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:
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