From martin.senger at gmail.com  Tue May  6 05:07:20 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 6 May 2008 10:07:20 +0100
Subject: [MOBY-dev] building jMoby on Mac - help needed
Message-ID: <4d93f07c0805060207t18802a74i3f59b00fff99c5f6@mail.gmail.com>

I am looking for Mac-ists who can help with the building/compiling jMoby on
Mac OS X.

The problem (as identified already during the last Biohackathon in Tokyo) is
the tools.jar library. On Mac, there is no such file because its contents is
part of the default library classes.jar. On other platforms we have to add
the tools.jar separately. That's why there is a "mac profile" in the
xmls/project.pom. But it does not work... (I wonder if it was working in the
past, at all; was it?).

The problematic (the one causing an error under Mac OS X) are the lines (in
build.xml):

    <fileset dir="${java.home}/../lib">
      <include name="tools.jar"/>
    </fileset>

I really do not understand how the profile tag in xmls/project.pom works, or
should work, to make the lines above working. Any help around?

Many thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From martin.senger at gmail.com  Tue May  6 05:58:20 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 6 May 2008 10:58:20 +0100
Subject: [MOBY-dev] where is the service 'ping' documented?
Message-ID: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>

I am looking for the documentation how the 'ping' should work. I think that
it should work like this: "Send an empty mobyContent and get back the
same.". Is this correct?

The only remark about this being documented I found is this one (from Paul):

In any case, the API doc is now up to date in CVS, it will take a while
> to propagate to the Web site...


But I still cannot find where it is. Does anybody know?

Thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From groscurt at mpiz-koeln.mpg.de  Tue May  6 07:52:27 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 06 May 2008 13:52:27 +0200
Subject: [MOBY-dev] biomoby.org gone white
In-Reply-To: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>
References: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>
Message-ID: <4820467B.2010609@mpiz-koeln.mpg.de>

Hi,

if we call biomoby.org (at least in germany) we get a white page....

intended ? ;-)

best
andreas

From martin.senger at gmail.com  Tue May  6 07:57:58 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 6 May 2008 12:57:58 +0100
Subject: [MOBY-dev] biomoby.org gone white
In-Reply-To: <4820467B.2010609@mpiz-koeln.mpg.de>
References: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>
	<4820467B.2010609@mpiz-koeln.mpg.de>
Message-ID: <4d93f07c0805060457m7c4fb0bcxad98543ac1e3ea7d@mail.gmail.com>

> if we call biomoby.org (at least in germany) we get a white page....
>

Interesting. It was still there about a two hours ago...
M.

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From groscurt at mpiz-koeln.mpg.de  Tue May  6 08:07:18 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 06 May 2008 14:07:18 +0200
Subject: [MOBY-dev] biomoby.org gone white
In-Reply-To: <4d93f07c0805060457m7c4fb0bcxad98543ac1e3ea7d@mail.gmail.com>
References: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>	<4820467B.2010609@mpiz-koeln.mpg.de>
	<4d93f07c0805060457m7c4fb0bcxad98543ac1e3ea7d@mail.gmail.com>
Message-ID: <482049F6.9090508@mpiz-koeln.mpg.de>

and now its back to normal.... weird ;-9

Martin Senger wrote:
>> if we call biomoby.org (at least in germany) we get a white page....
>>
>>     
>
> Interesting. It was still there about a two hours ago...
> M.
>
>   


From edward.kawas at gmail.com  Tue May  6 09:10:56 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 6 May 2008 06:10:56 -0700
Subject: [MOBY-dev] where is the service 'ping' documented?
In-Reply-To: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>
References: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>
Message-ID: <482058ef.2a528c0a.7ee6.ffffedda@mx.google.com>

Hi Martin,

You are correct in the behaviour of the pinger; send empty mobyContent and
get one back.

The only documentation that I am aware of is located at
http://moby.ucalgary.ca/moby/ValidateService?getDeadServices which is
produced by the script.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
Sent: May-06-08 2:58 AM
To: Core developer announcements
Cc: Skofic, Milko (Bioversity)
Subject: [MOBY-dev] where is the service 'ping' documented?

I am looking for the documentation how the 'ping' should work. I think that
it should work like this: "Send an empty mobyContent and get back the
same.". Is this correct?

The only remark about this being documented I found is this one (from Paul):

In any case, the API doc is now up to date in CVS, it will take a while
> to propagate to the Web site...


But I still cannot find where it is. Does anybody know?

Thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From edward.kawas at gmail.com  Tue May  6 09:12:58 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 6 May 2008 06:12:58 -0700
Subject: [MOBY-dev] building jMoby on Mac - help needed
In-Reply-To: <4d93f07c0805060207t18802a74i3f59b00fff99c5f6@mail.gmail.com>
References: <4d93f07c0805060207t18802a74i3f59b00fff99c5f6@mail.gmail.com>
Message-ID: <48205969.0abd720a.6d3e.664c@mx.google.com>

Hi Martin,

Have you seen this link before?
http://maven.apache.org/general.html#tools-jar-dependency

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
Sent: May-06-08 2:07 AM
To: Core developer announcements
Cc: Skofic, Milko (Bioversity)
Subject: [MOBY-dev] building jMoby on Mac - help needed

I am looking for Mac-ists who can help with the building/compiling jMoby on
Mac OS X.

The problem (as identified already during the last Biohackathon in Tokyo) is
the tools.jar library. On Mac, there is no such file because its contents is
part of the default library classes.jar. On other platforms we have to add
the tools.jar separately. That's why there is a "mac profile" in the
xmls/project.pom. But it does not work... (I wonder if it was working in the
past, at all; was it?).

The problematic (the one causing an error under Mac OS X) are the lines (in
build.xml):

    <fileset dir="${java.home}/../lib">
      <include name="tools.jar"/>
    </fileset>

I really do not understand how the profile tag in xmls/project.pom works, or
should work, to make the lines above working. Any help around?

Many thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From martin.senger at gmail.com  Tue May  6 09:26:22 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 6 May 2008 14:26:22 +0100
Subject: [MOBY-dev] building jMoby on Mac - help needed
In-Reply-To: <48205969.0abd720a.6d3e.664c@mx.google.com>
References: <4d93f07c0805060207t18802a74i3f59b00fff99c5f6@mail.gmail.com>
	<48205969.0abd720a.6d3e.664c@mx.google.com>
Message-ID: <4d93f07c0805060626laa1b54x39454275ad1fa633@mail.gmail.com>

> Have you seen this link before?
> http://maven.apache.org/general.html#tools-jar-dependency
>

We have a very similar lines in our dependencies file. They are using
slightly different, perhaps wrong, test for the platform name (roughly
speaking we say "if this is not a Mac" and your link says "if this is a
Sun"). We need a person with a Mac to find what is right and what works.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From martin.senger at gmail.com  Tue May  6 09:37:35 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 6 May 2008 14:37:35 +0100
Subject: [MOBY-dev] data type suitable as a search filter
Message-ID: <4d93f07c0805060637h5db4c555wc60f384a8b5a0287@mail.gmail.com>

I wonder if somebody can give me an advise.

I have a data type A (whose structure is very close to a simple name/value
pair). In one service, I would like to use this data type as a search
filter. In order to do it, I would need to add there an operator (to
indicate how to treat the value - like, equal, greater than etc.).
Therefore, I think about a new, more specialized data type AWithOperator. My
questions now are:

a) Is there already a data type that can be used to represent an operator
(so I would add it as a new article name into my new AWithOperator?

b) If not, does it mean that I am doing something which I should not? In
which case, what would be the correct way to do so? [Note that the usage of
secondary parameters is out of the question - I think - because the service
will have a collection of search filters and each of them can have different
operator while the secondary parameter is just one for the whole collection.
Correct?]

Thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From hao.chen at uni-bielefeld.de  Tue May  6 17:00:20 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Tue, 06 May 2008 23:00:20 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <4d93f07c0805060637h5db4c555wc60f384a8b5a0287@mail.gmail.com>
References: <4d93f07c0805060637h5db4c555wc60f384a8b5a0287@mail.gmail.com>
Message-ID: <1210107620.3268.14.camel@wasser-laptop>

hi, all

 Now I want to register service from XML file with jmoby. and I use the
existing method registerService(), which can receive xmlString as
Parameter. Here is part of my code.

          RegistryImpl register =new RegistryImpl();
          register.registerService(smlString);

but it seems not to work. I am sure that the smlString I used is
correct, because I can register the same one using Dashboard without nay
problem. Did I do something wrong? 

cheers,
hao chen

       


   


From edward.kawas at gmail.com  Tue May  6 23:51:48 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 6 May 2008 20:51:48 -0700
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <1210107620.3268.14.camel@wasser-laptop>
References: <4d93f07c0805060637h5db4c555wc60f384a8b5a0287@mail.gmail.com>
	<1210107620.3268.14.camel@wasser-laptop>
Message-ID: <48212756.1aba720a.21cc.40fc@mx.google.com>

Can you post the XML or send it to the list as an attachment?

Thanks,

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of wasser
Sent: May-06-08 2:00 PM
To: Core developer announcements
Subject: [MOBY-dev] Service registration from XML

hi, all

 Now I want to register service from XML file with jmoby. and I use the
existing method registerService(), which can receive xmlString as
Parameter. Here is part of my code.

          RegistryImpl register =new RegistryImpl();
          register.registerService(smlString);

but it seems not to work. I am sure that the smlString I used is
correct, because I can register the same one using Dashboard without nay
problem. Did I do something wrong? 

cheers,
hao chen

       


   

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From hao.chen at uni-bielefeld.de  Wed May  7 04:22:06 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Wed, 07 May 2008 10:22:06 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <48212756.1aba720a.21cc.40fc@mx.google.com>
References: <4d93f07c0805060637h5db4c555wc60f384a8b5a0287@mail.gmail.com>
	<1210107620.3268.14.camel@wasser-laptop>
	<48212756.1aba720a.21cc.40fc@mx.google.com>
Message-ID: <1210148526.5959.16.camel@wasser-laptop>

Hi, Eddie, 

Here is the XML file named ?TestXMLReg.xml I used.

<registerService>
<Category>moby</Category>
<serviceName>TestXMLReg</serviceName>
<serviceType>Testing</serviceType>
<serviceLSID/>
<authURI>www.techfak.uni-bielefeld.de</authURI>
<signatureURL/>
<URL>http://localhost:8080/axis/services/TestXMLReg</URL>
<contactEmail>webmaster at uni-bielefeld.de</contactEmail>
<authoritativeService>1</authoritativeService>
<Description>a test service.</Description>
<Input>
<Simple articleName="SequenceML">
<objectType>SequenceML</objectType>
</Simple>
</Input>
<secondaryArticles>
<Parameter articleName="Name">
<datatype>String</datatype>
<description/>
</Parameter>
<Parameter articleName="star">
<datatype>Integer</datatype>
<description/>
<default>0</default>
<max>25</max>
<min>0</min>
<enum/>
</Parameter>
<Parameter articleName="isEmpty">
<datatype>Boolean</datatype>
<description/>
<default>false</default>
</Parameter>
</secondaryArticles>
<Output>
<Simple articleName="FASTA_Text">
<objectType>FASTA_Text</objectType>
</Simple>
</Output>
</registerService>

and I write following code to generate XML String within a try block
String regXML="";
BufferedReader in = new BufferedReader(new InputStreamReader(new
FileInputStream("//home//wasser//workspace//TestXMLReg.xml")));
       String str="";
       while((str=in.readLine())!=null){ 
                           regXML+=str;}
cheers
hao chen


On Tue, 2008-05-06 at 20:51 -0700, Edward Kawas wrote:
> Can you post the XML or send it to the list as an attachment?
> 
> Thanks,
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of wasser
> Sent: May-06-08 2:00 PM
> To: Core developer announcements
> Subject: [MOBY-dev] Service registration from XML
> 
> hi, all
> 
>  Now I want to register service from XML file with jmoby. and I use the
> existing method registerService(), which can receive xmlString as
> Parameter. Here is part of my code.
> 
>           RegistryImpl register =new RegistryImpl();
>           register.registerService(smlString);
> 
> but it seems not to work. I am sure that the smlString I used is
> correct, because I can register the same one using Dashboard without nay
> problem. Did I do something wrong? 
> 
> cheers,
> hao chen
> 
>        
> 
> 
>    
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From dmitry.repchevski at bsc.es  Wed May  7 05:26:12 2008
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Wed, 07 May 2008 11:26:12 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <1210148526.5959.16.camel@wasser-laptop>
References: <1210148526.5959.16.camel@wasser-laptop>
Message-ID: <482175B4.50300@bsc.es>

Hello!

I don't know about JMoby, but at first glance you don't add "/n" (for 
unix) into your regXML (must not matter, but...).
[advice] Never concatenate strings with "+" operator - use StringBuffer 
or StringBuilder (java5) instead...
[advice] Also it is always a good idea to close files :-)

|String linebreak = System.getProperty("line.separator"));|

StringBuilder buf = new StringBuilder();
BufferedReader in = new BufferedReader(new FileReader("//home//wasser//workspace//TestXMLReg.xml"));

try {
    String str;
    while((str=in.readLine())!=null) { 
    buf.append(str).append(linebreak);
    }
}
finally { in.close(); }

String regXML = buf.toString();

P.S. sorry for offtopic





From hao.chen at uni-bielefeld.de  Wed May  7 07:10:39 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Wed, 07 May 2008 13:10:39 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <482175B4.50300@bsc.es>
References: <1210148526.5959.16.camel@wasser-laptop> <482175B4.50300@bsc.es>
Message-ID: <1210158639.5959.37.camel@wasser-laptop>


hallo,

thank you for your advice. Yes, I should use methode stringBuffer()
instead  "+" operator. I wrote this code just for test and want to know
if I can register service from xml with methode ?registerService(). 

and if it works , xml string  should be constructed directly without
reading XML from a file. 

cheers 
hao chen

On Wed, 2008-05-07 at 11:26 +0200, Dmitry Repchevsky wrote:
> Hello!
> 
> I don't know about JMoby, but at first glance you don't add "/n" (for 
> unix) into your regXML (must not matter, but...).
> [advice] Never concatenate strings with "+" operator - use StringBuffer 
> or StringBuilder (java5) instead...
> [advice] Also it is always a good idea to close files :-)
> 
> |String linebreak = System.getProperty("line.separator"));|
> 
> StringBuilder buf = new StringBuilder();
> BufferedReader in = new BufferedReader(new FileReader("//home//wasser//workspace//TestXMLReg.xml"));
> 
> try {
>     String str;
>     while((str=in.readLine())!=null) { 
>     buf.append(str).append(linebreak);
>     }
> }
> finally { in.close(); }
> 
> String regXML = buf.toString();
> 
> P.S. sorry for offtopic
> 
> 
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From dmitry.repchevski at bsc.es  Wed May  7 07:37:06 2008
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Wed, 07 May 2008 13:37:06 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <1210158639.5959.37.camel@wasser-laptop>
References: <1210158639.5959.37.camel@wasser-laptop>
Message-ID: <48219462.9040302@bsc.es>

It is just happened to me,
Have you tried to put XML header? (<?xml version='1.0' encoding='UTF-8'?>)
Formally your document is not an XML document without it...

Cheers,

Dmitry



From dmitry.repchevski at bsc.es  Wed May  7 07:52:27 2008
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Wed, 07 May 2008 13:52:27 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <1210158639.5959.37.camel@wasser-laptop>
References: <1210158639.5959.37.camel@wasser-laptop>
Message-ID: <482197FB.40105@bsc.es>

I have tested it with my API and got:

"Malformed email - must be a valid email address of the form 
name at organization.foo"

Error... So this is the error with XML itself :-)

Cheers,

Dmitry

From hao.chen at uni-bielefeld.de  Wed May  7 08:02:28 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Wed, 07 May 2008 14:02:28 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <48219462.9040302@bsc.es>
References: <1210158639.5959.37.camel@wasser-laptop> <48219462.9040302@bsc.es>
Message-ID: <1210161748.14207.10.camel@wasser-laptop>

hi, Dmitry

according to Biomoby API
(http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/org/biomoby/registry/Central/Registry.html) is an XML string with the following structure:

<registerService>
          <Category>moby</Category> <!-- one of 'moby', 'cgi', 'soap' -->
          <serviceName>YourServiceNameHere</serviceName>
          <serviceType>TypeOntologyTerm</serviceType>
          <authURI>your.URI.here</authURI>
          <signatureURL> http://some.URL.org/path/to/RDF/file </signatureURL>
          <URL>http://URL.to.your/Service.script</URL>;
          <contactEmail>your_name at contact.address.com</contactEmail>
          <authoritativeService>1 | 0 </authoritativeService>
          <Description><![CDATA[
                human readable COMPREHENSIVE description of your service]]>
          </Description>
          <Input>
               <!-- zero or more Primary (Simple and/or Collection) articles -->
               <!-- each of these articles will appear EXACTLY ONCE in the input to the service -->
          </Input>
          <secondaryArticles>
               <!-- zero or more INPUT Secondary (Parameter) articles -->
               <!-- each of these articles will appear EXACTLY ONCE in the output from the service -->
          </secondaryArticles>
          <Output>
               <!-- zero or more Primary (Simple and/or Collection) articles --> 
          </Output>
</registerService>

I think the XML String for the method registerService() should be used without XML header.

cheers
hao chen


On Wed, 2008-05-07 at 13:37 +0200, Dmitry Repchevsky wrote:
> It is just happened to me,
> Have you tried to put XML header? (<?xml version='1.0' encoding='UTF-8'?>)
> Formally your document is not an XML document without it...
> 
> Cheers,
> 
> Dmitry
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From hao.chen at uni-bielefeld.de  Wed May  7 09:12:01 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Wed, 07 May 2008 15:12:01 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <482197FB.40105@bsc.es>
References: <1210158639.5959.37.camel@wasser-laptop> <482197FB.40105@bsc.es>
Message-ID: <1210165921.14645.11.camel@wasser-laptop>

hi,? Dmitry

I use the correct email address Format. It seems that the program of our
Forum changed email symbol to "at", so you get the "Malformed email"
Error. I send the Email now as attachment to the list. 

On Wed, 2008-05-07 at 13:52 +0200, Dmitry Repchevsky wrote:
> I have tested it with my API and got:
> 
> "Malformed email - must be a valid email address of the form 
> name at organization.foo"
> 
> Error... So this is the error with XML itself :-)
> 
> Cheers,
> 
> Dmitry
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
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From edward.kawas at gmail.com  Wed May  7 09:52:21 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 7 May 2008 06:52:21 -0700
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <1210165921.14645.11.camel@wasser-laptop>
References: <1210158639.5959.37.camel@wasser-laptop> <482197FB.40105@bsc.es>
	<1210165921.14645.11.camel@wasser-laptop>
Message-ID: <4821b419.1dba720a.0a3f.65eb@mx.google.com>

Hi Hao Chen,

Okay, now that I have examined how you are trying to do things, I have a few things to say:

The class RegistryImpl in org.biomoby.registry was never implemented. I created that class a long time ago when I was going to try to write the registry in JAVA. Sorry for the confusion.

You should try using org.biomoby.client.CentralImpl and the method registerService(). Unfortunately, it doesn?t consume a string of XML, but I am sure that you could dig deeper and see how that method performs the registerService and mimic it.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of wasser
Sent: May-07-08 6:12 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Service registration from XML

hi,? Dmitry

I use the correct email address Format. It seems that the program of our Forum changed email symbol to "at", so you get the "Malformed email"
Error. I send the Email now as attachment to the list. 

On Wed, 2008-05-07 at 13:52 +0200, Dmitry Repchevsky wrote:
> I have tested it with my API and got:
> 
> "Malformed email - must be a valid email address of the form 
> name at organization.foo"
> 
> Error... So this is the error with XML itself :-)
> 
> Cheers,
> 
> Dmitry
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From gordonp at ucalgary.ca  Wed May  7 10:42:31 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 07 May 2008 08:42:31 -0600
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <4821b419.1dba720a.0a3f.65eb@mx.google.com>
References: <1210158639.5959.37.camel@wasser-laptop>
	<482197FB.40105@bsc.es>	<1210165921.14645.11.camel@wasser-laptop>
	<4821b419.1dba720a.0a3f.65eb@mx.google.com>
Message-ID: <4821BFD7.4050507@ucalgary.ca>

Or preferably, create a MobyService object and call all the set() 
methods to populate it.  Then call registerService on the MobyService 
object.  There is an example of this in 
moby-live/Java/src/Clients/ServletTester.java.  No manual XML required, 
which is part of the point of having an Java API ;-)

Edward Kawas wrote:
> Hi Hao Chen,
>
> Okay, now that I have examined how you are trying to do things, I have a few things to say:
>
> The class RegistryImpl in org.biomoby.registry was never implemented. I created that class a long time ago when I was going to try to write the registry in JAVA. Sorry for the confusion.
>
> You should try using org.biomoby.client.CentralImpl and the method registerService(). Unfortunately, it doesn?t consume a string of XML, but I am sure that you could dig deeper and see how that method performs the registerService and mimic it.
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of wasser
> Sent: May-07-08 6:12 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Service registration from XML
>
> hi,? Dmitry
>
> I use the correct email address Format. It seems that the program of our Forum changed email symbol to "at", so you get the "Malformed email"
> Error. I send the Email now as attachment to the list. 
>
> On Wed, 2008-05-07 at 13:52 +0200, Dmitry Repchevsky wrote:
>   
>> I have tested it with my API and got:
>>
>> "Malformed email - must be a valid email address of the form 
>> name at organization.foo"
>>
>> Error... So this is the error with XML itself :-)
>>
>> Cheers,
>>
>> Dmitry
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>     
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> !DSPAM:60005,4821b1ba109503177825363!
>
>
>
>   

From martin.senger at gmail.com  Thu May  8 04:22:04 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 8 May 2008 09:22:04 +0100
Subject: [MOBY-dev] can not generate service skeleton
In-Reply-To: <1203522403.11381.6.camel@andreas.dhcp.studentenwerk-bielefeld.de>
References: <1203522403.11381.6.camel@andreas.dhcp.studentenwerk-bielefeld.de>
Message-ID: <4d93f07c0805080122i47acb60dg98986d9b28d14cfe@mail.gmail.com>

>  I got this error


Could you paste the error here, please?

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From hao.chen at uni-bielefeld.de  Thu May  8 05:08:50 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Thu, 08 May 2008 11:08:50 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <4821BFD7.4050507@ucalgary.ca>
References: <1210158639.5959.37.camel@wasser-laptop> <482197FB.40105@bsc.es>
	<1210165921.14645.11.camel@wasser-laptop>
	<4821b419.1dba720a.0a3f.65eb@mx.google.com>
	<4821BFD7.4050507@ucalgary.ca>
Message-ID: <1210237730.13084.2.camel@wasser-laptop>

hi, Paul

Thanks for the hint. It works great. 


From sneumann at ipb-halle.de  Fri May  9 04:03:49 2008
From: sneumann at ipb-halle.de (sneumann)
Date: Fri, 09 May 2008 10:03:49 +0200
Subject: [MOBY-dev] Dashboard Service Results missing Tab
Message-ID: <1210320229.31656.135.camel@lathan.ipb-sub.ipb-halle.de>

Hi,

we have a moby service which we'd like to test drive 
in the moby-dashboard. Invocation is fine, 
and I see the "Service Results -> All" tab with my data.

We have a second Dashboard (on windows, which shouldn't matter) 
which shows -- for the same service and the same input --
a second tab "Record" with a "moby-whale-icon" 
next to the "All" tab. This contains the preformatted text instead of 

<moby:Simple moby:articleName="record">
        <moby:String moby:id="ACCESSION: PB000122&#xA;RECORD_TITLE: ...
</moby:Simple>

This dashboard also has a "Simple Moby Text"
in the drop-down box in the lower right of the "Service Results",
whereas I have only Plain Text and XML Tree. 

I checked CVS logs and docs/ChangeLog, but couldn't spot 
anything relevant. Have there been any changes recently ?

The service in question is MassBank_Simple_2 on testing registry.

Yours,
Steffen


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

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From martin.senger at gmail.com  Fri May  9 05:54:12 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 9 May 2008 10:54:12 +0100
Subject: [MOBY-dev] Dashboard Service Results missing Tab
In-Reply-To: <1210320229.31656.135.camel@lathan.ipb-sub.ipb-halle.de>
References: <1210320229.31656.135.camel@lathan.ipb-sub.ipb-halle.de>
Message-ID: <4d93f07c0805090254k5bf9ecdbqdf4db7327db596e3@mail.gmail.com>

Hi,

The differences in the number of result viewers in the SimpleClient panel in
the Dashboard are caused by the presence (or not presence) of the Java
classes representing the bIomoby data type. These classes are part of the
MoSeS system (more about it can be found on the jMoby pages). You can have
these classes on every machine by invoking:

ant moses-datatypes

(make sure that your build.properties file contains a property
"registry.cache.dir" pointing to a directory with your local cache - the
same directory that you can see in the Dashboard in the RegistryBrowser
panel).

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From sneumann at ipb-halle.de  Fri May  9 06:58:02 2008
From: sneumann at ipb-halle.de (sneumann)
Date: Fri, 09 May 2008 12:58:02 +0200
Subject: [MOBY-dev] Dashboard Service Results missing Tab
In-Reply-To: <4d93f07c0805090254k5bf9ecdbqdf4db7327db596e3@mail.gmail.com>
References: <1210320229.31656.135.camel@lathan.ipb-sub.ipb-halle.de>
	<4d93f07c0805090254k5bf9ecdbqdf4db7327db596e3@mail.gmail.com>
Message-ID: <1210330682.31656.151.camel@lathan.ipb-sub.ipb-halle.de>

On Fr, 2008-05-09 at 10:54 +0100, Martin Senger wrote:
> ant moses-datatypes
Yup, worked like a charm!

Thanks,
Steffen


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

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From sneumann at ipb-halle.de  Fri May  9 07:21:07 2008
From: sneumann at ipb-halle.de (sneumann)
Date: Fri, 09 May 2008 13:21:07 +0200
Subject: [MOBY-dev] Calling Moby from R / SSOAP
Message-ID: <1210332068.1475.8.camel@lathan.ipb-sub.ipb-halle.de>

Hi again, 

I am currently figuring how to call Moby Services manually 
using the R client package SSOAP:

Creating the service object works fine:

wsdl = "http://.../axis/services/myservice?wsdl"
service <- processWSDL(wsdl)

but the SSOAP has some kind of WSDL compiler 
which wants to create R classes as stubs to the SOAP:

client = genSOAPClientInterface(def=service, verbose = TRUE)

and this breaks, AFAICS because SSOAP is trying to map input 
and output types for the method calls. An example for the KEGG WSDL 
is given below. 

Do I see it correctly that the SSOAP stub writing has to be changed,
so that in the absence of <type> definitions I pass the arguments 
as encoded stuff in the body ? Has anybody experience with that,
or could give me (specific) links into documentation ?

Yours,
Steffen

from KEGG.wsdl:

	<definitions name="KEGG_v4.1" ... targetNamespace="SOAP/KEGG">
	  <types>
	    <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" targetNamespace="SOAP/KEGG">
	      <xsd:import namespace="http://schemas.xmlsoap.org/soap/encoding/"/>
	      <xsd:import namespace="http://schemas.xmlsoap.org/wsdl/"/>
	      <!-- common variable -->
	      <xsd:complexType name="ArrayOfstring">
	      ...

translates into:

	str(KEGG at types)	
	Formal class 'SchemaCollection' [package "SSOAP"] with 1 slots
	  ..@ .Data:List of 1
	  .. ..$ :Formal class 'SchemaTypes' [package "SSOAP"] with 1 slots
	  .. .. .. ..@ .Data:List of 9
	  .. .. .. .. ..$ :List of 2
	  .. .. .. .. .. ..$ name      : chr "ArrayOfstring"
	  .. .. .. .. .. ..$ definition:Formal class 'ArrayType' [package "SSOAP"] with 8 slots
	  .. .. .. .. .. .. .. ..@ elementType  : chr "xsd:string"
	  .. .. .. .. .. .. .. ..@ elType       :Formal class 'PrimitiveSOAPType' [package "SSOAP"] with 5 slots
	  .. .. .. .. .. .. .. .. .. ..@ fromConverter:function ()
	  .. .. .. .. .. .. .. .. .. ..@ toConverter  :function (x, ...)
	  .. .. .. .. .. .. .. .. .. ..@ name         : chr "string"
	  .. .. .. .. .. .. .. .. .. ..@ ns           : chr "xsd"
	  .. .. .. .. .. .. .. .. .. ..@ nsuri        : chr "http://www.w3.org/2001/XMLSchema"
	  .. .. .. .. .. .. .. ..@ dims         : int NA
	  .. .. .. .. .. .. .. ..@ fromConverter:function ()
	  .. .. .. .. .. .. .. ..@ toConverter  :function ()
	  .. .. .. .. .. .. .. ..@ name         : chr "ArrayOfstring"
	  .. .. .. .. .. .. .. ..@ ns           : chr(0)
	  .. .. .. .. .. .. .. ..@ nsuri        : chr(0)
	  .. .. .. .. .. ..- attr(*, "class")= chr "WSDLTypeDescription"
... 

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

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From gordonp at ucalgary.ca  Fri May  9 10:00:24 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 09 May 2008 08:00:24 -0600
Subject: [MOBY-dev] Calling Moby from R / SSOAP
In-Reply-To: <1210332068.1475.8.camel@lathan.ipb-sub.ipb-halle.de>
References: <1210332068.1475.8.camel@lathan.ipb-sub.ipb-halle.de>
Message-ID: <482458F8.4080808@ucalgary.ca>

Hi Steffen,

Yes, there is no XML Schema for Moby WSDL, because we allow inheritence 
at the tag level, which would make such a schema impossible.  So you 
would need to create an R library that creates the Moby XML message 
envelope, and send that string-encoded (as well as a parser for 
receiving).  While I'm quite familiar with R (I rewrote part of RMA), I 
haven't used any XML parsing facilities, so I can't provide any advice 
there...

Regards,

Paul

sneumann wrote:
> Hi again, 
>
> I am currently figuring how to call Moby Services manually 
> using the R client package SSOAP:
>
> Creating the service object works fine:
>
> wsdl = "http://.../axis/services/myservice?wsdl"
> service <- processWSDL(wsdl)
>
> but the SSOAP has some kind of WSDL compiler 
> which wants to create R classes as stubs to the SOAP:
>
> client = genSOAPClientInterface(def=service, verbose = TRUE)
>
> and this breaks, AFAICS because SSOAP is trying to map input 
> and output types for the method calls. An example for the KEGG WSDL 
> is given below. 
>
> Do I see it correctly that the SSOAP stub writing has to be changed,
> so that in the absence of <type> definitions I pass the arguments 
> as encoded stuff in the body ? Has anybody experience with that,
> or could give me (specific) links into documentation ?
>
> Yours,
> Steffen
>
> from KEGG.wsdl:
>
> 	<definitions name="KEGG_v4.1" ... targetNamespace="SOAP/KEGG">
> 	  <types>
> 	    <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" targetNamespace="SOAP/KEGG">
> 	      <xsd:import namespace="http://schemas.xmlsoap.org/soap/encoding/"/>
> 	      <xsd:import namespace="http://schemas.xmlsoap.org/wsdl/"/>
> 	      <!-- common variable -->
> 	      <xsd:complexType name="ArrayOfstring">
> 	      ...
>
> translates into:
>
> 	str(KEGG at types)	
> 	Formal class 'SchemaCollection' [package "SSOAP"] with 1 slots
> 	  ..@ .Data:List of 1
> 	  .. ..$ :Formal class 'SchemaTypes' [package "SSOAP"] with 1 slots
> 	  .. .. .. ..@ .Data:List of 9
> 	  .. .. .. .. ..$ :List of 2
> 	  .. .. .. .. .. ..$ name      : chr "ArrayOfstring"
> 	  .. .. .. .. .. ..$ definition:Formal class 'ArrayType' [package "SSOAP"] with 8 slots
> 	  .. .. .. .. .. .. .. ..@ elementType  : chr "xsd:string"
> 	  .. .. .. .. .. .. .. ..@ elType       :Formal class 'PrimitiveSOAPType' [package "SSOAP"] with 5 slots
> 	  .. .. .. .. .. .. .. .. .. ..@ fromConverter:function ()
> 	  .. .. .. .. .. .. .. .. .. ..@ toConverter  :function (x, ...)
> 	  .. .. .. .. .. .. .. .. .. ..@ name         : chr "string"
> 	  .. .. .. .. .. .. .. .. .. ..@ ns           : chr "xsd"
> 	  .. .. .. .. .. .. .. .. .. ..@ nsuri        : chr "http://www.w3.org/2001/XMLSchema"
> 	  .. .. .. .. .. .. .. ..@ dims         : int NA
> 	  .. .. .. .. .. .. .. ..@ fromConverter:function ()
> 	  .. .. .. .. .. .. .. ..@ toConverter  :function ()
> 	  .. .. .. .. .. .. .. ..@ name         : chr "ArrayOfstring"
> 	  .. .. .. .. .. .. .. ..@ ns           : chr(0)
> 	  .. .. .. .. .. .. .. ..@ nsuri        : chr(0)
> 	  .. .. .. .. .. ..- attr(*, "class")= chr "WSDLTypeDescription"
> ... 
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
> !DSPAM:60005,48243206109502520622991!
>   

From jason.e.stewart at gmail.com  Sat May 10 02:02:55 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Sat, 10 May 2008 11:32:55 +0530
Subject: [MOBY-dev] Calling Moby from R / SSOAP
In-Reply-To: <482458F8.4080808@ucalgary.ca>
References: <1210332068.1475.8.camel@lathan.ipb-sub.ipb-halle.de>
	<482458F8.4080808@ucalgary.ca>
Message-ID: <41c1ade50805092302x1b1ad07bnc2d5e52557fad012@mail.gmail.com>

Hi Paul,

2008/5/9 Paul Gordon <gordonp at ucalgary.ca>:

> Yes, there is no XML Schema for Moby WSDL, because we allow inheritence at
> the tag level, which would make such a schema impossible.  So you would need
> to create an R library that creates the Moby XML message envelope, and send
> that string-encoded (as well as a parser for receiving).

I've run into this same problem with XML::Compile with Perl... it
assumes the existence of WSDL and XML schemas to do its mapping
between Perl <=> XML...

I guess I'm needing to know how the object mapping should be done. Is
there a recommendation someplace for how to map MOBY objects to XML
and back?

Thanks, jas.

From gordonp at ucalgary.ca  Sat May 10 18:39:06 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Sat, 10 May 2008 16:39:06 -0600
Subject: [MOBY-dev] Calling Moby from R / SSOAP
In-Reply-To: <41c1ade50805092302x1b1ad07bnc2d5e52557fad012@mail.gmail.com>
References: <1210332068.1475.8.camel@lathan.ipb-sub.ipb-halle.de>	<482458F8.4080808@ucalgary.ca>
	<41c1ade50805092302x1b1ad07bnc2d5e52557fad012@mail.gmail.com>
Message-ID: <4826240A.9020306@ucalgary.ca>

Hi Jason,

There is no canonical object format (e.g. DOM) for Moby, but the XML 
format is.  You might want to check out how I did it in Java to give you 
an idea of the doxen or so envelope, job, container and primitive 
objects you need to create:

 The |org.biomoby.shared.data| package "In Anger": creating data 
instances 
<http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAnger.html>

http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAnger.html

Jason Stewart wrote:
> Hi Paul,
>
> 2008/5/9 Paul Gordon <gordonp at ucalgary.ca>:
>
>   
>> Yes, there is no XML Schema for Moby WSDL, because we allow inheritence at
>> the tag level, which would make such a schema impossible.  So you would need
>> to create an R library that creates the Moby XML message envelope, and send
>> that string-encoded (as well as a parser for receiving).
>>     
>
> I've run into this same problem with XML::Compile with Perl... it
> assumes the existence of WSDL and XML schemas to do its mapping
> between Perl <=> XML...
>
> I guess I'm needing to know how the object mapping should be done. Is
> there a recommendation someplace for how to map MOBY objects to XML
> and back?
>
> Thanks, jas.
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>   

From pieter.neerincx at gmail.com  Mon May 12 07:20:22 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Mon, 12 May 2008 13:20:22 +0200
Subject: [MOBY-dev] Perl BioMoby install
In-Reply-To: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>
Message-ID: <98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>

Hi,

I upgraded my Perl BioMoby install yesterday and noticed two minor  
problems:

1. Failed test t/MOBY:

t/MOBY........................
#   Failed test 'use MOBY;'
#   in t/MOBY.t at line 9.
#     Tried to use 'MOBY'.
#     Error:  Can't locate MOBY.pm in @INC (@INC contains:
.....<cut>.....
# BEGIN failed--compilation aborted at t/MOBY.t line 9.
t/MOBY........................NOK 1/1# Looks like you failed 1 test of  
1.
t/MOBY........................dubious
         Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 1
         Failed 1/1 tests, 0.00% okay


This test doesn't seem to be very useful. All it does is try a "use  
MOBY;", which fails as MOBY.pm doesn't exist and as far is I know  
shouldn't exist. Can I remove this test from the CVS tree or did I  
miss something and is the test correctly reporting a failure  
indicating a problem?

