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 <johns...@umn.edu> 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

     <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


--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
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