connotea-code-devel — Discussion and devlopment of the core Connotea code and plug-ins.

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[Barracuda S. F. <pos...@cl...>]

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[Connotea-code-devel] Feature requests for Connotea

[Nehdia S. <neh...@gm...>]

Hello all,

I've been trying out Connotea for some time and have been on a search for an
open source web-based reference management system for a while now. I want to
install Connotea on my own web portal rather than using the main Connotea
site. I checked out some of the projects at
http://bibliophile.sourceforge.net/projects.php, and found most to be
wanting. Connotea looks to me to hold the greatest promise, but there are
quite a few changes that I would want to make to it. My feature requests:

   - Save offline or print-only resources (i.e. resources with no URL) --
   http://www.connotea.org/wiki/RequestBookmarkNoURL
   - Make the description field HTML-friendly --
   http://www.connotea.org/wiki/RequestLargerDescFieldWithHTML
   - Allow Connotea to store links to related pages or bookmarks for each
   bookmark -- http://www.connotea.org/wiki/RequestRelatedLinks
   - Allow users to decide what should be syndicated in the RSS feeds --
   right now the authors field is omitted in the RSS feeds for bookmarks --
   http://www.connotea.org/wiki/RequestCustomizedRSS
   - Allow the creation of a separate page dedicated to each bookmark,
   where the abstract, private PDF file, Amazon Web API info if applicable,
   related attachments, notes, quotations, related links and so forth may be
   displayed in one place, such as in the PHP-based open-source bookmark
   manager Basilic --
   http://www.connotea.org/wiki/RequestDedicatedBookmarkPage
      - An elaboration on the above: as a future grad student, I would
      really like to have a web-based reference manager where I can not only
      manage my references but also notes, annotations, links and references
      related to a particular reference
      - I've been experimenting with Basilic, a PHP-based bookmark
      manager, but it is really limited, though I like the way it displays a
      dedicated page for each reference, which is very useful for us students.
      Here's an example of the sort of pages I'm generating with
Basilic for each
      reference I store:
      http://naqsh.org/basilic/biblio/2006/MT06/
      - There's already been a feature request regarding online
   storage of a private PDF copy of a journal article for instance. I would
   also like to be able to store additional attachments with each entry, such
   documents, presentations, images, movies, etc. I guess this is less
   appropriate for the main Connotea site and more appropriate for my own
   personal web portal on which I want to install Connotea. --
   http://www.connotea.org/wiki/RequestStoreAttachments
   - In the case of books linked to from Amazon.com, interface with the
   Amazon.com Web Services API to download book information such as the
   cover photograph, ratings, pricing information, etc. --
   http://www.connotea.org/wiki/RequestAmazonWebAPIIntegration

I posted some of these feature requests on the Connotea Community Pages
(links given above), but I would be interested in working on some of them
myself as well. I've downloaded the Connotea code, but I was wondering, can
anyone tell me where I can get some detailed documentation on Connotea's
source code and architecture?

Thanks very much for your cooperation!

With very best regards,
Nehdia Sameen.

[Connotea-code-devel] Adding Connotea friendly metadata to pages

[Adie, E. <e....@na...>]

(forgot to send this to the list instead of just to Thomas:)

Hi Thomas,

Connotea has code modules specifically written for each publisher, as well
as some general solutions to picking up document metadata.

The quickest (but not necessarily the best!) thing to do if you want
Connotea to pick up the right metadata is to include some RDF inside an html
comment somewhere in the header.

Here's an example of what I mean from biomedcentral.com:

<html>
<head>
 ... 

<!-- <rdf:RDF xmlns:cc="http://web.resource.org/cc/"
xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
xmlns:prism="http://prismstandard.org/namespaces/1.2/basic/"
xmlns:dc="http://purl.org/dc/elements/1.1/"
xmlns="http://purl.org/rss/1.0/">

<item rdf:about="http://www.biomedcentral.com/1471-2431/7/13">

    <title>Preliminary outcomes of a paediatric highly active antiretroviral
therapy cohort from KwaZulu-Natal, South Africa</title>

    <dc:title>Preliminary outcomes of a paediatric highly active
antiretroviral therapy cohort from KwaZulu-Natal, South Africa</dc:title>

    <dc:creator>Reddi, Anand</dc:creator>
    <dc:creator>Leeper, Sarah C</dc:creator>
    <dc:creator>Grobler, Anneke C</dc:creator>
    <dc:creator>Geddes, Rosemary</dc:creator>
    <dc:creator>France, K. Holly</dc:creator>
    <dc:creator>Dorse, Gillian L</dc:creator>

    <dc:identifier>info:doi/10.1186/1471-2431-7-13</dc:identifier>
    <dc:source>BMC Pediatrics 2007, 7:13</dc:source>
    <dc:date>2007-03-17</dc:date>

    <prism:publicationName>BMC Pediatrics</prism:publicationName>
    <prism:publicationDate>2007-03-17</prism:publicationDate>
    <prism:volume>7</prism:volume>
    <prism:number>1</prism:number>
    <prism:section>Research article</prism:section>
    <prism:startingPage>13</prism:startingPage>

</item>
</rdf:RDF> -->

....

</head>
.... etc.


Hope that helps,

Cheers,

Euan


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[Connotea-code-devel] making an HTML page ready for Connotea?

