[BioMart Users] Setting proxy servers to get around firewall

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[BioMart Users] Setting proxy servers to get around firewall

Estrella, Heather
Setting proxy servers to get around firewall

Has anyone used a proxy server within BioMart to get around an internal firewall? Ive set the proxy parameters in dist/conf/xml/biomart.all.properties

http.proxyHost=proxyserver.com

http.proxyPort=8080

I am able to set the http_proxy environment variable and access the external site using curl from the command line, but when I try to run the same query from within BioMart it fails.

Error in stdouterror log file:

org.biomart.common.exceptions.BioMartException: HTTP Error 404 - <HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html;charset=ISO-8859-1"><TITLE>Not Found</TITLE></HEAD>

<H1>Not Found</H1> The requested object does not exist on this server. The link you followed is either outdated, inaccurate, or the server has been instructed not to let you have it.

My guess is that Im not setting something correctly in the biomart.all.properties file or there is another setting that Im missing. If anyone has experience with proxy settings within BioMart, it would be great to get some input from anyone who has Biomart going through a proxy server.

Thanks,

Heather


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Re: [BioMart Users] Setting proxy servers to get around firewall

Jack Hsu
Hi Heather,

Unfortunately we do not currently officially support proxy servers.

We have tested some arguments on the JVM, but none was reliable enough for us to recommend. We found that only a limited number of proxy servers were easily supported natively on the JVM.

You can pass extra JVM arguments to the biomart-server.sh script.

E.g. ./scripts/biomart-server.sh start -Dhttp.proxyHost=... -Dhttp.proxyPort=... 

We are looking at more sophisticated solutions to handle proxy servers in the future.


-jack


From: "Estrella, Heather" <[hidden email]>
Date: Fri, 2 Sep 2011 13:39:16 -0400
To: BioMart Users <[hidden email]>
Subject: [BioMart Users] Setting proxy servers to get around firewall

Has anyone used a proxy server within BioMart to get around an internal firewall? Ive set the proxy parameters in dist/conf/xml/biomart.all.properties

http.proxyHost=proxyserver.com

http.proxyPort=8080

I am able to set the http_proxy environment variable and access the external site using curl from the command line, but when I try to run the same query from within BioMart it fails.

Error in stdouterror log file:

org.biomart.common.exceptions.BioMartException: HTTP Error 404 - <HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html;charset=ISO-8859-1"><TITLE>Not Found</TITLE></HEAD>

<H1>Not Found</H1> The requested object does not exist on this server. The link you followed is either outdated, inaccurate, or the server has been instructed not to let you have it.

My guess is that Im not setting something correctly in the biomart.all.properties file or there is another setting that Im missing. If anyone has experience with proxy settings within BioMart, it would be great to get some input fromanyone who has Biomart going through a proxy server.

Thanks,

Heather


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Re: [BioMart Users] Setting proxy servers to get around firewall

Estrella, Heather

Hi Jack,

 

Thanks for the tip. I’ve tried to specify the proxy settings at both the shell command line as you suggest below. I’ve also tried to specify them within the actual biomart-server.sh script that calls java. I don’t get errors, but the BioMart interface doesn’t return anything. It just keeps running and eventually times out. The log file doesn’t provide much help except to say that the connection timed out.

 

2011-09-02T11:21:00-0700 INFO  [2119867878@qtp-259943062-4:Log.java:165]: Incoming XML query: <!DOCTYPE Query><Query client="webbrowser" processor="TSVX" limit="1000" header="1"><Dataset name="sample_tcgaCOAD" config="sample_config_quick"><Attribute name="cancertype"/><Attribute name="sample__sample__main__donor_id"/><Attribute name="sample__sample__main__diagnosis_id"/><Attribute name="sample__sample__main__sample_id"/><Attribute name="sample__sample__main__sample_type"/></Dataset></Query>

