From maliha.aziz at yahoo.com  Mon Oct  1 19:30:31 2007
From: maliha.aziz at yahoo.com (maliha aziz)
Date: Mon, 1 Oct 2007 16:30:31 -0700 (PDT)
Subject: [MOBY-l] need help in populating a simple DB with biomoby
	services
In-Reply-To: <op.tzi5y3lunbznux@personalpc>
Message-ID: <234093.4149.qm@web57404.mail.re1.yahoo.com>

Hello Dr Wilkinson :)
 nope noone answered but I figured out the packages and all... I just want to confirm the thought process and the LSID part... All services and all datatypes do have LSIDs right?  I need a unique primary key and LSID is my best shot here :)
One more question the "HAS" and "HASA" relationship types allow me to determine if there are multiple instances of the same datatypes i.e. whether it is a record or a bag... right?

I dont think (at the moment ) that implementing whether a datatype is a record list or a bag etc for biomoby in my project is realistic. I dont know maybe a lot of brain storming is needed for this part... (maybe i need to clear my own concepts on this part first)

Thanks

Maliha 

Mark Wilkinson <markw at illuminae.com> wrote: Did anyone ever answer you?



On Wed, 26 Sep 2007 15:19:07 -0700, maliha aziz   
wrote:

> Hi
> the datatypes in biomoby are either
>
>    records or
>
>    sets (has only one instance of a particular child e.g. geneSNP that  
> is composed of
>
>        aa_pos (HASA) => Integer
>        strain (HASA) => String
>        codon_ref (HASA) => String
>        aa_ref (HASA) => String
>        codon_var (HASA) => String
>        aa_var (HASA) => String
>        aa_change (HASA) => String)     or
>
>    bags ( allows repeat of the same instance within it .g DNA sequence  
> Holder )
> correct?
>
> I have a simple Database that is composed of 5 tables
>
> The first table is called the "Concept class". It will hold the  
> datatypes declared in biomoby and their LSID
> The Second table is called the "Concept structure". It will hold the  
> information about the datatype itself whether it is a record , a set or  
> a bag....
> the third table is the "Concept Components". This table would hold the  
> child information i.e. for geneSNP datatype this table would hold
>    aa_pos (HASA) => Integer
>        strain (HASA) => String
>        codon_ref (HASA) => String
>        aa_ref (HASA) => String
>        codon_var (HASA) => String
>        aa_var (HASA) => String
>        aa_change (HASA) => String)
> LSID of each component would be stored along with other info.
>
> Now this takes care of the datatype. To look at the tool itself
> I have a table "Tools" that hold the information about the webservice  
> registered in biomoby its name the LSID etc
> Another table called the "Tools_io" holds the information about the  
> input and out puts of this particular tool . This is basically a  
> relational entity between the Tools and the Concept compnents.
>
> My first question... Am I on the right track?
> About the concept structure table I would have to find out  
> programmatically myself whether the datatype is a record or a set or a  
> bag by looking at the LSIDz right? (does a simple string have a LSID?)
> Secondly , right now I have just downloaded the webservices in a simple  
> file from biomoby so am not really sure if  this is going to work  
> although the work is pretty simple. It is the biomoby end that is a bit  
> confusing.
> If I download the datatypes and populate the Concept table and then  
> venture towards downloading the tools themselves Can I link the  
> datatypes with the tool IO through the LSID?
> Could someone tell me what packages am I looking at over here while  
> tryin to accomplish this.
>
> There is one thing missing here and that is the declaration of Tools_IO  
> to be collections or enumerated etc at the time of declaring the tool. I  
> still have to figure that out
>
> I would be really grateful if someone could help me out in this... :)
>
> regards
>
> Maliha
>
> ---------------------------------
> Shape Yahoo! in your own image.  Join our Network Research Panel today!
> _______________________________________________
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> moby-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-l



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
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From edward.kawas at gmail.com  Mon Oct  1 19:41:13 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 1 Oct 2007 16:41:13 -0700
Subject: [MOBY-l] need help in populating a simple DB with
	biomobyservices
In-Reply-To: <234093.4149.qm@web57404.mail.re1.yahoo.com>
References: <op.tzi5y3lunbznux@personalpc>
	<234093.4149.qm@web57404.mail.re1.yahoo.com>
Message-ID: <000601c80484$8eef70f0$6400a8c0@notebook>

> All services and all datatypes do have LSIDs 
> right?  I need a unique primary key and LSID is my best shot 
Yes they do each have an LSID. Make sure to read up on the lsid spec! an
lsid can uniquely identify something, but there can be revision information
associated with the LSID. BioMOBY uses revision information.

> here :) One more question the "HAS" and "HASA" relationship 
> types allow me to determine if there are multiple instances 
> of the same datatypes i.e. whether it is a record or a bag... right?
Yes, a record of a bag of records.

