Ok thanks! On 10/23/2018 11:14 AM, Marius van den Beek wrote: > 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 > <mailto: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://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 > > <http://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 <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. > > > ___________________________________________________________ > 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/ >
-- *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.
___________________________________________________________ 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/
