Uncaught exception in exposed API method:

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Uncaught exception in exposed API method:

Jochen
Hi,

I'm having this error since some minutes. The error message is coming in
the moment I click to any tool (e.g.: featurecounts) that provides data
collections. I think it has to do with a collection in my history. Here
some detail of my log file:

galaxy.web.framework.decorators ERROR 2019-02-06 15:50:09,026 Uncaught
exception in exposed API method:
Traceback (most recent call last):
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/web/framework/decorators.py",
line 283, in decorator
     rval = func(self, trans, *args, **kwargs)
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py",
line 113, in build
     return tool.to_json(trans, kwd.get('inputs', kwd))
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py", line
1903, in to_json
     self.populate_model(request_context, self.inputs, state_inputs,
tool_model['inputs'])
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py", line
1951, in populate_model
     tool_dict = input.to_dict(request_context)
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 701, in to_dict
     cond_dict["cases"] = list(map(nested_to_dict, self.cases))
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 699, in nested_to_dict
     return input.to_dict(trans)
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 719, in to_dict
     when_dict["inputs"] = list(map(input_to_dict, self.inputs.values()))
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
line 717, in input_to_dict
     return input.to_dict(trans)
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
line 1966, in to_dict
     match = dataset_collection_matcher.hdca_match(hdca)
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/dataset_matcher.py",
line 226, in hdca_match
     converted_ext, _ =
datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension,
formats)
   File
"/opt/galaxy/production/galaxy-dist/lib/galaxy/datatypes/registry.py",
line 892, in find_conversion_destination_for_dataset_by_extensions
     self.log.warning("Datatype class not found for extension '%s',
which is used as target for conversion from datatype '%s'" %
(convert_ext, dataset.ext))
AttributeError: 'NoneType' object has no attribute 'ext'
82.130.95.243 - - [06/Feb/2019:15:50:08 +0200] "GET
/api/tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3%2Bgalaxy2/build?version=1.6.3%2Bgalaxy2&__identifer=ku6ydfn1c8&tool_version=1.6.3%252Bgalaxy2
HTTP/1.1" 500 -
"http://green-l-bio.ethz.ch:8090/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F1.6.3%2Bgalaxy2&version=1.6.3%2Bgalaxy2&__identifer=ku6ydfn1c8"
"Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like Gecko)
Chrome/72.0.3626.81 Safari/537.36"


Any ideas? Errors only occur if I'm in that history. I can also provide
more information. This is running on a Galaxy 18.09.

The data collections contains 8 fastq files.

Cheers Jochen


--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone +41 52 354 92 06
[hidden email] <mailto:[hidden email]>
www.ap.ethz.ch

___________________________________________________________
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Re: Uncaught exception in exposed API method:

Jochen
UPDATE:

I think it is the combination of data collection and Bam files in a data
collection. If I delete the HISAT result the error is gone. Any idea?

Cheers Jochen

On 06.02.19 16:02, Jochen Bick wrote:

> Hi,
>
> I'm having this error since some minutes. The error message is coming
> in the moment I click to any tool (e.g.: featurecounts) that provides
> data collections. I think it has to do with a collection in my
> history. Here some detail of my log file:
>
> galaxy.web.framework.decorators ERROR 2019-02-06 15:50:09,026 Uncaught
> exception in exposed API method:
> Traceback (most recent call last):
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/web/framework/decorators.py",
> line 283, in decorator
>     rval = func(self, trans, *args, **kwargs)
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py",
> line 113, in build
>     return tool.to_json(trans, kwd.get('inputs', kwd))
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 1903, in to_json
>     self.populate_model(request_context, self.inputs, state_inputs,
> tool_model['inputs'])
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py",
> line 1951, in populate_model
>     tool_dict = input.to_dict(request_context)
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
> line 701, in to_dict
>     cond_dict["cases"] = list(map(nested_to_dict, self.cases))
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
> line 699, in nested_to_dict
>     return input.to_dict(trans)
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
> line 719, in to_dict
>     when_dict["inputs"] = list(map(input_to_dict, self.inputs.values()))
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
> line 717, in input_to_dict
>     return input.to_dict(trans)
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
> line 1966, in to_dict
>     match = dataset_collection_matcher.hdca_match(hdca)
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/dataset_matcher.py",
> line 226, in hdca_match
>     converted_ext, _ =
> datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension,
> formats)
>   File
> "/opt/galaxy/production/galaxy-dist/lib/galaxy/datatypes/registry.py",
> line 892, in find_conversion_destination_for_dataset_by_extensions
>     self.log.warning("Datatype class not found for extension '%s',
> which is used as target for conversion from datatype '%s'" %
> (convert_ext, dataset.ext))
> AttributeError: 'NoneType' object has no attribute 'ext'
> 82.130.95.243 - - [06/Feb/2019:15:50:08 +0200] "GET
> /api/tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3%2Bgalaxy2/build?version=1.6.3%2Bgalaxy2&__identifer=ku6ydfn1c8&tool_version=1.6.3%252Bgalaxy2
> HTTP/1.1" 500 -
> "http://green-l-bio.ethz.ch:8090/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F1.6.3%2Bgalaxy2&version=1.6.3%2Bgalaxy2&__identifer=ku6ydfn1c8"
> "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like
> Gecko) Chrome/72.0.3626.81 Safari/537.36"
>
>
> Any ideas? Errors only occur if I'm in that history. I can also
> provide more information. This is running on a Galaxy 18.09.
>
> The data collections contains 8 fastq files.
>
> Cheers Jochen
>
>
--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone +41 52 354 92 06
[hidden email] <mailto:[hidden email]>
www.ap.ethz.ch

