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 inhttps://bitbucket.org/galaxy/galaxy-central/pull-request/343/need-to-traverse-the-other_value-dict-to
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: |||||https://bitbucket.org/galaxy/galaxy-central/pull-request/343/need-to-traverse-the-other_value-dict-to |||||$ 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