regarding galaxy kickstart

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regarding galaxy kickstart

Rui Wang
Hi Folks,

I spent sometime playing with the kickstart, and sort of got it working. Still a couple things not clear:

1. Is it true that there is no start/stop? My guess is that whenever you need to restart, just re-run the playbook? Anything you want to update(for example add new tools), you re-run the updated playbook too, correct? Before you re-run it, do you have to manually kill everything?

2. Seems tools could easily added by editing the tool list. How about genome data? What if I want to add a specific repo or genome data? Is there a role for this purpose?

Please give me a hand if you could. Any input will be greatly appreciated. :-)

Thanks so much,
Rui

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Re: regarding galaxy kickstart

Peter van Heusden
I don't have an answer to your 2. but Galaxy Kickstart sets up Galaxy controlled by supervisord. So you can restart e.g. the Galaxy web front end with:

sudo supervisorctl restart galaxy:galaxy_web

On Tue, 16 Oct 2018 at 08:16 Rui Wang <[hidden email]> wrote:
Hi Folks,

I spent sometime playing with the kickstart, and sort of got it working. Still a couple things not clear:

1. Is it true that there is no start/stop? My guess is that whenever you need to restart, just re-run the playbook? Anything you want to update(for example add new tools), you re-run the updated playbook too, correct? Before you re-run it, do you have to manually kill everything?

2. Seems tools could easily added by editing the tool list. How about genome data? What if I want to add a specific repo or genome data? Is there a role for this purpose?

Please give me a hand if you could. Any input will be greatly appreciated. :-)

Thanks so much,
Rui
___________________________________________________________
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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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  http://galaxyproject.org/search/

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Error after creating dataset list of bam files in v18.05

Previti
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.previti@...
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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Error after creating dataset list of bam files in v18.05

Previti
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@...
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/

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Re: Error after creating dataset list of bam files in v18.05

Marius van den Beek
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 <[hidden email]> 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@...
www.dkfz.de

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

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Sie kann vertrauliche und/oder nur für den/die Empfänger bestimmte Informationen enthalten. Sollten Sie nicht
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Re: Error after creating dataset list of bam files in v18.05

Previti
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 <[hidden email]> 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@...
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.previti@...
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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in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
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To search Galaxy mailing lists use the unified search at:
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