From mleigh at gmail.com  Tue Apr  8 15:49:27 2008
From: mleigh at gmail.com (Matthew Leigh)
Date: Tue, 08 Apr 2008 12:49:27 -0700
Subject: Problem with data lookup for PDF documents
Message-ID: <1207684167.9715.19.camel@dell>

I have a number of PDF papers from reputable science journals that I
want to organize.  A few days ago I compiled Referencer 1.1.1, and I am
using it on Ubuntu 7.04, and I ran it hoping it would fill in the
metadata for my papers.  My papers are organized into a few folders, and
I named them using the format "abbreviated title~first
author~journal~year."  

Referencer was able to fill in the doi in some cases.  However, mostly
it just stuck the file name as the article title, and it filled in the
year either correctly or with 2008.  When I try to look up a reference,
I get the file below (launching referencer from the command line).  It
seems to connect with PubMed and CrossRef, and it seems to enter my
"ourl" successfully. However, the only way I have been getting data
entered is manually, and I keep getting "the resolver is unable to
process your request" error messages whenever I hit the "lookup" or "get
metadata" buttons.

Can anyone help me out here?  What am I missing?

Thanks, 

Matt



Output for a 
----------------------------------
Document::getMetaData: module 'lyx' has no suitable capabilities
Document::getMetaData: trying module 'pubmed'
Waiting...Waiting...Waiting...Waiting... 
openCB: result OK, opened
Done!
Waiting...
Woo, read 679 bytes
readCB: result OK
Waiting...
Woo, read 0 bytes
readCB: EOF
Done!
Waiting...Waiting...
closeCB: result OK, closed
Done!
referencer_download: got 679 characters
pubmed.py:resolve_metadata: Got no metadata
>> referencer_document_dealloc
Document::getMetaData: module 'arxiv' has no suitable capabilities
Document::getMetaData: trying module 'crossref'
CrossRefPlugin::resolve: using url
'http://www.crossref.org/openurl/?pid=ourl-mleigh1:crossref&id=doi:10.1063/1.2357551&noredirect=true'
Waiting...Waiting...
openCB: result OK, opened
Done!
Waiting...
Woo, read 91 bytes
readCB: result OK
Waiting...
Woo, read 0 bytes
readCB: EOF
Done!
Waiting...
closeCB: result OK, closed
Done!
Error: the resolver is unable to process your request <br>Missing
WWW-Authenticate header
CrossRefParser: Parse Error!
Markuperror while parsing:
'''
Error: the resolver is unable to process your request <br>Missing
WWW-Authenticate header
'''
>> end_parse
<< end_parse
resolve returning 0




From jcspray at icculus.org  Tue Apr  8 16:02:18 2008
From: jcspray at icculus.org (John Spray)
Date: Tue, 08 Apr 2008 21:02:18 +0100
Subject: [referencer] Problem with data lookup for PDF documents
In-Reply-To: <1207684167.9715.19.camel@dell>
References: <1207684167.9715.19.camel@dell>
Message-ID: <1207684938.6742.2.camel@thermite>

On Tue, 2008-04-08 at 12:49 -0700, Matthew Leigh wrote:
> Can anyone help me out here?  What am I missing?

Crossref isn't letting you in.  My crossref username starts ourl_, yours
seems to start ourl-: perhaps that is a typo?

John



From mleigh at gmail.com  Fri Apr 11 13:33:21 2008
From: mleigh at gmail.com (Matthew Leigh)
Date: Fri, 11 Apr 2008 10:33:21 -0700
Subject: [referencer] Problem with data lookup for PDF documents
In-Reply-To: <1207684938.6742.2.camel@thermite>
References: <1207684167.9715.19.camel@dell> <1207684938.6742.2.camel@thermite>
Message-ID: <328357950804111033i4abb77c4y8729ace73e2fb981@mail.gmail.com>

Thanks for catching the underscore/dash problem, as after that CrossRef did
work.  I did still have problems with two journals from the same
organization - Optics Letters and Optics Express.  Though both are part of
CrossRef, they still didn't load for some reason.  I just went to the OSA
website, searched for each paper, clicked on the website option to download
paper into BibTex, then copied using the "paste BibTex" button.  Though not
totally automatic, it worked well enough, and I now have a full
bibliography.

Thank you for making such a useful program.