2. Perl module version number fishiness:

-----------------------------------------
*** Module::AutoInstall version 1.03
*** Checking for Perl dependencies...
[Core Features]
- Test::More               ...loaded. (0.62 >= 0.42)
- Test::Simple             ...loaded. (0.62 >= 0.44)
- ExtUtils::MakeMaker      ...loaded. (6.17 >= 6.11)
- Carp                     ...loaded. (1.01)
- File::Spec               ...loaded. (3.19 >= 0.80)
- SOAP::Lite               ...loaded. (0.69 >= 0.69)
- XML::LibXML              ...loaded. (1.66 >= 1.62)
- IO::Stringy              ...loaded. (2.110 >= 2.110)
- Unicode::String          ...loaded. (2.09 >= 2.09)
- File::ShareDir           ...loaded. (0.05 >= 0.05)
- Template                 ...loaded. (2.19)
- Class::Inspector         ...loaded. (1.18 >= 1.17)
- RDF::Core                ...loaded. (0.51 >= 0.51)
- XML::XPath               ...loaded. (1.13 >= 1.12)
- Text::Shellwords         ...loaded. (1.08 >= 1.00)
- HTML::Entities           ...loaded. (1.27 >= 0.01)
- LS                       ...loaded. (1.1.7 >= 1.1.7)
- DBI                      ...loaded. (1.410 >= 0.01)
- DBD::mysql               ...loaded. (2.900300 >= 0.01)
- IO::Prompt               ...loaded. (0.099004 >= 0.99.2)
- IPC::Shareable           ...loaded. (0.600 >= 0.6)
- WSRF::Lite               ...missing. (would need 0.008.2.2)
- XML::DOM                 ...loaded. (1.430)
- DateTime::Format::Epoch  ...loaded. (0.100)
- DateTime::Format::W3CDTF ...loaded. (0.040)
- HTTP::Daemon             ...loaded. (1.360)
- HTTP::Daemon::SSL        ...loaded. (1.020)
- MIME::Base64             ...loaded. (3.050)
- Digest::SHA1             ...loaded. (2.070)
- Crypt::OpenSSL::RSA      ...loaded. (0.250)
- XML::CanonicalizeXML     ...loaded. (0.030 >= 0.02)
- Sys::Hostname::Long      ...loaded. (1.400)
- Crypt::OpenSSL::X509     ...loaded. (0.500)
==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
==> The module(s) are mandatory! Really skip? [n] y
*** Module::AutoInstall configuration finished.
-----------------------------------------
So far so good. It only complains about WSRF::Lite. I have version  
0.8.2.2 installed, but this module doesn't report a version number and  
therefore the dependency check fails. But now it continues:

-----------------------------------------

Checking if your kit is complete...

Looks good

Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have unknown  
version.

>
-----------------------------------------

This is weird. First it finds LS and IO::Prompt and detects the  
version numbers correctly, but apparently it checks them slightly  
differently now and fails to notice the versions I have are just fine...

Cheers,

Pi





From pieter.neerincx at gmail.com  Mon May 12 08:21:12 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Mon, 12 May 2008 14:21:12 +0200
Subject: [MOBY-dev] MOBY::Client::Central::Dump()
In-Reply-To: <47ff6755.14da600a.27c7.3af5@mx.google.com>
References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net>
	<96656174-1315-4B6D-871B-2F8F6047AF7A@wur.nl>
	<47ff6755.14da600a.27c7.3af5@mx.google.com>
Message-ID: <9FADB5D4-300E-40B3-9A12-E22FBFCFE2A1@gmail.com>

Hi Eddie & Mark,

Eh well it works, but not the way it is supposed to. When I call  
MOBY::Client::Central::Dump() on the public Central in Calgary I get  
the following error:

	Not an ARRAY reference at /geninf/prog/lib/perl/MOBY/Client/ 
Central.pm line 1927

Indeed what I get back is a hash reference. This hash contains only a  
single item with the key 'item'. If I change:

1927    my (
                $mobycentral,   $mobyobject, $mobyservice,
                $mobynamespace, $mobyrelationship
           )
           = @{$SQLs};

Into:

1927      my (
                 $mobycentral,   $mobyobject, $mobyservice,
                 $mobynamespace, $mobyrelationship
           )
           = @{${$SQLs}{item}};

...it does work. I checked the MOBY::Central.pm module from CVS and it  
is supposed to return an array ref as before. I upgraded BioMoby + all  
dependancies and compared the behaviour of the official Central with  
my local test Central and the latter still produces an array ref as  
expected... Looks to me like the official Central got a custom patch  
of some sort. Could one of you please have a look at this?

Thanks,

Pi



On 11?Apr?2008, at 3:27 PM, Edward Kawas wrote:

> Hi Pieter,
>
> Dump on mobycentral should work now (once mobycentral is back up and
> running). This was fixed a while back.
>
> Eddie


From edward.kawas at gmail.com  Mon May 12 09:14:23 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 12 May 2008 06:14:23 -0700
Subject: [MOBY-dev] Perl BioMoby install
In-Reply-To: <98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>
	<98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>
Message-ID: <482842bc.02578c0a.1808.ffff8dfe@mx.google.com>

Hi Pieter,

I have fixed the first problem that you have encountered, but I haven't
gotten around to a new cpan release. I have been waiting on a few things
first.

The second problem with regards to versioning may also be fixed. I am not
sure if the versioning for wsrf has been fixed for our makefile, but the
io::prompt and LS should be.

Thanks,

Eddie 

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx
Sent: May-12-08 4:20 AM
To: Core developer announcements
Subject: [MOBY-dev] Perl BioMoby install

Hi,

I upgraded my Perl BioMoby install yesterday and noticed two minor  
problems:

1. Failed test t/MOBY:

t/MOBY........................
#   Failed test 'use MOBY;'
#   in t/MOBY.t at line 9.
#     Tried to use 'MOBY'.
#     Error:  Can't locate MOBY.pm in @INC (@INC contains:
.....<cut>.....
# BEGIN failed--compilation aborted at t/MOBY.t line 9.
t/MOBY........................NOK 1/1# Looks like you failed 1 test of  
1.
t/MOBY........................dubious
         Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 1
         Failed 1/1 tests, 0.00% okay


This test doesn't seem to be very useful. All it does is try a "use  
MOBY;", which fails as MOBY.pm doesn't exist and as far is I know  
shouldn't exist. Can I remove this test from the CVS tree or did I  
miss something and is the test correctly reporting a failure  
indicating a problem?

2. Perl module version number fishiness:

-----------------------------------------
*** Module::AutoInstall version 1.03
*** Checking for Perl dependencies...
[Core Features]
- Test::More               ...loaded. (0.62 >= 0.42)
- Test::Simple             ...loaded. (0.62 >= 0.44)
- ExtUtils::MakeMaker      ...loaded. (6.17 >= 6.11)
- Carp                     ...loaded. (1.01)
- File::Spec               ...loaded. (3.19 >= 0.80)
- SOAP::Lite               ...loaded. (0.69 >= 0.69)
- XML::LibXML              ...loaded. (1.66 >= 1.62)
- IO::Stringy              ...loaded. (2.110 >= 2.110)
- Unicode::String          ...loaded. (2.09 >= 2.09)
- File::ShareDir           ...loaded. (0.05 >= 0.05)
- Template                 ...loaded. (2.19)
- Class::Inspector         ...loaded. (1.18 >= 1.17)
- RDF::Core                ...loaded. (0.51 >= 0.51)
- XML::XPath               ...loaded. (1.13 >= 1.12)
- Text::Shellwords         ...loaded. (1.08 >= 1.00)
- HTML::Entities           ...loaded. (1.27 >= 0.01)
- LS                       ...loaded. (1.1.7 >= 1.1.7)
- DBI                      ...loaded. (1.410 >= 0.01)
- DBD::mysql               ...loaded. (2.900300 >= 0.01)
- IO::Prompt               ...loaded. (0.099004 >= 0.99.2)
- IPC::Shareable           ...loaded. (0.600 >= 0.6)
- WSRF::Lite               ...missing. (would need 0.008.2.2)
- XML::DOM                 ...loaded. (1.430)
- DateTime::Format::Epoch  ...loaded. (0.100)
- DateTime::Format::W3CDTF ...loaded. (0.040)
- HTTP::Daemon             ...loaded. (1.360)
- HTTP::Daemon::SSL        ...loaded. (1.020)
- MIME::Base64             ...loaded. (3.050)
- Digest::SHA1             ...loaded. (2.070)
- Crypt::OpenSSL::RSA      ...loaded. (0.250)
- XML::CanonicalizeXML     ...loaded. (0.030 >= 0.02)
- Sys::Hostname::Long      ...loaded. (1.400)
- Crypt::OpenSSL::X509     ...loaded. (0.500)
==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
==> The module(s) are mandatory! Really skip? [n] y
*** Module::AutoInstall configuration finished.
-----------------------------------------
So far so good. It only complains about WSRF::Lite. I have version  
0.8.2.2 installed, but this module doesn't report a version number and  
therefore the dependency check fails. But now it continues:

-----------------------------------------

Checking if your kit is complete...

Looks good

Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have unknown  
version.

>
-----------------------------------------

This is weird. First it finds LS and IO::Prompt and detects the  
version numbers correctly, but apparently it checks them slightly  
differently now and fails to notice the versions I have are just fine...

Cheers,

Pi




_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From pieter.neerincx at gmail.com  Mon May 12 09:31:47 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Mon, 12 May 2008 15:31:47 +0200
Subject: [MOBY-dev] Perl BioMoby install
In-Reply-To: <482842bc.02578c0a.1808.ffff8dfe@mx.google.com>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>
	<98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>
	<482842bc.02578c0a.1808.ffff8dfe@mx.google.com>
Message-ID: <244159DE-A626-4B08-AF7A-A31E58334FAB@gmail.com>

Hi Eddie,

On 12?May?2008, at 3:14 PM, Edward Kawas wrote:

> Hi Pieter,
>
> I have fixed the first problem that you have encountered, but I  
> haven't
> gotten around to a new cpan release. I have been waiting on a few  
> things
> first.

Thanks!

> The second problem with regards to versioning may also be fixed. I  
> am not
> sure if the versioning for wsrf has been fixed for our makefile, but  
> the
> io::prompt and LS should be.

Thanks again! I e-mailed the maintainer of the WSRF::Lite module and  
requested the addition of a $VERSION variable... So that might get  
fixed in the near future too :) We'll see...

Cheers,

Pi

> Thanks,
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter  
> Neerincx
> Sent: May-12-08 4:20 AM
> To: Core developer announcements
> Subject: [MOBY-dev] Perl BioMoby install
>
> Hi,
>
> I upgraded my Perl BioMoby install yesterday and noticed two minor
> problems:
>
> 1. Failed test t/MOBY:
>
> t/MOBY........................
> #   Failed test 'use MOBY;'
> #   in t/MOBY.t at line 9.
> #     Tried to use 'MOBY'.
> #     Error:  Can't locate MOBY.pm in @INC (@INC contains:
> .....<cut>.....
> # BEGIN failed--compilation aborted at t/MOBY.t line 9.
> t/MOBY........................NOK 1/1# Looks like you failed 1 test of
> 1.
> t/MOBY........................dubious
>         Test returned status 1 (wstat 256, 0x100)
> DIED. FAILED test 1
>         Failed 1/1 tests, 0.00% okay
>
>
> This test doesn't seem to be very useful. All it does is try a "use
> MOBY;", which fails as MOBY.pm doesn't exist and as far is I know
> shouldn't exist. Can I remove this test from the CVS tree or did I
> miss something and is the test correctly reporting a failure
> indicating a problem?
>
> 2. Perl module version number fishiness:
>
> -----------------------------------------
> *** Module::AutoInstall version 1.03
> *** Checking for Perl dependencies...
> [Core Features]
> - Test::More               ...loaded. (0.62 >= 0.42)
> - Test::Simple             ...loaded. (0.62 >= 0.44)
> - ExtUtils::MakeMaker      ...loaded. (6.17 >= 6.11)
> - Carp                     ...loaded. (1.01)
> - File::Spec               ...loaded. (3.19 >= 0.80)
> - SOAP::Lite               ...loaded. (0.69 >= 0.69)
> - XML::LibXML              ...loaded. (1.66 >= 1.62)
> - IO::Stringy              ...loaded. (2.110 >= 2.110)
> - Unicode::String          ...loaded. (2.09 >= 2.09)
> - File::ShareDir           ...loaded. (0.05 >= 0.05)
> - Template                 ...loaded. (2.19)
> - Class::Inspector         ...loaded. (1.18 >= 1.17)
> - RDF::Core                ...loaded. (0.51 >= 0.51)
> - XML::XPath               ...loaded. (1.13 >= 1.12)
> - Text::Shellwords         ...loaded. (1.08 >= 1.00)
> - HTML::Entities           ...loaded. (1.27 >= 0.01)
> - LS                       ...loaded. (1.1.7 >= 1.1.7)
> - DBI                      ...loaded. (1.410 >= 0.01)
> - DBD::mysql               ...loaded. (2.900300 >= 0.01)
> - IO::Prompt               ...loaded. (0.099004 >= 0.99.2)
> - IPC::Shareable           ...loaded. (0.600 >= 0.6)
> - WSRF::Lite               ...missing. (would need 0.008.2.2)
> - XML::DOM                 ...loaded. (1.430)
> - DateTime::Format::Epoch  ...loaded. (0.100)
> - DateTime::Format::W3CDTF ...loaded. (0.040)
> - HTTP::Daemon             ...loaded. (1.360)
> - HTTP::Daemon::SSL        ...loaded. (1.020)
> - MIME::Base64             ...loaded. (3.050)
> - Digest::SHA1             ...loaded. (2.070)
> - Crypt::OpenSSL::RSA      ...loaded. (0.250)
> - XML::CanonicalizeXML     ...loaded. (0.030 >= 0.02)
> - Sys::Hostname::Long      ...loaded. (1.400)
> - Crypt::OpenSSL::X509     ...loaded. (0.500)
> ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
> ==> The module(s) are mandatory! Really skip? [n] y
> *** Module::AutoInstall configuration finished.
> -----------------------------------------
> So far so good. It only complains about WSRF::Lite. I have version
> 0.8.2.2 installed, but this module doesn't report a version number and
> therefore the dependency check fails. But now it continues:
>
> -----------------------------------------
>
> Checking if your kit is complete...
>
> Looks good
>
> Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
> Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
> Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have unknown
> version.
>
>>
> -----------------------------------------
>
> This is weird. First it finds LS and IO::Prompt and detects the
> version numbers correctly, but apparently it checks them slightly
> differently now and fails to notice the versions I have are just  
> fine...
>
> Cheers,
>
> Pi
>
>
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From edward.kawas at gmail.com  Mon May 12 11:11:09 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 12 May 2008 08:11:09 -0700
Subject: [MOBY-dev] MOBY::Client::Central::Dump()
In-Reply-To: <9FADB5D4-300E-40B3-9A12-E22FBFCFE2A1@gmail.com>
References: <47FF108F.4020006@toulouse.inra.fr>
	<20080411074010.173560@gmx.net>	<96656174-1315-4B6D-871B-2F8F6047AF7A@wur.nl>	<47ff6755.14da600a.27c7.3af5@mx.google.com>
	<9FADB5D4-300E-40B3-9A12-E22FBFCFE2A1@gmail.com>
Message-ID: <48285e1a.1f538c0a.7e36.3e14@mx.google.com>

Thanks Pieter,

I made changes (based on what you found out) to MOBY::Client::Central that
should now take care of the DUMP problem. The changes are in the CVS and
will soon be in cpan.

Thanks again!

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx
Sent: May-12-08 5:21 AM
To: Core developer announcements
Subject: [MOBY-dev] MOBY::Client::Central::Dump()

Hi Eddie & Mark,

Eh well it works, but not the way it is supposed to. When I call  
MOBY::Client::Central::Dump() on the public Central in Calgary I get  
the following error:

	Not an ARRAY reference at /geninf/prog/lib/perl/MOBY/Client/ 
Central.pm line 1927

Indeed what I get back is a hash reference. This hash contains only a  
single item with the key 'item'. If I change:

1927    my (
                $mobycentral,   $mobyobject, $mobyservice,
                $mobynamespace, $mobyrelationship
           )
           = @{$SQLs};

Into:

1927      my (
                 $mobycentral,   $mobyobject, $mobyservice,
                 $mobynamespace, $mobyrelationship
           )
           = @{${$SQLs}{item}};

...it does work. I checked the MOBY::Central.pm module from CVS and it  
is supposed to return an array ref as before. I upgraded BioMoby + all  
dependancies and compared the behaviour of the official Central with  
my local test Central and the latter still produces an array ref as  
expected... Looks to me like the official Central got a custom patch  
of some sort. Could one of you please have a look at this?

Thanks,

Pi



On 11.Apr.2008, at 3:27 PM, Edward Kawas wrote:

> Hi Pieter,
>
> Dump on mobycentral should work now (once mobycentral is back up and
> running). This was fixed a while back.
>
> Eddie

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From jmfernandez at cnio.es  Tue May 13 05:51:09 2008
From: jmfernandez at cnio.es (=?windows-1252?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=)
Date: Tue, 13 May 2008 11:51:09 +0200
Subject: [MOBY-dev] Perl BioMoby install
In-Reply-To: <244159DE-A626-4B08-AF7A-A31E58334FAB@gmail.com>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>	<98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>	<482842bc.02578c0a.1808.ffff8dfe@mx.google.com>
	<244159DE-A626-4B08-AF7A-A31E58334FAB@gmail.com>
Message-ID: <4829648D.1000306@cnio.es>

Hi everybody,
	although WSRF::Lite already has a $VERSION variable, it is not defined as a 
string, which is a problem for installation packages. It is set as:

$VERSION=0.8.2.2;

instead of

$VERSION='0.8.2.2';

	Jos? Manuel Rodr?guez and I made some tries fixing that for Makefile.PL (see 
jmrc commits).

	The main problem is that more and more Perl packages are migrating from 
string representation to 'literal' one (IO::Prompt for instance, I guess).

	Best Regards,
		Jos? Mar?a

Pieter Neerincx wrote:
> Hi Eddie,
> 
> On 12?May?2008, at 3:14 PM, Edward Kawas wrote:
> 
>> Hi Pieter,
>>
>> I have fixed the first problem that you have encountered, but I haven't
>> gotten around to a new cpan release. I have been waiting on a few things
>> first.
> 
> Thanks!
> 
>> The second problem with regards to versioning may also be fixed. I am not
>> sure if the versioning for wsrf has been fixed for our makefile, but the
>> io::prompt and LS should be.
> 
> Thanks again! I e-mailed the maintainer of the WSRF::Lite module and 
> requested the addition of a $VERSION variable... So that might get fixed 
> in the near future too :) We'll see...
> 
> Cheers,
> 
> Pi
> 
>> Thanks,
>>
>> Eddie
>>
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org
>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx
>> Sent: May-12-08 4:20 AM
>> To: Core developer announcements
>> Subject: [MOBY-dev] Perl BioMoby install
>>
>> Hi,
>>
>> I upgraded my Perl BioMoby install yesterday and noticed two minor
>> problems:
>>
>> 1. Failed test t/MOBY:
>>
>> t/MOBY........................
>> #   Failed test 'use MOBY;'
>> #   in t/MOBY.t at line 9.
>> #     Tried to use 'MOBY'.
>> #     Error:  Can't locate MOBY.pm in @INC (@INC contains:
>> .....<cut>.....
>> # BEGIN failed--compilation aborted at t/MOBY.t line 9.
>> t/MOBY........................NOK 1/1# Looks like you failed 1 test of
>> 1.
>> t/MOBY........................dubious
>>         Test returned status 1 (wstat 256, 0x100)
>> DIED. FAILED test 1
>>         Failed 1/1 tests, 0.00% okay
>>
>>
>> This test doesn't seem to be very useful. All it does is try a "use
>> MOBY;", which fails as MOBY.pm doesn't exist and as far is I know
>> shouldn't exist. Can I remove this test from the CVS tree or did I
>> miss something and is the test correctly reporting a failure
>> indicating a problem?
>>
>> 2. Perl module version number fishiness:
>>
>> -----------------------------------------
>> *** Module::AutoInstall version 1.03
>> *** Checking for Perl dependencies...
>> [Core Features]
>> - Test::More               ...loaded. (0.62 >= 0.42)
>> - Test::Simple             ...loaded. (0.62 >= 0.44)
>> - ExtUtils::MakeMaker      ...loaded. (6.17 >= 6.11)
>> - Carp                     ...loaded. (1.01)
>> - File::Spec               ...loaded. (3.19 >= 0.80)
>> - SOAP::Lite               ...loaded. (0.69 >= 0.69)
>> - XML::LibXML              ...loaded. (1.66 >= 1.62)
>> - IO::Stringy              ...loaded. (2.110 >= 2.110)
>> - Unicode::String          ...loaded. (2.09 >= 2.09)
>> - File::ShareDir           ...loaded. (0.05 >= 0.05)
>> - Template                 ...loaded. (2.19)
>> - Class::Inspector         ...loaded. (1.18 >= 1.17)
>> - RDF::Core                ...loaded. (0.51 >= 0.51)
>> - XML::XPath               ...loaded. (1.13 >= 1.12)
>> - Text::Shellwords         ...loaded. (1.08 >= 1.00)
>> - HTML::Entities           ...loaded. (1.27 >= 0.01)
>> - LS                       ...loaded. (1.1.7 >= 1.1.7)
>> - DBI                      ...loaded. (1.410 >= 0.01)
>> - DBD::mysql               ...loaded. (2.900300 >= 0.01)
>> - IO::Prompt               ...loaded. (0.099004 >= 0.99.2)
>> - IPC::Shareable           ...loaded. (0.600 >= 0.6)
>> - WSRF::Lite               ...missing. (would need 0.008.2.2)
>> - XML::DOM                 ...loaded. (1.430)
>> - DateTime::Format::Epoch  ...loaded. (0.100)
>> - DateTime::Format::W3CDTF ...loaded. (0.040)
>> - HTTP::Daemon             ...loaded. (1.360)
>> - HTTP::Daemon::SSL        ...loaded. (1.020)
>> - MIME::Base64             ...loaded. (3.050)
>> - Digest::SHA1             ...loaded. (2.070)
>> - Crypt::OpenSSL::RSA      ...loaded. (0.250)
>> - XML::CanonicalizeXML     ...loaded. (0.030 >= 0.02)
>> - Sys::Hostname::Long      ...loaded. (1.400)
>> - Crypt::OpenSSL::X509     ...loaded. (0.500)
>> ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
>> ==> The module(s) are mandatory! Really skip? [n] y
>> *** Module::AutoInstall configuration finished.
>> -----------------------------------------
>> So far so good. It only complains about WSRF::Lite. I have version
>> 0.8.2.2 installed, but this module doesn't report a version number and
>> therefore the dependency check fails. But now it continues:
>>
>> -----------------------------------------
>>
>> Checking if your kit is complete...
>>
>> Looks good
>>
>> Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
>> Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
>> Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have unknown
>> version.
>>
>>>
>> -----------------------------------------
>>
>> This is weird. First it finds LS and IO::Prompt and detects the
>> version numbers correctly, but apparently it checks them slightly
>> differently now and fails to notice the versions I have are just fine...
>>
>> Cheers,
>>
>> Pi
>>
>>
>>
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 

-- 
"There is no reason why anybody would want a computer in their home" -
	Ken Olson, founder of DEC 1977
"640K ought to be enough for anybody" - Bill Gates, 1981
"Nobody will ever outgrow a 20Mb hard drive." - ???

"Premature optimization is the root of all evil." - Donald Knuth

Jos? Mar?a Fern?ndez Gonz?lez
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
e-mail: jmfernandez at cnio.es		Fax: (+34) 91 224 69 76
Unidad del Instituto Nacional de Bioinform?tica
Biolog?a Estructural y Biocomputaci?n	Structural Biology and Biocomputing
Centro Nacional de Investigaciones Oncol?gicas
C.P.: 28029				Zip Code: 28029
C/. Melchor Fern?ndez Almagro, 3	Madrid (Spain)

**NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.


From pieter.neerincx at gmail.com  Tue May 13 06:28:32 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Tue, 13 May 2008 12:28:32 +0200
Subject: [MOBY-dev] Perl BioMoby install
In-Reply-To: <4829648D.1000306@cnio.es>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>	<98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>	<482842bc.02578c0a.1808.ffff8dfe@mx.google.com>
	<244159DE-A626-4B08-AF7A-A31E58334FAB@gmail.com>
	<4829648D.1000306@cnio.es>
Message-ID: <EAD19377-C879-4F04-9A82-2EC21DD7EB27@gmail.com>

Hi Jos? Mar?a,

On 13?May?2008, at 11:51 AM, Jos? Mar?a Fern?ndez Gonz?lez wrote:

> Hi everybody,
> 	although WSRF::Lite already has a $VERSION variable, it is not  
> defined as a string, which is a problem for installation packages.  
> It is set as:
>
> $VERSION=0.8.2.2;

Ok my bad. I thought I had installed 0.8.2.2, which I did but not in  
the proper path. Mix that with an outdated WSRF::Lite 0.6 in the  
correct path that reports it's version number in the wrong context and  
this is what you get :(. Problem solved :)

Pi

> instead of
>
> $VERSION='0.8.2.2';
>
> 	Jos? Manuel Rodr?guez and I made some tries fixing that for  
> Makefile.PL (see jmrc commits).
>
> 	The main problem is that more and more Perl packages are migrating  
> from string representation to 'literal' one (IO::Prompt for  
> instance, I guess).
>
> 	Best Regards,
> 		Jos? Mar?a
>
> Pieter Neerincx wrote:
>> Hi Eddie,
>> On 12?May?2008, at 3:14 PM, Edward Kawas wrote:
>>> Hi Pieter,
>>>
>>> I have fixed the first problem that you have encountered, but I  
>>> haven't
>>> gotten around to a new cpan release. I have been waiting on a few  
>>> things
>>> first.
>> Thanks!
>>> The second problem with regards to versioning may also be fixed. I  
>>> am not
>>> sure if the versioning for wsrf has been fixed for our makefile,  
>>> but the
>>> io::prompt and LS should be.
>> Thanks again! I e-mailed the maintainer of the WSRF::Lite module  
>> and requested the addition of a $VERSION variable... So that might  
>> get fixed in the near future too :) We'll see...
>> Cheers,
>> Pi
>>> Thanks,
>>>
>>> Eddie
>>>
>>> -----Original Message-----
>>> From: moby-dev-bounces at lists.open-bio.org
>>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter  
>>> Neerincx
>>> Sent: May-12-08 4:20 AM
>>> To: Core developer announcements
>>> Subject: [MOBY-dev] Perl BioMoby install
>>>
>>> Hi,
>>>
>>> I upgraded my Perl BioMoby install yesterday and noticed two minor
>>> problems:
>>>
>>> 1. Failed test t/MOBY:
>>>
>>> t/MOBY........................
>>> #   Failed test 'use MOBY;'
>>> #   in t/MOBY.t at line 9.
>>> #     Tried to use 'MOBY'.
>>> #     Error:  Can't locate MOBY.pm in @INC (@INC contains:
>>> .....<cut>.....
>>> # BEGIN failed--compilation aborted at t/MOBY.t line 9.
>>> t/MOBY........................NOK 1/1# Looks like you failed 1  
>>> test of
>>> 1.
>>> t/MOBY........................dubious
>>>        Test returned status 1 (wstat 256, 0x100)
>>> DIED. FAILED test 1
>>>        Failed 1/1 tests, 0.00% okay
>>>
>>>
>>> This test doesn't seem to be very useful. All it does is try a "use
>>> MOBY;", which fails as MOBY.pm doesn't exist and as far is I know
>>> shouldn't exist. Can I remove this test from the CVS tree or did I
>>> miss something and is the test correctly reporting a failure
>>> indicating a problem?
>>>
>>> 2. Perl module version number fishiness:
>>>
>>> -----------------------------------------
>>> *** Module::AutoInstall version 1.03
>>> *** Checking for Perl dependencies...
>>> [Core Features]
>>> - Test::More               ...loaded. (0.62 >= 0.42)
>>> - Test::Simple             ...loaded. (0.62 >= 0.44)
>>> - ExtUtils::MakeMaker      ...loaded. (6.17 >= 6.11)
>>> - Carp                     ...loaded. (1.01)
>>> - File::Spec               ...loaded. (3.19 >= 0.80)
>>> - SOAP::Lite               ...loaded. (0.69 >= 0.69)
>>> - XML::LibXML              ...loaded. (1.66 >= 1.62)
>>> - IO::Stringy              ...loaded. (2.110 >= 2.110)
>>> - Unicode::String          ...loaded. (2.09 >= 2.09)
>>> - File::ShareDir           ...loaded. (0.05 >= 0.05)
>>> - Template                 ...loaded. (2.19)
>>> - Class::Inspector         ...loaded. (1.18 >= 1.17)
>>> - RDF::Core                ...loaded. (0.51 >= 0.51)
>>> - XML::XPath               ...loaded. (1.13 >= 1.12)
>>> - Text::Shellwords         ...loaded. (1.08 >= 1.00)
>>> - HTML::Entities           ...loaded. (1.27 >= 0.01)
>>> - LS                       ...loaded. (1.1.7 >= 1.1.7)
>>> - DBI                      ...loaded. (1.410 >= 0.01)
>>> - DBD::mysql               ...loaded. (2.900300 >= 0.01)
>>> - IO::Prompt               ...loaded. (0.099004 >= 0.99.2)
>>> - IPC::Shareable           ...loaded. (0.600 >= 0.6)
>>> - WSRF::Lite               ...missing. (would need 0.008.2.2)
>>> - XML::DOM                 ...loaded. (1.430)
>>> - DateTime::Format::Epoch  ...loaded. (0.100)
>>> - DateTime::Format::W3CDTF ...loaded. (0.040)
>>> - HTTP::Daemon             ...loaded. (1.360)
>>> - HTTP::Daemon::SSL        ...loaded. (1.020)
>>> - MIME::Base64             ...loaded. (3.050)
>>> - Digest::SHA1             ...loaded. (2.070)
>>> - Crypt::OpenSSL::RSA      ...loaded. (0.250)
>>> - XML::CanonicalizeXML     ...loaded. (0.030 >= 0.02)
>>> - Sys::Hostname::Long      ...loaded. (1.400)
>>> - Crypt::OpenSSL::X509     ...loaded. (0.500)
>>> ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
>>> ==> The module(s) are mandatory! Really skip? [n] y
>>> *** Module::AutoInstall configuration finished.
>>> -----------------------------------------
>>> So far so good. It only complains about WSRF::Lite. I have version
>>> 0.8.2.2 installed, but this module doesn't report a version number  
>>> and
>>> therefore the dependency check fails. But now it continues:
>>>
>>> -----------------------------------------
>>>
>>> Checking if your kit is complete...
>>>
>>> Looks good
>>>
>>> Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
>>> Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
>>> Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have  
>>> unknown
>>> version.
>>>
>>>>
>>> -----------------------------------------
>>>
>>> This is weird. First it finds LS and IO::Prompt and detects the
>>> version numbers correctly, but apparently it checks them slightly
>>> differently now and fails to notice the versions I have are just  
>>> fine...
>>>
>>> Cheers,
>>>
>>> Pi
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> -- 
> "There is no reason why anybody would want a computer in their home" -
> 	Ken Olson, founder of DEC 1977
> "640K ought to be enough for anybody" - Bill Gates, 1981
> "Nobody will ever outgrow a 20Mb hard drive." - ???
>
> "Premature optimization is the root of all evil." - Donald Knuth
>
> Jos? Mar?a Fern?ndez Gonz?lez
> Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
> e-mail: jmfernandez at cnio.es		Fax: (+34) 91 224 69 76
> Unidad del Instituto Nacional de Bioinform?tica
> Biolog?a Estructural y Biocomputaci?n	Structural Biology and  
> Biocomputing
> Centro Nacional de Investigaciones Oncol?gicas
> C.P.: 28029				Zip Code: 28029
> C/. Melchor Fern?ndez Almagro, 3	Madrid (Spain)
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso  
> los ficheros adjuntos, pueden contener informaci?n protegida para el  
> uso exclusivo de su destinatario. Se proh?be la distribuci?n,  
> reproducci?n o cualquier otro tipo de transmisi?n por parte de otra  
> persona que no sea el destinatario. Si usted recibe por error este  
> correo, se ruega comunicarlo al remitente y borrar el mensaje  
> recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any  
> attachments may contain confidential and privileged information for  
> the sole use of the designated recipient named above. Distribution,  
> reproduction or any other use of this transmission by any party  
> other than the intended recipient is prohibited. If you are not the  
> intended recipient please contact the sender and delete all copies.
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From markw at illuminae.com  Thu May 15 13:53:15 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 15 May 2008 10:53:15 -0700
Subject: [MOBY-dev] the use-case for xml:lang
Message-ID: <op.ua7im1f5nbznux@mark.ubic.ca>

Hi all,

at the last Moby meeting we decided that there was a need for MOBY Central  
to observe the xml:lang attribute.  Can someone please send me an explicit  
use-case so that I am sure I understand why/where this attribute is going  
to appear and what changes to MOBY Central and the database might be  
necessary to accommodate this change?

Thanks!

Mark


-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre

From gordonp at ucalgary.ca  Thu May 15 14:32:51 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 15 May 2008 12:32:51 -0600
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <op.ua7im1f5nbznux@mark.ubic.ca>
References: <op.ua7im1f5nbznux@mark.ubic.ca>
Message-ID: <482C81D3.1030106@ucalgary.ca>

Some services are registered in other languages for their free-text 
descriptions for example.  In some places (I can't remember where 
exactly at the moment), the registry assumes that the description is 
English and uses the xml:lang tag to say so when returning XML.  It's 
probably a good idea to have the xml:lang in the returned info, but it 
should maintain the xml:lang tag used to register the service. 

Mark Wilkinson wrote:
> Hi all,
>
> at the last Moby meeting we decided that there was a need for MOBY 
> Central to observe the xml:lang attribute.  Can someone please send me 
> an explicit use-case so that I am sure I understand why/where this 
> attribute is going to appear and what changes to MOBY Central and the 
> database might be necessary to accommodate this change?
>
> Thanks!
>
> Mark
>
>

From gordonp at ucalgary.ca  Thu May 15 14:32:51 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 15 May 2008 12:32:51 -0600
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <op.ua7im1f5nbznux@mark.ubic.ca>
References: <op.ua7im1f5nbznux@mark.ubic.ca>
Message-ID: <482C81D3.1030106@ucalgary.ca>

Some services are registered in other languages for their free-text 
descriptions for example.  In some places (I can't remember where 
exactly at the moment), the registry assumes that the description is 
English and uses the xml:lang tag to say so when returning XML.  It's 
probably a good idea to have the xml:lang in the returned info, but it 
should maintain the xml:lang tag used to register the service. 

Mark Wilkinson wrote:
> Hi all,
>
> at the last Moby meeting we decided that there was a need for MOBY 
> Central to observe the xml:lang attribute.  Can someone please send me 
> an explicit use-case so that I am sure I understand why/where this 
> attribute is going to appear and what changes to MOBY Central and the 
> database might be necessary to accommodate this change?
>
> Thanks!
>
> Mark
>
>

From markw at illuminae.com  Thu May 15 14:54:26 2008
From: markw at illuminae.com (markw at illuminae.com)
Date: Thu, 15 May 2008 18:54:26 +0000
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <482C81D3.1030106@ucalgary.ca>
References: <op.ua7im1f5nbznux@mark.ubic.ca><482C81D3.1030106@ucalgary.ca>
Message-ID: <51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>

So... Should we allow more than one "description" element per service/obect/namespace to allow multiple languages per registration?  This would be a change to the API, but it would make sense to do so if this is the route we're going...

M


On the Road!

-----Original Message-----
From: Paul Gordon <gordonp at ucalgary.ca>

Date: Thu, 15 May 2008 12:32:51 
To:Core developer announcements <moby-dev at lists.open-bio.org>
Cc:moby-dev at biomoby.org
Subject: Re: [MOBY-dev] the use-case for xml:lang


Some services are registered in other languages for their free-text
descriptions for example.  In some places (I can't remember where
exactly at the moment), the registry assumes that the description is
English and uses the xml:lang tag to say so when returning XML.  It's
probably a good idea to have the xml:lang in the returned info, but it
should maintain the xml:lang tag used to register the service.

