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
jochen.b...@usys.ethz.ch <mailto:jochen.b...@usys.ethz.ch>
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/
