>Could I suggest a Skype chat , with interested developers involved , so
>you could get an idea what technologies are used by partners and we can
>discuss what technology will best suit IBMC team?

Dear Nina,

It is a good idea! Thank you for your suggestion! Now, we try to integrate
Cake PHP and Rest framework on our web-server, with realized on Windows. I
think Skype chat will be more productive after our experience on this field.
My Skype is alexey_zakharov_v.


>Welcome on board! Just a small thing I noticed: A request on
>http://195.178.ox/feature/compound/1/feature_definition/MNA returns
>Nothing while a request on
>http://195.178.207.160:8080/OpenTox/feature/compound/1/feature_definition/M
>NA/ is successful. The difference is clearly the / in the end of the second
>URI. The same holds for other URIs as well!

Dear Pantelis,

Thank you answer! We know about this problem. The slash (/) in the end of
the URI is necessary to use for Windows. So, cURL commands for Windows could
not work with out this slash, but POSTER (Mozilla Firefox) could work!

Yours sincerely,
Alexey Zakharov.
 
 

-----Original Message-----
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Sent: Wednesday, November 04, 2009 2:00 PM
To: development at opentox.org
Subject: Development Digest, Vol 10, Issue 5

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Today's Topics:

   1. Re: IBMC services (Nina Jeliazkova)
   2. Re: IBMC services (chung)


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

Message: 1
Date: Tue, 03 Nov 2009 16:26:24 +0200
From: Nina Jeliazkova <nina at acad.bg>
Subject: Re: [OTDev] IBMC services
To: opentox development mailing list <development at opentox.org>
Cc: joerg.wicker at in.tum.de
Message-ID: <4AF03D90.2050609 at acad.bg>
Content-Type: text/plain; charset=ISO-8859-1

Dear Alexey,

Few comments from my side, which I hope will help clarify your questions
and partners experience.

Regarding the service:
1) It is great yet another partner is becoming online :)
2) You are claiming implementation of following OpenTox resources:
feature definitions, feature, references, and algorithms.  So far the
only service running is one that retrieves feature value for specific
(hidden) compound and MNA descriptor, i.e. the one at

http://195.178.207.160:8080/OpenTox/feature/compound/{compound-id}/feature_d
efinition/{descr_id}/

>From your email it is not clear if other services are accessible and from
where.  The obvious URLs for the rest of the services are not working. 

http://195.178.207.160:8080/OpenTox/feature/
http://195.178.207.160:8080/OpenTox/feature_definition
http://195.178.207.160:8080/OpenTox/reference
http://195.178.207.160:8080/OpenTox/algorithm

http://195.178.207.160:8080/OpenTox/compound/1   - it is not clear now
how to retrieve the compound you are calculating descriptors for.

At this moment this is obviously an work in progress, therefore I expect
in next version your will be providing the claimed services. 

3) Another issue is your service return information under text/uri-list,
but the values returned are not URIs.  Therefore, you should support
different representation for the returned MNA values, rather than URI-list.

Regarding the underlying technology, I am not sure I understand your
questions completely.    Briefly, some of the partners are using java
and Restlet library and the some application server (tomcat or
similar).  The rest of the services are implemented and run with Ruby on
Rails framework. Both Java and Ruby applications can run on different
operating systems, so we are not locked into a single OS.

Could I suggest a Skype chat , with interested developers involved , so
you could get an idea what technologies are used by partners and we can
discuss what technology will best suit IBMC team?


Best regards,
Nina

 