[Thomas B. <pro...@gm...>]

I am new, just joined this list, but have been on the Connotea- 
discuss list since about Sept. 2005.

I would like to know:  How does one make an HTML page ready for  
Connotea, so that the 'Add to Connotea' bookmarklet picks up more  
than just the page title?

I just spent an hour trying to sort through the source code for an  
article in Nature that I have in my Connotea library.  However, I  
cannot figure out exactly how that page gives back author, journal  
etc. to Connotea.  Do I have to embed metadata in my HTML file?  I am  
used to slapping a script or metadata into the head of an HTML file.   
But if something else is required, I would like to know.

I am not very knowledgeable in XML, so if that is required, I would  
have to learn up on that, too.

Gracias!

- Thomas Brueckner

[Connotea-code-devel] A suggestion on PubMed links in Connotea

[Mohsen S. (GMail) <moh...@gm...>]

Hi Everybody,

 

First of all, thanks to the Connotea dev team for this wonderful service.

 

There has been some discussion recently on handling the redundat links to
PubMed articles in Connotea, with suggestons on using 'normalized' urls or
making Connotea smart enough to detect PMIDs from the url instead of working
with exact url string.

 

I think the problem is two fold as currently:

1. One user can bookmark a pubmed article several times.

2. It is almost impossible to query all posts related to a single pubmed
article.

 

Both of them are currently limiting the usefulness of connotea for
bookmarking pubmed astracts. 

 

I have a suggestion for handling these problems: that a new filtering
criterion be added specifically for PMID. For example, the request

 

http://www.connotea.org/pmid/12569935
 
should return all posts to the corrsponding article in PubMed. This will
immediately solve the second problem. For the first problem, this filter
also provides a descent solution: when a user bookmarks a pubmed abstract,
the code should first check through this filter that if the user has already
bookmarked this article:
 
http://www.connotea.org/user/harrytruman/pmid/12569935
 
and if yes, then the existing post should be edited instead of adding a new
post. 
 
As Connotea does understand PMID (and probably has a separate field in its
database for PMID), this approach shouldn't be that difficult to implement.
It also makes programs using Connotea API able to handle this issue as
efficiently as possible.
 

Thanks,

Mohsen

[Connotea-code-devel] Unable to import citations from file: antispam_score.csv: Permission denied

[Luke G. <luk...@gm...>]

Hi,

When trying to import a single entry from an RIS file this morning, I
encountered the error

> cannot open /var/www/html/connotea/antispam_score.csv: Permission denied at /var/www/perl/connotea/bibliotech/Bibliotech/Antispam.pm line 191.

I had the same problem with the file format set to either AutoDetect or RIS.

Is this caused by some fault in the RIS file or has the import feature
of Connotea broken since I last used it (a few months ago)?

Luke

(Just as an aside 'cause I need to vent a little: I'm only having to
import from a file as the ScienceDirect article's URI was 298
characters long and the DOI was broken - can you not hash long URIs to
get around the 255 character limit for table indices? I love the Add
to Connotea popup when it works. It's a real nuisance when it
doesn't.)

Re: [Connotea-code-devel] [Connotea-discuss] Online Reference Management as soft peer review?

[Adie, E. <e....@na...>]

Just to plug this a bit: Dario's post is a good read - if you're interested
in academic social bookmarking then go check it out :).

Euan


On 22/2/07 09:52, "Dario Taraborelli" <dar...@gm...> wrote:

> I've posted on the AcademicProductivity blog a few considerations on
> what Connotea and similar services might become in the near future:
> 
> http://www.academicproductivity.com/blog/2007/soft-peer-review-social-
> software-and-distributed-scientific-evaluation/
> 
> The post has also a number of development ideas.
> 
> Feedback welcome,
> 
> Best,
> Dario
> 
> 
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys-and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
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> https://lists.sourceforge.net/lists/listinfo/connotea-discuss

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not the original intended recipient. If you have received this e-mail in error
please inform the sender and delete it from your mailbox or any other storage
mechanism. Neither Macmillan Publishers Limited nor any of its agents accept
liability for any statements made which are clearly the sender's own and not
expressly made on behalf of Macmillan Publishers Limited or one of its agents.
Please note that neither Macmillan Publishers Limited nor any of its agents
accept any responsibility for viruses that may be contained in this e-mail or
its attachments and it is your responsibility to scan the e-mail and 
attachments (if any). No contracts may be concluded on behalf of Macmillan 
Publishers Limited or its agents by means of e-mail communication. Macmillan 
Publishers Limited Registered in England and Wales with registered number 785998 
Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS   
********************************************************************************

[Connotea-code-devel] Online Reference Management as soft peer review?

[Dario T. <dar...@gm...>]

I've posted on the AcademicProductivity blog a few considerations on  
what Connotea and similar services might become in the near future:

http://www.academicproductivity.com/blog/2007/soft-peer-review-social- 
software-and-distributed-scientific-evaluation/

The post has also a number of development ideas.

