[OTDev] Authorisation error

Philip Doganis filipposd at gmail.com
Sat Oct 5 00:07:22 CEST 2013 

Dear all,  
it certainly is nice to have the help of the group in this! So, please check my replies to the instructions from Pantelis.
Best regards,
Philip

-- 
Philip Doganis
Sent with Sparrow (http://www.sparrowmailapp.com/?sig)


On Friday, October 4, 2013 at 6:33 PM, Pantelis Sopasakis wrote:

> Dear Micha, Philip,
> 
> Thanks a lot for the help. I think this is a shortcoming of our implementation; We had never thought that there could be multiple instances of our services wanting to create policies with the same name. This is something to be fixed. However, in order to understand and reproduce the error and tell whether it is related to our implementation or to the SSO services I would recommend that the following action is taken from Philip who has access to his account:
> 
> 1. Verify that the user "filipposd" is a member of the group "member" (see my previous email)
The output I get is:
< HTTP/1.1 200 OK
< Server: nginx/0.7.67
< Date: Fri, 04 Oct 2013 21:41:55 GMT
< Content-Type: text/plain;charset=UTF-8
< Connection: keep-alive
< Content-Length: 232
< 
identitydetails.name=filipposd
identitydetails.type=user
identitydetails.realm=dc=opensso,dc=java,dc=net
identitydetails.group=development
identitydetails.group=member
identitydetails.attribute=
identitydetails.attribute.name=group
* Connection #0 to host opensso.in-silico.ch left intact
* Closing connection #0
* SSLv3, TLS alert, Client hello (1):

(A more detailed version of the output can be found at:  https://github.com/filipd/StrayCode/edit/master/output.rtf)
> 2. Check whether "filipposd" is allowed to perform a POST at http://147.102.82.124:8080/algorithm/mlr using the authorization API. (Although if I remember well, JAQPOT will just check whether you are authenticated as all users are allowed to use our algorithms.
 I gave curl -X POST -d 'dataset_uri=http://apps.ideaconsult.net:8080/ambit2/dataset/1037' -d 'prediction_feature=http://apps.ideaconsult.net:8080/ambit2/feature/26701' -d 'dataset_service=http://apps.ideaconsult.net:8080/ambit2/dataset' http://147.102.82.124:8080/algorithm/mlr

