Error when exporting history to file
Hi all, I get the following error when I try to export a specific history to file: 10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24" Error - <type 'exceptions.TypeError'>: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file... Any help is greatly appreciated! Best regards, Sarah
Sarah, What tool was used to create the problematic dataset? Thanks, J. On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
Hi all,
I get the following error when I try to export a specific history to file:
10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24" Error - <type 'exceptions.TypeError'>: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError: <galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable
I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file...
Any help is greatly appreciated!
Best regards, Sarah ___________________________________________________________ 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:
Sort (version 1.0.1) on column: c5 with flavor: Numerical sort everything in: Descending order On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
Sarah,
What tool was used to create the problematic dataset?
Thanks, J.
On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
Hi all,
I get the following error when I try to export a specific history to file:
10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24" Error -<type 'exceptions.TypeError'>:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable
I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file...
Any help is greatly appreciated!
Best regards, Sarah ___________________________________________________________ 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:
Sarah, I'm not able to reproduce your issue using galaxy-central. This could mean that this bug has been fixed in galaxy-central but hasn't made it to galaxy-dist yet—it appears you are using galaxy-dist—or there's other information needed to reproduce this issue. A couple more questions: Are you using galaxy-dist? Can you reproduce the issue on our public server using the problematic dataset and/or workflow? Thanks, J. On May 7, 2012, at 12:33 PM, Sarah Diehl wrote:
Sort (version 1.0.1)
on column: c5 with flavor: Numerical sort everything in: Descending order
On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
Sarah,
What tool was used to create the problematic dataset?
Thanks, J.
On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
Hi all,
I get the following error when I try to export a specific history to file:
10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24" Error -<type 'exceptions.TypeError'>:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable
I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file...
Any help is greatly appreciated!
Best regards, Sarah ___________________________________________________________ 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:
___________________________________________________________ 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:
Sarah, I'm not able to reproduce your issue using galaxy-central. This could mean that this bug has been fixed in galaxy-central but hasn't made it to galaxy-dist yet—it appears you are using galaxy-dist—or there's other information needed to reproduce this issue. A couple more questions: Are you using galaxy-dist? Can you reproduce the issue on our public server using the problematic dataset and/or workflow? Thanks, J. On May 7, 2012, at 12:33 PM, Sarah Diehl wrote:
Sort (version 1.0.1)
on column: c5 with flavor: Numerical sort everything in: Descending order
On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
Sarah,
What tool was used to create the problematic dataset?
Thanks, J.
On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
Hi all,
I get the following error when I try to export a specific history to file:
10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24" Error -<type 'exceptions.TypeError'>:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable
I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file...
Any help is greatly appreciated!
Best regards, Sarah ___________________________________________________________ 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:
___________________________________________________________ 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 Jeremy, I'm using galaxy-dist, but it's quite possible that I'm a version or two behind. I'm not yet able to reproduce the problem on the public server, but I'm still missing some steps from the input to the problematic dataset. I'll get back to you if I'm able to reproduce it or if it still persist when I have updated our Galaxy server. Thanks for your help! Best regards, Sarah On 05/09/2012 02:09 AM, Jeremy Goecks wrote:
Sarah,
I'm not able to reproduce your issue using galaxy-central. This could mean that this bug has been fixed in galaxy-central but hasn't made it to galaxy-dist yet—it appears you are using galaxy-dist—or there's other information needed to reproduce this issue. A couple more questions:
Are you using galaxy-dist? Can you reproduce the issue on our public server using the problematic dataset and/or workflow?
Thanks, J.
On May 7, 2012, at 12:33 PM, Sarah Diehl wrote:
Sort (version 1.0.1)
on column: c5 with flavor: Numerical sort everything in: Descending order
On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
Sarah,
What tool was used to create the problematic dataset?
Thanks, J.
On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
Hi all,
I get the following error when I try to export a specific history to file:
10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24" Error -<type 'exceptions.TypeError'>:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable
I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file...
Any help is greatly appreciated!
Best regards, Sarah ___________________________________________________________ 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:
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 Jeremy, I was able to reproduce the error on the public Galaxy server. I shared the history with you (jeremy.goecks@emory.edu). It's named "export history to file bug". Thanks. Sarah ----- Original Message ----- From: "Sarah Diehl" <diehl@immunbio.mpg.de> To: "Jeremy Goecks" <jeremy.goecks@emory.edu> Cc: "galaxy-dev@lists.bx.psu.edu List" <galaxy-dev@lists.bx.psu.edu> Sent: Wednesday, May 9, 2012 11:40:50 AM Subject: Re: [galaxy-dev] Error when exporting history to file Hi Jeremy, I'm using galaxy-dist, but it's quite possible that I'm a version or two behind. I'm not yet able to reproduce the problem on the public server, but I'm still missing some steps from the input to the problematic dataset. I'll get back to you if I'm able to reproduce it or if it still persist when I have updated our Galaxy server. Thanks for your help! Best regards, Sarah On 05/09/2012 02:09 AM, Jeremy Goecks wrote:
Sarah,
I'm not able to reproduce your issue using galaxy-central. This could mean that this bug has been fixed in galaxy-central but hasn't made it to galaxy-dist yet—it appears you are using galaxy-dist—or there's other information needed to reproduce this issue. A couple more questions:
Are you using galaxy-dist? Can you reproduce the issue on our public server using the problematic dataset and/or workflow?