Mark Wilkinson wrote:
> Hi all,
>
> at the last Moby meeting we decided that there was a need for MOBY
> Central to observe the xml:lang attribute.  Can someone please send me
> an explicit use-case so that I am sure I understand why/where this
> attribute is going to appear and what changes to MOBY Central and the
> database might be necessary to accommodate this change?
>
> Thanks!
>
> Mark
>
>
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From markw at illuminae.com  Thu May 15 14:54:26 2008
From: markw at illuminae.com (markw at illuminae.com)
Date: Thu, 15 May 2008 18:54:26 +0000
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <482C81D3.1030106@ucalgary.ca>
References: <op.ua7im1f5nbznux@mark.ubic.ca><482C81D3.1030106@ucalgary.ca>
Message-ID: <51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>

So... Should we allow more than one "description" element per service/obect/namespace to allow multiple languages per registration?  This would be a change to the API, but it would make sense to do so if this is the route we're going...

M


On the Road!

-----Original Message-----
From: Paul Gordon <gordonp at ucalgary.ca>

Date: Thu, 15 May 2008 12:32:51 
To:Core developer announcements <moby-dev at lists.open-bio.org>
Cc:moby-dev at biomoby.org
Subject: Re: [MOBY-dev] the use-case for xml:lang


Some services are registered in other languages for their free-text
descriptions for example.  In some places (I can't remember where
exactly at the moment), the registry assumes that the description is
English and uses the xml:lang tag to say so when returning XML.  It's
probably a good idea to have the xml:lang in the returned info, but it
should maintain the xml:lang tag used to register the service.

Mark Wilkinson wrote:
> Hi all,
>
> at the last Moby meeting we decided that there was a need for MOBY
> Central to observe the xml:lang attribute.  Can someone please send me
> an explicit use-case so that I am sure I understand why/where this
> attribute is going to appear and what changes to MOBY Central and the
> database might be necessary to accommodate this change?
>
> Thanks!
>
> Mark
>
>
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From martin.senger at gmail.com  Thu May 15 15:13:35 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 15 May 2008 20:13:35 +0100
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>
References: <op.ua7im1f5nbznux@mark.ubic.ca> <482C81D3.1030106@ucalgary.ca>
	<51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>
Message-ID: <4d93f07c0805151213m7ef4e967i6f3d4c0b249ac7b6@mail.gmail.com>

> So... Should we allow more than one "description" element per
> service/obect/namespace to allow multiple languages per registration?


I do not know... Do we really need it? I think the main point is allow a
*different* language, but not  necessarily more than one. The registry needs
to remember what xml:lang was given together with description and return the
same back when the description is going out.

And perhaps to do it in all descriptions, not only the service
description...

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From martin.senger at gmail.com  Thu May 15 15:13:35 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 15 May 2008 20:13:35 +0100
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>
References: <op.ua7im1f5nbznux@mark.ubic.ca> <482C81D3.1030106@ucalgary.ca>
	<51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>
Message-ID: <4d93f07c0805151213m7ef4e967i6f3d4c0b249ac7b6@mail.gmail.com>

> So... Should we allow more than one "description" element per
> service/obect/namespace to allow multiple languages per registration?


I do not know... Do we really need it? I think the main point is allow a
*different* language, but not  necessarily more than one. The registry needs
to remember what xml:lang was given together with description and return the
same back when the description is going out.

And perhaps to do it in all descriptions, not only the service
description...

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From martin.senger at gmail.com  Fri May 16 06:48:11 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 16 May 2008 11:48:11 +0100
Subject: [MOBY-dev] biomoby.org down?
Message-ID: <4d93f07c0805160348m7ba6ae11x489aca1922b41fd7@mail.gmail.com>

At least from the UK... (no http server responding, but I can ssh there).

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From pieter.neerincx at gmail.com  Fri May 16 07:07:10 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Fri, 16 May 2008 13:07:10 +0200
Subject: [MOBY-dev] biomoby.org down?
In-Reply-To: <4d93f07c0805160348m7ba6ae11x489aca1922b41fd7@mail.gmail.com>
References: <4d93f07c0805160348m7ba6ae11x489aca1922b41fd7@mail.gmail.com>
Message-ID: <CF52418B-3E57-47F7-AE86-89BFE5A9C785@gmail.com>

It's working overhere. So it either got fixed or it's a local problem...

Cheers,

Pi

On 16 May 2008, at 12:48, Martin Senger wrote:

> At least from the UK... (no http server responding, but I can ssh  
> there).
>
> Martin
>
> -- 
> Martin Senger
> email: martin.senger at gmail.com,m.senger at cgiar.org
> skype: martinsenger
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From edward.kawas at gmail.com  Wed May 21 11:38:21 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 21 May 2008 08:38:21 -0700
Subject: [MOBY-dev] Important note for MOBY-Async developers
In-Reply-To: <480F50D4.5000907@cnio.es>
References: <480F498A.4060902@cnio.es> <480F50D4.5000907@cnio.es>
Message-ID: <483441fa.15528c0a.1950.ffffddd5@mx.google.com>

Hi Jose Manual,

I noticed that the pdf document on async services seems to be corrupt (at
least for me). All the images are shown as smears.

Can you verify if this is the case?

Thanks,

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jose Manuel
rodriguez
Sent: April-23-08 8:08 AM
To: moby-dev at lists.open-bio.org; moby-dev-bounces at lists.open-bio.org;
inb-tecnico at lists.cnio.es
Cc: Dmitry Repchevsky; "=?ISO-8859-1?Q?Jos=E9_?="@portal.open-bio.org
Subject: [MOBY-dev] Important note for MOBY-Async developers

Hello,


The dispatcher of MOBY-Async services has to be modified.

The MOBY-Async developers have to add the next method to
SOAP::Transport::HTTP::CGI
    $server->on_action(sub{});

Inside of dispatcher he/she has to add:

$WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' 
=>' {Service Package}',
$WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP
ropertiesRequest' 
=> '{Service Package}',
$WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' 
=> '{Service Package}',

Then,
        $WSRF::Constants::WSRL => '{Service Package}',
        $WSRF::Constants::WSRP => '{Service Package}',

could be deleted.

I have attached you one CGI example.



For more information:
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/asyncDocs/BioMOBY%20A
synchronous%20Service%20Specification%20v2.4.2.pdf
(Maybe the CVS via web is not updated)

Best Regads,
Jos? Manuel.



Jose Manuel rodriguez wrote:
> Hello,
>
> We have fixed some problems that there were in our MOBY-async proposal.
>
> We found some inconsistencies in the specifications and implementations:
>
> * The "GetResourceProperty" and "GetMultipleResourceProperties" 
> messages returned QNames (both status and results) without prefixes.
>
> * During WSA messages, in the MOBY-Async Perl API we had:
>         
> <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
> roperties/GetMultipleResourceProperties</wsa:Action>
>    
>     When the WSRF specifications says that:
>         
> <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
> roperties/GetMultipleResourceProperties*Request*</wsa:Action>
>
> * In the WSDL for MOBY-Async services we have add the "soapAction" 
> address that SOAP 1.1 specifications says.
>
> * The MOBY-Async client and MOBY-Async sample have been updated from 
> these modifications. As soon as possible, we will sent you one 
> MOBY-Async sample which you could test it.
>
> * The MOBY-Async document has been updated (I have attached you the 
> MOBY-Async document v2.4.2).
>
> All these modifications have been committed to MOBY CVS.
>
> I think is all.
>
> Best Regards,
> Jos? Manuel.
>
>
>
> -- 
> Jos? Manuel Rodr?guez Carrasco            e-mail: jmrodriguez at cnio.es
> Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
> Bioinformatic Unit
> Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 
> 28029
> Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain)
>   


-- 
Jos? Manuel Rodr?guez Carrasco            e-mail: jmrodriguez at cnio.es
Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
Bioinformatic Unit
Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029
Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain) 



**NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los
ficheros adjuntos, pueden contener informaci?n protegida para el uso
exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o
cualquier otro tipo de transmisi?n por parte de otra persona que no sea el
destinatario. Si usted recibe por error este correo, se ruega comunicarlo al
remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may
contain confidential and privileged information for the sole use of the
designated recipient named above. Distribution, reproduction or any other
use of this transmission by any party other than the intended recipient is
prohibited. If you are not the intended recipient please contact the sender
and delete all copies.




From jmrodriguez at cnio.es  Wed May 21 12:11:45 2008
From: jmrodriguez at cnio.es (Jose Manuel rodriguez)
Date: Wed, 21 May 2008 18:11:45 +0200
Subject: [MOBY-dev] Important note for MOBY-Async developers
In-Reply-To: <483441fa.15528c0a.1950.ffffddd5@mx.google.com>
References: <480F498A.4060902@cnio.es> <480F50D4.5000907@cnio.es>
	<483441fa.15528c0a.1950.ffffddd5@mx.google.com>
Message-ID: <483449C1.6080709@cnio.es>

Hi Eddie,


It is strange. I have just make a checkout and the pdf looks good...I 
don't know.
We are checking now if the CVS has problems adding Binary Files.
We know that Binary files need to be added to CVS in a special way:
"cvs add -kb 'binary filename'"

But how I said I can read the pdf document perfectly.

Cheers,
Jos?.


Edward Kawas wrote:
> Hi Jose Manual,
>
> I noticed that the pdf document on async services seems to be corrupt (at
> least for me). All the images are shown as smears.
>
> Can you verify if this is the case?
>
> Thanks,
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jose Manuel
> rodriguez
> Sent: April-23-08 8:08 AM
> To: moby-dev at lists.open-bio.org; moby-dev-bounces at lists.open-bio.org;
> inb-tecnico at lists.cnio.es
> Cc: Dmitry Repchevsky; "=?ISO-8859-1?Q?Jos=E9_?="@portal.open-bio.org
> Subject: [MOBY-dev] Important note for MOBY-Async developers
>
> Hello,
>
>
> The dispatcher of MOBY-Async services has to be modified.
>
> The MOBY-Async developers have to add the next method to
> SOAP::Transport::HTTP::CGI
>     $server->on_action(sub{});
>
> Inside of dispatcher he/she has to add:
>
> $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' 
> =>' {Service Package}',
> $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP
> ropertiesRequest' 
> => '{Service Package}',
> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' 
> => '{Service Package}',
>
> Then,
>         $WSRF::Constants::WSRL => '{Service Package}',
>         $WSRF::Constants::WSRP => '{Service Package}',
>
> could be deleted.
>
> I have attached you one CGI example.
>
>
>
> For more information:
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/asyncDocs/BioMOBY%20A
> synchronous%20Service%20Specification%20v2.4.2.pdf
> (Maybe the CVS via web is not updated)
>
> Best Regads,
> Jos? Manuel.
>
>
>
> Jose Manuel rodriguez wrote:
>   
>> Hello,
>>
>> We have fixed some problems that there were in our MOBY-async proposal.
>>
>> We found some inconsistencies in the specifications and implementations:
>>
>> * The "GetResourceProperty" and "GetMultipleResourceProperties" 
>> messages returned QNames (both status and results) without prefixes.
>>
>> * During WSA messages, in the MOBY-Async Perl API we had:
>>         
>> <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
>> roperties/GetMultipleResourceProperties</wsa:Action>
>>    
>>     When the WSRF specifications says that:
>>         
>> <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
>> roperties/GetMultipleResourceProperties*Request*</wsa:Action>
>>
>> * In the WSDL for MOBY-Async services we have add the "soapAction" 
>> address that SOAP 1.1 specifications says.
>>
>> * The MOBY-Async client and MOBY-Async sample have been updated from 
>> these modifications. As soon as possible, we will sent you one 
>> MOBY-Async sample which you could test it.
>>
>> * The MOBY-Async document has been updated (I have attached you the 
>> MOBY-Async document v2.4.2).
>>
>> All these modifications have been committed to MOBY CVS.
>>
>> I think is all.
>>
>> Best Regards,
>> Jos? Manuel.
>>
>>
>>
>> -- 
>> Jos? Manuel Rodr?guez Carrasco            e-mail: jmrodriguez at cnio.es
>> Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
>> Bioinformatic Unit
>> Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 
>> 28029
>> Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain)
>>   
>>     
>
>
>   


-- 
Jos? Manuel Rodr?guez Carrasco            e-mail: jmrodriguez at cnio.es
Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
Bioinformatic Unit
Spanish National Cancer Center (CNIO) http://www.cnio.es
Zip Code: 28029
Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain) 


**NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.


From pieter.neerincx at gmail.com  Wed May 21 17:40:56 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Wed, 21 May 2008 23:40:56 +0200
Subject: [MOBY-dev] Important note for MOBY-Async developers
In-Reply-To: <483449C1.6080709@cnio.es>
References: <480F498A.4060902@cnio.es> <480F50D4.5000907@cnio.es>
	<483441fa.15528c0a.1950.ffffddd5@mx.google.com>
	<483449C1.6080709@cnio.es>
Message-ID: <6035FA51-858D-4E39-9F59-D96C5DD56F51@gmail.com>

Hi Eddie & Jos?,

On 21 May 2008, at 18:11, Jose Manuel rodriguez wrote:

> Hi Eddie,
>
>
> It is strange. I have just make a checkout and the pdf looks  
> good...I don't know.
> We are checking now if the CVS has problems adding Binary Files.
> We know that Binary files need to be added to CVS in a special way:
> "cvs add -kb 'binary filename'"
>
> But how I said I can read the pdf document perfectly.

Check, me too. So I don't think it's a problem with the way the  
document was checked in... Could it be a problem specific to a certain  
PDF viewer. There are many different versions of the PDF "standard" by  
now :(. Maybe Eddie's PDF viewer has a problem with this specific  
version. (I tried the official Adobe Acrobat Reader as well as Preview  
both on Mac OS X)

Cheers,

Pi

> Cheers,
> Jos?.
>
>
> Edward Kawas wrote:
>> Hi Jose Manual,
>>
>> I noticed that the pdf document on async services seems to be  
>> corrupt (at
>> least for me). All the images are shown as smears.
>>
>> Can you verify if this is the case?
>>
>> Thanks,
>>
>> Eddie
>>
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org
>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jose Manuel
>> rodriguez
>> Sent: April-23-08 8:08 AM
>> To: moby-dev at lists.open-bio.org; moby-dev-bounces at lists.open-bio.org;
>> inb-tecnico at lists.cnio.es
>> Cc: Dmitry Repchevsky; "=?ISO-8859-1?Q?Jos=E9_?="@portal.open-bio.org
>> Subject: [MOBY-dev] Important note for MOBY-Async developers
>>
>> Hello,
>>
>>
>> The dispatcher of MOBY-Async services has to be modified.
>>
>> The MOBY-Async developers have to add the next method to
>> SOAP::Transport::HTTP::CGI
>>    $server->on_action(sub{});
>>
>> Inside of dispatcher he/she has to add:
>>
>> $WSRF::Constants::WSRPW.'/GetResourceProperty/ 
>> GetResourcePropertyRequest' =>' {Service Package}',
>> $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/ 
>> GetMultipleResourceP
>> ropertiesRequest' => '{Service Package}',
>> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/ 
>> DestroyRequest' => '{Service Package}',
>>
>> Then,
>>        $WSRF::Constants::WSRL => '{Service Package}',
>>        $WSRF::Constants::WSRP => '{Service Package}',
>>
>> could be deleted.
>>
>> I have attached you one CGI example.
>>
>>
>>
>> For more information:
>> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/asyncDocs/BioMOBY%20A
>> synchronous%20Service%20Specification%20v2.4.2.pdf
>> (Maybe the CVS via web is not updated)
>>
>> Best Regads,
>> Jos? Manuel.
>>
>>
>>
>> Jose Manuel rodriguez wrote:
>>
>>> Hello,
>>>
>>> We have fixed some problems that there were in our MOBY-async  
>>> proposal.
>>>
>>> We found some inconsistencies in the specifications and  
>>> implementations:
>>>
>>> * The "GetResourceProperty" and "GetMultipleResourceProperties"  
>>> messages returned QNames (both status and results) without prefixes.
>>>
>>> * During WSA messages, in the MOBY-Async Perl API we had:
>>>        <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
>>> roperties/GetMultipleResourceProperties</wsa:Action>
>>>       When the WSRF specifications says that:
>>>        <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
>>> roperties/GetMultipleResourceProperties*Request*</wsa:Action>
>>>
>>> * In the WSDL for MOBY-Async services we have add the "soapAction"  
>>> address that SOAP 1.1 specifications says.
>>>
>>> * The MOBY-Async client and MOBY-Async sample have been updated  
>>> from these modifications. As soon as possible, we will sent you  
>>> one MOBY-Async sample which you could test it.
>>>
>>> * The MOBY-Async document has been updated (I have attached you  
>>> the MOBY-Async document v2.4.2).
>>>
>>> All these modifications have been committed to MOBY CVS.
>>>
>>> I think is all.
>>>
>>> Best Regards,
>>> Jos? Manuel.
>>>
>>>
>>>
>>> -- 
>>> Jos? Manuel Rodr?guez Carrasco            e-mail:  
>>> jmrodriguez at cnio.es
>>> Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
>>> Bioinformatic Unit
>>> Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code:  
>>> 28029
>>> Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain)
>>>
>>
>>
>>
>
>
> -- 
> Jos? Manuel Rodr?guez Carrasco            e-mail: jmrodriguez at cnio.es
> Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
> Bioinformatic Unit
> Spanish National Cancer Center (CNIO) http://www.cnio.es
> Zip Code: 28029
> Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain)
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso  
> los ficheros adjuntos, pueden contener informaci?n protegida para el  
> uso exclusivo de su destinatario. Se proh?be la distribuci?n,  
> reproducci?n o cualquier otro tipo de transmisi?n por parte de otra  
> persona que no sea el destinatario. Si usted recibe por error este  
> correo, se ruega comunicarlo al remitente y borrar el mensaje  
> recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any  
> attachments may contain confidential and privileged information for  
> the sole use of the designated recipient named above. Distribution,  
> reproduction or any other use of this transmission by any party  
> other than the intended recipient is prohibited. If you are not the  
> intended recipient please contact the sender and delete all copies.
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From jflo at imim.es  Thu May 22 12:12:55 2008
From: jflo at imim.es (Judith Flo)
Date: Thu, 22 May 2008 18:12:55 +0200
Subject: [MOBY-dev] problem registering with dashboard
Message-ID: <48359B87.8070705@imim.es>

Hi,
I'm getting this error when i try to register something using an xml file

===ERROR===

Fault details:

[stackTrace: null]

[hostname: null]

Fault string: Failed to locate method (registerDataType) in class 
(MOBY::Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm 
line 2586, <IN> line 54.


Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Client

Fault actor:  null

When calling:

    http://moby.ucalgary.ca/moby/MOBY-Central.pl

===========


It happens always, I just can register new Data Types when I fill all 
boxes in the registration view...(I don't have any problems registering 
new services or namespaces)
The xml files that I'm using are the ones that i got when I use the 
"show raw XML" button, so I assume that they are correct...

Any help will be appreciatted.
Cheers,
j


From edward.kawas at gmail.com  Thu May 22 12:33:24 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 22 May 2008 09:33:24 -0700
Subject: [MOBY-dev] problem registering with dashboard
In-Reply-To: <48359B87.8070705@imim.es>
References: <48359B87.8070705@imim.es>
Message-ID: <4835a065.08b38c0a.4751.6f48@mx.google.com>

Hi Judith,

The problem is that registerDataType is not the correct name. Try
registerObjectClass instead.

Thanks,

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Judith Flo
Sent: May-22-08 9:13 AM
To: Core developer announcements
Subject: [MOBY-dev] problem registering with dashboard

Hi,
I'm getting this error when i try to register something using an xml file

===ERROR===

Fault details:

[stackTrace: null]

[hostname: null]

Fault string: Failed to locate method (registerDataType) in class 
(MOBY::Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm 
line 2586, <IN> line 54.


Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Client

Fault actor:  null

When calling:

    http://moby.ucalgary.ca/moby/MOBY-Central.pl

===========


It happens always, I just can register new Data Types when I fill all 
boxes in the registration view...(I don't have any problems registering 
new services or namespaces)
The xml files that I'm using are the ones that i got when I use the 
"show raw XML" button, so I assume that they are correct...

Any help will be appreciatted.
Cheers,
j

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev


From martin.senger at gmail.com  Thu May 22 12:35:03 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 23 May 2008 00:35:03 +0800
Subject: [MOBY-dev] problem registering with dashboard
In-Reply-To: <48359B87.8070705@imim.es>
References: <48359B87.8070705@imim.es>
Message-ID: <4d93f07c0805220935k1660fb79ud5a7cb7ff33514dc@mail.gmail.com>

I'm getting this error when i try to register something using an xml file


I am glad that you got this error :-)
Because I got the same error several hours ago, and I have asked Eddie to
help me to find what is wrong. He has not replied yet. But the problem is
being solved...

M.

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From martin.senger at gmail.com  Thu May 22 12:39:23 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 23 May 2008 00:39:23 +0800
Subject: [MOBY-dev] problem registering with dashboard
In-Reply-To: <4835a065.08b38c0a.4751.6f48@mx.google.com>
References: <48359B87.8070705@imim.es>
	<4835a065.08b38c0a.4751.6f48@mx.google.com>
Message-ID: <4d93f07c0805220939w594d3185i32b8298545af3856@mail.gmail.com>

>
> The problem is that registerDataType is not the correct name. Try
> registerObjectClass instead.


Not possible - because it is the Dashboard who uses this wrong method, not
Judith.
Read my email please.

M.

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From martin.senger at gmail.com  Thu May 22 13:15:34 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 23 May 2008 01:15:34 +0800
Subject: [MOBY-dev] problem registering with dashboard
In-Reply-To: <4d93f07c0805220939w594d3185i32b8298545af3856@mail.gmail.com>
References: <48359B87.8070705@imim.es>
	<4835a065.08b38c0a.4751.6f48@mx.google.com>
	<4d93f07c0805220939w594d3185i32b8298545af3856@mail.gmail.com>
Message-ID: <4d93f07c0805221015p106c30d0r24b63ed350a2696a@mail.gmail.com>

It is fixed now. Please do cvs update.

But I cannot believe it: the bug was there for two years. It was never
working properly. Which means that nobody has used it. Until today! When we
both tried it *in the same day*, within about five hours. The planet Gaia
syndrome (http://en.wikipedia.org/wiki/Gaia_hypothesis) is here again!

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From jflo at imim.es  Fri May 23 03:49:54 2008
From: jflo at imim.es (Judith Flo)
Date: Fri, 23 May 2008 09:49:54 +0200
Subject: [MOBY-dev] problem registering with dashboard
In-Reply-To: <4d93f07c0805221015p106c30d0r24b63ed350a2696a@mail.gmail.com>
References: <48359B87.8070705@imim.es>	<4835a065.08b38c0a.4751.6f48@mx.googl
	e.com>	<4d93f07c0805220939w594d3185i32b8298545af3856@mail.gmail.com> 
	<4d93f07c0805221015p106c30d0r24b63ed350a2696a@mail.gmail.com>
Message-ID: <48367722.9030006@imim.es>

Hi,

[this is just for information] I didn't change any configuration and now 
when I cvs-update the moby project and try to start the dashboard (on 
Eclipse) I got this:

Buildfile: /home/judith/workspace3/moby/build.xml

checkmaven:


BUILD FAILED

/home/judith/workspace3/moby/xmls/maven.xml:62: Sorry...

    Missing Maven library. It can be fetched from the Internet.

    Type: ant bootstrap

    This is needed to be done only once.


Updates were working before without problem...

After running the bootstrap task I got my dashboard working properly and 
the data-type registration_from_xml_file button is working perfectly 
(lazy people (like me) will be happy ;)), it is a very useful tool when 
one wants to register its data-types, namespaces and services to 
different repositories, i don't understand why people don't use it... )

Thanks to all of you for your work!
j


Martin Senger wrote:
> It is fixed now. Please do cvs update.
>
> But I cannot believe it: the bug was there for two years. It was never
> working properly. Which means that nobody has used it. Until today! When we
> both tried it *in the same day*, within about five hours. The planet Gaia
> syndrome (http://en.wikipedia.org/wiki/Gaia_hypothesis) is here again!
>
> Martin
>
>   

From jason.e.stewart at gmail.com  Fri May 23 06:46:24 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Fri, 23 May 2008 16:16:24 +0530
Subject: [MOBY-dev] Error Registering service with Dashboard: malformed
	authURI
Message-ID: <41c1ade50805230346v1140a2ech9b2d208464efd00@mail.gmail.com>

Hey,

I'm feeling a bit stupid, but no matter what authURI I use, I get the error:

  Malformed authURI - must not have an http:// prefix

but my authURI doesn't have an 'http://' prefix... and I still get the error.

I tried registering with XML first, and then tried with the dashboard
second. Don't know what I'm doing I guess. Clues gratefully
accepted...

Cheers, jas.

From jason.e.stewart at gmail.com  Fri May 23 06:54:58 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Fri, 23 May 2008 16:24:58 +0530
Subject: [MOBY-dev] malformed authURI [solved]
Message-ID: <41c1ade50805230354l2318bc98s8087b79b64771c0b@mail.gmail.com>

Hey,

OK. It was an incomplet error message text...

Here is what the docs say:

authURI - a URI representing your organization (e.g. yourdomain.com);
no http-prefix, and no trailing path information is allowed.

but the code looks like this:

	return &_error( "Malformed authURI - must not have an http:// prefix", "" )
	  if $AuthURI =~ '[/:]';

Ah... I had a trailing '/'... but not a 'http://'  prefix... That was
confusing me...

So if I have a ':' or a '/' then the authURI is rejected. I'd be happy
to offer a patch for the error message to make it a bit more complete.
Is that helpful?

Cheers, jas.

From markw at illuminae.com  Fri May 23 11:58:41 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 23 May 2008 08:58:41 -0700
Subject: [MOBY-dev] malformed authURI [solved]
In-Reply-To: <41c1ade50805230354l2318bc98s8087b79b64771c0b@mail.gmail.com>
References: <41c1ade50805230354l2318bc98s8087b79b64771c0b@mail.gmail.com>
Message-ID: <op.ubl6n3uvnbznux@dd0710001l.icapture.ubc.ca>

the authURI is really intended to be the authority's domain name... so  
whatever regexp/error message changes you think will indicate that please  
go ahead :-)

Mark



On Fri, 23 May 2008 03:54:58 -0700, Jason Stewart  
<jason.e.stewart at gmail.com> wrote:

> Hey,
>
> OK. It was an incomplet error message text...
>
> Here is what the docs say:
>
> authURI - a URI representing your organization (e.g. yourdomain.com);
> no http-prefix, and no trailing path information is allowed.
>
> but the code looks like this:
>
> 	return &_error( "Malformed authURI - must not have an http:// prefix",  
> "" )
> 	  if $AuthURI =~ '[/:]';
>
> Ah... I had a trailing '/'... but not a 'http://'  prefix... That was
> confusing me...
>
> So if I have a ':' or a '/' then the authURI is rejected. I'd be happy
> to offer a patch for the error message to make it a bit more complete.
> Is that helpful?
>
> Cheers, jas.
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada


From jason.e.stewart at gmail.com  Fri May 23 13:19:54 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Fri, 23 May 2008 22:49:54 +0530
Subject: [MOBY-dev] DNS expired for open-bio.org
Message-ID: <41c1ade50805231019u45eed94awa6c56eb49c3991e2@mail.gmail.com>

Hey,

Just got this error:

ZoneEdit DNS services for this domain have expired.
To reactivate service for
OPEN-BIO.ORG/CVS_CONTENT/MOBY-LIVE/JAVA/DOCS/DASHBOARD.HTML, log into
your account and add credits.
Thank you for using ZoneEdit

Cheers, jas.

From gordonp at ucalgary.ca  Fri May 23 17:28:44 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 23 May 2008 15:28:44 -0600
Subject: [MOBY-dev] DNS expired for open-bio.org
In-Reply-To: <41c1ade50805231019u45eed94awa6c56eb49c3991e2@mail.gmail.com>
References: <41c1ade50805231019u45eed94awa6c56eb49c3991e2@mail.gmail.com>
Message-ID: <4837370C.5040207@ucalgary.ca>

I assume Chris is on vacation, or low on cash? :-)

Jason Stewart wrote:
> Hey,
>
> Just got this error:
>
> ZoneEdit DNS services for this domain have expired.
> To reactivate service for
> OPEN-BIO.ORG/CVS_CONTENT/MOBY-LIVE/JAVA/DOCS/DASHBOARD.HTML, log into
> your account and add credits.
> Thank you for using ZoneEdit
>
> Cheers, jas.
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> !DSPAM:60005,4837335d109501765921693!
>
>
>
>   

From jason.e.stewart at gmail.com  Sat May 24 07:13:37 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Sat, 24 May 2008 16:43:37 +0530
Subject: [MOBY-dev] malformed authURI [solved]
In-Reply-To: <op.ubl6n3uvnbznux@dd0710001l.icapture.ubc.ca>
References: <41c1ade50805230354l2318bc98s8087b79b64771c0b@mail.gmail.com>
	<op.ubl6n3uvnbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <41c1ade50805240413n55d11d8eu83ce112c0342a8e2@mail.gmail.com>

Hey Mark,

2008/5/23 Mark Wilkinson <markw at illuminae.com>:
> the authURI is really intended to be the authority's domain name... so
> whatever regexp/error message changes you think will indicate that please go
> ahead :-)

The regex checking for email and authURI is the same in three
different places so I thought I would centralize it to use a
subroutine that dies on error - so the code can be shared (in case the
messages or the regex's want to get changed later.

The subs look like this:

sub _validateAuthURI {
    my $auth = shift @_;

    my $error = "";
    if ($auth =~ '[/:]') {
	$error = "has a colon or a slash - must not have an http:// prefix,
and must not have trailing path info";
    } elsif ($auth =~ /\./) {
	$error = "must take the form NNN.NNN.NNN";
    }
    die "Malformed authURI - $error" if $error;
}

sub _validateEmail {
    my $email = shift @_;

    my $error = "";
    if ($email !~ /\S\@\S+\.\S+/) {
	$error = "Malformed email - must be a valid email address of the form
name\@organization.foo";
    }
    die $error if $error;
}

and they replace this code:

	return &_error( "Malformed authURI - must not have an http:// prefix", "" )
	  if $AuthURI =~ '[/:]';
	return &_error( "Malformed authURI - must take the form NNN.NNN.NNN", "" )
	  unless $AuthURI =~ /\./;
	return &_error("Malformed email - must be a valid email address of
the form name\@organization.foo","")
	  unless $contactEmail =~ /\S\@\S+\.\S+/;

with this:

	eval {_validateAuthURI($auth)};
	&_error($@) if $@;
	eval {_validateEmail($email)};
	&_error($@) if $@;

Does that look acceptable?

Mark and Eddie, I had one question about using that code in
registerService() - there seems to be two different error handling
strategies going on - there is an $error variable that is being added
to if any payload errors are found, but then authURI and email
validation causes _error() to be called immediately ... I was
wondering if this was accidental or on purpose? Should I changed the
authURI and email validation failure to also add to $error instead of
calling _error() immediately?

Cheers, jas.

From markw at illuminae.com  Sat May 24 10:59:39 2008
From: markw at illuminae.com (Mark)
Date: Sat, 24 May 2008 07:59:39 -0700
Subject: [MOBY-dev] malformed authURI [solved]
In-Reply-To: <41c1ade50805240413n55d11d8eu83ce112c0342a8e2@mail.gmail.com>
References: <41c1ade50805230354l2318bc98s8087b79b64771c0b@mail.gmail.com>
	<op.ubl6n3uvnbznux@dd0710001l.icapture.ubc.ca>
	<41c1ade50805240413n55d11d8eu83ce112c0342a8e2@mail.gmail.com>
Message-ID: <op.ubnylpmkdeqt07@bighome>

On Sat, 24 May 2008 04:13:37 -0700, Jason Stewart  
<jason.e.stewart at gmail.com> wrote:

> Does that look acceptable?

Fantastic!  Thanks!



> validation causes _error() to be called immediately ... I was
> wondering if this was accidental or on purpose? Should I changed the

Accidental.  Please change it to be consistent.

Cheers Jas!

M

From jason.e.stewart at gmail.com  Mon May 26 03:21:23 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Mon, 26 May 2008 12:51:23 +0530
Subject: [MOBY-dev] xml:lang explored
Message-ID: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>

Hey all,

Here's what I have found out.

I don't believe that changing the current parser for Central.pm is
going to help the situation. I have looked and besides special API's
like the one implemented by LibXML::Reader, the application is always
required to maintain the status of xml:lang using the standard SAX and
DOM API's - for Java or for Perl.

We will have to preserve the information in the DB, so a decision
needs to be made on what level the xml:lang should be used - only for
descriptions?? or for the whole registration?? At the moment I don't
see any reason to use it for more than the description - how do people
feel about this? Changing this should require adding one column to the
DB.

Finally, do we want registration with multiple descriptions? That will
probably require a significant change in the DB - a new table for
linking descriptions to registrations. Are people happy about that?

Cheers, jas.

From jason.e.stewart at gmail.com  Mon May 26 04:42:37 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Mon, 26 May 2008 14:12:37 +0530
Subject: [MOBY-dev] MOBY Central DB optimization
In-Reply-To: <480de11b.14b48c0a.0dfc.ffff9cdd@mx.google.com>
References: <41c1ade50804220313n1de734f0ldae2d077c97f5326@mail.gmail.com>
	<480de11b.14b48c0a.0dfc.ffff9cdd@mx.google.com>
Message-ID: <41c1ade50805260142q46b7893byfe3995d3d0342560@mail.gmail.com>

Hey Ed,

Just to let you know - it all worked fine, the cvs checkout, and the
make install. I did get some test failures - I can post them if you'd
like.

But now that things are installed... I'm not sure how to initiate the
repository - is there a web page for doing this?

Cheers, jas.

2008/4/22 Ed Kawas <ed.kawas at gmail.com>:
> Hi Jason,
>
> While it is now easier to install than before, it's still a little involved.
>
> If I were you, I would checkout moby from the cvs then:
>
> cd moby-live/Perl/MOBY-Server
> perl Makefile.PL
> make test
> make install
>
> then after the install, do a 'moby-s-install.pl' from the command line. That
> script is placed on you path during the make install phase.
>
> The 'make' part of things will prompt you to auto install some modules. This
> isn't full proof. I usually just download them myself and use the list that
> it provides as a guide.
>
> Before starting make sure that you have installed apache, mysql and have
> libxml2 on your system.
>
> Let me know if there is anything else that you need.
>
> Eddie
>
> -----Original Message-----
> From: Jason Stewart [mailto:jason.e.stewart at gmail.com]
> Sent: April-22-08 3:14 AM
> To: Core developer announcements; Ed Kawas
> Subject: MOBY Central DB optimization
>
> Hey Eddie,
>
> Just got the following from Mark:
>
> "THe MOBY Central issue would also be nice to work-out.  It will be in
> the MOBY-Server/lib/MOBY/Central.pm module.  The findService
> subroutine.  What I currently do is take each parameter that is passed
> into MOBY Central and do a database query on that parameter, hold the
> indexes of the discovered services in a hash where I increment the
> value of that hash elemnt by +1 each time it passes a test of being
> discovered in a single-parameter search, and then figure out which
> hash elements have been discovered on every search, and pass those
> back as the successfully discovered services.  This was done *only* to
> save me having to do nasty and largely unpredictable joins depending
> on which search parameters were passed-in.  If you can think of a way
> to optimize that, then please go ahead!  You will have to install a
> MOBY Central instance yourself - please talk to Eddie, as he has just
> finished writing an installer... should be simply "make install"."
>
> I'm wanting to setup a MOBY Central instance and debug findService()
> to see if there is a more efficient way to run it. Do you have a
> HOWTO?
>
> Cheers, jas.
>
>

From ed.kawas at gmail.com  Mon May 26 09:14:51 2008
From: ed.kawas at gmail.com (Ed Kawas)
Date: Mon, 26 May 2008 06:14:51 -0700
Subject: [MOBY-dev] MOBY Central DB optimization
In-Reply-To: <41c1ade50805260142q46b7893byfe3995d3d0342560@mail.gmail.com>
References: <41c1ade50804220313n1de734f0ldae2d077c97f5326@mail.gmail.com>	
	<480de11b.14b48c0a.0dfc.ffff9cdd@mx.google.com>
	<41c1ade50805260142q46b7893byfe3995d3d0342560@mail.gmail.com>
Message-ID: <483ab7d4.2a528c0a.6e50.3223@mx.google.com>

Hi Jason,

If you run the moby-s-install.pl from the command line, and enter 'yes' when
prompted to set up mysql, you can mirror a central registry. This should
help you fill up your local registry.