Matt

On Tue, Apr 8, 2008 at 1:02 PM, John Spray <jcspray at icculus.org> wrote:

> On Tue, 2008-04-08 at 12:49 -0700, Matthew Leigh wrote:
> > Can anyone help me out here?  What am I missing?
>
> Crossref isn't letting you in.  My crossref username starts ourl_, yours
> seems to start ourl-: perhaps that is a typo?
>
> John
>
>
> ---
> To unsubscribe, send a blank email to referencer-unsubscribe at icculus.org
> Mailing list archives: http://icculus.org/cgi-bin/ezmlm/ezmlm-cgi?60
>
>
>


-- 
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
My homepage: http://mleigh.googlepages.com/
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
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From andreas.dalsgaard at gmail.com  Mon Apr 14 06:28:31 2008
From: andreas.dalsgaard at gmail.com (Andreas Dalsgaard)
Date: Mon, 14 Apr 2008 12:28:31 +0200
Subject: [referencer] Referencer moving from svn to hg
In-Reply-To: <20080318055853.6crukyk2ogs0sgs0@mail.icculus.org>
References: <1205792187.6908.19.camel@thermite>
	 <47DF9084.3080504@liris.cnrs.fr>
	 <20080318055853.6crukyk2ogs0sgs0@mail.icculus.org>
Message-ID: <7e54b1b40804140328w57ba01a1g9ce67c8da8780d20@mail.gmail.com>

Btw. the web page still says:

hg clone http://hg.icculus.org/hgspace/jcspray/referencer/

instead of :

hg clone http://hg.icculus.org/jcspray/referencer/

Regards,
Andreas Dalsgaard

On 18/03/2008, jcspray at icculus.org <jcspray at icculus.org> wrote:
> Quoting David Coeurjolly <david.coeurjolly at liris.cnrs.fr>:
>
>
> > Hi John,
> >
> > something wrong with your hg repo ?
> >
> > ###% hg clone
> http://hg.icculus.org/hgspace/jcspray/referencer/
> > destination directory: referencer
> > abort:
> 'http://hg.icculus.org/hgspace/jcspray/referencer/' does
> not
> > appear to be an hg repository!
> >
>
>  Oops, take out the "hgspace/" and it should work.
>
>  John
>
>
>  ---
>  To unsubscribe, send a blank email to
> referencer-unsubscribe at icculus.org
>  Mailing list archives:
> http://icculus.org/cgi-bin/ezmlm/ezmlm-cgi?60
>
>
>


From jcspray at icculus.org  Mon Apr 14 06:42:48 2008
From: jcspray at icculus.org (jcspray at icculus.org)
Date: Mon, 14 Apr 2008 06:42:48 -0400
Subject: [referencer] Referencer moving from svn to hg
In-Reply-To: <7e54b1b40804140328w57ba01a1g9ce67c8da8780d20@mail.gmail.com>
References: <1205792187.6908.19.camel@thermite>
	<47DF9084.3080504@liris.cnrs.fr>
	<20080318055853.6crukyk2ogs0sgs0@mail.icculus.org>
	<7e54b1b40804140328w57ba01a1g9ce67c8da8780d20@mail.gmail.com>
Message-ID: <20080414064248.c9nixw534w4c800k@mail.icculus.org>


Oops.  Thanks for pointing that out, I think I fixed it and then  
overwrote the fix.  I'll sort it out when I'm at the right machine.

John

Quoting Andreas Dalsgaard <andreas.dalsgaard at gmail.com>:
> Btw. the web page still says:
>
> hg clone http://hg.icculus.org/hgspace/jcspray/referencer/
>
> instead of :
>
> hg clone http://hg.icculus.org/jcspray/referencer/
>
> Regards,
> Andreas Dalsgaard
>
> On 18/03/2008, jcspray at icculus.org <jcspray at icculus.org> wrote:
>> Quoting David Coeurjolly <david.coeurjolly at liris.cnrs.fr>:
>>
>>
>> > Hi John,
>> >
>> > something wrong with your hg repo ?
>> >
>> > ###% hg clone
>> http://hg.icculus.org/hgspace/jcspray/referencer/
>> > destination directory: referencer
>> > abort:
>> 'http://hg.icculus.org/hgspace/jcspray/referencer/' does
>> not
>> > appear to be an hg repository!
>> >
>>
>>  Oops, take out the "hgspace/" and it should work.
>>
>>  John
>>
>>
>>  ---
>>  To unsubscribe, send a blank email to
>> referencer-unsubscribe at icculus.org
>>  Mailing list archives:
>> http://icculus.org/cgi-bin/ezmlm/ezmlm-cgi?60
>>
>>
>>
>
> ---
> To unsubscribe, send a blank email to referencer-unsubscribe at icculus.org
> Mailing list archives: http://icculus.org/cgi-bin/ezmlm/ezmlm-cgi?60
>
>
>




