subject:"\[galaxy\-dev\] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow"

Re: [galaxy-dev] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow

2014-03-18 Thread John Chilton

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=cachedLocally installed reference
 genome/option
 option value=historyReference genome from your
 history/option
 option value=namedNamed on demand/option
 /param
 when value=cached
 param name=genomeVersion type=select label=Genome
 !--GENOMEDESCRIPTION--
 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
helpThese 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.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 =

Re: [galaxy-dev] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow

2014-03-18 Thread Jim Johnson


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=cachedLocally installed reference
genome/option
 option value=historyReference genome from your
history/option
 option value=namedNamed on demand/option
 /param
 when value=cached
 param name=genomeVersion type=select label=Genome
 !--GENOMEDESCRIPTION--
 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
helpThese 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.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,

[galaxy-dev] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow

2014-02-28 Thread Jim Johnson



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=cachedLocally installed reference 
genome/option
option value=historyReference genome from your 
history/option
option value=namedNamed on demand/option
/param
when value=cached
param name=genomeVersion type=select label=Genome
!--GENOMEDESCRIPTION--
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
   helpThese 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


--
James E. Johnson, Minnesota Supercomputing Institute, University of Minnesota
___
Please keep all replies on the list by using reply all
in your mail client.  To manage your subscriptions to this
and other Galaxy lists, please use the interface at:
  http://lists.bx.psu.edu/

To

Re: [galaxy-dev] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow

Re: [galaxy-dev] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow

[galaxy-dev] BugFix for dynamic_options ParamValueFilter to run IUC SnpEff in a workflow

3 matches

Site Navigation

Mail list logo

Footer information