Thanks,

Eddie

-----Original Message-----
From: Jason Stewart [mailto:jason.e.stewart at gmail.com] 
Sent: May-26-08 1:43 AM
To: Ed Kawas; Core developer announcements
Subject: Re: MOBY Central DB optimization

Hey Ed,

Just to let you know - it all worked fine, the cvs checkout, and the
make install. I did get some test failures - I can post them if you'd
like.

But now that things are installed... I'm not sure how to initiate the
repository - is there a web page for doing this?

Cheers, jas.

2008/4/22 Ed Kawas <ed.kawas at gmail.com>:
> Hi Jason,
>
> While it is now easier to install than before, it's still a little
involved.
>
> If I were you, I would checkout moby from the cvs then:
>
> cd moby-live/Perl/MOBY-Server
> perl Makefile.PL
> make test
> make install
>
> then after the install, do a 'moby-s-install.pl' from the command line.
That
> script is placed on you path during the make install phase.
>
> The 'make' part of things will prompt you to auto install some modules.
This
> isn't full proof. I usually just download them myself and use the list
that
> it provides as a guide.
>
> Before starting make sure that you have installed apache, mysql and have
> libxml2 on your system.
>
> Let me know if there is anything else that you need.
>
> Eddie
>
> -----Original Message-----
> From: Jason Stewart [mailto:jason.e.stewart at gmail.com]
> Sent: April-22-08 3:14 AM
> To: Core developer announcements; Ed Kawas
> Subject: MOBY Central DB optimization
>
> Hey Eddie,
>
> Just got the following from Mark:
>
> "THe MOBY Central issue would also be nice to work-out.  It will be in
> the MOBY-Server/lib/MOBY/Central.pm module.  The findService
> subroutine.  What I currently do is take each parameter that is passed
> into MOBY Central and do a database query on that parameter, hold the
> indexes of the discovered services in a hash where I increment the
> value of that hash elemnt by +1 each time it passes a test of being
> discovered in a single-parameter search, and then figure out which
> hash elements have been discovered on every search, and pass those
> back as the successfully discovered services.  This was done *only* to
> save me having to do nasty and largely unpredictable joins depending
> on which search parameters were passed-in.  If you can think of a way
> to optimize that, then please go ahead!  You will have to install a
> MOBY Central instance yourself - please talk to Eddie, as he has just
> finished writing an installer... should be simply "make install"."
>
> I'm wanting to setup a MOBY Central instance and debug findService()
> to see if there is a more efficient way to run it. Do you have a
> HOWTO?
>
> Cheers, jas.
>
>


From markw at illuminae.com  Mon May 26 13:52:33 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 26 May 2008 10:52:33 -0700
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
Message-ID: <op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>

Should we allow registration of objects, service-types and namespaces in  
foreign languages also?  If so, then we need to re-think the entire way we  
manage the ontology, and assign unique id numbers to each node, where the  
rdf:label of the node can have multiple languages, rather than having the  
node named by its label.

...can... worms... but it's probably the "right thing to do"...

M



On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart  
<jason.e.stewart at gmail.com> wrote:

> Hey all,
>
> Here's what I have found out.
>
> I don't believe that changing the current parser for Central.pm is
> going to help the situation. I have looked and besides special API's
> like the one implemented by LibXML::Reader, the application is always
> required to maintain the status of xml:lang using the standard SAX and
> DOM API's - for Java or for Perl.
>
> We will have to preserve the information in the DB, so a decision
> needs to be made on what level the xml:lang should be used - only for
> descriptions?? or for the whole registration?? At the moment I don't
> see any reason to use it for more than the description - how do people
> feel about this? Changing this should require adding one column to the
> DB.
>
> Finally, do we want registration with multiple descriptions? That will
> probably require a significant change in the DB - a new table for
> linking descriptions to registrations. Are people happy about that?
>
> Cheers, jas.
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada

From markw at illuminae.com  Wed May 14 12:15:27 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 14 May 2008 09:15:27 -0700
Subject: [MOBY-dev] For hosts of MOBY Central
In-Reply-To: <482B0F0E.90807@ucalgary.ca>
References: <482B0F0E.90807@ucalgary.ca>
Message-ID: <op.ua5jf102nbznux@dd0710001l.icapture.ubc.ca>

Just FYI - this is a graph showing the CPU usage before and after that  
last fix I did on MOBY Central... just for anyone who didn't believe that  
it was an important fix :-)

M



------- Forwarded message -------
From: "Theron Dekok" <tcdekok at ucalgary.ca>
To: "Mark Wilkinson" <markw at illuminae.com>
Cc:
Subject: Moby Graph
Date: Wed, 14 May 2008 09:10:54 -0700

Hi Mark,

I thought the attached graph might be of interest. It's really amazing
how things have changed since the fix :-)

-Theron



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada
-------------- next part --------------
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Size: 39142 bytes
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From gordonp at ucalgary.ca  Mon May 26 14:59:42 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 26 May 2008 12:59:42 -0600
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <483B089E.20602@ucalgary.ca>

I think we are mostly polyglots on this list, but for the sake of 
technical simplicity, I'd stick with just tracking the language rather 
than having multiple values in the registry.  Multilingual descriptions 
could be offloaded to the LSID metadata perhaps if people really want it.

Mes 0.02$ canadiens,

Paul

Mark Wilkinson wrote:
> Should we allow registration of objects, service-types and namespaces 
> in foreign languages also?  If so, then we need to re-think the entire 
> way we manage the ontology, and assign unique id numbers to each node, 
> where the rdf:label of the node can have multiple languages, rather 
> than having the node named by its label.
>
> ...can... worms... but it's probably the "right thing to do"...
>
> M
>
>
>
> On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart 
> <jason.e.stewart at gmail.com> wrote:
>
>> Hey all,
>>
>> Here's what I have found out.
>>
>> I don't believe that changing the current parser for Central.pm is
>> going to help the situation. I have looked and besides special API's
>> like the one implemented by LibXML::Reader, the application is always
>> required to maintain the status of xml:lang using the standard SAX and
>> DOM API's - for Java or for Perl.
>>
>> We will have to preserve the information in the DB, so a decision
>> needs to be made on what level the xml:lang should be used - only for
>> descriptions?? or for the whole registration?? At the moment I don't
>> see any reason to use it for more than the description - how do people
>> feel about this? Changing this should require adding one column to the
>> DB.
>>
>> Finally, do we want registration with multiple descriptions? That will
>> probably require a significant change in the DB - a new table for
>> linking descriptions to registrations. Are people happy about that?
>>
>> Cheers, jas.
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>

From pieter.neerincx at gmail.com  Mon May 26 17:04:19 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Mon, 26 May 2008 23:04:19 +0200
Subject: [MOBY-dev] For hosts of MOBY Central
In-Reply-To: <op.ua5jf102nbznux@dd0710001l.icapture.ubc.ca>
References: <482B0F0E.90807@ucalgary.ca>
	<op.ua5jf102nbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <C086F783-E537-4C30-8827-940453A12511@gmail.com>

Bummer, funding agencies will be a lot less impressed after looking at  
the new graphs: "Is anybody actually using this BioMoby thing?" :)

Cheers,

Pi

On 14 May 2008, at 18:15, Mark Wilkinson wrote:

> Just FYI - this is a graph showing the CPU usage before and after  
> that last fix I did on MOBY Central... just for anyone who didn't  
> believe that it was an important fix :-)
>
> M
>
>
>
> ------- Forwarded message -------
> From: "Theron Dekok" <tcdekok at ucalgary.ca>
> To: "Mark Wilkinson" <markw at illuminae.com>
> Cc:
> Subject: Moby Graph
> Date: Wed, 14 May 2008 09:10:54 -0700
>
> Hi Mark,
>
> I thought the attached graph might be of interest. It's really amazing
> how things have changed since the fix :-)
>
> -Theron
>
>
>
> -- 
> Mark D Wilkinson, PI Bioinformatics
> Assistant Professor, Medical Genetics
> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary  
> Research
> Providence Heart + Lung Institute
> University of British Columbia - St. Paul's Hospital
> Vancouver, BC,  
> Canada<mobyGraph.png>_______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev


From markw at illuminae.com  Mon May 26 17:09:53 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 26 May 2008 14:09:53 -0700
Subject: [MOBY-dev] For hosts of MOBY Central
In-Reply-To: <C086F783-E537-4C30-8827-940453A12511@gmail.com>
References: <482B0F0E.90807@ucalgary.ca>
	<op.ua5jf102nbznux@dd0710001l.icapture.ubc.ca>
	<C086F783-E537-4C30-8827-940453A12511@gmail.com>
Message-ID: <op.ubr42rmvnbznux@dd0710001l.icapture.ubc.ca>

damn!  Never thought of that!

;-)

M


On Mon, 26 May 2008 14:04:19 -0700, Pieter Neerincx  
<pieter.neerincx at gmail.com> wrote:

> Bummer, funding agencies will be a lot less impressed after looking at  
> the new graphs: "Is anybody actually using this BioMoby thing?" :)
>
> Cheers,
>
> Pi
>
> On 14 May 2008, at 18:15, Mark Wilkinson wrote:
>
>> Just FYI - this is a graph showing the CPU usage before and after that  
>> last fix I did on MOBY Central... just for anyone who didn't believe  
>> that it was an important fix :-)
>>
>> M
>>
>>
>>
>> ------- Forwarded message -------
>> From: "Theron Dekok" <tcdekok at ucalgary.ca>
>> To: "Mark Wilkinson" <markw at illuminae.com>
>> Cc:
>> Subject: Moby Graph
>> Date: Wed, 14 May 2008 09:10:54 -0700
>>
>> Hi Mark,
>>
>> I thought the attached graph might be of interest. It's really amazing
>> how things have changed since the fix :-)
>>
>> -Theron
>>
>>
>>
>> --Mark D Wilkinson, PI Bioinformatics
>> Assistant Professor, Medical Genetics
>> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
>> Providence Heart + Lung Institute
>> University of British Columbia - St. Paul's Hospital
>> Vancouver, BC,  
>> Canada<mobyGraph.png>_______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada

From pieter.neerincx at gmail.com  Mon May 26 18:41:34 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Tue, 27 May 2008 00:41:34 +0200
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <483B089E.20602@ucalgary.ca>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
Message-ID: <76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>

Hi all,

On 26 May 2008, at 20:59, Paul Gordon wrote:

> I think we are mostly polyglots on this list,

I'm a polyglot when I'm on holiday or in a pub maybe, but when I'm  
talking bioinformatics stuff I'm a strict monoglot! Before we open  
that can of worms: do we actually need translations? Did anyone  
request support for different languages? Mark mentioned someone did on  
the last developer meeting, but I didn't see anyone chime in on this  
list with a request for other languages. I only noticed a few objects  
and services in the official public Central containing descriptions in  
Spanish (or is it Portugese?), which renders them useless for the  
majority of users.

BioMoby web services are all about creating interoperable resources.  
Introducing the Tower of Babel effect isn't going to help. I hope I  
don't sound arrogant, but unless there are scientists out there using  
BioMoby for research into language itself, archeology or culture, I  
really fail to see why we need anything but the "de facto" standard  
language for research. (No, I'm not a native Englisch speaker...)

Is there actually any major bioinformatics resource that supports  
translations? I can't think of any, but maybe I should write an e-mail  
to the NCBI, DDBJ, EBI et al. and request Dutch translations of  
Genbank, PubMed, KEGG, Uniprot, Ensembl, etc. Might be fun to see if  
and how they repsond :)...

> but for the sake of technical simplicity, I'd stick with just  
> tracking the language rather than having multiple values in the  
> registry.

For even more simplicity I'd opt for hardcoding the language to  
English. Now let's hope the native English speakers are not going to  
fight over whether international English means Australian, UK,  
American, Canadian, or yet another English. If that happens I'm voting  
for Dinglish :).

Just my ? 0.02

Cheers,

Pi

>  Multilingual descriptions could be offloaded to the LSID metadata  
> perhaps if people really want it.
>
> Mes 0.02$ canadiens,
>
> Paul
>
> Mark Wilkinson wrote:
>> Should we allow registration of objects, service-types and  
>> namespaces in foreign languages also?  If so, then we need to re- 
>> think the entire way we manage the ontology, and assign unique id  
>> numbers to each node, where the rdf:label of the node can have  
>> multiple languages, rather than having the node named by its label.
>>
>> ...can... worms... but it's probably the "right thing to do"...
>>
>> M
>>
>>
>>
>> On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart <jason.e.stewart at gmail.com 
>> > wrote:
>>
>>> Hey all,
>>>
>>> Here's what I have found out.
>>>
>>> I don't believe that changing the current parser for Central.pm is
>>> going to help the situation. I have looked and besides special API's
>>> like the one implemented by LibXML::Reader, the application is  
>>> always
>>> required to maintain the status of xml:lang using the standard SAX  
>>> and
>>> DOM API's - for Java or for Perl.
>>>
>>> We will have to preserve the information in the DB, so a decision
>>> needs to be made on what level the xml:lang should be used - only  
>>> for
>>> descriptions?? or for the whole registration?? At the moment I don't
>>> see any reason to use it for more than the description - how do  
>>> people
>>> feel about this? Changing this should require adding one column to  
>>> the
>>> DB.
>>>
>>> Finally, do we want registration with multiple descriptions? That  
>>> will
>>> probably require a significant change in the DB - a new table for
>>> linking descriptions to registrations. Are people happy about that?
>>>
>>> Cheers, jas.
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From markw at illuminae.com  Mon May 26 18:58:53 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 26 May 2008 15:58:53 -0700
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
Message-ID: <op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>

personally, I tend to think we *should* be using the multi-lingual  
capabilities of XML more than we are!  The idea is not to introduce a  
tower of Babel, but rather to embrace as many languages as possible in our  
infrastructure!  to be inclusive, rather than exclusive!

this does, however, require extensive re-tooling of the software.  I  
wonder if it is something that is best left for Moby 2.0 (and planned from  
the start) rather than hacked into Moby 1.0?

M




On Mon, 26 May 2008 15:41:34 -0700, Pieter Neerincx  
<pieter.neerincx at gmail.com> wrote:

> Hi all,
>
> On 26 May 2008, at 20:59, Paul Gordon wrote:
>
>> I think we are mostly polyglots on this list,
>
> I'm a polyglot when I'm on holiday or in a pub maybe, but when I'm  
> talking bioinformatics stuff I'm a strict monoglot! Before we open that  
> can of worms: do we actually need translations? Did anyone request  
> support for different languages? Mark mentioned someone did on the last  
> developer meeting, but I didn't see anyone chime in on this list with a  
> request for other languages. I only noticed a few objects and services  
> in the official public Central containing descriptions in Spanish (or is  
> it Portugese?), which renders them useless for the majority of users.
>
> BioMoby web services are all about creating interoperable resources.  
> Introducing the Tower of Babel effect isn't going to help. I hope I  
> don't sound arrogant, but unless there are scientists out there using  
> BioMoby for research into language itself, archeology or culture, I  
> really fail to see why we need anything but the "de facto" standard  
> language for research. (No, I'm not a native Englisch speaker...)
>
> Is there actually any major bioinformatics resource that supports  
> translations? I can't think of any, but maybe I should write an e-mail  
> to the NCBI, DDBJ, EBI et al. and request Dutch translations of Genbank,  
> PubMed, KEGG, Uniprot, Ensembl, etc. Might be fun to see if and how they  
> repsond :)...
>
>> but for the sake of technical simplicity, I'd stick with just tracking  
>> the language rather than having multiple values in the registry.
>
> For even more simplicity I'd opt for hardcoding the language to English.  
> Now let's hope the native English speakers are not going to fight over  
> whether international English means Australian, UK, American, Canadian,  
> or yet another English. If that happens I'm voting for Dinglish :).
>
> Just my ? 0.02
>
> Cheers,
>
> Pi
>
>>  Multilingual descriptions could be offloaded to the LSID metadata  
>> perhaps if people really want it.
>>
>> Mes 0.02$ canadiens,
>>
>> Paul
>>
>> Mark Wilkinson wrote:
>>> Should we allow registration of objects, service-types and namespaces  
>>> in foreign languages also?  If so, then we need to re-think the entire  
>>> way we manage the ontology, and assign unique id numbers to each node,  
>>> where the rdf:label of the node can have multiple languages, rather  
>>> than having the node named by its label.
>>>
>>> ...can... worms... but it's probably the "right thing to do"...
>>>
>>> M
>>>
>>>
>>>
>>> On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart  
>>> <jason.e.stewart at gmail.com> wrote:
>>>
>>>> Hey all,
>>>>
>>>> Here's what I have found out.
>>>>
>>>> I don't believe that changing the current parser for Central.pm is
>>>> going to help the situation. I have looked and besides special API's
>>>> like the one implemented by LibXML::Reader, the application is always
>>>> required to maintain the status of xml:lang using the standard SAX and
>>>> DOM API's - for Java or for Perl.
>>>>
>>>> We will have to preserve the information in the DB, so a decision
>>>> needs to be made on what level the xml:lang should be used - only for
>>>> descriptions?? or for the whole registration?? At the moment I don't
>>>> see any reason to use it for more than the description - how do people
>>>> feel about this? Changing this should require adding one column to the
>>>> DB.
>>>>
>>>> Finally, do we want registration with multiple descriptions? That will
>>>> probably require a significant change in the DB - a new table for
>>>> linking descriptions to registrations. Are people happy about that?
>>>>
>>>> Cheers, jas.
>>>> _______________________________________________
>>>> MOBY-dev mailing list
>>>> MOBY-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>>
>>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada

From gordonp at ucalgary.ca  Mon May 26 19:10:58 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 26 May 2008 17:10:58 -0600
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>	<483B089E.20602@ucalgary.ca>	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <483B4382.8020108@ucalgary.ca>

I will reiterate that I think the language of the text should be noted 
in the database somewhere, but that we shouldn't support multi-liguality 
for a single entry (that's too much work).  While we can pressure people 
into using English for the public central registry, I see no reason to 
force English on a boutique registry in Botswana (for example) just 
because we were too lazy to program in an extra column in the DB.  I am 
also thinking about the potential usefulness of Moby outside of science...

Mark Wilkinson wrote:
> personally, I tend to think we *should* be using the multi-lingual 
> capabilities of XML more than we are!  The idea is not to introduce a 
> tower of Babel, but rather to embrace as many languages as possible in 
> our infrastructure!  to be inclusive, rather than exclusive!
>
> this does, however, require extensive re-tooling of the software.  I 
> wonder if it is something that is best left for Moby 2.0 (and planned 
> from the start) rather than hacked into Moby 1.0?
>
> M
>
>
>
>
> On Mon, 26 May 2008 15:41:34 -0700, Pieter Neerincx 
> <pieter.neerincx at gmail.com> wrote:
>
>> Hi all,
>>
>> On 26 May 2008, at 20:59, Paul Gordon wrote:
>>
>>> I think we are mostly polyglots on this list,
>>
>> I'm a polyglot when I'm on holiday or in a pub maybe, but when I'm 
>> talking bioinformatics stuff I'm a strict monoglot! Before we open 
>> that can of worms: do we actually need translations? Did anyone 
>> request support for different languages? Mark mentioned someone did 
>> on the last developer meeting, but I didn't see anyone chime in on 
>> this list with a request for other languages. I only noticed a few 
>> objects and services in the official public Central containing 
>> descriptions in Spanish (or is it Portugese?), which renders them 
>> useless for the majority of users.
>>
>> BioMoby web services are all about creating interoperable resources. 
>> Introducing the Tower of Babel effect isn't going to help. I hope I 
>> don't sound arrogant, but unless there are scientists out there using 
>> BioMoby for research into language itself, archeology or culture, I 
>> really fail to see why we need anything but the "de facto" standard 
>> language for research. (No, I'm not a native Englisch speaker...)
>>
>> Is there actually any major bioinformatics resource that supports 
>> translations? I can't think of any, but maybe I should write an 
>> e-mail to the NCBI, DDBJ, EBI et al. and request Dutch translations 
>> of Genbank, PubMed, KEGG, Uniprot, Ensembl, etc. Might be fun to see 
>> if and how they repsond :)...
>>
>>> but for the sake of technical simplicity, I'd stick with just 
>>> tracking the language rather than having multiple values in the 
>>> registry.
>>
>> For even more simplicity I'd opt for hardcoding the language to 
>> English. Now let's hope the native English speakers are not going to 
>> fight over whether international English means Australian, UK, 
>> American, Canadian, or yet another English. If that happens I'm 
>> voting for Dinglish :).
>>
>> Just my ? 0.02
>>
>> Cheers,
>>
>> Pi
>>
>>>  Multilingual descriptions could be offloaded to the LSID metadata 
>>> perhaps if people really want it.
>>>
>>> Mes 0.02$ canadiens,
>>>
>>> Paul
>>>
>>> Mark Wilkinson wrote:
>>>> Should we allow registration of objects, service-types and 
>>>> namespaces in foreign languages also?  If so, then we need to 
>>>> re-think the entire way we manage the ontology, and assign unique 
>>>> id numbers to each node, where the rdf:label of the node can have 
>>>> multiple languages, rather than having the node named by its label.
>>>>
>>>> ...can... worms... but it's probably the "right thing to do"...
>>>>
>>>> M
>>>>
>>>>
>>>>
>>>> On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart 
>>>> <jason.e.stewart at gmail.com> wrote:
>>>>
>>>>> Hey all,
>>>>>
>>>>> Here's what I have found out.
>>>>>
>>>>> I don't believe that changing the current parser for Central.pm is
>>>>> going to help the situation. I have looked and besides special API's
>>>>> like the one implemented by LibXML::Reader, the application is always
>>>>> required to maintain the status of xml:lang using the standard SAX 
>>>>> and
>>>>> DOM API's - for Java or for Perl.
>>>>>
>>>>> We will have to preserve the information in the DB, so a decision
>>>>> needs to be made on what level the xml:lang should be used - only for
>>>>> descriptions?? or for the whole registration?? At the moment I don't
>>>>> see any reason to use it for more than the description - how do 
>>>>> people
>>>>> feel about this? Changing this should require adding one column to 
>>>>> the
>>>>> DB.
>>>>>
>>>>> Finally, do we want registration with multiple descriptions? That 
>>>>> will
>>>>> probably require a significant change in the DB - a new table for
>>>>> linking descriptions to registrations. Are people happy about that?
>>>>>
>>>>> Cheers, jas.
>>>>> _______________________________________________
>>>>> MOBY-dev mailing list
>>>>> MOBY-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>
>>>>
>>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>

From jason.e.stewart at gmail.com  Wed May 28 06:30:09 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Wed, 28 May 2008 16:00:09 +0530
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <483B4382.8020108@ucalgary.ca>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
	<483B4382.8020108@ucalgary.ca>
Message-ID: <41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>

Hey All,

I have heard three ideas:

1) allow registration with multiple languages per instance
2) stick with english only
3) register with one language, but record the language

Of these cases I believe that using xml:lang is only valuable if 1) is chosen.

My understanding of the i18n support in general and xml:lang in
particular is to support a user setting his/her preferred language and
getting data in that language if it is available. So if the Dashboard
allowed us to set our preferred language to German and then retrieved
descriptions in German or fell back to English then I think we could
argue the effort was valuable.

But for case 3) I feel it would be a waste of effort - it wouldn't
change the existing user experience - it would just put a label on
what we already know. I don't believe users would search for services
with Spanish-only descriptions - but I do believe they would ask for
descriptions in Spanish if they existed.

I'm not here to advise whether we should or shouldn't support xml:lang
- only to advise that my personal opinion is that level of re-coding
is only useful if we support multiple descriptions in different
languages.

Personally I don't think there is a high demand in bioinformatics for
this feature - so I would advise against it. On the other hand - Mark
has pointed out that he hopes this work will have impact outside
bioinformataics. I can also add that the amount of code change is
pretty small for MOBY Central - the real impact is the change in the
clients to set language preferences.

So I am torn. I'm happy to make the change in MOBY Central - but it
won't be useful until the clients support it.

What do people say?

Cheers, jas.

2008/5/27 Paul Gordon <gordonp at ucalgary.ca>:
> I will reiterate that I think the language of the text should be noted in
> the database somewhere, but that we shouldn't support multi-liguality for a
> single entry (that's too much work).  While we can pressure people into
> using English for the public central registry, I see no reason to force
> English on a boutique registry in Botswana (for example) just because we
> were too lazy to program in an extra column in the DB.  I am also thinking
> about the potential usefulness of Moby outside of science...
>
> Mark Wilkinson wrote:
>>
>> personally, I tend to think we *should* be using the multi-lingual
>> capabilities of XML more than we are!  The idea is not to introduce a tower
>> of Babel, but rather to embrace as many languages as possible in our
>> infrastructure!  to be inclusive, rather than exclusive!
>>
>> this does, however, require extensive re-tooling of the software.  I
>> wonder if it is something that is best left for Moby 2.0 (and planned from
>> the start) rather than hacked into Moby 1.0?
>>
>> M
>>
>>
>>
>>
>> On Mon, 26 May 2008 15:41:34 -0700, Pieter Neerincx
>> <pieter.neerincx at gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> On 26 May 2008, at 20:59, Paul Gordon wrote:
>>>
>>>> I think we are mostly polyglots on this list,
>>>
>>> I'm a polyglot when I'm on holiday or in a pub maybe, but when I'm
>>> talking bioinformatics stuff I'm a strict monoglot! Before we open that can
>>> of worms: do we actually need translations? Did anyone request support for
>>> different languages? Mark mentioned someone did on the last developer
>>> meeting, but I didn't see anyone chime in on this list with a request for
>>> other languages. I only noticed a few objects and services in the official
>>> public Central containing descriptions in Spanish (or is it Portugese?),
>>> which renders them useless for the majority of users.
>>>
>>> BioMoby web services are all about creating interoperable resources.
>>> Introducing the Tower of Babel effect isn't going to help. I hope I don't
>>> sound arrogant, but unless there are scientists out there using BioMoby for
>>> research into language itself, archeology or culture, I really fail to see
>>> why we need anything but the "de facto" standard language for research. (No,
>>> I'm not a native Englisch speaker...)
>>>
>>> Is there actually any major bioinformatics resource that supports
>>> translations? I can't think of any, but maybe I should write an e-mail to
>>> the NCBI, DDBJ, EBI et al. and request Dutch translations of Genbank,
>>> PubMed, KEGG, Uniprot, Ensembl, etc. Might be fun to see if and how they
>>> repsond :)...
>>>
>>>> but for the sake of technical simplicity, I'd stick with just tracking
>>>> the language rather than having multiple values in the registry.
>>>
>>> For even more simplicity I'd opt for hardcoding the language to English.
>>> Now let's hope the native English speakers are not going to fight over
>>> whether international English means Australian, UK, American, Canadian, or
>>> yet another English. If that happens I'm voting for Dinglish :).
>>>
>>> Just my ? 0.02
>>>
>>> Cheers,
>>>
>>> Pi
>>>
>>>>  Multilingual descriptions could be offloaded to the LSID metadata
>>>> perhaps if people really want it.
>>>>
>>>> Mes 0.02$ canadiens,
>>>>
>>>> Paul
>>>>
>>>> Mark Wilkinson wrote:
>>>>>
>>>>> Should we allow registration of objects, service-types and namespaces
>>>>> in foreign languages also?  If so, then we need to re-think the entire way
>>>>> we manage the ontology, and assign unique id numbers to each node, where the
>>>>> rdf:label of the node can have multiple languages, rather than having the
>>>>> node named by its label.
>>>>>
>>>>> ...can... worms... but it's probably the "right thing to do"...
>>>>>
>>>>> M
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart
>>>>> <jason.e.stewart at gmail.com> wrote:
>>>>>
>>>>>> Hey all,
>>>>>>
>>>>>> Here's what I have found out.
>>>>>>
>>>>>> I don't believe that changing the current parser for Central.pm is
>>>>>> going to help the situation. I have looked and besides special API's
>>>>>> like the one implemented by LibXML::Reader, the application is always
>>>>>> required to maintain the status of xml:lang using the standard SAX and
>>>>>> DOM API's - for Java or for Perl.
>>>>>>
>>>>>> We will have to preserve the information in the DB, so a decision
>>>>>> needs to be made on what level the xml:lang should be used - only for
>>>>>> descriptions?? or for the whole registration?? At the moment I don't
>>>>>> see any reason to use it for more than the description - how do people
>>>>>> feel about this? Changing this should require adding one column to the
>>>>>> DB.
>>>>>>
>>>>>> Finally, do we want registration with multiple descriptions? That will
>>>>>> probably require a significant change in the DB - a new table for
>>>>>> linking descriptions to registrations. Are people happy about that?
>>>>>>
>>>>>> Cheers, jas.
>>>>>> _______________________________________________
>>>>>> MOBY-dev mailing list
>>>>>> MOBY-dev at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> MOBY-dev mailing list
>>>> MOBY-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>


From martin.senger at gmail.com  Wed May 28 06:42:20 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 28 May 2008 18:42:20 +0800
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
	<483B4382.8020108@ucalgary.ca>
	<41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>
Message-ID: <4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>

> 1) allow registration with multiple languages per instance
> 2) stick with english only
> 3) register with one language, but record the language


> Of these cases I believe that using xml:lang is only valuable if 1) is
> chosen.
>

When we met in February, I understood that we decided to have option 3. And
doing it by using xml:lang - I do not see why you are saying that it cannot
be used for option 3.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From jason.e.stewart at gmail.com  Wed May 28 08:11:15 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Wed, 28 May 2008 17:41:15 +0530
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
	<483B4382.8020108@ucalgary.ca>
	<41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>
	<4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>
Message-ID: <41c1ade50805280511l1173a54ao20b1ee6ed7395920@mail.gmail.com>

Hey Martin,

2008/5/28 Martin Senger <martin.senger at gmail.com>:
>> 1) allow registration with multiple languages per instance
>> 2) stick with english only
>> 3) register with one language, but record the language
>
>
>> Of these cases I believe that using xml:lang is only valuable if 1) is
>> chosen.

> When we met in February, I understood that we decided to have option 3. And
> doing it by using xml:lang - I do not see why you are saying that it cannot
> be used for option 3.

Thanks - I guess I need to clarify. I'm definitely new to the scene
and so I am trying to play catchup with what has already been
discussed.

Yes, xml:lang can be used without any problem for 3) - but my point
was that it wouldn't change the current user experience of MOBY. I
wasn't understanding how it would change what users do. If a user
registers a service and provides the description in Spanish - it will
be stored as xml:lang="es" in the DB. But I don't believe that users
will look for services based on the value of that xml:lang attribute -
the description will be returned to them (in Spanish) just as it was
without storing the xml:lang. Perhaps I am missing something important
- so please help me understand if I don't get it.

In my mind, the real value of xml:lang is when it can be used to
return the user information in their preferred language - only
supporting a single language defeats that purpose. That way the
returned descriptions of any registered service will all be in Spanish
if they exist - or English if they do not, or whatever language is
available if English is not present.

I hope this helps clarify what I meant.

Cheers, jas.

From martin.senger at gmail.com  Wed May 28 09:06:11 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 28 May 2008 21:06:11 +0800
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <41c1ade50805280511l1173a54ao20b1ee6ed7395920@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
	<483B4382.8020108@ucalgary.ca>
	<41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>
	<4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>
	<41c1ade50805280511l1173a54ao20b1ee6ed7395920@mail.gmail.com>
Message-ID: <4d93f07c0805280606g2caab44bo4158ca4e29c5020a@mail.gmail.com>

> Yes, xml:lang can be used without any problem for 3) - but my point
> was that it wouldn't change the current user experience of MOBY.


Yes, you are completely right. [That's why I have never taken this language
discussion - and decision - too seriously :-)]

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger

From gordonp at ucalgary.ca  Wed May 28 09:44:29 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 28 May 2008 07:44:29 -0600
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <4d93f07c0805280606g2caab44bo4158ca4e29c5020a@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>	<483B089E.20602@ucalgary.ca>	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>	<483B4382.8020108@ucalgary.ca>	<41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>	<4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>	<41c1ade50805280511l1173a54ao20b1ee6ed7395920@mail.gmail.com>
	<4d93f07c0805280606g2caab44bo4158ca4e29c5020a@mail.gmail.com>
Message-ID: <483D61BD.9090507@ucalgary.ca>

This originally came up because there were places in the Central XML 
that used the xml:lang="en" attribute, but the contents was Spanish.  I 
cannot find these attributes anymore, so the conflict appears to have 
been removed...

Martin Senger wrote:
>> Yes, xml:lang can be used without any problem for 3) - but my point
>> was that it wouldn't change the current user experience of MOBY.
>>     
>
>
> Yes, you are completely right. [That's why I have never taken this language
> discussion - and decision - too seriously :-)]
>
> Martin
>
>   

From markw at illuminae.com  Wed May 28 11:51:50 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 28 May 2008 08:51:50 -0700
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <4d93f07c0805280606g2caab44bo4158ca4e29c5020a@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
	<483B4382.8020108@ucalgary.ca>
	<41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>
	<4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>
	<41c1ade50805280511l1173a54ao20b1ee6ed7395920@mail.gmail.com>
	<4d93f07c0805280606g2caab44bo4158ca4e29c5020a@mail.gmail.com>
Message-ID: <op.ubvfooconbznux@dd0710001l.icapture.ubc.ca>

On Wed, 28 May 2008 06:06:11 -0700, Martin Senger  
<martin.senger at gmail.com> wrote:

> [That's why I have never taken this languag discussion - and decision -  
> too seriously :-)]


Martin set's his e-value cutoff to 10e-45 for these kinds of debates ;-)

LOL!

M



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada

From martin.senger at gmail.com  Tue May  6 09:07:20 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 6 May 2008 10:07:20 +0100
Subject: [MOBY-dev] building jMoby on Mac - help needed
Message-ID: <4d93f07c0805060207t18802a74i3f59b00fff99c5f6@mail.gmail.com>

I am looking for Mac-ists who can help with the building/compiling jMoby on
Mac OS X.

The problem (as identified already during the last Biohackathon in Tokyo) is
the tools.jar library. On Mac, there is no such file because its contents is
part of the default library classes.jar. On other platforms we have to add
the tools.jar separately. That's why there is a "mac profile" in the
xmls/project.pom. But it does not work... (I wonder if it was working in the
past, at all; was it?).

The problematic (the one causing an error under Mac OS X) are the lines (in
build.xml):

    <fileset dir="${java.home}/../lib">
      <include name="tools.jar"/>
    </fileset>

I really do not understand how the profile tag in xmls/project.pom works, or
should work, to make the lines above working. Any help around?

Many thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From martin.senger at gmail.com  Tue May  6 09:58:20 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 6 May 2008 10:58:20 +0100
Subject: [MOBY-dev] where is the service 'ping' documented?
Message-ID: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>

I am looking for the documentation how the 'ping' should work. I think that
it should work like this: "Send an empty mobyContent and get back the
same.". Is this correct?

The only remark about this being documented I found is this one (from Paul):

In any case, the API doc is now up to date in CVS, it will take a while
> to propagate to the Web site...


But I still cannot find where it is. Does anybody know?

Thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From groscurt at mpiz-koeln.mpg.de  Tue May  6 11:52:27 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 06 May 2008 13:52:27 +0200
Subject: [MOBY-dev] biomoby.org gone white
In-Reply-To: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>
References: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>
Message-ID: <4820467B.2010609@mpiz-koeln.mpg.de>

Hi,

if we call biomoby.org (at least in germany) we get a white page....

intended ? ;-)

best
andreas


From martin.senger at gmail.com  Tue May  6 11:57:58 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 6 May 2008 12:57:58 +0100
Subject: [MOBY-dev] biomoby.org gone white
In-Reply-To: <4820467B.2010609@mpiz-koeln.mpg.de>
References: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>
	<4820467B.2010609@mpiz-koeln.mpg.de>
Message-ID: <4d93f07c0805060457m7c4fb0bcxad98543ac1e3ea7d@mail.gmail.com>

> if we call biomoby.org (at least in germany) we get a white page....
>

Interesting. It was still there about a two hours ago...
M.

