Fwd: Failure to set attributes_type metadata for interval files / error in gff_filter_by_attribute tool
Hello all,
Not sure if the mailing list or trello would be appropriate for this. I had a problem using the gff_filter_by_attribute tool, both locally and on usegalaxy.org. Neither filtering for GTF or GFF were working.
The error message was:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 158, in prepare_job job_wrapper.prepare() File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 832, in prepare self.command_line, self.extra_filenames = tool_evaluator.build() File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 408, in build self.__build_command_line( ) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 424, in __build_command_line command_line = fill_template( command, context=param_dict ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 92, in respond NotFound: cannot find 'attribute_types' while searching for 'input.metadata.attribute_types'
I could fix it by importing safe_dumps from galaxy.util.json, which apparently was not imported. The next problem occurred because gff_filter_by_attribute expects GTF attribute name-value separators (" ") but allowed GFF input, which uses ("=") as separator. I added a logic to switch between seperators based on the file extension. Everything works smoothly now, the code changes are here: https://github.com/mvdbeek/galaxy Should I create a pull request?
Hi Marius,
It'd be great if you wanted to submit a PR for the json issue separately -- I can confirm that that's a working fix. I'll let someone else speak to the tool change.
-Dannon
On Thu, Apr 30, 2015 at 2:30 PM Marius van den Beek m.vandenbeek@gmail.com wrote:
Hello all,
Not sure if the mailing list or trello would be appropriate for this. I had a problem using the gff_filter_by_attribute tool, both locally and on usegalaxy.org. Neither filtering for GTF or GFF were working.
The error message was:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 158, in prepare_job job_wrapper.prepare() File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 832, in prepare self.command_line, self.extra_filenames = tool_evaluator.build() File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 408, in build self.__build_command_line( ) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 424, in __build_command_line command_line = fill_template( command, context=param_dict ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 92, in respond NotFound: cannot find 'attribute_types' while searching for 'input.metadata.attribute_types'
I could fix it by importing safe_dumps from galaxy.util.json, which apparently was not imported. The next problem occurred because gff_filter_by_attribute expects GTF attribute name-value separators (" ") but allowed GFF input, which uses ("=") as separator. I added a logic to switch between seperators based on the file extension. Everything works smoothly now, the code changes are here: https://github.com/mvdbeek/galaxy Should I create a pull request?
-- Marius van den Beek, PhD
Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 01 44 27 34 01
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Hi Marius,
I hope you don't mind, but I went ahead and pulled your change in as https://github.com/galaxyproject/galaxy/pull/199, since there's a bit of backport-fixing required to get this applied correctly.
-Dannon
On Thu, Apr 30, 2015 at 2:37 PM Dannon Baker dannon.baker@gmail.com wrote:
Hi Marius,
It'd be great if you wanted to submit a PR for the json issue separately -- I can confirm that that's a working fix. I'll let someone else speak to the tool change.
-Dannon
On Thu, Apr 30, 2015 at 2:30 PM Marius van den Beek < m.vandenbeek@gmail.com> wrote:
Hello all,
Not sure if the mailing list or trello would be appropriate for this. I had a problem using the gff_filter_by_attribute tool, both locally and on usegalaxy.org. Neither filtering for GTF or GFF were working.
The error message was:
Traceback (most recent call last): File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/__init__.py", line 158, in prepare_job job_wrapper.prepare() File "/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line 832, in prepare self.command_line, self.extra_filenames = tool_evaluator.build() File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 408, in build self.__build_command_line( ) File "/home/galaxy/galaxy-dist/lib/galaxy/tools/evaluation.py", line 424, in __build_command_line command_line = fill_template( command, context=param_dict ) File "/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line 9, in fill_template return str( Template( source=template_text, searchList=[context] ) ) File "/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.7-linux-x86_64-ucs4.egg/Cheetah/Template.py", line 1004, in __str__ return getattr(self, mainMethName)() File "DynamicallyCompiledCheetahTemplate.py", line 92, in respond NotFound: cannot find 'attribute_types' while searching for 'input.metadata.attribute_types'
I could fix it by importing safe_dumps from galaxy.util.json, which apparently was not imported. The next problem occurred because gff_filter_by_attribute expects GTF attribute name-value separators (" ") but allowed GFF input, which uses ("=") as separator. I added a logic to switch between seperators based on the file extension. Everything works smoothly now, the code changes are here: https://github.com/mvdbeek/galaxy Should I create a pull request?
-- Marius van den Beek, PhD
Drosophila Genetics and Epigenetics Institut de Biologie Paris Seine http://www.ibps.upmc.fr/fr/Recherche/umr-biologie-developpement/genetique-et-epigenetique-de-la-drosophile 9, Quai St Bernard, Boîte courrier 24 75252 Paris Cedex 05 Tel +33 01 44 27 34 01
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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galaxy-dev@lists.galaxyproject.org
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Dannon Baker -
Marius van den Beek