Feedback welcome,

Best,
Dario

[Connotea-code-devel] Performance problems adding a bookmark using WebAPI

[Oliver M. <o.m...@tu...>]

Hi all,

I have a problem with the WebAPI. I wrote a PHP-class to integrate some
Connotea features into one of our projects. This works quite good, but
when I try to add a bookmark with my class the browser needs up to three
minutes to perform this action.
All I do is posting an uri and some tags to www.connotea.org/data/add
Here is the HTTP-packet I am sending:

-----------
POST /data/add HTTP/1.1
Host: www.connotea.org
Content-type: application/x-www-form-urlencoded
Content-length: 125
User-Agent: Mozilla/5.0 (X11; U; Linux i686; en-US; rv:1.8.1.1)
Gecko/20061208 Firefox/2.0.0.1
Authorization: Basic $base64-encoded-userdata
Connection: Close

uri=3Dhttp%3A%2F%2Fdoku.b.tu-harburg.de%2Fvolltexte%2F2006%2F24%2F&tags=3D=
TUB%20TUBdok%20TUHH%20%22meine%20kleine%20welt%22
-------------

Perhaps someone can give me a hint what's slowing down this simple
request...

Any help is appreciated. Thanks in advance
    Oliver

--=20
Oliver Marahrens
TU Hamburg-Harburg / Universit=E4tsbibliothek / Digitale Dienste
Denickestr. 22
21071 Hamburg - Harburg
Tel. 	+49 (0)40 / 428 78 - 32 91
eMail	o.m...@tu...
--
GPG/PGP-Schl=FCssel:=20
http://www.tub.tu-harburg.de/keys/Oliver_Marahrens_pub.asc
--
Projekt DISCUS http://discus.tu-harburg.de
Projekt TUBdok http://doku.b.tu-harburg.de

[Connotea-code-devel] Apache2.pm

[Tjeerd v. d. L. <t....@oc...>]

I try to get connotea running on OpenSUSE 10.1 with Apache 2.2.0-21 and
mod_perl 2.02-14. Apache won't start because mod_perl can't find
Apache2.pm. It seems that from mod_perl2 package version 1.999_22 on
parts of the mod_perl API are renamed (see also
http://perl.apache.org/docs/2.0/rename.html). Does this mean that
Connotea definitely requires a mod_perl version prior to 1.999_22?=20
=20
Thanks in advance for any help.
*************************************************************************=
*************************

Re: [Connotea-code-devel] RSS feeds?

[Martin F. <ma...@ne...>]

Ah, yes, this was reported as a bug. The Content-Encoding field is 
apparently only to be used for compression algorithms, not character 
sets. I'm really sorry that did not come to mind and you had to 
rediscover it.

We fixed the biblio_rdf problem by adding another accessor called 
xmlnoun() which is used there.

Sounds like it's time for a new open source release.

I hadn't seen the XML::RSS problem yet but we try not to upgrade the 
CPAN modules very often once things are working.

Martin

Hilary Spencer wrote:
>   Hi Martin,
> 
> I managed to fix the problem I mentioned before.  I was also surprised 
> to find out that the problem was with the headers, as I had looked at 
> them before and didn't see (what I thought were) any significant 
> differences.  In addition, the Firefox documentation claims that the 
> browser recognizes RSS feeds based on the content of the document, and 
> not the headers.
> 
> Anyway, according to LiveHeaders, the only difference was that the my 
> RSS file had:
> "Content-Type: application/xml"
> "Content-Encoding: utf-8"
> 
> While the RSS file on Connotea.org has:
> Content-Type: application/xml; charset=UTF-8"
> 
> It seems that the extra header was causing the problem (just changing 
> the content type didn't help).  So, I commented out the line in 
> Apache.pm which adds the Content-Encoding header (in sub query_handler):
> 487: #  $r->content_encoding('utf-8');
> 
> And in Const.pm, I added the charset to the content-type constant:
> 30: use constant RSS_MIME_TYPE          => 'application/xml; charset=UTF-8';
> 
> And now it works correctly.  Apparently, if the media type given in the 
> Content-Type header is 'application/xml', the browser ought to ignore 
> the Content-Encoding header and use either the charset specified in the 
> content-type header, or in the XML document itself, or default to UTF-8 
> (see http://diveintomark.org/archives/2004/02/13/xml-media-types).  But 
> either way, the content-encoding header is unnecessary.
> 
> In regard to your other question, I commented out the following lines in 
> DBI.pm (sub biblio_rdf):
> 2326: #       $model->addStmt(new RDF::Core::Statement($node,
> 2327: #                                                new 
> RDF::Core::Resource($RDF.'type'),
> 2328: #                                                new 
> RDF::Core::Resource($CONNOTEA.$id->noun)));
> 
> Finally, I had problems after updating the cpan module XML::RSS, 
> although I'm not sure why.  For some reason, XML::RSS::encode_text (line 
> 274 in Util.pm) was not a function in the module any more, so I had to 
> write my own local function.
> 
> Hilary
> 
> Martin Flack wrote:
>> Hi Hilary,
>>
>> Hilary Spencer wrote:
>>   
>>> I'm having problems with the RSS feeds in the open source code.  First, 
>>> I noticed that some tags were malformed/empty "<:>".  I fixed this by 
>>> commenting out a line in DBI.pm, although I'm not sure what was causing 
>>> the problem in the first place.
>>>     
>> I think we caught the same bug independently, but can you tell me what 
>> it was that you changed so I can compare?
>>
>>   
>>> Now, the only problem seems to be that the resulting file is not 
>>> recognized/displayed as an RSS file by Firefox (2.0), so I can't use the 
>>> live bookmarks feature.  This is not a problem on the main Connotea 
>>> site, so I'm hoping someone will be able to help me fix it.
>>>     
>> [snip]
>>
>> We were a bit surprised by Firefox's new behaviour, but as you say, on 
>> connotea.org it's recognizing the RSS. I can't fathom why your instance 
>> would behave differently...? Have you tried using the Live Headers 
>> module for Firefox and compared all the HTTP headers in the exchange?
>>
>> Martin
>>
>>
>> -------------------------------------------------------------------------
>> Take Surveys. Earn Cash. Influence the Future of IT
>> Join SourceForge.net's Techsay panel and you'll get the chance to share your
>> opinions on IT & business topics through brief surveys - and earn cash
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>>
>>   
> 