Alexey wrote:
> Dear Joerg,
>
> At present time our server is working.
>
> We used cURL version 7.19.6 ssl and Poster (Mozilla Firefox) for
> implementation of following query:
>
> A Linux example call (command line) to retrieve a list of MNA descriptors
> for compounds would be:
>
> curl -X GET -H 'Accept:text/uri-list'
>
http://195.178.207.160:8080/OpenTox/feature/compound/1/feature_definition/MN
> A/
>
> For Poster (Mozilla Firefox) using GET method you could be obtained list
of
> MNA descriptors for compounds:
>
>
http://195.178.207.160:8080/OpenTox/feature/compound/1/feature_definition/MN
> A/
>
> I send you print screens of Poster and cURL working.
>
> How we understand use of curl command for curl -X POST -d
> "dataset_id=http://test.server.com/input.sdf" -H 'Accept:text/xml'
>
http://opentox.informatik.tu-muenchen.de:8080/OpenTox/algorithm/descriptorca
> lculation/physicochemical/CDKPhysChem activate working of XML-parser for
> descriptors calculation. Could you write, what does XML-parser initiate
for
> working of XML algorithm which are located in
>
http://opentox.informatik.tu-muenchen.de:8080/OpenTox/algorithm/descriptorca
> lculation/physicochemical/CDKPhysChem. Is it especial program or may be
you
> use XML-server for this purpose (I mean executable module is realized in
> XML-server)? 
>
> For example, we try to realize such path: curl->php>socket>php>place on
> server or user interface
>
> Yours sincerely,
> Alexey Zakharov.
>  
>
> -----Original Message-----
> From: Poroikov V.V. [mailto:vladimir.poroikov at ibmc.msk.ru] 
> Sent: Tuesday, November 03, 2009 4:04 PM
> To: alexey.zakharov at ibmc.msk.ru; alexey.lagunin at ibmc.msk.ru
> Cc: dmitry.filimonov at ibmc.msk.ru
> Subject: Fw: [OTDev] IBMC services
>
>
> ----- Original Message ----- 
> From: "Joerg Wicker" <joerg.wicker at in.tum.de>
> To: "opentox development mailing list" <development at opentox.org>
> Sent: Monday, November 02, 2009 5:31 PM
> Subject: Re: [OTDev] IBMC services
>
>
>   
>> Dear Alex,
>>
>> we tried to run some of your examples you send in your
>> email. Unfortunately, we do not get any reply. The port seems to be open
>> but we wait really long and nothing happens. If there something wrong on
>> our side or is maybe the service down?
>>
>> Thank you and regards,
>>
>> Joerg
>>
>> -- 
>> Dipl.-Bioinf.  Joerg Wicker              phone: +49-89-289-19440
>> Technische Universitaet Muenchen           fax: +49-89-289-19414
>> Institut fuer Informatik/I12             email: joerg.wicker at in.tum.de
>> Boltzmannstr. 3                           room: MI 01.08.039
>> D-85748 Garching b. Muenchen, Germany
>> http://wwwkramer.in.tum.de/wicker/
>> _______________________________________________
>> Development mailing list
>> Development at opentox.org
>> http://www.opentox.org/mailman/listinfo/development
>>     
>>
>> ------------------------------------------------------------------------
>>
>>
>>
>> ------------------------------------------------------------------------
>>
>>
>> ------------------------------------------------------------------------
>>
>> _______________________________________________
>> Development mailing list
>> Development at opentox.org
>> http://www.opentox.org/mailman/listinfo/development
>>     



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

Message: 2
Date: Tue, 03 Nov 2009 18:14:03 +0200
From: chung <chvng at mail.ntua.gr>
Subject: Re: [OTDev] IBMC services
To: opentox development mailing list <development at opentox.org>
Cc: joerg.wicker at in.tum.de
Message-ID: <1257264843.9058.34.camel at chungX>
Content-Type: text/plain

Dear Alexey,
  Welcome on board! Just a small thing I noticed: A request on
http://195.178.ox/feature/compound/1/feature_definition/MNA returns
Nothing while a request on
http://195.178.207.160:8080/OpenTox/feature/compound/1/feature_definition/MN
A/ is successful. The difference is clearly the / in the end of the second
URI. The same holds for other URIs as well!

