upload of local file ends up with a broken pipe.
I am having difficulties with my local instance of Galaxy on Mac OS X. Upon using the local file upload tool I get an error resultant of a broken pipe in python. The command-line output is as follows. 127.0.0.1 - - [25/Feb/2013:12:36:32 -0400] "GET /history HTTP/1.1" 500 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 50438) Traceback (most recent call last): File "/Users/jjevans/Work/Tools/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 "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 641, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 694, in finish self.wfile.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [25/Feb/2013:12:36:34 -0400] "GET /api/histories/2a56795cad3c7db3 HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" galaxy.jobs.manager DEBUG 2013-02-25 12:36:35,289 (77) Job assigned to handler 'upload_handler' My instance has worked for this task in the past, but I'm not sure if it has been since my last Galaxy update or perhaps something with my configuration changed. thanks for your help, Jason
Hello, Jason At which revision of galaxy-central or galaxy-dist is your installation? Does this happen intermittently or regularly (with every upload)? Thanks, Carl On Mon, Feb 25, 2013 at 1:49 PM, Jason Evans <jason.j.evans@gmail.com>wrote:
I am having difficulties with my local instance of Galaxy on Mac OS X. Upon using the local file upload tool I get an error resultant of a broken pipe in python.
The command-line output is as follows.
127.0.0.1 - - [25/Feb/2013:12:36:32 -0400] "GET /history HTTP/1.1" 500 - " http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 50438) Traceback (most recent call last): File "/Users/jjevans/Work/Tools/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 "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 641, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 694, in finish self.wfile.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [25/Feb/2013:12:36:34 -0400] "GET /api/histories/2a56795cad3c7db3 HTTP/1.1" 200 - " http://localhost:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" galaxy.jobs.manager DEBUG 2013-02-25 12:36:35,289 (77) Job assigned to handler 'upload_handler'
My instance has worked for this task in the past, but I'm not sure if it has been since my last Galaxy update or perhaps something with my configuration changed.
thanks for your help,
Jason
___________________________________________________________ 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:
Greetings Carl, Thanks for your response. I pulled and updated and the broken pipe error still occurs. I am using revision 9fd7fe0c5712 . The error was regular, but now seems intermittent. I've been trying to reproduce it and could only see it cause an error once. I don't think it was doing this before, but the upload completes properly now. It still gives an error in the output, but finishes and the data is there. thanks again, Jason Jason Evans jason.j.evans@gmail.com On Mar 7, 2013, at 9:52 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hello, Jason
At which revision of galaxy-central or galaxy-dist is your installation? Does this happen intermittently or regularly (with every upload)?
Thanks, Carl
On Mon, Feb 25, 2013 at 1:49 PM, Jason Evans <jason.j.evans@gmail.com> wrote: I am having difficulties with my local instance of Galaxy on Mac OS X. Upon using the local file upload tool I get an error resultant of a broken pipe in python.
The command-line output is as follows.
127.0.0.1 - - [25/Feb/2013:12:36:32 -0400] "GET /history HTTP/1.1" 500 - "http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 50438) Traceback (most recent call last): File "/Users/jjevans/Work/Tools/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 "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 641, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 694, in finish self.wfile.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [25/Feb/2013:12:36:34 -0400] "GET /api/histories/2a56795cad3c7db3 HTTP/1.1" 200 - "http://localhost:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" galaxy.jobs.manager DEBUG 2013-02-25 12:36:35,289 (77) Job assigned to handler 'upload_handler'
My instance has worked for this task in the past, but I'm not sure if it has been since my last Galaxy update or perhaps something with my configuration changed.
thanks for your help,
Jason
___________________________________________________________ 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:
Hello, Jason, The broken pipe can happen when a client stops listening to the servers response (e.g. when a user closes a tab). In general it won't cause any long term problems. I'm glad that the uploads are working now, however. Let us know if you see any further problems, Carl On Thu, Mar 7, 2013 at 4:31 PM, Jason Evans <jason.j.evans@gmail.com> wrote:
Greetings Carl,
Thanks for your response. I pulled and updated and the broken pipe error still occurs. I am using revision 9fd7fe0c5712 .
The error was regular, but now seems intermittent. I've been trying to reproduce it and could only see it cause an error once.
I don't think it was doing this before, but the upload completes properly now. It still gives an error in the output, but finishes and the data is there.
thanks again,
Jason
Jason Evans jason.j.evans@gmail.com
On Mar 7, 2013, at 9:52 AM, Carl Eberhard <carlfeberhard@gmail.com> wrote:
Hello, Jason
At which revision of galaxy-central or galaxy-dist is your installation? Does this happen intermittently or regularly (with every upload)?
Thanks, Carl
On Mon, Feb 25, 2013 at 1:49 PM, Jason Evans <jason.j.evans@gmail.com>wrote:
I am having difficulties with my local instance of Galaxy on Mac OS X. Upon using the local file upload tool I get an error resultant of a broken pipe in python.
The command-line output is as follows.
127.0.0.1 - - [25/Feb/2013:12:36:32 -0400] "GET /history HTTP/1.1" 500 - " http://localhost:8080/tool_runner/upload_async_message" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" ---------------------------------------- Exception happened during processing of request from ('127.0.0.1', 50438) Traceback (most recent call last): File "/Users/jjevans/Work/Tools/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 "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 323, in finish_request self.RequestHandlerClass(request, client_address, self) File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 641, in __init__ self.finish() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/SocketServer.py", line 694, in finish self.wfile.flush() File "/System/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/socket.py", line 303, in flush self._sock.sendall(view[write_offset:write_offset+buffer_size]) error: [Errno 32] Broken pipe ---------------------------------------- 127.0.0.1 - - [25/Feb/2013:12:36:34 -0400] "GET /api/histories/2a56795cad3c7db3 HTTP/1.1" 200 - " http://localhost:8080/history" "Mozilla/5.0 (Macintosh; Intel Mac OS X 10_8_2) AppleWebKit/536.26.17 (KHTML, like Gecko) Version/6.0.2 Safari/536.26.17" galaxy.jobs.manager DEBUG 2013-02-25 12:36:35,289 (77) Job assigned to handler 'upload_handler'
My instance has worked for this task in the past, but I'm not sure if it has been since my last Galaxy update or perhaps something with my configuration changed.
thanks for your help,
Jason
___________________________________________________________ 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:
participants (2)
-
Carl Eberhard -
Jason Evans