Eddie


From clushbou at usd.edu  Mon Oct  8 13:08:07 2007
From: clushbou at usd.edu (Carol Lushbough)
Date: Mon, 08 Oct 2007 12:08:07 -0500
Subject: [MOBY-l] Java CentralImpl call problem
Message-ID: <470A63F7.3030003@usd.edu>

All,

I was wondering if someone could help me with this problem  I'm trying 
to execute a BioMoby service using XML in a java applicaiton

When I try to execute the following code:

                String response = new 
CentralImpl("http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl", 
"http://biomoby.org/").call(mr.getService().getName(),inputXMLString);

I receive the following error message:

http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.plnull
org.biomoby.shared.MobyException: 
http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.plnull
        at org.biomoby.client.CentralImpl.doCall(CentralImpl.java:221)
        at org.biomoby.client.CentralImpl.call(CentralImpl.java:1506)

Caused by: Denied access to method (ClustalWFastaCollection) in class 
(main) at /usr/lib/perl5/site_perl/5.8.5/SOAP/Lite.pm line 2509, <IN> 
line 131440.

I"m pretty sure my inputXMLString is OK because when I use it in 
dashboard, it works fine.

I also tried creating a MobyContentInstance object and calling 
MobyRequest setInput but the ">" in my FASTA records doesn't get 
formated correctly.

Thanks!

Carol



               

-- 
Carol Lushbough
Assistant Professor of Computer Science
University of South Dakota
Vermillion, SD 57069
(605) 677-6138 



From martin.senger at gmail.com  Mon Oct  8 13:37:33 2007
From: martin.senger at gmail.com (Martin Senger)
Date: Mon, 8 Oct 2007 18:37:33 +0100
Subject: [MOBY-l] Java CentralImpl call problem
In-Reply-To: <470A63F7.3030003@usd.edu>
References: <470A63F7.3030003@usd.edu>
Message-ID: <4d93f07c0710081037l44891c0dp42e20a42987d1d00@mail.gmail.com>

Hi,

                String response = new
> CentralImpl("
> http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl",
> "http://biomoby.org/").call(mr.getService().getName(),inputXMLString);


The problem may be with your parameters to the constructor of the
CentralImpl. They should be an endpoint and a registry namespace. Therefore,
at least for the default registry, the second parameter should be
http://mobycentral.icapture.ubc.ca/MOBY/Central. However, if you wish to
call the default registry, better to use the no-arg constructor (just new
CentralImpl() ).

I wonder if this does it solve your problem... [if not, we will find a
different solution :-) ]

Cheers,
Martin

-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger

From edward.kawas at gmail.com  Tue Oct  9 09:23:18 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 9 Oct 2007 06:23:18 -0700
Subject: [MOBY-l] Java CentralImpl call problem
In-Reply-To: <470A63F7.3030003@usd.edu>
References: <470A63F7.3030003@usd.edu>
Message-ID: <000f01c80a77$8f82a930$0401a8c0@notebook>

Hi,

>                 String response = new
> CentralImpl("http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05
> /mobycentral.pl",
> "http://biomoby.org/").call(mr.getService().getName(),inputXMLString);

What you have as http://mobycentral.icapture.ubc.ca/... should actually be
the endpoint of your service, since you are hoping to call the physical
service and not the registry. The following page might be useful:
https://biomoby.tigr.org/wiki/index.php/Discovering_and_Invoking_Moby_Servic
es

Hope that helps!

Eddie


From maliha.aziz at yahoo.com  Tue Oct  9 15:23:21 2007
From: maliha.aziz at yahoo.com (maliha aziz)
Date: Tue, 9 Oct 2007 12:23:21 -0700 (PDT)
Subject: [MOBY-l] services and their data types
Message-ID: <702272.85874.qm@web57406.mail.re1.yahoo.com>

Hi
sorry to bother you again. I was wondering if you could help me in figuring out how to link the the input output datatypes of a service with the entries in the main table that might be holding all known data types . oh and all of this is pertaining to biomoby ofcourse. I am actually confused because I donot have the biomoby schema infront of me so it all becomes kind of a guessing game.
My question is that if I retrieve a service and it has some inputs and outputs with certain data types how do I link these data types to the data types in the main repository (u know a table that holds all declared data types). Do you give IDz to the datatypes while declaring them that become foreign keys for the service inputs and outputs? If yes how do i retreive these IDz? 
What I thought I could use were LSIDz. But then they are strings and although I am treating them as keys(not primary), I donot want to base my searching on LSIDz as they are strings and strings are not very reliable keys.

My question might have confused you here a bit ....

