[OTDev] validating web services

chung chvng at mail.ntua.gr
Wed Apr 21 16:32:52 CEST 2010 

Hi Nina,
  This was because I wasn't expecting such a lengthy URI. I'm modifying
the length of VARCHAR in the database and I think this will be fixed.
Thanks for pointing out this problem.

Regards,
Pantelis


On Wed, 2010-04-21 at 08:05 +0300, Nina Jeliazkova wrote:
> Dear Pantelis,
> 
> chung wrote:
> > Dear Martin, All,
> >   I have made some changes regarding the NTUA services to provide full
> > compatibility with the recent changes in the Task API. I was a bit
> > dubious as to whether I should deploy the new version of the services
> > lest these would ruin the integration with ToxPredict. So I deployed the
> > latest version of YAQP on another URI: http://opentox.ntua.gr:3003 (Note
> > the different port: its 3003 instead of 3000).
> >
> > @Martin: Could you please try the validation services using the above
> > URI? (Hope this works...). Note that there are some changes as far as
> > the redirections are concerned! Let me know if you encounter any
> > problems and we'll be in touch to make the services work.
> >
> > @Nina: Could you please check if the new services are compliant with the
> > new API (status codes, response messages, RDF content etc)? Then we
> > could officially switch to the new API.
> >   
> The task RDF is fine. 
> 
> I have tried creating a new model by following curl commands:
> 
>     nina at ambit:~$ curl -X POST -d
>     "dataset_uri=http%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Fdataset%2F595%3Ffeature_uris%5B%5D%3Dhttp%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Ffeature%2F255508%26feature_uris%5B%5D%3Dhttp%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Ffeature%2F255509%26feature_uris%5B%5D%3Dhttp%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Ffeature%2F255511%26feature_uris%5B%5D%3Dhttp%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Ffeature%2F255512%26feature_uris%5B%5D%3Dhttp%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Ffeature%2F255510&prediction_feature=http%3A%2F%2Fambit.uni-plovdiv.bg%3A8080%2Fambit2%2Ffeature%2F255510"
>     http://opentox.ntua.gr:3003/algorithm/mlr -vi >
>     test-create-ntua-model-1.txt
>     * About to connect() to opentox.ntua.gr port 3003 (#0)
>     *   Trying 147.102.82.32... connected
>     * Connected to opentox.ntua.gr (147.102.82.32) port 3003 (#0)
>     > POST /algorithm/mlr HTTP/1.1
>     > User-Agent: curl/7.18.2 (x86_64-pc-linux-gnu) libcurl/7.18.2
>     OpenSSL/0.9.8g zlib/1.2.3.3 libidn/1.8 libssh2/0.18
>     > Host: opentox.ntua.gr:3003
>     > Accept: */*
>     > Content-Length: 625
>     > Content-Type: application/x-www-form-urlencoded
>     >
>     } [data not shown]
>       % Total    % Received % Xferd  Average Speed   Time    Time    
>     Time  Current
>                                      Dload  Upload   Total   Spent   
>     Left  Speed
>     100   625    0     0    0   625      0  25051 --:--:-- --:--:--
>     --:--:-- 25051< HTTP/1.1 202 The request has been accepted for
>     processing, but the processing has not been completed
>     < Content-Language: en, en-us
>     < Content-Type: application/rdf+xml
>     < Date: Wed, 21 Apr 2010 04:47:05 GMT
>     < Accept-Ranges: bytes
>     < Server: Restlet-Framework/2.0m7
>     < Vary: Accept-Charset, Accept-Encoding, Accept-Language, Accept
>     < Connection: close
>     < Transfer-Encoding: chunked
>     <
>     { [data not shown]
>     100  4390    0  3765    0   625  24513   4069 --:--:-- --:--:--
>     --:--:-- 24531* Closing connection #0
> 
> 
>     nina at ambit:~$ curl -iv
>     http://opentox.ntua.gr:3003/task/acc51ac8-7872-40e1-9837-9784537a1777
