Re: [galaxy-dev] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow
Nice work John.
This fixed issues for running workflows for both SnpEff and XYPlot.
Please reject my pull requests : #336 and #343 in favor of #349
Thanks,
JJ
On 3/18/14, 11:44 AM, John Chilton wrote:
Hey JJ,
Thanks for the bug report. I can confirm the issue. I think the
problem probably is that the other_values thing you are printing out
there is very different when rendering tools (it is the value of
things at that depth of the tool state tree) versus workflows (in
which it is the global state of the tree from the top). The tool
variant is probably the "right" approach since they work and has the
nice advantage of avoiding ambiguities that arise otherwise.
https://bitbucket.org/galaxy/galaxy-central/pull-request/349/bring-workflow-parameter-context/diff
I have opened a pull request with an attempt to bring workflows in
line with tools - it seems to fix snpEff for me locally - can you
confirm? Any chance this also solves your other problem with the XY
plotting tool (Pull Request #336)?
-John
On Fri, Feb 28, 2014 at 12:12 PM, Jim Johnson wrote:
The current code in: lib/galaxy/tools/parameters/dynamic_options.py
only searches the top layer of the dict to find the dependency value.
A fix is provide in pull request:
#343: Need to traverse the other_value dict to find dependencies for
ParamValueFilter in
SnpEff tool_config
...
Locally installed reference
genome
Reference genome from your
history
Named on demand
These are available for only a few
genomes
When running workflow: input.vcf -> SnpEff
The values in ParamValueFilter filter_options function:
self.ref_name
'genomeVersion'
other_values
{u'spliceSiteSize': '1', u'filterHomHet': 'no_filter', u'outputFormat':
'vcf', u'filterOut': None, u'inputFormat': 'vcf', u'filterIn': 'no_filter',
u'udLength': '5000', u'generate_stats': True, u'noLog': True, u'chr':
'None', u'intervals': None, u'snpDb': {'extra_annotations': None,
'regulation': None, 'genomeVersion': 'GRCh37.71', 'genomeSrc': 'cached',
'__current_case__': 0}, u'offset': '', u'input':
,
u'transcripts': None, u'annotations': ['-canon', '-lof', '-onlyReg']}
Since 'genomeVersion' isn't in the keys of other_values, but rather in
other_values['snpDb']
this failed the assertion:
assert self.ref_name in other_values, "Required dependency '%s' not
found in incoming values" % self.ref_name
Pull request 343:
$ hg diff lib/galaxy/tools/parameters/dynamic_options.py
diff -r 95517f976cca lib/galaxy/tools/parameters/dynamic_options.py
--- a/lib/galaxy/tools/parameters/dynamic_options.pyThu Feb 27 16:56:25
2014 -0500
+++ b/lib/galaxy/tools/parameters/dynamic_options.pyFri Feb 28 11:37:04
2014 -0600
@@ -177,8 +177,27 @@
return self.ref_name
def filter_options( self, options, trans, other_values ):
if trans is not None and trans.workflow_building_mode: return []
-assert self.ref_name in other_values, "Required dependency '%s' not
found in incoming values" % self.ref_name
-ref = other_values.get( self.ref_name, None )
+## Depth first traversal to find the value for a dependency
+def get_dep_value(param_name, dep_name, cur_val, layer):
+dep_val = cur_val
+if isinstance(layer, dict ):
+if dep_name in layer:
+dep_val = layer[dep_name]
+if param_name in layer:
+return dep_val
+else:
+for l in layer.itervalues():
+dep_val = get_dep_value(param_name, dep_name,
dep_val, l)
+if dep_val:
+break
+elif isinstance( layer, list):
+for l in layer:
+dep_val = get_dep_value(param_name, dep_name, dep_val,
l)
+if dep_val:
+break
+return None
+ref = get_dep_value(self.dynamic_option.tool_param.name,
self.ref_name, None, other_values)
+assert not ref, "Required dependency '%s' not found in incoming
values" % self.ref_name
for ref_attribute in self.ref_attribute:
if not hasattr( ref, ref_attribute ):
return [] #ref does not have attribute, so we cannot
filter, return empty list
--
James E. Johnson, Minnesota Supercomputing Institute, University of
Minnesota
--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
___
Please keep all replies on the list by using "reply all"
in
Re: [galaxy-dev] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow
Hey JJ,
Thanks for the bug report. I can confirm the issue. I think the
problem probably is that the other_values thing you are printing out
there is very different when rendering tools (it is the value of
things at that depth of the tool state tree) versus workflows (in
which it is the global state of the tree from the top). The tool
variant is probably the "right" approach since they work and has the
nice advantage of avoiding ambiguities that arise otherwise.
https://bitbucket.org/galaxy/galaxy-central/pull-request/349/bring-workflow-parameter-context/diff
I have opened a pull request with an attempt to bring workflows in
line with tools - it seems to fix snpEff for me locally - can you
confirm? Any chance this also solves your other problem with the XY
plotting tool (Pull Request #336)?