Would be really grateful if you could help me out :)

Regards

Maliha

       
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From maliha.aziz at yahoo.com  Wed Oct 10 18:19:50 2007
From: maliha.aziz at yahoo.com (maliha aziz)
Date: Wed, 10 Oct 2007 15:19:50 -0700 (PDT)
Subject: [MOBY-l] collections
Message-ID: <282688.95093.qm@web57406.mail.re1.yahoo.com>

hi

I use the org.biomoby.client.CentralDigestCachedImpl package's getServices() function to get all services. Then for each service I use the function getPrimaryInputs() to retrieve all the primary inputs... now how do i find out whether this primary input is a collection or not?.

maliha
       
---------------------------------
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From martin.senger at gmail.com  Wed Oct 10 18:31:14 2007
From: martin.senger at gmail.com (Martin Senger)
Date: Wed, 10 Oct 2007 23:31:14 +0100
Subject: [MOBY-l] collections
In-Reply-To: <282688.95093.qm@web57406.mail.re1.yahoo.com>
References: <282688.95093.qm@web57406.mail.re1.yahoo.com>
Message-ID: <4d93f07c0710101531j6f609852wd4cbefb09b849f3f@mail.gmail.com>

On 10/10/07, maliha aziz <maliha.aziz at yahoo.com> wrote:
>
> hi
>
> I use the org.biomoby.client.CentralDigestCachedImpl package's
> getServices() function to get all services. Then for each service I use the
> function getPrimaryInputs() to retrieve all the primary inputs... now how do
> i find out whether this primary input is a collection or not?.


if (inputs[i] instanceof MobyPrimaryDataSet) {
   // you have a collection
} else {
   // you have a Simple
}

Martin

-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger

From clushbou at usd.edu  Fri Oct 12 08:52:41 2007
From: clushbou at usd.edu (Carol Lushbough)
Date: Fri, 12 Oct 2007 07:52:41 -0500
Subject: [MOBY-l] Verifying a Service
Message-ID: <470F6E19.9030705@usd.edu>

So sorry to bother you but it is still not clear to me how to best test 
a service in a Java Client.  Given the following statement:

The status of all services is tested hourly, and is recorded in the 
      LSID metadata for each service as a boolean value in the RDF tag
       "isAlive", which may be used by client software to filter-out
       non-functional services.

Is there a Java method that I can call to ask is the service "alive".  
The following code verifies that I can find the service but doesn't 
guarantee that the service is functional.

try {
	Central central = new CentralImpl(url, uri);
 	if (central.findService(s).length > 0)
 		return true;
} catch (MobyException e) {

Am I correct in thinking that once I locate a service, if the following code 
 
String inputXML = "<MOBY><mobyContent></mobyContent></MOBY>";              
String response = new CentralImpl(serviceURL,"http://biomoby.org/").call(serviceName,inputXML );

throws an exception or does not return a response in the form:
     
            <MOBY>
            	<mobyContent></mobyContent>
            </MOBY>

indicates that the service is dead?

Thank you very much!

Carol

-- 
Carol Lushbough
Assistant Professor of Computer Science
University of South Dakota
Vermillion, SD 57069
(605) 677-6138 



From dmitry.repchevski at bsc.es  Mon Oct 15 08:46:50 2007
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Mon, 15 Oct 2007 14:46:50 +0200
Subject: [MOBY-l] wsdl for MOBY Central
Message-ID: <4713613A.6050806@bsc.es>

Hello!

As far as I understand Moby Central (Registry) is implemented as
web-service itself isn't it?
How (where) can I get a wsdl for it? I have an endpoint (suppose
webservice) URL, then I have some examples of messages in XML with a
notion that this is a "SOAP payload".
So the part I miss is the SOAP message or better the wsdl...

Cheers,

Dmitry


From edward.kawas at gmail.com  Mon Oct 15 09:37:36 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Mon, 15 Oct 2007 06:37:36 -0700
Subject: [MOBY-l] wsdl for MOBY Central
References: <4713613A.6050806@bsc.es> 
Message-ID: <000e01c80f30$8c917950$6400a8c0@notebook>

I just realized that I hit reply, rather than reply to all!