From A.Wagner at stud.uni-frankfurt.de  Tue Apr 15 06:34:21 2008
From: A.Wagner at stud.uni-frankfurt.de (Andreas Wagner)
Date: Tue, 15 Apr 2008 12:34:21 +0200
Subject: Ubuntu (and others) dropping python-xml
Message-ID: <20080415103421.GC5346@hermes.commontology.de>

Hi,
when trying to understand a bit more about the dependencies of referencer I came across this 
ubuntu bug:
https://bugs.launchpad.net/ubuntu/+source/elisa/+bug/199014

In short, they are going to drop python-xml from the distribution and recommend to either drop 
python-xml as an explicit build dependency and rely on the core python package which by now 
includes much of the functionality, or use python-lxml (,or finally to include the needed 
functionality with your own package, but I'm not sure I got that right).

Can you check and adapt referencer to that (and/or change the development page 
(http://icculus.org/referencer/development.html) to reflect the new dependencies)?

Thanks,
Andreas



From jcspray at icculus.org  Tue Apr 15 10:00:35 2008
From: jcspray at icculus.org (jcspray at icculus.org)
Date: Tue, 15 Apr 2008 10:00:35 -0400
Subject: [referencer] Ubuntu (and others) dropping python-xml
In-Reply-To: <20080415103421.GC5346@hermes.commontology.de>
References: <20080415103421.GC5346@hermes.commontology.de>
Message-ID: <20080415100035.5amcb6fvy8sccwwg@mail.icculus.org>

Quoting Andreas Wagner <A.Wagner at stud.uni-frankfurt.de>:
> In short, they are going to drop python-xml from the distribution and
> recommend to either drop python-xml as an explicit build dependency and
> rely on the core python package which by now includes much of the
> functionality, or use python-lxml (,or finally to include the needed
> functionality with your own package, but I'm not sure I got that right).


So it seems that minidom is included in python 2.5?  In that case it's  
simply a case of removing the dependency for python >= 2.5.

Good spot though, I was running Hardy but hadn't noticed this.

John



From frederik.elwert at web.de  Tue Apr 15 14:51:13 2008
From: frederik.elwert at web.de (Frederik Elwert)
Date: Tue, 15 Apr 2008 20:51:13 +0200
Subject: [referencer] Ubuntu (and others) dropping python-xml
In-Reply-To: <20080415100035.5amcb6fvy8sccwwg@mail.icculus.org>
References: <20080415103421.GC5346@hermes.commontology.de>
	 <20080415100035.5amcb6fvy8sccwwg@mail.icculus.org>
Message-ID: <1208285473.7251.8.camel@FredDesk>

Hi!

Am Dienstag, den 15.04.2008, 10:00 -0400 schrieb jcspray at icculus.org:
> Quoting Andreas Wagner <A.Wagner at stud.uni-frankfurt.de>:
> > In short, they are going to drop python-xml from the distribution and
> > recommend to either drop python-xml as an explicit build dependency and
> > rely on the core python package which by now includes much of the
> > functionality, or use python-lxml (,or finally to include the needed
> > functionality with your own package, but I'm not sure I got that right).
> 
> 
> So it seems that minidom is included in python 2.5?  In that case it's  
> simply a case of removing the dependency for python >= 2.5.

As far as I can tell, minidom is included in Python since 2.0. And since
2.5, Python contains the new ElementTree API, which lxml also uses and
extends. Those are a really innovative, easy way to handle XML, but if
you just want to go with minidom, you should be able to use the one from
python instead of the one from python-xml.

