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
<inputs>
<param format="vcf,tabular,pileup,bed" name="input" type="data"
label="Sequence changes (SNPs, MNPs, InDels)"/>
...
<conditional name="snpDb">
<param name="genomeSrc" type="select" label="Genome source">
<option value="cached">Locally installed reference
genome</option>
<option value="history">Reference genome from your
history</option>
<option value="named">Named on demand</option>
</param>
<when value="cached">
<param name="genomeVersion" type="select" label="Genome">
<!--GENOME DESCRIPTION-->
<options from_data_table="snpeff_genomedb">
<filter type="unique_value" column="0" />
</options>
</param>
<param name="extra_annotations" type="select"
display="checkboxes" multiple="true" label="Additional Annotations">
<help>These are available for only a few
genomes</help>
<options from_data_table="snpeff_annotations">
<filter type="param_value" ref="genomeVersion"
key="genome" column="0" />
<filter type="unique_value" column="1" />
</options>
</param>
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':
<galaxy.tools.parameters.basic.DummyDataset object at 0x11451b8d0>,
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.py Thu Feb 27 16:56:25
2014 -0500
+++ b/lib/galaxy/tools/parameters/dynamic_options.py Fri 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
