Attribute Error when uploading data on local
Hi, I get the following error when trying to upload data to Galaxy AttributeError: 'NoneType' object has no attribute 'lower' Same error for many different types of files (fastq, sam, bam) some of which uploaded last week. What I've tried: Deleting browser cache Deleting cookie Deleting database/compiled_templates Deleting eggs/ Please let me know what else I should try / what I am doing wrong. More info below. Thank you! More information: TRACEBACK: URL: http://127.0.0.1:8080/datasets/59c76a119581e190/display/?preview=True File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 361 in display mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) AttributeError: 'NoneType' object has no attribute 'lower' Extra Data CGI Variables CONTENT_LENGTH '0' HTTP_ACCEPT 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING 'gzip, deflate' HTTP_ACCEPT_LANGUAGE 'en-us,en;q=0.5' HTTP_CONNECTION 'keep-alive' HTTP_COOKIE 'galaxysession=c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c' HTTP_HOST '127.0.0.1:8080' HTTP_REFERER 'http://127.0.0.1:8080/history' HTTP_USER_AGENT 'Mozilla/5.0 (X11; Linux x86_64; rv:6.0.2) Gecko/20100101 Firefox/6.0.2' PATH_INFO '/datasets/59c76a119581e190/display/' QUERY_STRING 'preview=True' REMOTE_ADDR '127.0.0.1' REQUEST_METHOD 'GET' SERVER_NAME '127.0.0.1' SERVER_PORT '8080' SERVER_PROTOCOL 'HTTP/1.1' Extra Data WSGI Variables application <paste.debug.prints.PrintDebugMiddleware object at 0x7834350> paste.cookies (<SimpleCookie: galaxysession='c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c'>, 'galaxysession=c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c') paste.evalexception <weberror.evalexception.middleware.EvalException object at 0x6dd11d0> paste.evalexception.debug_count 1316648566 paste.expected_exceptions [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions <paste.httpexceptions.HTTPExceptionHandler object at 0x7823090> paste.httpserver.thread_pool <paste.httpserver.ThreadPool object at 0x2b66f90> paste.printdebug_listeners [<cStringIO.StringO object at 0x6e24fb8>, <open file '<stderr>', mode 'w' at 0x7fb208c901e0>] paste.recursive.forward <paste.recursive.Forwarder from /> paste.recursive.include <paste.recursive.Includer from /> paste.recursive.include_app_iter <paste.recursive.IncluderAppIter from /> paste.recursive.script_name '' paste.remove_printdebug <function remove_printdebug at 0x6e23a28> paste.throw_errors True weberror.evalexception <weberror.evalexception.middleware.EvalException object at 0x6dd11d0> weberror.evalexception.debug_count 1316648566 webob._parsed_query_vars (MultiDict([('preview', 'True')]), 'preview=True') wsgi process 'Multithreaded'
Colleen Doherty wrote:
Hi, I get the following error when trying to upload data to Galaxy AttributeError: 'NoneType' object has no attribute 'lower'
Same error for many different types of files (fastq, sam, bam) some of which uploaded last week.
What I've tried: Deleting browser cache Deleting cookie Deleting database/compiled_templates Deleting eggs/
Please let me know what else I should try / what I am doing wrong. More info below. Thank you!
Hi Colleen, I don't think the error below is the true cause of the upload problem - this is indicating that the file's extension is unset and we are not properly handling displaying a dataset when this is the case. I've fixed this in changeset 6054:e28ebc25b2e7. But there's presumably a failure further up since the extension is unset. Is the uploaded dataset red? If so, is there an error displayed when you click on the dataset's "bug" icon? If not, were there any other errors logged in the Galaxy server output when you uploaded the file? Thanks, --nate
More information: TRACEBACK:
URL: http://127.0.0.1:8080/datasets/59c76a119581e190/display/?preview=True File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 361 in display mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) AttributeError: 'NoneType' object has no attribute 'lower'
Extra Data CGI Variables CONTENT_LENGTH '0' HTTP_ACCEPT 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING 'gzip, deflate' HTTP_ACCEPT_LANGUAGE 'en-us,en;q=0.5' HTTP_CONNECTION 'keep-alive' HTTP_COOKIE 'galaxysession=c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c' HTTP_HOST '127.0.0.1:8080' HTTP_REFERER 'http://127.0.0.1:8080/history' HTTP_USER_AGENT 'Mozilla/5.0 (X11; Linux x86_64; rv:6.0.2) Gecko/20100101 Firefox/6.0.2' PATH_INFO '/datasets/59c76a119581e190/display/' QUERY_STRING 'preview=True' REMOTE_ADDR '127.0.0.1' REQUEST_METHOD 'GET' SERVER_NAME '127.0.0.1' SERVER_PORT '8080' SERVER_PROTOCOL 'HTTP/1.1' Extra Data WSGI Variables application <paste.debug.prints.PrintDebugMiddleware object at 0x7834350> paste.cookies (<SimpleCookie: galaxysession='c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c'>, 'galaxysession=c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c') paste.evalexception <weberror.evalexception.middleware.EvalException object at 0x6dd11d0> paste.evalexception.debug_count 1316648566 paste.expected_exceptions [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions <paste.httpexceptions.HTTPExceptionHandler object at 0x7823090> paste.httpserver.thread_pool <paste.httpserver.ThreadPool object at 0x2b66f90> paste.printdebug_listeners [<cStringIO.StringO object at 0x6e24fb8>, <open file '<stderr>', mode 'w' at 0x7fb208c901e0>] paste.recursive.forward <paste.recursive.Forwarder from /> paste.recursive.include <paste.recursive.Includer from /> paste.recursive.include_app_iter <paste.recursive.IncluderAppIter from /> paste.recursive.script_name '' paste.remove_printdebug <function remove_printdebug at 0x6e23a28> paste.throw_errors True weberror.evalexception <weberror.evalexception.middleware.EvalException object at 0x6dd11d0> weberror.evalexception.debug_count 1316648566 webob._parsed_query_vars (MultiDict([('preview', 'True')]), 'preview=True') wsgi process 'Multithreaded' ___________________________________________________________ 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:
Hi Nate, thanks for responding. After reading your e-mail I realized I was making a stupid mistake and not uploading these via http. Sorry for the trouble! Thanks, Colleen . On Wed, Sep 28, 2011 at 7:58 AM, Nate Coraor <nate@bx.psu.edu> wrote:
Colleen Doherty wrote:
Hi, I get the following error when trying to upload data to Galaxy AttributeError: 'NoneType' object has no attribute 'lower'
Same error for many different types of files (fastq, sam, bam) some of which uploaded last week.
