Hi,

I had the same problem and also wrote within this mailing list, but got no reply yet. This was my message:

" Hi,

I maybe found a bug or misunderstand something in the debugging/logging section of universal_wsgi.ini

I wanted to disable any logging and so commented everything within the logging section:

|# ---- Logging and Debugging ------------------------------------------------

# Verbosity of log messages #log_level = DEBUG

# Log memory usage #log_memory_usage = False

# Log events #log_events = True

# Log user actions #log_actions = False

# Configuration for debugging middleware #debug = True #use_lint = False

# Interactive debugging - NEVER enable this on a public site #use_interactive = False

# Write thread status periodically to 'heartbeat.log' (careful, uses disk space rapidly!) #use_heartbeat = False

# Enable the memory debugging interface (careful, negatively impacts server performance) #use_memdump = False

# Profiling middleware (cProfile based) #use_profile = False |

When I then start Galaxy the complete History shows only "Internal Server Error" and the Galaxy Log:

|Starting server in PID 5470. serving on http://127.0.0.1:8080 192.168.3.90 - - [15/Jul/2010:17:29:23 +0200] "GET / HTTP/1.1" 200 - "-" "Mozilla/5.0 (X11; U; Linux x86_64; de; rv:1.9.0.19) Gecko/2010040121 Ubuntu/9.04 (jaunty) Firefox/3.0.19" 192.168.3.90 - - [15/Jul/2010:17:29:23 +0200] "GET /history HTTP/1.1" 200 - "http://bioapp07/" "Mozilla/5.0 (X11; U; Linux x86_64; de; rv:1.9.0.19) Gecko/2010040121 Ubuntu/9.04 (jaunty) Firefox/3.0.19" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 38584) Traceback (most recent call last): File "/r1/people/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.6/SocketServer.py", line 320, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.6/SocketServer.py", line 615, in __init__ self.handle() File "/r1/people/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/r1/people/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/r1/people/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 290, in wsgi_execute self.wsgi_write_chunk(chunk) File "/r1/people/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 125, in wsgi_write_chunk "Content returned before start_response called") RuntimeError: Content returned before start_response called ---------------------------------------- 192.168.3.90 - - [15/Jul/2010:17:29:23 +0200] "GET /root/tool_menu HTTP/1.1" 200 - "http://bioapp07/" "Mozilla/5.0 (X11; U; Linux x86_64; de; rv:1.9.0.19) Gecko/2010040121 Ubuntu/9.04 (jaunty) Firefox/3.0.19" | After uncommenting everything in the logging section, galaxy works fine again. Whats the matter and how can I disable the debug messages, and especially: |192.168.3.90 - - [15/Jul/2010:17:29:23 +0200] "GET /root/tool_menu HTTP/1.1" 200 - "http://bioapp07/" "Mozilla/5.0 (X11; U; Linux x86_64; de; rv:1.9.0.19) Gecko/2010040121 Ubuntu/9.04 (jaunty) Firefox/3.0.19"|

I use Galaxy behind a Apache with NIS userauthentification.

Regards, Michael ;-)

Am 10/21/2010 03:34 AM, schrieb Nate Coraor:

Hi Isabelle,

Could you send your config file off-list (directly to me at nate@bx.psu.edu) with any identifying or secure information removed (like the database user and password, the id_secret, and your admin_users).

Also, are you able to load the same history with debug = True?

--nate

Isabelle Phan wrote:

...

...

http://gmod.827538.n3.nabble.com/Possible-Bug-tt969896.html

are there plans to address this issue or is this not affecting others besides Michael and myself?

This is currently a complete blocker for me:

• downloading large files from Galaxy fails with an out of memory error
• trying to fix that by setting

debug = False causes galaxy to be unusable. The application starts up, but the History panel shows 'internal server error' and the app throws a RuntimeError:

Traceback (most recent call last): File "/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.6/SocketServer.py", line 320, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.6/SocketServer.py", line 615, in __init__ self.handle() File "/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 290, in wsgi_execute self.wsgi_write_chunk(chunk) File "/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 125, in wsgi_write_chunk "Content returned before start_response called") RuntimeError: Content returned before start_response called

I did an update of galaxy, migrated the database to version 58, and am still unable to switch off debugging. Galaxy is not running behind apache at present.

Without the ability to download large-ish files, I am losing support to have Galaxy in production *sob*.

Any help greatly appreciated.

Isabelle

---

galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

Michael Siebauer wrote:

Sorry for double posting. I've did'nt noticed your link to my old email. :-(

Hi Michael,

Sorry for overlooking your earlier post. The solution is to disable 'filter-with = gzip' in the config, as it turns out it's incompatible with the way we stream templates like the history (streaming is enabled when debug is disabled). I have updated this information on the ProductionServer wiki page.

Note this does not mean you can't use on-the-fly compression - but it should be done in the proxy server instead (where it would probably be more efficient anyway).

--nate

Am 10/21/2010 03:34 AM, schrieb Nate Coraor:

...

Hi Isabelle,

Could you send your config file off-list (directly to me at nate@bx.psu.edu) with any identifying or secure information removed (like the database user and password, the id_secret, and your admin_users).

Also, are you able to load the same history with debug = True?

--nate

Isabelle Phan wrote:

...

...

http://gmod.827538.n3.nabble.com/Possible-Bug-tt969896.html

are there plans to address this issue or is this not affecting others besides Michael and myself?

This is currently a complete blocker for me:

• downloading large files from Galaxy fails with an out of memory error
• trying to fix that by setting

debug = False causes galaxy to be unusable. The application starts up, but the History panel shows 'internal server error' and the app throws a RuntimeError:

Traceback (most recent call last): File "/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 1053, in process_request_in_thread self.finish_request(request, client_address) File "/usr/lib/python2.6/SocketServer.py", line 320, in finish_request self.RequestHandlerClass(request, client_address, self) File "/usr/lib/python2.6/SocketServer.py", line 615, in __init__ self.handle() File "/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 432, in handle BaseHTTPRequestHandler.handle(self) File "/usr/lib/python2.6/BaseHTTPServer.py", line 329, in handle self.handle_one_request() File "/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 427, in handle_one_request self.wsgi_execute() File "/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 290, in wsgi_execute self.wsgi_write_chunk(chunk) File "/home/galaxy/galaxy_dist/eggs/Paste-1.6-py2.6.egg/paste/httpserver.py", line 125, in wsgi_write_chunk "Content returned before start_response called") RuntimeError: Content returned before start_response called

I did an update of galaxy, migrated the database to version 58, and am still unable to switch off debugging. Galaxy is not running behind apache at present.

Without the ability to download large-ish files, I am losing support to have Galaxy in production *sob*.

Any help greatly appreciated.

Isabelle

---

galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev

---

galaxy-dev mailing list galaxy-dev@lists.bx.psu.edu http://lists.bx.psu.edu/listinfo/galaxy-dev