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:8
30)
at
org.biomart.queryEngine.SubQuery.executeQuery(SubQuery.java:739)
at
org.biomart.queryEngine.QueryRunnerThread.recurseSubQueries(QueryRunnerT
hread.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$Sync.innerRun(FutureTask.java:334)
at java.util.concurrent.FutureTask.run(FutureTask.java:166)
at
java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.jav
a:1110)
at
java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.ja
va: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(UR
LConnectionClientHandler.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:[email protected]]
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" <[email protected]>
Date: Fri, 2 Sep 2011 13:39:16 -0400
To: BioMart Users <[email protected]>
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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