I'm having a pretty torrid time with this because we've had to implement active
directory authentication for Apache. It works and users can log in with their
AD accounts and that is all fine. The problems arise when I try and get UCSC
to pick up a BAM file. The first problem is that although the Galaxy server is
configured to for UCSC as a display server, putting the following into the
Apache conf as recommended here
http://wiki.galaxyproject.org/Admin/Config/Apache%20Proxy doesn't work.
1 <Location "/root/display_as">
2 Satisfy Any
3 Order deny,allow
4 Deny from all
5 Allow from hgw1.cse.ucsc.edu
6 Allow from hgw2.cse.ucsc.edu
7 Allow from hgw3.cse.ucsc.edu
8 Allow from hgw4.cse.ucsc.edu
9 Allow from hgw5.cse.ucsc.edu
10 Allow from hgw6.cse.ucsc.edu
11 Allow from hgw7.cse.ucsc.edu
12 Allow from hgw8.cse.ucsc.edu
13 </Location>
All that happens is you get 401 Authorization Required errors indicating that
the Apache server isn't letting the UCSC servers non-authenticated access.
Now, if I add the Allow from hgw etc into the <Location "/"> block then it gets
through and then I hit the next problem which is that although I've mapped some
read data against dm3 I'm getting failures inside Galaxy itself related to
serving the bai file UCSC is requesting. Here's the galaxy_access log:
192.168.240.21 - shane [23/May/2013:15:22:24 +1200] "GET
/display_application/d3a4d6a5256f2d9a/ucsc_bam/main HTTP/1.1" 302 406
hgw4.cse.ucsc.edu - - [23/May/2013:15:22:24 +1200] "GET
/dataset/display_application?app_action=param&user_id=207edd50b8d72f8b&app_name=ucsc_bam&action_param=track&link_name=main&dataset_id=d3a4d6a5256f2d9a
HTTP/1.0" 200 311
hgw4.cse.ucsc.edu - - [23/May/2013:15:22:29 +1200] "HEAD
/dataset/display_application?app_action=data&user_id=207edd50b8d72f8b&app_name=ucsc_bam&action_param=galaxy_d3a4d6a5256f2d9a.bam&link_name=main&dataset_id=d3a4d6a5256f2d9a
HTTP/1.0" 200 -
hgw4.cse.ucsc.edu - - [23/May/2013:15:22:31 +1200] "HEAD
/dataset/display_application?app_action=data&user_id=207edd50b8d72f8b&app_name=ucsc_bam&action_param=galaxy_d3a4d6a5256f2d9a.bam&link_name=main&dataset_id=d3a4d6a5256f2d9a.bai
HTTP/1.0" 500 -
hgw4.cse.ucsc.edu - - [23/May/2013:15:22:30 +1200] "GET
/dataset/display_application?app_action=data&user_id=207edd50b8d72f8b&app_name=ucsc_bam&action_param=galaxy_d3a4d6a5256f2d9a.bam&link_name=main&dataset_id=d3a4d6a5256f2d9a
HTTP/1.0" 200 472000
Note the 500 when requesting the bai file.
This is what my manager.log is showing when this happens.
128.114.119.134 - - [23/May/2013:15:22:29 +1300] "HEAD
/dataset/display_application?app_action=data&user_id=207edd50b8d72f8b&app_name=ucsc_bam&action_param=galaxy_d3a4d6a5256f2d9a.bam&link_name=main&dataset_id=d3a4d6a5256f2d9a
HTTP/1.1" 200 3301004 "-" "genome.ucsc.edu/net.c"
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 60484)
Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__
self.finish()
File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish
self.wfile.flush()
File "/usr/lib64/python2.6/socket.py", line 303, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
----------------------------------------
128.114.119.134 - - [23/May/2013:15:22:30 +1300] "GET
/dataset/display_application?app_action=data&user_id=207edd50b8d72f8b&app_name=ucsc_bam&action_param=galaxy_d3a4d6a5256f2d9a.bam&link_name=main&dataset_id=d3a4d6a5256f2d9a
HTTP/1.1" 200 3301004 "-" "genome.ucsc.edu/net.c"
128.114.119.134 - - [23/May/2013:15:22:31 +1300] "HEAD
/dataset/display_application?app_action=data&user_id=207edd50b8d72f8b&app_name=ucsc_bam&action_param=galaxy_d3a4d6a5256f2d9a.bam&link_name=main&dataset_id=d3a4d6a5256f2d9a.bai
HTTP/1.1" 500 - "-" "genome.ucsc.edu/net.c"
Error - <type 'exceptions.TypeError'>: Non-hexadecimal digit found
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 60486)
Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__
self.finish()
File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish
self.wfile.flush()
File "/usr/lib64/python2.6/socket.py", line 303, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
----------------------------------------
----------------------------------------
Exception happened during processing of request from ('127.0.0.1', 60485)
Traceback (most recent call last):
File
"/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpserver.py",
line 1068, in process_request_in_thread
self.finish_request(request, client_address)
File "/usr/lib64/python2.6/SocketServer.py", line 322, in finish_request
self.RequestHandlerClass(request, client_address, self)
File "/usr/lib64/python2.6/SocketServer.py", line 618, in __init__
self.finish()
File "/usr/lib64/python2.6/SocketServer.py", line 661, in finish
self.wfile.flush()
File "/usr/lib64/python2.6/socket.py", line 303, in flush
self._sock.sendall(buffer(data, write_offset, buffer_size))
error: [Errno 32] Broken pipe
----------------------------------------
And here's the text version in the browser (edited out our server's hostname
though):
URL:
https://<ourgalaxyserver>/dataset/display_application?app_action=data&user_id=207edd50b8d72f8b&app_name=ucsc_bam&action_param=galaxy_d3a4d6a5256f2d9a.bam&link_name=main&dataset_id=d3a4d6a5256f2d9a.bai
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/error.py',
line 149 in __call__
app_iter = self.application(environ, sr_checker)
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/recursive.py',
line 84 in __call__
return self.application(environ, start_response)
File
'/home/galaxy/galaxy-dist/lib/galaxy/web/framework/middleware/remoteuser.py',
line 91 in __call__
return self.app( environ, start_response )
File
'/home/galaxy/galaxy-dist/eggs/Paste-1.7.5.1-py2.6.egg/paste/httpexceptions.py',
line 633 in __call__
return self.application(environ, start_response)
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in
__call__
return self.handle_request( environ, start_response )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/framework/base.py', line 182 in
handle_request
body = method( trans, **kwargs )
File
'/home/galaxy/galaxy-dist/lib/galaxy/webapps/galaxy/controllers/dataset.py',
line 727 in display_application
data, user = decode_dataset_user( trans, dataset_id, user_id )
File
'/home/galaxy/galaxy-dist/lib/galaxy/datatypes/display_applications/util.py',
line 22 in decode_dataset_user
dataset_id = trans.security.decode_id( dataset_hash )
File '/home/galaxy/galaxy-dist/lib/galaxy/web/security/__init__.py', line 60 in
decode_id
return int( self.id_cipher.decrypt( obj_id.decode( 'hex' ) ).lstrip( "!" ) )
File '/home/galaxy/galaxy_env/lib64/python2.6/encodings/hex_codec.py', line 42
in hex_decode
output = binascii.a2b_hex(input)
TypeError: Non-hexadecimal digit found
I've been banging my head against this all day :-(
Shane Sturrock
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