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
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