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startup bug in lib/galaxy/tools/toolbox/base.py

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startup bug in lib/galaxy/tools/toolbox/base.py

Matthias Bernt
Dear galaxy developers,

I sent this originally to the galaxy-bugs list and was asked to forward
this also to this list. What is the best way to report bugs? There is
galaxy-bugs, galaxy-dev and also the issue tracker on galaxy.

During startup of my galaxy 17.01 installation an error message pops up:

galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,605 Error reading
tool from path:
toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa/bwa.xml
Traceback (most recent call last):
   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
560, in _load_tool_tag_set
     tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'

Seems that tool_shed_repository is still None at this point. This
happens for some tools.

galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,764 Error reading
tool from path:
toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa/bwa-mem.xml
Traceback (most recent call last):
   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
560, in _load_tool_tag_set
     tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'
galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,768 Error reading
tool from path:
toolshed.g2.bx.psu.edu/repos/devteam/fastqc/a00a6402d09a/fastqc/rgFastQC.xml
Traceback (most recent call last):
   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
560, in _load_tool_tag_set
     tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'
galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,773 Error reading
tool from path:
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.xml
Traceback (most recent call last):
   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
560, in _load_tool_tag_set
     tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'
galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,779 Error reading
tool from path:
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/04a609b0fdf6/fastq_trimmer_by_quality/fastq_trimmer_by_quality.xml
Traceback (most recent call last):
   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
560, in _load_tool_tag_set
     tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'
galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,788 Error reading
tool from path:
toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/e0cfb5a703ce/fastq_trimmer/fastq_trimmer.xml
Traceback (most recent call last):
   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
560, in _load_tool_tag_set
     tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'
galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,793 Error reading
tool from path:
toolshed.g2.bx.psu.edu/repos/geert-vandeweyer/fastq_qc_trimmer/cba6282b5dc8/fastq_qc_trimmer/Paired_fastQ_trimmer.xml
Traceback (most recent call last):
   File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
560, in _load_tool_tag_set
     tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'

Best,
Matthias

--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone +49 341 235 482296,
[hidden email], www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board:
MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------


___________________________________________________________
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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  http://galaxyproject.org/search/

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Re: startup bug in lib/galaxy/tools/toolbox/base.py

Marius van den Beek
Hi Matthias,

so typically what's happening there is that there is no tool_shed_respository entry in the database for this tool.
I see this in my development instance when I setup a new database, but keep my old shed_tool_conf.xml.

If you want to get rid of these errors you can uninstall the tools in question and install them again from the toolshed.

It could be worth thinking about relaxing the assumption that tools in the shed_tool_conf.xml should have an entry in the database.
I'd encourage you to open an issue on https://github.com/galaxyproject/galaxy/issues to get some more opinions on this.


Best,
Marius

On 16 March 2017 at 09:33, Matthias Bernt <[hidden email]> wrote:
Dear galaxy developers,

I sent this originally to the galaxy-bugs list and was asked to forward this also to this list. What is the best way to report bugs? There is galaxy-bugs, galaxy-dev and also the issue tracker on galaxy.

During startup of my galaxy 17.01 installation an error message pops up:

galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,605 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa/bwa.xml
Traceback (most recent call last):
  File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560, in _load_tool_tag_set
    tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'

Seems that tool_shed_repository is still None at this point. This happens for some tools.

galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,764 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa/bwa-mem.xml
Traceback (most recent call last):
  File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560, in _load_tool_tag_set
    tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'
galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,768 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/fastqc/a00a6402d09a/fastqc/rgFastQC.xml
Traceback (most recent call last):
  File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560, in _load_tool_tag_set
    tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'
galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,773 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.xml
Traceback (most recent call last):
  File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560, in _load_tool_tag_set
    tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'
galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,779 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/04a609b0fdf6/fastq_trimmer_by_quality/fastq_trimmer_by_quality.xml
Traceback (most recent call last):
  File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560, in _load_tool_tag_set
    tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'
galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,788 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/e0cfb5a703ce/fastq_trimmer/fastq_trimmer.xml
Traceback (most recent call last):
  File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560, in _load_tool_tag_set
    tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'
galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,793 Error reading tool from path: toolshed.g2.bx.psu.edu/repos/geert-vandeweyer/fastq_qc_trimmer/cba6282b5dc8/fastq_qc_trimmer/Paired_fastQ_trimmer.xml
Traceback (most recent call last):
  File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line 560, in _load_tool_tag_set
    tool.tool_shed = tool_shed_repository.tool_shed
AttributeError: 'NoneType' object has no attribute 'tool_shed'

Best,
Matthias

--

-------------------------------------------
Matthias Bernt
Bioinformatics Service
Molekulare Systembiologie (MOLSYB)
Helmholtz-Zentrum für Umweltforschung GmbH - UFZ/
Helmholtz Centre for Environmental Research GmbH - UFZ
Permoserstraße 15, 04318 Leipzig, Germany
Phone <a href="tel:%2B49%20341%20235%20482296" value="+49341235482296" target="_blank">+49 341 235 482296,
[hidden email], www.ufz.de

Sitz der Gesellschaft/Registered Office: Leipzig
Registergericht/Registration Office: Amtsgericht Leipzig
Handelsregister Nr./Trade Register Nr.: B 4703
Vorsitzender des Aufsichtsrats/Chairman of the Supervisory Board: MinDirig Wilfried Kraus
Wissenschaftlicher Geschäftsführer/Scientific Managing Director:
Prof. Dr. Dr. h.c. Georg Teutsch
Administrative Geschäftsführerin/ Administrative Managing Director:
Prof. Dr. Heike Graßmann
-------------------------------------------


___________________________________________________________
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/


___________________________________________________________
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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Re: startup bug in lib/galaxy/tools/toolbox/base.py

Matthias Bernt
Dear Marius,

thanks for the information. You are right, there are entries in
shed_tool_conf.xml for tools which I have uninstalled. I can manually
remove them. I will file an issue because in the best case these
entries would be removed when tools are uninstalled.

