Hello everybody, 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"; "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.prev...@dkfz.de <http://www.dkfz.de/> www.dkfz.de <http://www.dkfz.de/> Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta VAT-ID No.: DE143293537 Vertraulichkeitshinweis: Diese Nachricht ist ausschließlich für die Personen bestimmt, an die sie adressiert ist. Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht der bestimmungsgemäße Empfänger sein, kontaktieren Sie bitte den Absender und löschen Sie die Mitteilung. Jegliche unbefugte Verwendung der Informationen in dieser Nachricht ist untersagt.
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