Re: [Connotea-code-devel] RSS feeds?

[Hilary S. <hil...@st...>]

Hi Martin,

I managed to fix the problem I mentioned before.  I was also surprised 
to find out that the problem was with the headers, as I had looked at 
them before and didn't see (what I thought were) any significant 
differences.  In addition, the Firefox documentation claims that the 
browser recognizes RSS feeds based on the content of the document, and 
not the headers.

Anyway, according to LiveHeaders, the only difference was that the my 
RSS file had:
"Content-Type: application/xml"
"Content-Encoding: utf-8"

While the RSS file on Connotea.org has:
Content-Type: application/xml; charset=UTF-8"

It seems that the extra header was causing the problem (just changing 
the content type didn't help).  So, I commented out the line in 
Apache.pm which adds the Content-Encoding header (in sub query_handler):
487: #  $r->content_encoding('utf-8');

And in Const.pm, I added the charset to the content-type constant:
30: use constant RSS_MIME_TYPE          => 'application/xml; charset=UTF-8';

And now it works correctly.  Apparently, if the media type given in the 
Content-Type header is 'application/xml', the browser ought to ignore 
the Content-Encoding header and use either the charset specified in the 
content-type header, or in the XML document itself, or default to UTF-8 
(see http://diveintomark.org/archives/2004/02/13/xml-media-types).  But 
either way, the content-encoding header is unnecessary.

In regard to your other question, I commented out the following lines in 
DBI.pm (sub biblio_rdf):
2326: #       $model->addStmt(new RDF::Core::Statement($node,
2327: #                                                new 
RDF::Core::Resource($RDF.'type'),
2328: #                                                new 
RDF::Core::Resource($CONNOTEA.$id->noun)));

Finally, I had problems after updating the cpan module XML::RSS, 
although I'm not sure why.  For some reason, XML::RSS::encode_text (line 
274 in Util.pm) was not a function in the module any more, so I had to 
write my own local function.

Hilary

Martin Flack wrote:
> Hi Hilary,
>
> Hilary Spencer wrote:
>   
>> I'm having problems with the RSS feeds in the open source code.  First, 
>> I noticed that some tags were malformed/empty "<:>".  I fixed this by 
>> commenting out a line in DBI.pm, although I'm not sure what was causing 
>> the problem in the first place.
>>     
>
> I think we caught the same bug independently, but can you tell me what 
> it was that you changed so I can compare?
>
>   
>> Now, the only problem seems to be that the resulting file is not 
>> recognized/displayed as an RSS file by Firefox (2.0), so I can't use the 
>> live bookmarks feature.  This is not a problem on the main Connotea 
>> site, so I'm hoping someone will be able to help me fix it.
>>     
> [snip]
>
> We were a bit surprised by Firefox's new behaviour, but as you say, on 
> connotea.org it's recognizing the RSS. I can't fathom why your instance 
> would behave differently...? Have you tried using the Live Headers 
> module for Firefox and compared all the HTTP headers in the exchange?
>
> Martin
>
>
> -------------------------------------------------------------------------
> Take Surveys. Earn Cash. Influence the Future of IT
> Join SourceForge.net's Techsay panel and you'll get the chance to share your
> opinions on IT & business topics through brief surveys - and earn cash
> http://www.techsay.com/default.php?page=join.php&p=sourceforge&CID=DEVDEV
> _______________________________________________
> Connotea-code-devel mailing list
> Con...@li...
> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel
>
>   

Re: [Connotea-code-devel] RSS feeds?

[Martin F. <ma...@ne...>]

Hi Hilary,

Hilary Spencer wrote:
> I'm having problems with the RSS feeds in the open source code.  First, 
> I noticed that some tags were malformed/empty "<:>".  I fixed this by 
> commenting out a line in DBI.pm, although I'm not sure what was causing 
> the problem in the first place.

I think we caught the same bug independently, but can you tell me what 
it was that you changed so I can compare?

> Now, the only problem seems to be that the resulting file is not 
> recognized/displayed as an RSS file by Firefox (2.0), so I can't use the 
> live bookmarks feature.  This is not a problem on the main Connotea 
> site, so I'm hoping someone will be able to help me fix it.
[snip]

We were a bit surprised by Firefox's new behaviour, but as you say, on 
connotea.org it's recognizing the RSS. I can't fathom why your instance 
would behave differently...? Have you tried using the Live Headers 
module for Firefox and compared all the HTTP headers in the exchange?