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From groscurt at mpiz-koeln.mpg.de  Tue May  6 12:07:18 2008
From: groscurt at mpiz-koeln.mpg.de (Andreas Groscurth)
Date: Tue, 06 May 2008 14:07:18 +0200
Subject: [MOBY-dev] biomoby.org gone white
In-Reply-To: <4d93f07c0805060457m7c4fb0bcxad98543ac1e3ea7d@mail.gmail.com>
References: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>	<4820467B.2010609@mpiz-koeln.mpg.de>
	<4d93f07c0805060457m7c4fb0bcxad98543ac1e3ea7d@mail.gmail.com>
Message-ID: <482049F6.9090508@mpiz-koeln.mpg.de>

and now its back to normal.... weird ;-9

Martin Senger wrote:
>> if we call biomoby.org (at least in germany) we get a white page....
>>
>>     
>
> Interesting. It was still there about a two hours ago...
> M.
>
>   



From edward.kawas at gmail.com  Tue May  6 13:10:56 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 6 May 2008 06:10:56 -0700
Subject: [MOBY-dev] where is the service 'ping' documented?
In-Reply-To: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>
References: <4d93f07c0805060258o62f61211g1567cfb334294a56@mail.gmail.com>
Message-ID: <482058ef.2a528c0a.7ee6.ffffedda@mx.google.com>

Hi Martin,

You are correct in the behaviour of the pinger; send empty mobyContent and
get one back.

The only documentation that I am aware of is located at
http://moby.ucalgary.ca/moby/ValidateService?getDeadServices which is
produced by the script.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
Sent: May-06-08 2:58 AM
To: Core developer announcements
Cc: Skofic, Milko (Bioversity)
Subject: [MOBY-dev] where is the service 'ping' documented?

I am looking for the documentation how the 'ping' should work. I think that
it should work like this: "Send an empty mobyContent and get back the
same.". Is this correct?

The only remark about this being documented I found is this one (from Paul):

In any case, the API doc is now up to date in CVS, it will take a while
> to propagate to the Web site...


But I still cannot find where it is. Does anybody know?

Thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From edward.kawas at gmail.com  Tue May  6 13:12:58 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 6 May 2008 06:12:58 -0700
Subject: [MOBY-dev] building jMoby on Mac - help needed
In-Reply-To: <4d93f07c0805060207t18802a74i3f59b00fff99c5f6@mail.gmail.com>
References: <4d93f07c0805060207t18802a74i3f59b00fff99c5f6@mail.gmail.com>
Message-ID: <48205969.0abd720a.6d3e.664c@mx.google.com>

Hi Martin,

Have you seen this link before?
http://maven.apache.org/general.html#tools-jar-dependency

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Martin Senger
Sent: May-06-08 2:07 AM
To: Core developer announcements
Cc: Skofic, Milko (Bioversity)
Subject: [MOBY-dev] building jMoby on Mac - help needed

I am looking for Mac-ists who can help with the building/compiling jMoby on
Mac OS X.

The problem (as identified already during the last Biohackathon in Tokyo) is
the tools.jar library. On Mac, there is no such file because its contents is
part of the default library classes.jar. On other platforms we have to add
the tools.jar separately. That's why there is a "mac profile" in the
xmls/project.pom. But it does not work... (I wonder if it was working in the
past, at all; was it?).

The problematic (the one causing an error under Mac OS X) are the lines (in
build.xml):

    <fileset dir="${java.home}/../lib">
      <include name="tools.jar"/>
    </fileset>

I really do not understand how the profile tag in xmls/project.pom works, or
should work, to make the lines above working. Any help around?

Many thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From martin.senger at gmail.com  Tue May  6 13:26:22 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 6 May 2008 14:26:22 +0100
Subject: [MOBY-dev] building jMoby on Mac - help needed
In-Reply-To: <48205969.0abd720a.6d3e.664c@mx.google.com>
References: <4d93f07c0805060207t18802a74i3f59b00fff99c5f6@mail.gmail.com>
	<48205969.0abd720a.6d3e.664c@mx.google.com>
Message-ID: <4d93f07c0805060626laa1b54x39454275ad1fa633@mail.gmail.com>

> Have you seen this link before?
> http://maven.apache.org/general.html#tools-jar-dependency
>

We have a very similar lines in our dependencies file. They are using
slightly different, perhaps wrong, test for the platform name (roughly
speaking we say "if this is not a Mac" and your link says "if this is a
Sun"). We need a person with a Mac to find what is right and what works.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From martin.senger at gmail.com  Tue May  6 13:37:35 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Tue, 6 May 2008 14:37:35 +0100
Subject: [MOBY-dev] data type suitable as a search filter
Message-ID: <4d93f07c0805060637h5db4c555wc60f384a8b5a0287@mail.gmail.com>

I wonder if somebody can give me an advise.

I have a data type A (whose structure is very close to a simple name/value
pair). In one service, I would like to use this data type as a search
filter. In order to do it, I would need to add there an operator (to
indicate how to treat the value - like, equal, greater than etc.).
Therefore, I think about a new, more specialized data type AWithOperator. My
questions now are:

a) Is there already a data type that can be used to represent an operator
(so I would add it as a new article name into my new AWithOperator?

b) If not, does it mean that I am doing something which I should not? In
which case, what would be the correct way to do so? [Note that the usage of
secondary parameters is out of the question - I think - because the service
will have a collection of search filters and each of them can have different
operator while the secondary parameter is just one for the whole collection.
Correct?]

Thanks,
Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From hao.chen at uni-bielefeld.de  Tue May  6 21:00:20 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Tue, 06 May 2008 23:00:20 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <4d93f07c0805060637h5db4c555wc60f384a8b5a0287@mail.gmail.com>
References: <4d93f07c0805060637h5db4c555wc60f384a8b5a0287@mail.gmail.com>
Message-ID: <1210107620.3268.14.camel@wasser-laptop>

hi, all

 Now I want to register service from XML file with jmoby. and I use the
existing method registerService(), which can receive xmlString as
Parameter. Here is part of my code.

          RegistryImpl register =new RegistryImpl();
          register.registerService(smlString);

but it seems not to work. I am sure that the smlString I used is
correct, because I can register the same one using Dashboard without nay
problem. Did I do something wrong? 

cheers,
hao chen

       


   



From edward.kawas at gmail.com  Wed May  7 03:51:48 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 6 May 2008 20:51:48 -0700
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <1210107620.3268.14.camel@wasser-laptop>
References: <4d93f07c0805060637h5db4c555wc60f384a8b5a0287@mail.gmail.com>
	<1210107620.3268.14.camel@wasser-laptop>
Message-ID: <48212756.1aba720a.21cc.40fc@mx.google.com>

Can you post the XML or send it to the list as an attachment?

Thanks,

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of wasser
Sent: May-06-08 2:00 PM
To: Core developer announcements
Subject: [MOBY-dev] Service registration from XML

hi, all

 Now I want to register service from XML file with jmoby. and I use the
existing method registerService(), which can receive xmlString as
Parameter. Here is part of my code.

          RegistryImpl register =new RegistryImpl();
          register.registerService(smlString);

but it seems not to work. I am sure that the smlString I used is
correct, because I can register the same one using Dashboard without nay
problem. Did I do something wrong? 

cheers,
hao chen

       


   

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From hao.chen at uni-bielefeld.de  Wed May  7 08:22:06 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Wed, 07 May 2008 10:22:06 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <48212756.1aba720a.21cc.40fc@mx.google.com>
References: <4d93f07c0805060637h5db4c555wc60f384a8b5a0287@mail.gmail.com>
	<1210107620.3268.14.camel@wasser-laptop>
	<48212756.1aba720a.21cc.40fc@mx.google.com>
Message-ID: <1210148526.5959.16.camel@wasser-laptop>

Hi, Eddie, 

Here is the XML file named ?TestXMLReg.xml I used.

<registerService>
<Category>moby</Category>
<serviceName>TestXMLReg</serviceName>
<serviceType>Testing</serviceType>
<serviceLSID/>
<authURI>www.techfak.uni-bielefeld.de</authURI>
<signatureURL/>
<URL>http://localhost:8080/axis/services/TestXMLReg</URL>
<contactEmail>webmaster at uni-bielefeld.de</contactEmail>
<authoritativeService>1</authoritativeService>
<Description>a test service.</Description>
<Input>
<Simple articleName="SequenceML">
<objectType>SequenceML</objectType>
</Simple>
</Input>
<secondaryArticles>
<Parameter articleName="Name">
<datatype>String</datatype>
<description/>
</Parameter>
<Parameter articleName="star">
<datatype>Integer</datatype>
<description/>
<default>0</default>
<max>25</max>
<min>0</min>
<enum/>
</Parameter>
<Parameter articleName="isEmpty">
<datatype>Boolean</datatype>
<description/>
<default>false</default>
</Parameter>
</secondaryArticles>
<Output>
<Simple articleName="FASTA_Text">
<objectType>FASTA_Text</objectType>
</Simple>
</Output>
</registerService>

and I write following code to generate XML String within a try block
String regXML="";
BufferedReader in = new BufferedReader(new InputStreamReader(new
FileInputStream("//home//wasser//workspace//TestXMLReg.xml")));
       String str="";
       while((str=in.readLine())!=null){ 
                           regXML+=str;}
cheers
hao chen


On Tue, 2008-05-06 at 20:51 -0700, Edward Kawas wrote:
> Can you post the XML or send it to the list as an attachment?
> 
> Thanks,
> 
> Eddie
> 
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of wasser
> Sent: May-06-08 2:00 PM
> To: Core developer announcements
> Subject: [MOBY-dev] Service registration from XML
> 
> hi, all
> 
>  Now I want to register service from XML file with jmoby. and I use the
> existing method registerService(), which can receive xmlString as
> Parameter. Here is part of my code.
> 
>           RegistryImpl register =new RegistryImpl();
>           register.registerService(smlString);
> 
> but it seems not to work. I am sure that the smlString I used is
> correct, because I can register the same one using Dashboard without nay
> problem. Did I do something wrong? 
> 
> cheers,
> hao chen
> 
>        
> 
> 
>    
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From dmitry.repchevski at bsc.es  Wed May  7 09:26:12 2008
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Wed, 07 May 2008 11:26:12 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <1210148526.5959.16.camel@wasser-laptop>
References: <1210148526.5959.16.camel@wasser-laptop>
Message-ID: <482175B4.50300@bsc.es>

Hello!

I don't know about JMoby, but at first glance you don't add "/n" (for 
unix) into your regXML (must not matter, but...).
[advice] Never concatenate strings with "+" operator - use StringBuffer 
or StringBuilder (java5) instead...
[advice] Also it is always a good idea to close files :-)

|String linebreak = System.getProperty("line.separator"));|

StringBuilder buf = new StringBuilder();
BufferedReader in = new BufferedReader(new FileReader("//home//wasser//workspace//TestXMLReg.xml"));

try {
    String str;
    while((str=in.readLine())!=null) { 
    buf.append(str).append(linebreak);
    }
}
finally { in.close(); }

String regXML = buf.toString();

P.S. sorry for offtopic






From hao.chen at uni-bielefeld.de  Wed May  7 11:10:39 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Wed, 07 May 2008 13:10:39 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <482175B4.50300@bsc.es>
References: <1210148526.5959.16.camel@wasser-laptop> <482175B4.50300@bsc.es>
Message-ID: <1210158639.5959.37.camel@wasser-laptop>


hallo,

thank you for your advice. Yes, I should use methode stringBuffer()
instead  "+" operator. I wrote this code just for test and want to know
if I can register service from xml with methode ?registerService(). 

and if it works , xml string  should be constructed directly without
reading XML from a file. 

cheers 
hao chen

On Wed, 2008-05-07 at 11:26 +0200, Dmitry Repchevsky wrote:
> Hello!
> 
> I don't know about JMoby, but at first glance you don't add "/n" (for 
> unix) into your regXML (must not matter, but...).
> [advice] Never concatenate strings with "+" operator - use StringBuffer 
> or StringBuilder (java5) instead...
> [advice] Also it is always a good idea to close files :-)
> 
> |String linebreak = System.getProperty("line.separator"));|
> 
> StringBuilder buf = new StringBuilder();
> BufferedReader in = new BufferedReader(new FileReader("//home//wasser//workspace//TestXMLReg.xml"));
> 
> try {
>     String str;
>     while((str=in.readLine())!=null) { 
>     buf.append(str).append(linebreak);
>     }
> }
> finally { in.close(); }
> 
> String regXML = buf.toString();
> 
> P.S. sorry for offtopic
> 
> 
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From dmitry.repchevski at bsc.es  Wed May  7 11:37:06 2008
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Wed, 07 May 2008 13:37:06 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <1210158639.5959.37.camel@wasser-laptop>
References: <1210158639.5959.37.camel@wasser-laptop>
Message-ID: <48219462.9040302@bsc.es>

It is just happened to me,
Have you tried to put XML header? (<?xml version='1.0' encoding='UTF-8'?>)
Formally your document is not an XML document without it...

Cheers,

Dmitry




From dmitry.repchevski at bsc.es  Wed May  7 11:52:27 2008
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Wed, 07 May 2008 13:52:27 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <1210158639.5959.37.camel@wasser-laptop>
References: <1210158639.5959.37.camel@wasser-laptop>
Message-ID: <482197FB.40105@bsc.es>

I have tested it with my API and got:

"Malformed email - must be a valid email address of the form 
name at organization.foo"

Error... So this is the error with XML itself :-)

Cheers,

Dmitry


From hao.chen at uni-bielefeld.de  Wed May  7 12:02:28 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Wed, 07 May 2008 14:02:28 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <48219462.9040302@bsc.es>
References: <1210158639.5959.37.camel@wasser-laptop> <48219462.9040302@bsc.es>
Message-ID: <1210161748.14207.10.camel@wasser-laptop>

hi, Dmitry

according to Biomoby API
(http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/API/org/biomoby/registry/Central/Registry.html) is an XML string with the following structure:

<registerService>
          <Category>moby</Category> <!-- one of 'moby', 'cgi', 'soap' -->
          <serviceName>YourServiceNameHere</serviceName>
          <serviceType>TypeOntologyTerm</serviceType>
          <authURI>your.URI.here</authURI>
          <signatureURL> http://some.URL.org/path/to/RDF/file </signatureURL>
          <URL>http://URL.to.your/Service.script</URL>;
          <contactEmail>your_name at contact.address.com</contactEmail>
          <authoritativeService>1 | 0 </authoritativeService>
          <Description><![CDATA[
                human readable COMPREHENSIVE description of your service]]>
          </Description>
          <Input>
               <!-- zero or more Primary (Simple and/or Collection) articles -->
               <!-- each of these articles will appear EXACTLY ONCE in the input to the service -->
          </Input>
          <secondaryArticles>
               <!-- zero or more INPUT Secondary (Parameter) articles -->
               <!-- each of these articles will appear EXACTLY ONCE in the output from the service -->
          </secondaryArticles>
          <Output>
               <!-- zero or more Primary (Simple and/or Collection) articles --> 
          </Output>
</registerService>

I think the XML String for the method registerService() should be used without XML header.

cheers
hao chen


On Wed, 2008-05-07 at 13:37 +0200, Dmitry Repchevsky wrote:
> It is just happened to me,
> Have you tried to put XML header? (<?xml version='1.0' encoding='UTF-8'?>)
> Formally your document is not an XML document without it...
> 
> Cheers,
> 
> Dmitry
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From hao.chen at uni-bielefeld.de  Wed May  7 13:12:01 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Wed, 07 May 2008 15:12:01 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <482197FB.40105@bsc.es>
References: <1210158639.5959.37.camel@wasser-laptop> <482197FB.40105@bsc.es>
Message-ID: <1210165921.14645.11.camel@wasser-laptop>

hi,? Dmitry

I use the correct email address Format. It seems that the program of our
Forum changed email symbol to "at", so you get the "Malformed email"
Error. I send the Email now as attachment to the list. 

On Wed, 2008-05-07 at 13:52 +0200, Dmitry Repchevsky wrote:
> I have tested it with my API and got:
> 
> "Malformed email - must be a valid email address of the form 
> name at organization.foo"
> 
> Error... So this is the error with XML itself :-)
> 
> Cheers,
> 
> Dmitry
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
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From edward.kawas at gmail.com  Wed May  7 13:52:21 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 7 May 2008 06:52:21 -0700
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <1210165921.14645.11.camel@wasser-laptop>
References: <1210158639.5959.37.camel@wasser-laptop> <482197FB.40105@bsc.es>
	<1210165921.14645.11.camel@wasser-laptop>
Message-ID: <4821b419.1dba720a.0a3f.65eb@mx.google.com>

Hi Hao Chen,

Okay, now that I have examined how you are trying to do things, I have a few things to say:

The class RegistryImpl in org.biomoby.registry was never implemented. I created that class a long time ago when I was going to try to write the registry in JAVA. Sorry for the confusion.

You should try using org.biomoby.client.CentralImpl and the method registerService(). Unfortunately, it doesn?t consume a string of XML, but I am sure that you could dig deeper and see how that method performs the registerService and mimic it.

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of wasser
Sent: May-07-08 6:12 AM
To: Core developer announcements
Subject: Re: [MOBY-dev] Service registration from XML

hi,? Dmitry

I use the correct email address Format. It seems that the program of our Forum changed email symbol to "at", so you get the "Malformed email"
Error. I send the Email now as attachment to the list. 

On Wed, 2008-05-07 at 13:52 +0200, Dmitry Repchevsky wrote:
> I have tested it with my API and got:
> 
> "Malformed email - must be a valid email address of the form 
> name at organization.foo"
> 
> Error... So this is the error with XML itself :-)
> 
> Cheers,
> 
> Dmitry
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev




From gordonp at ucalgary.ca  Wed May  7 14:42:31 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 07 May 2008 08:42:31 -0600
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <4821b419.1dba720a.0a3f.65eb@mx.google.com>
References: <1210158639.5959.37.camel@wasser-laptop>
	<482197FB.40105@bsc.es>	<1210165921.14645.11.camel@wasser-laptop>
	<4821b419.1dba720a.0a3f.65eb@mx.google.com>
Message-ID: <4821BFD7.4050507@ucalgary.ca>

Or preferably, create a MobyService object and call all the set() 
methods to populate it.  Then call registerService on the MobyService 
object.  There is an example of this in 
moby-live/Java/src/Clients/ServletTester.java.  No manual XML required, 
which is part of the point of having an Java API ;-)

Edward Kawas wrote:
> Hi Hao Chen,
>
> Okay, now that I have examined how you are trying to do things, I have a few things to say:
>
> The class RegistryImpl in org.biomoby.registry was never implemented. I created that class a long time ago when I was going to try to write the registry in JAVA. Sorry for the confusion.
>
> You should try using org.biomoby.client.CentralImpl and the method registerService(). Unfortunately, it doesn?t consume a string of XML, but I am sure that you could dig deeper and see how that method performs the registerService and mimic it.
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of wasser
> Sent: May-07-08 6:12 AM
> To: Core developer announcements
> Subject: Re: [MOBY-dev] Service registration from XML
>
> hi,? Dmitry
>
> I use the correct email address Format. It seems that the program of our Forum changed email symbol to "at", so you get the "Malformed email"
> Error. I send the Email now as attachment to the list. 
>
> On Wed, 2008-05-07 at 13:52 +0200, Dmitry Repchevsky wrote:
>   
>> I have tested it with my API and got:
>>
>> "Malformed email - must be a valid email address of the form 
>> name at organization.foo"
>>
>> Error... So this is the error with XML itself :-)
>>
>> Cheers,
>>
>> Dmitry
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>     
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> !DSPAM:60005,4821b1ba109503177825363!
>
>
>
>   


From martin.senger at gmail.com  Thu May  8 08:22:04 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 8 May 2008 09:22:04 +0100
Subject: [MOBY-dev] can not generate service skeleton
In-Reply-To: <1203522403.11381.6.camel@andreas.dhcp.studentenwerk-bielefeld.de>
References: <1203522403.11381.6.camel@andreas.dhcp.studentenwerk-bielefeld.de>
Message-ID: <4d93f07c0805080122i47acb60dg98986d9b28d14cfe@mail.gmail.com>

>  I got this error


Could you paste the error here, please?

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From hao.chen at uni-bielefeld.de  Thu May  8 09:08:50 2008
From: hao.chen at uni-bielefeld.de (wasser)
Date: Thu, 08 May 2008 11:08:50 +0200
Subject: [MOBY-dev] Service registration from XML
In-Reply-To: <4821BFD7.4050507@ucalgary.ca>
References: <1210158639.5959.37.camel@wasser-laptop> <482197FB.40105@bsc.es>
	<1210165921.14645.11.camel@wasser-laptop>
	<4821b419.1dba720a.0a3f.65eb@mx.google.com>
	<4821BFD7.4050507@ucalgary.ca>
Message-ID: <1210237730.13084.2.camel@wasser-laptop>

hi, Paul

Thanks for the hint. It works great. 



From sneumann at ipb-halle.de  Fri May  9 08:03:49 2008
From: sneumann at ipb-halle.de (sneumann)
Date: Fri, 09 May 2008 10:03:49 +0200
Subject: [MOBY-dev] Dashboard Service Results missing Tab
Message-ID: <1210320229.31656.135.camel@lathan.ipb-sub.ipb-halle.de>

Hi,

we have a moby service which we'd like to test drive 
in the moby-dashboard. Invocation is fine, 
and I see the "Service Results -> All" tab with my data.

We have a second Dashboard (on windows, which shouldn't matter) 
which shows -- for the same service and the same input --
a second tab "Record" with a "moby-whale-icon" 
next to the "All" tab. This contains the preformatted text instead of 

<moby:Simple moby:articleName="record">
        <moby:String moby:id="ACCESSION: PB000122&#xA;RECORD_TITLE: ...
</moby:Simple>

This dashboard also has a "Simple Moby Text"
in the drop-down box in the lower right of the "Service Results",
whereas I have only Plain Text and XML Tree. 

I checked CVS logs and docs/ChangeLog, but couldn't spot 
anything relevant. Have there been any changes recently ?

The service in question is MassBank_Simple_2 on testing registry.

Yours,
Steffen


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

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From martin.senger at gmail.com  Fri May  9 09:54:12 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 9 May 2008 10:54:12 +0100
Subject: [MOBY-dev] Dashboard Service Results missing Tab
In-Reply-To: <1210320229.31656.135.camel@lathan.ipb-sub.ipb-halle.de>
References: <1210320229.31656.135.camel@lathan.ipb-sub.ipb-halle.de>
Message-ID: <4d93f07c0805090254k5bf9ecdbqdf4db7327db596e3@mail.gmail.com>

Hi,

The differences in the number of result viewers in the SimpleClient panel in
the Dashboard are caused by the presence (or not presence) of the Java
classes representing the bIomoby data type. These classes are part of the
MoSeS system (more about it can be found on the jMoby pages). You can have
these classes on every machine by invoking:

ant moses-datatypes

(make sure that your build.properties file contains a property
"registry.cache.dir" pointing to a directory with your local cache - the
same directory that you can see in the Dashboard in the RegistryBrowser
panel).

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From sneumann at ipb-halle.de  Fri May  9 10:58:02 2008
From: sneumann at ipb-halle.de (sneumann)
Date: Fri, 09 May 2008 12:58:02 +0200
Subject: [MOBY-dev] Dashboard Service Results missing Tab
In-Reply-To: <4d93f07c0805090254k5bf9ecdbqdf4db7327db596e3@mail.gmail.com>
References: <1210320229.31656.135.camel@lathan.ipb-sub.ipb-halle.de>
	<4d93f07c0805090254k5bf9ecdbqdf4db7327db596e3@mail.gmail.com>
Message-ID: <1210330682.31656.151.camel@lathan.ipb-sub.ipb-halle.de>

On Fr, 2008-05-09 at 10:54 +0100, Martin Senger wrote:
> ant moses-datatypes
Yup, worked like a charm!

Thanks,
Steffen


-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

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From sneumann at ipb-halle.de  Fri May  9 11:21:07 2008
From: sneumann at ipb-halle.de (sneumann)
Date: Fri, 09 May 2008 13:21:07 +0200
Subject: [MOBY-dev] Calling Moby from R / SSOAP
Message-ID: <1210332068.1475.8.camel@lathan.ipb-sub.ipb-halle.de>

Hi again, 

I am currently figuring how to call Moby Services manually 
using the R client package SSOAP:

Creating the service object works fine:

wsdl = "http://.../axis/services/myservice?wsdl"
service <- processWSDL(wsdl)

but the SSOAP has some kind of WSDL compiler 
which wants to create R classes as stubs to the SOAP:

client = genSOAPClientInterface(def=service, verbose = TRUE)

and this breaks, AFAICS because SSOAP is trying to map input 
and output types for the method calls. An example for the KEGG WSDL 
is given below. 

Do I see it correctly that the SSOAP stub writing has to be changed,
so that in the absence of <type> definitions I pass the arguments 
as encoded stuff in the body ? Has anybody experience with that,
or could give me (specific) links into documentation ?

Yours,
Steffen

from KEGG.wsdl:

	<definitions name="KEGG_v4.1" ... targetNamespace="SOAP/KEGG">
	  <types>
	    <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" targetNamespace="SOAP/KEGG">
	      <xsd:import namespace="http://schemas.xmlsoap.org/soap/encoding/"/>
	      <xsd:import namespace="http://schemas.xmlsoap.org/wsdl/"/>
	      <!-- common variable -->
	      <xsd:complexType name="ArrayOfstring">
	      ...

translates into:

	str(KEGG at types)	
	Formal class 'SchemaCollection' [package "SSOAP"] with 1 slots
	  ..@ .Data:List of 1
	  .. ..$ :Formal class 'SchemaTypes' [package "SSOAP"] with 1 slots
	  .. .. .. ..@ .Data:List of 9
	  .. .. .. .. ..$ :List of 2
	  .. .. .. .. .. ..$ name      : chr "ArrayOfstring"
	  .. .. .. .. .. ..$ definition:Formal class 'ArrayType' [package "SSOAP"] with 8 slots
	  .. .. .. .. .. .. .. ..@ elementType  : chr "xsd:string"
	  .. .. .. .. .. .. .. ..@ elType       :Formal class 'PrimitiveSOAPType' [package "SSOAP"] with 5 slots
	  .. .. .. .. .. .. .. .. .. ..@ fromConverter:function ()
	  .. .. .. .. .. .. .. .. .. ..@ toConverter  :function (x, ...)
	  .. .. .. .. .. .. .. .. .. ..@ name         : chr "string"
	  .. .. .. .. .. .. .. .. .. ..@ ns           : chr "xsd"
	  .. .. .. .. .. .. .. .. .. ..@ nsuri        : chr "http://www.w3.org/2001/XMLSchema"
	  .. .. .. .. .. .. .. ..@ dims         : int NA
	  .. .. .. .. .. .. .. ..@ fromConverter:function ()
	  .. .. .. .. .. .. .. ..@ toConverter  :function ()
	  .. .. .. .. .. .. .. ..@ name         : chr "ArrayOfstring"
	  .. .. .. .. .. .. .. ..@ ns           : chr(0)
	  .. .. .. .. .. .. .. ..@ nsuri        : chr(0)
	  .. .. .. .. .. ..- attr(*, "class")= chr "WSDLTypeDescription"
... 

-- 
IPB Halle                    AG Massenspektrometrie & Bioinformatik
Dr. Steffen Neumann          http://www.IPB-Halle.DE
Weinberg 3                   http://msbi.bic-gh.de
06120 Halle                  Tel. +49 (0) 345 5582 - 1470
                                  +49 (0) 345 5582 - 0
sneumann(at)IPB-Halle.DE     Fax. +49 (0) 345 5582 - 1409

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From gordonp at ucalgary.ca  Fri May  9 14:00:24 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 09 May 2008 08:00:24 -0600
Subject: [MOBY-dev] Calling Moby from R / SSOAP
In-Reply-To: <1210332068.1475.8.camel@lathan.ipb-sub.ipb-halle.de>
References: <1210332068.1475.8.camel@lathan.ipb-sub.ipb-halle.de>
Message-ID: <482458F8.4080808@ucalgary.ca>

Hi Steffen,

Yes, there is no XML Schema for Moby WSDL, because we allow inheritence 
at the tag level, which would make such a schema impossible.  So you 
would need to create an R library that creates the Moby XML message 
envelope, and send that string-encoded (as well as a parser for 
receiving).  While I'm quite familiar with R (I rewrote part of RMA), I 
haven't used any XML parsing facilities, so I can't provide any advice 
there...

Regards,

Paul

sneumann wrote:
> Hi again, 
>
> I am currently figuring how to call Moby Services manually 
> using the R client package SSOAP:
>
> Creating the service object works fine:
>
> wsdl = "http://.../axis/services/myservice?wsdl"
> service <- processWSDL(wsdl)
>
> but the SSOAP has some kind of WSDL compiler 
> which wants to create R classes as stubs to the SOAP:
>
> client = genSOAPClientInterface(def=service, verbose = TRUE)
>
> and this breaks, AFAICS because SSOAP is trying to map input 
> and output types for the method calls. An example for the KEGG WSDL 
> is given below. 
>
> Do I see it correctly that the SSOAP stub writing has to be changed,
> so that in the absence of <type> definitions I pass the arguments 
> as encoded stuff in the body ? Has anybody experience with that,
> or could give me (specific) links into documentation ?
>
> Yours,
> Steffen
>
> from KEGG.wsdl:
>
> 	<definitions name="KEGG_v4.1" ... targetNamespace="SOAP/KEGG">
> 	  <types>
> 	    <xsd:schema xmlns:xsd="http://www.w3.org/2001/XMLSchema" targetNamespace="SOAP/KEGG">
> 	      <xsd:import namespace="http://schemas.xmlsoap.org/soap/encoding/"/>
> 	      <xsd:import namespace="http://schemas.xmlsoap.org/wsdl/"/>
> 	      <!-- common variable -->
> 	      <xsd:complexType name="ArrayOfstring">
> 	      ...
>
> translates into:
>
> 	str(KEGG at types)	
> 	Formal class 'SchemaCollection' [package "SSOAP"] with 1 slots
> 	  ..@ .Data:List of 1
> 	  .. ..$ :Formal class 'SchemaTypes' [package "SSOAP"] with 1 slots
> 	  .. .. .. ..@ .Data:List of 9
> 	  .. .. .. .. ..$ :List of 2
> 	  .. .. .. .. .. ..$ name      : chr "ArrayOfstring"
> 	  .. .. .. .. .. ..$ definition:Formal class 'ArrayType' [package "SSOAP"] with 8 slots
> 	  .. .. .. .. .. .. .. ..@ elementType  : chr "xsd:string"
> 	  .. .. .. .. .. .. .. ..@ elType       :Formal class 'PrimitiveSOAPType' [package "SSOAP"] with 5 slots
> 	  .. .. .. .. .. .. .. .. .. ..@ fromConverter:function ()
> 	  .. .. .. .. .. .. .. .. .. ..@ toConverter  :function (x, ...)
> 	  .. .. .. .. .. .. .. .. .. ..@ name         : chr "string"
> 	  .. .. .. .. .. .. .. .. .. ..@ ns           : chr "xsd"
> 	  .. .. .. .. .. .. .. .. .. ..@ nsuri        : chr "http://www.w3.org/2001/XMLSchema"
> 	  .. .. .. .. .. .. .. ..@ dims         : int NA
> 	  .. .. .. .. .. .. .. ..@ fromConverter:function ()
> 	  .. .. .. .. .. .. .. ..@ toConverter  :function ()
> 	  .. .. .. .. .. .. .. ..@ name         : chr "ArrayOfstring"
> 	  .. .. .. .. .. .. .. ..@ ns           : chr(0)
> 	  .. .. .. .. .. .. .. ..@ nsuri        : chr(0)
> 	  .. .. .. .. .. ..- attr(*, "class")= chr "WSDLTypeDescription"
> ... 
>
>   
> ------------------------------------------------------------------------
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
> !DSPAM:60005,48243206109502520622991!
>   


From jason.e.stewart at gmail.com  Sat May 10 06:02:55 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Sat, 10 May 2008 11:32:55 +0530
Subject: [MOBY-dev] Calling Moby from R / SSOAP
In-Reply-To: <482458F8.4080808@ucalgary.ca>
References: <1210332068.1475.8.camel@lathan.ipb-sub.ipb-halle.de>
	<482458F8.4080808@ucalgary.ca>
Message-ID: <41c1ade50805092302x1b1ad07bnc2d5e52557fad012@mail.gmail.com>

Hi Paul,

2008/5/9 Paul Gordon <gordonp at ucalgary.ca>:

> Yes, there is no XML Schema for Moby WSDL, because we allow inheritence at
> the tag level, which would make such a schema impossible.  So you would need
> to create an R library that creates the Moby XML message envelope, and send
> that string-encoded (as well as a parser for receiving).

I've run into this same problem with XML::Compile with Perl... it
assumes the existence of WSDL and XML schemas to do its mapping
between Perl <=> XML...

I guess I'm needing to know how the object mapping should be done. Is
there a recommendation someplace for how to map MOBY objects to XML
and back?

Thanks, jas.


From gordonp at ucalgary.ca  Sat May 10 22:39:06 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Sat, 10 May 2008 16:39:06 -0600
Subject: [MOBY-dev] Calling Moby from R / SSOAP
In-Reply-To: <41c1ade50805092302x1b1ad07bnc2d5e52557fad012@mail.gmail.com>
References: <1210332068.1475.8.camel@lathan.ipb-sub.ipb-halle.de>	<482458F8.4080808@ucalgary.ca>
	<41c1ade50805092302x1b1ad07bnc2d5e52557fad012@mail.gmail.com>
Message-ID: <4826240A.9020306@ucalgary.ca>

Hi Jason,

There is no canonical object format (e.g. DOM) for Moby, but the XML 
format is.  You might want to check out how I did it in Java to give you 
an idea of the doxen or so envelope, job, container and primitive 
objects you need to create:

 The |org.biomoby.shared.data| package "In Anger": creating data 
instances 
<http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAnger.html>

http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Java/docs/DataPackageInAnger.html

Jason Stewart wrote:
> Hi Paul,
>
> 2008/5/9 Paul Gordon <gordonp at ucalgary.ca>:
>
>   
>> Yes, there is no XML Schema for Moby WSDL, because we allow inheritence at
>> the tag level, which would make such a schema impossible.  So you would need
>> to create an R library that creates the Moby XML message envelope, and send
>> that string-encoded (as well as a parser for receiving).
>>     
>
> I've run into this same problem with XML::Compile with Perl... it
> assumes the existence of WSDL and XML schemas to do its mapping
> between Perl <=> XML...
>
> I guess I'm needing to know how the object mapping should be done. Is
> there a recommendation someplace for how to map MOBY objects to XML
> and back?
>
> Thanks, jas.
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>   


From pieter.neerincx at gmail.com  Mon May 12 11:20:22 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Mon, 12 May 2008 13:20:22 +0200
Subject: [MOBY-dev] Perl BioMoby install
In-Reply-To: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>
Message-ID: <98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>

Hi,

I upgraded my Perl BioMoby install yesterday and noticed two minor  
problems:

1. Failed test t/MOBY:

t/MOBY........................
#   Failed test 'use MOBY;'
#   in t/MOBY.t at line 9.
#     Tried to use 'MOBY'.
#     Error:  Can't locate MOBY.pm in @INC (@INC contains:
.....<cut>.....
# BEGIN failed--compilation aborted at t/MOBY.t line 9.
t/MOBY........................NOK 1/1# Looks like you failed 1 test of  
1.
t/MOBY........................dubious
         Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 1
         Failed 1/1 tests, 0.00% okay


This test doesn't seem to be very useful. All it does is try a "use  
MOBY;", which fails as MOBY.pm doesn't exist and as far is I know  
shouldn't exist. Can I remove this test from the CVS tree or did I  
miss something and is the test correctly reporting a failure  
indicating a problem?

2. Perl module version number fishiness:

-----------------------------------------
*** Module::AutoInstall version 1.03
*** Checking for Perl dependencies...
[Core Features]
- Test::More               ...loaded. (0.62 >= 0.42)
- Test::Simple             ...loaded. (0.62 >= 0.44)
- ExtUtils::MakeMaker      ...loaded. (6.17 >= 6.11)
- Carp                     ...loaded. (1.01)
- File::Spec               ...loaded. (3.19 >= 0.80)
- SOAP::Lite               ...loaded. (0.69 >= 0.69)
- XML::LibXML              ...loaded. (1.66 >= 1.62)
- IO::Stringy              ...loaded. (2.110 >= 2.110)
- Unicode::String          ...loaded. (2.09 >= 2.09)
- File::ShareDir           ...loaded. (0.05 >= 0.05)
- Template                 ...loaded. (2.19)
- Class::Inspector         ...loaded. (1.18 >= 1.17)
- RDF::Core                ...loaded. (0.51 >= 0.51)
- XML::XPath               ...loaded. (1.13 >= 1.12)
- Text::Shellwords         ...loaded. (1.08 >= 1.00)
- HTML::Entities           ...loaded. (1.27 >= 0.01)
- LS                       ...loaded. (1.1.7 >= 1.1.7)
- DBI                      ...loaded. (1.410 >= 0.01)
- DBD::mysql               ...loaded. (2.900300 >= 0.01)
- IO::Prompt               ...loaded. (0.099004 >= 0.99.2)
- IPC::Shareable           ...loaded. (0.600 >= 0.6)
- WSRF::Lite               ...missing. (would need 0.008.2.2)
- XML::DOM                 ...loaded. (1.430)
- DateTime::Format::Epoch  ...loaded. (0.100)
- DateTime::Format::W3CDTF ...loaded. (0.040)
- HTTP::Daemon             ...loaded. (1.360)
- HTTP::Daemon::SSL        ...loaded. (1.020)
- MIME::Base64             ...loaded. (3.050)
- Digest::SHA1             ...loaded. (2.070)
- Crypt::OpenSSL::RSA      ...loaded. (0.250)
- XML::CanonicalizeXML     ...loaded. (0.030 >= 0.02)
- Sys::Hostname::Long      ...loaded. (1.400)
- Crypt::OpenSSL::X509     ...loaded. (0.500)
==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
==> The module(s) are mandatory! Really skip? [n] y
*** Module::AutoInstall configuration finished.
-----------------------------------------
So far so good. It only complains about WSRF::Lite. I have version  
0.8.2.2 installed, but this module doesn't report a version number and  
therefore the dependency check fails. But now it continues:

-----------------------------------------

Checking if your kit is complete...