Eddie 

> -----Original Message-----
> From: Edward Kawas [mailto:edward.kawas at gmail.com] 
> Sent: Monday, October 15, 2007 6:14 AM
> To: 'Dmitry Repchevsky'
> Subject: RE: [MOBY-l] wsdl for MOBY Central
> 
> Hi Dmitry,
> 
> We don't have wsdls just yet for the registry, but we do have 
> xml schemas for the in/outputs to mobycentral (the wsdls will 
> follow shortly).
> 
> You can find the schemas at 
> moby-live/Docs/Schemas/RegistryAPI in the moby cvs.
> 
> Hope this helps,
> 
> Eddie 
> 
> > -----Original Message-----
> > From: moby-l-bounces at lists.open-bio.org 
> > [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Dmitry 
> > Repchevsky
> > Sent: Monday, October 15, 2007 5:47 AM
> > To: moby-l at lists.open-bio.org
> > Subject: [MOBY-l] wsdl for MOBY Central
> > 
> > Hello!
> > 
> > As far as I understand Moby Central (Registry) is implemented as 
> > web-service itself isn't it?
> > How (where) can I get a wsdl for it? I have an endpoint (suppose
> > webservice) URL, then I have some examples of messages in 
> XML with a 
> > notion that this is a "SOAP payload".
> > So the part I miss is the SOAP message or better the wsdl...
> > 
> > Cheers,
> > 
> > Dmitry
> > 
> > _______________________________________________
> > moby-l mailing list
> > moby-l at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/moby-l


From dmitry.repchevski at bsc.es  Tue Oct 16 09:41:29 2007
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Tue, 16 Oct 2007 15:41:29 +0200
Subject: [MOBY-l] registry messages
Message-ID: <4714BF89.8080306@bsc.es>

Hello!

I was able to connect the registry using the schema (thx 2 Edward) in 
moby docs.
The schemas look to be generated from XML messages (not vice versa).
No problem - it's simple enough to get in.
The problem I have is that different services (schemas) uses similar 
objects (Simple, Input, Output...).
As far as I understand they supposed to be the same, but not exactly :-(.
Sometimes the difference is only in namespace (i.e in RegistryService 
"Simple.articleName" decrared within a namespace, but not in FindService).
Is this a schema inconsistence or it's really the situation?
Because (by now I tested only findService) in schema we have 
[targetNamespace="http://mobycentral.icapture.ubc.ca/MOBY/Central"]
but if I try to send the message with this namespace the service 
fails... (works OK without).

The question is. DOES this schema reflects the real API?
If not, is it correct to omit namespaces? (I checked it looks like the 
Central is easy about it, even it's wrong from xml point of view).

Sincerely Yours,

Dmitry

From edward.kawas at gmail.com  Tue Oct 16 09:45:47 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 16 Oct 2007 06:45:47 -0700
Subject: [MOBY-l] registry messages
In-Reply-To: <4714BF89.8080306@bsc.es>
References: <4714BF89.8080306@bsc.es>
Message-ID: <000901c80ffa$dbcc5060$6400a8c0@notebook>

Hi Dmitry, 

> -----Original Message-----
> From: moby-l-bounces at lists.open-bio.org 
> [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of 
> Dmitry Repchevsky
> Sent: Tuesday, October 16, 2007 6:41 AM
> To: moby-l at lists.open-bio.org
> Subject: [MOBY-l] registry messages
> 
> Hello!
> 
> I was able to connect the registry using the schema (thx 2 
> Edward) in moby docs.
> The schemas look to be generated from XML messages (not vice versa).
> No problem - it's simple enough to get in.
> The problem I have is that different services (schemas) uses 
> similar objects (Simple, Input, Output...).
> As far as I understand they supposed to be the same, but not 
> exactly :-(.
> Sometimes the difference is only in namespace (i.e in 
> RegistryService "Simple.articleName" decrared within a 
> namespace, but not in FindService).
> Is this a schema inconsistence or it's really the situation?

Probably an inconsistency.

Could you point me to those inconsistencies? I created the schemas and I
would love to make them as correct as possible.


> Because (by now I tested only findService) in schema we have 
> [targetNamespace="http://mobycentral.icapture.ubc.ca/MOBY/Central"]
> but if I try to send the message with this namespace the 
> service fails... (works OK without).
> 
> The question is. DOES this schema reflects the real API?
> If not, is it correct to omit namespaces? (I checked it looks 
> like the Central is easy about it, even it's wrong from xml 
> point of view).
> 
Omitting the namespaces should be okay.

> Sincerely Yours,
> 

Eddie

> Dmitry
> _______________________________________________
> moby-l mailing list
> moby-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-l


From edward.kawas at gmail.com  Tue Oct 16 10:31:30 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Tue, 16 Oct 2007 07:31:30 -0700
Subject: [MOBY-l] registry messages
In-Reply-To: <4714C92B.7050305@bsc.es>
References: <4714BF89.8080306@bsc.es> <000901c80ffa$dbcc5060$6400a8c0@notebook>
	<4714C92B.7050305@bsc.es>
Message-ID: <000d01c81001$3e914a60$6400a8c0@notebook>

Thanks for replying! 

> most notably the <xs:attribute name="articleName"> is 
> specified with namespace in first example and without in second.

That was done because of restrictions on articleName; specifically, that
each articleName must be unique. Hence when you register a service, the
constraint appears, but not for finding services. I think that you are
right, in that perhaps while I did constrain the value, I introduced a
namespace inadvertently. I will see what I can do about that.