>     > test-query-task-1.txt
>     * About to connect() to opentox.ntua.gr port 3003 (#0)
>     *   Trying 147.102.82.32... connected
>     * Connected to opentox.ntua.gr (147.102.82.32) port 3003 (#0)
>     > GET /task/acc51ac8-7872-40e1-9837-9784537a1777 HTTP/1.1
>     > User-Agent: curl/7.18.2 (x86_64-pc-linux-gnu) libcurl/7.18.2
>     OpenSSL/0.9.8g zlib/1.2.3.3 libidn/1.8 libssh2/0.18
>     > Host: opentox.ntua.gr:3003
>     > Accept: */*
>     >
>     < HTTP/1.1 200 The request has succeeded
>     < Content-Language: en, en-us
>     < Content-Type: application/rdf+xml
>     < Date: Wed, 21 Apr 2010 04:47:50 GMT
>     < Accept-Ranges: bytes
>     < Server: Restlet-Framework/2.0m7
>     < Vary: Accept-Charset, Accept-Encoding, Accept-Language, Accept
>     < Connection: close
>     < Transfer-Encoding: chunked
>     <
>       % Total    % Received % Xferd  Average Speed   Time    Time    
>     Time  Current
>                                      Dload  Upload   Total   Spent   
>     Left  Speed
>       0     0    0     0    0     0      0      0 --:--:-- --:--:--
>     --:--:--     0{ [data not shown]
>     100  4063    0  4063    0     0  44055      0 --:--:-- --:--:--
>     --:--:-- 99097* Closing connection #0
> 
> 
> 
> The outcome seems fine (200 OK result code),  but when looking into the
> RDF, returned by the last command (output in the attached
> test-query-task-1.txt) , the URL of the created model is not a valid one
> http://opentox.ntua.gr:3003/model/0  - excerpt below, as well as full
> output in the attached file.
> 
>       <rdf:Description
>     rdf:about="http://opentox.ntua.gr:3003/task/acc51ac8-7872-40e1-9837-9784537a1777">
>         <ot:hasStatus
>     rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Completed</ot:hasStatus>
>         <ot:resultURI
>     rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003/model/0</ot:resultURI>
>         <dc:date
>     rdf:datatype="http://www.w3.org/2001/XMLSchema#date">Wed Apr 21
>     00:47:50 EDT 2010</dc:date>
>         <dc:relation
>     rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.org</dc:relation>
>         <dc:contributor
>     rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.org</dc:contributor>
>         <dc:publisher
>     rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003</dc:publisher>
>         <dc:creator
>     rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003</dc:creator>
>         <dc:title
>     rdf:datatype="http://www.w3.org/2001/XMLSchema#string">YAQP
>     Task</dc:title>
>         <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Task"/>
>         <dc:identifier
>     rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003/task/acc51ac8-7872-40e1-9837-9784537a1777</dc:identifie
>     r>
> 
> 
> I might be well submitting something wrong , although this is caco-2
> dataset from the model we had tried to reproduce, and result codes don't
> indicate possible errors.
> 
> Could you please have a look?
> 
> Best regards,
> Nina
> > Best regards,
> > Pantelis 
> >
> > On Mon, 2010-04-19 at 18:29 +0200, Martin Guetlein wrote:
> >   
> >> Dear All,
> >>
> >> I created a new website that makes it easier for you to get your
> >> models and the validation web service working together:
> >> http://opentox.informatik.uni-freiburg.de/validation/nightly
> >> This website is for developers of OT web services and shows the
> >> results of a daily validation of your model web service/s. So far it
> >> is only a first initial version, it will be extended further.
> >>
> >> To all developers: please send to me URIs of models and/or datasets to
> >> extend the tests.
