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
_______________________________________________ Users mailing list [email protected] https://lists.biomart.org/mailman/listinfo/users