> As far as I understand you (?) are trying to make a FORMAL 
> message specification based on schema, manually (?) coz  the 
> only specification I found so far is some obscure XML examples... :-(

I guess so. the idea was that the schemas would be the inputs/outputs for
WSDLs that have yet to be created.

> 
> if you are interested the java class describing "findService" 
> below. I'm using inner static classes to avoid interference 
> with another services, but I think classes like Input?/Output 
> should have the same structure for any service?!! The cool 
> thing is that JAXB marshall/unmarshall it automagically... so 
> actually there is almos no API...
> 

Thanks. I haven't actually ever used JAXB. Looks like something that could
be a lot of fun.

> Sincerely Yours,
> 

Eddie




From ola.spjuth at farmbio.uu.se  Fri Oct 19 08:41:26 2007
From: ola.spjuth at farmbio.uu.se (Ola Spjuth)
Date: Fri, 19 Oct 2007 14:41:26 +0200
Subject: [MOBY-l] MobyDataType 'Object'
Message-ID: <9D92A08D-B47D-4E29-A8E8-776EF3192BC5@farmbio.uu.se>

Hi,

How should the primitive MobyDataType 'Object' be treated? If a  
service only has a input with a primitive 'Object', what does it expect?

Example (implemented in jMoby):
The service 'getKeggPathwayAsGif' has primary input name='pathway'  
with MobyDataType 'object', hence instantiating from this  
datatypeName creates a MobyDataObject, which cannot contain a value  
(the static method createInstanceFromString(typename, value) sets the  
'value' parameter as ID for the MobyDataObject). Is this intentional  
and in that case what is the intention?

Why does not the service use the DataType 'String' if that's what it  
expects? Is the dirty workaround to always supply a MobyDataString if  
a DataType is set to Object?

Cheers,

    .../Ola

From edward.kawas at gmail.com  Fri Oct 19 09:20:28 2007
From: edward.kawas at gmail.com (Edward Kawas)
Date: Fri, 19 Oct 2007 06:20:28 -0700
Subject: [MOBY-l] MobyDataType 'Object'
In-Reply-To: <9D92A08D-B47D-4E29-A8E8-776EF3192BC5@farmbio.uu.se>
References: <9D92A08D-B47D-4E29-A8E8-776EF3192BC5@farmbio.uu.se>
Message-ID: <000f01c81252$d8ea9690$6400a8c0@notebook>

Hi Ola,

The service that you mention expects an identifier (Kegg pathway id) set in
the id portion of the datatype Object. The combination of the id/ns portion
of Object usually specifies a db/id into that db. So when service providers
want to create a service that queries some db, they usually have input of
object. They would expect that you provide the query identifier as the id in
object.

Hope this makes sense,

Eddie

> -----Original Message-----
> From: moby-l-bounces at lists.open-bio.org 
> [mailto:moby-l-bounces at lists.open-bio.org] On Behalf Of Ola Spjuth
> Sent: Friday, October 19, 2007 5:41 AM
> To: moby-l at lists.open-bio.org
> Subject: [MOBY-l] MobyDataType 'Object'
> 
> Hi,
> 
> How should the primitive MobyDataType 'Object' be treated? If 
> a service only has a input with a primitive 'Object', what 
> does it expect?
> 
> Example (implemented in jMoby):
> The service 'getKeggPathwayAsGif' has primary input name='pathway'  
> with MobyDataType 'object', hence instantiating from this 
> datatypeName creates a MobyDataObject, which cannot contain a 
> value (the static method createInstanceFromString(typename, 
> value) sets the 'value' parameter as ID for the 
> MobyDataObject). Is this intentional and in that case what is 
> the intention?
> 
> Why does not the service use the DataType 'String' if that's 
> what it expects? Is the dirty workaround to always supply a 
> MobyDataString if a DataType is set to Object?
> 
> Cheers,
> 
>     .../Ola
> _______________________________________________
> moby-l mailing list
> moby-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-l


From groscurt at mpiz-koeln.mpg.de  Fri Oct 19 09:29:16 2007
From: groscurt at mpiz-koeln.mpg.de (groscurt at mpiz-koeln.mpg.de)
Date: Fri, 19 Oct 2007 15:29:16 +0200 (CEST)
Subject: [MOBY-l] MobyDataType 'Object'
In-Reply-To: <9D92A08D-B47D-4E29-A8E8-776EF3192BC5@farmbio.uu.se>
References: <9D92A08D-B47D-4E29-A8E8-776EF3192BC5@farmbio.uu.se>
Message-ID: <56036.195.37.46.22.1192800556.squirrel@mpizmail.mpiz-koeln.mpg.de>

Hi,

In the moby world the basic datatype is an object. Any object can be
identified by its id and a namespace. Both values guarantee to describe
the object explicitly.

