.tar.gz.  So what
 > depends on what?
 > 

That wasn't exactly easy to untangle. I've created a graph real quick
showing the dependencies:

http://refdb.sourceforge.net/refdb-dependencies.png

External applications or packages are shown in yellow. Perl modules
are shown in red.

Please correct me if there are any problems.

regards,
Markus

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Torsten Bronger | 22 Aug 2009 17:24
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RefDB for Ubuntu

Hallöchen!

At https://launchpad.net/~bronger/+archive/ppa you can get RefDB for
Ubuntu Jaunty.  It is possible to add support for Hardy or Intrepid
if someone requests it.

If someone needs support for Debian, he must do it himself.  It
should be very easy since the source of the package is available
there, too.

I packaged only the big rectangle in
<http://refdb.sourceforge.net/refdb-dependencies.png>.  This means
that there are some programs in /usr/bin which won't work.

After installation, there is no configuration file.  The server runs
in Sqlite mode without database, so you must create configuration
files according to the manual.  A slightly modified refdb-init is
available but difficult to use.  For example, refdbd runs as user
"refdb", which must have admin access to PostgreSQL.

There is no refdbctl.  Instead, there is /etc/init.d/refdb with the
usual options.

Tschö,
Torsten.

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Wei-Wei Guo | 23 Aug 2009 03:41
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Making RefDB cooperating with Zotero

Hi Markus,

I searched the mailing list and found there are some discussions about Zotero years ago. The Zotero becomes very
popular recently, but, due to my experience, it has a major flaw. The Zotero has limited ability in managing
it 
database, since its only an extension of Firefox. RefDB is powerful in managing reference database. If
RefDB could 
managing the database of Zotero directly, which is a sqlite3 database, it will boost RefDB a lot.

It's just my immature thinking. Hope it's not unreality and bother you much.

Best wishes,
Wei-Wei

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Bruce D'Arcus | 23 Aug 2009 15:45
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Re: Making RefDB cooperating with Zotero

On Sat, Aug 22, 2009 at 9:41 PM, Wei-Wei Guo<wwguocn <at> gmail.com> wrote:

> I searched the mailing list and found there are some discussions about Zotero years ago. The Zotero
becomes very
> popular recently, but, due to my experience, it has a major flaw. The Zotero has limited ability in
managing it
> database, since its only an extension of Firefox.

What do you mean by "managing [the] database"? Why is this a "major
flaw"? For whom?

> RefDB is powerful in managing reference database. If RefDB could
> managing the database of Zotero directly, which is a sqlite3 database, it will boost RefDB a lot.

I think the ability to easily move data around between systems is
probably the better approach.

Bruce

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Markus Hoenicka | 23 Aug 2009 17:28
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Re: Making RefDB cooperating with Zotero

Quoting Bruce D'Arcus <bdarcus.lists <at> gmail.com>:

> On Sat, Aug 22, 2009 at 9:41 PM, Wei-Wei Guo<wwguocn <at> gmail.com> wrote:
>
>> RefDB is powerful in managing reference database. If RefDB could
>> managing the database of Zotero directly, which is a sqlite3  
>> database, it will boost RefDB a lot.
>
> I think the ability to easily move data around between systems is
> probably the better approach.
>

I second that. I've had a look at Zotero's internal data model, which  
isn't really documented anywhere except in the SQL script which  
creates the database. At first glance there are so many differences to  
the data model currently used by RefDB that it would come close to  
rewriting the app in order to make it handle Zotero databases.  
Moreover, the Zotero developers discourage external access to the  
database as Zotero may end up in an undefined state if the database is  
fiddled with while the browser is open.

How good are Zotero's import and export capabilities?

regards,
Markus

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Bruce D'Arcus | 24 Aug 2009 16:58
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Re: Making RefDB cooperating with Zotero

On Sun, Aug 23, 2009 at 11:28 AM, Markus
Hoenicka<markus.hoenicka <at> mhoenicka.de> wrote:
> Quoting Bruce D'Arcus <bdarcus.lists <at> gmail.com>:
>
>> On Sat, Aug 22, 2009 at 9:41 PM, Wei-Wei Guo<wwguocn <at> gmail.com> wrote:
>>
>>> RefDB is powerful in managing reference database. If RefDB could
>>> managing the database of Zotero directly, which is a sqlite3 database, it
>>> will boost RefDB a lot.
>>
>> I think the ability to easily move data around between systems is
>> probably the better approach.
>>
>
> I second that. I've had a look at Zotero's internal data model, which isn't
> really documented anywhere except in the SQL script which creates the
> database. At first glance there are so many differences to the data model
> currently used by RefDB that it would come close to rewriting the app in
> order to make it handle Zotero databases. Moreover, the Zotero developers
> discourage external access to the database as Zotero may end up in an
> undefined state if the database is fiddled with while the browser is open.
>
> How good are Zotero's import and export capabilities?

Keep in mind that Zotero is now split between a client, and a server.

The client has supported good import/export of standard formats like
RIS, BibTeX, MODS for awhile. Their primary (e.g. lossless) format is
RDF, which is about to get an upgrade (to the BIBO vocab I've worked
with them and others on), and be accessible via a server API as well.
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Torsten Bronger | 24 Aug 2009 17:27
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Re: Making RefDB cooperating with Zotero

Hallöchen!

Bruce D'Arcus writes:

> [...]
>
> Keep in mind that Zotero is now split between a client, and a
> server.
>
> [...]
>
> Upshot is that I would assume some kind of server API interop
> might be worth exploring.

It could be implemented with URIs:

    addref zotero://login <at> localhost
    getref -o zotero://login <at> localhost :ID:>0

Of course, the Zotero server must meet the following requirements:

* serve in RIS format

* serve only datasets that have changed after a certain timestamp
  (namely the last synchronisation)

Zotero's IDs become citation keys in RefDB.

This also means that RefDB must introduce last-modified (and maybe
created) fields for its datasets.  This is something that I could
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