OK, thanks Arek! Isaac
2012/1/25 Arek Kasprzyk <[email protected]> > Hi Isaac, > someone will be able to assist you with this during your visit in London > > a > > > On Fri, Jan 20, 2012 at 10:25 AM, Isaac cano <[email protected]> wrote: > >> Hi Jack, >> >> Did you progress any more on the openid-proxy issue? >> >> Thanks! >> >> Isaac >> >> >> 2012/1/12 Arek Kasprzyk <[email protected]> >> >>> Hi Isaac, >>> Jack will be in a better position to provide you with an update you on >>> this. I see from his email that he was planning to do some testing >>> beforehand and then commit the fix. I am not sure how far he has got with >>> that >>> >>> >>> a >>> >>> >>> On Tue, Jan 10, 2012 at 8:28 AM, Isaac cano <[email protected]> wrote: >>> >>>> Hi Jack and Arek, >>>> >>>> I'm currently working with rc7 trying to get the OpenID working through >>>> proxy but I cannot make it work. Did you introduce the OpenID proxy fix in >>>> rc7? Where can I find the list of new things in rc7? >>>> >>>> Thanks! >>>> >>>> Isaac >>>> >>>> >>>> 2011/10/13 Arek Kasprzyk <[email protected]> >>>> >>>>> Hi Jack, >>>>> sure, whatever works correctly for you. >>>>> >>>>> thank you >>>>> a >>>>> >>>>> >>>>> On Thu, Oct 13, 2011 at 2:53 PM, Jack Hsu <[email protected]> wrote: >>>>> >>>>>> Hi Arek, >>>>>> >>>>>> We'll have to do a bit more testing before making any commits to rc6 >>>>>> and rc7. >>>>>> >>>>>> Seems like there may be some problems with SOCKS proxy, even with the >>>>>> proposed solution. >>>>>> >>>>>> -jack >>>>>> >>>>>> From: Arek Kasprzyk <[email protected]> >>>>>> Date: Thu, 13 Oct 2011 11:45:52 -0400 >>>>>> To: Jack Hsu <[email protected]> >>>>>> Cc: Isaac cano <[email protected]>, BioMart Users <[email protected]> >>>>>> >>>>>> Subject: Re: [BioMart Users] OpenID -- Error 400 - Bad request >>>>>> >>>>>> Hi Jack, >>>>>> perhaps it would be useful to add this small fix into rc6 so other >>>>>> users could also benefit from it? >>>>>> >>>>>> >>>>>> a >>>>>> >>>>>> >>>>>> On Thu, Oct 13, 2011 at 10:15 AM, Jack Hsu <[email protected]>wrote: >>>>>> >>>>>>> Hi Isaac, >>>>>>> >>>>>>> I think the issue is with the openid4java library we are using for >>>>>>> OpenID communication. >>>>>>> >>>>>>> If you have the source code available you can try inserting the >>>>>>> following code in the org.biomart.api.rest.UserResource class, at the >>>>>>> beginning of the constructor (before instantiating ConsumerManager). >>>>>>> >>>>>>> >>>>>>> String proxyHost = System.getProperty( "http.proxyHost", >>>>>>> System.getProperty("socksProxyHost") ); >>>>>>> String proxyPort = System.getProperty( "http.proxyPort", >>>>>>> System.getProperty("socksProxyPort") ); >>>>>>> >>>>>>> if (proxyHost != null && proxyPort != null) { >>>>>>> org.openid4java.util.ProxyProperties proxyProps = new >>>>>>> org.openid4java.util.ProxyProperties(); >>>>>>> proxyProps.setProxyHostName(proxyHost); >>>>>>> proxyProps.setProxyPort( Integer.parseInt(proxyPort) ); >>>>>>> >>>>>>> org.openid4java.util.HttpClientFactory.setProxyProperties(proxyProps); >>>>>>> } >>>>>>> >>>>>>> http://code.google.com/p/openid4java/wiki/ConsumerForwardProxy >>>>>>> >>>>>>> -jack >>>>>>> >>>>>>> >>>>>>> From: Isaac cano <[email protected]> >>>>>>> Date: Thu, 13 Oct 2011 04:04:28 -0400 >>>>>>> To: Jack Hsu <[email protected]> >>>>>>> Cc: BioMart Users <[email protected]> >>>>>>> Subject: Re: [BioMart Users] OpenID -- Error 400 - Bad request >>>>>>> >>>>>>> Hi Jack, >>>>>>> >>>>>>> Thanks for your answer. I assume then that the openID functionality >>>>>>> is also supported when using proxy settings. I'll continue investigating >>>>>>> why I can't use the openID functionality when using proxies, both HTTP >>>>>>> or >>>>>>> SOCKS (other communications such us accessing to other marts works for >>>>>>> me >>>>>>> when setting the proxy). >>>>>>> >>>>>>> Thanks! >>>>>>> >>>>>>> Isaac >>>>>>> >>>>>>> 2011/10/11 Jack Hsu <[email protected]> >>>>>>> >>>>>>>> Hi Isaac, >>>>>>>> >>>>>>>> BioMart only supports proxy settings that is built into Java >>>>>>>> networking. ( >>>>>>>> http://download.oracle.com/javase/6/docs/technotes/guides/net/proxies.html >>>>>>>> ) >>>>>>>> >>>>>>>> It may be the case here that the default Java settings are not >>>>>>>> enough to use the SOCKS proxy