Re: [galaxy-dev] 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 > 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/53646fef/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/53646fef/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:

Re: [galaxy-dev] 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  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/53646fef/bwa/bw
> a.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/53646fef/bwa/bw
> a-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/fas
> tqc/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_qualit
> y/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_qualit
> y/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/e0cfb5a70
> 3ce/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_trimm
> er/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,
> m.be...@ufz.de, 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