Looks good

Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have unknown  
version.

>
-----------------------------------------

This is weird. First it finds LS and IO::Prompt and detects the  
version numbers correctly, but apparently it checks them slightly  
differently now and fails to notice the versions I have are just fine...

Cheers,

Pi






From pieter.neerincx at gmail.com  Mon May 12 12:21:12 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Mon, 12 May 2008 14:21:12 +0200
Subject: [MOBY-dev] MOBY::Client::Central::Dump()
In-Reply-To: <47ff6755.14da600a.27c7.3af5@mx.google.com>
References: <47FF108F.4020006@toulouse.inra.fr> <20080411074010.173560@gmx.net>
	<96656174-1315-4B6D-871B-2F8F6047AF7A@wur.nl>
	<47ff6755.14da600a.27c7.3af5@mx.google.com>
Message-ID: <9FADB5D4-300E-40B3-9A12-E22FBFCFE2A1@gmail.com>

Hi Eddie & Mark,

Eh well it works, but not the way it is supposed to. When I call  
MOBY::Client::Central::Dump() on the public Central in Calgary I get  
the following error:

	Not an ARRAY reference at /geninf/prog/lib/perl/MOBY/Client/ 
Central.pm line 1927

Indeed what I get back is a hash reference. This hash contains only a  
single item with the key 'item'. If I change:

1927    my (
                $mobycentral,   $mobyobject, $mobyservice,
                $mobynamespace, $mobyrelationship
           )
           = @{$SQLs};

Into:

1927      my (
                 $mobycentral,   $mobyobject, $mobyservice,
                 $mobynamespace, $mobyrelationship
           )
           = @{${$SQLs}{item}};

...it does work. I checked the MOBY::Central.pm module from CVS and it  
is supposed to return an array ref as before. I upgraded BioMoby + all  
dependancies and compared the behaviour of the official Central with  
my local test Central and the latter still produces an array ref as  
expected... Looks to me like the official Central got a custom patch  
of some sort. Could one of you please have a look at this?

Thanks,

Pi



On 11?Apr?2008, at 3:27 PM, Edward Kawas wrote:

> Hi Pieter,
>
> Dump on mobycentral should work now (once mobycentral is back up and
> running). This was fixed a while back.
>
> Eddie



From edward.kawas at gmail.com  Mon May 12 13:14:23 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 12 May 2008 06:14:23 -0700
Subject: [MOBY-dev] Perl BioMoby install
In-Reply-To: <98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>
	<98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>
Message-ID: <482842bc.02578c0a.1808.ffff8dfe@mx.google.com>

Hi Pieter,

I have fixed the first problem that you have encountered, but I haven't
gotten around to a new cpan release. I have been waiting on a few things
first.

The second problem with regards to versioning may also be fixed. I am not
sure if the versioning for wsrf has been fixed for our makefile, but the
io::prompt and LS should be.

Thanks,

Eddie 

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx
Sent: May-12-08 4:20 AM
To: Core developer announcements
Subject: [MOBY-dev] Perl BioMoby install

Hi,

I upgraded my Perl BioMoby install yesterday and noticed two minor  
problems:

1. Failed test t/MOBY:

t/MOBY........................
#   Failed test 'use MOBY;'
#   in t/MOBY.t at line 9.
#     Tried to use 'MOBY'.
#     Error:  Can't locate MOBY.pm in @INC (@INC contains:
.....<cut>.....
# BEGIN failed--compilation aborted at t/MOBY.t line 9.
t/MOBY........................NOK 1/1# Looks like you failed 1 test of  
1.
t/MOBY........................dubious
         Test returned status 1 (wstat 256, 0x100)
DIED. FAILED test 1
         Failed 1/1 tests, 0.00% okay


This test doesn't seem to be very useful. All it does is try a "use  
MOBY;", which fails as MOBY.pm doesn't exist and as far is I know  
shouldn't exist. Can I remove this test from the CVS tree or did I  
miss something and is the test correctly reporting a failure  
indicating a problem?

2. Perl module version number fishiness:

-----------------------------------------
*** Module::AutoInstall version 1.03
*** Checking for Perl dependencies...
[Core Features]
- Test::More               ...loaded. (0.62 >= 0.42)
- Test::Simple             ...loaded. (0.62 >= 0.44)
- ExtUtils::MakeMaker      ...loaded. (6.17 >= 6.11)
- Carp                     ...loaded. (1.01)
- File::Spec               ...loaded. (3.19 >= 0.80)
- SOAP::Lite               ...loaded. (0.69 >= 0.69)
- XML::LibXML              ...loaded. (1.66 >= 1.62)
- IO::Stringy              ...loaded. (2.110 >= 2.110)
- Unicode::String          ...loaded. (2.09 >= 2.09)
- File::ShareDir           ...loaded. (0.05 >= 0.05)
- Template                 ...loaded. (2.19)
- Class::Inspector         ...loaded. (1.18 >= 1.17)
- RDF::Core                ...loaded. (0.51 >= 0.51)
- XML::XPath               ...loaded. (1.13 >= 1.12)
- Text::Shellwords         ...loaded. (1.08 >= 1.00)
- HTML::Entities           ...loaded. (1.27 >= 0.01)
- LS                       ...loaded. (1.1.7 >= 1.1.7)
- DBI                      ...loaded. (1.410 >= 0.01)
- DBD::mysql               ...loaded. (2.900300 >= 0.01)
- IO::Prompt               ...loaded. (0.099004 >= 0.99.2)
- IPC::Shareable           ...loaded. (0.600 >= 0.6)
- WSRF::Lite               ...missing. (would need 0.008.2.2)
- XML::DOM                 ...loaded. (1.430)
- DateTime::Format::Epoch  ...loaded. (0.100)
- DateTime::Format::W3CDTF ...loaded. (0.040)
- HTTP::Daemon             ...loaded. (1.360)
- HTTP::Daemon::SSL        ...loaded. (1.020)
- MIME::Base64             ...loaded. (3.050)
- Digest::SHA1             ...loaded. (2.070)
- Crypt::OpenSSL::RSA      ...loaded. (0.250)
- XML::CanonicalizeXML     ...loaded. (0.030 >= 0.02)
- Sys::Hostname::Long      ...loaded. (1.400)
- Crypt::OpenSSL::X509     ...loaded. (0.500)
==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
==> The module(s) are mandatory! Really skip? [n] y
*** Module::AutoInstall configuration finished.
-----------------------------------------
So far so good. It only complains about WSRF::Lite. I have version  
0.8.2.2 installed, but this module doesn't report a version number and  
therefore the dependency check fails. But now it continues:

-----------------------------------------

Checking if your kit is complete...

Looks good

Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have unknown  
version.

>
-----------------------------------------

This is weird. First it finds LS and IO::Prompt and detects the  
version numbers correctly, but apparently it checks them slightly  
differently now and fails to notice the versions I have are just fine...

Cheers,

Pi




_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From pieter.neerincx at gmail.com  Mon May 12 13:31:47 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Mon, 12 May 2008 15:31:47 +0200
Subject: [MOBY-dev] Perl BioMoby install
In-Reply-To: <482842bc.02578c0a.1808.ffff8dfe@mx.google.com>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>
	<98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>
	<482842bc.02578c0a.1808.ffff8dfe@mx.google.com>
Message-ID: <244159DE-A626-4B08-AF7A-A31E58334FAB@gmail.com>

Hi Eddie,

On 12?May?2008, at 3:14 PM, Edward Kawas wrote:

> Hi Pieter,
>
> I have fixed the first problem that you have encountered, but I  
> haven't
> gotten around to a new cpan release. I have been waiting on a few  
> things
> first.

Thanks!

> The second problem with regards to versioning may also be fixed. I  
> am not
> sure if the versioning for wsrf has been fixed for our makefile, but  
> the
> io::prompt and LS should be.

Thanks again! I e-mailed the maintainer of the WSRF::Lite module and  
requested the addition of a $VERSION variable... So that might get  
fixed in the near future too :) We'll see...

Cheers,

Pi

> Thanks,
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter  
> Neerincx
> Sent: May-12-08 4:20 AM
> To: Core developer announcements
> Subject: [MOBY-dev] Perl BioMoby install
>
> Hi,
>
> I upgraded my Perl BioMoby install yesterday and noticed two minor
> problems:
>
> 1. Failed test t/MOBY:
>
> t/MOBY........................
> #   Failed test 'use MOBY;'
> #   in t/MOBY.t at line 9.
> #     Tried to use 'MOBY'.
> #     Error:  Can't locate MOBY.pm in @INC (@INC contains:
> .....<cut>.....
> # BEGIN failed--compilation aborted at t/MOBY.t line 9.
> t/MOBY........................NOK 1/1# Looks like you failed 1 test of
> 1.
> t/MOBY........................dubious
>         Test returned status 1 (wstat 256, 0x100)
> DIED. FAILED test 1
>         Failed 1/1 tests, 0.00% okay
>
>
> This test doesn't seem to be very useful. All it does is try a "use
> MOBY;", which fails as MOBY.pm doesn't exist and as far is I know
> shouldn't exist. Can I remove this test from the CVS tree or did I
> miss something and is the test correctly reporting a failure
> indicating a problem?
>
> 2. Perl module version number fishiness:
>
> -----------------------------------------
> *** Module::AutoInstall version 1.03
> *** Checking for Perl dependencies...
> [Core Features]
> - Test::More               ...loaded. (0.62 >= 0.42)
> - Test::Simple             ...loaded. (0.62 >= 0.44)
> - ExtUtils::MakeMaker      ...loaded. (6.17 >= 6.11)
> - Carp                     ...loaded. (1.01)
> - File::Spec               ...loaded. (3.19 >= 0.80)
> - SOAP::Lite               ...loaded. (0.69 >= 0.69)
> - XML::LibXML              ...loaded. (1.66 >= 1.62)
> - IO::Stringy              ...loaded. (2.110 >= 2.110)
> - Unicode::String          ...loaded. (2.09 >= 2.09)
> - File::ShareDir           ...loaded. (0.05 >= 0.05)
> - Template                 ...loaded. (2.19)
> - Class::Inspector         ...loaded. (1.18 >= 1.17)
> - RDF::Core                ...loaded. (0.51 >= 0.51)
> - XML::XPath               ...loaded. (1.13 >= 1.12)
> - Text::Shellwords         ...loaded. (1.08 >= 1.00)
> - HTML::Entities           ...loaded. (1.27 >= 0.01)
> - LS                       ...loaded. (1.1.7 >= 1.1.7)
> - DBI                      ...loaded. (1.410 >= 0.01)
> - DBD::mysql               ...loaded. (2.900300 >= 0.01)
> - IO::Prompt               ...loaded. (0.099004 >= 0.99.2)
> - IPC::Shareable           ...loaded. (0.600 >= 0.6)
> - WSRF::Lite               ...missing. (would need 0.008.2.2)
> - XML::DOM                 ...loaded. (1.430)
> - DateTime::Format::Epoch  ...loaded. (0.100)
> - DateTime::Format::W3CDTF ...loaded. (0.040)
> - HTTP::Daemon             ...loaded. (1.360)
> - HTTP::Daemon::SSL        ...loaded. (1.020)
> - MIME::Base64             ...loaded. (3.050)
> - Digest::SHA1             ...loaded. (2.070)
> - Crypt::OpenSSL::RSA      ...loaded. (0.250)
> - XML::CanonicalizeXML     ...loaded. (0.030 >= 0.02)
> - Sys::Hostname::Long      ...loaded. (1.400)
> - Crypt::OpenSSL::X509     ...loaded. (0.500)
> ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
> ==> The module(s) are mandatory! Really skip? [n] y
> *** Module::AutoInstall configuration finished.
> -----------------------------------------
> So far so good. It only complains about WSRF::Lite. I have version
> 0.8.2.2 installed, but this module doesn't report a version number and
> therefore the dependency check fails. But now it continues:
>
> -----------------------------------------
>
> Checking if your kit is complete...
>
> Looks good
>
> Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
> Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
> Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have unknown
> version.
>
>>
> -----------------------------------------
>
> This is weird. First it finds LS and IO::Prompt and detects the
> version numbers correctly, but apparently it checks them slightly
> differently now and fails to notice the versions I have are just  
> fine...
>
> Cheers,
>
> Pi
>
>
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev




From edward.kawas at gmail.com  Mon May 12 15:11:09 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 12 May 2008 08:11:09 -0700
Subject: [MOBY-dev] MOBY::Client::Central::Dump()
In-Reply-To: <9FADB5D4-300E-40B3-9A12-E22FBFCFE2A1@gmail.com>
References: <47FF108F.4020006@toulouse.inra.fr>
	<20080411074010.173560@gmx.net>	<96656174-1315-4B6D-871B-2F8F6047AF7A@wur.nl>	<47ff6755.14da600a.27c7.3af5@mx.google.com>
	<9FADB5D4-300E-40B3-9A12-E22FBFCFE2A1@gmail.com>
Message-ID: <48285e1a.1f538c0a.7e36.3e14@mx.google.com>

Thanks Pieter,

I made changes (based on what you found out) to MOBY::Client::Central that
should now take care of the DUMP problem. The changes are in the CVS and
will soon be in cpan.

Thanks again!

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx
Sent: May-12-08 5:21 AM
To: Core developer announcements
Subject: [MOBY-dev] MOBY::Client::Central::Dump()

Hi Eddie & Mark,

Eh well it works, but not the way it is supposed to. When I call  
MOBY::Client::Central::Dump() on the public Central in Calgary I get  
the following error:

	Not an ARRAY reference at /geninf/prog/lib/perl/MOBY/Client/ 
Central.pm line 1927

Indeed what I get back is a hash reference. This hash contains only a  
single item with the key 'item'. If I change:

1927    my (
                $mobycentral,   $mobyobject, $mobyservice,
                $mobynamespace, $mobyrelationship
           )
           = @{$SQLs};

Into:

1927      my (
                 $mobycentral,   $mobyobject, $mobyservice,
                 $mobynamespace, $mobyrelationship
           )
           = @{${$SQLs}{item}};

...it does work. I checked the MOBY::Central.pm module from CVS and it  
is supposed to return an array ref as before. I upgraded BioMoby + all  
dependancies and compared the behaviour of the official Central with  
my local test Central and the latter still produces an array ref as  
expected... Looks to me like the official Central got a custom patch  
of some sort. Could one of you please have a look at this?

Thanks,

Pi



On 11.Apr.2008, at 3:27 PM, Edward Kawas wrote:

> Hi Pieter,
>
> Dump on mobycentral should work now (once mobycentral is back up and
> running). This was fixed a while back.
>
> Eddie

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From jmfernandez at cnio.es  Tue May 13 09:51:09 2008
From: jmfernandez at cnio.es (=?windows-1252?Q?Jos=E9_Mar=EDa_Fern=E1ndez_Gonz=E1lez?=)
Date: Tue, 13 May 2008 11:51:09 +0200
Subject: [MOBY-dev] Perl BioMoby install
In-Reply-To: <244159DE-A626-4B08-AF7A-A31E58334FAB@gmail.com>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>	<98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>	<482842bc.02578c0a.1808.ffff8dfe@mx.google.com>
	<244159DE-A626-4B08-AF7A-A31E58334FAB@gmail.com>
Message-ID: <4829648D.1000306@cnio.es>

Hi everybody,
	although WSRF::Lite already has a $VERSION variable, it is not defined as a 
string, which is a problem for installation packages. It is set as:

$VERSION=0.8.2.2;

instead of

$VERSION='0.8.2.2';

	Jos? Manuel Rodr?guez and I made some tries fixing that for Makefile.PL (see 
jmrc commits).

	The main problem is that more and more Perl packages are migrating from 
string representation to 'literal' one (IO::Prompt for instance, I guess).

	Best Regards,
		Jos? Mar?a

Pieter Neerincx wrote:
> Hi Eddie,
> 
> On 12?May?2008, at 3:14 PM, Edward Kawas wrote:
> 
>> Hi Pieter,
>>
>> I have fixed the first problem that you have encountered, but I haven't
>> gotten around to a new cpan release. I have been waiting on a few things
>> first.
> 
> Thanks!
> 
>> The second problem with regards to versioning may also be fixed. I am not
>> sure if the versioning for wsrf has been fixed for our makefile, but the
>> io::prompt and LS should be.
> 
> Thanks again! I e-mailed the maintainer of the WSRF::Lite module and 
> requested the addition of a $VERSION variable... So that might get fixed 
> in the near future too :) We'll see...
> 
> Cheers,
> 
> Pi
> 
>> Thanks,
>>
>> Eddie
>>
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org
>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter Neerincx
>> Sent: May-12-08 4:20 AM
>> To: Core developer announcements
>> Subject: [MOBY-dev] Perl BioMoby install
>>
>> Hi,
>>
>> I upgraded my Perl BioMoby install yesterday and noticed two minor
>> problems:
>>
>> 1. Failed test t/MOBY:
>>
>> t/MOBY........................
>> #   Failed test 'use MOBY;'
>> #   in t/MOBY.t at line 9.
>> #     Tried to use 'MOBY'.
>> #     Error:  Can't locate MOBY.pm in @INC (@INC contains:
>> .....<cut>.....
>> # BEGIN failed--compilation aborted at t/MOBY.t line 9.
>> t/MOBY........................NOK 1/1# Looks like you failed 1 test of
>> 1.
>> t/MOBY........................dubious
>>         Test returned status 1 (wstat 256, 0x100)
>> DIED. FAILED test 1
>>         Failed 1/1 tests, 0.00% okay
>>
>>
>> This test doesn't seem to be very useful. All it does is try a "use
>> MOBY;", which fails as MOBY.pm doesn't exist and as far is I know
>> shouldn't exist. Can I remove this test from the CVS tree or did I
>> miss something and is the test correctly reporting a failure
>> indicating a problem?
>>
>> 2. Perl module version number fishiness:
>>
>> -----------------------------------------
>> *** Module::AutoInstall version 1.03
>> *** Checking for Perl dependencies...
>> [Core Features]
>> - Test::More               ...loaded. (0.62 >= 0.42)
>> - Test::Simple             ...loaded. (0.62 >= 0.44)
>> - ExtUtils::MakeMaker      ...loaded. (6.17 >= 6.11)
>> - Carp                     ...loaded. (1.01)
>> - File::Spec               ...loaded. (3.19 >= 0.80)
>> - SOAP::Lite               ...loaded. (0.69 >= 0.69)
>> - XML::LibXML              ...loaded. (1.66 >= 1.62)
>> - IO::Stringy              ...loaded. (2.110 >= 2.110)
>> - Unicode::String          ...loaded. (2.09 >= 2.09)
>> - File::ShareDir           ...loaded. (0.05 >= 0.05)
>> - Template                 ...loaded. (2.19)
>> - Class::Inspector         ...loaded. (1.18 >= 1.17)
>> - RDF::Core                ...loaded. (0.51 >= 0.51)
>> - XML::XPath               ...loaded. (1.13 >= 1.12)
>> - Text::Shellwords         ...loaded. (1.08 >= 1.00)
>> - HTML::Entities           ...loaded. (1.27 >= 0.01)
>> - LS                       ...loaded. (1.1.7 >= 1.1.7)
>> - DBI                      ...loaded. (1.410 >= 0.01)
>> - DBD::mysql               ...loaded. (2.900300 >= 0.01)
>> - IO::Prompt               ...loaded. (0.099004 >= 0.99.2)
>> - IPC::Shareable           ...loaded. (0.600 >= 0.6)
>> - WSRF::Lite               ...missing. (would need 0.008.2.2)
>> - XML::DOM                 ...loaded. (1.430)
>> - DateTime::Format::Epoch  ...loaded. (0.100)
>> - DateTime::Format::W3CDTF ...loaded. (0.040)
>> - HTTP::Daemon             ...loaded. (1.360)
>> - HTTP::Daemon::SSL        ...loaded. (1.020)
>> - MIME::Base64             ...loaded. (3.050)
>> - Digest::SHA1             ...loaded. (2.070)
>> - Crypt::OpenSSL::RSA      ...loaded. (0.250)
>> - XML::CanonicalizeXML     ...loaded. (0.030 >= 0.02)
>> - Sys::Hostname::Long      ...loaded. (1.400)
>> - Crypt::OpenSSL::X509     ...loaded. (0.500)
>> ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
>> ==> The module(s) are mandatory! Really skip? [n] y
>> *** Module::AutoInstall configuration finished.
>> -----------------------------------------
>> So far so good. It only complains about WSRF::Lite. I have version
>> 0.8.2.2 installed, but this module doesn't report a version number and
>> therefore the dependency check fails. But now it continues:
>>
>> -----------------------------------------
>>
>> Checking if your kit is complete...
>>
>> Looks good
>>
>> Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
>> Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
>> Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have unknown
>> version.
>>
>>>
>> -----------------------------------------
>>
>> This is weird. First it finds LS and IO::Prompt and detects the
>> version numbers correctly, but apparently it checks them slightly
>> differently now and fails to notice the versions I have are just fine...
>>
>> Cheers,
>>
>> Pi
>>
>>
>>
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 
> 
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
> 

-- 
"There is no reason why anybody would want a computer in their home" -
	Ken Olson, founder of DEC 1977
"640K ought to be enough for anybody" - Bill Gates, 1981
"Nobody will ever outgrow a 20Mb hard drive." - ???

"Premature optimization is the root of all evil." - Donald Knuth

Jos? Mar?a Fern?ndez Gonz?lez
Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
e-mail: jmfernandez at cnio.es		Fax: (+34) 91 224 69 76
Unidad del Instituto Nacional de Bioinform?tica
Biolog?a Estructural y Biocomputaci?n	Structural Biology and Biocomputing
Centro Nacional de Investigaciones Oncol?gicas
C.P.: 28029				Zip Code: 28029
C/. Melchor Fern?ndez Almagro, 3	Madrid (Spain)

**NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.



From pieter.neerincx at gmail.com  Tue May 13 10:28:32 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Tue, 13 May 2008 12:28:32 +0200
Subject: [MOBY-dev] Perl BioMoby install
In-Reply-To: <4829648D.1000306@cnio.es>
References: <1D200DE1A9A1614D99F25CF7DD78DE3512B0F9@scomp0040.wurnet.nl>	<98C4D878-6704-4EB0-80DF-AA8C885A18A3@gmail.com>	<482842bc.02578c0a.1808.ffff8dfe@mx.google.com>
	<244159DE-A626-4B08-AF7A-A31E58334FAB@gmail.com>
	<4829648D.1000306@cnio.es>
Message-ID: <EAD19377-C879-4F04-9A82-2EC21DD7EB27@gmail.com>

Hi Jos? Mar?a,

On 13?May?2008, at 11:51 AM, Jos? Mar?a Fern?ndez Gonz?lez wrote:

> Hi everybody,
> 	although WSRF::Lite already has a $VERSION variable, it is not  
> defined as a string, which is a problem for installation packages.  
> It is set as:
>
> $VERSION=0.8.2.2;

Ok my bad. I thought I had installed 0.8.2.2, which I did but not in  
the proper path. Mix that with an outdated WSRF::Lite 0.6 in the  
correct path that reports it's version number in the wrong context and  
this is what you get :(. Problem solved :)

Pi

> instead of
>
> $VERSION='0.8.2.2';
>
> 	Jos? Manuel Rodr?guez and I made some tries fixing that for  
> Makefile.PL (see jmrc commits).
>
> 	The main problem is that more and more Perl packages are migrating  
> from string representation to 'literal' one (IO::Prompt for  
> instance, I guess).
>
> 	Best Regards,
> 		Jos? Mar?a
>
> Pieter Neerincx wrote:
>> Hi Eddie,
>> On 12?May?2008, at 3:14 PM, Edward Kawas wrote:
>>> Hi Pieter,
>>>
>>> I have fixed the first problem that you have encountered, but I  
>>> haven't
>>> gotten around to a new cpan release. I have been waiting on a few  
>>> things
>>> first.
>> Thanks!
>>> The second problem with regards to versioning may also be fixed. I  
>>> am not
>>> sure if the versioning for wsrf has been fixed for our makefile,  
>>> but the
>>> io::prompt and LS should be.
>> Thanks again! I e-mailed the maintainer of the WSRF::Lite module  
>> and requested the addition of a $VERSION variable... So that might  
>> get fixed in the near future too :) We'll see...
>> Cheers,
>> Pi
>>> Thanks,
>>>
>>> Eddie
>>>
>>> -----Original Message-----
>>> From: moby-dev-bounces at lists.open-bio.org
>>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Pieter  
>>> Neerincx
>>> Sent: May-12-08 4:20 AM
>>> To: Core developer announcements
>>> Subject: [MOBY-dev] Perl BioMoby install
>>>
>>> Hi,
>>>
>>> I upgraded my Perl BioMoby install yesterday and noticed two minor
>>> problems:
>>>
>>> 1. Failed test t/MOBY:
>>>
>>> t/MOBY........................
>>> #   Failed test 'use MOBY;'
>>> #   in t/MOBY.t at line 9.
>>> #     Tried to use 'MOBY'.
>>> #     Error:  Can't locate MOBY.pm in @INC (@INC contains:
>>> .....<cut>.....
>>> # BEGIN failed--compilation aborted at t/MOBY.t line 9.
>>> t/MOBY........................NOK 1/1# Looks like you failed 1  
>>> test of
>>> 1.
>>> t/MOBY........................dubious
>>>        Test returned status 1 (wstat 256, 0x100)
>>> DIED. FAILED test 1
>>>        Failed 1/1 tests, 0.00% okay
>>>
>>>
>>> This test doesn't seem to be very useful. All it does is try a "use
>>> MOBY;", which fails as MOBY.pm doesn't exist and as far is I know
>>> shouldn't exist. Can I remove this test from the CVS tree or did I
>>> miss something and is the test correctly reporting a failure
>>> indicating a problem?
>>>
>>> 2. Perl module version number fishiness:
>>>
>>> -----------------------------------------
>>> *** Module::AutoInstall version 1.03
>>> *** Checking for Perl dependencies...
>>> [Core Features]
>>> - Test::More               ...loaded. (0.62 >= 0.42)
>>> - Test::Simple             ...loaded. (0.62 >= 0.44)
>>> - ExtUtils::MakeMaker      ...loaded. (6.17 >= 6.11)
>>> - Carp                     ...loaded. (1.01)
>>> - File::Spec               ...loaded. (3.19 >= 0.80)
>>> - SOAP::Lite               ...loaded. (0.69 >= 0.69)
>>> - XML::LibXML              ...loaded. (1.66 >= 1.62)
>>> - IO::Stringy              ...loaded. (2.110 >= 2.110)
>>> - Unicode::String          ...loaded. (2.09 >= 2.09)
>>> - File::ShareDir           ...loaded. (0.05 >= 0.05)
>>> - Template                 ...loaded. (2.19)
>>> - Class::Inspector         ...loaded. (1.18 >= 1.17)
>>> - RDF::Core                ...loaded. (0.51 >= 0.51)
>>> - XML::XPath               ...loaded. (1.13 >= 1.12)
>>> - Text::Shellwords         ...loaded. (1.08 >= 1.00)
>>> - HTML::Entities           ...loaded. (1.27 >= 0.01)
>>> - LS                       ...loaded. (1.1.7 >= 1.1.7)
>>> - DBI                      ...loaded. (1.410 >= 0.01)
>>> - DBD::mysql               ...loaded. (2.900300 >= 0.01)
>>> - IO::Prompt               ...loaded. (0.099004 >= 0.99.2)
>>> - IPC::Shareable           ...loaded. (0.600 >= 0.6)
>>> - WSRF::Lite               ...missing. (would need 0.008.2.2)
>>> - XML::DOM                 ...loaded. (1.430)
>>> - DateTime::Format::Epoch  ...loaded. (0.100)
>>> - DateTime::Format::W3CDTF ...loaded. (0.040)
>>> - HTTP::Daemon             ...loaded. (1.360)
>>> - HTTP::Daemon::SSL        ...loaded. (1.020)
>>> - MIME::Base64             ...loaded. (3.050)
>>> - Digest::SHA1             ...loaded. (2.070)
>>> - Crypt::OpenSSL::RSA      ...loaded. (0.250)
>>> - XML::CanonicalizeXML     ...loaded. (0.030 >= 0.02)
>>> - Sys::Hostname::Long      ...loaded. (1.400)
>>> - Crypt::OpenSSL::X509     ...loaded. (0.500)
>>> ==> Auto-install the 1 mandatory module(s) from CPAN? [y] n
>>> ==> The module(s) are mandatory! Really skip? [n] y
>>> *** Module::AutoInstall configuration finished.
>>> -----------------------------------------
>>> So far so good. It only complains about WSRF::Lite. I have version
>>> 0.8.2.2 installed, but this module doesn't report a version number  
>>> and
>>> therefore the dependency check fails. But now it continues:
>>>
>>> -----------------------------------------
>>>
>>> Checking if your kit is complete...
>>>
>>> Looks good
>>>
>>> Warning: prerequisite IO::Prompt 0.99.2 not found. We have 0.099004.
>>> Warning: prerequisite LS 1.1.7 not found. We have 1.001007.
>>> Warning: prerequisite WSRF::Lite 0.008.2.2 not found. We have  
>>> unknown
>>> version.
>>>
>>>>
>>> -----------------------------------------
>>>
>>> This is weird. First it finds LS and IO::Prompt and detects the
>>> version numbers correctly, but apparently it checks them slightly
>>> differently now and fails to notice the versions I have are just  
>>> fine...
>>>
>>> Cheers,
>>>
>>> Pi
>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> -- 
> "There is no reason why anybody would want a computer in their home" -
> 	Ken Olson, founder of DEC 1977
> "640K ought to be enough for anybody" - Bill Gates, 1981
> "Nobody will ever outgrow a 20Mb hard drive." - ???
>
> "Premature optimization is the root of all evil." - Donald Knuth
>
> Jos? Mar?a Fern?ndez Gonz?lez
> Tlfn: (+34) 91 732 80 00 / 91 224 69 00 (ext 3061)
> e-mail: jmfernandez at cnio.es		Fax: (+34) 91 224 69 76
> Unidad del Instituto Nacional de Bioinform?tica
> Biolog?a Estructural y Biocomputaci?n	Structural Biology and  
> Biocomputing
> Centro Nacional de Investigaciones Oncol?gicas
> C.P.: 28029				Zip Code: 28029
> C/. Melchor Fern?ndez Almagro, 3	Madrid (Spain)
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso  
> los ficheros adjuntos, pueden contener informaci?n protegida para el  
> uso exclusivo de su destinatario. Se proh?be la distribuci?n,  
> reproducci?n o cualquier otro tipo de transmisi?n por parte de otra  
> persona que no sea el destinatario. Si usted recibe por error este  
> correo, se ruega comunicarlo al remitente y borrar el mensaje  
> recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any  
> attachments may contain confidential and privileged information for  
> the sole use of the designated recipient named above. Distribution,  
> reproduction or any other use of this transmission by any party  
> other than the intended recipient is prohibited. If you are not the  
> intended recipient please contact the sender and delete all copies.
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev




From markw at illuminae.com  Thu May 15 17:53:15 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Thu, 15 May 2008 10:53:15 -0700
Subject: [MOBY-dev] the use-case for xml:lang
Message-ID: <op.ua7im1f5nbznux@mark.ubic.ca>

Hi all,

at the last Moby meeting we decided that there was a need for MOBY Central  
to observe the xml:lang attribute.  Can someone please send me an explicit  
use-case so that I am sure I understand why/where this attribute is going  
to appear and what changes to MOBY Central and the database might be  
necessary to accommodate this change?

Thanks!

Mark


-- 
Mark Wilkinson
Assistant Professor
Dept. of Medical Genetics, UBC
PI Bioinformatics, Heart and Lung Institute at St. Paul's Hospital
iCAPTURE Centre


From gordonp at ucalgary.ca  Thu May 15 18:32:51 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 15 May 2008 12:32:51 -0600
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <op.ua7im1f5nbznux@mark.ubic.ca>
References: <op.ua7im1f5nbznux@mark.ubic.ca>
Message-ID: <482C81D3.1030106@ucalgary.ca>

Some services are registered in other languages for their free-text 
descriptions for example.  In some places (I can't remember where 
exactly at the moment), the registry assumes that the description is 
English and uses the xml:lang tag to say so when returning XML.  It's 
probably a good idea to have the xml:lang in the returned info, but it 
should maintain the xml:lang tag used to register the service. 

Mark Wilkinson wrote:
> Hi all,
>
> at the last Moby meeting we decided that there was a need for MOBY 
> Central to observe the xml:lang attribute.  Can someone please send me 
> an explicit use-case so that I am sure I understand why/where this 
> attribute is going to appear and what changes to MOBY Central and the 
> database might be necessary to accommodate this change?
>
> Thanks!
>
> Mark
>
>


From gordonp at ucalgary.ca  Thu May 15 18:32:51 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Thu, 15 May 2008 12:32:51 -0600
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <op.ua7im1f5nbznux@mark.ubic.ca>
References: <op.ua7im1f5nbznux@mark.ubic.ca>
Message-ID: <482C81D3.1030106@ucalgary.ca>

Some services are registered in other languages for their free-text 
descriptions for example.  In some places (I can't remember where 
exactly at the moment), the registry assumes that the description is 
English and uses the xml:lang tag to say so when returning XML.  It's 
probably a good idea to have the xml:lang in the returned info, but it 
should maintain the xml:lang tag used to register the service. 

Mark Wilkinson wrote:
> Hi all,
>
> at the last Moby meeting we decided that there was a need for MOBY 
> Central to observe the xml:lang attribute.  Can someone please send me 
> an explicit use-case so that I am sure I understand why/where this 
> attribute is going to appear and what changes to MOBY Central and the 
> database might be necessary to accommodate this change?
>
> Thanks!
>
> Mark
>
>


From markw at illuminae.com  Thu May 15 18:54:26 2008
From: markw at illuminae.com (markw at illuminae.com)
Date: Thu, 15 May 2008 18:54:26 +0000
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <482C81D3.1030106@ucalgary.ca>
References: <op.ua7im1f5nbznux@mark.ubic.ca><482C81D3.1030106@ucalgary.ca>
Message-ID: <51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>

So... Should we allow more than one "description" element per service/obect/namespace to allow multiple languages per registration?  This would be a change to the API, but it would make sense to do so if this is the route we're going...

M


On the Road!

-----Original Message-----
From: Paul Gordon <gordonp at ucalgary.ca>

Date: Thu, 15 May 2008 12:32:51 
To:Core developer announcements <moby-dev at lists.open-bio.org>
Cc:moby-dev at biomoby.org
Subject: Re: [MOBY-dev] the use-case for xml:lang


Some services are registered in other languages for their free-text
descriptions for example.  In some places (I can't remember where
exactly at the moment), the registry assumes that the description is
English and uses the xml:lang tag to say so when returning XML.  It's
probably a good idea to have the xml:lang in the returned info, but it
should maintain the xml:lang tag used to register the service.

Mark Wilkinson wrote:
> Hi all,
>
> at the last Moby meeting we decided that there was a need for MOBY
> Central to observe the xml:lang attribute.  Can someone please send me
> an explicit use-case so that I am sure I understand why/where this
> attribute is going to appear and what changes to MOBY Central and the
> database might be necessary to accommodate this change?
>
> Thanks!
>
> Mark
>
>
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From markw at illuminae.com  Thu May 15 18:54:26 2008
From: markw at illuminae.com (markw at illuminae.com)
Date: Thu, 15 May 2008 18:54:26 +0000
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <482C81D3.1030106@ucalgary.ca>
References: <op.ua7im1f5nbznux@mark.ubic.ca><482C81D3.1030106@ucalgary.ca>
Message-ID: <51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>

So... Should we allow more than one "description" element per service/obect/namespace to allow multiple languages per registration?  This would be a change to the API, but it would make sense to do so if this is the route we're going...