<rdf:RDF
    xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
    xmlns:ot="http://www.opentox.org/api/1.1#"
    xmlns:otrs="http://opentox.org/opentox-rest.owl#"
    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:bibtex="http://purl.oclc.org/NET/nknouf/ns/bibtex#"
    xmlns:xsd="http://www.w3.org/2001/XMLSchema#"
    xmlns:jaqpot="http://opentox.ntua.gr:3000"
    xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" > 
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#Dataset">
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#OpenToxResource"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Provides access to chemical compounds and their features (e.g. structural, physical-chemical, biological, toxicological properties)</rdfs:comment>
    <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/description">
    <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#message">
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">For example: 'Prediction feature not provided'</rdfs:comment>
    <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">A simple message providing some simple description of the exceptional event.</dc:description>
    <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">error message</dc:title>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
    <rdfs:domain rdf:resource="http://www.opentox.org/api/1.1#ErrorReport"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#DataType">
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#OpenToxResource"/>
    <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/identifier">
    <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#Feature">
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#OpenToxResource"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#httpStatus">
    <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">HTTP status</dc:title>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#int"/>
    <rdfs:domain rdf:resource="http://www.opentox.org/api/1.1#ErrorReport"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#errorCode">
    <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Error codes of error reports are specified by the service providers that produce the error report. These are characteristic for every class of exceptional events.</dc:description>
    <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">error code</dc:title>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
    <rdfs:domain rdf:resource="http://www.opentox.org/api/1.1#ErrorReport"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://anonymous.org/error/625d13f4-2e21-4400-b77c-7fe2127d5d46">
    <ot:httpStatus rdf:datatype="http://www.w3.org/2001/XMLSchema#int">401</ot:httpStatus>
    <ot:errorCode rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anonymous</ot:errorCode>
    <ot:actor rdf:datatype="http://www.w3.org/2001/XMLSchema#string">(Client Error) 85.75.73.141 using curl/7.21.4 (universal-apple-darwin11.0) libcurl/7.21.4 OpenSSL/0.9.8y zlib/1.2.5</ot:actor>
    <ot:details rdf:datatype="http://www.w3.org/2001/XMLSchema#string">You have to authenticate yourself using the 'Authorization' Header according to the OpenTox API specifications</ot:details>
    <ot:message rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Anonymous predictions are now allowed</ot:message>
    <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Error report produced by '(Client Error) 85.75.73.141 using curl/7.21.4 (universal-apple-darwin11.0) libcurl/7.21.4 OpenSSL/0.9.8y zlib/1.2.5'</dc:title>
    <dc:identifier rdf:datatype="http://www.w3.org/2001/XMLSchema#anyURI">http://anonymous.org/error/625d13f4-2e21-4400-b77c-7fe2127d5d46</dc:identifier>
    <rdf:type rdf:resource="http://www.opentox.org/api/1.1#ErrorReport"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#OpenToxResource">
    <rdfs:subClassOf rdf:resource="http://www.w3.org/2002/07/owl#Thing"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Generic OpenTox Resource</rdfs:comment>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#actor">
    <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">URI of the peer that produces the exception.</dc:description>
    <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">error actor</dc:title>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
    <rdfs:domain rdf:resource="http://www.opentox.org/api/1.1#ErrorReport"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#Model">
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#OpenToxResource"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#Task">
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#String"/>
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#Feature"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#Algorithm">
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#OpenToxResource"/>
    <rdfs:comment rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Provides access to OpenTox algorithms</rdfs:comment>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#hasSource">
    <rdfs:range rdf:resource="http://www.opentox.org/api/1.1#Model"/>
    <rdfs:range rdf:resource="http://www.opentox.org/api/1.1#Dataset"/>
    <rdfs:range rdf:resource="http://www.opentox.org/api/1.1#Algorithm"/>
    <rdfs:domain rdf:resource="http://www.opentox.org/api/1.1#Feature"/>
    <rdfs:domain rdf:resource="http://www.opentox.org/api/1.1#Task"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#ObjectProperty"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#details">
    <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Detailed message including technical information about the exceptional event. Can be used to help both peers in the debugging.</dc:description>
    <dc:title rdf:datatype="http://www.w3.org/2001/XMLSchema#string">error details</dc:title>
    <rdfs:range rdf:resource="http://www.w3.org/2001/XMLSchema#string"/>
    <rdfs:domain rdf:resource="http://www.opentox.org/api/1.1#ErrorReport"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#DatatypeProperty"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#ErrorReport">
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#OpenToxResource"/>
    <dc:description rdf:datatype="http://www.w3.org/2001/XMLSchema#string">Instances of the class ErrorReport appear in ontological models to report some exceptional event that happened during the transaction of data from one server to another, request errors or internal server errors. An error report is characterized by its actor, the corresponding status code, some unique identifier for the exceptional event and possibly another error report that triggered its creation.</dc:description>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.opentox.org/api/1.1#String">
    <rdfs:subClassOf rdf:resource="http://www.opentox.org/api/1.1#DataType"/>
    <rdf:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
  </rdf:Description>
  <rdf:Description rdf:about="http://www.w3.org/2000/01/rdf-schema#comment">
    <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>
 