Cheers,
Frederik



From jcspray at icculus.org  Wed Apr 16 17:16:02 2008
From: jcspray at icculus.org (John Spray)
Date: Wed, 16 Apr 2008 22:16:02 +0100
Subject: [referencer] Ubuntu (and others) dropping python-xml
In-Reply-To: <1208285473.7251.8.camel@FredDesk>
References: <20080415103421.GC5346@hermes.commontology.de>
	 <20080415100035.5amcb6fvy8sccwwg@mail.icculus.org>
	 <1208285473.7251.8.camel@FredDesk>
Message-ID: <1208380562.9026.0.camel@thermite>

On Tue, 2008-04-15 at 20:51 +0200, Frederik Elwert wrote:
> Hi!
> 
> Am Dienstag, den 15.04.2008, 10:00 -0400 schrieb jcspray at icculus.org:
> > Quoting Andreas Wagner <A.Wagner at stud.uni-frankfurt.de>:
> > > In short, they are going to drop python-xml from the distribution and
> > > recommend to either drop python-xml as an explicit build dependency and
> > > rely on the core python package which by now includes much of the
> > > functionality, or use python-lxml (,or finally to include the needed
> > > functionality with your own package, but I'm not sure I got that right).
> > 
> > 
> > So it seems that minidom is included in python 2.5?  In that case it's  
> > simply a case of removing the dependency for python >= 2.5.
> 
> As far as I can tell, minidom is included in Python since 2.0.

I've now removed all mention of python-xml from referencer.  Tested
without it on ubuntu 6.06, seems to be happy.

John




From jcspray at icculus.org  Sat Apr 19 11:09:00 2008
From: jcspray at icculus.org (John Spray)
Date: Sat, 19 Apr 2008 16:09:00 +0100
Subject: Plugin documentation
Message-ID: <1208617740.6816.1.camel@thermite>

Dear all,

Anyone interested in extending referencer may be interested in some
documentation I have written for the forthcoming 1.1.2 release with some
extensions to the API:
http://icculus.org/referencer/plugins.pdf

John



From lists at volker-gaibler.de  Sun Apr 20 14:04:47 2008
From: lists at volker-gaibler.de (Volker Gaibler)
Date: Sun, 20 Apr 2008 20:04:47 +0200
Subject: GUI behaviour changed?
Message-ID: <480B85BF.2020402@volker-gaibler.de>

Hi,

I just noticed that the GUI behaviour is different from the one before,
as I just updated Debian Sid: referencer 1.0.4-2 -> 1.1.1-1

Now, clicking on any item in the list view lets me change the specific
entry (key, title, ...). Clicking on the Key entry, adds an extra field
"key" with the respective name, but the key itself is not changed.
Also, I really liked the old behaviour of double clicking to open
linked files.

Can anyone confirm this "bug" - or is it intended behaviour?
Is this a bug on my system or also for others or is this intended
behaviour? And is there an easy way to change it?

Also, is there a way to sort entries in list view alphabetically by key 
or something similar?

Cheers,
   Volker

PS: I really like this program - it makes work so much nicer! :-)






From jcspray at icculus.org  Sun Apr 20 18:42:43 2008
From: jcspray at icculus.org (John Spray)
Date: Sun, 20 Apr 2008 23:42:43 +0100
Subject: [referencer] GUI behaviour changed?
In-Reply-To: <480B85BF.2020402@volker-gaibler.de>
References: <480B85BF.2020402@volker-gaibler.de>
Message-ID: <1208731363.6732.8.camel@thermite>

Hi Volker,

> Now, clicking on any item in the list view lets me change the specific
> entry (key, title, ...). Clicking on the Key entry, adds an extra field
> "key" with the respective name, but the key itself is not changed.

That was bug 208184: https://bugs.launchpad.net/referencer/+bug/208184

The original reporter did not seem to care enough to follow up so I let
it slip.  I've looked again and fixed it now.  Unfortunately it missed
1.1.2 by about 24 hours.


> Also, I really liked the old behaviour of double clicking to open
> linked files.

Well, it's either-or.  When double clicking opened files, I had people
asking for editable fields.  I think this way is a better compromise,
since the right-click menu still provides a fairly handy route for
opening files.

> Also, is there a way to sort entries in list view alphabetically by key 
> or something similar?

This got broken in 1.1.1, it's fixed in 1.1.2: you can click the title
of a column as you would expect.

You might be able to guess that personally I use the icon view.  The
list view was added because it wasn't very much extra work but I'm
starting to think it might be more trouble than it's worth.

Cheers,
John