-John
On Fri, Feb 28, 2014 at 12:12 PM, Jim Johnson wrote:
>
> The current code in: lib/galaxy/tools/parameters/dynamic_options.py
> only searches the top layer of the dict to find the dependency value.
>
> A fix is provide in pull request:
> #343: Need to traverse the other_value dict to find dependencies for
> ParamValueFilter in
>
>
> SnpEff tool_config
>
>
> label="Sequence changes (SNPs, MNPs, InDels)"/>
> ...
>
>
> Locally installed reference
> genome
> Reference genome from your
> history
> Named on demand
>
>
>
>
>
>
>
>
> display="checkboxes" multiple="true" label="Additional Annotations">
>These are available for only a few
> genomes
>
> key="genome" column="0" />
>
>
>
>
>
>
> When running workflow: input.vcf -> SnpEff
>
> The values in ParamValueFilter filter_options function:
>
self.ref_name
> 'genomeVersion'
>
other_values
> {u'spliceSiteSize': '1', u'filterHomHet': 'no_filter', u'outputFormat':
> 'vcf', u'filterOut': None, u'inputFormat': 'vcf', u'filterIn': 'no_filter',
> u'udLength': '5000', u'generate_stats': True, u'noLog': True, u'chr':
> 'None', u'intervals': None, u'snpDb': {'extra_annotations': None,
> 'regulation': None, 'genomeVersion': 'GRCh37.71', 'genomeSrc': 'cached',
> '__current_case__': 0}, u'offset': '', u'input':
> ,
> u'transcripts': None, u'annotations': ['-canon', '-lof', '-onlyReg']}
>
> Since 'genomeVersion' isn't in the keys of other_values, but rather in
> other_values['snpDb']
> this failed the assertion:
> assert self.ref_name in other_values, "Required dependency '%s' not
> found in incoming values" % self.ref_name
>
> Pull request 343:
>
> $ hg diff lib/galaxy/tools/parameters/dynamic_options.py
> diff -r 95517f976cca lib/galaxy/tools/parameters/dynamic_options.py
> --- a/lib/galaxy/tools/parameters/dynamic_options.pyThu Feb 27 16:56:25
> 2014 -0500
> +++ b/lib/galaxy/tools/parameters/dynamic_options.pyFri Feb 28 11:37:04
> 2014 -0600
> @@ -177,8 +177,27 @@
> return self.ref_name
> def filter_options( self, options, trans, other_values ):
> if trans is not None and trans.workflow_building_mode: return []
> -assert self.ref_name in other_values, "Required dependency '%s' not
> found in incoming values" % self.ref_name
> -ref = other_values.get( self.ref_name, None )
> +## Depth first traversal to find the value for a dependency
> +def get_dep_value(param_name, dep_name, cur_val, layer):
> +dep_val = cur_val
> +if isinstance(layer, dict ):
> +if dep_name in layer:
> +dep_val = layer[dep_name]
> +if param_name in layer:
> +return dep_val
> +else:
> +for l in layer.itervalues():
> +dep_val = get_dep_value(param_name, dep_name,
> dep_val, l)
> +if dep_val:
> +break
> +elif isinstance( layer, list):
> +for l in layer:
> +dep_val = get_dep_value(param_name, dep_name, dep_val,
> l)
> +if dep_val:
> +break
> +return None
> +ref = get_dep_value(self.dynamic_option.tool_param.name,
> self.ref_name, None, other_values)
> +assert not ref, "Required dependency '%s' not found in incoming
> values" % self.ref_name
> for ref_attribute in self.ref_attribute:
> if not hasattr( ref, ref_attribute ):
> return [] #ref does not have attribute, so we cannot
> filter, return empty list
>
>
> --
> James E. Johnson, Minnesota Supercomputing Institute, University of
> Minnesota
___
Please keep all replies o