Thanks, J.
On May 7, 2012, at 12:33 PM, Sarah Diehl wrote:
Sort (version 1.0.1)
on column: c5 with flavor: Numerical sort everything in: Descending order
On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
Sarah,
What tool was used to create the problematic dataset?
Thanks, J.
On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
Hi all,
I get the following error when I try to export a specific history to file:
10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24" Error -<type 'exceptions.TypeError'>:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable
I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file...
Any help is greatly appreciated!
Best regards, Sarah ___________________________________________________________ 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:
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:
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Fixed in galaxy-central changeset cc70c3dcd6f7 Sarah, thanks for taking the time to reproduce on the public server. Best, J. On May 10, 2012, at 10:17 AM, Sarah Diehl wrote:
Hi Jeremy,
I was able to reproduce the error on the public Galaxy server. I shared the history with you (jeremy.goecks@emory.edu). It's named "export history to file bug".
Thanks. Sarah
----- Original Message ----- From: "Sarah Diehl" <diehl@immunbio.mpg.de> To: "Jeremy Goecks" <jeremy.goecks@emory.edu> Cc: "galaxy-dev@lists.bx.psu.edu List" <galaxy-dev@lists.bx.psu.edu> Sent: Wednesday, May 9, 2012 11:40:50 AM Subject: Re: [galaxy-dev] Error when exporting history to file
Hi Jeremy,
I'm using galaxy-dist, but it's quite possible that I'm a version or two behind. I'm not yet able to reproduce the problem on the public server, but I'm still missing some steps from the input to the problematic dataset. I'll get back to you if I'm able to reproduce it or if it still persist when I have updated our Galaxy server. Thanks for your help!
Best regards, Sarah
On 05/09/2012 02:09 AM, Jeremy Goecks wrote:
Sarah,
I'm not able to reproduce your issue using galaxy-central. This could mean that this bug has been fixed in galaxy-central but hasn't made it to galaxy-dist yet—it appears you are using galaxy-dist—or there's other information needed to reproduce this issue. A couple more questions:
Are you using galaxy-dist? Can you reproduce the issue on our public server using the problematic dataset and/or workflow?
Thanks, J.
On May 7, 2012, at 12:33 PM, Sarah Diehl wrote:
Sort (version 1.0.1)
on column: c5 with flavor: Numerical sort everything in: Descending order
On 05/07/2012 06:28 PM, Jeremy Goecks wrote:
Sarah,
What tool was used to create the problematic dataset?
Thanks, J.
On May 7, 2012, at 12:17 PM, Sarah Diehl wrote:
Hi all,
I get the following error when I try to export a specific history to file:
10.1.5.190 - - [07/May/2012:18:01:08 +0200] "GET /history/export_archive HTTP/1.1" 500 - "http://galaxy.immunbio.mpg.de/" "Mozilla/5.0 (X11; U; Linux x86_64; en-US; rv:1.9.2.24) Gecko/20111108 Fedora/3.6.24-1.fc14 Firefox/3.6.24" Error -<type 'exceptions.TypeError'>:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable URL: http://galaxy.immunbio.mpg.de/history/export_archive File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/exceptions/errormiddleware.py', line 143 in __call__ app_iter = self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/recursive.py', line 80 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/eggs/Paste-1.6-py2.7.egg/paste/httpexceptions.py', line 632 in __call__ return self.application(environ, start_response) File '/galaxy/galaxy_server/lib/galaxy/web/framework/base.py', line 160 in __call__ body = method( trans, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/web/controllers/history.py', line 678 in export_archive history_exp_tool.execute( trans, incoming = params, set_output_hid = True ) File '/galaxy/galaxy_server/lib/galaxy/tools/__init__.py', line 1517 in execute return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) File '/galaxy/galaxy_server/lib/galaxy/tools/actions/history_imp_exp.py', line 106 in execute include_deleted=incoming[ 'include_deleted' ] ) File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 428 in setup_job jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/__init__.py', line 268 in dumps File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 214 in encode File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 282 in iterencode File '/galaxy/galaxy_server/lib/galaxy/tools/imp_exp/__init__.py', line 327 in default return simplejson.JSONEncoder.default( self, obj ) File '/galaxy/galaxy_server/eggs/simplejson-2.1.1-py2.7-linux-x86_64-ucs2.egg/simplejson/encoder.py', line 190 in default TypeError:<galaxy.tools.parameters.basic.UnvalidatedValue object at 0x8ba67d0> is not JSON serializable
I tracked the problem down to a single bed file. I copied it into a new empty history and I can still not export this history to a file. This file doesn't have any special characters in either its name, info or annotation. I can't find anything special about this file...
Any help is greatly appreciated!
Best regards, Sarah ___________________________________________________________ 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:
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:
___________________________________________________________ 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)
-
Jeremy Goecks -
Sarah Diehl