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.prev...@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.prev...@dkfz.de <http://www.dkfz.de/> > 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. > > > ___________________________________________________________ > 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/
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