IGV display_application configuration failed with require_login=TRUE

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IGV display_application configuration failed with require_login=TRUE

navratil
Dear galaxy-dev team,

We have configured a galaxy-dist  server (stable release) behind an Apache2 proxy (with mod_xsendfile) by following the galaxy wiki.

We would like to use the galaxy embeded user authentification with require_login=True option instead of a remote_user configuration on the proxy side.

With require_login = False it works but with require_login=True configuration we fail to load .bam files into IGV (local) :

The IGV (Version 2.3.18) send this error:
INFO [2014-02-04 16:05:56,660]  [MessageUtils.java:60] [Thread-9]  Error loading http://XXXXXX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam: An error occurred while accessing:    http://XXXXXX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam<br>Invalid GZIP header

and the galaxy-server send this error_log:

----------------------------------------
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "HEAD /display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "HEAD /root HTTP/1.1" 200 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 46142)
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 651, in __init__
    self.finish()
  File "/usr/lib/python2.7/SocketServer.py", line 710, in finish
    self.wfile.close()
  File "/usr/lib/python2.7/socket.py", line 279, in close
    self.flush()
  File "/usr/lib/python2.7/socket.py", line 303, in flush
    self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "GET /display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "GET /root HTTP/1.1" 200 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM

Any idea ?

Vincent

-- 
Vincent Navratil, PhD
IR UCBL - PRABI 
http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard – Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: +33 472432826

My 'ome' page http://vinavratil.free.fr

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Re: IGV display_application configuration failed with require_login=TRUE

Björn Grüning-3
Hi Vincent,

I think there was an error that was fixed recently. If you can, please try yo upgrade or wait a few more days until the new galaxy-dist version is released.

Bjoern


2014-02-04 navratil <[hidden email]>:
Dear galaxy-dev team,

We have configured a galaxy-dist  server (stable release) behind an Apache2 proxy (with mod_xsendfile) by following the galaxy wiki.

We would like to use the galaxy embeded user authentification with require_login=True option instead of a remote_user configuration on the proxy side.

With require_login = False it works but with require_login=True configuration we fail to load .bam files into IGV (local) :

The IGV (Version 2.3.18) send this error:
INFO [2014-02-04 16:05:56,660]  [MessageUtils.java:60] [Thread-9]  Error loading http://XXXXXX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam: An error occurred while accessing:    http://XXXXXX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam<br>Invalid GZIP header

and the galaxy-server send this error_log:

----------------------------------------
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "HEAD /display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "HEAD /root HTTP/1.1" 200 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 46142)
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 651, in __init__
    self.finish()
  File "/usr/lib/python2.7/SocketServer.py", line 710, in finish
    self.wfile.close()
  File "/usr/lib/python2.7/socket.py", line 279, in close
    self.flush()
  File "/usr/lib/python2.7/socket.py", line 303, in flush
    self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "GET /display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "GET /root HTTP/1.1" 200 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM

Any idea ?

Vincent

-- 
Vincent Navratil, PhD
IR UCBL - PRABI 
http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard – Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: <a href="tel:%2B33%20472432826" value="+33472432826" target="_blank">+33 472432826

My 'ome' page http://vinavratil.free.fr

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Re: IGV display_application configuration failed with require_login=TRUE

Thomas Bellembois
In reply to this post by navratil
On 04/02/2014 16:37, navratil wrote:
Dear galaxy-dev team,

We have configured a galaxy-dist  server (stable release) behind an Apache2 proxy (with mod_xsendfile) by following the galaxy wiki.

We would like to use the galaxy embeded user authentification with require_login=True option instead of a remote_user configuration on the proxy side.

With require_login = False it works but with require_login=True configuration we fail to load .bam files into IGV (local) :

The IGV (Version 2.3.18) send this error:
INFO [2014-02-04 16:05:56,660]  [MessageUtils.java:60] [Thread-9]  Error loading http://XXXXXX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam: An error occurred while accessing:    http://XXXXXX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam<br>Invalid GZIP header

and the galaxy-server send this error_log:

----------------------------------------
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "HEAD /display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "HEAD /root HTTP/1.1" 200 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 46142)
Traceback (most recent call last):
  File "/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread
    self.finish_request(request, client_address)
  File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request
    self.RequestHandlerClass(request, client_address, self)
  File "/usr/lib/python2.7/SocketServer.py", line 651, in __init__
    self.finish()
  File "/usr/lib/python2.7/SocketServer.py", line 710, in finish
    self.wfile.close()
  File "/usr/lib/python2.7/socket.py", line 279, in close
    self.flush()
  File "/usr/lib/python2.7/socket.py", line 303, in flush
    self._sock.sendall(view[write_offset:write_offset+buffer_size])
error: [Errno 32] Broken pipe
----------------------------------------
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "GET /display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"
XXXXXX - - [04/Feb/2014:16:05:40 +0200] "GET /root HTTP/1.1" 200 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM

Any idea ?