What I've tried: Deleting browser cache Deleting cookie Deleting database/compiled_templates Deleting eggs/
Please let me know what else I should try / what I am doing wrong. More info below. Thank you!
Hi Colleen,
I don't think the error below is the true cause of the upload problem - this is indicating that the file's extension is unset and we are not properly handling displaying a dataset when this is the case. I've fixed this in changeset 6054:e28ebc25b2e7.
But there's presumably a failure further up since the extension is unset. Is the uploaded dataset red? If so, is there an error displayed when you click on the dataset's "bug" icon? If not, were there any other errors logged in the Galaxy server output when you uploaded the file?
Thanks, --nate
More information: TRACEBACK:
URL: http://127.0.0.1:8080/datasets/59c76a119581e190/display/?preview=True File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/WebError-0.8a-py2.6.egg/weberror/evalexception/middleware.py', line 364 in respond app_iter = self.application(environ, detect_start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/debug/prints.py', line 98 in __call__ environ, self.app) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/wsgilib.py', line 539 in intercept_output app_iter = application(environ, replacement_start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/eggs/Paste-1.6-py2.6.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/lib/galaxy/web/framework/base.py', line 145 in __call__ body = method( trans, **kwargs ) File '/home/colleen/Work/workspace/ChIPSeq/tools/galaxy-dist/lib/galaxy/web/controllers/dataset.py', line 361 in display mime = trans.app.datatypes_registry.get_mimetype_by_extension( data.extension.lower() ) AttributeError: 'NoneType' object has no attribute 'lower'
Extra Data CGI Variables CONTENT_LENGTH '0' HTTP_ACCEPT 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8' HTTP_ACCEPT_CHARSET 'ISO-8859-1,utf-8;q=0.7,*;q=0.7' HTTP_ACCEPT_ENCODING 'gzip, deflate' HTTP_ACCEPT_LANGUAGE 'en-us,en;q=0.5' HTTP_CONNECTION 'keep-alive' HTTP_COOKIE 'galaxysession=c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c' HTTP_HOST '127.0.0.1:8080' HTTP_REFERER 'http://127.0.0.1:8080/history' HTTP_USER_AGENT 'Mozilla/5.0 (X11; Linux x86_64; rv:6.0.2) Gecko/20100101 Firefox/6.0.2' PATH_INFO '/datasets/59c76a119581e190/display/' QUERY_STRING 'preview=True' REMOTE_ADDR '127.0.0.1' REQUEST_METHOD 'GET' SERVER_NAME '127.0.0.1' SERVER_PORT '8080' SERVER_PROTOCOL 'HTTP/1.1' Extra Data WSGI Variables application <paste.debug.prints.PrintDebugMiddleware object at 0x7834350> paste.cookies (<SimpleCookie: galaxysession='c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c'>, 'galaxysession=c6ca0ddb55be603a2c2796e41769bc2412b1c87332f54f840b1876eab065f3113e1ca20ff6a4ab5c') paste.evalexception <weberror.evalexception.middleware.EvalException object at 0x6dd11d0> paste.evalexception.debug_count 1316648566 paste.expected_exceptions [<class 'paste.httpexceptions.HTTPException'>] paste.httpexceptions <paste.httpexceptions.HTTPExceptionHandler object at 0x7823090> paste.httpserver.thread_pool <paste.httpserver.ThreadPool object at 0x2b66f90> paste.printdebug_listeners [<cStringIO.StringO object at 0x6e24fb8>, <open file '<stderr>', mode 'w' at 0x7fb208c901e0>] paste.recursive.forward <paste.recursive.Forwarder from /> paste.recursive.include <paste.recursive.Includer from /> paste.recursive.include_app_iter <paste.recursive.IncluderAppIter from /> paste.recursive.script_name '' paste.remove_printdebug <function remove_printdebug at 0x6e23a28> paste.throw_errors True weberror.evalexception <weberror.evalexception.middleware.EvalException object at 0x6dd11d0> weberror.evalexception.debug_count 1316648566 webob._parsed_query_vars (MultiDict([('preview', 'True')]), 'preview=True') wsgi process 'Multithreaded' ___________________________________________________________ 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)
-
Colleen Doherty -
Nate Coraor