Martin

[Connotea-code-devel] Scheduled downtime on 2nd Jan, 6pm - 8pm EST

[Adie, E. <E....@na...>]

Hi all,

Early in the new year we'll be moving Connotea to bigger, better servers. U=
nfortunately this means that Connotea will be unavailable for two hours on =
the 2nd of January 2007, from around 6pm to 8pm EST, while we physically re=
locate some of the hardware that runs the site.

Please accept our apologies for any inconvenience this may cause you. If yo=
u encounter (or anticipate) any specific problems because of the downtime d=
o let us know at con...@na....

Happy holidays,

Euan

***************************************************************************=
*****  =20
DISCLAIMER: This e-mail is confidential and should not be used by anyone wh=
o is
not the original intended recipient. If you have received this e-mail in er=
ror
please inform the sender and delete it from your mailbox or any other stora=
ge
mechanism. Neither Macmillan Publishers Limited nor any of its agents accept
liability for any statements made which are clearly the sender's own and not
expressly made on behalf of Macmillan Publishers Limited or one of its agen=
ts.
Please note that neither Macmillan Publishers Limited nor any of its agents
accept any responsibility for viruses that may be contained in this e-mail =
or
its attachments and it is your responsibility to scan the e-mail and=20
attachments (if any). No contracts may be concluded on behalf of Macmillan=20
Publishers Limited or its agents by means of e-mail communication. Macmilla=
n=20
Publishers Limited Registered in England and Wales with registered number 7=
85998=20
Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS  =20
***************************************************************************=
*****

[Connotea-code-devel] RSS feeds?

[Hilary S. <hil...@st...>]

Hi,

I'm having problems with the RSS feeds in the open source code.  First, 
I noticed that some tags were malformed/empty "<:>".  I fixed this by 
commenting out a line in DBI.pm, although I'm not sure what was causing 
the problem in the first place.

Now, the only problem seems to be that the resulting file is not 
recognized/displayed as an RSS file by Firefox (2.0), so I can't use the 
live bookmarks feature.  This is not a problem on the main Connotea 
site, so I'm hoping someone will be able to help me fix it.

Here's a image of the problem:
  http://cirge.stanford.edu/connoteafiles/rss.html

The top image is what I see when I click the "RSS" link at the top of a 
list of bookmarks. The bottom image is what I should see.  Oddly enough, 
if I use curl to create a local copy of the rss feed (curl -o test.rss 
http://cirge.stanford.edu/bibliotech/rss/user/hilary/tag/aCGH) generated 
by connotea, it is recognized by Firefox to be an rss feed.  This has 
nothing to do with the file extension since "curl -o test http..." also 
generates a recognized rss feed.

I am using Apache's mod_mime (with the default configurations) although 
I don't think this should have any effect.  From my research, I think 
that Firefox guesses if a file is an RSS file or an HTML file by looking 
at the first couple of lines.  If the file begins with <? ?>followed by 
<rdf:RDF> or <rss>, then Firefox should treat the file as an RSS file.  
However, the content of both the file at 
http://cirge.stanford.edu/bibliotech/rss/user/hilary/tag/aCGH and the 
copied file generated by curl are identical.  So theoretically, Firefox 
should interpret them the same way, but doesn't.  I'm confused.

The only difference I can find is that the file header for the 
(correctly recognized) RSS feed says the file type is 
"application/xhtml+xml", while the file header for the unrecognized RSS 
feed says the file type is "application/xml".  Changing this in Const.pm 
so that the RSS feeds have "application/xhtml+xml" as the file type  
doesn't seem to make a difference.

Anyone else having this problem?  Any thoughts?

Please ask if any of the above is not clear.

Thanks so much,
Hilary

[Connotea-code-devel] =?iso-8859-1?q?Perl_-_Encoding_Problems_whi?= =?iso-8859-1?q?le_posting_with_german_=22Umlaute=22_=F6=E4=FC=DF?=

[Jan L <ein...@go...>]

Hi,
I am trying to post entries to connotea with perl on two ways. I am doing
this with the perl module and with LWP::UserAgent. In both I have problems,
that German Umlaute (diacritical marks) are not stored in the right way. So
there is a problem with the encoding but I currently do not have a clue to
solve this problem.

Does someone have a tipp on this?

Here is an example

http://www.connotea.org/uri/e2f5efbaa57e5a1b9a1567e9c44b8be6


Code for using the perl module:

use WWW::Connotea;

use constant USER =3D> 'xxxxxxx';
use constant PASSWORD =3D> 'xxxxxxx';

my $c =3D WWW::Connotea->new(user =3D> USER, password =3D> PASSWORD);
$c->authenticate;

my $p =3D WWW::Connotea::Post->new;
$p->link('http://www.somelinkwhichdoesnotexist.de');
$p->tags('=F6=E4=FC=DF=D6=C4=DC','testing');
$p->description('=F6=E4=FC=DF=D6=C4=DC');

my $location =3D $c->create($p);

print 'Successfuly created post at ', $location, "\n";


Code doing this with LWP post request:

use LWP::UserAgent;
my $ua =3D LWP::UserAgent->new();

my $url_post=3D'http://username:pas...@ww.../data/add';
my $response =3D $ua->post($url_post,['uri'=3D>'
http://www.somelinkwhichdoesnotexist.de','tags'=3D>'=E4=F6=FC=DF','descript=
ion'=3D>'=E4=F6=FC=DF','comment'=3D>'=E4=F6=FC=DF'],'Referer'
=3D>'');

[Connotea-code-devel] proxy systems

[Martin F. <ma...@ne...>]

Dear Connotea Users,

We've seen, and been notified, that some users are bookmarking URL's 
that they have "proxified"; that is, they have added arbitrary URL 
information such as appending a server at their institution to the 
hostname, mostly in order to facilitate off-premises access to protected 
resources. Because the proxified URL goes through the institution proxy 
it can yield the article/data when also given proper access credentials.