Vincent

-- 
Vincent Navratil, PhD
IR UCBL - PRABI 
http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard – Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: +33 472432826

My 'ome' page http://vinavratil.free.fr


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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Hi Vincent,

I had the same issue with NGINX.
Ensure that "#filter-with = gzip" is commented out in your universe_wsgi.ini.
I also have "upstream_gzip = False"

Hope this helps,

Regards,

Thomas
-- 
Thomas Bellembois, network and system administrator
ENS-Lyon/IGFL - 46, Allée d'Italie 69364 LYON CEDEX 07 FRANCE
+33 4 26 73 13 67

.The IGFL is a member of the "portail-labos" project (https://portail-labos.ens-lyon.fr/site/).
.IGFL IT documentation: http://itdoc.igfl.ens-lyon.fr/itdoc

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Re: IGV display_application configuration failed with require_login=TRUE

navratil
Thks Thomas,
Indeed the configuration you provide is the one we use here.
However we do not use the nginx proxy (yet ;-))
We are waiting for the next galaxy-dist release to see if it will fix our problem.
Vincent

Vincent Navratil, PhD
IR UCBL - PRABI 
http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard – Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: +33 472432826

My 'ome' page http://vinavratil.free.fr
Le 2/4/14 5:06 PM, Thomas Bellembois a écrit :
On 04/02/2014 16:37, navratil wrote:
Dear galaxy-dev team,

We have configured a galaxy-dist  server (stable release) behind an Apache2 proxy (with mod_xsendfile) by following the galaxy wiki.

We would like to use the galaxy embeded user authentification with require_login=True option instead of a remote_user configuration on the proxy side.

With require_login = False it works but with require_login=True configuration we fail to load .bam files into IGV (local) :

The IGV (Version 2.3.18) send this error:
*/INFO [2014-02-04 16:05:56,660]  [MessageUtils.java:60] [Thread-9]  Error loading http://XXXXXX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam: An error occurred while accessing: http://XXXXXX/display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam<br>Invalid GZIP/**/header/**/
/*
and the galaxy-server send this error_log:

*/----------------------------------------/**/
/**/XXXXXX - - [04/Feb/2014:16:05:40 +0200] "HEAD /display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"/**/
/**/XXXXXX - - [04/Feb/2014:16:05:40 +0200] "HEAD /root HTTP/1.1" 200 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"/**/
/**/----------------------------------------/**/
/**/Exception happened during processing of request from ('127.0.0.1', 46142)/**/
/**/Traceback (most recent call last):/**/
/**/  File "/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.7.egg/paste/httpserver.py", line 1068, in process_request_in_thread/**/
/**/    self.finish_request(request, client_address)/**/
/**/  File "/usr/lib/python2.7/SocketServer.py", line 334, in finish_request/**/
/**/    self.RequestHandlerClass(request, client_address, self)/**/
/**/  File "/usr/lib/python2.7/SocketServer.py", line 651, in __init__/**/
/**/    self.finish()/**/
/**/  File "/usr/lib/python2.7/SocketServer.py", line 710, in finish/**/
/**/    self.wfile.close()/**/
/**/  File "/usr/lib/python2.7/socket.py", line 279, in close/**/
/**/    self.flush()/**/
/**/  File "/usr/lib/python2.7/socket.py", line 303, in flush/**/
/**/self._sock.sendall(view[write_offset:write_offset+buffer_size])/**/
/**/error: [Errno 32] Broken pipe/**/
/**/----------------------------------------/**/
/**/XXXXXX - - [04/Feb/2014:16:05:40 +0200] "GET /display_application/03501d7626bd192f/igv_bam/local_default/845a235de3463571/data/galaxy_03501d7626bd192f.bam HTTP/1.1" 302 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM"/**/
/**/XXXXXX - - [04/Feb/2014:16:05:40 +0200] "GET /root HTTP/1.1" 200 - "-" "IGV Version 2.3.18 (20)09/05/2013 12:24 PM/*

Any idea ?

Vincent

-- 
Vincent Navratil, PhD
IR UCBL - PRABI
http://www.prabi.fr
Bâtiment Gregor Mendel
Université Claude Bernard -- Lyon 1
16, rue Raphaël Dubois
69622 VILLEURBANNE CEDEX
Tel: +33 472432826

My 'ome' pagehttp://vinavratil.free.fr


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
   http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
   http://galaxyproject.org/search/mailinglists/
Hi Vincent,

I had the same issue with NGINX.
Ensure that "#filter-with = gzip" is commented out in your universe_wsgi.ini.
I also have "upstream_gzip = False"

Hope this helps,

Regards,

Thomas



___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/


___________________________________________________________
Please keep all replies on the list by using "reply all"
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To search Galaxy mailing lists use the unified search at:
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