server. We currently don't have a way to >>>>>>>> support proxy settings beyond through JVM system properties. >>>>>>>> >>>>>>>> -jack >>>>>>>> >>>>>>>> >>>>>>>> From: Isaac cano <[email protected]> >>>>>>>> Date: Tue, 11 Oct 2011 04:53:48 -0400 >>>>>>>> To: BioMart Users <[email protected]> >>>>>>>> Subject: [BioMart Users] OpenID -- Error 400 - Bad request >>>>>>>> >>>>>>>> Dear BioMart users, >>>>>>>> >>>>>>>> I'm running BioMart 0.8 RC6 in a server that is connected to >>>>>>>> Internet through a proxy/socks server. I've configured the >>>>>>>> biomart.all.properties xml file with the corresponding proxy/socks >>>>>>>> setting >>>>>>>> and every connection from/to our BioMart server to other marts like >>>>>>>> Ensembl >>>>>>>> is working but the OpenID functionality is not. I receive the following >>>>>>>> error messages to the error log file: >>>>>>>> >>>>>>>> 2011-10-11 10:58:49,908 WARN >>>>>>>> [31538514@qtp-31278839-8:RealmVerifier.java:107]: >>>>>>>> RP discovery / realm validation disabled; >>>>>>>> 2011-10-11 10:58:49,912 INFO >>>>>>>> [31538514@qtp-31278839-8:ConsumerManager.java:286]: >>>>>>>> Associations disabled. >>>>>>>> 2011-10-11 10:58:49,912 WARN >>>>>>>> [31538514@qtp-31278839-8:RealmVerifier.java:107]: >>>>>>>> RP discovery / realm validation disabled; >>>>>>>> 2011-10-11 10:58:49,918 INFO >>>>>>>> [31538514@qtp-31278839-8:Discovery.java:128]: >>>>>>>> Starting discovery on URL identifier: >>>>>>>> https://www.google.com/accounts/o8/id >>>>>>>> 2011-10-11 10:58:50,023 INFO >>>>>>>> [31538514@qtp-31278839-8:HttpMethodDirector.java:438]: >>>>>>>> I/O exception (java.net.SocketException) caught when processing >>>>>>>> request: >>>>>>>> Can't connect to SOCKS proxy:Connection refused >>>>>>>> >>>>>>>> And the corresponding message that is shown in the biomart portal >>>>>>>> (openID pop-up) is the following: >>>>>>>> >>>>>>>> <html> <head> <meta http-equiv="Content-Type" content="text/html; >>>>>>>> charset=ISO-8859-1"/> <title>Error 400 Bad Request</title> </head> >>>>>>>> <body><h2>HTTP ERROR 400</h2> <p>Problem accessing >>>>>>>> /martservice/user/auth. >>>>>>>> Reason: <pre> Bad Request</pre></p><hr /><i><small>Powered by >>>>>>>> Jetty://</small></i><br/> <br/> <br/> <br/> <br/> <br/> <br/> <br/> >>>>>>>> <br/> >>>>>>>> <br/> <br/> <br/> <br/> <br/> <br/> <br/> <br/> <br/> <br/> <br/> >>>>>>>> </body> >>>>>>>> </html> >>>>>>>> >>>>>>>> Is the OpendID functionality supported in the current release when >>>>>>>> using proxy/socks servers? >>>>>>>> >>>>>>>> Thanks in advance, >>>>>>>> >>>>>>>> -- >>>>>>>> Isaac Cano >>>>>>>> Bioinformatics >>>>>>>> Linkcare Health Services SL >>>>>>>> C/Villarroel 170 >>>>>>>> 08036 - Barcelona >>>>>>>> Tel.: (+34)932 275 400, ext. 4182\4523 >>>>>>>> Mobile: (+34) 666 186 748 >>>>>>>> Fax: (+34) 932 275 455 >>>>>>>> [email protected] >>>>>>>> >>>>>>>> >>>>>>> >>>>>>> >>>>>>> -- >>>>>>> Isaac Cano >>>>>>> Bioinformatics >>>>>>> Linkcare Health Services SL >>>>>>> C/Villarroel 170 >>>>>>> 08036 - Barcelona >>>>>>> Tel.: (+34)932 275 400, ext. 4182\4523 >>>>>>> Mobile: (+34) 666 186 748 >>>>>>> Fax: (+34) 932 275 455 >>>>>>> [email protected] >>>>>>> >>>>>>> >>>>>>> _______________________________________________ >>>>>>> Users mailing list >>>>>>> [email protected] >>>>>>> https://lists.biomart.org/mailman/listinfo/users >>>>>>> >>>>>>> >>>>>> >>>>> >>>> >>>> >>>> -- >>>> Isaac Cano >>>> Bioinformatics >>>> Linkcare Health Services SL >>>> C/Villarroel 170 >>>> 08036 - Barcelona >>>> Tel.: (+34)932 275 400, ext. 4182\4523 >>>> Mobile: (+34) 666 186 748 >>>> Fax: (+34) 932 275 455 >>>> [email protected] >>>> >>>> >>> >>> >>> -- >>> >>> Arek Kasprzyk, MD, MSc, PhD >>> BioMart Project Lead >>> >>> >> >> >> -- >> Isaac Cano >> Bioinformatics >> Linkcare Health Services SL >> C/Villarroel 170 >> 08036 - Barcelona >> Tel.: (+34)932 275 400, ext. 4182\4523 >> Mobile: (+34) 666 186 748 >> Fax: (+34) 932 275 455 >> [email protected] >> >> > > > -- > > Arek Kasprzyk, MD, MSc, PhD > BioMart Project Lead > > -- Isaac Cano Bioinformatics Linkcare Health Services SL C/Villarroel 170 08036 - Barcelona Tel.: (+34)932 275 400, ext. 4182\4523 Mobile: (+34) 666 186 748 Fax: (+34) 932 275 455 [email protected]
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