10:38 a.m.
Hi all,
I've got a patch to reduce the noise in the log output when a tool XML
file is missing, e.g.
galaxy.tools ERROR 2010-09-29 11:34:43,111 error reading tool from
path: ./tools/data_source/hapmapmart.xml
Traceback (most recent call last):
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 75, in load_tool
tool = self.load_tool( path )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 133, in load_tool
tree = util.parse_xml( config_file )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/util/__init__.py",
line 102, in parse_xml
tree = ElementTree.parse(fname)
File
"/Users/xxx/repositories/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.5.egg/elementtree/ElementTree.py",
line 859, in parse
tree.parse(source, parser)
File
"/Users/xxx/repositories/galaxy-central/eggs/elementtree-1.2.6_20050316-py2.5.egg/elementtree/ElementTree.py",
line 576, in parse
source = open(source, "rb")
IOError: [Errno 2] No such file or directory:
'./tools/data_source/hapmapmart.xml'
becomes:
galaxy.tools ERROR 2010-09-29 11:36:03,982 Tool file missing:
./tools/data_source/hapmapmart.xml
Changeset here:
http://bitbucket.org/peterjc/galaxy-central/changeset/5c9046c8bb08
Peter
11:11 a.m.
On Wed, Sep 29, 2010 at 11:38 AM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
Hi all,
I've got a patch to reduce the noise in the log output when a tool XML
file is missing, e.g.
Here is a follow up patch for the remaining two common error tracebacks
I see with a default galaxy-central installation. First, missing loc files in
dynamic options:
galaxy.tools ERROR 2010-09-29 11:36:04,606 error reading tool from
path: ./tools/human_genome_variation/funDo.xml
Traceback (most recent call last):
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 75, in load_tool
tool = self.load_tool( path )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 146, in load_tool
return ToolClass( config_file, root, self.app )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 288, in __init__
self.parse( root )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 381, in parse
self.parse_inputs( root )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 468, in parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 607, in parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 687, in parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 697, in parse_param_elem
param = ToolParameter.build( self, input_elem )
File
"/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/parameters/basic.py",
line 148, in build
return parameter_types[param_type]( tool, param )
File
"/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/parameters/basic.py",
line 497, in __init__
self.options = dynamic_options.DynamicOptions( options, self )
File
"/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/parameters/dynamic_options.py",
line 426, in __init__
self.file_fields = self.parse_file_fields( open( data_file ) )
IOError: [Errno 2] No such file or directory:
'/Users/xxx/repositories/galaxy-central/tool-data/funDo.loc'
becomes:
galaxy.tools ERROR 2010-09-29 11:51:19,663 Tool
./tools/human_genome_variation/funDo.xml missing data file:
/Users/xxx/repositories/galaxy-central/tool-data/funDo.loc
Likewise for missing loc files in validation, this:
galaxy.tools ERROR 2010-09-29 11:59:23,003 error reading tool from
path: ./tools/human_genome_variation/sift.xml
Traceback (most recent call last):
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 77, in load_tool
tool = self.load_tool( path )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 150, in load_tool
return ToolClass( config_file, root, self.app )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 292, in __init__
self.parse( root )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 385, in parse
self.parse_inputs( root )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 472, in parse_inputs
display, inputs = self.parse_input_page( page, enctypes )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 611, in parse_input_page
inputs = self.parse_input_elem( input_elem, enctypes )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 691, in parse_input_elem
param = self.parse_param_elem( elem, enctypes, context )
File "/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/__init__.py",
line 701, in parse_param_elem
param = ToolParameter.build( self, input_elem )
File
"/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/parameters/basic.py",
line 153, in build
return parameter_types[param_type]( tool, param )
File
"/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/parameters/basic.py",
line 1152, in __init__
ToolParameter.__init__( self, tool, elem )
File
"/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/parameters/basic.py",
line 46, in __init__
self.validators.append( validation.Validator.from_element( self, elem ) )
File
"/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/parameters/validation.py",
line 23, in from_element
return validator_types[type].from_element( param, elem )
File
"/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/parameters/validation.py",
line 251, in from_element
return cls( filename, metadata_name, metadata_column, message,
line_startswith )
File
"/Users/xxx/repositories/galaxy-central/lib/galaxy/tools/parameters/validation.py",
line 256, in __init__
for line in open( filename ):
IOError: [Errno 2] No such file or directory:
'/Users/pjcock/repositories/galaxy-central/tool-data/sift_db.loc'
becomes:
galaxy.tools ERROR 2010-09-29 12:03:13,383 Tool
./tools/human_genome_variation/sift.xml missing data file:
/Users/xxx/repositories/galaxy-central/tool-data/sift_db.loc
In order to do this, I introduced a new exception - however I'm not sure which
module it would be best to define this in. I hope something based on this patch
will be committed:
http://bitbucket.org/peterjc/galaxy-central/changeset/35344d053267
Peter
11:45 a.m.