Best,
Matthias


On 16.03.2017 11:10, Marius van den Beek wrote:

> Hi Matthias,
>
> so typically what's happening there is that there is no
> tool_shed_respository entry in the database for this tool.
> I see this in my development instance when I setup a new database, but
> keep my old shed_tool_conf.xml.
>
> If you want to get rid of these errors you can uninstall the tools in
> question and install them again from the toolshed.
>
> It could be worth thinking about relaxing the assumption that tools in
> the shed_tool_conf.xml should have an entry in the database.
> I'd encourage you to open an issue
> on https://github.com/galaxyproject/galaxy/issues to get some more
> opinions on this.
>
>
> Best,
> Marius
>
> On 16 March 2017 at 09:33, Matthias Bernt <[hidden email]
> <mailto:[hidden email]>> wrote:
>
>     Dear galaxy developers,
>
>     I sent this originally to the galaxy-bugs list and was asked to
>     forward this also to this list. What is the best way to report bugs?
>     There is galaxy-bugs, galaxy-dev and also the issue tracker on galaxy.
>
>     During startup of my galaxy 17.01 installation an error message pops up:
>
>     galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,605 Error
>     reading tool from path:
>     toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa/bwa.xml
>     <http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa/bwa.xml>
>     Traceback (most recent call last):
>       File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
>     560, in _load_tool_tag_set
>         tool.tool_shed = tool_shed_repository.tool_shed
>     AttributeError: 'NoneType' object has no attribute 'tool_shed'
>
>     Seems that tool_shed_repository is still None at this point. This
>     happens for some tools.
>
>     galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,764 Error
>     reading tool from path:
>     toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa/bwa-mem.xml <http://toolshed.g2.bx.psu.edu/repos/devteam/bwa/53646aaaafef/bwa/bwa-mem.xml>
>     Traceback (most recent call last):
>       File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
>     560, in _load_tool_tag_set
>         tool.tool_shed = tool_shed_repository.tool_shed
>     AttributeError: 'NoneType' object has no attribute 'tool_shed'
>     galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,768 Error
>     reading tool from path:
>     toolshed.g2.bx.psu.edu/repos/devteam/fastqc/a00a6402d09a/fastqc/rgFastQC.xml
>     <http://toolshed.g2.bx.psu.edu/repos/devteam/fastqc/a00a6402d09a/fastqc/rgFastQC.xml>
>     Traceback (most recent call last):
>       File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
>     560, in _load_tool_tag_set
>         tool.tool_shed = tool_shed_repository.tool_shed
>     AttributeError: 'NoneType' object has no attribute 'tool_shed'
>     galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,773 Error
>     reading tool from path:
>     toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.xml
>     <http://toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/25c24379693a/fastq_trimmer_by_quality/fastq_trimmer_by_quality.xml>
>     Traceback (most recent call last):
>       File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
>     560, in _load_tool_tag_set
>         tool.tool_shed = tool_shed_repository.tool_shed
>     AttributeError: 'NoneType' object has no attribute 'tool_shed'
>     galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,779 Error
>     reading tool from path:
>     toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/04a609b0fdf6/fastq_trimmer_by_quality/fastq_trimmer_by_quality.xml
>     <http://toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer_by_quality/04a609b0fdf6/fastq_trimmer_by_quality/fastq_trimmer_by_quality.xml>
>     Traceback (most recent call last):
>       File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
>     560, in _load_tool_tag_set
>         tool.tool_shed = tool_shed_repository.tool_shed
>     AttributeError: 'NoneType' object has no attribute 'tool_shed'
>     galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,788 Error
>     reading tool from path:
>     toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/e0cfb5a703ce/fastq_trimmer/fastq_trimmer.xml
>     <http://toolshed.g2.bx.psu.edu/repos/devteam/fastq_trimmer/e0cfb5a703ce/fastq_trimmer/fastq_trimmer.xml>
>     Traceback (most recent call last):
>       File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
>     560, in _load_tool_tag_set
>         tool.tool_shed = tool_shed_repository.tool_shed
>     AttributeError: 'NoneType' object has no attribute 'tool_shed'
>     galaxy.tools.toolbox.base ERROR 2017-03-14 11:15:17,793 Error
>     reading tool from path:
>     toolshed.g2.bx.psu.edu/repos/geert-vandeweyer/fastq_qc_trimmer/cba6282b5dc8/fastq_qc_trimmer/Paired_fastQ_trimmer.xml
>     <http://toolshed.g2.bx.psu.edu/repos/geert-vandeweyer/fastq_qc_trimmer/cba6282b5dc8/fastq_qc_trimmer/Paired_fastQ_trimmer.xml>
>     Traceback (most recent call last):
>       File "/home/berntm/galaxy/lib/galaxy/tools/toolbox/base.py", line
>     560, in _load_tool_tag_set
>         tool.tool_shed = tool_shed_repository.tool_shed
>     AttributeError: 'NoneType' object has no attribute 'tool_shed'
>
>     Best,
>     Matthias
>



___________________________________________________________
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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