M


On the Road!

-----Original Message-----
From: Paul Gordon <gordonp at ucalgary.ca>

Date: Thu, 15 May 2008 12:32:51 
To:Core developer announcements <moby-dev at lists.open-bio.org>
Cc:moby-dev at biomoby.org
Subject: Re: [MOBY-dev] the use-case for xml:lang


Some services are registered in other languages for their free-text
descriptions for example.  In some places (I can't remember where
exactly at the moment), the registry assumes that the description is
English and uses the xml:lang tag to say so when returning XML.  It's
probably a good idea to have the xml:lang in the returned info, but it
should maintain the xml:lang tag used to register the service.

Mark Wilkinson wrote:
> Hi all,
>
> at the last Moby meeting we decided that there was a need for MOBY
> Central to observe the xml:lang attribute.  Can someone please send me
> an explicit use-case so that I am sure I understand why/where this
> attribute is going to appear and what changes to MOBY Central and the
> database might be necessary to accommodate this change?
>
> Thanks!
>
> Mark
>
>
_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From martin.senger at gmail.com  Thu May 15 19:13:35 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 15 May 2008 20:13:35 +0100
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>
References: <op.ua7im1f5nbznux@mark.ubic.ca> <482C81D3.1030106@ucalgary.ca>
	<51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>
Message-ID: <4d93f07c0805151213m7ef4e967i6f3d4c0b249ac7b6@mail.gmail.com>

> So... Should we allow more than one "description" element per
> service/obect/namespace to allow multiple languages per registration?


I do not know... Do we really need it? I think the main point is allow a
*different* language, but not  necessarily more than one. The registry needs
to remember what xml:lang was given together with description and return the
same back when the description is going out.

And perhaps to do it in all descriptions, not only the service
description...

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From martin.senger at gmail.com  Thu May 15 19:13:35 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Thu, 15 May 2008 20:13:35 +0100
Subject: [MOBY-dev] the use-case for xml:lang
In-Reply-To: <51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>
References: <op.ua7im1f5nbznux@mark.ubic.ca> <482C81D3.1030106@ucalgary.ca>
	<51256892-1210877669-cardhu_decombobulator_blackberry.rim.net-343697065-@bxe013.bisx.prod.on.blackberry>
Message-ID: <4d93f07c0805151213m7ef4e967i6f3d4c0b249ac7b6@mail.gmail.com>

> So... Should we allow more than one "description" element per
> service/obect/namespace to allow multiple languages per registration?


I do not know... Do we really need it? I think the main point is allow a
*different* language, but not  necessarily more than one. The registry needs
to remember what xml:lang was given together with description and return the
same back when the description is going out.

And perhaps to do it in all descriptions, not only the service
description...

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From martin.senger at gmail.com  Fri May 16 10:48:11 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 16 May 2008 11:48:11 +0100
Subject: [MOBY-dev] biomoby.org down?
Message-ID: <4d93f07c0805160348m7ba6ae11x489aca1922b41fd7@mail.gmail.com>

At least from the UK... (no http server responding, but I can ssh there).

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From pieter.neerincx at gmail.com  Fri May 16 11:07:10 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Fri, 16 May 2008 13:07:10 +0200
Subject: [MOBY-dev] biomoby.org down?
In-Reply-To: <4d93f07c0805160348m7ba6ae11x489aca1922b41fd7@mail.gmail.com>
References: <4d93f07c0805160348m7ba6ae11x489aca1922b41fd7@mail.gmail.com>
Message-ID: <CF52418B-3E57-47F7-AE86-89BFE5A9C785@gmail.com>

It's working overhere. So it either got fixed or it's a local problem...

Cheers,

Pi

On 16 May 2008, at 12:48, Martin Senger wrote:

> At least from the UK... (no http server responding, but I can ssh  
> there).
>
> Martin
>
> -- 
> Martin Senger
> email: martin.senger at gmail.com,m.senger at cgiar.org
> skype: martinsenger
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From edward.kawas at gmail.com  Wed May 21 15:38:21 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Wed, 21 May 2008 08:38:21 -0700
Subject: [MOBY-dev] Important note for MOBY-Async developers
In-Reply-To: <480F50D4.5000907@cnio.es>
References: <480F498A.4060902@cnio.es> <480F50D4.5000907@cnio.es>
Message-ID: <483441fa.15528c0a.1950.ffffddd5@mx.google.com>

Hi Jose Manual,

I noticed that the pdf document on async services seems to be corrupt (at
least for me). All the images are shown as smears.

Can you verify if this is the case?

Thanks,

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jose Manuel
rodriguez
Sent: April-23-08 8:08 AM
To: moby-dev at lists.open-bio.org; moby-dev-bounces at lists.open-bio.org;
inb-tecnico at lists.cnio.es
Cc: Dmitry Repchevsky; "=?ISO-8859-1?Q?Jos=E9_?="@portal.open-bio.org
Subject: [MOBY-dev] Important note for MOBY-Async developers

Hello,


The dispatcher of MOBY-Async services has to be modified.

The MOBY-Async developers have to add the next method to
SOAP::Transport::HTTP::CGI
    $server->on_action(sub{});

Inside of dispatcher he/she has to add:

$WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' 
=>' {Service Package}',
$WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP
ropertiesRequest' 
=> '{Service Package}',
$WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' 
=> '{Service Package}',

Then,
        $WSRF::Constants::WSRL => '{Service Package}',
        $WSRF::Constants::WSRP => '{Service Package}',

could be deleted.

I have attached you one CGI example.



For more information:
http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/asyncDocs/BioMOBY%20A
synchronous%20Service%20Specification%20v2.4.2.pdf
(Maybe the CVS via web is not updated)

Best Regads,
Jos? Manuel.



Jose Manuel rodriguez wrote:
> Hello,
>
> We have fixed some problems that there were in our MOBY-async proposal.
>
> We found some inconsistencies in the specifications and implementations:
>
> * The "GetResourceProperty" and "GetMultipleResourceProperties" 
> messages returned QNames (both status and results) without prefixes.
>
> * During WSA messages, in the MOBY-Async Perl API we had:
>         
> <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
> roperties/GetMultipleResourceProperties</wsa:Action>
>    
>     When the WSRF specifications says that:
>         
> <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
> roperties/GetMultipleResourceProperties*Request*</wsa:Action>
>
> * In the WSDL for MOBY-Async services we have add the "soapAction" 
> address that SOAP 1.1 specifications says.
>
> * The MOBY-Async client and MOBY-Async sample have been updated from 
> these modifications. As soon as possible, we will sent you one 
> MOBY-Async sample which you could test it.
>
> * The MOBY-Async document has been updated (I have attached you the 
> MOBY-Async document v2.4.2).
>
> All these modifications have been committed to MOBY CVS.
>
> I think is all.
>
> Best Regards,
> Jos? Manuel.
>
>
>
> -- 
> Jos? Manuel Rodr?guez Carrasco            e-mail: jmrodriguez at cnio.es
> Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
> Bioinformatic Unit
> Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 
> 28029
> Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain)
>   


-- 
Jos? Manuel Rodr?guez Carrasco            e-mail: jmrodriguez at cnio.es
Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
Bioinformatic Unit
Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 28029
Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain) 



**NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los
ficheros adjuntos, pueden contener informaci?n protegida para el uso
exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o
cualquier otro tipo de transmisi?n por parte de otra persona que no sea el
destinatario. Si usted recibe por error este correo, se ruega comunicarlo al
remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may
contain confidential and privileged information for the sole use of the
designated recipient named above. Distribution, reproduction or any other
use of this transmission by any party other than the intended recipient is
prohibited. If you are not the intended recipient please contact the sender
and delete all copies.





From jmrodriguez at cnio.es  Wed May 21 16:11:45 2008
From: jmrodriguez at cnio.es (Jose Manuel rodriguez)
Date: Wed, 21 May 2008 18:11:45 +0200
Subject: [MOBY-dev] Important note for MOBY-Async developers
In-Reply-To: <483441fa.15528c0a.1950.ffffddd5@mx.google.com>
References: <480F498A.4060902@cnio.es> <480F50D4.5000907@cnio.es>
	<483441fa.15528c0a.1950.ffffddd5@mx.google.com>
Message-ID: <483449C1.6080709@cnio.es>

Hi Eddie,


It is strange. I have just make a checkout and the pdf looks good...I 
don't know.
We are checking now if the CVS has problems adding Binary Files.
We know that Binary files need to be added to CVS in a special way:
"cvs add -kb 'binary filename'"

But how I said I can read the pdf document perfectly.

Cheers,
Jos?.


Edward Kawas wrote:
> Hi Jose Manual,
>
> I noticed that the pdf document on async services seems to be corrupt (at
> least for me). All the images are shown as smears.
>
> Can you verify if this is the case?
>
> Thanks,
>
> Eddie
>
> -----Original Message-----
> From: moby-dev-bounces at lists.open-bio.org
> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jose Manuel
> rodriguez
> Sent: April-23-08 8:08 AM
> To: moby-dev at lists.open-bio.org; moby-dev-bounces at lists.open-bio.org;
> inb-tecnico at lists.cnio.es
> Cc: Dmitry Repchevsky; "=?ISO-8859-1?Q?Jos=E9_?="@portal.open-bio.org
> Subject: [MOBY-dev] Important note for MOBY-Async developers
>
> Hello,
>
>
> The dispatcher of MOBY-Async services has to be modified.
>
> The MOBY-Async developers have to add the next method to
> SOAP::Transport::HTTP::CGI
>     $server->on_action(sub{});
>
> Inside of dispatcher he/she has to add:
>
> $WSRF::Constants::WSRPW.'/GetResourceProperty/GetResourcePropertyRequest' 
> =>' {Service Package}',
> $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/GetMultipleResourceP
> ropertiesRequest' 
> => '{Service Package}',
> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/DestroyRequest' 
> => '{Service Package}',
>
> Then,
>         $WSRF::Constants::WSRL => '{Service Package}',
>         $WSRF::Constants::WSRP => '{Service Package}',
>
> could be deleted.
>
> I have attached you one CGI example.
>
>
>
> For more information:
> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/asyncDocs/BioMOBY%20A
> synchronous%20Service%20Specification%20v2.4.2.pdf
> (Maybe the CVS via web is not updated)
>
> Best Regads,
> Jos? Manuel.
>
>
>
> Jose Manuel rodriguez wrote:
>   
>> Hello,
>>
>> We have fixed some problems that there were in our MOBY-async proposal.
>>
>> We found some inconsistencies in the specifications and implementations:
>>
>> * The "GetResourceProperty" and "GetMultipleResourceProperties" 
>> messages returned QNames (both status and results) without prefixes.
>>
>> * During WSA messages, in the MOBY-Async Perl API we had:
>>         
>> <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
>> roperties/GetMultipleResourceProperties</wsa:Action>
>>    
>>     When the WSRF specifications says that:
>>         
>> <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
>> roperties/GetMultipleResourceProperties*Request*</wsa:Action>
>>
>> * In the WSDL for MOBY-Async services we have add the "soapAction" 
>> address that SOAP 1.1 specifications says.
>>
>> * The MOBY-Async client and MOBY-Async sample have been updated from 
>> these modifications. As soon as possible, we will sent you one 
>> MOBY-Async sample which you could test it.
>>
>> * The MOBY-Async document has been updated (I have attached you the 
>> MOBY-Async document v2.4.2).
>>
>> All these modifications have been committed to MOBY CVS.
>>
>> I think is all.
>>
>> Best Regards,
>> Jos? Manuel.
>>
>>
>>
>> -- 
>> Jos? Manuel Rodr?guez Carrasco            e-mail: jmrodriguez at cnio.es
>> Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
>> Bioinformatic Unit
>> Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code: 
>> 28029
>> Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain)
>>   
>>     
>
>
>   


-- 
Jos? Manuel Rodr?guez Carrasco            e-mail: jmrodriguez at cnio.es
Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
Bioinformatic Unit
Spanish National Cancer Center (CNIO) http://www.cnio.es
Zip Code: 28029
Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain) 


**NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso los ficheros adjuntos, pueden contener informaci?n protegida para el uso exclusivo de su destinatario. Se proh?be la distribuci?n, reproducci?n o cualquier otro tipo de transmisi?n por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido.
**CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies.



From pieter.neerincx at gmail.com  Wed May 21 21:40:56 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Wed, 21 May 2008 23:40:56 +0200
Subject: [MOBY-dev] Important note for MOBY-Async developers
In-Reply-To: <483449C1.6080709@cnio.es>
References: <480F498A.4060902@cnio.es> <480F50D4.5000907@cnio.es>
	<483441fa.15528c0a.1950.ffffddd5@mx.google.com>
	<483449C1.6080709@cnio.es>
Message-ID: <6035FA51-858D-4E39-9F59-D96C5DD56F51@gmail.com>

Hi Eddie & Jos?,

On 21 May 2008, at 18:11, Jose Manuel rodriguez wrote:

> Hi Eddie,
>
>
> It is strange. I have just make a checkout and the pdf looks  
> good...I don't know.
> We are checking now if the CVS has problems adding Binary Files.
> We know that Binary files need to be added to CVS in a special way:
> "cvs add -kb 'binary filename'"
>
> But how I said I can read the pdf document perfectly.

Check, me too. So I don't think it's a problem with the way the  
document was checked in... Could it be a problem specific to a certain  
PDF viewer. There are many different versions of the PDF "standard" by  
now :(. Maybe Eddie's PDF viewer has a problem with this specific  
version. (I tried the official Adobe Acrobat Reader as well as Preview  
both on Mac OS X)

Cheers,

Pi

> Cheers,
> Jos?.
>
>
> Edward Kawas wrote:
>> Hi Jose Manual,
>>
>> I noticed that the pdf document on async services seems to be  
>> corrupt (at
>> least for me). All the images are shown as smears.
>>
>> Can you verify if this is the case?
>>
>> Thanks,
>>
>> Eddie
>>
>> -----Original Message-----
>> From: moby-dev-bounces at lists.open-bio.org
>> [mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Jose Manuel
>> rodriguez
>> Sent: April-23-08 8:08 AM
>> To: moby-dev at lists.open-bio.org; moby-dev-bounces at lists.open-bio.org;
>> inb-tecnico at lists.cnio.es
>> Cc: Dmitry Repchevsky; "=?ISO-8859-1?Q?Jos=E9_?="@portal.open-bio.org
>> Subject: [MOBY-dev] Important note for MOBY-Async developers
>>
>> Hello,
>>
>>
>> The dispatcher of MOBY-Async services has to be modified.
>>
>> The MOBY-Async developers have to add the next method to
>> SOAP::Transport::HTTP::CGI
>>    $server->on_action(sub{});
>>
>> Inside of dispatcher he/she has to add:
>>
>> $WSRF::Constants::WSRPW.'/GetResourceProperty/ 
>> GetResourcePropertyRequest' =>' {Service Package}',
>> $WSRF::Constants::WSRPW.'/GetMultipleResourceProperties/ 
>> GetMultipleResourceP
>> ropertiesRequest' => '{Service Package}',
>> $WSRF::Constants::WSRLW.'/ImmediateResourceTermination/ 
>> DestroyRequest' => '{Service Package}',
>>
>> Then,
>>        $WSRF::Constants::WSRL => '{Service Package}',
>>        $WSRF::Constants::WSRP => '{Service Package}',
>>
>> could be deleted.
>>
>> I have attached you one CGI example.
>>
>>
>>
>> For more information:
>> http://biomoby.open-bio.org/CVS_CONTENT/moby-live/Docs/asyncDocs/BioMOBY%20A
>> synchronous%20Service%20Specification%20v2.4.2.pdf
>> (Maybe the CVS via web is not updated)
>>
>> Best Regads,
>> Jos? Manuel.
>>
>>
>>
>> Jose Manuel rodriguez wrote:
>>
>>> Hello,
>>>
>>> We have fixed some problems that there were in our MOBY-async  
>>> proposal.
>>>
>>> We found some inconsistencies in the specifications and  
>>> implementations:
>>>
>>> * The "GetResourceProperty" and "GetMultipleResourceProperties"  
>>> messages returned QNames (both status and results) without prefixes.
>>>
>>> * During WSA messages, in the MOBY-Async Perl API we had:
>>>        <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
>>> roperties/GetMultipleResourceProperties</wsa:Action>
>>>       When the WSRF specifications says that:
>>>        <wsa:Action>http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceP
>>> roperties/GetMultipleResourceProperties*Request*</wsa:Action>
>>>
>>> * In the WSDL for MOBY-Async services we have add the "soapAction"  
>>> address that SOAP 1.1 specifications says.
>>>
>>> * The MOBY-Async client and MOBY-Async sample have been updated  
>>> from these modifications. As soon as possible, we will sent you  
>>> one MOBY-Async sample which you could test it.
>>>
>>> * The MOBY-Async document has been updated (I have attached you  
>>> the MOBY-Async document v2.4.2).
>>>
>>> All these modifications have been committed to MOBY CVS.
>>>
>>> I think is all.
>>>
>>> Best Regards,
>>> Jos? Manuel.
>>>
>>>
>>>
>>> -- 
>>> Jos? Manuel Rodr?guez Carrasco            e-mail:  
>>> jmrodriguez at cnio.es
>>> Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
>>> Bioinformatic Unit
>>> Spanish National Cancer Center (CNIO) http://www.cnio.es Zip Code:  
>>> 28029
>>> Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain)
>>>
>>
>>
>>
>
>
> -- 
> Jos? Manuel Rodr?guez Carrasco            e-mail: jmrodriguez at cnio.es
> Tlfn:    (+34) 91 732 80 00 ext: 2256     Fax:    (+34) 91 224 69 76
> Bioinformatic Unit
> Spanish National Cancer Center (CNIO) http://www.cnio.es
> Zip Code: 28029
> Address: C/. Melchor Fernandez Almagro n? 3, Madrid (Spain)
>
> **NOTA DE CONFIDENCIALIDAD** Este correo electr?nico, y en su caso  
> los ficheros adjuntos, pueden contener informaci?n protegida para el  
> uso exclusivo de su destinatario. Se proh?be la distribuci?n,  
> reproducci?n o cualquier otro tipo de transmisi?n por parte de otra  
> persona que no sea el destinatario. Si usted recibe por error este  
> correo, se ruega comunicarlo al remitente y borrar el mensaje  
> recibido.
> **CONFIDENTIALITY NOTICE** This email communication and any  
> attachments may contain confidential and privileged information for  
> the sole use of the designated recipient named above. Distribution,  
> reproduction or any other use of this transmission by any party  
> other than the intended recipient is prohibited. If you are not the  
> intended recipient please contact the sender and delete all copies.
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev




From jflo at imim.es  Thu May 22 16:12:55 2008
From: jflo at imim.es (Judith Flo)
Date: Thu, 22 May 2008 18:12:55 +0200
Subject: [MOBY-dev] problem registering with dashboard
Message-ID: <48359B87.8070705@imim.es>

Hi,
I'm getting this error when i try to register something using an xml file

===ERROR===

Fault details:

[stackTrace: null]

[hostname: null]

Fault string: Failed to locate method (registerDataType) in class 
(MOBY::Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm 
line 2586, <IN> line 54.


Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Client

Fault actor:  null

When calling:

    http://moby.ucalgary.ca/moby/MOBY-Central.pl

===========


It happens always, I just can register new Data Types when I fill all 
boxes in the registration view...(I don't have any problems registering 
new services or namespaces)
The xml files that I'm using are the ones that i got when I use the 
"show raw XML" button, so I assume that they are correct...

Any help will be appreciatted.
Cheers,
j



From edward.kawas at gmail.com  Thu May 22 16:33:24 2008
From: edward.kawas at gmail.com (Edward Kawas)
Date: Thu, 22 May 2008 09:33:24 -0700
Subject: [MOBY-dev] problem registering with dashboard
In-Reply-To: <48359B87.8070705@imim.es>
References: <48359B87.8070705@imim.es>
Message-ID: <4835a065.08b38c0a.4751.6f48@mx.google.com>

Hi Judith,

The problem is that registerDataType is not the correct name. Try
registerObjectClass instead.

Thanks,

Eddie

-----Original Message-----
From: moby-dev-bounces at lists.open-bio.org
[mailto:moby-dev-bounces at lists.open-bio.org] On Behalf Of Judith Flo
Sent: May-22-08 9:13 AM
To: Core developer announcements
Subject: [MOBY-dev] problem registering with dashboard

Hi,
I'm getting this error when i try to register something using an xml file

===ERROR===

Fault details:

[stackTrace: null]

[hostname: null]

Fault string: Failed to locate method (registerDataType) in class 
(MOBY::Central) at /opt/coolstack/lib/perl5/site_perl/5.8.8/SOAP/Lite.pm 
line 2586, <IN> line 54.


Fault code:   {http://schemas.xmlsoap.org/soap/envelope/}Client

Fault actor:  null

When calling:

    http://moby.ucalgary.ca/moby/MOBY-Central.pl

===========


It happens always, I just can register new Data Types when I fill all 
boxes in the registration view...(I don't have any problems registering 
new services or namespaces)
The xml files that I'm using are the ones that i got when I use the 
"show raw XML" button, so I assume that they are correct...

Any help will be appreciatted.
Cheers,
j

_______________________________________________
MOBY-dev mailing list
MOBY-dev at lists.open-bio.org
http://lists.open-bio.org/mailman/listinfo/moby-dev



From martin.senger at gmail.com  Thu May 22 16:35:03 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 23 May 2008 00:35:03 +0800
Subject: [MOBY-dev] problem registering with dashboard
In-Reply-To: <48359B87.8070705@imim.es>
References: <48359B87.8070705@imim.es>
Message-ID: <4d93f07c0805220935k1660fb79ud5a7cb7ff33514dc@mail.gmail.com>

I'm getting this error when i try to register something using an xml file


I am glad that you got this error :-)
Because I got the same error several hours ago, and I have asked Eddie to
help me to find what is wrong. He has not replied yet. But the problem is
being solved...

M.

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From martin.senger at gmail.com  Thu May 22 16:39:23 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 23 May 2008 00:39:23 +0800
Subject: [MOBY-dev] problem registering with dashboard
In-Reply-To: <4835a065.08b38c0a.4751.6f48@mx.google.com>
References: <48359B87.8070705@imim.es>
	<4835a065.08b38c0a.4751.6f48@mx.google.com>
Message-ID: <4d93f07c0805220939w594d3185i32b8298545af3856@mail.gmail.com>

>
> The problem is that registerDataType is not the correct name. Try
> registerObjectClass instead.


Not possible - because it is the Dashboard who uses this wrong method, not
Judith.
Read my email please.

M.

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From martin.senger at gmail.com  Thu May 22 17:15:34 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Fri, 23 May 2008 01:15:34 +0800
Subject: [MOBY-dev] problem registering with dashboard
In-Reply-To: <4d93f07c0805220939w594d3185i32b8298545af3856@mail.gmail.com>
References: <48359B87.8070705@imim.es>
	<4835a065.08b38c0a.4751.6f48@mx.google.com>
	<4d93f07c0805220939w594d3185i32b8298545af3856@mail.gmail.com>
Message-ID: <4d93f07c0805221015p106c30d0r24b63ed350a2696a@mail.gmail.com>

It is fixed now. Please do cvs update.

But I cannot believe it: the bug was there for two years. It was never
working properly. Which means that nobody has used it. Until today! When we
both tried it *in the same day*, within about five hours. The planet Gaia
syndrome (http://en.wikipedia.org/wiki/Gaia_hypothesis) is here again!

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From jflo at imim.es  Fri May 23 07:49:54 2008
From: jflo at imim.es (Judith Flo)
Date: Fri, 23 May 2008 09:49:54 +0200
Subject: [MOBY-dev] problem registering with dashboard
In-Reply-To: <4d93f07c0805221015p106c30d0r24b63ed350a2696a@mail.gmail.com>
References: <48359B87.8070705@imim.es>	<4835a065.08b38c0a.4751.6f48@mx.googl
	e.com>	<4d93f07c0805220939w594d3185i32b8298545af3856@mail.gmail.com> 
	<4d93f07c0805221015p106c30d0r24b63ed350a2696a@mail.gmail.com>
Message-ID: <48367722.9030006@imim.es>

Hi,

[this is just for information] I didn't change any configuration and now 
when I cvs-update the moby project and try to start the dashboard (on 
Eclipse) I got this:

Buildfile: /home/judith/workspace3/moby/build.xml

checkmaven:


BUILD FAILED

/home/judith/workspace3/moby/xmls/maven.xml:62: Sorry...

    Missing Maven library. It can be fetched from the Internet.

    Type: ant bootstrap

    This is needed to be done only once.


Updates were working before without problem...

After running the bootstrap task I got my dashboard working properly and 
the data-type registration_from_xml_file button is working perfectly 
(lazy people (like me) will be happy ;)), it is a very useful tool when 
one wants to register its data-types, namespaces and services to 
different repositories, i don't understand why people don't use it... )

Thanks to all of you for your work!
j


Martin Senger wrote:
> It is fixed now. Please do cvs update.
>
> But I cannot believe it: the bug was there for two years. It was never
> working properly. Which means that nobody has used it. Until today! When we
> both tried it *in the same day*, within about five hours. The planet Gaia
> syndrome (http://en.wikipedia.org/wiki/Gaia_hypothesis) is here again!
>
> Martin
>
>   


From jason.e.stewart at gmail.com  Fri May 23 10:46:24 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Fri, 23 May 2008 16:16:24 +0530
Subject: [MOBY-dev] Error Registering service with Dashboard: malformed
	authURI
Message-ID: <41c1ade50805230346v1140a2ech9b2d208464efd00@mail.gmail.com>

Hey,

I'm feeling a bit stupid, but no matter what authURI I use, I get the error:

  Malformed authURI - must not have an http:// prefix

but my authURI doesn't have an 'http://' prefix... and I still get the error.

I tried registering with XML first, and then tried with the dashboard
second. Don't know what I'm doing I guess. Clues gratefully
accepted...

Cheers, jas.


From jason.e.stewart at gmail.com  Fri May 23 10:54:58 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Fri, 23 May 2008 16:24:58 +0530
Subject: [MOBY-dev] malformed authURI [solved]
Message-ID: <41c1ade50805230354l2318bc98s8087b79b64771c0b@mail.gmail.com>

Hey,

OK. It was an incomplet error message text...

Here is what the docs say:

authURI - a URI representing your organization (e.g. yourdomain.com);
no http-prefix, and no trailing path information is allowed.

but the code looks like this:

	return &_error( "Malformed authURI - must not have an http:// prefix", "" )
	  if $AuthURI =~ '[/:]';

Ah... I had a trailing '/'... but not a 'http://'  prefix... That was
confusing me...

So if I have a ':' or a '/' then the authURI is rejected. I'd be happy
to offer a patch for the error message to make it a bit more complete.
Is that helpful?

Cheers, jas.


From markw at illuminae.com  Fri May 23 15:58:41 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Fri, 23 May 2008 08:58:41 -0700
Subject: [MOBY-dev] malformed authURI [solved]
In-Reply-To: <41c1ade50805230354l2318bc98s8087b79b64771c0b@mail.gmail.com>
References: <41c1ade50805230354l2318bc98s8087b79b64771c0b@mail.gmail.com>
Message-ID: <op.ubl6n3uvnbznux@dd0710001l.icapture.ubc.ca>

the authURI is really intended to be the authority's domain name... so  
whatever regexp/error message changes you think will indicate that please  
go ahead :-)

Mark



On Fri, 23 May 2008 03:54:58 -0700, Jason Stewart  
<jason.e.stewart at gmail.com> wrote:

> Hey,
>
> OK. It was an incomplet error message text...
>
> Here is what the docs say:
>
> authURI - a URI representing your organization (e.g. yourdomain.com);
> no http-prefix, and no trailing path information is allowed.
>
> but the code looks like this:
>
> 	return &_error( "Malformed authURI - must not have an http:// prefix",  
> "" )
> 	  if $AuthURI =~ '[/:]';
>
> Ah... I had a trailing '/'... but not a 'http://'  prefix... That was
> confusing me...
>
> So if I have a ':' or a '/' then the authURI is rejected. I'd be happy
> to offer a patch for the error message to make it a bit more complete.
> Is that helpful?
>
> Cheers, jas.
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada



From jason.e.stewart at gmail.com  Fri May 23 17:19:54 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Fri, 23 May 2008 22:49:54 +0530
Subject: [MOBY-dev] DNS expired for open-bio.org
Message-ID: <41c1ade50805231019u45eed94awa6c56eb49c3991e2@mail.gmail.com>

Hey,

Just got this error:

ZoneEdit DNS services for this domain have expired.
To reactivate service for
OPEN-BIO.ORG/CVS_CONTENT/MOBY-LIVE/JAVA/DOCS/DASHBOARD.HTML, log into
your account and add credits.
Thank you for using ZoneEdit

Cheers, jas.


From gordonp at ucalgary.ca  Fri May 23 21:28:44 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Fri, 23 May 2008 15:28:44 -0600
Subject: [MOBY-dev] DNS expired for open-bio.org
In-Reply-To: <41c1ade50805231019u45eed94awa6c56eb49c3991e2@mail.gmail.com>
References: <41c1ade50805231019u45eed94awa6c56eb49c3991e2@mail.gmail.com>
Message-ID: <4837370C.5040207@ucalgary.ca>

I assume Chris is on vacation, or low on cash? :-)

Jason Stewart wrote:
> Hey,
>
> Just got this error:
>
> ZoneEdit DNS services for this domain have expired.
> To reactivate service for
> OPEN-BIO.ORG/CVS_CONTENT/MOBY-LIVE/JAVA/DOCS/DASHBOARD.HTML, log into
> your account and add credits.
> Thank you for using ZoneEdit
>
> Cheers, jas.
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> !DSPAM:60005,4837335d109501765921693!
>
>
>
>   


From jason.e.stewart at gmail.com  Sat May 24 11:13:37 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Sat, 24 May 2008 16:43:37 +0530
Subject: [MOBY-dev] malformed authURI [solved]
In-Reply-To: <op.ubl6n3uvnbznux@dd0710001l.icapture.ubc.ca>
References: <41c1ade50805230354l2318bc98s8087b79b64771c0b@mail.gmail.com>
	<op.ubl6n3uvnbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <41c1ade50805240413n55d11d8eu83ce112c0342a8e2@mail.gmail.com>

Hey Mark,

2008/5/23 Mark Wilkinson <markw at illuminae.com>:
> the authURI is really intended to be the authority's domain name... so
> whatever regexp/error message changes you think will indicate that please go
> ahead :-)

The regex checking for email and authURI is the same in three
different places so I thought I would centralize it to use a
subroutine that dies on error - so the code can be shared (in case the
messages or the regex's want to get changed later.

The subs look like this:

sub _validateAuthURI {
    my $auth = shift @_;

    my $error = "";
    if ($auth =~ '[/:]') {
	$error = "has a colon or a slash - must not have an http:// prefix,
and must not have trailing path info";
    } elsif ($auth =~ /\./) {
	$error = "must take the form NNN.NNN.NNN";
    }
    die "Malformed authURI - $error" if $error;
}

sub _validateEmail {
    my $email = shift @_;

    my $error = "";
    if ($email !~ /\S\@\S+\.\S+/) {
	$error = "Malformed email - must be a valid email address of the form
name\@organization.foo";
    }
    die $error if $error;
}

and they replace this code:

	return &_error( "Malformed authURI - must not have an http:// prefix", "" )
	  if $AuthURI =~ '[/:]';
	return &_error( "Malformed authURI - must take the form NNN.NNN.NNN", "" )
	  unless $AuthURI =~ /\./;
	return &_error("Malformed email - must be a valid email address of
the form name\@organization.foo","")
	  unless $contactEmail =~ /\S\@\S+\.\S+/;

with this:

	eval {_validateAuthURI($auth)};
	&_error($@) if $@;
	eval {_validateEmail($email)};
	&_error($@) if $@;

Does that look acceptable?

Mark and Eddie, I had one question about using that code in
registerService() - there seems to be two different error handling
strategies going on - there is an $error variable that is being added
to if any payload errors are found, but then authURI and email
validation causes _error() to be called immediately ... I was
wondering if this was accidental or on purpose? Should I changed the
authURI and email validation failure to also add to $error instead of
calling _error() immediately?

Cheers, jas.


From markw at illuminae.com  Sat May 24 14:59:39 2008
From: markw at illuminae.com (Mark)
Date: Sat, 24 May 2008 07:59:39 -0700
Subject: [MOBY-dev] malformed authURI [solved]
In-Reply-To: <41c1ade50805240413n55d11d8eu83ce112c0342a8e2@mail.gmail.com>
References: <41c1ade50805230354l2318bc98s8087b79b64771c0b@mail.gmail.com>
	<op.ubl6n3uvnbznux@dd0710001l.icapture.ubc.ca>
	<41c1ade50805240413n55d11d8eu83ce112c0342a8e2@mail.gmail.com>
Message-ID: <op.ubnylpmkdeqt07@bighome>

On Sat, 24 May 2008 04:13:37 -0700, Jason Stewart  
<jason.e.stewart at gmail.com> wrote:

> Does that look acceptable?

Fantastic!  Thanks!



> validation causes _error() to be called immediately ... I was
> wondering if this was accidental or on purpose? Should I changed the

Accidental.  Please change it to be consistent.

Cheers Jas!

M


From jason.e.stewart at gmail.com  Mon May 26 07:21:23 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Mon, 26 May 2008 12:51:23 +0530
Subject: [MOBY-dev] xml:lang explored
Message-ID: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>

Hey all,

Here's what I have found out.

I don't believe that changing the current parser for Central.pm is
going to help the situation. I have looked and besides special API's
like the one implemented by LibXML::Reader, the application is always
required to maintain the status of xml:lang using the standard SAX and
DOM API's - for Java or for Perl.

We will have to preserve the information in the DB, so a decision
needs to be made on what level the xml:lang should be used - only for
descriptions?? or for the whole registration?? At the moment I don't
see any reason to use it for more than the description - how do people
feel about this? Changing this should require adding one column to the
DB.

Finally, do we want registration with multiple descriptions? That will
probably require a significant change in the DB - a new table for
linking descriptions to registrations. Are people happy about that?

Cheers, jas.


From jason.e.stewart at gmail.com  Mon May 26 08:42:37 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Mon, 26 May 2008 14:12:37 +0530
Subject: [MOBY-dev] MOBY Central DB optimization
In-Reply-To: <480de11b.14b48c0a.0dfc.ffff9cdd@mx.google.com>
References: <41c1ade50804220313n1de734f0ldae2d077c97f5326@mail.gmail.com>
	<480de11b.14b48c0a.0dfc.ffff9cdd@mx.google.com>
Message-ID: <41c1ade50805260142q46b7893byfe3995d3d0342560@mail.gmail.com>

Hey Ed,

Just to let you know - it all worked fine, the cvs checkout, and the
make install. I did get some test failures - I can post them if you'd
like.

But now that things are installed... I'm not sure how to initiate the
repository - is there a web page for doing this?

Cheers, jas.

2008/4/22 Ed Kawas <ed.kawas at gmail.com>:
> Hi Jason,
>
> While it is now easier to install than before, it's still a little involved.
>
> If I were you, I would checkout moby from the cvs then:
>
> cd moby-live/Perl/MOBY-Server
> perl Makefile.PL
> make test
> make install
>
> then after the install, do a 'moby-s-install.pl' from the command line. That
> script is placed on you path during the make install phase.
>
> The 'make' part of things will prompt you to auto install some modules. This
> isn't full proof. I usually just download them myself and use the list that
> it provides as a guide.
>
> Before starting make sure that you have installed apache, mysql and have
> libxml2 on your system.
>
> Let me know if there is anything else that you need.
>
> Eddie
>
> -----Original Message-----
> From: Jason Stewart [mailto:jason.e.stewart at gmail.com]
> Sent: April-22-08 3:14 AM
> To: Core developer announcements; Ed Kawas
> Subject: MOBY Central DB optimization
>
> Hey Eddie,
>
> Just got the following from Mark:
>
> "THe MOBY Central issue would also be nice to work-out.  It will be in
> the MOBY-Server/lib/MOBY/Central.pm module.  The findService
> subroutine.  What I currently do is take each parameter that is passed
> into MOBY Central and do a database query on that parameter, hold the
> indexes of the discovered services in a hash where I increment the
> value of that hash elemnt by +1 each time it passes a test of being
> discovered in a single-parameter search, and then figure out which
> hash elements have been discovered on every search, and pass those
> back as the successfully discovered services.  This was done *only* to
> save me having to do nasty and largely unpredictable joins depending
> on which search parameters were passed-in.  If you can think of a way
> to optimize that, then please go ahead!  You will have to install a
> MOBY Central instance yourself - please talk to Eddie, as he has just
> finished writing an installer... should be simply "make install"."
>
> I'm wanting to setup a MOBY Central instance and debug findService()
> to see if there is a more efficient way to run it. Do you have a
> HOWTO?
>
> Cheers, jas.
>
>


From ed.kawas at gmail.com  Mon May 26 13:14:51 2008
From: ed.kawas at gmail.com (Ed Kawas)
Date: Mon, 26 May 2008 06:14:51 -0700
Subject: [MOBY-dev] MOBY Central DB optimization
In-Reply-To: <41c1ade50805260142q46b7893byfe3995d3d0342560@mail.gmail.com>
References: <41c1ade50804220313n1de734f0ldae2d077c97f5326@mail.gmail.com>	
	<480de11b.14b48c0a.0dfc.ffff9cdd@mx.google.com>
	<41c1ade50805260142q46b7893byfe3995d3d0342560@mail.gmail.com>
Message-ID: <483ab7d4.2a528c0a.6e50.3223@mx.google.com>

Hi Jason,

If you run the moby-s-install.pl from the command line, and enter 'yes' when
prompted to set up mysql, you can mirror a central registry. This should
help you fill up your local registry.