As an example:

00492215062447

does not tell you anything for what this number / string stands for. With
the namespace "telephone number" it becomes clearly what its for.

The same id can be used differently - e.g. with the namespace "social
number" it is a different object than the one with the namespace
"telephone number" - so with the same content (the id), they are
semantically different (because of the namespace).

If a MobyService has as input such kind of object - e.g. a database
identifier - the MobyObject has to be used. There is no more information
one needs, because its all defined with these object.

The DataType String is semantically incorrect because not all identifiers
are Strings (see telephone examples).

Therefore dont use MobyDataString if an Object is needed.


Thats my point of view - please correct me or add to that
andreas



On Friday 19 October 2007 14:41, Ola Spjuth wrote:
> Hi,
>
> How should the primitive MobyDataType 'Object' be treated? If a
> service only has a input with a primitive 'Object', what does it expect?
>
> Example (implemented in jMoby):
> The service 'getKeggPathwayAsGif' has primary input name='pathway'
> with MobyDataType 'object', hence instantiating from this
> datatypeName creates a MobyDataObject, which cannot contain a value
> (the static method createInstanceFromString(typename, value) sets the
> 'value' parameter as ID for the MobyDataObject). Is this intentional
> and in that case what is the intention?
>
> Why does not the service use the DataType 'String' if that's what it
> expects? Is the dirty workaround to always supply a MobyDataString if
> a DataType is set to Object?
>
> Cheers,
>
>     .../Ola
> _______________________________________________
> moby-l mailing list
> moby-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-l

-- 
Andreas Groscurth
Diplom Bioinformatik - PhD Student
Max Planck Institute for Plant Breeding Research
Carl-von-Linn?-Weg 10
50829 Cologne
Germany
E-mail:    groscurt at mpiz-koeln.mpg.de
Phone:    +49(0)221-5062-447


From ola.spjuth at farmbio.uu.se  Fri Oct 19 12:36:24 2007
From: ola.spjuth at farmbio.uu.se (Ola Spjuth)
Date: Fri, 19 Oct 2007 18:36:24 +0200
Subject: [MOBY-l] MobyDataType 'Object'
In-Reply-To: <56036.195.37.46.22.1192800556.squirrel@mpizmail.mpiz-koeln.mpg.de>
References: <9D92A08D-B47D-4E29-A8E8-776EF3192BC5@farmbio.uu.se>
	<56036.195.37.46.22.1192800556.squirrel@mpizmail.mpiz-koeln.mpg.de>
Message-ID: <D74AED60-A879-4278-AF7D-FC5E9C1B04EF@farmbio.uu.se>

Thanks for the help, I understand a lot better now.

Cheers,

    .../Ola

On Oct 19, 2007, at 15:29 , groscurt at mpiz-koeln.mpg.de wrote:

> Hi,
>
> In the moby world the basic datatype is an object. Any object can be
> identified by its id and a namespace. Both values guarantee to  
> describe
> the object explicitly.
>
> As an example:
>
> 00492215062447
>
> does not tell you anything for what this number / string stands  
> for. With
> the namespace "telephone number" it becomes clearly what its for.
>
> The same id can be used differently - e.g. with the namespace "social
> number" it is a different object than the one with the namespace
> "telephone number" - so with the same content (the id), they are
> semantically different (because of the namespace).
>
> If a MobyService has as input such kind of object - e.g. a database
> identifier - the MobyObject has to be used. There is no more  
> information
> one needs, because its all defined with these object.
>
> The DataType String is semantically incorrect because not all  
> identifiers
> are Strings (see telephone examples).
>
> Therefore dont use MobyDataString if an Object is needed.
>
>
> Thats my point of view - please correct me or add to that
> andreas
>
>
>
> On Friday 19 October 2007 14:41, Ola Spjuth wrote:
>> Hi,
>>
>> How should the primitive MobyDataType 'Object' be treated? If a
>> service only has a input with a primitive 'Object', what does it  
>> expect?
>>
>> Example (implemented in jMoby):
>> The service 'getKeggPathwayAsGif' has primary input name='pathway'
>> with MobyDataType 'object', hence instantiating from this
>> datatypeName creates a MobyDataObject, which cannot contain a value
>> (the static method createInstanceFromString(typename, value) sets the
>> 'value' parameter as ID for the MobyDataObject). Is this intentional
>> and in that case what is the intention?
>>
>> Why does not the service use the DataType 'String' if that's what it
>> expects? Is the dirty workaround to always supply a MobyDataString if
>> a DataType is set to Object?
>>
>> Cheers,
>>
>>     .../Ola
>> _______________________________________________
>> moby-l mailing list
>> moby-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-l
>
> -- 
> Andreas Groscurth
> Diplom Bioinformatik - PhD Student
> Max Planck Institute for Plant Breeding Research
> Carl-von-Linn?-Weg 10
> 50829 Cologne
> Germany
> E-mail:    groscurt at mpiz-koeln.mpg.de
> Phone:    +49(0)221-5062-447
>