Peter;
> I've got a patch to reduce the noise in the log output when
a tool XML
> file is missing, e.g.
Here is a follow up patch for the remaining two common error tracebacks
I see with a default galaxy-central installation. First, missing loc files in
dynamic options:
Is it a good thing to be making this messages less noisy? Your
proposal makes them easier to miss amongst all of the logging
messages that are displayed when Galaxy starts up. These are issues
that you'd want to identify and fix, instead of getting confused
later wondering why a tool doesn't show up in the menu or have data
files associated with it.
Brad
2:33 p.m.
On Wed, Sep 29, 2010 at 12:45 PM, Brad Chapman <chapmanb(a)50mail.com> wrote:
Peter;
> > I've got a patch to reduce the noise in the log output when a tool XML
> > file is missing, e.g.
>
> Here is a follow up patch for the remaining two common error tracebacks
> I see with a default galaxy-central installation. First, missing loc files in
> dynamic options:
Is it a good thing to be making this messages less noisy? Your
proposal makes them easier to miss amongst all of the logging
messages that are displayed when Galaxy starts up. These are issues
that you'd want to identify and fix, instead of getting confused
later wondering why a tool doesn't show up in the menu or have data
files associated with it.
Hi Brad,
They are still logged at ERROR priority, so if you are sending the
logging somewhere central nothing important is lost. In these
specific examples the traceback really is just noise.
Rather than making the errors stand out by printing tracebacks,
I would suggest the default Galaxy behaviour of printing the
logging to stdout should ignore the DEBUG log entries - they
make up the bulk of the output and (thus far) are not of interest
to me, and really do hide any errors.
Peter
2:41 p.m.
Peter, fortunately you may be able to adjust that in your
universe_wsgi.ini by changing log_level from the out of the box
default of DEBUG to something less chatty like ERROR:
# Specifies the factory for the universe WSGI application
paste.app_factory = galaxy.web.buildapp:app_factory
log_level = DEBUG
On Wed, Sep 29, 2010 at 10:33 AM, Peter <peter(a)maubp.freeserve.co.uk> wrote:
On Wed, Sep 29, 2010 at 12:45 PM, Brad Chapman
<chapmanb(a)50mail.com> wrote:
>
> Peter;
>
>> > I've got a patch to reduce the noise in the log output when a tool XML
>> > file is missing, e.g.
>>
>> Here is a follow up patch for the remaining two common error tracebacks
>> I see with a default galaxy-central installation. First, missing loc files in
>> dynamic options:
>
> Is it a good thing to be making this messages less noisy? Your
> proposal makes them easier to miss amongst all of the logging
> messages that are displayed when Galaxy starts up. These are issues
> that you'd want to identify and fix, instead of getting confused
> later wondering why a tool doesn't show up in the menu or have data
> files associated with it.
4506
days inactive
4506
days old
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3 participants
participants (3)
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