> 3. Check the logs of our services for additional error messages.
> 
> 

will do that... 
> 
> Best regards,
> Pantelis
> 
> 
> On 04/ott/2013, at 11:37, Micha Rautenberg <mr at mrautenberg.de (mailto:mr at mrautenberg.de)> wrote:
> 
> > Hello Philip,
> > 
> > I checked the OpenSSO logs and found some lines with the following error:
> > 
> > S: Create pol[Policy service] Resolved to user: 'filipposd'[Policy service] Create Policy 'user_filipposd at opensso.in-silico.ch (mailto:user_filipposd at opensso.in-silico.ch)'Policy 'user_filipposd at opensso.in-silico.ch (mailto:user_filipposd at opensso.in-silico.ch)' already exists
> > 
> > please have in mind that each policy must have a different name.
> > e.G.: in the XML policy template https://github.com/opentox/opentox-client/blob/master/lib/templates/default_policy.xml#L5 <Policy name="policy_user" and later: <Policy name="policy_group" has to be replaced before creating a new policy.
> > 
> > Cheers,
> > Micha
> > 
> > 
> > Am 04.10.2013 09:46, schrieb Micha Rautenberg:
> > > 
> > > Am 04.10.2013 09:22, schrieb Nina Jeliazkova:
> > > > On 4 October 2013 10:18, Micha Rautenberg <mr at mrautenberg.de (mailto:mr at mrautenberg.de)> wrote:
> > > > 
> > > > > Hi Pantelis,
> > > > > Am 04.10.2013 02:14, schrieb Pantelis Sopasakis:
> > > > > 
> > > > > @Barry: Could you add Philip (in CC) to the development mailing list?
> > > > > Philip is already in the development mailing list.
> > > > > 
> > > > > 
> > > > > > @Philip, All,
> > > > > > 
> > > > > > Some instructions on how to obtain group membership data using the
> > > > > > OpenTox A&A API (required authentication):
> > > > > > 
> > > > > 
> > > > > I hope this excellent example is already somewhere in our documentation :-)
> > > > > 
> > > > 
> > > > +1
> > > > 
> > > > Or perhaps we could start a repository with such examples at
> > > > https://github.com/opentox-api ?
> > > > 
> > > 
> > > good idea
> > > > 
> > > > Nina
> > > > 
> > > > 
> > > > > best, Micha
> > > > > 
> > > > > 
> > > > > > #Your username:
> > > > > > export username=guest
> > > > > > $Your password:
> > > > > > export password=guest
> > > > > > export token=`curl -X POST -k 'https://opensso.in-silico.ch:**
> > > > > > 443/auth/authenticate?uri=**service=openldap<https://opensso.in-silico.ch:443/auth/authenticate?uri=service=openldap>' 
> > > > > > -d username=$username -d password=$password`
> > > > > > token=`echo $token | cut -c10-80`;
> > > > > > curl -k -v -d name=$username -d attributes_names="group" -d admin=$token
> > > > > > https://opensso.in-silico.ch/**opensso/identity/read<https://opensso.in-silico.ch/opensso/identity/read> 
> > > > > > 
> > > > > > This will produce an output like this:
> > > > > > 
> > > > > > < HTTP/1.1 200 OK
> > > > > > < Server: nginx/0.7.67
> > > > > > < Date: Fri, 04 Oct 2013 00:25:35 GMT
> > > > > > < Content-Type: text/plain;charset=UTF-8
> > > > > > < Connection: keep-alive
> > > > > > < Content-Length: 194
> > > > > > <
> > > > > > identitydetails.name (http://identitydetails.name)=guest
> > > > > > identitydetails.type=user
> > > > > > identitydetails.realm=dc=**opensso,dc=java,dc=net
> > > > > > identitydetails.group=member
> > > > > > identitydetails.attribute=
> > > > > > identitydetails.attribute.name (http://identitydetails.attribute.name)**=group
> > > > > > 
> > > > > > A more detailed report is returned by:
> > > > > > 
> > > > > > curl -k -v -d name=$username -d admin=$token
> > > > > > https://opensso.in-silico.ch/**opensso/identity/read<https://opensso.in-silico.ch/opensso/identity/read> 
> > > > > > 
> > > > > > and finally, logout:
> > > > > > 
> > > > > > curl -i -d subjectid=$token http://opensso.in-silico.ch/**
> > > > > > opensso/identity/logout<http://opensso.in-silico.ch/opensso/identity/logout>
> > > > > > 
> > > > > > Best regards,
> > > > > > Pantelis
> > > > > > 
> > > > > > 
> > > > > > On 03/ott/2013, at 14:05, Nina Jeliazkova <jeliazkova.nina at gmail.com (mailto:jeliazkova.nina at gmail.com)>
> > > > > > wrote:
> > > > > > 
> > > > > > Philip,
> > > > > > > Most probably Pantelis is right, this is something related to the group
> > > > > > > memberships. You could check the access rights by yourself via the
> > > > > > > OpenTox
> > > > > > > AA .
> > > > > > > 
> > > > > > > I am usually using the command line application (this is a library as
> > > > > > > well)
> > > > > > > in such cases
> > > > > > > 
> > > > > > > http://vedina.github.io/**opentox-aa-cli/#cli.html<http://vedina.github.io/opentox-aa-cli/#cli.html> 
> > > > > > > 
> > > > > > > Best regards,
> > > > > > > Nina
> > > > > > > 
> > > > > > > 
> > > > > > > On 3 October 2013 14:57, Philip Doganis <filipposd at gmail.com (mailto:filipposd at gmail.com)> wrote:
> > > > > > > 
> > > > > > > Hello Nina,
> > > > > > > > Many thanks for your reply.
> > > > > > > > 