From maliha.aziz at yahoo.com  Fri Oct 19 19:19:12 2007
From: maliha.aziz at yahoo.com (maliha aziz)
Date: Fri, 19 Oct 2007 16:19:12 -0700 (PDT)
Subject: [MOBY-l] visualise data types
Message-ID: <175993.90029.qm@web57413.mail.re1.yahoo.com>

Hi 

Is there a tool that anyone knows of by which I could dump in all the biomoby datatypes and it returns me a tree type of structure (actual visual tree) .... I normally use dashboard if i want any sort of information but i usually get lost while tracing the ISA  hierarchy 

Maliha

 __________________________________________________
Do You Yahoo!?
Tired of spam?  Yahoo! Mail has the best spam protection around 
http://mail.yahoo.com 

From martin.senger at gmail.com  Fri Oct 19 19:45:29 2007
From: martin.senger at gmail.com (Martin Senger)
Date: Sat, 20 Oct 2007 00:45:29 +0100
Subject: [MOBY-l] visualise data types
In-Reply-To: <175993.90029.qm@web57413.mail.re1.yahoo.com>
References: <175993.90029.qm@web57413.mail.re1.yahoo.com>
Message-ID: <4d93f07c0710191645p1051de2dm7551b490a0e6d21e@mail.gmail.com>

> Is there a tool that anyone knows of by which I could dump in all the
> biomoby datatypes and it returns me a tree type of structure (actual visual
> tree)


Yes, it is. But it has not been updated for a long time. I have just tried
and it still work (at least most of the options) - but it can produce too
big pictures (for example with the option -d you get *all* data types). I
was planning to make it better browsable. But it has now a low priority -
but perhaps one day I will return to it by exploring Google maps API for
it...

Anyway, here is how you can use it (of course, you can also read about it
quite comprehensive documentation on the jMoby pages):

cd jMoby
build/run/run-graphs-client -h | less
build/run/run-graphs-client -cachedir myCache -q -d > data.dot
dot -Tpng data.dot > data.png
display data.png

[You need to fill first your local cache. You can use the one created by
dashboard, or update it by another command-line client.

And you need program 'dot' that can convert the created tree into an image.]

Cheers,
Martin


-- 
Martin Senger
   email: martin.senger at gmail.com
   skype: martinsenger

From dmitry.repchevski at bsc.es  Mon Oct 22 08:38:22 2007
From: dmitry.repchevski at bsc.es (Dmitry Repchevsky)
Date: Mon, 22 Oct 2007 14:38:22 +0200
Subject: [MOBY-l] Registry "Relationships" return is wrong?
Message-ID: <471C99BE.1020703@bsc.es>

Hello!

I'm trying to get a relationship for ObjectType, but got the wrong 
answer... (?)

Here is the xml I send:

********************************************************
<?xml version="1.0" encoding="UTF-8" standalone="yes"?>
<Relationships xmlns:moby="http://www.biomoby.org/moby">
    <direction>root</direction>
    <expandRelationship>0</expandRelationship>
    <objectType>PepinfoReport</objectType>
    <relationshipType>ISA</relationshipType>
    <relationshipType>HAS</relationshipType>
    <relationshipType>HASA</relationshipType>
</Relationships>
********************************************************

And the answer is:

********************************************************
<Relationships>
<Relationship relationshipType='HASA' 
lsid='urn:lsid:biomoby.org:objectrelation:hasa'>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z' 
articleName='Aromatic'>FeatureAASequence</objectType>
</Relationship>
<Relationship relationshipType='ISA' 
lsid='urn:lsid:biomoby.org:objectrelation:isa'>
<objectType 
lsid='urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z' 
 >Object</objectType>
</Relationship>
</Relationships>
********************************************************
As you can notice the articleName is the same for ALL FeatureAASequence[s]

I tried to use two endpoints:
http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl
and
http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl


Thank you,

Dmitry

From markw at illuminae.com  Mon Oct 22 13:12:29 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 22 Oct 2007 10:12:29 -0700
Subject: [MOBY-l] Registry "Relationships" return is wrong?
In-Reply-To: <471C99BE.1020703@bsc.es>
References: <471C99BE.1020703@bsc.es>
Message-ID: <op.t0lze3frnbznux@personalpc>

I'll look into this and get back to you.

Sorry you're having troubles!

