I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question . When I try to "Get Data" from UCSC or any other external site, I get a 407 error from our proxy as I need to authenticate. Is the request going out as the 'galaxy' user or 'apache' or the user that's logged in? I already have http_proxy and ftp_proxy configured in /etc/profile (we're running Centos 6) but I assume there a correct place to configure this for Galaxy? The error message I'm seeing is: An error occurred running this job: The remote data source application may be off line, please try again later. Error: ('http error', 407, 'Proxy Access Denied', <httplib.HTTPMessage instance at 0x35d2998>) Any ideas? Thanx, Russell Smithies ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. =======================================================================
Found the cure - just required adding urllib2.ProxyHandler in the data_source tools. Why doesn't Galaxy pick up the system http_proxy variables? --Russell Smithies From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Smithies, Russell Sent: Wednesday, 30 November 2011 9:09 a.m. To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] proxy settings? I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question . When I try to "Get Data" from UCSC or any other external site, I get a 407 error from our proxy as I need to authenticate. Is the request going out as the 'galaxy' user or 'apache' or the user that's logged in? I already have http_proxy and ftp_proxy configured in /etc/profile (we're running Centos 6) but I assume there a correct place to configure this for Galaxy? The error message I'm seeing is: An error occurred running this job: The remote data source application may be off line, please try again later. Error: ('http error', 407, 'Proxy Access Denied', <httplib.HTTPMessage instance at 0x35d2998>) Any ideas? Thanx, Russell Smithies ________________________________ Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ________________________________
On Nov 29, 2011, at 9:35 PM, Smithies, Russell wrote:
Found the cure – just required adding urllib2.ProxyHandler in the data_source tools. Why doesn’t Galaxy pick up the system http_proxy variables?
Hi Russell, Thanks for tracking down the problem. Could you send a patch for this? --nate
--Russell Smithies
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Smithies, Russell Sent: Wednesday, 30 November 2011 9:09 a.m. To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] proxy settings?
I’m new to Galaxy so I’m not sure if this a Galaxy or linux/apache question .
When I try to “Get Data” from UCSC or any other external site, I get a 407 error from our proxy as I need to authenticate. Is the request going out as the ‘galaxy’ user or ‘apache’ or the user that’s logged in? I already have http_proxy and ftp_proxy configured in /etc/profile (we’re running Centos 6) but I assume there a correct place to configure this for Galaxy?
The error message I’m seeing is: An error occurred running this job: The remote data source application may be off line, please try again later. Error: ('http error', 407, 'Proxy Access Denied', <httplib.HTTPMessage instance at 0x35d2998>)
Any ideas?
Thanx,
Russell Smithies
Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately.
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Hi Nate, My "solution" was a bit of a hack and there may be better ways of doing it (I haven't read all the docs yet - just started with Galaxy last week) Python is not my strong suit and there may be more elegant ways, but here's how I usually connect thru our proxy: ---------------------------------- proxy_info = { 'user' : 'DOMAIN\\username', 'pass' : 'thisismypassword', 'host' : "proxy.yoyodyne.com", 'port' : 8080 } # build a new opener that uses a proxy requiring authorization proxy_support = urllib2.ProxyHandler({"http" : "http://%(user)s:%(pass)s@%(host)s:%(port)d" % proxy_info}) opener = urllib2.build_opener(proxy_support, urllib2.HTTPHandler) # install it urllib2.install_opener(opener) #then open the page with urllib2 page = urllib2.urlopen( cur_URL ) ---------------------------------- I was in a hurry so tweaked data_source.py, fetch.py, genomespace_file_browser.py, ucsc_proxy.py, and upload.py but it would make more sense to read the proxy_info from universe_wsgi.ini If you can point me at an example of a tool that reads from the config, I'll try and put it together. The best solution would be for Python to pick up the local $http_proxy env settings but I've never managed to get that working! --Russell
-----Original Message----- From: Nate Coraor [mailto:nate@bx.psu.edu] Sent: Friday, 2 December 2011 7:03 a.m. To: Smithies, Russell Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] proxy settings?
On Nov 29, 2011, at 9:35 PM, Smithies, Russell wrote:
Found the cure - just required adding urllib2.ProxyHandler in the data_source tools. Why doesn't Galaxy pick up the system http_proxy variables?
Hi Russell,
Thanks for tracking down the problem. Could you send a patch for this?
--nate
--Russell Smithies
From: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] On Behalf Of Smithies, Russell Sent: Wednesday, 30 November 2011 9:09 a.m. To: galaxy-dev@lists.bx.psu.edu Subject: [galaxy-dev] proxy settings?
I'm new to Galaxy so I'm not sure if this a Galaxy or linux/apache question .
When I try to "Get Data" from UCSC or any other external site, I get a 407
Is the request going out as the 'galaxy' user or 'apache' or the user that's logged in? I already have http_proxy and ftp_proxy configured in /etc/profile (we're running Centos 6) but I assume there a correct place to configure this for Galaxy?
The error message I'm seeing is: An error occurred running this job: The remote data source application may be off line, please try again later. Error: ('http error', 407, 'Proxy Access Denied', <httplib.HTTPMessage instance at 0x35d2998>)
Any ideas?
Thanx,
Russell Smithies
Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received
error from our proxy as I need to authenticate. this message in error, please notify the sender immediately.
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Smithies, Russell