> >>
> >> Best regards,
> >> Martin
> >>
> >>
> >>     
> >
> >
> > _______________________________________________
> > Development mailing list
> > Development at opentox.org
> > http://www.opentox.org/mailman/listinfo/development
> >   
> 
> plain text document attachment (test-query-task-1.txt)
> HTTP/1.1 200 The request has succeeded
> Content-Language: en, en-us
> Content-Type: application/rdf+xml
> Date: Wed, 21 Apr 2010 04:47:50 GMT
> Accept-Ranges: bytes
> Server: Restlet-Framework/2.0m7
> Vary: Accept-Charset, Accept-Encoding, Accept-Language, Accept
> Connection: close
> Transfer-Encoding: chunked
> 
> <rdf:RDF
>     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>     xmlns:ot="http://www.opentox.org/api/1.1#"
>     xmlns:ota="http://www.opentox.org/algorithmTypes.owl/#"
>     xmlns:owl="http://www.w3.org/2002/07/owl#"
>     xmlns:dc="http://purl.org/dc/elements/1.1/"
>     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" > 
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/relation">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/identifier">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/contributor">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://www.opentox.org/api/1.1#hasStatus">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/rights">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/creator">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://www.opentox.org/api/1.1#Task">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/date">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://www.opentox.org/api/1.1#resultURI">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/publisher">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#type">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://opentox.ntua.gr:3003/task/acc51ac8-7872-40e1-9837-9784537a1777">
>     <ot:hasStatus rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Completed</ot:hasStatus>
>     <ot:resultURI rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003/model/0</ot:resultURI>
>     <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#date">Wed Apr 21 00:47:50 EDT 2010</dc:date>
>     <dc:relation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.org</dc:relation>
>     <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.org</dc:contributor>
>     <dc:publisher rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003</dc:publisher>
>     <dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003</dc:creator>
>     <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">YAQP Task</dc:title>
>     <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Task"/>
>     <dc:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003/task/acc51ac8-7872-40e1-9837-9784537a1777</dc:identifier>
>     <dc:source rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003</dc:source>
>     <dc:rights rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://www.gnu.org/licenses/</dc:rights>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/source">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/title">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
> </rdf:RDF>
> plain text document attachment (test-create-ntua-model-1.txt)
> HTTP/1.1 202 The request has been accepted for processing, but the processing has not been completed
> Content-Language: en, en-us
> Content-Type: application/rdf+xml
> Date: Wed, 21 Apr 2010 04:47:05 GMT
> Accept-Ranges: bytes
> Server: Restlet-Framework/2.0m7
> Vary: Accept-Charset, Accept-Encoding, Accept-Language, Accept
> Connection: close
> Transfer-Encoding: chunked
> 
> <rdf:RDF
>     xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>     xmlns:ot="http://www.opentox.org/api/1.1#"
>     xmlns:ota="http://www.opentox.org/algorithmTypes.owl/#"
>     xmlns:owl="http://www.w3.org/2002/07/owl#"
>     xmlns:dc="http://purl.org/dc/elements/1.1/"
>     xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
>     xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" > 
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/relation">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/identifier">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/contributor">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://www.opentox.org/api/1.1#hasStatus">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/rights">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/creator">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://www.opentox.org/api/1.1#Task">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/date">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/publisher">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://www.w3.org/1999/02/22-rdf-syntax-ns#type">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://opentox.ntua.gr:3003/task/acc51ac8-7872-40e1-9837-9784537a1777">
>     <dc:relation rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.org</dc:relation>
>     <dc:contributor rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.org</dc:contributor>
>     <dc:publisher rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003</dc:publisher>
>     <dc:creator rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003</dc:creator>
>     <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">YAQP Task</dc:title>
>     <ot:hasStatus rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Running</ot:hasStatus>
>     <rdf:type rdf:resource="http://www.opentox.org/api/1.1#Task"/>
>     <dc:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003/task/acc51ac8-7872-40e1-9837-9784537a1777</dc:identifier>
>     <dc:source rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://opentox.ntua.gr:3003</dc:source>
>     <dc:rights rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://www.gnu.org/licenses/</dc:rights>
>     <dc:date rdf:datatype="http://www.w3.org/2001/XMLSchema#date">Wed Apr 21 00:47:05 EDT 2010</dc:date>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/source">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
>   <rdf:Description rdf:about="http://purl.org/dc/elements/1.1/title">
>     <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#AnnotationProperty"/>
>   </rdf:Description>
> </rdf:RDF>
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