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%2Fiu..." "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
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%2Fiu..." "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
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%2Fiu..." "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
galaxy-dev@lists.galaxyproject.org