Best Regards,
Pantelis

On Tue, 2009-11-03 at 16:26 +0200, Nina Jeliazkova wrote:
> Dear Alexey,
> 
> Few comments from my side, which I hope will help clarify your questions
> and partners experience.
> 
> Regarding the service:
> 1) It is great yet another partner is becoming online :)
> 2) You are claiming implementation of following OpenTox resources:
> feature definitions, feature, references, and algorithms.  So far the
> only service running is one that retrieves feature value for specific
> (hidden) compound and MNA descriptor, i.e. the one at
> 
>
http://195.178.207.160:8080/OpenTox/feature/compound/{compound-id}/feature_d
efinition/{descr_id}/
> 
> >From your email it is not clear if other services are accessible and from
where.  The obvious URLs for the rest of the services are not working. 
> 
> http://195.178.207.160:8080/OpenTox/feature/
> http://195.178.207.160:8080/OpenTox/feature_definition
> http://195.178.207.160:8080/OpenTox/reference
> http://195.178.207.160:8080/OpenTox/algorithm
> 
> http://195.178.207.160:8080/OpenTox/compound/1   - it is not clear now
> how to retrieve the compound you are calculating descriptors for.
> 
> At this moment this is obviously an work in progress, therefore I expect
> in next version your will be providing the claimed services. 
> 
> 3) Another issue is your service return information under text/uri-list,
> but the values returned are not URIs.  Therefore, you should support
> different representation for the returned MNA values, rather than
URI-list.
> 
> Regarding the underlying technology, I am not sure I understand your
> questions completely.    Briefly, some of the partners are using java
> and Restlet library and the some application server (tomcat or
> similar).  The rest of the services are implemented and run with Ruby on
> Rails framework. Both Java and Ruby applications can run on different
> operating systems, so we are not locked into a single OS.
> 
> Could I suggest a Skype chat , with interested developers involved , so
> you could get an idea what technologies are used by partners and we can
> discuss what technology will best suit IBMC team?
> 
> 
> Best regards,
> Nina
> 
>  
> 
> 
> Alexey wrote:
> > Dear Joerg,
> >
> > At present time our server is working.
> >
> > We used cURL version 7.19.6 ssl and Poster (Mozilla Firefox) for
> > implementation of following query:
> >
> > A Linux example call (command line) to retrieve a list of MNA
descriptors
> > for compounds would be:
> >
> > curl -X GET -H 'Accept:text/uri-list'
> >
http://195.178.207.160:8080/OpenTox/feature/compound/1/feature_definition/MN
> > A/
> >
> > For Poster (Mozilla Firefox) using GET method you could be obtained list
of
> > MNA descriptors for compounds:
> >
> >
http://195.178.207.160:8080/OpenTox/feature/compound/1/feature_definition/MN
> > A/
> >
> > I send you print screens of Poster and cURL working.
> >
> > How we understand use of curl command for curl -X POST -d
> > "dataset_id=http://test.server.com/input.sdf" -H 'Accept:text/xml'
> >
http://opentox.informatik.tu-muenchen.de:8080/OpenTox/algorithm/descriptorca
> > lculation/physicochemical/CDKPhysChem activate working of XML-parser for
> > descriptors calculation. Could you write, what does XML-parser initiate
for
> > working of XML algorithm which are located in
> >
http://opentox.informatik.tu-muenchen.de:8080/OpenTox/algorithm/descriptorca
> > lculation/physicochemical/CDKPhysChem. Is it especial program or may be
you
> > use XML-server for this purpose (I mean executable module is realized in
> > XML-server)? 
> >
> > For example, we try to realize such path: curl->php>socket>php>place on
> > server or user interface
> >
> > Yours sincerely,
> > Alexey Zakharov.
> >  
> >
> > -----Original Message-----
> > From: Poroikov V.V. [mailto:vladimir.poroikov at ibmc.msk.ru] 
> > Sent: Tuesday, November 03, 2009 4:04 PM
> > To: alexey.zakharov at ibmc.msk.ru; alexey.lagunin at ibmc.msk.ru
> > Cc: dmitry.filimonov at ibmc.msk.ru
> > Subject: Fw: [OTDev] IBMC services
> >
> >
> > ----- Original Message ----- 
> > From: "Joerg Wicker" <joerg.wicker at in.tum.de>
> > To: "opentox development mailing list" <development at opentox.org>
> > Sent: Monday, November 02, 2009 5:31 PM
> > Subject: Re: [OTDev] IBMC services
> >
> >
> >   
> >> Dear Alex,
> >>
> >> we tried to run some of your examples you send in your
> >> email. Unfortunately, we do not get any reply. The port seems to be
open
> >> but we wait really long and nothing happens. If there something wrong
on
> >> our side or is maybe the service down?
> >>
> >> Thank you and regards,
> >>
> >> Joerg
> >>
> >> -- 
> >> Dipl.-Bioinf.  Joerg Wicker              phone: +49-89-289-19440
> >> Technische Universitaet Muenchen           fax: +49-89-289-19414
> >> Institut fuer Informatik/I12             email: joerg.wicker at in.tum.de
> >> Boltzmannstr. 3                           room: MI 01.08.039
> >> D-85748 Garching b. Muenchen, Germany
> >> http://wwwkramer.in.tum.de/wicker/
> >> _______________________________________________
> >> Development mailing list
> >> Development at opentox.org
> >> http://www.opentox.org/mailman/listinfo/development
> >>     
> >>
> >>
------------------------------------------------------------------------
> >>
> >>
> >>
> >>
------------------------------------------------------------------------
> >>
> >>
> >>
------------------------------------------------------------------------
> >>
> >> _______________________________________________
> >> Development mailing list
> >> Development at opentox.org
> >> http://www.opentox.org/mailman/listinfo/development
> >>     
> 
> _______________________________________________
> Development mailing list
> Development at opentox.org
> http://www.opentox.org/mailman/listinfo/development
> 



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

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