Internally we're discussing the best way to support these URL's, with 
the primary issue being that we'd like these URL's to be recognized by 
our citation data retrieval system. There are other issues, such as 
merging theses bookmarks with other versions that point to the same 
article/data, but since that involves a wider issue of multiple (or no) 
URL's to the same data, we have decided not to treat the proxy issue 
specially in that regard until we address it for the whole system, as 
that problem exists with lots of URL's for other reasons.

So, the system that we're currently designing uses a plugin architecture 
and accomplishes the following:

1. An URL is accepted.
2. Our proxy modules scan the URL and decide if they can "unproxify" it.
3. If so, they do it, and the simpler URL is passed on to the citation 
module system, but not stored.
4. The HTML title of the URL is grabbed and saved.
5. The citation modules scan the URL and decide if they can fetch 
authoritative data for it (this part is working now).
6. Citation data is fetched.
7. In some cases, the citation module can (and should) simplify the URL, 
e.g. to strip out a user's username or session identifier. This is 
normally passed back and saved.
8. In the case that the proxy system unproxified the original URL, and 
the citation system simplified the URL, the proxy module chosen would 
now have to reproxify the simpler URL. So unlike citation modules which 
are essentially one-way, proxy modules have to potentially go two ways.
9. The URL and citation data is saved.

The proxy module architecture is actually similar but simpler than the 
citation module architecture: understands() and filter(), etc.

Does this sound like a good system?

Would those of you who happen to be using proxies be willing to write a 
short perl module, or help us write one, that understands your proxy 
URL's and rewrites them? In our testing we have found these to be quite 
short.

Thanks for any feedback.

Regards,
Martin Flack

[Connotea-code-devel] Goodbye from Ben

[Lund, B. <b....@na...>]

Hi All,

Almost two years ago Connotea was launched as an early, experimental,
alpha-version service.  Since then I've had a lot of fun working on
Connotea, and seeing it change into the highly used and highly useful
service it is now.

However, now the time has come for me to move on, and so tomorrow (Thursday
9th) will be my last day here at Nature.  I will, of course, continue to be
a Connotea user, but I'll no longer be involved in the day-to-day running of
the project.

But other people will!  So everything will continue as normal here -- Joanna
Scott will continue to gather your feedback and help create and test new
features, Martin Flack from NeoReality will continue to develop the core
Connotea Code, Euan Adie (of postgenomic.com fame) will be helping out, and
there may be some new faces coming on board too.

A lot of the work we've done on Connotea has been as a direct result of the
feedback we've received from these lists, both publicly and privately.  So
thanks very much for that, and please do continue to discuss the present and
future of Connotea with Joanna, Euan and the others here at NPG.

What am I going to be doing now?  Well, as Holmes said to Watson, "I have my
eye on a suite in Baker Street."

All the best,
Ta,
Ben


---
-- Ben Lund
-- Soon-to-be-ex-Product Development Manager
-- Web Publishing
-- Nature Publishing Group
-- http://www.connotea.org/user/ben
-- http://blogs.nature.com/wp/nascent/

---

********************************************************************************   
DISCLAIMER: This e-mail is confidential and should not be used by anyone who is
not the original intended recipient. If you have received this e-mail in error
please inform the sender and delete it from your mailbox or any other storage
mechanism. Neither Macmillan Publishers Limited nor any of its agents accept
liability for any statements made which are clearly the sender's own and not
expressly made on behalf of Macmillan Publishers Limited or one of its agents.
Please note that neither Macmillan Publishers Limited nor any of its agents
accept any responsibility for viruses that may be contained in this e-mail or
its attachments and it is your responsibility to scan the e-mail and 
attachments (if any). No contracts may be concluded on behalf of Macmillan 
Publishers Limited or its agents by means of e-mail communication. Macmillan 
Publishers Limited Registered in England and Wales with registered number 785998 
Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS   
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[Connotea-code-devel] Help!connotea does not work

[Fan <va...@12...>]

Hello everyone
For a long week, I install connotea code on my computer, but there is still not successful to run.

My apache server has accepted connotea after configuring apache2.conf(Ubuntu platform).

Test in local environment http://localhost/bibliotech/
Here is Error Exception Report:
Visitor requests /bibliotech bringing load to 1 with db at 1162802747
must pass in Apache::RequestRec Object at  /var/www/bibliotech//Bibliotech/Component/Inc.pm line 24

I thought a lot but not find a way to resolve.

Please help me , thank you all the time!

Wei 
va...@12... 