Thanks,

Eddie

-----Original Message-----
From: Jason Stewart [mailto:jason.e.stewart at gmail.com] 
Sent: May-26-08 1:43 AM
To: Ed Kawas; Core developer announcements
Subject: Re: MOBY Central DB optimization

Hey Ed,

Just to let you know - it all worked fine, the cvs checkout, and the
make install. I did get some test failures - I can post them if you'd
like.

But now that things are installed... I'm not sure how to initiate the
repository - is there a web page for doing this?

Cheers, jas.

2008/4/22 Ed Kawas <ed.kawas at gmail.com>:
> Hi Jason,
>
> While it is now easier to install than before, it's still a little
involved.
>
> If I were you, I would checkout moby from the cvs then:
>
> cd moby-live/Perl/MOBY-Server
> perl Makefile.PL
> make test
> make install
>
> then after the install, do a 'moby-s-install.pl' from the command line.
That
> script is placed on you path during the make install phase.
>
> The 'make' part of things will prompt you to auto install some modules.
This
> isn't full proof. I usually just download them myself and use the list
that
> it provides as a guide.
>
> Before starting make sure that you have installed apache, mysql and have
> libxml2 on your system.
>
> Let me know if there is anything else that you need.
>
> Eddie
>
> -----Original Message-----
> From: Jason Stewart [mailto:jason.e.stewart at gmail.com]
> Sent: April-22-08 3:14 AM
> To: Core developer announcements; Ed Kawas
> Subject: MOBY Central DB optimization
>
> Hey Eddie,
>
> Just got the following from Mark:
>
> "THe MOBY Central issue would also be nice to work-out.  It will be in
> the MOBY-Server/lib/MOBY/Central.pm module.  The findService
> subroutine.  What I currently do is take each parameter that is passed
> into MOBY Central and do a database query on that parameter, hold the
> indexes of the discovered services in a hash where I increment the
> value of that hash elemnt by +1 each time it passes a test of being
> discovered in a single-parameter search, and then figure out which
> hash elements have been discovered on every search, and pass those
> back as the successfully discovered services.  This was done *only* to
> save me having to do nasty and largely unpredictable joins depending
> on which search parameters were passed-in.  If you can think of a way
> to optimize that, then please go ahead!  You will have to install a
> MOBY Central instance yourself - please talk to Eddie, as he has just
> finished writing an installer... should be simply "make install"."
>
> I'm wanting to setup a MOBY Central instance and debug findService()
> to see if there is a more efficient way to run it. Do you have a
> HOWTO?
>
> Cheers, jas.
>
>



From markw at illuminae.com  Mon May 26 17:52:33 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 26 May 2008 10:52:33 -0700
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
Message-ID: <op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>

Should we allow registration of objects, service-types and namespaces in  
foreign languages also?  If so, then we need to re-think the entire way we  
manage the ontology, and assign unique id numbers to each node, where the  
rdf:label of the node can have multiple languages, rather than having the  
node named by its label.

...can... worms... but it's probably the "right thing to do"...

M



On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart  
<jason.e.stewart at gmail.com> wrote:

> Hey all,
>
> Here's what I have found out.
>
> I don't believe that changing the current parser for Central.pm is
> going to help the situation. I have looked and besides special API's
> like the one implemented by LibXML::Reader, the application is always
> required to maintain the status of xml:lang using the standard SAX and
> DOM API's - for Java or for Perl.
>
> We will have to preserve the information in the DB, so a decision
> needs to be made on what level the xml:lang should be used - only for
> descriptions?? or for the whole registration?? At the moment I don't
> see any reason to use it for more than the description - how do people
> feel about this? Changing this should require adding one column to the
> DB.
>
> Finally, do we want registration with multiple descriptions? That will
> probably require a significant change in the DB - a new table for
> linking descriptions to registrations. Are people happy about that?
>
> Cheers, jas.
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada


From markw at illuminae.com  Wed May 14 16:15:27 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 14 May 2008 09:15:27 -0700
Subject: [MOBY-dev] For hosts of MOBY Central
In-Reply-To: <482B0F0E.90807@ucalgary.ca>
References: <482B0F0E.90807@ucalgary.ca>
Message-ID: <op.ua5jf102nbznux@dd0710001l.icapture.ubc.ca>

Just FYI - this is a graph showing the CPU usage before and after that  
last fix I did on MOBY Central... just for anyone who didn't believe that  
it was an important fix :-)

M



------- Forwarded message -------
From: "Theron Dekok" <tcdekok at ucalgary.ca>
To: "Mark Wilkinson" <markw at illuminae.com>
Cc:
Subject: Moby Graph
Date: Wed, 14 May 2008 09:10:54 -0700

Hi Mark,

I thought the attached graph might be of interest. It's really amazing
how things have changed since the fix :-)

-Theron



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada
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From gordonp at ucalgary.ca  Mon May 26 18:59:42 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 26 May 2008 12:59:42 -0600
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <483B089E.20602@ucalgary.ca>

I think we are mostly polyglots on this list, but for the sake of 
technical simplicity, I'd stick with just tracking the language rather 
than having multiple values in the registry.  Multilingual descriptions 
could be offloaded to the LSID metadata perhaps if people really want it.

Mes 0.02$ canadiens,

Paul

Mark Wilkinson wrote:
> Should we allow registration of objects, service-types and namespaces 
> in foreign languages also?  If so, then we need to re-think the entire 
> way we manage the ontology, and assign unique id numbers to each node, 
> where the rdf:label of the node can have multiple languages, rather 
> than having the node named by its label.
>
> ...can... worms... but it's probably the "right thing to do"...
>
> M
>
>
>
> On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart 
> <jason.e.stewart at gmail.com> wrote:
>
>> Hey all,
>>
>> Here's what I have found out.
>>
>> I don't believe that changing the current parser for Central.pm is
>> going to help the situation. I have looked and besides special API's
>> like the one implemented by LibXML::Reader, the application is always
>> required to maintain the status of xml:lang using the standard SAX and
>> DOM API's - for Java or for Perl.
>>
>> We will have to preserve the information in the DB, so a decision
>> needs to be made on what level the xml:lang should be used - only for
>> descriptions?? or for the whole registration?? At the moment I don't
>> see any reason to use it for more than the description - how do people
>> feel about this? Changing this should require adding one column to the
>> DB.
>>
>> Finally, do we want registration with multiple descriptions? That will
>> probably require a significant change in the DB - a new table for
>> linking descriptions to registrations. Are people happy about that?
>>
>> Cheers, jas.
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>


From pieter.neerincx at gmail.com  Mon May 26 21:04:19 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Mon, 26 May 2008 23:04:19 +0200
Subject: [MOBY-dev] For hosts of MOBY Central
In-Reply-To: <op.ua5jf102nbznux@dd0710001l.icapture.ubc.ca>
References: <482B0F0E.90807@ucalgary.ca>
	<op.ua5jf102nbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <C086F783-E537-4C30-8827-940453A12511@gmail.com>

Bummer, funding agencies will be a lot less impressed after looking at  
the new graphs: "Is anybody actually using this BioMoby thing?" :)

Cheers,

Pi

On 14 May 2008, at 18:15, Mark Wilkinson wrote:

> Just FYI - this is a graph showing the CPU usage before and after  
> that last fix I did on MOBY Central... just for anyone who didn't  
> believe that it was an important fix :-)
>
> M
>
>
>
> ------- Forwarded message -------
> From: "Theron Dekok" <tcdekok at ucalgary.ca>
> To: "Mark Wilkinson" <markw at illuminae.com>
> Cc:
> Subject: Moby Graph
> Date: Wed, 14 May 2008 09:10:54 -0700
>
> Hi Mark,
>
> I thought the attached graph might be of interest. It's really amazing
> how things have changed since the fix :-)
>
> -Theron
>
>
>
> -- 
> Mark D Wilkinson, PI Bioinformatics
> Assistant Professor, Medical Genetics
> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary  
> Research
> Providence Heart + Lung Institute
> University of British Columbia - St. Paul's Hospital
> Vancouver, BC,  
> Canada<mobyGraph.png>_______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



From markw at illuminae.com  Mon May 26 21:09:53 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 26 May 2008 14:09:53 -0700
Subject: [MOBY-dev] For hosts of MOBY Central
In-Reply-To: <C086F783-E537-4C30-8827-940453A12511@gmail.com>
References: <482B0F0E.90807@ucalgary.ca>
	<op.ua5jf102nbznux@dd0710001l.icapture.ubc.ca>
	<C086F783-E537-4C30-8827-940453A12511@gmail.com>
Message-ID: <op.ubr42rmvnbznux@dd0710001l.icapture.ubc.ca>

damn!  Never thought of that!

;-)

M


On Mon, 26 May 2008 14:04:19 -0700, Pieter Neerincx  
<pieter.neerincx at gmail.com> wrote:

> Bummer, funding agencies will be a lot less impressed after looking at  
> the new graphs: "Is anybody actually using this BioMoby thing?" :)
>
> Cheers,
>
> Pi
>
> On 14 May 2008, at 18:15, Mark Wilkinson wrote:
>
>> Just FYI - this is a graph showing the CPU usage before and after that  
>> last fix I did on MOBY Central... just for anyone who didn't believe  
>> that it was an important fix :-)
>>
>> M
>>
>>
>>
>> ------- Forwarded message -------
>> From: "Theron Dekok" <tcdekok at ucalgary.ca>
>> To: "Mark Wilkinson" <markw at illuminae.com>
>> Cc:
>> Subject: Moby Graph
>> Date: Wed, 14 May 2008 09:10:54 -0700
>>
>> Hi Mark,
>>
>> I thought the attached graph might be of interest. It's really amazing
>> how things have changed since the fix :-)
>>
>> -Theron
>>
>>
>>
>> --Mark D Wilkinson, PI Bioinformatics
>> Assistant Professor, Medical Genetics
>> The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
>> Providence Heart + Lung Institute
>> University of British Columbia - St. Paul's Hospital
>> Vancouver, BC,  
>> Canada<mobyGraph.png>_______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada


From pieter.neerincx at gmail.com  Mon May 26 22:41:34 2008
From: pieter.neerincx at gmail.com (Pieter Neerincx)
Date: Tue, 27 May 2008 00:41:34 +0200
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <483B089E.20602@ucalgary.ca>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
Message-ID: <76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>

Hi all,

On 26 May 2008, at 20:59, Paul Gordon wrote:

> I think we are mostly polyglots on this list,

I'm a polyglot when I'm on holiday or in a pub maybe, but when I'm  
talking bioinformatics stuff I'm a strict monoglot! Before we open  
that can of worms: do we actually need translations? Did anyone  
request support for different languages? Mark mentioned someone did on  
the last developer meeting, but I didn't see anyone chime in on this  
list with a request for other languages. I only noticed a few objects  
and services in the official public Central containing descriptions in  
Spanish (or is it Portugese?), which renders them useless for the  
majority of users.

BioMoby web services are all about creating interoperable resources.  
Introducing the Tower of Babel effect isn't going to help. I hope I  
don't sound arrogant, but unless there are scientists out there using  
BioMoby for research into language itself, archeology or culture, I  
really fail to see why we need anything but the "de facto" standard  
language for research. (No, I'm not a native Englisch speaker...)

Is there actually any major bioinformatics resource that supports  
translations? I can't think of any, but maybe I should write an e-mail  
to the NCBI, DDBJ, EBI et al. and request Dutch translations of  
Genbank, PubMed, KEGG, Uniprot, Ensembl, etc. Might be fun to see if  
and how they repsond :)...

> but for the sake of technical simplicity, I'd stick with just  
> tracking the language rather than having multiple values in the  
> registry.

For even more simplicity I'd opt for hardcoding the language to  
English. Now let's hope the native English speakers are not going to  
fight over whether international English means Australian, UK,  
American, Canadian, or yet another English. If that happens I'm voting  
for Dinglish :).

Just my ? 0.02

Cheers,

Pi

>  Multilingual descriptions could be offloaded to the LSID metadata  
> perhaps if people really want it.
>
> Mes 0.02$ canadiens,
>
> Paul
>
> Mark Wilkinson wrote:
>> Should we allow registration of objects, service-types and  
>> namespaces in foreign languages also?  If so, then we need to re- 
>> think the entire way we manage the ontology, and assign unique id  
>> numbers to each node, where the rdf:label of the node can have  
>> multiple languages, rather than having the node named by its label.
>>
>> ...can... worms... but it's probably the "right thing to do"...
>>
>> M
>>
>>
>>
>> On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart <jason.e.stewart at gmail.com 
>> > wrote:
>>
>>> Hey all,
>>>
>>> Here's what I have found out.
>>>
>>> I don't believe that changing the current parser for Central.pm is
>>> going to help the situation. I have looked and besides special API's
>>> like the one implemented by LibXML::Reader, the application is  
>>> always
>>> required to maintain the status of xml:lang using the standard SAX  
>>> and
>>> DOM API's - for Java or for Perl.
>>>
>>> We will have to preserve the information in the DB, so a decision
>>> needs to be made on what level the xml:lang should be used - only  
>>> for
>>> descriptions?? or for the whole registration?? At the moment I don't
>>> see any reason to use it for more than the description - how do  
>>> people
>>> feel about this? Changing this should require adding one column to  
>>> the
>>> DB.
>>>
>>> Finally, do we want registration with multiple descriptions? That  
>>> will
>>> probably require a significant change in the DB - a new table for
>>> linking descriptions to registrations. Are people happy about that?
>>>
>>> Cheers, jas.
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev




From markw at illuminae.com  Mon May 26 22:58:53 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 26 May 2008 15:58:53 -0700
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
Message-ID: <op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>

personally, I tend to think we *should* be using the multi-lingual  
capabilities of XML more than we are!  The idea is not to introduce a  
tower of Babel, but rather to embrace as many languages as possible in our  
infrastructure!  to be inclusive, rather than exclusive!

this does, however, require extensive re-tooling of the software.  I  
wonder if it is something that is best left for Moby 2.0 (and planned from  
the start) rather than hacked into Moby 1.0?

M




On Mon, 26 May 2008 15:41:34 -0700, Pieter Neerincx  
<pieter.neerincx at gmail.com> wrote:

> Hi all,
>
> On 26 May 2008, at 20:59, Paul Gordon wrote:
>
>> I think we are mostly polyglots on this list,
>
> I'm a polyglot when I'm on holiday or in a pub maybe, but when I'm  
> talking bioinformatics stuff I'm a strict monoglot! Before we open that  
> can of worms: do we actually need translations? Did anyone request  
> support for different languages? Mark mentioned someone did on the last  
> developer meeting, but I didn't see anyone chime in on this list with a  
> request for other languages. I only noticed a few objects and services  
> in the official public Central containing descriptions in Spanish (or is  
> it Portugese?), which renders them useless for the majority of users.
>
> BioMoby web services are all about creating interoperable resources.  
> Introducing the Tower of Babel effect isn't going to help. I hope I  
> don't sound arrogant, but unless there are scientists out there using  
> BioMoby for research into language itself, archeology or culture, I  
> really fail to see why we need anything but the "de facto" standard  
> language for research. (No, I'm not a native Englisch speaker...)
>
> Is there actually any major bioinformatics resource that supports  
> translations? I can't think of any, but maybe I should write an e-mail  
> to the NCBI, DDBJ, EBI et al. and request Dutch translations of Genbank,  
> PubMed, KEGG, Uniprot, Ensembl, etc. Might be fun to see if and how they  
> repsond :)...
>
>> but for the sake of technical simplicity, I'd stick with just tracking  
>> the language rather than having multiple values in the registry.
>
> For even more simplicity I'd opt for hardcoding the language to English.  
> Now let's hope the native English speakers are not going to fight over  
> whether international English means Australian, UK, American, Canadian,  
> or yet another English. If that happens I'm voting for Dinglish :).
>
> Just my ? 0.02
>
> Cheers,
>
> Pi
>
>>  Multilingual descriptions could be offloaded to the LSID metadata  
>> perhaps if people really want it.
>>
>> Mes 0.02$ canadiens,
>>
>> Paul
>>
>> Mark Wilkinson wrote:
>>> Should we allow registration of objects, service-types and namespaces  
>>> in foreign languages also?  If so, then we need to re-think the entire  
>>> way we manage the ontology, and assign unique id numbers to each node,  
>>> where the rdf:label of the node can have multiple languages, rather  
>>> than having the node named by its label.
>>>
>>> ...can... worms... but it's probably the "right thing to do"...
>>>
>>> M
>>>
>>>
>>>
>>> On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart  
>>> <jason.e.stewart at gmail.com> wrote:
>>>
>>>> Hey all,
>>>>
>>>> Here's what I have found out.
>>>>
>>>> I don't believe that changing the current parser for Central.pm is
>>>> going to help the situation. I have looked and besides special API's
>>>> like the one implemented by LibXML::Reader, the application is always
>>>> required to maintain the status of xml:lang using the standard SAX and
>>>> DOM API's - for Java or for Perl.
>>>>
>>>> We will have to preserve the information in the DB, so a decision
>>>> needs to be made on what level the xml:lang should be used - only for
>>>> descriptions?? or for the whole registration?? At the moment I don't
>>>> see any reason to use it for more than the description - how do people
>>>> feel about this? Changing this should require adding one column to the
>>>> DB.
>>>>
>>>> Finally, do we want registration with multiple descriptions? That will
>>>> probably require a significant change in the DB - a new table for
>>>> linking descriptions to registrations. Are people happy about that?
>>>>
>>>> Cheers, jas.
>>>> _______________________________________________
>>>> MOBY-dev mailing list
>>>> MOBY-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>>
>>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada


From gordonp at ucalgary.ca  Mon May 26 23:10:58 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Mon, 26 May 2008 17:10:58 -0600
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>	<483B089E.20602@ucalgary.ca>	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
Message-ID: <483B4382.8020108@ucalgary.ca>

I will reiterate that I think the language of the text should be noted 
in the database somewhere, but that we shouldn't support multi-liguality 
for a single entry (that's too much work).  While we can pressure people 
into using English for the public central registry, I see no reason to 
force English on a boutique registry in Botswana (for example) just 
because we were too lazy to program in an extra column in the DB.  I am 
also thinking about the potential usefulness of Moby outside of science...

Mark Wilkinson wrote:
> personally, I tend to think we *should* be using the multi-lingual 
> capabilities of XML more than we are!  The idea is not to introduce a 
> tower of Babel, but rather to embrace as many languages as possible in 
> our infrastructure!  to be inclusive, rather than exclusive!
>
> this does, however, require extensive re-tooling of the software.  I 
> wonder if it is something that is best left for Moby 2.0 (and planned 
> from the start) rather than hacked into Moby 1.0?
>
> M
>
>
>
>
> On Mon, 26 May 2008 15:41:34 -0700, Pieter Neerincx 
> <pieter.neerincx at gmail.com> wrote:
>
>> Hi all,
>>
>> On 26 May 2008, at 20:59, Paul Gordon wrote:
>>
>>> I think we are mostly polyglots on this list,
>>
>> I'm a polyglot when I'm on holiday or in a pub maybe, but when I'm 
>> talking bioinformatics stuff I'm a strict monoglot! Before we open 
>> that can of worms: do we actually need translations? Did anyone 
>> request support for different languages? Mark mentioned someone did 
>> on the last developer meeting, but I didn't see anyone chime in on 
>> this list with a request for other languages. I only noticed a few 
>> objects and services in the official public Central containing 
>> descriptions in Spanish (or is it Portugese?), which renders them 
>> useless for the majority of users.
>>
>> BioMoby web services are all about creating interoperable resources. 
>> Introducing the Tower of Babel effect isn't going to help. I hope I 
>> don't sound arrogant, but unless there are scientists out there using 
>> BioMoby for research into language itself, archeology or culture, I 
>> really fail to see why we need anything but the "de facto" standard 
>> language for research. (No, I'm not a native Englisch speaker...)
>>
>> Is there actually any major bioinformatics resource that supports 
>> translations? I can't think of any, but maybe I should write an 
>> e-mail to the NCBI, DDBJ, EBI et al. and request Dutch translations 
>> of Genbank, PubMed, KEGG, Uniprot, Ensembl, etc. Might be fun to see 
>> if and how they repsond :)...
>>
>>> but for the sake of technical simplicity, I'd stick with just 
>>> tracking the language rather than having multiple values in the 
>>> registry.
>>
>> For even more simplicity I'd opt for hardcoding the language to 
>> English. Now let's hope the native English speakers are not going to 
>> fight over whether international English means Australian, UK, 
>> American, Canadian, or yet another English. If that happens I'm 
>> voting for Dinglish :).
>>
>> Just my ? 0.02
>>
>> Cheers,
>>
>> Pi
>>
>>>  Multilingual descriptions could be offloaded to the LSID metadata 
>>> perhaps if people really want it.
>>>
>>> Mes 0.02$ canadiens,
>>>
>>> Paul
>>>
>>> Mark Wilkinson wrote:
>>>> Should we allow registration of objects, service-types and 
>>>> namespaces in foreign languages also?  If so, then we need to 
>>>> re-think the entire way we manage the ontology, and assign unique 
>>>> id numbers to each node, where the rdf:label of the node can have 
>>>> multiple languages, rather than having the node named by its label.
>>>>
>>>> ...can... worms... but it's probably the "right thing to do"...
>>>>
>>>> M
>>>>
>>>>
>>>>
>>>> On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart 
>>>> <jason.e.stewart at gmail.com> wrote:
>>>>
>>>>> Hey all,
>>>>>
>>>>> Here's what I have found out.
>>>>>
>>>>> I don't believe that changing the current parser for Central.pm is
>>>>> going to help the situation. I have looked and besides special API's
>>>>> like the one implemented by LibXML::Reader, the application is always
>>>>> required to maintain the status of xml:lang using the standard SAX 
>>>>> and
>>>>> DOM API's - for Java or for Perl.
>>>>>
>>>>> We will have to preserve the information in the DB, so a decision
>>>>> needs to be made on what level the xml:lang should be used - only for
>>>>> descriptions?? or for the whole registration?? At the moment I don't
>>>>> see any reason to use it for more than the description - how do 
>>>>> people
>>>>> feel about this? Changing this should require adding one column to 
>>>>> the
>>>>> DB.
>>>>>
>>>>> Finally, do we want registration with multiple descriptions? That 
>>>>> will
>>>>> probably require a significant change in the DB - a new table for
>>>>> linking descriptions to registrations. Are people happy about that?
>>>>>
>>>>> Cheers, jas.
>>>>> _______________________________________________
>>>>> MOBY-dev mailing list
>>>>> MOBY-dev at lists.open-bio.org
>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>
>>>>
>>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>> _______________________________________________
>> MOBY-dev mailing list
>> MOBY-dev at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>
>
>


From jason.e.stewart at gmail.com  Wed May 28 10:30:09 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Wed, 28 May 2008 16:00:09 +0530
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <483B4382.8020108@ucalgary.ca>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
	<483B4382.8020108@ucalgary.ca>
Message-ID: <41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>

Hey All,

I have heard three ideas:

1) allow registration with multiple languages per instance
2) stick with english only
3) register with one language, but record the language

Of these cases I believe that using xml:lang is only valuable if 1) is chosen.

My understanding of the i18n support in general and xml:lang in
particular is to support a user setting his/her preferred language and
getting data in that language if it is available. So if the Dashboard
allowed us to set our preferred language to German and then retrieved
descriptions in German or fell back to English then I think we could
argue the effort was valuable.

But for case 3) I feel it would be a waste of effort - it wouldn't
change the existing user experience - it would just put a label on
what we already know. I don't believe users would search for services
with Spanish-only descriptions - but I do believe they would ask for
descriptions in Spanish if they existed.

I'm not here to advise whether we should or shouldn't support xml:lang
- only to advise that my personal opinion is that level of re-coding
is only useful if we support multiple descriptions in different
languages.

Personally I don't think there is a high demand in bioinformatics for
this feature - so I would advise against it. On the other hand - Mark
has pointed out that he hopes this work will have impact outside
bioinformataics. I can also add that the amount of code change is
pretty small for MOBY Central - the real impact is the change in the
clients to set language preferences.

So I am torn. I'm happy to make the change in MOBY Central - but it
won't be useful until the clients support it.

What do people say?

Cheers, jas.

2008/5/27 Paul Gordon <gordonp at ucalgary.ca>:
> I will reiterate that I think the language of the text should be noted in
> the database somewhere, but that we shouldn't support multi-liguality for a
> single entry (that's too much work).  While we can pressure people into
> using English for the public central registry, I see no reason to force
> English on a boutique registry in Botswana (for example) just because we
> were too lazy to program in an extra column in the DB.  I am also thinking
> about the potential usefulness of Moby outside of science...
>
> Mark Wilkinson wrote:
>>
>> personally, I tend to think we *should* be using the multi-lingual
>> capabilities of XML more than we are!  The idea is not to introduce a tower
>> of Babel, but rather to embrace as many languages as possible in our
>> infrastructure!  to be inclusive, rather than exclusive!
>>
>> this does, however, require extensive re-tooling of the software.  I
>> wonder if it is something that is best left for Moby 2.0 (and planned from
>> the start) rather than hacked into Moby 1.0?
>>
>> M
>>
>>
>>
>>
>> On Mon, 26 May 2008 15:41:34 -0700, Pieter Neerincx
>> <pieter.neerincx at gmail.com> wrote:
>>
>>> Hi all,
>>>
>>> On 26 May 2008, at 20:59, Paul Gordon wrote:
>>>
>>>> I think we are mostly polyglots on this list,
>>>
>>> I'm a polyglot when I'm on holiday or in a pub maybe, but when I'm
>>> talking bioinformatics stuff I'm a strict monoglot! Before we open that can
>>> of worms: do we actually need translations? Did anyone request support for
>>> different languages? Mark mentioned someone did on the last developer
>>> meeting, but I didn't see anyone chime in on this list with a request for
>>> other languages. I only noticed a few objects and services in the official
>>> public Central containing descriptions in Spanish (or is it Portugese?),
>>> which renders them useless for the majority of users.
>>>
>>> BioMoby web services are all about creating interoperable resources.
>>> Introducing the Tower of Babel effect isn't going to help. I hope I don't
>>> sound arrogant, but unless there are scientists out there using BioMoby for
>>> research into language itself, archeology or culture, I really fail to see
>>> why we need anything but the "de facto" standard language for research. (No,
>>> I'm not a native Englisch speaker...)
>>>
>>> Is there actually any major bioinformatics resource that supports
>>> translations? I can't think of any, but maybe I should write an e-mail to
>>> the NCBI, DDBJ, EBI et al. and request Dutch translations of Genbank,
>>> PubMed, KEGG, Uniprot, Ensembl, etc. Might be fun to see if and how they
>>> repsond :)...
>>>
>>>> but for the sake of technical simplicity, I'd stick with just tracking
>>>> the language rather than having multiple values in the registry.
>>>
>>> For even more simplicity I'd opt for hardcoding the language to English.
>>> Now let's hope the native English speakers are not going to fight over
>>> whether international English means Australian, UK, American, Canadian, or
>>> yet another English. If that happens I'm voting for Dinglish :).
>>>
>>> Just my ? 0.02
>>>
>>> Cheers,
>>>
>>> Pi
>>>
>>>>  Multilingual descriptions could be offloaded to the LSID metadata
>>>> perhaps if people really want it.
>>>>
>>>> Mes 0.02$ canadiens,
>>>>
>>>> Paul
>>>>
>>>> Mark Wilkinson wrote:
>>>>>
>>>>> Should we allow registration of objects, service-types and namespaces
>>>>> in foreign languages also?  If so, then we need to re-think the entire way
>>>>> we manage the ontology, and assign unique id numbers to each node, where the
>>>>> rdf:label of the node can have multiple languages, rather than having the
>>>>> node named by its label.
>>>>>
>>>>> ...can... worms... but it's probably the "right thing to do"...
>>>>>
>>>>> M
>>>>>
>>>>>
>>>>>
>>>>> On Mon, 26 May 2008 00:21:23 -0700, Jason Stewart
>>>>> <jason.e.stewart at gmail.com> wrote:
>>>>>
>>>>>> Hey all,
>>>>>>
>>>>>> Here's what I have found out.
>>>>>>
>>>>>> I don't believe that changing the current parser for Central.pm is
>>>>>> going to help the situation. I have looked and besides special API's
>>>>>> like the one implemented by LibXML::Reader, the application is always
>>>>>> required to maintain the status of xml:lang using the standard SAX and
>>>>>> DOM API's - for Java or for Perl.
>>>>>>
>>>>>> We will have to preserve the information in the DB, so a decision
>>>>>> needs to be made on what level the xml:lang should be used - only for
>>>>>> descriptions?? or for the whole registration?? At the moment I don't
>>>>>> see any reason to use it for more than the description - how do people
>>>>>> feel about this? Changing this should require adding one column to the
>>>>>> DB.
>>>>>>
>>>>>> Finally, do we want registration with multiple descriptions? That will
>>>>>> probably require a significant change in the DB - a new table for
>>>>>> linking descriptions to registrations. Are people happy about that?
>>>>>>
>>>>>> Cheers, jas.
>>>>>> _______________________________________________
>>>>>> MOBY-dev mailing list
>>>>>> MOBY-dev at lists.open-bio.org
>>>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>>>
>>>>>
>>>>>
>>>> _______________________________________________
>>>> MOBY-dev mailing list
>>>> MOBY-dev at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>>
>>>
>>> _______________________________________________
>>> MOBY-dev mailing list
>>> MOBY-dev at lists.open-bio.org
>>> http://lists.open-bio.org/mailman/listinfo/moby-dev
>>
>>
>>
> _______________________________________________
> MOBY-dev mailing list
> MOBY-dev at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-dev
>



From martin.senger at gmail.com  Wed May 28 10:42:20 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 28 May 2008 18:42:20 +0800
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
	<483B4382.8020108@ucalgary.ca>
	<41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>
Message-ID: <4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>

> 1) allow registration with multiple languages per instance
> 2) stick with english only
> 3) register with one language, but record the language


> Of these cases I believe that using xml:lang is only valuable if 1) is
> chosen.
>

When we met in February, I understood that we decided to have option 3. And
doing it by using xml:lang - I do not see why you are saying that it cannot
be used for option 3.

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From jason.e.stewart at gmail.com  Wed May 28 12:11:15 2008
From: jason.e.stewart at gmail.com (Jason Stewart)
Date: Wed, 28 May 2008 17:41:15 +0530
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
	<483B4382.8020108@ucalgary.ca>
	<41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>
	<4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>
Message-ID: <41c1ade50805280511l1173a54ao20b1ee6ed7395920@mail.gmail.com>

Hey Martin,

2008/5/28 Martin Senger <martin.senger at gmail.com>:
>> 1) allow registration with multiple languages per instance
>> 2) stick with english only
>> 3) register with one language, but record the language
>
>
>> Of these cases I believe that using xml:lang is only valuable if 1) is
>> chosen.

> When we met in February, I understood that we decided to have option 3. And
> doing it by using xml:lang - I do not see why you are saying that it cannot
> be used for option 3.

Thanks - I guess I need to clarify. I'm definitely new to the scene
and so I am trying to play catchup with what has already been
discussed.

Yes, xml:lang can be used without any problem for 3) - but my point
was that it wouldn't change the current user experience of MOBY. I
wasn't understanding how it would change what users do. If a user
registers a service and provides the description in Spanish - it will
be stored as xml:lang="es" in the DB. But I don't believe that users
will look for services based on the value of that xml:lang attribute -
the description will be returned to them (in Spanish) just as it was
without storing the xml:lang. Perhaps I am missing something important
- so please help me understand if I don't get it.

In my mind, the real value of xml:lang is when it can be used to
return the user information in their preferred language - only
supporting a single language defeats that purpose. That way the
returned descriptions of any registered service will all be in Spanish
if they exist - or English if they do not, or whatever language is
available if English is not present.

I hope this helps clarify what I meant.

Cheers, jas.


From martin.senger at gmail.com  Wed May 28 13:06:11 2008
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 28 May 2008 21:06:11 +0800
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <41c1ade50805280511l1173a54ao20b1ee6ed7395920@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
	<483B4382.8020108@ucalgary.ca>
	<41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>
	<4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>
	<41c1ade50805280511l1173a54ao20b1ee6ed7395920@mail.gmail.com>
Message-ID: <4d93f07c0805280606g2caab44bo4158ca4e29c5020a@mail.gmail.com>

> Yes, xml:lang can be used without any problem for 3) - but my point
> was that it wouldn't change the current user experience of MOBY.


Yes, you are completely right. [That's why I have never taken this language
discussion - and decision - too seriously :-)]

Martin

-- 
Martin Senger
email: martin.senger at gmail.com,m.senger at cgiar.org
skype: martinsenger


From gordonp at ucalgary.ca  Wed May 28 13:44:29 2008
From: gordonp at ucalgary.ca (Paul Gordon)
Date: Wed, 28 May 2008 07:44:29 -0600
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <4d93f07c0805280606g2caab44bo4158ca4e29c5020a@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>	<483B089E.20602@ucalgary.ca>	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>	<483B4382.8020108@ucalgary.ca>	<41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>	<4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>	<41c1ade50805280511l1173a54ao20b1ee6ed7395920@mail.gmail.com>
	<4d93f07c0805280606g2caab44bo4158ca4e29c5020a@mail.gmail.com>
Message-ID: <483D61BD.9090507@ucalgary.ca>

This originally came up because there were places in the Central XML 
that used the xml:lang="en" attribute, but the contents was Spanish.  I 
cannot find these attributes anymore, so the conflict appears to have 
been removed...

Martin Senger wrote:
>> Yes, xml:lang can be used without any problem for 3) - but my point
>> was that it wouldn't change the current user experience of MOBY.
>>     
>
>
> Yes, you are completely right. [That's why I have never taken this language
> discussion - and decision - too seriously :-)]
>
> Martin
>
>   


From markw at illuminae.com  Wed May 28 15:51:50 2008
From: markw at illuminae.com (Mark Wilkinson)
Date: Wed, 28 May 2008 08:51:50 -0700
Subject: [MOBY-dev] xml:lang explored
In-Reply-To: <4d93f07c0805280606g2caab44bo4158ca4e29c5020a@mail.gmail.com>
References: <41c1ade50805260021l6b88de2an9eff38cb79101d6b@mail.gmail.com>
	<op.ubrvxvb0nbznux@dd0710001l.icapture.ubc.ca>
	<483B089E.20602@ucalgary.ca>
	<76618742-4E1E-4FB6-9D36-21030491C164@gmail.com>
	<op.ubr94fbsnbznux@dd0710001l.icapture.ubc.ca>
	<483B4382.8020108@ucalgary.ca>
	<41c1ade50805280330h3e6eb737wbafa3752b7cb6468@mail.gmail.com>
	<4d93f07c0805280342h632bc93ewecc57ad050a6966b@mail.gmail.com>
	<41c1ade50805280511l1173a54ao20b1ee6ed7395920@mail.gmail.com>
	<4d93f07c0805280606g2caab44bo4158ca4e29c5020a@mail.gmail.com>
Message-ID: <op.ubvfooconbznux@dd0710001l.icapture.ubc.ca>

On Wed, 28 May 2008 06:06:11 -0700, Martin Senger  
<martin.senger at gmail.com> wrote:

> [That's why I have never taken this languag discussion - and decision -  
> too seriously :-)]


Martin set's his e-value cutoff to 10e-45 for these kinds of debates ;-)

LOL!

M



-- 
Mark D Wilkinson, PI Bioinformatics
Assistant Professor, Medical Genetics
The James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research
Providence Heart + Lung Institute
University of British Columbia - St. Paul's Hospital
Vancouver, BC, Canada