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" "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
www.dkfz.de

Management Board: Prof. Dr. Michael Baumann, Prof. Dr. Josef Puchta
VAT-ID No.: DE143293537

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