startup bug in lib/galaxy/tools/toolbox/base.py
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, m.bernt@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 Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------
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 <m.bernt@ufz.de> 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/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/53646aaaafef/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.bernt@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 Managing Director: Prof. Dr. Heike Graßmann -------------------------------------------
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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 <m.bernt@ufz.de <mailto:m.bernt@ufz.de>> 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
participants (2)
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Marius van den Beek -
Matthias Bernt