	

Re: [Connotea-code-devel] Can't locate WWW/Connotea.pm

[Jing T. <ti...@gm...>]

Hi Kieren,

Thank you very much for your answer.

I installed all the necessary classes in Linux, but when perl
post_something.pl, there is an error:
Invalid content type in response: "application/xml; charset=UTF-8" at
post_something.pl line 25 (this line: my $location = $c->create($p);)

I have no idea why it happens. Would you please give some help?

Thanks for your time!

Jing

On 10/30/06, Kieren Diment <ki...@di...> wrote:
>
> You don't have Class::Accessor installed.
>
> You need to install it via cpan or ActivePerl equivalent.  However,
> I"m not sure whether Connotea will work with ActiveState Perl.
>
>
> On 31 Oct 2006, at 14:56, Jing Tie wrote:
>
> > Dear All,
> >
> > I am a very beginner of perl, and met some problem to create a new
> > post
> > using webapi.
> >
> > When I am compiling sample file "post_something.pl" by ActivePerl
> > perlcc, it
> > failed: "Can't locate WWW/Connotea.pm in @INC". So I changed "use lib
> > '../lib' " into absolute address, but another failure occured:
> > "Can't locate
> > Class/Accessor.pm in @INC at D:/code/connotea/lib/WWW/Connotea.pm".
> >
> > I think maybe I missed some configuration...? But I couldn't find
> > it on the
> > webpage.
> >
> > Thanks for your help!
> >
> > Sincerely,
> > Jing
> > ----------------------------------------------------------------------
> > ---
> > 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
> > http://sel.as-us.falkag.net/sel?
> > cmd=lnk&kid=120709&bid=263057&dat=121642______________________________
> > _________________
> > Connotea-code-devel mailing list
> > Con...@li...
> > https://lists.sourceforge.net/lists/listinfo/connotea-code-devel
>

Re: [Connotea-code-devel] Notes: Questionnaire: are you in collections, Do you need help - Chris607311619

[Vicente J. <Div...@gm...>]

soy massage
Our attorneys have discovered a loop hole in the banking laws. tonsil.

Using this discovery we have been successful at totally eliminating peoples CreditCardDebt with out them paying another dime. handel.

We GuaranteeThat we can do this for you. josephson.

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Re: [Connotea-code-devel] Can't locate WWW/Connotea.pm

[Kieren D. <ki...@di...>]

You don't have Class::Accessor installed.

You need to install it via cpan or ActivePerl equivalent.  However,  
I"m not sure whether Connotea will work with ActiveState Perl.


On 31 Oct 2006, at 14:56, Jing Tie wrote:

> Dear All,
>
> I am a very beginner of perl, and met some problem to create a new  
> post
> using webapi.
>
> When I am compiling sample file "post_something.pl" by ActivePerl  
> perlcc, it
> failed: "Can't locate WWW/Connotea.pm in @INC". So I changed "use lib
> '../lib' " into absolute address, but another failure occured:  
> "Can't locate
> Class/Accessor.pm in @INC at D:/code/connotea/lib/WWW/Connotea.pm".
>
> I think maybe I missed some configuration...? But I couldn't find  
> it on the
> webpage.
>
> Thanks for your help!
>
> Sincerely,
> Jing
> ---------------------------------------------------------------------- 
> ---
> 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
> http://sel.as-us.falkag.net/sel? 
> cmd=lnk&kid=120709&bid=263057&dat=121642______________________________ 
> _________________
> Connotea-code-devel mailing list
> Con...@li...
> https://lists.sourceforge.net/lists/listinfo/connotea-code-devel

[Connotea-code-devel] Can't locate WWW/Connotea.pm

[Jing T. <ti...@gm...>]

Dear All,

I am a very beginner of perl, and met some problem to create a new post
using webapi.

When I am compiling sample file "post_something.pl" by ActivePerl perlcc, it
failed: "Can't locate WWW/Connotea.pm in @INC". So I changed "use lib
'../lib' " into absolute address, but another failure occured: "Can't locate
Class/Accessor.pm in @INC at D:/code/connotea/lib/WWW/Connotea.pm".

I think maybe I missed some configuration...? But I couldn't find it on the
webpage.

Thanks for your help!

Sincerely,
Jing

[Connotea-code-devel] fwd: GSNH Closes Up Friday, After-Market News Release - acct Leo Sweeney

[Kathleen W. <Hor...@gm...>]

recusant megohm

Up On the News - GSNH closes Up Friday, After-Market News Release - Get GSNH Quote Here. then.
http://moneycentral.msn.com/detail/stock_quote?Symbol=gsnh

After weeks of speculation it's finally here, and the news is even bigger than we thought. antioch.

We first knew something was up with GSNH when news came out Thursday regarding Drill LOMT #1. But GSNH really popped up on our radar with Friday's After-Market news. GSNH has announced its partners for the LOMT #1 sidetrack well and you are not going to believe who they are. arrange.