2011-09-02T11:21:00-0700 INFO  [2119867878@qtp-259943062-4:Log.java:165]: PSEUDO attribute's value: Colon Adenocarcinoma (TCGA, US)

2011-09-02T11:21:00-0700 INFO  [2119867878@qtp-259943062-4:Log.java:165]: PSEUDO attribute's value: sample_report

2011-09-02T11:21:00-0700 INFO  [2119867878@qtp-259943062-4:Log.java:165]: PSEUDO attribute's value: sample_tcgaCOAD

2011-09-02T11:21:00-0700 INFO  [2119867878@qtp-259943062-4:Log.java:165]: PSEUDO attribute's value: sample_tcgaCOAD

2011-09-02T11:21:00-0700 INFO  [2119867878@qtp-259943062-4:Log.java:165]: PSEUDO attribute's value: sample_tcgaCOAD

org.biomart.common.exceptions.BioMartException: Error while connection to HTTP source

        at org.biomart.queryEngine.SubQuery.executeMartServiceQuery(SubQuery.java:830)

        at org.biomart.queryEngine.SubQuery.executeQuery(SubQuery.java:739)

        at org.biomart.queryEngine.QueryRunnerThread.recurseSubQueries(QueryRunnerThread.java:171)

        at org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:73)

        at org.biomart.queryEngine.QueryRunnerThread.call(QueryRunnerThread.java:37)

        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)

        at java.util.concurrent.FutureTask.run(FutureTask.java:166)

        at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)

        at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)

        at java.util.concurrent.FutureTask.run(FutureTask.java:166)

        at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)

        at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)

        at java.lang.Thread.run(Thread.java:636)

Caused by: com.sun.jersey.api.client.ClientHandlerException: java.net.ConnectException: Connection timed out

        at com.sun.jersey.client.urlconnection.URLConnectionClientHandler.handle(URLConnectionClientHandler.java:131)

 

Please keep me updated as you find new options to test out for the proxy servers as I would like to give them a try here as well.

 

Many thanks,

Heather

 

From: Jack Hsu [mailto:[hidden email]]
Sent: Friday, September 02, 2011 10:53 AM
To: Estrella, Heather; BioMart Users
Subject: Re: [BioMart Users] Setting proxy servers to get around firewall

 

Hi Heather,

 

Unfortunately we do not currently officially support proxy servers.

 

We have tested some arguments on the JVM, but none was reliable enough for us to recommend. We found that only a limited number of proxy servers were easily supported natively on the JVM.

 

You can pass extra JVM arguments to the biomart-server.sh script.

 

E.g. ./scripts/biomart-server.sh start -Dhttp.proxyHost=... -Dhttp.proxyPort=... 

 

We are looking at more sophisticated solutions to handle proxy servers in the future.

 

 

-jack

 

 

From: "Estrella, Heather" <[hidden email]>
Date: Fri, 2 Sep 2011 13:39:16 -0400
To: BioMart Users <[hidden email]>
Subject: [BioMart Users] Setting proxy servers to get around firewall

 

Has anyone used a proxy server within BioMart to get around an internal firewall? I’ve set the proxy parameters in dist/conf/xml/biomart.all.properties

http.proxyHost=proxyserver.com

http.proxyPort=8080

I am able to set the http_proxy environment variable and access the external site using curl from the command line, but when I try to run the same query from within BioMart it fails.

Error in stdouterror log file:

org.biomart.common.exceptions.BioMartException: HTTP Error 404 - <HEAD><META HTTP-EQUIV="Content-Type" CONTENT="text/html;charset=ISO-8859-1"><TITLE>Not Found</TITLE></HEAD>

<H1>Not Found</H1> The requested object does not exist on this server. The link you followed is either outdated, inaccurate, or the server has been instructed not to let you have it.

My guess is that I’m not setting something correctly in the biomart.all.properties file or there is another setting that I’m missing. If anyone has experience with proxy settings within BioMart, it would be great to get some input fromanyone who has Biomart going through a proxy server.

Thanks,

Heather


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