___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: Uncaught exception in exposed API method:

Jochen
I found the solution:

http://dev.list.galaxyproject.org/regarding-galaxy-kickstart-td4671625.html

we were running an old datatypes_conf.xml

I guess it was not updated when we updated galaxy.

Cheers Jochen

On 06.02.19 18:45, Jochen Bick wrote:

> UPDATE:
>
> I think it is the combination of data collection and Bam files in a
> data collection. If I delete the HISAT result the error is gone. Any
> idea?
>
> Cheers Jochen
>
> On 06.02.19 16:02, Jochen Bick wrote:
>> Hi,
>>
>> I'm having this error since some minutes. The error message is coming
>> in the moment I click to any tool (e.g.: featurecounts) that provides
>> data collections. I think it has to do with a collection in my
>> history. Here some detail of my log file:
>>
>> galaxy.web.framework.decorators ERROR 2019-02-06 15:50:09,026
>> Uncaught exception in exposed API method:
>> Traceback (most recent call last):
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/web/framework/decorators.py",
>> line 283, in decorator
>>     rval = func(self, trans, *args, **kwargs)
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/webapps/galaxy/api/tools.py",
>> line 113, in build
>>     return tool.to_json(trans, kwd.get('inputs', kwd))
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py",
>> line 1903, in to_json
>>     self.populate_model(request_context, self.inputs, state_inputs,
>> tool_model['inputs'])
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/__init__.py",
>> line 1951, in populate_model
>>     tool_dict = input.to_dict(request_context)
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
>> line 701, in to_dict
>>     cond_dict["cases"] = list(map(nested_to_dict, self.cases))
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
>> line 699, in nested_to_dict
>>     return input.to_dict(trans)
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
>> line 719, in to_dict
>>     when_dict["inputs"] = list(map(input_to_dict, self.inputs.values()))
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/grouping.py",
>> line 717, in input_to_dict
>>     return input.to_dict(trans)
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/basic.py",
>> line 1966, in to_dict
>>     match = dataset_collection_matcher.hdca_match(hdca)
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/tools/parameters/dataset_matcher.py",
>> line 226, in hdca_match
>>     converted_ext, _ =
>> datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension,
>> formats)
>>   File
>> "/opt/galaxy/production/galaxy-dist/lib/galaxy/datatypes/registry.py",
>> line 892, in find_conversion_destination_for_dataset_by_extensions
>>     self.log.warning("Datatype class not found for extension '%s',
>> which is used as target for conversion from datatype '%s'" %
>> (convert_ext, dataset.ext))
>> AttributeError: 'NoneType' object has no attribute 'ext'
>> 82.130.95.243 - - [06/Feb/2019:15:50:08 +0200] "GET
>> /api/tools/toolshed.g2.bx.psu.edu/repos/iuc/featurecounts/featurecounts/1.6.3%2Bgalaxy2/build?version=1.6.3%2Bgalaxy2&__identifer=ku6ydfn1c8&tool_version=1.6.3%252Bgalaxy2
>> HTTP/1.1" 500 -
>> "http://green-l-bio.ethz.ch:8090/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Ffeaturecounts%2Ffeaturecounts%2F1.6.3%2Bgalaxy2&version=1.6.3%2Bgalaxy2&__identifer=ku6ydfn1c8"
>> "Mozilla/5.0 (X11; Linux x86_64) AppleWebKit/537.36 (KHTML, like
>> Gecko) Chrome/72.0.3626.81 Safari/537.36"
>>
>>
>> Any ideas? Errors only occur if I'm in that history. I can also
>> provide more information. This is running on a Galaxy 18.09.
>>
>> The data collections contains 8 fastq files.
>>
>> Cheers Jochen
>>
>>
--
ETH Zurich
*Jochen Bick*
Animal Physiology
Institute of Agricultural Sciences
Postal address: Universitätstrasse 2 / LFW B 58.1
8092 Zurich, Switzerland
Office: Eschikon 27
8315 Lindau, Switzerland

Phone +41 52 354 92 06
[hidden email] <mailto:[hidden email]>
www.ap.ethz.ch

___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/