GSNH Names Partners for LOMT #1 Sidetrack Well merrimack.
Friday October 27, 4:05 pm ET squeamish.
HOUSTON, Texas--(BUSINESS WIRE) - GSNH announces...has awarded drilling services for the LOMT #1 Sidetrack well to the following providers: doneck
* Patterson-UTI (Nasdaq: PTEN), Revenue: 2.23 billion, UP 63.30% gogh
* Schlumberger (NYSE: SLB), Revenue: 17.90 billion, UP 34.00% defiant
* Halliburton (NYSE: HAL), Revenue: 22.90 billion, UP 13.40% phd

Oct. 27, 2006 (BUSINESS WIRE) - GSNH Names Partners for Sidetrack Well... schnabel
http://biz.yahoo.com/bw/061027/20061027005324.html?.v=1

GSNH has been releasing steady news worldwide, from Yahoo Finance, AOL, & MSN Money to Marketwatch & Bloomberg---even the NYSE & the NASDAQ have gotten in on the action. Exposure for GSNH is expansive. The increased frequency of news led us to believe that something big was coming for GSNH, and as usual, we were dead-on right. blackbird

Oct. 26, 2006 (BUSINESS WIRE) – GSNH to Drill LOMT #1... tier.
http://money.aol.com/news/articles/_a/greater-sooner-holdings-inc-to-drill/n20061026162609990029

Oct. 12, 2006 (BUSINESS WIRE) – GSNH Reports Drilling Success... darn.
http://www.marketwatch.com/News/Story/Story.aspx?guid={05206016-17D5-4077-B8A3-3D8A763487E2}&siteid=mktw&sid=2133723&symb=

Oct. 11, 2006 (BUSINESS WIRE) – GSNH Announces the Anthony 33... brow.
http://news.moneycentral.msn.com/ticker/article.asp?Feed=BW&Date=20061011&ID=6094112&Symbol=US:GSNH

Oct. 4, 2006 (BUSINESS WIRE) – GSNH...285 million in Probable Reserves... crouch.
http://bloomberg.com/apps/news?pid=conewsstory&refer=conews&tkr=GSNH:US&sid=a6F2jO13PWCU

Friday's After-Market news on GSNH and its newfound partnership with these major corporations (over 43 billion in revenue combined) is just the beginning. We believe that there is even bigger news coming, and as always, we are bringing you the news ahead of time, ahead of everyone else, and ahead of a major spike in GSNH stock price.

shrug return erratum

[Connotea-code-devel] Notea: A Firefox Extension for Connotea

[Lund, B. <b....@na...>]

Hi All,

[Apologies if you receive this twice -- I'm posting to both the discussion
list and the code-devel list.  Please include only the code-devel list if
you reply.]

I'm happy to announce a new Connotea-related project that you might be
interested in trying out.  I'm not announcing this more generally than these
lists at the moment, since this is still at an early phase. However, you
should feel free to pass this on to anyone you think will want to try it
out.

Notea ( http://www.connotea.org/wiki/Notea ) is a Firefox Extension that
helps you store and organise local copies of online works. It integrates
with Connotea to allow you to (optionally) add a bookmark for anything you
store locally to your Connotea library.

How it works:

 * The extension allows you to add a nice big button to your browser toolbar

 * To save a local copy of any web page that you visit, click that Notea
button
   - note that this is different to the Connotea browser button

 * This reveals a simple form, similar to the Connotea bookmarking form

 * Type in some tags, just like in Connotea, and select the other
appropriate options

 * Depending on your preferences, as well as saving a local copy, Notea will
bookmark the article you saved to your Connotea library.


See the Notea community page for more details and instructions on how to
install it:

http://www.connotea.org/wiki/Notea

Some important things to note:

  * There are some instructions on how to make the button visible on the
Notea community page.  Have a look at those, since after installation the
button isn't visible by default.

  * This is an alpha version of the extension, so don't be surprised if
there are a few things that need to be polished (there are many!).  We're
releasing it now so as to get some early feedback on the idea, and to allow
you to get involved in the future development of the tool.

  * It currently only works with Firefox 1.5.*

  * It's open source.  If you're a programmer and like the sound of the
extension, please do get involved.  Have a look at
http://www.connotea.org/wiki/NoteaDevelopment for more details.


Why is it called "Notea"?
 
  1) It's like "Connotea" but without the con- prefix that means "all in
one place" 
  2) Also, I hadn't had my morning cup of tea when I was trying to decide
what to name the first file...


Have fun,

All the best,
Ben


--- 
-- Ben Lund
-- Product Development Manager
-- Web Publishing
-- Nature Publishing Group
-- http://www.connotea.org/user/ben
-- http://blogs.nature.com/wp/nascent/



********************************************************************************   
DISCLAIMER: This e-mail is confidential and should not be used by anyone who is
not the original intended recipient. If you have received this e-mail in error
please inform the sender and delete it from your mailbox or any other storage
mechanism. Neither Macmillan Publishers Limited nor any of its agents accept
liability for any statements made which are clearly the sender's own and not
expressly made on behalf of Macmillan Publishers Limited or one of its agents.
Please note that neither Macmillan Publishers Limited nor any of its agents
accept any responsibility for viruses that may be contained in this e-mail or
its attachments and it is your responsibility to scan the e-mail and 
attachments (if any). No contracts may be concluded on behalf of Macmillan 
Publishers Limited or its agents by means of e-mail communication. Macmillan 
Publishers Limited Registered in England and Wales with registered number 785998 
Registered Office Brunel Road, Houndmills, Basingstoke RG21 6XS   
********************************************************************************