Mark


On Mon, 22 Oct 2007 05:38:22 -0700, Dmitry Repchevsky  
<dmitry.repchevski at bsc.es> wrote:

> Hello!
>
> I'm trying to get a relationship for ObjectType, but got the wrong
> answer... (?)
>
> Here is the xml I send:
>
> ********************************************************
> <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
> <Relationships xmlns:moby="http://www.biomoby.org/moby">
>     <direction>root</direction>
>     <expandRelationship>0</expandRelationship>
>     <objectType>PepinfoReport</objectType>
>     <relationshipType>ISA</relationshipType>
>     <relationshipType>HAS</relationshipType>
>     <relationshipType>HASA</relationshipType>
> </Relationships>
> ********************************************************
>
> And the answer is:
>
> ********************************************************
> <Relationships>
> <Relationship relationshipType='HASA'
> lsid='urn:lsid:biomoby.org:objectrelation:hasa'>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
> articleName='Aromatic'>FeatureAASequence</objectType>
> </Relationship>
> <Relationship relationshipType='ISA'
> lsid='urn:lsid:biomoby.org:objectrelation:isa'>
> <objectType
> lsid='urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z'
>  >Object</objectType>
> </Relationship>
> </Relationships>
> ********************************************************
> As you can notice the articleName is the same for ALL  
> FeatureAASequence[s]
>
> I tried to use two endpoints:
> http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl
> and
> http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl
>
>
> Thank you,
>
> Dmitry
> _______________________________________________
> moby-l mailing list
> moby-l at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/moby-l



-- 
--
Mark Wilkinson
Assistant Professor, Dept. Medical Genetics
University of British Columbia
PI Bioinformatics
iCAPTURE Centre, St. Paul's Hospital
Tel:  604 682 2344 x62129
Fax:  604 806 9274

***CONFIDENTIALITY NOTICE***
This electronic message is intended only for the use of the addressee and  
may contain information that is privileged and confidential.  Any  
dissemination, distribution or copying of this communication by  
unauthorized individuals is strictly prohibited. If you have received this  
communication in error, please notify the sender immediately by reply  
e-mail and delete the original and all copies from your system.
 


From markw at illuminae.com  Mon Oct 22 20:40:07 2007
From: markw at illuminae.com (Mark Wilkinson)
Date: Mon, 22 Oct 2007 17:40:07 -0700
Subject: [MOBY-l] Registry "Relationships" return is wrong?
In-Reply-To: <op.t0lze3frnbznux@personalpc>
References: <471C99BE.1020703@bsc.es> <op.t0lze3frnbznux@personalpc>
Message-ID: <op.t0mj45hunbznux@homecomp>

Problem is fixed.  Let me know if you notice any other errors.

Best wishes!

Mark



On Mon, 22 Oct 2007 10:12:29 -0700, Mark Wilkinson <markw at illuminae.com>  
wrote:

> I'll look into this and get back to you.
>
> Sorry you're having troubles!
>
> Mark
>
>
> On Mon, 22 Oct 2007 05:38:22 -0700, Dmitry Repchevsky
> <dmitry.repchevski at bsc.es> wrote:
>
>> Hello!
>>
>> I'm trying to get a relationship for ObjectType, but got the wrong
>> answer... (?)
>>
>> Here is the xml I send:
>>
>> ********************************************************
>> <?xml version="1.0" encoding="UTF-8" standalone="yes"?>
>> <Relationships xmlns:moby="http://www.biomoby.org/moby">
>>     <direction>root</direction>
>>     <expandRelationship>0</expandRelationship>
>>     <objectType>PepinfoReport</objectType>
>>     <relationshipType>ISA</relationshipType>
>>     <relationshipType>HAS</relationshipType>
>>     <relationshipType>HASA</relationshipType>
>> </Relationships>
>> ********************************************************
>>
>> And the answer is:
>>
>> ********************************************************
>> <Relationships>
>> <Relationship relationshipType='HASA'
>> lsid='urn:lsid:biomoby.org:objectrelation:hasa'>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:FeatureAASequence:2001-09-21T16-00-00Z'
>> articleName='Aromatic'>FeatureAASequence</objectType>
>> </Relationship>
>> <Relationship relationshipType='ISA'
>> lsid='urn:lsid:biomoby.org:objectrelation:isa'>
>> <objectType
>> lsid='urn:lsid:biomoby.org:objectclass:Object:2001-09-21T16-00-00Z'
>>  >Object</objectType>
>> </Relationship>
>> </Relationships>
>> ********************************************************
>> As you can notice the articleName is the same for ALL
>> FeatureAASequence[s]
>>
>> I tried to use two endpoints:
>> http://moby-dev.inab.org/cgi-bin/MOBY-Central.pl
>> and
>> http://mobycentral.icapture.ubc.ca/cgi-bin/MOBY05/mobycentral.pl
>>
>>
>> Thank you,
>>
>> Dmitry
>> _______________________________________________
>> moby-l mailing list
>> moby-l at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/moby-l
>
>
>