Dear Christopher, You need to copy the shipped datatypes_conf.xml.sample to the appropriate location(s) for your installation. Best, Marius On Tue, Oct 23, 2018, 11:08 AM Previti < christopher.previti@dkfz-heidelberg.de> wrote:
Dear all,
We're in the process of testing version 18.05 before updating our production server. The update process went fine but now I'm getting a "curious" error:
Every time I make a dataset list of bam files the interfaces gives me following error when I try to run any tool:
"Uncaught exception in exposed API method:"
The error message in the galaxy.log is the following (here I just wanted to run hisat2, but it doesn't really matter which tool I try):
172.22.24.119 - - [19/Oct/2018:13:21:05 +0200] "POST /api/tools/ toolshed.g2.bx.psu.edu/repos/iuc/hisat2/hisat2/2.0.5.2/build HTTP/1.1" 500 - "http://galaxy-test.inet.dkfz-heidelberg.de/?tool_id=toolshed.g2.bx. psu.edu%2Frepos%2Fiuc%2Fhisat2%2Fhisat2%2F2.0.5.2&version=2.0.5.2&__identifer=froqct2i1h" "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:62.0) Gecko/20100101 Firefox/62.0" 172.22.24.119 - - [19/Oct/2018:13:21:07 +0200] "GET /api/histories/1cd8e2f6b131e891/contents?order=hid&v=dev&q=update_time-ge&qv=2018-10-19T11%3A21%3A03.000Z HTTP/1.1" 200 - "http://galaxy-test.inet.dkfz-heidelberg.de/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhisat2%2Fhisat2%2F2.0.5.2&version=2.0.5.2&__identifer=froqct2i1h" <http://galaxy-test.inet.dkfz-heidelberg.de/?tool_id=toolshed.g2.bx.psu.edu%2Frepos%2Fiuc%2Fhisat2%2Fhisat2%2F2.0.5.2&version=2.0.5.2&__identifer=froqct2i1h> "Mozilla/5.0 (X11; Fedora; Linux x86_64; rv:62.0) Gecko/20100101 Firefox/62.0" galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,014 Datatype class not found for extension 'bai', which is used as target for conversion from datatype 'bam' galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,015 Datatype class not found for extension 'bai', which is used as target for conversion from datatype 'bam' galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,015 Datatype class not found for extension 'bai', which is used as target for conversion from datatype 'bam' galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,015 Datatype class not found for extension 'bai', which is used as target for conversion from datatype 'bam' galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,016 Datatype class not found for extension 'bai', which is used as target for conversion from datatype 'bam' galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,016 Datatype class not found for extension 'bai', which is used as target for conversion from datatype 'bam' galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,016 Datatype class not found for extension 'bai', which is used as target for conversion from datatype 'bam' galaxy.datatypes.registry WARNING 2018-10-19 13:21:08,019 Datatype class not found for extension 'bai', which is used as target for conversion from datatype 'bam' galaxy.web.framework.decorators ERROR 2018-10-19 13:21:08,038 Uncaught exception in exposed API method: Traceback (most recent call last): File "/opt/galaxy/galaxy/lib/galaxy/web/framework/decorators.py", line 281, in decorator rval = func(self, trans, *args, **kwargs) File "/opt/galaxy/galaxy/lib/galaxy/webapps/galaxy/api/tools.py", line 113, in build return tool.to_json(trans, kwd.get('inputs', kwd)) File "/opt/galaxy/galaxy/lib/galaxy/tools/__init__.py", line 1883, in to_json self.populate_model(request_context, self.inputs, state_inputs, tool_model['inputs']) File "/opt/galaxy/galaxy/lib/galaxy/tools/__init__.py", line 1933, in populate_model tool_dict = input.to_dict(request_context) File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py", line 701, in to_dict cond_dict["cases"] = list(map(nested_to_dict, self.cases)) File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py", line 699, in nested_to_dict return input.to_dict(trans) File "/opt/galaxy/galaxy/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/galaxy/lib/galaxy/tools/parameters/grouping.py", line 717, in input_to_dict return input.to_dict(trans) File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py", line 701, in to_dict cond_dict["cases"] = list(map(nested_to_dict, self.cases)) File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py", line 699, in nested_to_dict return input.to_dict(trans) File "/opt/galaxy/galaxy/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/galaxy/lib/galaxy/tools/parameters/grouping.py", line 717, in input_to_dict return input.to_dict(trans) File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py", line 701, in to_dict cond_dict["cases"] = list(map(nested_to_dict, self.cases)) File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/grouping.py", line 699, in nested_to_dict return input.to_dict(trans) File "/opt/galaxy/galaxy/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/galaxy/lib/galaxy/tools/parameters/grouping.py", line 717, in input_to_dict return input.to_dict(trans) File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line 2005, in to_dict d = super(DataCollectionToolParameter, self).to_dict(trans) File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line 227, in to_dict tool_dict['value'] = self.value_to_basic(self.get_initial_value(trans, other_values), trans.app, use_security=True) File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/basic.py", line 1524, in get_initial_value if dataset_collection_matcher.hdca_match(hdca): File "/opt/galaxy/galaxy/lib/galaxy/tools/parameters/dataset_matcher.py", line 225, in hdca_match converted_ext, _ = datatypes_registry.find_conversion_destination_for_dataset_by_extensions(extension, formats) File "/opt/galaxy/galaxy/lib/galaxy/datatypes/registry.py", line 891, 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'
Has anybody dealt with this issue before? Cheers and thanks,
Christopher
-- *Dr. Christopher Previti* Genomics and Proteomics Core Facility High Throughput Sequencing (W190) Bioinformatician
German Cancer Research Center (DKFZ) Foundation under Public Law Im Neuenheimer Feld 580 69120 Heidelberg Germany Room: B2.102 (INF580/TP3) Phone: +49 6221 42-4661
christopher.previti@dkfz.de <http://www.dkfz.de/> www.dkfz.de
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