> > > > > > > > Earlier today, I was trying to find the source of the problem and I
> > > > > > > > logged
> > > > > > > > on to the opentox ntua service with my credentials and operated
> > > > > > > > successfully! I still get an error when trying to access
> > > > > > > > http://opentox.ntua.gr:8080/**user <http://opentox.ntua.gr:8080/user>, but I can access the User Quota Report.
> > > > > > > > 
> > > > > > > > My main goal is to set up the successor of NTUA opentox server and for
> > > > > > > > that purpose I am setting it up an another machine.
> > > > > > > > While I can construct models using the guest account and someone
> > > > > > > > else's, I
> > > > > > > > can't do that with mine.
> > > > > > > > Pantelis sent a message while I was typing this message, some info can
> > > > > > > > be
> > > > > > > > found in his e-mail...
> > > > > > > > 
> > > > > > > > Since this is a public forum, I can give more info in a private message.
> > > > > > > > 
> > > > > > > > Thanks for your help.
> > > > > > > > 
> > > > > > > > Best regards,
> > > > > > > > Philip
> > > > > > > > 
> > > > > > > > -- 
> > > > > > > > Philip Doganis
> > > > > > > > Sent with Sparrow (http://www.sparrowmailapp.**com/?sig<http://www.sparrowmailapp.com/?sig>
> > > > > > > > )
> > > > > > > > 
> > > > > > > > 
> > > > > > > > On Thursday, October 3, 2013 at 2:15 PM, Nina Jeliazkova wrote:
> > > > > > > > 
> > > > > > > > Dear Philip,
> > > > > > > > > This seems to be an error when creating a policy at the OpenSSO server,
> > > > > > > > > probably when creating a new model, but this is not explicit in the
> > > > > > > > > error
> > > > > > > > > log. Do I understand you use the "guest" user, or do you use your own
> > > > > > > > > OpenTox user?
> > > > > > > > > 
> > > > > > > > > Micha, could you have a look at the OpenSSO and policy server logs.
> > > > > > > > > 
> > > > > > > > > Thanks,
> > > > > > > > > Nina
> > > > > > > > > 
> > > > > > > > > 
> > > > > > > > > 
> > > > > > > > > 
> > > > > > > > > On 1 October 2013 20:00, Philip Doganis <filipposd at gmail.com (mailto:filipposd at gmail.com) (mailto:
> > > > > > > > filipposd at gmail.com (mailto:filipposd at gmail.com))> wrote:
> > > > > > > > 
> > > > > > > > > Dear Opentox community,
> > > > > > > > > > My name is Philip Doganis, I am a postgraduate researcher working at
> > > > > > > > > 
> > > > > > > > > NTUA
> > > > > > > > > with Prof. Sarimveis.
> > > > > > > > > > I am writing about the problem I encountered in my effort to use the
> > > > > > > > > > opentox service. I have created the user filipposd but I am unable to
> > > > > > > > > > perform any action, other than receive a token. As a guest user, I can
> > > > > > > > > > create and manage models and I have checked my cookie settings (I
> > > > > > > > > > 
> > > > > > > > > 
> > > > > > > > > accept
> > > > > > > > > everything). I get this error:
> > > > > > > > > > https://gist.github.com/**alphaville/**07536df6f3b8e252832a<https://gist.github.com/alphaville/07536df6f3b8e252832a>. 
> > > > > > > > > > Please check any problems there might be with my account, so I can
> > > > > > > > > > make
> > > > > > > > > > use of the services. Thanks in advance for your time.
> > > > > > > > > > 
> > > > > > > > > > Best regards,
> > > > > > > > > > Philip Doganis
> > > > > > > > > > 
> > > > > > > > > > 
> > > > > > > > > > 
> > > > > > > > > > -- 
> > > > > > > > > > Philip Doganis
> > > > > > > > > > Sent with Sparrow (http://www.sparrowmailapp.**com/?sig<http://www.sparrowmailapp.com/?sig>
> > > > > > > > > > )
> > > > > > > > > > 
> > > > > > > > > > ______________________________**_________________
> > > > > > > > > > Development mailing list
> > > > > > > > > > Development at opentox.org (mailto:Development at opentox.**org<Development at opentox.org (mailto:Development at opentox.org)>
> > > > > > > > > > )
> > > > > > > > > > http://www.opentox.org/**mailman/listinfo/development<http://www.opentox.org/mailman/listinfo/development> 
> > > > > > > > > > 
> > > > > > > > > > ______________________________**_________________
> > > > > > > > > Development mailing list
> > > > > > > > > Development at opentox.org (mailto:Development at opentox.**org<Development at opentox.org (mailto:Development at opentox.org)>
> > > > > > > > > )
> > > > > > > > > http://www.opentox.org/**mailman/listinfo/development<http://www.opentox.org/mailman/listinfo/development> 
> > > > > > > > > 
> > > > > > > > 
> > > > > > > > ______________________________**_________________
> > > > > > > > Development mailing list
> > > > > > > > Development at opentox.org (mailto:Development at opentox.org)
> > > > > > > > http://www.opentox.org/**mailman/listinfo/development<http://www.opentox.org/mailman/listinfo/development> 
> > > > > > > > 
> > > > > > > > ______________________________**_________________
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